voro_explo_mod15.patch
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	Martin Felke (scorpion81)
	Nov 13 2013, 5:24 PM

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voro_explo_mod15.patch
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	Index: release/scripts/startup/bl_ui/properties_data_modifier.py
	===================================================================
	--- release/scripts/startup/bl_ui/properties_data_modifier.py (revision 53656)
	+++ release/scripts/startup/bl_ui/properties_data_modifier.py (working copy)
	@@ -277,26 +277,42 @@
	split.prop(md, "use_edge_sharp", text="Sharp Edges")

	def EXPLODE(self, layout, ob, md):
	+ layout.prop(md, "mode")
	split = layout.split()

	- col = split.column()
	- col.label(text="Vertex group:")
	- col.prop_search(md, "vertex_group", ob, "vertex_groups", text="")
	- sub = col.column()
	- sub.active = bool(md.vertex_group)
	- sub.prop(md, "protect")
	- col.label(text="Particle UV")
	- col.prop_search(md, "particle_uv", ob.data, "uv_textures", text="")
	+ if (md.mode == 'CELLS'):
	+ col = split.column()
	+ col.label("Point Source:")
	+ col.prop(md, "point_source")
	+ col.prop(md, "use_boolean")
	+ if (md.use_boolean == True):
	+ col.prop(md, "flip_normal")
	+ col.prop(md, "inner_material")
	+ if (md.refracture == False):
	+ col.prop(md, "use_cache")
	+ if (md.use_cache == False):
	+ col.prop(md, "refracture")
	+ col.prop(md, "emit_continuously")
	+ if (md.emit_continuously == False):
	+ col.prop(md, "map_delay")
	+ elif (md.mode == 'FACES'):
	+ col = split.column()
	+ col.label(text="Vertex group:")
	+ col.prop_search(md, "vertex_group", ob, "vertex_groups", text="")
	+ sub = col.column()
	+ sub.active = bool(md.vertex_group)
	+ sub.prop(md, "protect")
	+ col.label(text="Particle UV")
	+ col.prop_search(md, "particle_uv", ob.data, "uv_textures", text="")

	- col = split.column()
	- col.prop(md, "use_edge_cut")
	- col.prop(md, "show_unborn")
	- col.prop(md, "show_alive")
	- col.prop(md, "show_dead")
	- col.prop(md, "use_size")
	+ col = split.column()
	+ col.prop(md, "use_edge_cut")
	+ col.prop(md, "show_unborn")
	+ col.prop(md, "show_alive")
	+ col.prop(md, "show_dead")
	+ col.prop(md, "use_size")
	+ layout.operator("object.explode_refresh", text="Refresh")

	- layout.operator("object.explode_refresh", text="Refresh")
	-
	def FLUID_SIMULATION(self, layout, ob, md):
	layout.label(text="Settings can be found inside the Physics context")

	@@ -782,6 +798,7 @@
	sub = col.column(align=True)
	sub.prop(md, "scale_x", text="Scale X")
	sub.prop(md, "scale_y", text="Scale Y")
	+

	def WARP(self, layout, ob, md):
	use_falloff = (md.falloff_type != 'NONE')
	Index: source/creator/CMakeLists.txt
	===================================================================
	--- source/creator/CMakeLists.txt (revision 53656)
	+++ source/creator/CMakeLists.txt (working copy)
	@@ -969,6 +969,10 @@
	if(WITH_INTERNATIONAL)
	list(APPEND BLENDER_SORTED_LIBS bf_intern_locale)
	endif()
	+
	+ if(WITH_MOD_VORONOI)
	+ list(APPEND BLENDER_SORTED_LIBS extern_voro++)
	+ endif()

	if(WITH_BULLET AND NOT WITH_BULLET_SYSTEM)
	list_insert_after(BLENDER_SORTED_LIBS "ge_logic_ngnetwork" "extern_bullet")
	Index: source/blenderplayer/CMakeLists.txt
	===================================================================
	--- source/blenderplayer/CMakeLists.txt (revision 53656)
	+++ source/blenderplayer/CMakeLists.txt (working copy)
	@@ -195,6 +195,10 @@
	if(WITH_INTERNATIONAL)
	list(APPEND BLENDER_SORTED_LIBS bf_intern_locale)
	endif()
	+
	+ if(WITH_MOD_VORONOI)
	+ list(APPEND BLENDER_SORTED_LIBS extern_voro++)
	+ endif()

	foreach(SORTLIB ${BLENDER_SORTED_LIBS})
	set(REMLIB ${SORTLIB})
	Index: source/blender/modifiers/intern/MOD_explode.c
	===================================================================
	--- source/blender/modifiers/intern/MOD_explode.c (revision 53656)
	+++ source/blender/modifiers/intern/MOD_explode.c (working copy)
	@@ -22,7 +22,8 @@
	* Ton Roosendaal,
	* Ben Batt,
	* Brecht Van Lommel,
	- * Campbell Barton
	+ * Campbell Barton,
	+ * Martin Felke
	*
	* *** END GPL LICENSE BLOCK ***
	*
	@@ -34,6 +35,7 @@


	#include "DNA_meshdata_types.h"
	+#include "DNA_mesh_types.h"
	#include "DNA_scene_types.h"
	#include "DNA_object_types.h"

	@@ -57,19 +59,131 @@

	#include "MOD_util.h"

	+#include "MOD_boolean_util.h"
	+#include "../../../../extern/voro++/src/c_interface.hh"
	+#include "bmesh.h"
	+#include "BLI_path_util.h"
	+#include <ctype.h>
	+#include "DNA_material_types.h"
	+#include "BKE_material.h"
	+#include "DNA_gpencil_types.h"
	+#include "../../editors/include/ED_object.h"
	+#include "BKE_global.h"
	+#include "../../editors/include/ED_physics.h"
	+#include "BKE_main.h"
	+#include "BKE_library.h"
	+
	+void updateMesh(VoronoiCell* cell, Object* ob);
	+
	static void initData(ModifierData *md)
	{
	ExplodeModifierData emd = (ExplodeModifierData ) md;

	+ emd->mode = eFractureMode_Faces;
	+ emd->use_boolean = FALSE;
	+ emd->use_cache = MOD_VORONOI_USECACHE;
	+ emd->refracture = FALSE;
	+ emd->fracMesh = NULL;
	+ emd->tempOb = NULL;
	+ emd->cells = NULL;
	+ emd->flip_normal = FALSE;
	+
	+ emd->last_part = 0;
	+ emd->last_bool = FALSE;
	+ emd->last_flip = FALSE;
	+
	emd->facepa = NULL;
	+ emd->emit_continuously = FALSE;
	emd->flag \|= eExplodeFlag_Unborn + eExplodeFlag_Alive + eExplodeFlag_Dead;
	+ emd->patree = NULL;
	+ emd->map_delay = 1;
	+ emd->last_map_delay = 1;
	+ emd->inner_material = NULL;
	+ emd->point_source = eOwnParticles;
	+ emd->last_point_source = eOwnParticles;
	}
	+
	+static void freeCells(ExplodeModifierData* emd)
	+{
	+ int c = 0;
	+
	+ if ((emd->cells) && (emd->mode == eFractureMode_Cells))
	+ {
	+ if (emd->cells->data)
	+ {
	+ for (c = 0; c < emd->cells->count; c++)
	+ {
	+ MEM_freeN(emd->cells->data[c].vertco);
	+ emd->cells->data[c].vertco = NULL;
	+ MEM_freeN(emd->cells->data[c].vertices);
	+ emd->cells->data[c].vertices = NULL;
	+ DM_release(emd->cells->data[c].cell_mesh);
	+ MEM_freeN(emd->cells->data[c].cell_mesh);
	+ emd->cells->data[c].cell_mesh = NULL;
	+ }
	+
	+ MEM_freeN(emd->cells->data);
	+ emd->cells->data = NULL;
	+ }
	+
	+ MEM_freeN(emd->cells);
	+ emd->cells = NULL;
	+ }
	+}
	+
	+#ifdef WITH_MOD_VORONOI
	+
	static void freeData(ModifierData *md)
	{
	ExplodeModifierData emd = (ExplodeModifierData ) md;
	+
	+ freeCells(emd);
	+
	+ if ((emd->fracMesh) && (emd->mode == eFractureMode_Cells))
	+ {
	+ BM_mesh_free(emd->fracMesh);
	+ emd->fracMesh = NULL;
	+ }
	+
	+ if ((emd->tempOb) && (emd->mode == eFractureMode_Cells))
	+ {
	+ BKE_libblock_free_us(&(G.main->object), emd->tempOb);
	+ BKE_object_unlink(emd->tempOb);
	+ BKE_object_free(emd->tempOb);
	+ emd->tempOb = NULL;
	+ }
	+
	+ //if (emd->mode == eFractureMode_Faces)
	+ {
	+ if (emd->facepa) MEM_freeN(emd->facepa);
	+ }

	- if (emd->facepa) MEM_freeN(emd->facepa);
	+ if (emd->patree)
	+ {
	+ BLI_kdtree_free(emd->patree);
	+ emd->patree = NULL;
	+ }
	+
	+ if (emd->inner_material)
	+ { //will be freed by walk/foreachIDLink ?
	+ emd->inner_material = NULL;
	+ }
	+
	}
	+
	+#else
	+
	+static void freeData(ModifierData *md)
	+{
	+ ExplodeModifierData emd = (ExplodeModifierData ) md;
	+ if (emd->mode == eFractureMode_Faces)
	+ {
	+ if (emd->facepa) MEM_freeN(emd->facepa);
	+ }
	+}
	+
	+#endif
	+
	static void copyData(ModifierData md, ModifierData target)
	{
	ExplodeModifierData emd = (ExplodeModifierData ) md;
	@@ -79,7 +193,26 @@
	temd->flag = emd->flag;
	temd->protect = emd->protect;
	temd->vgroup = emd->vgroup;
	+
	+ temd->mode = emd->mode;
	+ temd->use_boolean = emd->use_boolean;
	+ temd->fracMesh = emd->fracMesh;
	+ temd->use_cache = emd->use_cache;
	+ temd->refracture = emd->refracture;
	+ temd->tempOb = emd->tempOb;
	+ temd->cells = emd->cells;
	+ temd->flip_normal = emd->flip_normal;
	+ temd->last_part = emd->last_part;
	+ temd->last_bool = emd->last_bool;
	+ temd->last_flip = emd->last_flip;
	+ temd->emit_continuously = emd->emit_continuously;
	+ temd->map_delay = emd->map_delay;
	+ temd->last_map_delay = emd->last_map_delay;
	+ temd->inner_material = emd->inner_material;
	+ temd->point_source = emd->point_source;
	+ temd->last_point_source = emd->last_point_source;
	}
	+
	static int dependsOnTime(ModifierData *UNUSED(md))
	{
	return 1;
	@@ -989,6 +1122,888 @@
	}
	return psmd;
	}
	+
	+static int dm_minmax(DerivedMesh* dm, float min[3], float max[3])
	+{
	+
	+ int verts = dm->getNumVerts(dm);
	+ MVert *mverts = dm->getVertArray(dm);
	+ MVert *mvert;
	+ int i = 0;
	+
	+ INIT_MINMAX(min, max);
	+ for (i = 0; i < verts; i++) {
	+ mvert = &mverts[i];
	+ minmax_v3v3_v3(min, max, mvert->co);
	+ }
	+
	+ return (verts != 0);
	+}
	+
	+static int points_from_verts(Object* ob, int totobj, float** points, int p_exist)
	+{
	+ int v, o, pt = p_exist;
	+ float co[3];
	+
	+ for (o = 0; o < totobj; o++)
	+ {
	+ if (ob[o].type == OB_MESH)
	+ {
	+ Mesh* me = (Mesh*)ob[o].data;
	+ for (v = 0; v < me->totvert; v++)
	+ {
	+ points = MEM_reallocN(points, ((pt+1)3)sizeof(float));
	+
	+ co[0] = me->mvert[v].co[0];
	+ co[1] = me->mvert[v].co[1];
	+ co[2] = me->mvert[v].co[2];
	+
	+ mul_m4_v3(ob->obmat, co);
	+
	+ (points)[pt3] = co[0];
	+ (points)[pt3+1] = co[1];
	+ (points)[pt3+2] = co[2];
	+ pt++;
	+ }
	+ }
	+ }
	+
	+ return pt;
	+}
	+
	+static int points_from_particles(Object* ob, int totobj, Scene* scene, float** points, int p_exist)
	+{
	+ int o, p, pt = p_exist;
	+ ParticleSystemModifierData* psmd;
	+ ParticleData* pa;
	+ ParticleSimulationData sim = {NULL};
	+ ParticleKey birth;
	+ ModifierData* mod;
	+
	+ for (o = 0; o < totobj; o++)
	+ {
	+ for (mod = ob[o].modifiers.first; mod; mod = mod->next)
	+ {
	+ if (mod->type == eModifierType_ParticleSystem)
	+ {
	+ psmd = (ParticleSystemModifierData*)mod;
	+ sim.scene = scene;
	+ sim.ob = ob;
	+ sim.psys = psmd->psys;
	+ sim.psmd = psmd;
	+
	+ for (p = 0, pa = psmd->psys->particles; p < psmd->psys->totpart; p++, pa++)
	+ {
	+ psys_get_birth_coordinates(&sim, pa, &birth, 0, 0);
	+ points = MEM_reallocN(points, ((pt+1)3) sizeof(float));
	+ (points)[pt3] = birth.co[0];
	+ (points)[pt3+1] = birth.co[1];
	+ (points)[pt3+2] = birth.co[2];
	+ pt++;
	+ }
	+ }
	+ }
	+ }
	+
	+ return pt;
	+}
	+
	+static int points_from_greasepencil(Object* ob, int totobj, float** points, int p_exist)
	+{
	+ bGPDlayer* gpl;
	+ bGPDframe* gpf;
	+ bGPDstroke* gps;
	+ int pt = p_exist, p, o;
	+
	+ for (o = 0; o < totobj; o++)
	+ {
	+ if ((ob[o].gpd) && (ob[o].gpd->layers.first))
	+ {
	+ for (gpl = ob[o].gpd->layers.first; gpl; gpl = gpl->next)
	+ {
	+ gpf = gpl->actframe;
	+ for (gps = gpf->strokes.first; gps; gps = gps->next)
	+ {
	+ for (p = 0; p < gps->totpoints; p++)
	+ {
	+ points = MEM_reallocN(points, ((pt+1)3)sizeof(float));
	+ (points)[pt3] = gps->points[p].x;
	+ (points)[pt3+1] = gps->points[p].y;
	+ (points)[pt3+2] = gps->points[p].z;
	+ pt++;
	+ }
	+ }
	+ }
	+ }
	+ }
	+
	+ return pt;
	+}
	+
	+static int isChild(Object* ob, Object* child)
	+{
	+ Object *par;
	+ if (child->parent && child->parent == ob)
	+ {
	+ return TRUE;
	+ }
	+
	+ for (par = child->parent; par; par = par->parent) {
	+ if (par == ob) {
	+ return TRUE;
	+ }
	+ }
	+ return FALSE;
	+}
	+
	+static int getChildren(Scene* scene, Object* ob, Object* children)
	+{
	+ Base* base;
	+ int ctr = 0;
	+
	+ for (base = scene->base.first; base; base = base->next)
	+ {
	+ if (isChild(ob, base->object))
	+ {
	+ children = MEM_reallocN(children, sizeof(Object) * (ctr+1));
	+ children[ctr] = *(base->object);
	+ ctr++;
	+ }
	+ }
	+
	+ return ctr;
	+}
	+
	+static int get_points(ExplodeModifierData emd, Scene scene, Object ob, float *points)
	+{
	+ int totpoint = 0, totchildren = 0;
	+ //int fallback = FALSE;
	+ Object* children = NULL;
	+
	+ if (emd->point_source & (eChildParticles \| eChildVerts ))
	+ {
	+ children = MEM_mallocN(sizeof(Object), "get_points->children");
	+ totchildren += getChildren(scene, ob, children);
	+ }
	+
	+ if (emd->point_source & eOwnParticles)
	+ {
	+ totpoint += points_from_particles(ob, 1, scene, points, totpoint);
	+ }
	+
	+ if (emd->point_source & eChildParticles)
	+ {
	+ totpoint += points_from_particles(children, totchildren, scene, points , totpoint);
	+ /*if ((totpoint == 0) && (!(emd->point_source & eOwnVerts)) && (!fallback))
	+ { // if no child particles available, return original geometry
	+ totpoint += points_from_verts(ob, 1, points, totpoint);
	+ fallback = TRUE;
	+ }*/
	+ }
	+
	+ if (emd->point_source & eChildVerts)
	+ {
	+ totpoint += points_from_verts(children, totchildren, points, totpoint);
	+ /*if ((totpoint == 0) && (!(emd->point_source & eOwnVerts)) && (!fallback))
	+ { // if no childverts available, return original geometry
	+ totpoint += points_from_verts(ob, 1, points, totpoint);
	+ fallback = TRUE;
	+ }*/
	+ }
	+
	+ if (emd->point_source & eGreasePencil)
	+ {
	+ totpoint += points_from_greasepencil(ob, 1, points, totpoint);
	+
	+ /*if ((totpoint == 0) && (!(emd->point_source & eOwnVerts)) && (!fallback))
	+ { // if no greasepencil available, return original geometry
	+ totpoint += points_from_verts(ob, 1, points, totpoint);
	+ fallback = TRUE;
	+ }*/
	+ }
	+
	+ if (emd->point_source & eOwnVerts)
	+ {
	+ totpoint += points_from_verts(ob, 1, points, totpoint);
	+ }
	+
	+
	+ if (children)
	+ {
	+ MEM_freeN(children);
	+ children = NULL;
	+ }
	+
	+ return totpoint;
	+}
	+
	+
	+
	+// create the voronoi cell faces inside the existing mesh
	+static BMesh* fractureToCells(Object ob, DerivedMesh derivedData, ParticleSystemModifierData* psmd, ExplodeModifierData* emd)
	+{
	+ void* container = NULL;
	+ void* particle_order = NULL;
	+ float min[3], max[3];
	+ int p = 0;
	+ ParticleData *pa = NULL;
	+ //ParticleSimulationData sim = {NULL};
	+ //ParticleKey birth;
	+ float co[3], vco[3];//, cfra;
	+ BMesh bm = NULL, bmtemp = NULL;
	+
	+ FILE *fp = NULL;
	+ int vert_index = 0;
	+ int read = 0;
	+ BMVert faceverts = NULL, tempvert = NULL, vert = NULL, *localverts = NULL;
	+ BMEdge *faceedges = NULL, edge = NULL;
	+ int *facevert_indexes = NULL;
	+ int face_index = 0;
	+ int edge_index = 0;
	+ char c;
	+ int facevert_index = 0;
	+ BMFace *face = NULL;
	+
	+ DerivedMesh dm = NULL, boolresult = NULL;
	+ MEdge* ed = NULL;
	+ MFace* fa = NULL;
	+
	+ int totvert, totedge, totface;
	+ int v, e, f;
	+ int tempvert_index;
	+ const char *file;
	+ char path, fullpath;
	+ float imat[4][4];
	+ float theta = 0.0f;
	+ int n_size = 8;
	+
	+ float* points = NULL;
	+ int totpoint = 0;
	+
	+ if (emd->use_boolean)
	+ {
	+ //theta = -0.01f;
	+ //make container bigger for boolean case,so cube and container dont have equal size which can lead to boolean errors
	+ if (emd->flip_normal)
	+ { //cubes usually need flip_normal, so enable theta only here, otherwise it will be subtracted
	+ theta = 0.01f;
	+ }
	+
	+ INIT_MINMAX(min, max);
	+ BKE_mesh_minmax(ob->data, min, max);
	+ }
	+ else
	+ {
	+ //con = voronoi.domain(xmin-theta,xmax+theta,ymin-theta,ymax+theta,zmin-theta,zmax+theta,nx,ny,nz,False, False, False, particles)
	+ dm_minmax(derivedData, min, max);
	+ }
	+
	+ //use global coordinates for container
	+ mul_v3_m4v3(min, ob->obmat, min);
	+ mul_v3_m4v3(max, ob->obmat, max);
	+
	+
	+ // printf("Container: %f;%f;%f;%f;%f;%f \n", min[0], max[0], min[1], max[1], min[2], max[2]);
	+ //TODO: maybe support simple shapes without boolean, but eh...
	+ container = container_new(min[0]-theta, max[0]+theta, min[1]-theta, max[1]+theta, min[2]-theta, max[2]+theta,
	+ n_size, n_size, n_size, FALSE, FALSE, FALSE, psmd->psys->totpart); //add number of parts here!
	+ // particle_order = particle_order_new();
	+
	+
	+ /* sim.scene = emd->modifier.scene;
	+ sim.ob = ob;
	+ sim.psys = psmd->psys;
	+ sim.psmd = psmd;*/
	+
	+
	+ //choose from point sources here
	+ if (!emd->refracture)
	+ {
	+ points = MEM_mallocN(sizeof(float), "points");
	+ totpoint = get_points(emd, emd->modifier.scene, ob, &points);
	+
	+ //no points, cant do anything
	+ if (totpoint == 0) return DM_to_bmesh(derivedData);
	+
	+ if (emd->point_source == eOwnVerts)
	+ {
	+ //make container a little bigger ?
	+ theta = 0.01f;
	+ }
	+ container = container_new(min[0]-theta, max[0]+theta, min[1]-theta, max[1]+theta, min[2]-theta, max[2]+theta,
	+ n_size, n_size, n_size, FALSE, FALSE, FALSE, totpoint);
	+
	+ for (p = 0; p < totpoint; p++)
	+ {
	+ co[0] = points[p*3];
	+ co[1] = points[p*3+1];
	+ co[2] = points[p*3+2];
	+ container_put(container, particle_order, p, co[0], co[1], co[2]);
	+ }
	+ }
	+ else
	+ {
	+ container = container_new(min[0]-theta, max[0]+theta, min[1]-theta, max[1]+theta, min[2]-theta, max[2]+theta,
	+ n_size, n_size, n_size, FALSE, FALSE, FALSE, psmd->psys->totpart);
	+ for (p = 0, pa = psmd->psys->particles; p < psmd->psys->totpart; p++, pa++)
	+ {
	+ co[0] = pa->state.co[0];
	+ co[1] = pa->state.co[1];
	+ co[2] = pa->state.co[2];
	+
	+ /*else
	+ {
	+ psys_get_birth_coordinates(&sim, pa, &birth, 0, 0);
	+ co[0] = birth.co[0];
	+ co[1] = birth.co[1];
	+ co[2] = birth.co[2];
	+ }*/
	+
	+ // printf("Particle: %f, %f, %f \n", co[0], co[1], co[2]);
	+
	+ //use particle positions to fracture the object, tell those to the voronoi container
	+ container_put(container, particle_order, p, co[0], co[1], co[2]);
	+ }
	+ }
	+
	+ //TODO: write results to temp file, ensure using the systems temp dir...
	+ // this prints out vertex positions and face indexes
	+ file = "test.out";
	+ path = MEM_mallocN(((strlen(BLI_temporary_dir()) + strlen(file) + 2) * sizeof(char)), "path");
	+ path = strcpy(path, BLI_temporary_dir());
	+ fullpath = strcat(path, file);
	+ fp = fopen(fullpath, "w+");
	+
	+
	+ //this triggers computation of the voronoi cells and produces the desired data:
	+ //see voro++ homepage for detailed description
	+ //TODO: insert link here
	+
	+ // %P global vertex coordinates of voronoi vertices
	+ // v the vertex -> face delimiter
	+ // %t the indexes to the cell vertices, describes which vertices build each face
	+ // f the face -> centroid section delimiter
	+ // %C the centroid of the voronoi cell, used to find nearest particle in createCellpa
	+
	+ //%i the particle index
	+ container_print_custom(container, "%P v %t f %C", fp);
	+ fflush(fp);
	+ rewind(fp);
	+
	+ if (points)
	+ {
	+ MEM_freeN(points);
	+ points = NULL;
	+ }
	+
	+
	+ bm = DM_to_bmesh(derivedData);
	+
	+ //empty the mesh
	+ BM_mesh_clear(bm);
	+
	+ //TODO: maybe put variable declarations at top of function ? C90 ?
	+ //TODO: check for setting in psys to volume
	+ //vert_index = 0;
	+
	+ if (emd->cells)
	+ {
	+ freeCells(emd);
	+ }
	+
	+ emd->cells = MEM_mallocN(sizeof(VoronoiCells), "emd->cells");
	+ emd->cells->data = MEM_mallocN(sizeof(VoronoiCell), "emd->cells->data");
	+ emd->cells->count = 0;
	+
	+
	+ while(feof(fp) == 0)
	+ {
	+ //printf("Reading line...\n");
	+
	+ //store cell data: centroid and associated vertex coords
	+ emd->cells->data = MEM_reallocN(emd->cells->data, sizeof(VoronoiCell) * (emd->cells->count + 1));
	+ emd->cells->data[emd->cells->count].vertices = MEM_mallocN(sizeof(BMVert), "vertices");// (float)malloc(3 * sizeof(float));
	+ emd->cells->data[emd->cells->count].vertco = MEM_mallocN(sizeof(float), "vertco");
	+ emd->cells->data[emd->cells->count].vertex_count = 0;
	+ emd->cells->data[emd->cells->count].particle_index = -1;
	+
	+
	+ bmtemp = BM_mesh_create(&bm_mesh_chunksize_default);
	+ tempvert = MEM_mallocN(sizeof(BMVert*), "tempvert");
	+ tempvert_index = 0;
	+
	+ // Read in the cell data, each line in the output file represents a voronoi cell
	+ while (1)
	+ {
	+ // Read in the vertex coordinates of the cell vertices
	+ read = fscanf(fp, "(%f,%f,%f) ", &vco[0], &vco[1], &vco[2]);
	+ if (read < 3) break;
	+
	+ //back to object space
	+
	+ invert_m4_m4(imat, ob->obmat);
	+ mul_v3_m4v3(vco, imat, vco);
	+
	+
	+ tempvert = MEM_reallocN(tempvert, sizeof(BMVert) (tempvert_index + 1));
	+ vert = BM_vert_create(bmtemp, vco, NULL, 0);
	+ tempvert[tempvert_index] = vert;
	+
	+ tempvert_index++;
	+ }
	+
	+ faceverts = MEM_mallocN(sizeof(BMVert*), "faceverts");
	+ faceedges = MEM_mallocN(sizeof(BMEdge*), "faceedges");
	+ facevert_indexes = MEM_mallocN(sizeof(int), "facevert_indexes");
	+
	+ face_index = 0;
	+ edge_index = 0;
	+
	+ while(1)
	+ {
	+ // printf ("Reading faces...\n");
	+ c = fgetc(fp);
	+ if (isdigit(c)) //maybe atoi !! (ascii value to int ?)
	+ {
	+ //put/seek back and better do fscanf !
	+ fseek(fp, -sizeof(char), SEEK_CUR);
	+ facevert_index = 0;
	+ fscanf(fp, "%d", &facevert_index);
	+ faceverts = MEM_reallocN(faceverts, (face_index + 1) * sizeof(BMVert*));
	+ // find vertices for each face, store indexes here
	+ faceverts[face_index] = tempvert[facevert_index];//emd->cells->data[emd->cells->count].vertices[facevert_index];
	+
	+ facevert_indexes = MEM_reallocN(facevert_indexes, sizeof(int) * (face_index+1));
	+ facevert_indexes[face_index] = facevert_index;
	+
	+ if (face_index > 0)
	+ {
	+ //argh, need to determine edges manually...
	+ faceedges = MEM_reallocN(faceedges, (edge_index + 1) * sizeof(BMEdge*));
	+ edge = BM_edge_create(bmtemp, faceverts[face_index - 1], faceverts[face_index], NULL, 0);
	+ faceedges[edge_index] = edge;
	+ edge_index++;
	+
	+ }
	+
	+ face_index++;
	+
	+ }
	+ else if ( c == ')')
	+ {
	+ //end of face tuple, can create face now, but before create last edge to close the circle
	+ faceedges = MEM_reallocN(faceedges, (edge_index + 1) * sizeof(BMEdge*));
	+ edge = BM_edge_create(bmtemp, faceverts[face_index-1], faceverts[0], NULL, 0);
	+ faceedges[edge_index] = edge;
	+
	+ face = BM_face_create(bmtemp, faceverts, faceedges, face_index, 0);
	+ if (emd->flip_normal)
	+ {
	+ BM_face_normal_flip(bmtemp, face);
	+ }
	+
	+ // MEM_freeN(faceedges);
	+ // MEM_freeN(faceverts);
	+ // MEM_freeN(facevert_indexes);
	+ edge_index = 0;
	+ face_index = 0;
	+ //faceverts = MEM_mallocN(sizeof(BMVert*), "faceverts");
	+ //faceedges = MEM_mallocN(sizeof(BMEdge*), "faceedges");
	+ //facevert_indexes = MEM_mallocN(sizeof(int), "facevert_indexes");
	+ }
	+ else if ((c == 'f') \|\| (feof(fp) != 0))
	+ {
	+ if (c == 'f')
	+ {
	+ //Intersection, use elements from temporary per-cell bmeshes and write to global bmesh, which
	+ //is passed around and whose vertices are manipulated directly.
	+ int mat_index = 0;
	+ dm = CDDM_from_bmesh(bmtemp, TRUE);
	+ BM_mesh_free(bmtemp);
	+ bmtemp = NULL;
	+
	+ DM_ensure_tessface(derivedData);
	+ CDDM_calc_edges_tessface(derivedData);
	+ CDDM_tessfaces_to_faces(derivedData);
	+ CDDM_calc_normals(derivedData);
	+
	+ DM_ensure_tessface(dm);
	+ CDDM_calc_edges_tessface(dm);
	+ CDDM_tessfaces_to_faces(dm);
	+ CDDM_calc_normals(dm);
	+
	+ if (emd->use_boolean)
	+ {
	+ //put temp bmesh to temp object ? Necessary ? Seems so.
	+ //TODO: maybe get along without temp object ?
	+ if (!emd->tempOb)
	+ {
	+ emd->tempOb = BKE_object_add_only_object(OB_MESH, "Intersect");
	+ //emd->tempOb = BKE_object_add(emd->modifier.scene, OB_MESH);
	+ }
	+
	+ if (!emd->tempOb->data)
	+ {
	+ emd->tempOb->data = BKE_object_obdata_add_from_type(OB_MESH);
	+ //object_add_material_slot(emd->tempOb);
	+ }
	+
	+
	+ //assign inner material to temp Object
	+ if (emd->inner_material)
	+ {
	+ //assign inner material as secondary mat to ob if not there already
	+ mat_index = find_material_index(ob, emd->inner_material);
	+ if (mat_index == 0)
	+ {
	+ object_add_material_slot(ob);
	+ assign_material(ob, emd->inner_material, ob->totcol, BKE_MAT_ASSIGN_OBDATA);
	+ }
	+
	+ //shard gets inner material, maybe assign to all faces as well (in case this does not happen automatically
	+ assign_material(emd->tempOb, emd->inner_material, 1, BKE_MAT_ASSIGN_OBDATA);
	+ }
	+
	+ DM_to_mesh(dm, emd->tempOb->data, emd->tempOb);
	+ copy_m4_m4(emd->tempOb->obmat, ob->obmat);
	+
	+ //CustomData_merge(&derivedData->faceData, &dm->faceData, CD_MASK_DERIVEDMESH & ~(CD_MASK_NORMAL \| CD_MASK_ORIGINDEX), CD_DUPLICATE, derivedData->numTessFaceData);
	+
	+ boolresult = NewBooleanDerivedMesh(dm, emd->tempOb, derivedData, ob, eBooleanModifierOp_Intersect);
	+
	+ //if boolean fails, return original mesh, emit a warning
	+ if (!boolresult)
	+ {
	+ boolresult = dm;
	+ printf("Boolean Operation failed, using original mesh !\n");
	+ }
	+ else
	+ {
	+ DM_release(dm);
	+ MEM_freeN(dm);
	+ }
	+ }
	+ else
	+ {
	+ boolresult = dm;
	+ }
	+
	+
	+ //DM_ensure_tessface(boolresult);
	+ CDDM_calc_edges_tessface(boolresult);
	+ CDDM_tessfaces_to_faces(boolresult);
	+ CDDM_calc_normals(boolresult);
	+ DM_ensure_tessface(boolresult);
	+
	+ emd->cells->data[emd->cells->count].cell_mesh = boolresult;// CDDM_copy(boolresult);
	+ //CustomData_merge(&boolresult->faceData, &emd->cells->data[emd->cells->count].cell_mesh->faceData,
	+ // CD_MASK_DERIVEDMESH & ~(CD_MASK_NORMAL \| CD_MASK_ORIGINDEX), CD_DUPLICATE, boolresult->numTessFaceData);
	+
	+ totvert = boolresult->getNumVerts(boolresult);
	+ totedge = boolresult->getNumEdges(boolresult);
	+ totface = boolresult->getNumTessFaces(boolresult);
	+
	+ localverts = MEM_mallocN(sizeof(BMVert) totvert, "localverts");
	+ ed = boolresult->getEdgeArray(boolresult);
	+ fa = boolresult->getTessFaceArray(boolresult);
	+
	+ for (v = 0; v < totvert; v++)
	+ {
	+ boolresult->getVertCo(boolresult, v, co);
	+
	+ emd->cells->data[emd->cells->count].vertices =
	+ MEM_reallocN(emd->cells->data[emd->cells->count].vertices, (vert_index + 1)* sizeof(BMVert));
	+
	+ emd->cells->data[emd->cells->count].vertex_count++;
	+
	+
	+ vert = BM_vert_create(bm, co, NULL, 0);
	+ localverts[v] = vert;
	+
	+ emd->cells->data[emd->cells->count].vertices[vert_index] = vert;
	+
	+ //store original coordinates for later re-use
	+
	+ emd->cells->data[emd->cells->count].vertco =
	+ MEM_reallocN(emd->cells->data[emd->cells->count].vertco, (vert_index + 1)* (3*sizeof(float)));
	+
	+ emd->cells->data[emd->cells->count].vertco[3*vert_index] = vert->co[0];
	+ emd->cells->data[emd->cells->count].vertco[3*vert_index+1] = vert->co[1];
	+ emd->cells->data[emd->cells->count].vertco[3*vert_index+2] = vert->co[2];
	+
	+ vert_index++;
	+ }
	+
	+ for (e = 0; e < totedge; e++)
	+ {
	+ BM_edge_create(bm, localverts[ed[e].v1], localverts[ed[e].v2], NULL, 0);
	+ }
	+
	+ for (f = 0; f < totface; f++)
	+ {
	+ if ((fa[f].v4 > 0) && (fa[f].v4 < totvert))
	+ { //create quad
	+ face = BM_face_create_quad_tri(bm, localverts[fa[f].v1], localverts[fa[f].v2], localverts[fa[f].v3], localverts[fa[f].v4], NULL, 0);
	+ face->mat_nr = fa[f].mat_nr;
	+
	+ }
	+ else
	+ { //triangle only
	+ face = BM_face_create_quad_tri(bm, localverts[fa[f].v1], localverts[fa[f].v2], localverts[fa[f].v3], NULL, NULL, 0);
	+ face->mat_nr = fa[f].mat_nr;
	+ }
	+ }
	+
	+
	+ MEM_freeN(localverts);
	+ }
	+
	+ edge_index = 0;
	+ face_index = 0;
	+ // MEM_freeN(faceedges);
	+ // MEM_freeN(faceverts);
	+ // faceverts = MEM_mallocN(sizeof(BMVert*), "faceverts");
	+ // faceedges = MEM_mallocN(sizeof(BMEdge*), "faceverts");
	+ break;
	+ }
	+ }
	+
	+ //read centroid
	+ fscanf(fp, " %f %f %f", &emd->cells->data[emd->cells->count].centroid[0],
	+ &emd->cells->data[emd->cells->count].centroid[1],
	+ &emd->cells->data[emd->cells->count].centroid[2]);
	+
	+ invert_m4_m4(imat, ob->obmat);
	+ mul_m4_v3(imat, emd->cells->data[emd->cells->count].centroid);
	+
	+ //skip newline
	+ if (feof(fp) == 0)
	+ {
	+
	+#ifdef _WIN32
	+ //skip \r\n
	+ fseek(fp, 2*sizeof(char), SEEK_CUR);
	+#else
	+ //skip \n
	+ fseek(fp, sizeof(char), SEEK_CUR);
	+#endif
	+ emd->cells->count++;
	+ }
	+ else
	+ {
	+ //EOF reached, free last vertco/vertices
	+ MEM_freeN(emd->cells->data[emd->cells->count].vertco);
	+ MEM_freeN(emd->cells->data[emd->cells->count].vertices);
	+ }
	+
	+ vert_index = 0;
	+ MEM_freeN(tempvert);
	+ if (bmtemp) BM_mesh_free(bmtemp);
	+ MEM_freeN(faceverts);
	+ MEM_freeN(facevert_indexes);
	+ MEM_freeN(faceedges);
	+ }
	+
	+ fclose(fp);
	+ MEM_freeN(path);
	+
	+ printf("%d cells missing\n", totpoint - emd->cells->count); //use totpoint here
	+
	+ return bm;
	+}
	+
	+static void createParticleTree(ExplodeModifierData emd, ParticleSystemModifierData psmd, Scene* scene, Object* ob)
	+{
	+ ParticleSimulationData sim = {NULL};
	+ ParticleSystem *psys = psmd->psys;
	+ ParticleData *pa;
	+ ParticleKey birth;
	+ int p = 0, totpart = 0;
	+
	+ totpart = psys->totpart;
	+ sim.scene = scene;
	+ sim.ob = ob;
	+ sim.psys = psmd->psys;
	+ sim.psmd = psmd;
	+
	+ /* make tree of emitter locations */
	+ if (emd->patree)
	+ {
	+ BLI_kdtree_free(emd->patree);
	+ emd->patree = NULL;
	+ }
	+
	+ emd->patree = BLI_kdtree_new(totpart);
	+ for (p = 0, pa = psys->particles; p < totpart; p++, pa++)
	+ {
	+ if (emd->emit_continuously)
	+ {
	+ psys_get_birth_coordinates(&sim, pa, &birth, 0, 0);
	+ BLI_kdtree_insert(emd->patree, p, birth.co, NULL);
	+ }
	+ else if (ELEM3(pa->alive, PARS_ALIVE, PARS_DYING, PARS_DEAD))
	+ {
	+ //psys_particle_on_emitter(psmd, psys->part->from, pa->num, pa->num_dmcache, pa->fuv, pa->foffset, co, NULL, NULL, NULL, NULL, NULL);
	+ psys_get_birth_coordinates(&sim, pa, &birth, 0, 0);
	+ BLI_kdtree_insert(emd->patree, p, birth.co, NULL);
	+ }
	+ }
	+
	+ BLI_kdtree_balance(emd->patree);
	+}
	+
	+
	+static void mapCellsToParticles(ExplodeModifierData emd, ParticleSystemModifierData psmd, Scene* scene, Object* ob)
	+{
	+ ParticleSystem *psys = psmd->psys;
	+ float center[3];
	+ int p = 0, c;
	+ // if voronoi: need to set centroids of cells to nearest particle, apply same(?) matrix to a group of verts
	+ float cfra;
	+ cfra = BKE_scene_frame_get(scene);
	+
	+ for(c = 0; c < emd->cells->count; c++)
	+ {
	+ center[0] = emd->cells->data[c].centroid[0];
	+ center[1] = emd->cells->data[c].centroid[1];
	+ center[2] = emd->cells->data[c].centroid[2];
	+
	+ //centroids were stored in object space, go to global space (particles are in global space)
	+ mul_m4_v3(ob->obmat, center);
	+ p = BLI_kdtree_find_nearest(emd->patree, center, NULL, NULL);
	+
	+ if (emd->emit_continuously)
	+ {
	+ if (ELEM3(psys->particles[p].alive, PARS_ALIVE, PARS_DYING, PARS_DEAD))
	+ {
	+ emd->cells->data[c].particle_index = p;
	+ }
	+ else
	+ {
	+ emd->cells->data[c].particle_index = -1;
	+ }
	+ }
	+ else
	+ {
	+ if ((emd->cells->data[c].particle_index == -1) && (cfra > (psys->part->sta + emd->map_delay)))
	+ {
	+ //map once, with delay, the larger the delay, the more smaller chunks !
	+ emd->cells->data[c].particle_index = p;
	+ }
	+ }
	+ }
	+}
	+
	+static void explodeCells(ExplodeModifierData *emd,
	+ ParticleSystemModifierData psmd, Scene scene, Object *ob)
	+{
	+ ParticleSimulationData sim = {NULL};
	+ ParticleData pa = NULL, pars = psmd->psys->particles;
	+ ParticleKey state, birth;
	+ float imat[4][4];
	+ float rot[4];
	+ int totpart = 0;
	+ int i, j, p;
	+
	+ totpart = psmd->psys->totpart;
	+
	+ sim.scene = scene;
	+ sim.ob = ob;
	+ sim.psys = psmd->psys;
	+ sim.psmd = psmd;
	+
	+ if (emd->cells == NULL)
	+ {
	+ return;
	+ }
	+
	+ /* getting back to object space */ // do i need this ?
	+ invert_m4_m4(imat, ob->obmat);
	+ psmd->psys->lattice = psys_get_lattice(&sim);
	+
	+ //create a new mesh aka "explode" from new vertex positions. use bmesh for that now.
	+
	+ //since we dont have real access to tessfaces we can deal with from our cells, need to recreate the edges
	+ //and faces now the bmesh way. Or ... simply move the verts ? and recreate the DerivedMesh.
	+
	+ //but... need the Verts objects... hopefully global indexes are the same as in DerivedMesh, if not, need to deal with BMesh there too.
	+
	+ for (i = 0; i < emd->cells->count; i++)
	+ {
	+ p = emd->cells->data[i].particle_index;
	+ if ((p >= 0) && (p < totpart))
	+ {
	+ pa = pars + p;
	+ }
	+
	+ for (j = 0; j < emd->cells->data[i].vertex_count; j++)
	+ {
	+ // BMVert *vert = BM_vert_at_index(bm, ind);
	+ BMVert* vert = emd->cells->data[i].vertices[j];
	+
	+ //reset to original coords // stored at fracture time
	+ vert->co[0] = emd->cells->data[i].vertco[j*3];
	+ vert->co[1] = emd->cells->data[i].vertco[j*3+1];
	+ vert->co[2] = emd->cells->data[i].vertco[j*3+2];
	+
	+ if ((p < 0) \|\| (p > totpart-1) \|\| ((!emd->emit_continuously) && (pa->alive == PARS_UNBORN)))
	+ {
	+ continue;
	+ }
	+
	+ //do recalc here ! what about uv maps and such.... ? let boolean (initially) handle this, but
	+ //i HOPE vertex movement will update the uvs as well... or bust
	+
	+ //particle CACHE causes lots of problems with this kind of calculation.
	+ psys_get_birth_coordinates(&sim, pa, &birth, 0, 0);
	+ // psys_particle_on_emitter(psmd, psmd->psys->part->from, pa->num, pa->num_dmcache, pa->fuv, pa->foffset, co, NULL, NULL, NULL, NULL, NULL);
	+
	+ //birth.time = cfra;
	+ //psys_get_particle_state(&sim, p, &birth, 1);
	+ //birth = pa->prev_state;
	+ state = pa->state;
	+
	+ //vertco = vert->co;
	+ mul_m4_v3(ob->obmat, vert->co);
	+ sub_v3_v3(vert->co, birth.co);
	+
	+ /* apply rotation, size & location */
	+ //only if defined, means if checked in psys
	+ if (psmd->psys->part->flag & PART_ROTATIONS)
	+ {
	+ sub_qt_qtqt(rot, state.rot, birth.rot);
	+ mul_qt_v3(rot, vert->co);
	+ }
	+
	+ //TODO: maybe apply size flag, alive / unborn / dead flags
	+ // if (emd->flag & eExplodeFlag_PaSize)
	+ // mul_v3_fl(vert->co, pa->size);
	+
	+ add_v3_v3(vert->co, state.co);
	+
	+ mul_m4_v3(imat, vert->co);
	+
	+ }
	+ }
	+
	+ if (psmd->psys->lattice) {
	+ end_latt_deform(psmd->psys->lattice);
	+ psmd->psys->lattice = NULL;
	+ }
	+
	+ //return bm;
	+}
	+
	+static void resetCells(ExplodeModifierData *emd)
	+{
	+ int c;
	+
	+ for (c = 0; c < emd->cells->count; c++)
	+ {
	+ emd->cells->data[c].particle_index = -1;
	+ }
	+}
	+
	static DerivedMesh applyModifier(ModifierData md, Object *ob,
	DerivedMesh *derivedData,
	ModifierApplyFlag UNUSED(flag))
	@@ -996,54 +2011,261 @@
	DerivedMesh *dm = derivedData;
	ExplodeModifierData emd = (ExplodeModifierData ) md;
	ParticleSystemModifierData *psmd = findPrecedingParticlesystem(ob, md);
	+
	+ DerivedMesh result = NULL, d = NULL;
	+ int i = 0, j = 0, f, f_index = 0, ml_index = 0;
	+ MTFace* mtface = NULL;
	+ MTFace* mtf = NULL;
	+ MTFace tf;
	+ //MTFaces not used in BMesh/further modifier processing , so need to split to MTexPoly/MLoopUV
	+ MTexPoly* mtps, mtp;
	+ MLoopUV* mluvs, mluv;
	+ MLoop* mla = NULL, *ml;
	+ MPoly* mpa = NULL, *mp;
	+ float imat[4][4], oldobmat[4][4];
	+
	+ if (psmd)
	+ {
	+ if (emd->mode == eFractureMode_Cells)
	+ {
	+#ifdef WITH_MOD_VORONOI
	+
	+ if ((emd->cells == NULL) \|\|
	+ (emd->last_part != psmd->psys->totpart) \|\|
	+ (emd->last_bool != emd->use_boolean) \|\|
	+ (emd->last_flip != emd->flip_normal) \|\|
	+ (emd->last_point_source != emd->point_source) \|\|
	+ (emd->use_cache == FALSE))
	+ {
	+ invert_m4_m4(imat, ob->obmat);
	+ copy_m4_m4(oldobmat, ob->obmat);
	+ mult_m4_m4m4(ob->obmat, imat, ob->obmat); //neutralize obmat
	+
	+ if (emd->cells) BM_mesh_free(emd->fracMesh);
	+ emd->fracMesh = fractureToCells(ob, derivedData, psmd, emd);
	+
	+ copy_m4_m4(ob->obmat, oldobmat); // restore obmat
	+
	+ emd->last_part = psmd->psys->totpart;
	+ emd->last_bool = emd->use_boolean;
	+ emd->last_flip = emd->flip_normal;
	+ emd->last_point_source = emd->point_source;
	+
	+ }
	+
	+ if (emd->refracture)
	+ {
	+ if ((emd->cells == NULL) \|\|
	+ (emd->last_part != psmd->psys->totpart) \|\|
	+ (emd->last_bool != emd->use_boolean) \|\|
	+ (emd->last_flip != emd->flip_normal) \|\|
	+ (emd->last_point_source != emd->point_source) \|\|
	+ (emd->use_cache == FALSE))
	+ {
	+ if (emd->fracMesh) BM_mesh_free(emd->fracMesh);
	+ emd->fracMesh = fractureToCells(ob, derivedData, psmd, emd);
	+ }
	+
	+ emd->last_part = psmd->psys->totpart;
	+ emd->last_bool = emd->use_boolean;
	+ emd->last_flip = emd->flip_normal;
	+
	+ result = CDDM_from_bmesh(emd->fracMesh, TRUE);
	+ BM_mesh_free(emd->fracMesh);
	+ emd->fracMesh = NULL;
	+ return result;
	+
	+ }
	+ else
	+ {
	+ //BM_mesh_copy(emd->fracMesh); loses some faces too, hrm.
	+ if (emd->map_delay != emd->last_map_delay) resetCells(emd);
	+ emd->last_map_delay = emd->map_delay;
	+ createParticleTree(emd, psmd, md->scene, ob);
	+ mapCellsToParticles(emd, psmd, md->scene, ob);
	+ explodeCells(emd, psmd, md->scene, ob);
	+ result = CDDM_from_bmesh(emd->fracMesh, TRUE);
	+
	+ DM_ensure_tessface(result);
	+ CDDM_calc_edges_tessface(result);
	+ CDDM_tessfaces_to_faces(result);
	+ CDDM_calc_normals(result);
	+
	+ if (emd->use_boolean)
	+ {
	+ mtface = MEM_mallocN(sizeof(MTFace), "mtface");
	+ mtps = MEM_mallocN(sizeof(MTexPoly), "mtps");
	+ mluvs = MEM_mallocN(sizeof(MLoopUV), "mluvs");
	+
	+ f_index = 0;
	+ ml_index = 0;
	+ //Image* img;
	+
	+ for (i = 0; i < emd->cells->count; i++)
	+ {
	+ d = emd->cells->data[i].cell_mesh;
	+ //f = d->numTessFaceData;
	+
	+ //if (mtf) MEM_freeN(mtf);
	+ //hope this merges the MTFace data... successfully...
	+ mtf = DM_get_tessface_data_layer(d, CD_MTFACE);
	+ if (!mtf)
	+ {
	+ //argh, something went wrong, data will be missing...
	+ MEM_freeN(mtface);
	+ mtface = NULL;
	+ break;
	+ }
	+
	+
	+ /*CDDM_calc_edges_tessface(d);
	+ CDDM_tessfaces_to_faces(d);
	+ CDDM_calc_normals(d);
	+ DM_ensure_tessface(d);*/
	+ //if (mpa) MEM_freeN(mpa);
	+ //if (mla) MEM_freeN(mla);
	+ mpa = d->getPolyArray(d);
	+ mla = d->getLoopArray(d);
	+
	+ for (f = 0; f < d->numTessFaceData; f++)
	+ {
	+ mtface = MEM_reallocN(mtface, sizeof(MTFace) * (f_index+1));
	+ tf = mtf[f];
	+
	+ //setting image with the crowbar, hrm...
	+ /*if (tf.tpage)
	+ {
	+ img = tf.tpage;
	+ }
	+ if (!tf.tpage)
	+ {
	+ //free(mtface);
	+ //mtface = NULL;
	+ //break;
	+ tf.tpage = img;
	+ }*/
	+ mtps = MEM_reallocN(mtps, sizeof(MTexPoly) * (f_index+1));
	+ mtp.tpage = tf.tpage;
	+ mtp.flag = tf.flag;
	+ mtp.mode = tf.mode;
	+ mtp.tile = tf.tile;
	+ mtp.transp = tf.transp;
	+ mtps[f_index] = mtp;
	+
	+ //assume facecount = polycount and faces = polys since only tris and quads available
	+ //because of boolean
	+
	+ mp = mpa + f; // get Polygon according to face index
	+ mluvs = MEM_reallocN(mluvs, sizeof(MLoopUV)* (mp->totloop + ml_index));
	+
	+ for (j = mp->loopstart; j < mp->loopstart + mp->totloop; j++)
	+ {
	+ //assume vertindex = uvindex, sigh, is that so ?, and no more than 4 loops !
	+ ml = mla + j;
	+ //mluv.flag = MLOOPUV_PINNED;//; MLOOPUV_EDGESEL;// MLOOPUV_VERTSEL;
	+ mluv.uv[0] = tf.uv[j-mp->loopstart][0];
	+ mluv.uv[1] = tf.uv[j-mp->loopstart][1];
	+ mluvs[ml_index] = mluv;
	+ ml_index++;
	+ }
	+
	+ mtface[f_index] = tf;
	+ f_index++;
	+ }
	+ //MEM_freeN(mtf);
	+ //MEM_freeN(mla);
	+ //MEM_freeN(mpa);
	+
	+ //if(!mtface)
	+ // break;
	+ }
	+
	+ if (mtface)
	+ {
	+ CustomData fdata, pdata, *ldata;
	+ fdata = &result->faceData;
	+ ldata = &result->loopData;
	+ pdata = &result->polyData;
	+
	+ CustomData_add_layer(fdata, CD_MTFACE , CD_DUPLICATE, mtface, f_index);
	+ CustomData_add_layer(pdata, CD_MTEXPOLY, CD_DUPLICATE, mtps, f_index);
	+ CustomData_add_layer(ldata, CD_MLOOPUV, CD_DUPLICATE, mluvs, ml_index);
	+
	+ MEM_freeN(mtface);
	+ MEM_freeN(mtps);
	+ MEM_freeN(mluvs);
	+ //MEM_freeN(mtf);
	+ //MEM_freeN(mla);
	+ //MEM_freeN(mpa);
	+ }
	+ }
	+
	+ return result;
	+ }
	+#else
	+ emd->mode = eFractureMode_Faces;
	+ return derivedData;
	+#endif
	+ }

	- DM_ensure_tessface(dm); /* BMESH - UNTIL MODIFIER IS UPDATED FOR MPoly */
	+
	+ else if (emd->mode == eFractureMode_Faces)
	+ {
	+ ParticleSystem *psys = psmd->psys;
	+ DM_ensure_tessface(dm); /* BMESH - UNTIL MODIFIER IS UPDATED FOR MPoly */

	- if (psmd) {
	- ParticleSystem *psys = psmd->psys;
	+ if (psys == NULL \|\| psys->totpart == 0) return derivedData;
	+ if (psys->part == NULL \|\| psys->particles == NULL) return derivedData;
	+ if (psmd->dm == NULL) return derivedData;

	- if (psys == NULL \|\| psys->totpart == 0) return derivedData;
	- if (psys->part == NULL \|\| psys->particles == NULL) return derivedData;
	- if (psmd->dm == NULL) return derivedData;
	+ /* 1. find faces to be exploded if needed */
	+ if (emd->facepa == NULL \|\|
	+ psmd->flag & eParticleSystemFlag_Pars \|\|
	+ emd->flag & eExplodeFlag_CalcFaces \|\|
	+ MEM_allocN_len(emd->facepa) / sizeof(int) != dm->getNumTessFaces(dm))
	+ {
	+ if (psmd->flag & eParticleSystemFlag_Pars)
	+ psmd->flag &= ~eParticleSystemFlag_Pars;
	+
	+ if (emd->flag & eExplodeFlag_CalcFaces)
	+ emd->flag &= ~eExplodeFlag_CalcFaces;

	- /* 1. find faces to be exploded if needed */
	- if (emd->facepa == NULL \|\|
	- psmd->flag & eParticleSystemFlag_Pars \|\|
	- emd->flag & eExplodeFlag_CalcFaces \|\|
	- MEM_allocN_len(emd->facepa) / sizeof(int) != dm->getNumTessFaces(dm))
	- {
	- if (psmd->flag & eParticleSystemFlag_Pars)
	- psmd->flag &= ~eParticleSystemFlag_Pars;
	-
	- if (emd->flag & eExplodeFlag_CalcFaces)
	- emd->flag &= ~eExplodeFlag_CalcFaces;
	+ createFacepa(emd, psmd, derivedData);
	+ }
	+ /* 2. create new mesh */
	+ if (emd->flag & eExplodeFlag_EdgeCut) {
	+ int *facepa = emd->facepa;
	+ DerivedMesh *splitdm = cutEdges(emd, dm);
	+ DerivedMesh *explode = explodeMesh(emd, psmd, md->scene, ob, splitdm);

	- createFacepa(emd, psmd, derivedData);
	- }
	- /* 2. create new mesh */
	- if (emd->flag & eExplodeFlag_EdgeCut) {
	- int *facepa = emd->facepa;
	- DerivedMesh *splitdm = cutEdges(emd, dm);
	- DerivedMesh *explode = explodeMesh(emd, psmd, md->scene, ob, splitdm);
	-
	- MEM_freeN(emd->facepa);
	- emd->facepa = facepa;
	- splitdm->release(splitdm);
	- return explode;
	- }
	- else
	- return explodeMesh(emd, psmd, md->scene, ob, derivedData);
	+ MEM_freeN(emd->facepa);
	+ emd->facepa = facepa;
	+ splitdm->release(splitdm);
	+ return explode;
	+ }
	+ else
	+ return explodeMesh(emd, psmd, md->scene, ob, derivedData);
	+ }
	}
	return derivedData;
	}

	+static void foreachIDLink(ModifierData md, Object ob,
	+ IDWalkFunc walk, void *userData)
	+{
	+ ExplodeModifierData emd = (ExplodeModifierData ) md;
	+
	+ walk(userData, ob, (ID **)&emd->inner_material);
	+}

	+
	ModifierTypeInfo modifierType_Explode = {
	/* name */ "Explode",
	/* structName */ "ExplodeModifierData",
	/* structSize */ sizeof(ExplodeModifierData),
	/* type */ eModifierTypeType_Constructive,
	- /* flags */ eModifierTypeFlag_AcceptsMesh,
	+ /* flags */ eModifierTypeFlag_AcceptsMesh \|
	+ eModifierTypeFlag_Single, //more modifiers dont really make sense
	/* copyData */ copyData,
	/* deformVerts */ NULL,
	/* deformMatrices */ NULL,
	@@ -1059,6 +2281,6 @@
	/* dependsOnTime */ dependsOnTime,
	/* dependsOnNormals */ NULL,
	/* foreachObjectLink */ NULL,
	- /* foreachIDLink */ NULL,
	+ /* foreachIDLink */ foreachIDLink,
	/* foreachTexLink */ NULL,
	};
	Index: source/blender/modifiers/SConscript
	===================================================================
	--- source/blender/modifiers/SConscript (revision 53656)
	+++ source/blender/modifiers/SConscript (working copy)
	@@ -52,6 +52,10 @@
	if env['WITH_BF_OCEANSIM']:
	defs.append('WITH_OCEANSIM')

	+if env['WITH_BF_VORONOI']:
	+ incs += ' #/extern/voro++'
	+ defs.append('WITH_MOD_VORONOI')
	+
	if env['WITH_BF_GAMEENGINE']:
	incs += ' #/extern/recastnavigation'
	defs.append('WITH_GAMEENGINE')
	Index: source/blender/modifiers/CMakeLists.txt
	===================================================================
	--- source/blender/modifiers/CMakeLists.txt (revision 53656)
	+++ source/blender/modifiers/CMakeLists.txt (working copy)
	@@ -129,6 +129,13 @@
	add_definitions(-DWITH_OCEANSIM)
	endif()

	+if(WITH_MOD_VORONOI)
	+ add_definitions(-DWITH_MOD_VORONOI)
	+ list(APPEND INC
	+ ../../../extern/voro++
	+ )
	+endif()
	+
	if(WITH_GAMEENGINE)
	# for MOD_navmesh.c
	add_definitions(-DWITH_GAMEENGINE)
	Index: source/blender/makesdna/DNA_modifier_types.h
	===================================================================
	--- source/blender/makesdna/DNA_modifier_types.h (revision 53656)
	+++ source/blender/makesdna/DNA_modifier_types.h (working copy)
	@@ -631,12 +631,67 @@
	eExplodeFlag_Dead = (1<<5),
	} ExplodeModifierFlag;

	+typedef enum {
	+ eFractureMode_Cells = 0,
	+ eFractureMode_Faces = 1,
	+} eFractureMode;
	+
	+enum {
	+ MOD_VORONOI_USEBOOLEAN = (1 << 1),
	+ MOD_VORONOI_REFRACTURE = (1 << 2),
	+ MOD_VORONOI_USECACHE = (1 << 3),
	+ MOD_VORONOI_FLIPNORMAL = (1 << 4),
	+ MOD_VORONOI_EMITCONTINUOUSLY = (1 << 5)
	+};
	+
	+typedef struct VoronoiCell {
	+ struct BMVert **vertices;
	+ float *vertco;
	+ struct DerivedMesh *cell_mesh;
	+ int vertex_count;
	+ int particle_index;
	+ float centroid[3];
	+ char pad[4];
	+} VoronoiCell;
	+
	+typedef struct VoronoiCells {
	+ VoronoiCell *data;
	+ int count;
	+ char pad[4];
	+} VoronoiCells;
	+
	+typedef enum {
	+ eOwnVerts = (1 << 0),
	+ eOwnParticles = (1 << 1),
	+ eChildVerts = (1 << 2),
	+ eChildParticles = (1 << 3),
	+ eGreasePencil = (1 << 4),
	+
	+} eVoronoiPointSource;
	+
	typedef struct ExplodeModifierData {
	ModifierData modifier;
	- int *facepa;
	+
	+ //for voronoi cell mode
	+ VoronoiCells *cells;
	+ struct BMesh *fracMesh;
	+ struct Object *tempOb;
	+ struct KDTree *patree;
	+ struct Material *inner_material;
	+
	+ //for face mode
	+ int *facepa;
	short flag, vgroup;
	float protect;
	- char uvname[64]; /* MAX_CUSTOMDATA_LAYER_NAME */
	+ char uvname[64]; /* MAX_CUSTOMDATA_LAYER_NAME */
	+
	+ //for voronoi cell mode
	+ int use_boolean, refracture, use_cache, flip_normal;
	+ int last_part, last_bool, last_flip, emit_continuously;
	+ int mode, map_delay, last_map_delay, point_source;
	+ int last_point_source;
	+ char pad[4];
	+
	} ExplodeModifierData;

	typedef struct MultiresModifierData {
	Index: source/blender/makesrna/intern/rna_modifier.c
	===================================================================
	--- source/blender/makesrna/intern/rna_modifier.c (revision 53656)
	+++ source/blender/makesrna/intern/rna_modifier.c (working copy)
	@@ -2120,7 +2120,23 @@
	{
	StructRNA *srna;
	PropertyRNA *prop;
	+
	+ static EnumPropertyItem prop_mode_items[] = {
	+ {eFractureMode_Cells, "CELLS", 0, "Voronoi Cells", "Fracture to voronoi cells and move them with particles"},
	+ {eFractureMode_Faces, "FACES", 0, "Mesh Faces", "Move mesh faces with particles"},
	+ {0, NULL, 0, NULL, NULL}
	+ };
	+
	+ static EnumPropertyItem prop_point_source_items[] = {
	+ {eOwnParticles, "OWN_PARTICLES", 0, "Own Particles", "Use own particles as point cloud"},
	+ {eOwnVerts, "OWN_VERTS", 0, "Own Vertices", "Use own vertices as point cloud"},
	+ {eChildParticles, "CHILD_PARTICLES", 0, "Child Particles", "Use particles of child objects as point cloud"},
	+ {eChildVerts, "CHILD_VERTS", 0, "Child Vertices", "Use child vertices as point cloud"},
	+ {eGreasePencil, "GREASE_PENCIL", 0, "Grease Pencil", "Use grease pencil points as point cloud"},
	+ {0, NULL, 0, NULL, NULL}
	+ };

	+
	srna = RNA_def_struct(brna, "ExplodeModifier", "Modifier");
	RNA_def_struct_ui_text(srna, "Explode Modifier", "Explosion effect modifier based on a particle system");
	RNA_def_struct_sdna(srna, "ExplodeModifierData");
	@@ -2166,6 +2182,55 @@
	RNA_def_property_string_maxlength(prop, MAX_CUSTOMDATA_LAYER_NAME);
	RNA_def_property_ui_text(prop, "Particle UV", "UV map to change with particle age");
	RNA_def_property_update(prop, 0, "rna_Modifier_update");
	+
	+ prop = RNA_def_property(srna, "mode", PROP_ENUM, PROP_NONE);
	+ RNA_def_property_enum_items(prop, prop_mode_items);
	+ RNA_def_property_ui_text(prop, "Mode", "Mode of fracture");
	+ RNA_def_property_update(prop, 0, "rna_Modifier_update");
	+
	+ prop = RNA_def_property(srna, "point_source", PROP_ENUM, PROP_NONE);
	+ RNA_def_property_enum_items(prop, prop_point_source_items);
	+ RNA_def_property_flag(prop, PROP_ENUM_FLAG);
	+ RNA_def_property_enum_default(prop, eOwnParticles);
	+ RNA_def_property_ui_text(prop, "Point Source", "Source of point cloud");
	+ RNA_def_property_update(prop, 0, "rna_Modifier_update");
	+
	+ prop = RNA_def_property(srna, "use_boolean", PROP_BOOLEAN, PROP_NONE);
	+ RNA_def_property_boolean_sdna(prop, NULL, "use_boolean", MOD_VORONOI_USEBOOLEAN);
	+ RNA_def_property_ui_text(prop, "Use Boolean Intersection", "Intersect shards with original object shape");
	+ RNA_def_property_update(prop, 0, "rna_Modifier_update");
	+
	+ prop = RNA_def_property(srna, "refracture", PROP_BOOLEAN, PROP_NONE);
	+ RNA_def_property_boolean_sdna(prop, NULL, "refracture", MOD_VORONOI_REFRACTURE);
	+ RNA_def_property_ui_text(prop, "Keep Refracturing", "Refracture the object when particles move");
	+ RNA_def_property_update(prop, 0, "rna_Modifier_update");
	+
	+ prop = RNA_def_property(srna, "use_cache", PROP_BOOLEAN, PROP_NONE);
	+ RNA_def_property_boolean_sdna(prop, NULL, "use_cache", MOD_VORONOI_USECACHE);
	+ RNA_def_property_ui_text(prop, "Use Fracture Cache", "Store the fractured mesh in a cache for faster re-use");
	+ RNA_def_property_update(prop, 0, "rna_Modifier_update");
	+
	+ prop = RNA_def_property(srna, "flip_normal", PROP_BOOLEAN, PROP_NONE);
	+ RNA_def_property_boolean_sdna(prop, NULL, "flip_normal", MOD_VORONOI_FLIPNORMAL);
	+ RNA_def_property_ui_text(prop, "Flip Normals", "Flip the normals when using boolean intersection, to possibly fix odd looking shapes");
	+ RNA_def_property_update(prop, 0, "rna_Modifier_update");
	+
	+ prop = RNA_def_property(srna, "emit_continuously", PROP_BOOLEAN, PROP_NONE);
	+ RNA_def_property_boolean_sdna(prop, NULL, "emit_continuously", MOD_VORONOI_EMITCONTINUOUSLY);
	+ RNA_def_property_ui_text(prop, "Emit Continuously", "Keep re-emitting the voronoi cells until all particles are dead");
	+ RNA_def_property_update(prop, 0, "rna_Modifier_update");
	+
	+ prop = RNA_def_property(srna, "map_delay", PROP_INT, PROP_NONE);
	+ RNA_def_property_range(prop, 0, 1000); //TODO: get correct psys end value here ?
	+ RNA_def_property_ui_text(prop, "Map Delay", "Delay in frames after which the object is broken up intially ");
	+ RNA_def_property_update(prop, 0, "rna_Modifier_update");
	+
	+ prop = RNA_def_property(srna, "inner_material", PROP_POINTER, PROP_NONE);
	+ RNA_def_property_ui_text(prop, "Inner Material", "");
	+ RNA_def_property_flag(prop, PROP_EDITABLE);
	+ RNA_def_property_update(prop, 0, "rna_Modifier_update");
	+
	+
	}

	static void rna_def_modifier_cloth(BlenderRNA *brna)
	Index: source/blender/blenloader/intern/readfile.c
	===================================================================
	--- source/blender/blenloader/intern/readfile.c (revision 53656)
	+++ source/blender/blenloader/intern/readfile.c (working copy)
	@@ -4632,6 +4632,13 @@
	ExplodeModifierData psmd = (ExplodeModifierData )md;

	psmd->facepa = NULL;
	+
	+ //should all be regenerated
	+ psmd->fracMesh = NULL;
	+ psmd->cells = NULL;
	+ psmd->tempOb = NULL;
	+ psmd->patree = NULL;
	+ psmd->inner_material = NULL;
	}
	else if (md->type == eModifierType_MeshDeform) {
	MeshDeformModifierData mmd = (MeshDeformModifierData )md;
	Index: build_files/scons/tools/btools.py
	===================================================================
	--- build_files/scons/tools/btools.py (revision 53656)
	+++ build_files/scons/tools/btools.py (working copy)
	@@ -156,6 +156,7 @@
	'WITH_BF_BOOLEAN',
	'WITH_BF_REMESH',
	'WITH_BF_OCEANSIM',
	+ 'WITH_BF_VORONOI',
	'WITH_BF_SMOKE',
	'WITH_BF_CXX_GUARDEDALLOC',
	'WITH_BF_JEMALLOC', 'WITH_BF_STATICJEMALLOC', 'BF_JEMALLOC', 'BF_JEMALLOC_INC', 'BF_JEMALLOC_LIBPATH', 'BF_JEMALLOC_LIB', 'BF_JEMALLOC_LIB_STATIC',
	@@ -271,6 +272,7 @@
	(BoolVariable('WITH_BF_REMESH', 'Build with remesh modifier', True)),
	(BoolVariable('WITH_BF_OCEANSIM', 'Build with ocean simulation', False)),
	(BoolVariable('WITH_BF_SMOKE', 'Build with smoke simulation', True)),
	+ (BoolVariable('WITH_BF_VORONOI', 'Build with voronoi cells in explo modifier', True)),
	('BF_PROFILE_FLAGS', 'Profiling compiler flags', ''),
	(BoolVariable('WITH_BF_OPENAL', 'Use OpenAL if true', False)),
	('BF_OPENAL', 'Base path for OpenAL', ''),
	Index: extern/SConscript
	===================================================================
	--- extern/SConscript (revision 53656)
	+++ extern/SConscript (working copy)
	@@ -43,3 +43,6 @@
	# FreeBSD doesn't seems to support XDND protocol
	if env['OURPLATFORM'] in ('linux', 'openbsd3', 'sunos5', 'aix4', 'aix5'):
	SConscript(['xdnd/SConscript'])
	+
	+if env ['WITH_BF_VORONOI']:
	+ SConscript(['voro++/SConscript'])
	Index: extern/voro++/LICENSE
	===================================================================
	--- extern/voro++/LICENSE (revision 0)
	+++ extern/voro++/LICENSE (revision 0)
	@@ -0,0 +1,39 @@
	+Voro++ Copyright (c) 2008, The Regents of the University of California, through
	+Lawrence Berkeley National Laboratory (subject to receipt of any required
	+approvals from the U.S. Dept. of Energy). All rights reserved.
	+
	+Redistribution and use in source and binary forms, with or without
	+modification, are permitted provided that the following conditions are met:
	+
	+(1) Redistributions of source code must retain the above copyright notice, this
	+list of conditions and the following disclaimer.
	+
	+(2) Redistributions in binary form must reproduce the above copyright notice,
	+this list of conditions and the following disclaimer in the documentation
	+and/or other materials provided with the distribution.
	+
	+(3) Neither the name of the University of California, Lawrence Berkeley
	+National Laboratory, U.S. Dept. of Energy nor the names of its contributors may
	+be used to endorse or promote products derived from this software without
	+specific prior written permission.
	+
	+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
	+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
	+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
	+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
	+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
	+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
	+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
	+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
	+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
	+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
	+
	+You are under no obligation whatsoever to provide any bug fixes, patches, or
	+upgrades to the features, functionality or performance of the source code
	+("Enhancements") to anyone; however, if you choose to make your Enhancements
	+available either publicly, or directly to Lawrence Berkeley National
	+Laboratory, without imposing a separate written license agreement for such
	+Enhancements, then you hereby grant the following license: a non-exclusive,
	+royalty-free perpetual license to install, use, modify, prepare derivative
	+works, incorporate into other computer software, distribute, and sublicense
	+such enhancements or derivative works thereof, in binary and source code form.
	Index: extern/voro++/SConscript
	===================================================================
	--- extern/voro++/SConscript (revision 0)
	+++ extern/voro++/SConscript (revision 0)
	@@ -0,0 +1,12 @@
	+#!/usr/bin/python
	+
	+import os
	+Import ('env')
	+
	+sources = env.Glob('src/*.cc')
	+sources.remove('src'+os.sep+'v_base_wl.cc')
	+defs = []
	+incs = ['src']
	+
	+
	+env.BlenderLib ('extern_voro++', Split(sources), incs, defs, libtype=['extern'], priority=[40] )
	Index: extern/voro++/src/container.hh
	===================================================================
	--- extern/voro++/src/container.hh (revision 0)
	+++ extern/voro++/src/container.hh (revision 0)
	@@ -0,0 +1,687 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file container.hh
	+ * \brief Header file for the container_base and related classes. */
	+
	+#ifndef VOROPP_CONTAINER_HH
	+#define VOROPP_CONTAINER_HH
	+
	+#include <cstdio>
	+#include <vector>
	+
	+#include "config.hh"
	+#include "common.hh"
	+#include "v_base.hh"
	+#include "cell.hh"
	+#include "c_loops.hh"
	+#include "v_compute.hh"
	+#include "rad_option.hh"
	+
	+namespace voro {
	+
	+/** \brief Pure virtual class from which wall objects are derived.
	+ *
	+ * This is a pure virtual class for a generic wall object. A wall object
	+ * can be specified by deriving a new class from this and specifying the
	+ * functions.*/
	+class wall {
	+ public:
	+ virtual ~wall() {}
	+ /** A pure virtual function for testing whether a point is
	+ * inside the wall object. */
	+ virtual bool point_inside(double x,double y,double z) = 0;
	+ /** A pure virtual function for cutting a cell without
	+ * neighbor-tracking with a wall. */
	+ virtual bool cut_cell(voronoicell &c,double x,double y,double z) = 0;
	+ /** A pure virtual function for cutting a cell with
	+ * neighbor-tracking enabled with a wall. */
	+ virtual bool cut_cell(voronoicell_neighbor &c,double x,double y,double z) = 0;
	+};
	+
	+/** \brief A class for storing a list of pointers to walls.
	+ *
	+ * This class stores a list of pointers to wall classes. It contains several
	+ * simple routines that make use of the wall classes (such as telling whether a
	+ * given position is inside all of the walls or not). It can be used by itself,
	+ * but also forms part of container_base, for associating walls with this
	+ * class. */
	+class wall_list {
	+ public:
	+ /** An array holding pointers to wall objects. */
	+ wall **walls;
	+ /** A pointer to the next free position to add a wall pointer.
	+ */
	+ wall **wep;
	+ wall_list();
	+ ~wall_list();
	+ /** Adds a wall to the list.
	+ * \param[in] w the wall to add. */
	+ inline void add_wall(wall *w) {
	+ if(wep==wel) increase_wall_memory();
	+ *(wep++)=w;
	+ }
	+ /** Adds a wall to the list.
	+ * \param[in] w a reference to the wall to add. */
	+ inline void add_wall(wall &w) {add_wall(&w);}
	+ void add_wall(wall_list &wl);
	+ /** Determines whether a given position is inside all of the
	+ * walls on the list.
	+ * \param[in] (x,y,z) the position to test.
	+ * \return True if it is inside, false if it is outside. */
	+ inline bool point_inside_walls(double x,double y,double z) {
	+ for(wall *wp=walls;wp<wep;wp++) if(!((wp)->point_inside(x,y,z))) return false;
	+ return true;
	+ }
	+ /** Cuts a Voronoi cell by all of the walls currently on
	+ * the list.
	+ * \param[in] c a reference to the Voronoi cell class.
	+ * \param[in] (x,y,z) the position of the cell.
	+ * \return True if the cell still exists, false if the cell is
	+ * deleted. */
	+ template<class c_class>
	+ bool apply_walls(c_class &c,double x,double y,double z) {
	+ for(wall *wp=walls;wp<wep;wp++) if(!((wp)->cut_cell(c,x,y,z))) return false;
	+ return true;
	+ }
	+ void deallocate();
	+ protected:
	+ void increase_wall_memory();
	+ /** A pointer to the limit of the walls array, used to
	+ * determine when array is full. */
	+ wall **wel;
	+ /** The current amount of memory allocated for walls. */
	+ int current_wall_size;
	+};
	+
	+/** \brief Class for representing a particle system in a three-dimensional
	+ * rectangular box.
	+ *
	+ * This class represents a system of particles in a three-dimensional
	+ * rectangular box. Any combination of non-periodic and periodic coordinates
	+ * can be used in the three coordinate directions. The class is not intended
	+ * for direct use, but instead forms the base of the container and
	+ * container_poly classes that add specialized routines for computing the
	+ * regular and radical Voronoi tessellations respectively. It contains routines
	+ * that are commonly between these two classes, such as those for drawing the
	+ * domain, and placing particles within the internal data structure.
	+ *
	+ * The class is derived from the wall_list class, which encapsulates routines
	+ * for associating walls with the container, and the voro_base class, which
	+ * encapsulates routines about the underlying computational grid. */
	+class container_base : public voro_base, public wall_list {
	+ public:
	+ /** The minimum x coordinate of the container. */
	+ const double ax;
	+ /** The maximum x coordinate of the container. */
	+ const double bx;
	+ /** The minimum y coordinate of the container. */
	+ const double ay;
	+ /** The maximum y coordinate of the container. */
	+ const double by;
	+ /** The minimum z coordinate of the container. */
	+ const double az;
	+ /** The maximum z coordinate of the container. */
	+ const double bz;
	+ /** A boolean value that determines if the x coordinate in
	+ * periodic or not. */
	+ const bool xperiodic;
	+ /** A boolean value that determines if the y coordinate in
	+ * periodic or not. */
	+ const bool yperiodic;
	+ /** A boolean value that determines if the z coordinate in
	+ * periodic or not. */
	+ const bool zperiodic;
	+ /** This array holds the numerical IDs of each particle in each
	+ * computational box. */
	+ int **id;
	+ /** A two dimensional array holding particle positions. For the
	+ * derived container_poly class, this also holds particle
	+ * radii. */
	+ double **p;
	+ /** This array holds the number of particles within each
	+ * computational box of the container. */
	+ int *co;
	+ /** This array holds the maximum amount of particle memory for
	+ * each computational box of the container. If the number of
	+ * particles in a particular box ever approaches this limit,
	+ * more is allocated using the add_particle_memory() function.
	+ */
	+ int *mem;
	+ /** The amount of memory in the array structure for each
	+ * particle. This is set to 3 when the basic class is
	+ * initialized, so that the array holds (x,y,z) positions. If
	+ * the container class is initialized as part of the derived
	+ * class container_poly, then this is set to 4, to also hold
	+ * the particle radii. */
	+ const int ps;
	+ container_base(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
	+ int nx_,int ny_,int nz_,bool xperiodic_,bool yperiodic_,bool zperiodic_,
	+ int init_mem,int ps_);
	+ ~container_base();
	+ bool point_inside(double x,double y,double z);
	+ void region_count();
	+ /** Initializes the Voronoi cell prior to a compute_cell
	+ * operation for a specific particle being carried out by a
	+ * voro_compute class. The cell is initialized to fill the
	+ * entire container. For non-periodic coordinates, this is set
	+ * by the position of the walls. For periodic coordinates, the
	+ * space is equally divided in either direction from the
	+ * particle's initial position. Plane cuts made by any walls
	+ * that have been added are then applied to the cell.
	+ * \param[in,out] c a reference to a voronoicell object.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] q the index of the particle within its block.
	+ * \param[in] (ci,cj,ck) the coordinates of the block in the
	+ * container coordinate system.
	+ * \param[out] (i,j,k) the coordinates of the test block
	+ * relative to the voro_compute
	+ * coordinate system.
	+ * \param[out] (x,y,z) the position of the particle.
	+ * \param[out] disp a block displacement used internally by the
	+ * compute_cell routine.
	+ * \return False if the plane cuts applied by walls completely
	+ * removed the cell, true otherwise. */
	+ template<class v_cell>
	+ inline bool initialize_voronoicell(v_cell &c,int ijk,int q,int ci,int cj,int ck,
	+ int &i,int &j,int &k,double &x,double &y,double &z,int &disp) {
	+ double x1,x2,y1,y2,z1,z2,pp=p[ijk]+psq;
	+ x=(pp++);y=(pp++);z=*pp;
	+ if(xperiodic) {x1=-(x2=0.5*(bx-ax));i=nx;} else {x1=ax-x;x2=bx-x;i=ci;}
	+ if(yperiodic) {y1=-(y2=0.5*(by-ay));j=ny;} else {y1=ay-y;y2=by-y;j=cj;}
	+ if(zperiodic) {z1=-(z2=0.5*(bz-az));k=nz;} else {z1=az-z;z2=bz-z;k=ck;}
	+ c.init(x1,x2,y1,y2,z1,z2);
	+ if(!apply_walls(c,x,y,z)) return false;
	+ disp=ijk-i-nx(j+nyk);
	+ return true;
	+ }
	+ /** Initializes parameters for a find_voronoi_cell call within
	+ * the voro_compute template.
	+ * \param[in] (ci,cj,ck) the coordinates of the test block in
	+ * the container coordinate system.
	+ * \param[in] ijk the index of the test block
	+ * \param[out] (i,j,k) the coordinates of the test block
	+ * relative to the voro_compute
	+ * coordinate system.
	+ * \param[out] disp a block displacement used internally by the
	+ * find_voronoi_cell routine. */
	+ inline void initialize_search(int ci,int cj,int ck,int ijk,int &i,int &j,int &k,int &disp) {
	+ i=xperiodic?nx:ci;
	+ j=yperiodic?ny:cj;
	+ k=zperiodic?nz:ck;
	+ disp=ijk-i-nx(j+nyk);
	+ }
	+ /** Returns the position of a particle currently being computed
	+ * relative to the computational block that it is within. It is
	+ * used to select the optimal worklist entry to use.
	+ * \param[in] (x,y,z) the position of the particle.
	+ * \param[in] (ci,cj,ck) the block that the particle is within.
	+ * \param[out] (fx,fy,fz) the position relative to the block.
	+ */
	+ inline void frac_pos(double x,double y,double z,double ci,double cj,double ck,
	+ double &fx,double &fy,double &fz) {
	+ fx=x-ax-boxx*ci;
	+ fy=y-ay-boxy*cj;
	+ fz=z-az-boxz*ck;
	+ }
	+ /** Calculates the index of block in the container structure
	+ * corresponding to given coordinates.
	+ * \param[in] (ci,cj,ck) the coordinates of the original block
	+ * in the current computation, relative
	+ * to the container coordinate system.
	+ * \param[in] (ei,ej,ek) the displacement of the current block
	+ * from the original block.
	+ * \param[in,out] (qx,qy,qz) the periodic displacement that
	+ * must be added to the particles
	+ * within the computed block.
	+ * \param[in] disp a block displacement used internally by the
	+ * find_voronoi_cell and compute_cell routines.
	+ * \return The block index. */
	+ inline int region_index(int ci,int cj,int ck,int ei,int ej,int ek,double &qx,double &qy,double &qz,int &disp) {
	+ if(xperiodic) {if(ci+ei<nx) {ei+=nx;qx=-(bx-ax);} else if(ci+ei>=(nx<<1)) {ei-=nx;qx=bx-ax;} else qx=0;}
	+ if(yperiodic) {if(cj+ej<ny) {ej+=ny;qy=-(by-ay);} else if(cj+ej>=(ny<<1)) {ej-=ny;qy=by-ay;} else qy=0;}
	+ if(zperiodic) {if(ck+ek<nz) {ek+=nz;qz=-(bz-az);} else if(ck+ek>=(nz<<1)) {ek-=nz;qz=bz-az;} else qz=0;}
	+ return disp+ei+nx(ej+nyek);
	+ }
	+ void draw_domain_gnuplot(FILE *fp=stdout);
	+ /** Draws an outline of the domain in Gnuplot format.
	+ * \param[in] filename the filename to write to. */
	+ inline void draw_domain_gnuplot(const char* filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_domain_gnuplot(fp);
	+ fclose(fp);
	+ }
	+ void draw_domain_pov(FILE *fp=stdout);
	+ /** Draws an outline of the domain in Gnuplot format.
	+ * \param[in] filename the filename to write to. */
	+ inline void draw_domain_pov(const char* filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_domain_pov(fp);
	+ fclose(fp);
	+ }
	+ /** Sums up the total number of stored particles.
	+ * \return The number of particles. */
	+ inline int total_particles() {
	+ int tp=*co;
	+ for(int cop=co+1;cop<co+nxyz;cop++) tp+=cop;
	+ return tp;
	+ }
	+ protected:
	+ void add_particle_memory(int i);
	+ inline bool put_locate_block(int &ijk,double &x,double &y,double &z);
	+ inline bool put_remap(int &ijk,double &x,double &y,double &z);
	+ inline bool remap(int &ai,int &aj,int &ak,int &ci,int &cj,int &ck,double &x,double &y,double &z,int &ijk);
	+};
	+
	+/** \brief Extension of the container_base class for computing regular Voronoi
	+ * tessellations.
	+ *
	+ * This class is an extension of the container_base class that has routines
	+ * specifically for computing the regular Voronoi tessellation with no
	+ * dependence on particle radii. */
	+class container : public container_base, public radius_mono {
	+ public:
	+ container(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
	+ int nx_,int ny_,int nz_,bool xperiodic_,bool yperiodic_,bool zperiodic_,int init_mem);
	+ void clear();
	+ void put(int n,double x,double y,double z);
	+ void put(particle_order &vo,int n,double x,double y,double z);
	+ void import(FILE *fp=stdin);
	+ void import(particle_order &vo,FILE *fp=stdin);
	+ /** Imports a list of particles from an open file stream into
	+ * the container. Entries of four numbers (Particle ID, x
	+ * position, y position, z position) are searched for. If the
	+ * file cannot be successfully read, then the routine causes a
	+ * fatal error.
	+ * \param[in] filename the name of the file to open and read
	+ * from. */
	+ inline void import(const char* filename) {
	+ FILE *fp=safe_fopen(filename,"r");
	+ import(fp);
	+ fclose(fp);
	+ }
	+ /** Imports a list of particles from an open file stream into
	+ * the container. Entries of four numbers (Particle ID, x
	+ * position, y position, z position) are searched for. In
	+ * addition, the order in which particles are read is saved
	+ * into an ordering class. If the file cannot be successfully
	+ * read, then the routine causes a fatal error.
	+ * \param[in,out] vo the ordering class to use.
	+ * \param[in] filename the name of the file to open and read
	+ * from. */
	+ inline void import(particle_order &vo,const char* filename) {
	+ FILE *fp=safe_fopen(filename,"r");
	+ import(vo,fp);
	+ fclose(fp);
	+ }
	+ void compute_all_cells();
	+ double sum_cell_volumes();
	+ /** Dumps particle IDs and positions to a file.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_particles(c_loop &vl,FILE *fp) {
	+ double *pp;
	+ if(vl.start()) do {
	+ pp=p[vl.ijk]+3*vl.q;
	+ fprintf(fp,"%d %g %g %g\n",id[vl.ijk][vl.q],*pp,pp[1],pp[2]);
	+ } while(vl.inc());
	+ }
	+ /** Dumps all of the particle IDs and positions to a file.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_particles(FILE *fp=stdout) {
	+ c_loop_all vl(*this);
	+ draw_particles(vl,fp);
	+ }
	+ /** Dumps all of the particle IDs and positions to a file.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_particles(const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_particles(fp);
	+ fclose(fp);
	+ }
	+ /** Dumps particle positions in POV-Ray format.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_particles_pov(c_loop &vl,FILE *fp) {
	+ double *pp;
	+ if(vl.start()) do {
	+ pp=p[vl.ijk]+3*vl.q;
	+ fprintf(fp,"// id %d\nsphere{<%g,%g,%g>,s}\n",
	+ id[vl.ijk][vl.q],*pp,pp[1],pp[2]);
	+ } while(vl.inc());
	+ }
	+ /** Dumps all particle positions in POV-Ray format.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_particles_pov(FILE *fp=stdout) {
	+ c_loop_all vl(*this);
	+ draw_particles_pov(vl,fp);
	+ }
	+ /** Dumps all particle positions in POV-Ray format.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_particles_pov(const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_particles_pov(fp);
	+ fclose(fp);
	+ }
	+ /** Computes Voronoi cells and saves the output in gnuplot
	+ * format.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_cells_gnuplot(c_loop &vl,FILE *fp) {
	+ voronoicell c;double *pp;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ pp=p[vl.ijk]+ps*vl.q;
	+ c.draw_gnuplot(*pp,pp[1],pp[2],fp);
	+ } while(vl.inc());
	+ }
	+ /** Computes all Voronoi cells and saves the output in gnuplot
	+ * format.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_cells_gnuplot(FILE *fp=stdout) {
	+ c_loop_all vl(*this);
	+ draw_cells_gnuplot(vl,fp);
	+ }
	+ /** Computes all Voronoi cells and saves the output in gnuplot
	+ * format.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_cells_gnuplot(const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_cells_gnuplot(fp);
	+ fclose(fp);
	+ }
	+ /** Computes Voronoi cells and saves the output in POV-Ray
	+ * format.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_cells_pov(c_loop &vl,FILE *fp) {
	+ voronoicell c;double *pp;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ fprintf(fp,"// cell %d\n",id[vl.ijk][vl.q]);
	+ pp=p[vl.ijk]+ps*vl.q;
	+ c.draw_pov(*pp,pp[1],pp[2],fp);
	+ } while(vl.inc());
	+ }
	+ /** Computes all Voronoi cells and saves the output in POV-Ray
	+ * format.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_cells_pov(FILE *fp=stdout) {
	+ c_loop_all vl(*this);
	+ draw_cells_pov(vl,fp);
	+ }
	+ /** Computes all Voronoi cells and saves the output in POV-Ray
	+ * format.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_cells_pov(const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_cells_pov(fp);
	+ fclose(fp);
	+ }
	+ /** Computes the Voronoi cells and saves customized information
	+ * about them.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] format the custom output string to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void print_custom(c_loop &vl,const char format,FILE fp) {
	+ int ijk,q;double *pp;
	+ if(contains_neighbor(format)) {
	+ voronoicell_neighbor c;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
	+ c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],default_radius,fp);
	+ } while(vl.inc());
	+ } else {
	+ voronoicell c;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
	+ c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],default_radius,fp);
	+ } while(vl.inc());
	+ }
	+ }
	+ void print_custom(const char format,FILE fp=stdout);
	+ void print_custom(const char format,const char filename);
	+ bool find_voronoi_cell(double x,double y,double z,double &rx,double &ry,double &rz,int &pid);
	+ /** Computes the Voronoi cell for a particle currently being
	+ * referenced by a loop class.
	+ * \param[out] c a Voronoi cell class in which to store the
	+ * computed cell.
	+ * \param[in] vl the loop class to use.
	+ * \return True if the cell was computed. If the cell cannot be
	+ * computed, if it is removed entirely by a wall or boundary
	+ * condition, then the routine returns false. */
	+ template<class v_cell,class c_loop>
	+ inline bool compute_cell(v_cell &c,c_loop &vl) {
	+ return vc.compute_cell(c,vl.ijk,vl.q,vl.i,vl.j,vl.k);
	+ }
	+ /** Computes the Voronoi cell for given particle.
	+ * \param[out] c a Voronoi cell class in which to store the
	+ * computed cell.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] q the index of the particle within the block.
	+ * \return True if the cell was computed. If the cell cannot be
	+ * computed, if it is removed entirely by a wall or boundary
	+ * condition, then the routine returns false. */
	+ template<class v_cell>
	+ inline bool compute_cell(v_cell &c,int ijk,int q) {
	+ int k=ijk/nxy,ijkt=ijk-nxyk,j=ijkt/nx,i=ijkt-jnx;
	+ return vc.compute_cell(c,ijk,q,i,j,k);
	+ }
	+ private:
	+ voro_compute<container> vc;
	+ friend class voro_compute<container>;
	+};
	+
	+/** \brief Extension of the container_base class for computing radical Voronoi
	+ * tessellations.
	+ *
	+ * This class is an extension of container_base class that has routines
	+ * specifically for computing the radical Voronoi tessellation that depends on
	+ * the particle radii. */
	+class container_poly : public container_base, public radius_poly {
	+ public:
	+ container_poly(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
	+ int nx_,int ny_,int nz_,bool xperiodic_,bool yperiodic_,bool zperiodic_,int init_mem);
	+ void clear();
	+ void put(int n,double x,double y,double z,double r);
	+ void put(particle_order &vo,int n,double x,double y,double z,double r);
	+ void import(FILE *fp=stdin);
	+ void import(particle_order &vo,FILE *fp=stdin);
	+ /** Imports a list of particles from an open file stream into
	+ * the container_poly class. Entries of five numbers (Particle
	+ * ID, x position, y position, z position, radius) are searched
	+ * for. If the file cannot be successfully read, then the
	+ * routine causes a fatal error.
	+ * \param[in] filename the name of the file to open and read
	+ * from. */
	+ inline void import(const char* filename) {
	+ FILE *fp=safe_fopen(filename,"r");
	+ import(fp);
	+ fclose(fp);
	+ }
	+ /** Imports a list of particles from an open file stream into
	+ * the container_poly class. Entries of five numbers (Particle
	+ * ID, x position, y position, z position, radius) are searched
	+ * for. In addition, the order in which particles are read is
	+ * saved into an ordering class. If the file cannot be
	+ * successfully read, then the routine causes a fatal error.
	+ * \param[in,out] vo the ordering class to use.
	+ * \param[in] filename the name of the file to open and read
	+ * from. */
	+ inline void import(particle_order &vo,const char* filename) {
	+ FILE *fp=safe_fopen(filename,"r");
	+ import(vo,fp);
	+ fclose(fp);
	+ }
	+ void compute_all_cells();
	+ double sum_cell_volumes();
	+ /** Dumps particle IDs, positions and radii to a file.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_particles(c_loop &vl,FILE *fp) {
	+ double *pp;
	+ if(vl.start()) do {
	+ pp=p[vl.ijk]+4*vl.q;
	+ fprintf(fp,"%d %g %g %g %g\n",id[vl.ijk][vl.q],*pp,pp[1],pp[2],pp[3]);
	+ } while(vl.inc());
	+ }
	+ /** Dumps all of the particle IDs, positions and radii to a
	+ * file.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_particles(FILE *fp=stdout) {
	+ c_loop_all vl(*this);
	+ draw_particles(vl,fp);
	+ }
	+ /** Dumps all of the particle IDs, positions and radii to a
	+ * file.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_particles(const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_particles(fp);
	+ fclose(fp);
	+ }
	+ /** Dumps particle positions in POV-Ray format.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_particles_pov(c_loop &vl,FILE *fp) {
	+ double *pp;
	+ if(vl.start()) do {
	+ pp=p[vl.ijk]+4*vl.q;
	+ fprintf(fp,"// id %d\nsphere{<%g,%g,%g>,%g}\n",
	+ id[vl.ijk][vl.q],*pp,pp[1],pp[2],pp[3]);
	+ } while(vl.inc());
	+ }
	+ /** Dumps all the particle positions in POV-Ray format.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_particles_pov(FILE *fp=stdout) {
	+ c_loop_all vl(*this);
	+ draw_particles_pov(vl,fp);
	+ }
	+ /** Dumps all the particle positions in POV-Ray format.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_particles_pov(const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_particles_pov(fp);
	+ fclose(fp);
	+ }
	+ /** Computes Voronoi cells and saves the output in gnuplot
	+ * format.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_cells_gnuplot(c_loop &vl,FILE *fp) {
	+ voronoicell c;double *pp;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ pp=p[vl.ijk]+ps*vl.q;
	+ c.draw_gnuplot(*pp,pp[1],pp[2],fp);
	+ } while(vl.inc());
	+ }
	+ /** Compute all Voronoi cells and saves the output in gnuplot
	+ * format.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_cells_gnuplot(FILE *fp=stdout) {
	+ c_loop_all vl(*this);
	+ draw_cells_gnuplot(vl,fp);
	+ }
	+ /** Compute all Voronoi cells and saves the output in gnuplot
	+ * format.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_cells_gnuplot(const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_cells_gnuplot(fp);
	+ fclose(fp);
	+ }
	+ /** Computes Voronoi cells and saves the output in POV-Ray
	+ * format.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_cells_pov(c_loop &vl,FILE *fp) {
	+ voronoicell c;double *pp;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ fprintf(fp,"// cell %d\n",id[vl.ijk][vl.q]);
	+ pp=p[vl.ijk]+ps*vl.q;
	+ c.draw_pov(*pp,pp[1],pp[2],fp);
	+ } while(vl.inc());
	+ }
	+ /** Computes all Voronoi cells and saves the output in POV-Ray
	+ * format.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_cells_pov(FILE *fp=stdout) {
	+ c_loop_all vl(*this);
	+ draw_cells_pov(vl,fp);
	+ }
	+ /** Computes all Voronoi cells and saves the output in POV-Ray
	+ * format.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_cells_pov(const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_cells_pov(fp);
	+ fclose(fp);
	+ }
	+ /** Computes the Voronoi cells and saves customized information
	+ * about them.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] format the custom output string to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void print_custom(c_loop &vl,const char format,FILE fp) {
	+ int ijk,q;double *pp;
	+ if(contains_neighbor(format)) {
	+ voronoicell_neighbor c;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
	+ c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],pp[3],fp);
	+ } while(vl.inc());
	+ } else {
	+ voronoicell c;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
	+ c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],pp[3],fp);
	+ } while(vl.inc());
	+ }
	+ }
	+ /** Computes the Voronoi cell for a particle currently being
	+ * referenced by a loop class.
	+ * \param[out] c a Voronoi cell class in which to store the
	+ * computed cell.
	+ * \param[in] vl the loop class to use.
	+ * \return True if the cell was computed. If the cell cannot be
	+ * computed, if it is removed entirely by a wall or boundary
	+ * condition, then the routine returns false. */
	+ template<class v_cell,class c_loop>
	+ inline bool compute_cell(v_cell &c,c_loop &vl) {
	+ return vc.compute_cell(c,vl.ijk,vl.q,vl.i,vl.j,vl.k);
	+ }
	+ /** Computes the Voronoi cell for given particle.
	+ * \param[out] c a Voronoi cell class in which to store the
	+ * computed cell.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] q the index of the particle within the block.
	+ * \return True if the cell was computed. If the cell cannot be
	+ * computed, if it is removed entirely by a wall or boundary
	+ * condition, then the routine returns false. */
	+ template<class v_cell>
	+ inline bool compute_cell(v_cell &c,int ijk,int q) {
	+ int k=ijk/nxy,ijkt=ijk-nxyk,j=ijkt/nx,i=ijkt-jnx;
	+ return vc.compute_cell(c,ijk,q,i,j,k);
	+ }
	+ void print_custom(const char format,FILE fp=stdout);
	+ void print_custom(const char format,const char filename);
	+ bool find_voronoi_cell(double x,double y,double z,double &rx,double &ry,double &rz,int &pid);
	+ private:
	+ voro_compute<container_poly> vc;
	+ friend class voro_compute<container_poly>;
	+};
	+
	+}
	+
	+#endif
	Index: extern/voro++/src/Doxyfile
	===================================================================
	--- extern/voro++/src/Doxyfile (revision 0)
	+++ extern/voro++/src/Doxyfile (revision 0)
	@@ -0,0 +1,1793 @@
	+# Doxyfile 1.8.1.1
	+
	+# This file describes the settings to be used by the documentation system
	+# doxygen (www.doxygen.org) for a project.
	+#
	+# All text after a hash (#) is considered a comment and will be ignored.
	+# The format is:
	+# TAG = value [value, ...]
	+# For lists items can also be appended using:
	+# TAG += value [value, ...]
	+# Values that contain spaces should be placed between quotes (" ").
	+
	+#---------------------------------------------------------------------------
	+# Project related configuration options
	+#---------------------------------------------------------------------------
	+
	+# This tag specifies the encoding used for all characters in the config file
	+# that follow. The default is UTF-8 which is also the encoding used for all
	+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
	+# iconv built into libc) for the transcoding. See
	+# http://www.gnu.org/software/libiconv for the list of possible encodings.
	+
	+DOXYFILE_ENCODING = UTF-8
	+
	+# The PROJECT_NAME tag is a single word (or sequence of words) that should
	+# identify the project. Note that if you do not use Doxywizard you need
	+# to put quotes around the project name if it contains spaces.
	+
	+PROJECT_NAME = Voro++
	+
	+# The PROJECT_NUMBER tag can be used to enter a project or revision number.
	+# This could be handy for archiving the generated documentation or
	+# if some version control system is used.
	+
	+PROJECT_NUMBER =
	+
	+# Using the PROJECT_BRIEF tag one can provide an optional one line description
	+# for a project that appears at the top of each page and should give viewer
	+# a quick idea about the purpose of the project. Keep the description short.
	+
	+PROJECT_BRIEF =
	+
	+# With the PROJECT_LOGO tag one can specify an logo or icon that is
	+# included in the documentation. The maximum height of the logo should not
	+# exceed 55 pixels and the maximum width should not exceed 200 pixels.
	+# Doxygen will copy the logo to the output directory.
	+
	+PROJECT_LOGO =
	+
	+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
	+# base path where the generated documentation will be put.
	+# If a relative path is entered, it will be relative to the location
	+# where doxygen was started. If left blank the current directory will be used.
	+
	+OUTPUT_DIRECTORY = ..
	+
	+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
	+# 4096 sub-directories (in 2 levels) under the output directory of each output
	+# format and will distribute the generated files over these directories.
	+# Enabling this option can be useful when feeding doxygen a huge amount of
	+# source files, where putting all generated files in the same directory would
	+# otherwise cause performance problems for the file system.
	+
	+CREATE_SUBDIRS = NO
	+
	+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
	+# documentation generated by doxygen is written. Doxygen will use this
	+# information to generate all constant output in the proper language.
	+# The default language is English, other supported languages are:
	+# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
	+# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
	+# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
	+# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
	+# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
	+# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
	+
	+OUTPUT_LANGUAGE = English
	+
	+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
	+# include brief member descriptions after the members that are listed in
	+# the file and class documentation (similar to JavaDoc).
	+# Set to NO to disable this.
	+
	+BRIEF_MEMBER_DESC = YES
	+
	+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
	+# the brief description of a member or function before the detailed description.
	+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
	+# brief descriptions will be completely suppressed.
	+
	+REPEAT_BRIEF = NO
	+
	+# This tag implements a quasi-intelligent brief description abbreviator
	+# that is used to form the text in various listings. Each string
	+# in this list, if found as the leading text of the brief description, will be
	+# stripped from the text and the result after processing the whole list, is
	+# used as the annotated text. Otherwise, the brief description is used as-is.
	+# If left blank, the following values are used ("$name" is automatically
	+# replaced with the name of the entity): "The $name class" "The $name widget"
	+# "The $name file" "is" "provides" "specifies" "contains"
	+# "represents" "a" "an" "the"
	+
	+ABBREVIATE_BRIEF =
	+
	+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
	+# Doxygen will generate a detailed section even if there is only a brief
	+# description.
	+
	+ALWAYS_DETAILED_SEC = NO
	+
	+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
	+# inherited members of a class in the documentation of that class as if those
	+# members were ordinary class members. Constructors, destructors and assignment
	+# operators of the base classes will not be shown.
	+
	+INLINE_INHERITED_MEMB = NO
	+
	+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
	+# path before files name in the file list and in the header files. If set
	+# to NO the shortest path that makes the file name unique will be used.
	+
	+FULL_PATH_NAMES = YES
	+
	+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
	+# can be used to strip a user-defined part of the path. Stripping is
	+# only done if one of the specified strings matches the left-hand part of
	+# the path. The tag can be used to show relative paths in the file list.
	+# If left blank the directory from which doxygen is run is used as the
	+# path to strip.
	+
	+STRIP_FROM_PATH =
	+
	+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
	+# the path mentioned in the documentation of a class, which tells
	+# the reader which header file to include in order to use a class.
	+# If left blank only the name of the header file containing the class
	+# definition is used. Otherwise one should specify the include paths that
	+# are normally passed to the compiler using the -I flag.
	+
	+STRIP_FROM_INC_PATH =
	+
	+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
	+# (but less readable) file names. This can be useful if your file system
	+# doesn't support long names like on DOS, Mac, or CD-ROM.
	+
	+SHORT_NAMES = NO
	+
	+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
	+# will interpret the first line (until the first dot) of a JavaDoc-style
	+# comment as the brief description. If set to NO, the JavaDoc
	+# comments will behave just like regular Qt-style comments
	+# (thus requiring an explicit @brief command for a brief description.)
	+
	+JAVADOC_AUTOBRIEF = NO
	+
	+# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
	+# interpret the first line (until the first dot) of a Qt-style
	+# comment as the brief description. If set to NO, the comments
	+# will behave just like regular Qt-style comments (thus requiring
	+# an explicit \brief command for a brief description.)
	+
	+QT_AUTOBRIEF = NO
	+
	+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
	+# treat a multi-line C++ special comment block (i.e. a block of //! or ///
	+# comments) as a brief description. This used to be the default behaviour.
	+# The new default is to treat a multi-line C++ comment block as a detailed
	+# description. Set this tag to YES if you prefer the old behaviour instead.
	+
	+MULTILINE_CPP_IS_BRIEF = NO
	+
	+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
	+# member inherits the documentation from any documented member that it
	+# re-implements.
	+
	+INHERIT_DOCS = YES
	+
	+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
	+# a new page for each member. If set to NO, the documentation of a member will
	+# be part of the file/class/namespace that contains it.
	+
	+SEPARATE_MEMBER_PAGES = NO
	+
	+# The TAB_SIZE tag can be used to set the number of spaces in a tab.
	+# Doxygen uses this value to replace tabs by spaces in code fragments.
	+
	+TAB_SIZE = 8
	+
	+# This tag can be used to specify a number of aliases that acts
	+# as commands in the documentation. An alias has the form "name=value".
	+# For example adding "sideeffect=\par Side Effects:\n" will allow you to
	+# put the command \sideeffect (or @sideeffect) in the documentation, which
	+# will result in a user-defined paragraph with heading "Side Effects:".
	+# You can put \n's in the value part of an alias to insert newlines.
	+
	+ALIASES =
	+
	+# This tag can be used to specify a number of word-keyword mappings (TCL only).
	+# A mapping has the form "name=value". For example adding
	+# "class=itcl::class" will allow you to use the command class in the
	+# itcl::class meaning.
	+
	+TCL_SUBST =
	+
	+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
	+# sources only. Doxygen will then generate output that is more tailored for C.
	+# For instance, some of the names that are used will be different. The list
	+# of all members will be omitted, etc.
	+
	+OPTIMIZE_OUTPUT_FOR_C = YES
	+
	+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
	+# sources only. Doxygen will then generate output that is more tailored for
	+# Java. For instance, namespaces will be presented as packages, qualified
	+# scopes will look different, etc.
	+
	+OPTIMIZE_OUTPUT_JAVA = NO
	+
	+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
	+# sources only. Doxygen will then generate output that is more tailored for
	+# Fortran.
	+
	+OPTIMIZE_FOR_FORTRAN = NO
	+
	+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
	+# sources. Doxygen will then generate output that is tailored for
	+# VHDL.
	+
	+OPTIMIZE_OUTPUT_VHDL = NO
	+
	+# Doxygen selects the parser to use depending on the extension of the files it
	+# parses. With this tag you can assign which parser to use for a given extension.
	+# Doxygen has a built-in mapping, but you can override or extend it using this
	+# tag. The format is ext=language, where ext is a file extension, and language
	+# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
	+# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
	+# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
	+# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
	+# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
	+
	+EXTENSION_MAPPING =
	+
	+# If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all
	+# comments according to the Markdown format, which allows for more readable
	+# documentation. See http://daringfireball.net/projects/markdown/ for details.
	+# The output of markdown processing is further processed by doxygen, so you
	+# can mix doxygen, HTML, and XML commands with Markdown formatting.
	+# Disable only in case of backward compatibilities issues.
	+
	+MARKDOWN_SUPPORT = YES
	+
	+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
	+# to include (a tag file for) the STL sources as input, then you should
	+# set this tag to YES in order to let doxygen match functions declarations and
	+# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
	+# func(std::string) {}). This also makes the inheritance and collaboration
	+# diagrams that involve STL classes more complete and accurate.
	+
	+BUILTIN_STL_SUPPORT = YES
	+
	+# If you use Microsoft's C++/CLI language, you should set this option to YES to
	+# enable parsing support.
	+
	+CPP_CLI_SUPPORT = NO
	+
	+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
	+# Doxygen will parse them like normal C++ but will assume all classes use public
	+# instead of private inheritance when no explicit protection keyword is present.
	+
	+SIP_SUPPORT = NO
	+
	+# For Microsoft's IDL there are propget and propput attributes to indicate getter
	+# and setter methods for a property. Setting this option to YES (the default)
	+# will make doxygen replace the get and set methods by a property in the
	+# documentation. This will only work if the methods are indeed getting or
	+# setting a simple type. If this is not the case, or you want to show the
	+# methods anyway, you should set this option to NO.
	+
	+IDL_PROPERTY_SUPPORT = YES
	+
	+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
	+# tag is set to YES, then doxygen will reuse the documentation of the first
	+# member in the group (if any) for the other members of the group. By default
	+# all members of a group must be documented explicitly.
	+
	+DISTRIBUTE_GROUP_DOC = NO
	+
	+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
	+# the same type (for instance a group of public functions) to be put as a
	+# subgroup of that type (e.g. under the Public Functions section). Set it to
	+# NO to prevent subgrouping. Alternatively, this can be done per class using
	+# the \nosubgrouping command.
	+
	+SUBGROUPING = YES
	+
	+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
	+# unions are shown inside the group in which they are included (e.g. using
	+# @ingroup) instead of on a separate page (for HTML and Man pages) or
	+# section (for LaTeX and RTF).
	+
	+INLINE_GROUPED_CLASSES = NO
	+
	+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
	+# unions with only public data fields will be shown inline in the documentation
	+# of the scope in which they are defined (i.e. file, namespace, or group
	+# documentation), provided this scope is documented. If set to NO (the default),
	+# structs, classes, and unions are shown on a separate page (for HTML and Man
	+# pages) or section (for LaTeX and RTF).
	+
	+INLINE_SIMPLE_STRUCTS = NO
	+
	+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
	+# is documented as struct, union, or enum with the name of the typedef. So
	+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
	+# with name TypeT. When disabled the typedef will appear as a member of a file,
	+# namespace, or class. And the struct will be named TypeS. This can typically
	+# be useful for C code in case the coding convention dictates that all compound
	+# types are typedef'ed and only the typedef is referenced, never the tag name.
	+
	+TYPEDEF_HIDES_STRUCT = NO
	+
	+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
	+# determine which symbols to keep in memory and which to flush to disk.
	+# When the cache is full, less often used symbols will be written to disk.
	+# For small to medium size projects (<1000 input files) the default value is
	+# probably good enough. For larger projects a too small cache size can cause
	+# doxygen to be busy swapping symbols to and from disk most of the time
	+# causing a significant performance penalty.
	+# If the system has enough physical memory increasing the cache will improve the
	+# performance by keeping more symbols in memory. Note that the value works on
	+# a logarithmic scale so increasing the size by one will roughly double the
	+# memory usage. The cache size is given by this formula:
	+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
	+# corresponding to a cache size of 2^16 = 65536 symbols.
	+
	+SYMBOL_CACHE_SIZE = 0
	+
	+# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
	+# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
	+# their name and scope. Since this can be an expensive process and often the
	+# same symbol appear multiple times in the code, doxygen keeps a cache of
	+# pre-resolved symbols. If the cache is too small doxygen will become slower.
	+# If the cache is too large, memory is wasted. The cache size is given by this
	+# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
	+# corresponding to a cache size of 2^16 = 65536 symbols.
	+
	+LOOKUP_CACHE_SIZE = 0
	+
	+#---------------------------------------------------------------------------
	+# Build related configuration options
	+#---------------------------------------------------------------------------
	+
	+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
	+# documentation are documented, even if no documentation was available.
	+# Private class members and static file members will be hidden unless
	+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
	+
	+EXTRACT_ALL = NO
	+
	+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
	+# will be included in the documentation.
	+
	+EXTRACT_PRIVATE = NO
	+
	+# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal scope will be included in the documentation.
	+
	+EXTRACT_PACKAGE = NO
	+
	+# If the EXTRACT_STATIC tag is set to YES all static members of a file
	+# will be included in the documentation.
	+
	+EXTRACT_STATIC = NO
	+
	+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
	+# defined locally in source files will be included in the documentation.
	+# If set to NO only classes defined in header files are included.
	+
	+EXTRACT_LOCAL_CLASSES = YES
	+
	+# This flag is only useful for Objective-C code. When set to YES local
	+# methods, which are defined in the implementation section but not in
	+# the interface are included in the documentation.
	+# If set to NO (the default) only methods in the interface are included.
	+
	+EXTRACT_LOCAL_METHODS = NO
	+
	+# If this flag is set to YES, the members of anonymous namespaces will be
	+# extracted and appear in the documentation as a namespace called
	+# 'anonymous_namespace{file}', where file will be replaced with the base
	+# name of the file that contains the anonymous namespace. By default
	+# anonymous namespaces are hidden.
	+
	+EXTRACT_ANON_NSPACES = NO
	+
	+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
	+# undocumented members of documented classes, files or namespaces.
	+# If set to NO (the default) these members will be included in the
	+# various overviews, but no documentation section is generated.
	+# This option has no effect if EXTRACT_ALL is enabled.
	+
	+HIDE_UNDOC_MEMBERS = NO
	+
	+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
	+# undocumented classes that are normally visible in the class hierarchy.
	+# If set to NO (the default) these classes will be included in the various
	+# overviews. This option has no effect if EXTRACT_ALL is enabled.
	+
	+HIDE_UNDOC_CLASSES = NO
	+
	+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
	+# friend (class\|struct\|union) declarations.
	+# If set to NO (the default) these declarations will be included in the
	+# documentation.
	+
	+HIDE_FRIEND_COMPOUNDS = NO
	+
	+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
	+# documentation blocks found inside the body of a function.
	+# If set to NO (the default) these blocks will be appended to the
	+# function's detailed documentation block.
	+
	+HIDE_IN_BODY_DOCS = NO
	+
	+# The INTERNAL_DOCS tag determines if documentation
	+# that is typed after a \internal command is included. If the tag is set
	+# to NO (the default) then the documentation will be excluded.
	+# Set it to YES to include the internal documentation.
	+
	+INTERNAL_DOCS = NO
	+
	+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
	+# file names in lower-case letters. If set to YES upper-case letters are also
	+# allowed. This is useful if you have classes or files whose names only differ
	+# in case and if your file system supports case sensitive file names. Windows
	+# and Mac users are advised to set this option to NO.
	+
	+CASE_SENSE_NAMES = NO
	+
	+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
	+# will show members with their full class and namespace scopes in the
	+# documentation. If set to YES the scope will be hidden.
	+
	+HIDE_SCOPE_NAMES = NO
	+
	+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
	+# will put a list of the files that are included by a file in the documentation
	+# of that file.
	+
	+SHOW_INCLUDE_FILES = YES
	+
	+# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
	+# will list include files with double quotes in the documentation
	+# rather than with sharp brackets.
	+
	+FORCE_LOCAL_INCLUDES = NO
	+
	+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
	+# is inserted in the documentation for inline members.
	+
	+INLINE_INFO = YES
	+
	+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
	+# will sort the (detailed) documentation of file and class members
	+# alphabetically by member name. If set to NO the members will appear in
	+# declaration order.
	+
	+SORT_MEMBER_DOCS = YES
	+
	+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
	+# brief documentation of file, namespace and class members alphabetically
	+# by member name. If set to NO (the default) the members will appear in
	+# declaration order.
	+
	+SORT_BRIEF_DOCS = NO
	+
	+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
	+# will sort the (brief and detailed) documentation of class members so that
	+# constructors and destructors are listed first. If set to NO (the default)
	+# the constructors will appear in the respective orders defined by
	+# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
	+# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
	+# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
	+
	+SORT_MEMBERS_CTORS_1ST = NO
	+
	+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
	+# hierarchy of group names into alphabetical order. If set to NO (the default)
	+# the group names will appear in their defined order.
	+
	+SORT_GROUP_NAMES = NO
	+
	+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
	+# sorted by fully-qualified names, including namespaces. If set to
	+# NO (the default), the class list will be sorted only by class name,
	+# not including the namespace part.
	+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
	+# Note: This option applies only to the class list, not to the
	+# alphabetical list.
	+
	+SORT_BY_SCOPE_NAME = NO
	+
	+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
	+# do proper type resolution of all parameters of a function it will reject a
	+# match between the prototype and the implementation of a member function even
	+# if there is only one candidate or it is obvious which candidate to choose
	+# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
	+# will still accept a match between prototype and implementation in such cases.
	+
	+STRICT_PROTO_MATCHING = NO
	+
	+# The GENERATE_TODOLIST tag can be used to enable (YES) or
	+# disable (NO) the todo list. This list is created by putting \todo
	+# commands in the documentation.
	+
	+GENERATE_TODOLIST = YES
	+
	+# The GENERATE_TESTLIST tag can be used to enable (YES) or
	+# disable (NO) the test list. This list is created by putting \test
	+# commands in the documentation.
	+
	+GENERATE_TESTLIST = YES
	+
	+# The GENERATE_BUGLIST tag can be used to enable (YES) or
	+# disable (NO) the bug list. This list is created by putting \bug
	+# commands in the documentation.
	+
	+GENERATE_BUGLIST = YES
	+
	+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
	+# disable (NO) the deprecated list. This list is created by putting
	+# \deprecated commands in the documentation.
	+
	+GENERATE_DEPRECATEDLIST= YES
	+
	+# The ENABLED_SECTIONS tag can be used to enable conditional
	+# documentation sections, marked by \if sectionname ... \endif.
	+
	+ENABLED_SECTIONS =
	+
	+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
	+# the initial value of a variable or macro consists of for it to appear in
	+# the documentation. If the initializer consists of more lines than specified
	+# here it will be hidden. Use a value of 0 to hide initializers completely.
	+# The appearance of the initializer of individual variables and macros in the
	+# documentation can be controlled using \showinitializer or \hideinitializer
	+# command in the documentation regardless of this setting.
	+
	+MAX_INITIALIZER_LINES = 30
	+
	+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
	+# at the bottom of the documentation of classes and structs. If set to YES the
	+# list will mention the files that were used to generate the documentation.
	+
	+SHOW_USED_FILES = YES
	+
	+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
	+# This will remove the Files entry from the Quick Index and from the
	+# Folder Tree View (if specified). The default is YES.
	+
	+SHOW_FILES = YES
	+
	+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
	+# Namespaces page.
	+# This will remove the Namespaces entry from the Quick Index
	+# and from the Folder Tree View (if specified). The default is YES.
	+
	+SHOW_NAMESPACES = YES
	+
	+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
	+# doxygen should invoke to get the current version for each file (typically from
	+# the version control system). Doxygen will invoke the program by executing (via
	+# popen()) the command <command> <input-file>, where <command> is the value of
	+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
	+# provided by doxygen. Whatever the program writes to standard output
	+# is used as the file version. See the manual for examples.
	+
	+FILE_VERSION_FILTER =
	+
	+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
	+# by doxygen. The layout file controls the global structure of the generated
	+# output files in an output format independent way. To create the layout file
	+# that represents doxygen's defaults, run doxygen with the -l option.
	+# You can optionally specify a file name after the option, if omitted
	+# DoxygenLayout.xml will be used as the name of the layout file.
	+
	+LAYOUT_FILE =
	+
	+# The CITE_BIB_FILES tag can be used to specify one or more bib files
	+# containing the references data. This must be a list of .bib files. The
	+# .bib extension is automatically appended if omitted. Using this command
	+# requires the bibtex tool to be installed. See also
	+# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
	+# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
	+# feature you need bibtex and perl available in the search path.
	+
	+CITE_BIB_FILES =
	+
	+#---------------------------------------------------------------------------
	+# configuration options related to warning and progress messages
	+#---------------------------------------------------------------------------
	+
	+# The QUIET tag can be used to turn on/off the messages that are generated
	+# by doxygen. Possible values are YES and NO. If left blank NO is used.
	+
	+QUIET = NO
	+
	+# The WARNINGS tag can be used to turn on/off the warning messages that are
	+# generated by doxygen. Possible values are YES and NO. If left blank
	+# NO is used.
	+
	+WARNINGS = YES
	+
	+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
	+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
	+# automatically be disabled.
	+
	+WARN_IF_UNDOCUMENTED = YES
	+
	+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
	+# potential errors in the documentation, such as not documenting some
	+# parameters in a documented function, or documenting parameters that
	+# don't exist or using markup commands wrongly.
	+
	+WARN_IF_DOC_ERROR = YES
	+
	+# The WARN_NO_PARAMDOC option can be enabled to get warnings for
	+# functions that are documented, but have no documentation for their parameters
	+# or return value. If set to NO (the default) doxygen will only warn about
	+# wrong or incomplete parameter documentation, but not about the absence of
	+# documentation.
	+
	+WARN_NO_PARAMDOC = NO
	+
	+# The WARN_FORMAT tag determines the format of the warning messages that
	+# doxygen can produce. The string should contain the $file, $line, and $text
	+# tags, which will be replaced by the file and line number from which the
	+# warning originated and the warning text. Optionally the format may contain
	+# $version, which will be replaced by the version of the file (if it could
	+# be obtained via FILE_VERSION_FILTER)
	+
	+WARN_FORMAT = "$file:$line: $text"
	+
	+# The WARN_LOGFILE tag can be used to specify a file to which warning
	+# and error messages should be written. If left blank the output is written
	+# to stderr.
	+
	+WARN_LOGFILE =
	+
	+#---------------------------------------------------------------------------
	+# configuration options related to the input files
	+#---------------------------------------------------------------------------
	+
	+# The INPUT tag can be used to specify the files and/or directories that contain
	+# documented source files. You may enter file names like "myfile.cpp" or
	+# directories like "/usr/src/myproject". Separate the files or directories
	+# with spaces.
	+
	+INPUT = .
	+
	+# This tag can be used to specify the character encoding of the source files
	+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
	+# also the default input encoding. Doxygen uses libiconv (or the iconv built
	+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
	+# the list of possible encodings.
	+
	+INPUT_ENCODING = UTF-8
	+
	+# If the value of the INPUT tag contains directories, you can use the
	+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
	+# and *.h) to filter out the source-files in the directories. If left
	+# blank the following patterns are tested:
	+# .c .cc .cxx .cpp .c++ .d .java .ii .ixx .ipp .i++ .inl .h .hh
	+# .hxx .hpp .h++ .idl .odl .cs .php .php3 .inc .m .mm .dox *.py
	+# .f90 .f .for .vhd *.vhdl
	+
	+FILE_PATTERNS =
	+
	+# The RECURSIVE tag can be used to turn specify whether or not subdirectories
	+# should be searched for input files as well. Possible values are YES and NO.
	+# If left blank NO is used.
	+
	+RECURSIVE = NO
	+
	+# The EXCLUDE tag can be used to specify files and/or directories that should be
	+# excluded from the INPUT source files. This way you can easily exclude a
	+# subdirectory from a directory tree whose root is specified with the INPUT tag.
	+# Note that relative paths are relative to the directory from which doxygen is
	+# run.
	+
	+EXCLUDE = cmd_line.cc
	+
	+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
	+# directories that are symbolic links (a Unix file system feature) are excluded
	+# from the input.
	+
	+EXCLUDE_SYMLINKS = NO
	+
	+# If the value of the INPUT tag contains directories, you can use the
	+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
	+# certain files from those directories. Note that the wildcards are matched
	+# against the file with absolute path, so to exclude all test directories
	+# for example use the pattern /test/
	+
	+EXCLUDE_PATTERNS =
	+
	+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
	+# (namespaces, classes, functions, etc.) that should be excluded from the
	+# output. The symbol name can be a fully qualified name, a word, or if the
	+# wildcard * is used, a substring. Examples: ANamespace, AClass,
	+# AClass::ANamespace, ANamespace::*Test
	+
	+EXCLUDE_SYMBOLS =
	+
	+# The EXAMPLE_PATH tag can be used to specify one or more files or
	+# directories that contain example code fragments that are included (see
	+# the \include command).
	+
	+EXAMPLE_PATH =
	+
	+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
	+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
	+# and *.h) to filter out the source-files in the directories. If left
	+# blank all files are included.
	+
	+EXAMPLE_PATTERNS =
	+
	+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
	+# searched for input files to be used with the \include or \dontinclude
	+# commands irrespective of the value of the RECURSIVE tag.
	+# Possible values are YES and NO. If left blank NO is used.
	+
	+EXAMPLE_RECURSIVE = NO
	+
	+# The IMAGE_PATH tag can be used to specify one or more files or
	+# directories that contain image that are included in the documentation (see
	+# the \image command).
	+
	+IMAGE_PATH =
	+
	+# The INPUT_FILTER tag can be used to specify a program that doxygen should
	+# invoke to filter for each input file. Doxygen will invoke the filter program
	+# by executing (via popen()) the command <filter> <input-file>, where <filter>
	+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
	+# input file. Doxygen will then use the output that the filter program writes
	+# to standard output.
	+# If FILTER_PATTERNS is specified, this tag will be
	+# ignored.
	+
	+INPUT_FILTER =
	+
	+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
	+# basis.
	+# Doxygen will compare the file name with each pattern and apply the
	+# filter if there is a match.
	+# The filters are a list of the form:
	+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
	+# info on how filters are used. If FILTER_PATTERNS is empty or if
	+# non of the patterns match the file name, INPUT_FILTER is applied.
	+
	+FILTER_PATTERNS =
	+
	+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
	+# INPUT_FILTER) will be used to filter the input files when producing source
	+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
	+
	+FILTER_SOURCE_FILES = NO
	+
	+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
	+# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
	+# and it is also possible to disable source filtering for a specific pattern
	+# using *.ext= (so without naming a filter). This option only has effect when
	+# FILTER_SOURCE_FILES is enabled.
	+
	+FILTER_SOURCE_PATTERNS =
	+
	+#---------------------------------------------------------------------------
	+# configuration options related to source browsing
	+#---------------------------------------------------------------------------
	+
	+# If the SOURCE_BROWSER tag is set to YES then a list of source files will
	+# be generated. Documented entities will be cross-referenced with these sources.
	+# Note: To get rid of all source code in the generated output, make sure also
	+# VERBATIM_HEADERS is set to NO.
	+
	+SOURCE_BROWSER = YES
	+
	+# Setting the INLINE_SOURCES tag to YES will include the body
	+# of functions and classes directly in the documentation.
	+
	+INLINE_SOURCES = NO
	+
	+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
	+# doxygen to hide any special comment blocks from generated source code
	+# fragments. Normal C, C++ and Fortran comments will always remain visible.
	+
	+STRIP_CODE_COMMENTS = NO
	+
	+# If the REFERENCED_BY_RELATION tag is set to YES
	+# then for each documented function all documented
	+# functions referencing it will be listed.
	+
	+REFERENCED_BY_RELATION = NO
	+
	+# If the REFERENCES_RELATION tag is set to YES
	+# then for each documented function all documented entities
	+# called/used by that function will be listed.
	+
	+REFERENCES_RELATION = NO
	+
	+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
	+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
	+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
	+# link to the source code.
	+# Otherwise they will link to the documentation.
	+
	+REFERENCES_LINK_SOURCE = NO
	+
	+# If the USE_HTAGS tag is set to YES then the references to source code
	+# will point to the HTML generated by the htags(1) tool instead of doxygen
	+# built-in source browser. The htags tool is part of GNU's global source
	+# tagging system (see http://www.gnu.org/software/global/global.html). You
	+# will need version 4.8.6 or higher.
	+
	+USE_HTAGS = NO
	+
	+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
	+# will generate a verbatim copy of the header file for each class for
	+# which an include is specified. Set to NO to disable this.
	+
	+VERBATIM_HEADERS = YES
	+
	+#---------------------------------------------------------------------------
	+# configuration options related to the alphabetical class index
	+#---------------------------------------------------------------------------
	+
	+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
	+# of all compounds will be generated. Enable this if the project
	+# contains a lot of classes, structs, unions or interfaces.
	+
	+ALPHABETICAL_INDEX = NO
	+
	+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
	+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
	+# in which this list will be split (can be a number in the range [1..20])
	+
	+COLS_IN_ALPHA_INDEX = 5
	+
	+# In case all classes in a project start with a common prefix, all
	+# classes will be put under the same header in the alphabetical index.
	+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
	+# should be ignored while generating the index headers.
	+
	+IGNORE_PREFIX =
	+
	+#---------------------------------------------------------------------------
	+# configuration options related to the HTML output
	+#---------------------------------------------------------------------------
	+
	+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
	+# generate HTML output.
	+
	+GENERATE_HTML = YES
	+
	+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
	+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
	+# put in front of it. If left blank `html' will be used as the default path.
	+
	+HTML_OUTPUT = html
	+
	+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
	+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
	+# doxygen will generate files with .html extension.
	+
	+HTML_FILE_EXTENSION = .html
	+
	+# The HTML_HEADER tag can be used to specify a personal HTML header for
	+# each generated HTML page. If it is left blank doxygen will generate a
	+# standard header. Note that when using a custom header you are responsible
	+# for the proper inclusion of any scripts and style sheets that doxygen
	+# needs, which is dependent on the configuration options used.
	+# It is advised to generate a default header using "doxygen -w html
	+# header.html footer.html stylesheet.css YourConfigFile" and then modify
	+# that header. Note that the header is subject to change so you typically
	+# have to redo this when upgrading to a newer version of doxygen or when
	+# changing the value of configuration settings such as GENERATE_TREEVIEW!
	+
	+HTML_HEADER =
	+
	+# The HTML_FOOTER tag can be used to specify a personal HTML footer for
	+# each generated HTML page. If it is left blank doxygen will generate a
	+# standard footer.
	+
	+HTML_FOOTER =
	+
	+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
	+# style sheet that is used by each HTML page. It can be used to
	+# fine-tune the look of the HTML output. If the tag is left blank doxygen
	+# will generate a default style sheet. Note that doxygen will try to copy
	+# the style sheet file to the HTML output directory, so don't put your own
	+# style sheet in the HTML output directory as well, or it will be erased!
	+
	+HTML_STYLESHEET =
	+
	+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
	+# other source files which should be copied to the HTML output directory. Note
	+# that these files will be copied to the base HTML output directory. Use the
	+# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
	+# files. In the HTML_STYLESHEET file, use the file name only. Also note that
	+# the files will be copied as-is; there are no commands or markers available.
	+
	+HTML_EXTRA_FILES =
	+
	+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
	+# Doxygen will adjust the colors in the style sheet and background images
	+# according to this color. Hue is specified as an angle on a colorwheel,
	+# see http://en.wikipedia.org/wiki/Hue for more information.
	+# For instance the value 0 represents red, 60 is yellow, 120 is green,
	+# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
	+# The allowed range is 0 to 359.
	+
	+HTML_COLORSTYLE_HUE = 220
	+
	+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
	+# the colors in the HTML output. For a value of 0 the output will use
	+# grayscales only. A value of 255 will produce the most vivid colors.
	+
	+HTML_COLORSTYLE_SAT = 100
	+
	+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
	+# the luminance component of the colors in the HTML output. Values below
	+# 100 gradually make the output lighter, whereas values above 100 make
	+# the output darker. The value divided by 100 is the actual gamma applied,
	+# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
	+# and 100 does not change the gamma.
	+
	+HTML_COLORSTYLE_GAMMA = 80
	+
	+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
	+# page will contain the date and time when the page was generated. Setting
	+# this to NO can help when comparing the output of multiple runs.
	+
	+HTML_TIMESTAMP = YES
	+
	+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
	+# documentation will contain sections that can be hidden and shown after the
	+# page has loaded.
	+
	+HTML_DYNAMIC_SECTIONS = YES
	+
	+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
	+# entries shown in the various tree structured indices initially; the user
	+# can expand and collapse entries dynamically later on. Doxygen will expand
	+# the tree to such a level that at most the specified number of entries are
	+# visible (unless a fully collapsed tree already exceeds this amount).
	+# So setting the number of entries 1 will produce a full collapsed tree by
	+# default. 0 is a special value representing an infinite number of entries
	+# and will result in a full expanded tree by default.
	+
	+HTML_INDEX_NUM_ENTRIES = 100
	+
	+# If the GENERATE_DOCSET tag is set to YES, additional index files
	+# will be generated that can be used as input for Apple's Xcode 3
	+# integrated development environment, introduced with OSX 10.5 (Leopard).
	+# To create a documentation set, doxygen will generate a Makefile in the
	+# HTML output directory. Running make will produce the docset in that
	+# directory and running "make install" will install the docset in
	+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
	+# it at startup.
	+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
	+# for more information.
	+
	+GENERATE_DOCSET = NO
	+
	+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
	+# feed. A documentation feed provides an umbrella under which multiple
	+# documentation sets from a single provider (such as a company or product suite)
	+# can be grouped.
	+
	+DOCSET_FEEDNAME = "Doxygen generated docs"
	+
	+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
	+# should uniquely identify the documentation set bundle. This should be a
	+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
	+# will append .docset to the name.
	+
	+DOCSET_BUNDLE_ID = org.doxygen.Project
	+
	+# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
	+# the documentation publisher. This should be a reverse domain-name style
	+# string, e.g. com.mycompany.MyDocSet.documentation.
	+
	+DOCSET_PUBLISHER_ID = org.doxygen.Publisher
	+
	+# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
	+
	+DOCSET_PUBLISHER_NAME = Publisher
	+
	+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
	+# will be generated that can be used as input for tools like the
	+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
	+# of the generated HTML documentation.
	+
	+GENERATE_HTMLHELP = NO
	+
	+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
	+# be used to specify the file name of the resulting .chm file. You
	+# can add a path in front of the file if the result should not be
	+# written to the html output directory.
	+
	+CHM_FILE =
	+
	+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
	+# be used to specify the location (absolute path including file name) of
	+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
	+# the HTML help compiler on the generated index.hhp.
	+
	+HHC_LOCATION =
	+
	+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
	+# controls if a separate .chi index file is generated (YES) or that
	+# it should be included in the master .chm file (NO).
	+
	+GENERATE_CHI = NO
	+
	+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
	+# is used to encode HtmlHelp index (hhk), content (hhc) and project file
	+# content.
	+
	+CHM_INDEX_ENCODING =
	+
	+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
	+# controls whether a binary table of contents is generated (YES) or a
	+# normal table of contents (NO) in the .chm file.
	+
	+BINARY_TOC = NO
	+
	+# The TOC_EXPAND flag can be set to YES to add extra items for group members
	+# to the contents of the HTML help documentation and to the tree view.
	+
	+TOC_EXPAND = NO
	+
	+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
	+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
	+# that can be used as input for Qt's qhelpgenerator to generate a
	+# Qt Compressed Help (.qch) of the generated HTML documentation.
	+
	+GENERATE_QHP = NO
	+
	+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
	+# be used to specify the file name of the resulting .qch file.
	+# The path specified is relative to the HTML output folder.
	+
	+QCH_FILE =
	+
	+# The QHP_NAMESPACE tag specifies the namespace to use when generating
	+# Qt Help Project output. For more information please see
	+# http://doc.trolltech.com/qthelpproject.html#namespace
	+
	+QHP_NAMESPACE = org.doxygen.Project
	+
	+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
	+# Qt Help Project output. For more information please see
	+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
	+
	+QHP_VIRTUAL_FOLDER = doc
	+
	+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
	+# add. For more information please see
	+# http://doc.trolltech.com/qthelpproject.html#custom-filters
	+
	+QHP_CUST_FILTER_NAME =
	+
	+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
	+# custom filter to add. For more information please see
	+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
	+# Qt Help Project / Custom Filters</a>.
	+
	+QHP_CUST_FILTER_ATTRS =
	+
	+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
	+# project's
	+# filter section matches.
	+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
	+# Qt Help Project / Filter Attributes</a>.
	+
	+QHP_SECT_FILTER_ATTRS =
	+
	+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
	+# be used to specify the location of Qt's qhelpgenerator.
	+# If non-empty doxygen will try to run qhelpgenerator on the generated
	+# .qhp file.
	+
	+QHG_LOCATION =
	+
	+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
	+# will be generated, which together with the HTML files, form an Eclipse help
	+# plugin. To install this plugin and make it available under the help contents
	+# menu in Eclipse, the contents of the directory containing the HTML and XML
	+# files needs to be copied into the plugins directory of eclipse. The name of
	+# the directory within the plugins directory should be the same as
	+# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
	+# the help appears.
	+
	+GENERATE_ECLIPSEHELP = NO
	+
	+# A unique identifier for the eclipse help plugin. When installing the plugin
	+# the directory name containing the HTML and XML files should also have
	+# this name.
	+
	+ECLIPSE_DOC_ID = org.doxygen.Project
	+
	+# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
	+# at top of each HTML page. The value NO (the default) enables the index and
	+# the value YES disables it. Since the tabs have the same information as the
	+# navigation tree you can set this option to NO if you already set
	+# GENERATE_TREEVIEW to YES.
	+
	+DISABLE_INDEX = NO
	+
	+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
	+# structure should be generated to display hierarchical information.
	+# If the tag value is set to YES, a side panel will be generated
	+# containing a tree-like index structure (just like the one that
	+# is generated for HTML Help). For this to work a browser that supports
	+# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
	+# Windows users are probably better off using the HTML help feature.
	+# Since the tree basically has the same information as the tab index you
	+# could consider to set DISABLE_INDEX to NO when enabling this option.
	+
	+GENERATE_TREEVIEW = NO
	+
	+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
	+# (range [0,1..20]) that doxygen will group on one line in the generated HTML
	+# documentation. Note that a value of 0 will completely suppress the enum
	+# values from appearing in the overview section.
	+
	+ENUM_VALUES_PER_LINE = 4
	+
	+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
	+# used to set the initial width (in pixels) of the frame in which the tree
	+# is shown.
	+
	+TREEVIEW_WIDTH = 250
	+
	+# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
	+# links to external symbols imported via tag files in a separate window.
	+
	+EXT_LINKS_IN_WINDOW = NO
	+
	+# Use this tag to change the font size of Latex formulas included
	+# as images in the HTML documentation. The default is 10. Note that
	+# when you change the font size after a successful doxygen run you need
	+# to manually remove any form_*.png images from the HTML output directory
	+# to force them to be regenerated.
	+
	+FORMULA_FONTSIZE = 10
	+
	+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
	+# generated for formulas are transparent PNGs. Transparent PNGs are
	+# not supported properly for IE 6.0, but are supported on all modern browsers.
	+# Note that when changing this option you need to delete any form_*.png files
	+# in the HTML output before the changes have effect.
	+
	+FORMULA_TRANSPARENT = YES
	+
	+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
	+# (see http://www.mathjax.org) which uses client side Javascript for the
	+# rendering instead of using prerendered bitmaps. Use this if you do not
	+# have LaTeX installed or if you want to formulas look prettier in the HTML
	+# output. When enabled you may also need to install MathJax separately and
	+# configure the path to it using the MATHJAX_RELPATH option.
	+
	+USE_MATHJAX = NO
	+
	+# When MathJax is enabled you need to specify the location relative to the
	+# HTML output directory using the MATHJAX_RELPATH option. The destination
	+# directory should contain the MathJax.js script. For instance, if the mathjax
	+# directory is located at the same level as the HTML output directory, then
	+# MATHJAX_RELPATH should be ../mathjax. The default value points to
	+# the MathJax Content Delivery Network so you can quickly see the result without
	+# installing MathJax.
	+# However, it is strongly recommended to install a local
	+# copy of MathJax from http://www.mathjax.org before deployment.
	+
	+MATHJAX_RELPATH = http://www.mathjax.org/mathjax
	+
	+# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension
	+# names that should be enabled during MathJax rendering.
	+
	+MATHJAX_EXTENSIONS =
	+
	+# When the SEARCHENGINE tag is enabled doxygen will generate a search box
	+# for the HTML output. The underlying search engine uses javascript
	+# and DHTML and should work on any modern browser. Note that when using
	+# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
	+# (GENERATE_DOCSET) there is already a search function so this one should
	+# typically be disabled. For large projects the javascript based search engine
	+# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
	+
	+SEARCHENGINE = NO
	+
	+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
	+# implemented using a PHP enabled web server instead of at the web client
	+# using Javascript. Doxygen will generate the search PHP script and index
	+# file to put on the web server. The advantage of the server
	+# based approach is that it scales better to large projects and allows
	+# full text search. The disadvantages are that it is more difficult to setup
	+# and does not have live searching capabilities.
	+
	+SERVER_BASED_SEARCH = NO
	+
	+#---------------------------------------------------------------------------
	+# configuration options related to the LaTeX output
	+#---------------------------------------------------------------------------
	+
	+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
	+# generate Latex output.
	+
	+GENERATE_LATEX = NO
	+
	+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
	+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
	+# put in front of it. If left blank `latex' will be used as the default path.
	+
	+LATEX_OUTPUT = latex
	+
	+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
	+# invoked. If left blank `latex' will be used as the default command name.
	+# Note that when enabling USE_PDFLATEX this option is only used for
	+# generating bitmaps for formulas in the HTML output, but not in the
	+# Makefile that is written to the output directory.
	+
	+LATEX_CMD_NAME = latex
	+
	+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
	+# generate index for LaTeX. If left blank `makeindex' will be used as the
	+# default command name.
	+
	+MAKEINDEX_CMD_NAME = makeindex
	+
	+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
	+# LaTeX documents. This may be useful for small projects and may help to
	+# save some trees in general.
	+
	+COMPACT_LATEX = YES
	+
	+# The PAPER_TYPE tag can be used to set the paper type that is used
	+# by the printer. Possible values are: a4, letter, legal and
	+# executive. If left blank a4wide will be used.
	+
	+PAPER_TYPE = letter
	+
	+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
	+# packages that should be included in the LaTeX output.
	+
	+EXTRA_PACKAGES = fullpage, \
	+ palatino
	+
	+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
	+# the generated latex document. The header should contain everything until
	+# the first chapter. If it is left blank doxygen will generate a
	+# standard header. Notice: only use this tag if you know what you are doing!
	+
	+LATEX_HEADER =
	+
	+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
	+# the generated latex document. The footer should contain everything after
	+# the last chapter. If it is left blank doxygen will generate a
	+# standard footer. Notice: only use this tag if you know what you are doing!
	+
	+LATEX_FOOTER =
	+
	+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
	+# is prepared for conversion to pdf (using ps2pdf). The pdf file will
	+# contain links (just like the HTML output) instead of page references
	+# This makes the output suitable for online browsing using a pdf viewer.
	+
	+PDF_HYPERLINKS = YES
	+
	+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
	+# plain latex in the generated Makefile. Set this option to YES to get a
	+# higher quality PDF documentation.
	+
	+USE_PDFLATEX = YES
	+
	+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
	+# command to the generated LaTeX files. This will instruct LaTeX to keep
	+# running if errors occur, instead of asking the user for help.
	+# This option is also used when generating formulas in HTML.
	+
	+LATEX_BATCHMODE = YES
	+
	+# If LATEX_HIDE_INDICES is set to YES then doxygen will not
	+# include the index chapters (such as File Index, Compound Index, etc.)
	+# in the output.
	+
	+LATEX_HIDE_INDICES = YES
	+
	+# If LATEX_SOURCE_CODE is set to YES then doxygen will include
	+# source code with syntax highlighting in the LaTeX output.
	+# Note that which sources are shown also depends on other settings
	+# such as SOURCE_BROWSER.
	+
	+LATEX_SOURCE_CODE = NO
	+
	+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
	+# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
	+# http://en.wikipedia.org/wiki/BibTeX for more info.
	+
	+LATEX_BIB_STYLE = plain
	+
	+#---------------------------------------------------------------------------
	+# configuration options related to the RTF output
	+#---------------------------------------------------------------------------
	+
	+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
	+# The RTF output is optimized for Word 97 and may not look very pretty with
	+# other RTF readers or editors.
	+
	+GENERATE_RTF = NO
	+
	+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
	+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
	+# put in front of it. If left blank `rtf' will be used as the default path.
	+
	+RTF_OUTPUT = rtf
	+
	+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
	+# RTF documents. This may be useful for small projects and may help to
	+# save some trees in general.
	+
	+COMPACT_RTF = NO
	+
	+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
	+# will contain hyperlink fields. The RTF file will
	+# contain links (just like the HTML output) instead of page references.
	+# This makes the output suitable for online browsing using WORD or other
	+# programs which support those fields.
	+# Note: wordpad (write) and others do not support links.
	+
	+RTF_HYPERLINKS = NO
	+
	+# Load style sheet definitions from file. Syntax is similar to doxygen's
	+# config file, i.e. a series of assignments. You only have to provide
	+# replacements, missing definitions are set to their default value.
	+
	+RTF_STYLESHEET_FILE =
	+
	+# Set optional variables used in the generation of an rtf document.
	+# Syntax is similar to doxygen's config file.
	+
	+RTF_EXTENSIONS_FILE =
	+
	+#---------------------------------------------------------------------------
	+# configuration options related to the man page output
	+#---------------------------------------------------------------------------
	+
	+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
	+# generate man pages
	+
	+GENERATE_MAN = NO
	+
	+# The MAN_OUTPUT tag is used to specify where the man pages will be put.
	+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
	+# put in front of it. If left blank `man' will be used as the default path.
	+
	+MAN_OUTPUT = man
	+
	+# The MAN_EXTENSION tag determines the extension that is added to
	+# the generated man pages (default is the subroutine's section .3)
	+
	+MAN_EXTENSION = .3
	+
	+# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
	+# then it will generate one additional man file for each entity
	+# documented in the real man page(s). These additional files
	+# only source the real man page, but without them the man command
	+# would be unable to find the correct page. The default is NO.
	+
	+MAN_LINKS = NO
	+
	+#---------------------------------------------------------------------------
	+# configuration options related to the XML output
	+#---------------------------------------------------------------------------
	+
	+# If the GENERATE_XML tag is set to YES Doxygen will
	+# generate an XML file that captures the structure of
	+# the code including all documentation.
	+
	+GENERATE_XML = NO
	+
	+# The XML_OUTPUT tag is used to specify where the XML pages will be put.
	+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
	+# put in front of it. If left blank `xml' will be used as the default path.
	+
	+XML_OUTPUT = xml
	+
	+# The XML_SCHEMA tag can be used to specify an XML schema,
	+# which can be used by a validating XML parser to check the
	+# syntax of the XML files.
	+
	+XML_SCHEMA =
	+
	+# The XML_DTD tag can be used to specify an XML DTD,
	+# which can be used by a validating XML parser to check the
	+# syntax of the XML files.
	+
	+XML_DTD =
	+
	+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
	+# dump the program listings (including syntax highlighting
	+# and cross-referencing information) to the XML output. Note that
	+# enabling this will significantly increase the size of the XML output.
	+
	+XML_PROGRAMLISTING = YES
	+
	+#---------------------------------------------------------------------------
	+# configuration options for the AutoGen Definitions output
	+#---------------------------------------------------------------------------
	+
	+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
	+# generate an AutoGen Definitions (see autogen.sf.net) file
	+# that captures the structure of the code including all
	+# documentation. Note that this feature is still experimental
	+# and incomplete at the moment.
	+
	+GENERATE_AUTOGEN_DEF = NO
	+
	+#---------------------------------------------------------------------------
	+# configuration options related to the Perl module output
	+#---------------------------------------------------------------------------
	+
	+# If the GENERATE_PERLMOD tag is set to YES Doxygen will
	+# generate a Perl module file that captures the structure of
	+# the code including all documentation. Note that this
	+# feature is still experimental and incomplete at the
	+# moment.
	+
	+GENERATE_PERLMOD = NO
	+
	+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
	+# the necessary Makefile rules, Perl scripts and LaTeX code to be able
	+# to generate PDF and DVI output from the Perl module output.
	+
	+PERLMOD_LATEX = NO
	+
	+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
	+# nicely formatted so it can be parsed by a human reader.
	+# This is useful
	+# if you want to understand what is going on.
	+# On the other hand, if this
	+# tag is set to NO the size of the Perl module output will be much smaller
	+# and Perl will parse it just the same.
	+
	+PERLMOD_PRETTY = YES
	+
	+# The names of the make variables in the generated doxyrules.make file
	+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
	+# This is useful so different doxyrules.make files included by the same
	+# Makefile don't overwrite each other's variables.
	+
	+PERLMOD_MAKEVAR_PREFIX =
	+
	+#---------------------------------------------------------------------------
	+# Configuration options related to the preprocessor
	+#---------------------------------------------------------------------------
	+
	+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
	+# evaluate all C-preprocessor directives found in the sources and include
	+# files.
	+
	+ENABLE_PREPROCESSING = YES
	+
	+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
	+# names in the source code. If set to NO (the default) only conditional
	+# compilation will be performed. Macro expansion can be done in a controlled
	+# way by setting EXPAND_ONLY_PREDEF to YES.
	+
	+MACRO_EXPANSION = NO
	+
	+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
	+# then the macro expansion is limited to the macros specified with the
	+# PREDEFINED and EXPAND_AS_DEFINED tags.
	+
	+EXPAND_ONLY_PREDEF = NO
	+
	+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
	+# pointed to by INCLUDE_PATH will be searched when a #include is found.
	+
	+SEARCH_INCLUDES = YES
	+
	+# The INCLUDE_PATH tag can be used to specify one or more directories that
	+# contain include files that are not input files but should be processed by
	+# the preprocessor.
	+
	+INCLUDE_PATH =
	+
	+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
	+# patterns (like .h and .hpp) to filter out the header-files in the
	+# directories. If left blank, the patterns specified with FILE_PATTERNS will
	+# be used.
	+
	+INCLUDE_FILE_PATTERNS =
	+
	+# The PREDEFINED tag can be used to specify one or more macro names that
	+# are defined before the preprocessor is started (similar to the -D option of
	+# gcc). The argument of the tag is a list of macros of the form: name
	+# or name=definition (no spaces). If the definition and the = are
	+# omitted =1 is assumed. To prevent a macro definition from being
	+# undefined via #undef or recursively expanded use the := operator
	+# instead of the = operator.
	+
	+PREDEFINED =
	+
	+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
	+# this tag can be used to specify a list of macro names that should be expanded.
	+# The macro definition that is found in the sources will be used.
	+# Use the PREDEFINED tag if you want to use a different macro definition that
	+# overrules the definition found in the source code.
	+
	+EXPAND_AS_DEFINED =
	+
	+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
	+# doxygen's preprocessor will remove all references to function-like macros
	+# that are alone on a line, have an all uppercase name, and do not end with a
	+# semicolon, because these will confuse the parser if not removed.
	+
	+SKIP_FUNCTION_MACROS = YES
	+
	+#---------------------------------------------------------------------------
	+# Configuration::additions related to external references
	+#---------------------------------------------------------------------------
	+
	+# The TAGFILES option can be used to specify one or more tagfiles. For each
	+# tag file the location of the external documentation should be added. The
	+# format of a tag file without this location is as follows:
	+#
	+# TAGFILES = file1 file2 ...
	+# Adding location for the tag files is done as follows:
	+#
	+# TAGFILES = file1=loc1 "file2 = loc2" ...
	+# where "loc1" and "loc2" can be relative or absolute paths
	+# or URLs. Note that each tag file must have a unique name (where the name does
	+# NOT include the path). If a tag file is not located in the directory in which
	+# doxygen is run, you must also specify the path to the tagfile here.
	+
	+TAGFILES =
	+
	+# When a file name is specified after GENERATE_TAGFILE, doxygen will create
	+# a tag file that is based on the input files it reads.
	+
	+GENERATE_TAGFILE =
	+
	+# If the ALLEXTERNALS tag is set to YES all external classes will be listed
	+# in the class index. If set to NO only the inherited external classes
	+# will be listed.
	+
	+ALLEXTERNALS = NO
	+
	+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
	+# in the modules index. If set to NO, only the current project's groups will
	+# be listed.
	+
	+EXTERNAL_GROUPS = YES
	+
	+# The PERL_PATH should be the absolute path and name of the perl script
	+# interpreter (i.e. the result of `which perl').
	+
	+PERL_PATH = /usr/bin/perl
	+
	+#---------------------------------------------------------------------------
	+# Configuration options related to the dot tool
	+#---------------------------------------------------------------------------
	+
	+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
	+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
	+# or super classes. Setting the tag to NO turns the diagrams off. Note that
	+# this option also works with HAVE_DOT disabled, but it is recommended to
	+# install and use dot, since it yields more powerful graphs.
	+
	+CLASS_DIAGRAMS = YES
	+
	+# You can define message sequence charts within doxygen comments using the \msc
	+# command. Doxygen will then run the mscgen tool (see
	+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
	+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
	+# the mscgen tool resides. If left empty the tool is assumed to be found in the
	+# default search path.
	+
	+MSCGEN_PATH =
	+
	+# If set to YES, the inheritance and collaboration graphs will hide
	+# inheritance and usage relations if the target is undocumented
	+# or is not a class.
	+
	+HIDE_UNDOC_RELATIONS = YES
	+
	+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
	+# available from the path. This tool is part of Graphviz, a graph visualization
	+# toolkit from AT&T and Lucent Bell Labs. The other options in this section
	+# have no effect if this option is set to NO (the default)
	+
	+HAVE_DOT = NO
	+
	+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
	+# allowed to run in parallel. When set to 0 (the default) doxygen will
	+# base this on the number of processors available in the system. You can set it
	+# explicitly to a value larger than 0 to get control over the balance
	+# between CPU load and processing speed.
	+
	+DOT_NUM_THREADS = 0
	+
	+# By default doxygen will use the Helvetica font for all dot files that
	+# doxygen generates. When you want a differently looking font you can specify
	+# the font name using DOT_FONTNAME. You need to make sure dot is able to find
	+# the font, which can be done by putting it in a standard location or by setting
	+# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
	+# directory containing the font.
	+
	+DOT_FONTNAME = FreeSans
	+
	+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
	+# The default size is 10pt.
	+
	+DOT_FONTSIZE = 10
	+
	+# By default doxygen will tell dot to use the Helvetica font.
	+# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
	+# set the path where dot can find it.
	+
	+DOT_FONTPATH =
	+
	+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
	+# will generate a graph for each documented class showing the direct and
	+# indirect inheritance relations. Setting this tag to YES will force the
	+# CLASS_DIAGRAMS tag to NO.
	+
	+CLASS_GRAPH = YES
	+
	+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
	+# will generate a graph for each documented class showing the direct and
	+# indirect implementation dependencies (inheritance, containment, and
	+# class references variables) of the class with other documented classes.
	+
	+COLLABORATION_GRAPH = YES
	+
	+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
	+# will generate a graph for groups, showing the direct groups dependencies
	+
	+GROUP_GRAPHS = YES
	+
	+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
	+# collaboration diagrams in a style similar to the OMG's Unified Modeling
	+# Language.
	+
	+UML_LOOK = NO
	+
	+# If the UML_LOOK tag is enabled, the fields and methods are shown inside
	+# the class node. If there are many fields or methods and many nodes the
	+# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
	+# threshold limits the number of items for each type to make the size more
	+# managable. Set this to 0 for no limit. Note that the threshold may be
	+# exceeded by 50% before the limit is enforced.
	+
	+UML_LIMIT_NUM_FIELDS = 10
	+
	+# If set to YES, the inheritance and collaboration graphs will show the
	+# relations between templates and their instances.
	+
	+TEMPLATE_RELATIONS = YES
	+
	+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
	+# tags are set to YES then doxygen will generate a graph for each documented
	+# file showing the direct and indirect include dependencies of the file with
	+# other documented files.
	+
	+INCLUDE_GRAPH = YES
	+
	+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
	+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
	+# documented header file showing the documented files that directly or
	+# indirectly include this file.
	+
	+INCLUDED_BY_GRAPH = YES
	+
	+# If the CALL_GRAPH and HAVE_DOT options are set to YES then
	+# doxygen will generate a call dependency graph for every global function
	+# or class method. Note that enabling this option will significantly increase
	+# the time of a run. So in most cases it will be better to enable call graphs
	+# for selected functions only using the \callgraph command.
	+
	+CALL_GRAPH = NO
	+
	+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
	+# doxygen will generate a caller dependency graph for every global function
	+# or class method. Note that enabling this option will significantly increase
	+# the time of a run. So in most cases it will be better to enable caller
	+# graphs for selected functions only using the \callergraph command.
	+
	+CALLER_GRAPH = NO
	+
	+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
	+# will generate a graphical hierarchy of all classes instead of a textual one.
	+
	+GRAPHICAL_HIERARCHY = YES
	+
	+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
	+# then doxygen will show the dependencies a directory has on other directories
	+# in a graphical way. The dependency relations are determined by the #include
	+# relations between the files in the directories.
	+
	+DIRECTORY_GRAPH = YES
	+
	+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
	+# generated by dot. Possible values are svg, png, jpg, or gif.
	+# If left blank png will be used. If you choose svg you need to set
	+# HTML_FILE_EXTENSION to xhtml in order to make the SVG files
	+# visible in IE 9+ (other browsers do not have this requirement).
	+
	+DOT_IMAGE_FORMAT = png
	+
	+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
	+# enable generation of interactive SVG images that allow zooming and panning.
	+# Note that this requires a modern browser other than Internet Explorer.
	+# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you
	+# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files
	+# visible. Older versions of IE do not have SVG support.
	+
	+INTERACTIVE_SVG = NO
	+
	+# The tag DOT_PATH can be used to specify the path where the dot tool can be
	+# found. If left blank, it is assumed the dot tool can be found in the path.
	+
	+DOT_PATH =
	+
	+# The DOTFILE_DIRS tag can be used to specify one or more directories that
	+# contain dot files that are included in the documentation (see the
	+# \dotfile command).
	+
	+DOTFILE_DIRS =
	+
	+# The MSCFILE_DIRS tag can be used to specify one or more directories that
	+# contain msc files that are included in the documentation (see the
	+# \mscfile command).
	+
	+MSCFILE_DIRS =
	+
	+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
	+# nodes that will be shown in the graph. If the number of nodes in a graph
	+# becomes larger than this value, doxygen will truncate the graph, which is
	+# visualized by representing a node as a red box. Note that doxygen if the
	+# number of direct children of the root node in a graph is already larger than
	+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
	+# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
	+
	+DOT_GRAPH_MAX_NODES = 50
	+
	+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
	+# graphs generated by dot. A depth value of 3 means that only nodes reachable
	+# from the root by following a path via at most 3 edges will be shown. Nodes
	+# that lay further from the root node will be omitted. Note that setting this
	+# option to 1 or 2 may greatly reduce the computation time needed for large
	+# code bases. Also note that the size of a graph can be further restricted by
	+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
	+
	+MAX_DOT_GRAPH_DEPTH = 0
	+
	+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
	+# background. This is disabled by default, because dot on Windows does not
	+# seem to support this out of the box. Warning: Depending on the platform used,
	+# enabling this option may lead to badly anti-aliased labels on the edges of
	+# a graph (i.e. they become hard to read).
	+
	+DOT_TRANSPARENT = YES
	+
	+# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
	+# files in one run (i.e. multiple -o and -T options on the command line). This
	+# makes dot run faster, but since only newer versions of dot (>1.8.10)
	+# support this, this feature is disabled by default.
	+
	+DOT_MULTI_TARGETS = NO
	+
	+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
	+# generate a legend page explaining the meaning of the various boxes and
	+# arrows in the dot generated graphs.
	+
	+GENERATE_LEGEND = YES
	+
	+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
	+# remove the intermediate dot files that are used to generate
	+# the various graphs.
	+
	+DOT_CLEANUP = YES
	Index: extern/voro++/src/v_base_wl.cc
	===================================================================
	--- extern/voro++/src/v_base_wl.cc (revision 0)
	+++ extern/voro++/src/v_base_wl.cc (revision 0)
	@@ -0,0 +1,79 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file v_base_wl.cc
	+ * \brief The table of block worklists that are used during the cell
	+ * computation, which is part of the voro_base class.
	+ *
	+ * This file is automatically generated by worklist_gen.pl and it is not
	+ * intended to be edited by hand. */
	+
	+const unsigned int voro_base::wl[wl_seq_length*wl_hgridcu]={
	+ 7,0x10203f,0x101fc0,0xfe040,0xfe03f,0x101fbf,0xfdfc0,0xfdfbf,0x10fe0bf,0x11020bf,0x11020c0,0x10fe0c0,0x2fe041,0x302041,0x301fc1,0x2fdfc1,0x8105fc0,0x8106040,0x810603f,0x8105fbf,0x701fbe,0x70203e,0x6fe03e,0x6fdfbe,0x30fdf3f,0x3101f3f,0x3101f40,0x30fdf40,0x180f9fc0,0x180fa040,0x180fa03f,0x180f9fbf,0x12fe0c1,0x13020c1,0x91060c0,0x91060bf,0x8306041,0x8305fc1,0x3301f41,0x32fdf41,0x182f9fc1,0x182fa041,0x190fa0c0,0x190fa0bf,0x16fe0be,0x17020be,0x870603e,0x8705fbe,0xb105f3f,0xb105f40,0x3701f3e,0x36fdf3e,0x186f9fbe,0x186fa03e,0x1b0f9f3f,0x1b0f9f40,0x93060c1,0x192fa0c1,0x97060be,0xb305f41,0x1b2f9f41,0x196fa0be,0xb705f3e,0x1b6f9f3e,
	+ 11,0x101fc0,0xfe040,0xfdfc0,0x10203f,0x101fbf,0xfe03f,0xfdfbf,0xfdfc1,0x101fc1,0x102041,0xfe041,0x10fe0c0,0x11020c0,0x8106040,0x8105fc0,0x8105fbf,0x810603f,0x11020bf,0x10fe0bf,0x180fa040,0x180f9fc0,0x30fdf40,0x3101f40,0x3101f3f,0x30fdf3f,0x180f9fbf,0x180fa03f,0x6fe03e,0x70203e,0x701fbe,0x6fdfbe,0x8105fc1,0x8106041,0x11020c1,0x10fe0c1,0x180fa041,0x180f9fc1,0x30fdf41,0x3101f41,0x91060c0,0x91060bf,0x190fa0c0,0x190fa0bf,0xb105f40,0xb105f3f,0x8705fbe,0x870603e,0x97020be,0x16fe0be,0x1b0f9f40,0x1b0f9f3f,0x36fdf3e,0xb701f3e,0x1b6f9fbe,0x196fa03e,0x93060c1,0xb305f41,0x192fa0c1,0x1b2f9f41,0x1b2fdfc2,0xb301fc2,0x9302042,0x192fe042,
	+ 11,0x101fc0,0xfe040,0xfdfc0,0xfdfbf,0x101fbf,0x10203f,0xfe03f,0xfe041,0x102041,0x101fc1,0xfdfc1,0x8105fc0,0x8106040,0x11020c0,0x10fe0c0,0x10fe0bf,0x11020bf,0x810603f,0x8105fbf,0x3101f40,0x30fdf40,0x180f9fc0,0x180fa040,0x180fa03f,0x180f9fbf,0x30fdf3f,0x3101f3f,0x8105fc1,0x8106041,0x11020c1,0x10fe0c1,0x180fa041,0x180f9fc1,0x30fdf41,0x3101f41,0x701fbe,0x70203e,0x6fe03e,0x6fdfbe,0x91060c0,0x91060bf,0xb105f40,0xb105f3f,0x190fa0c0,0x190fa0bf,0x93060c1,0x1b0f9f40,0x1b0f9f3f,0xb305f41,0x192fa0c1,0x16fe0be,0x17020be,0x970603e,0x8705fbe,0xb701f3e,0x36fdf3e,0x1b2f9f41,0x1b2fdfc2,0x192fe042,0x9302042,0xb301fc2,0x1b6f9fbe,0x196fa03e,
	+ 11,0x101fc0,0xfe040,0xfdfc0,0xfdfbf,0x101fbf,0x10203f,0xfe03f,0xfe041,0x102041,0x101fc1,0xfdfc1,0x8105fc0,0x8106040,0x11020c0,0x10fe0c0,0x10fe0bf,0x11020bf,0x810603f,0x8105fbf,0x3101f40,0x30fdf40,0x180f9fc0,0x180fa040,0x10fe0c1,0x11020c1,0x8106041,0x8105fc1,0x3101f3f,0x30fdf3f,0x180f9fbf,0x180fa03f,0x180fa041,0x180f9fc1,0x30fdf41,0x3101f41,0x91060c0,0x91060bf,0x70203e,0x701fbe,0x6fdfbe,0x6fe03e,0x190fa0c0,0xb105f40,0xb105f3f,0x93060c1,0x190fa0bf,0x192fa0c1,0x1b0f9f40,0x1b0f9f3f,0xb305f41,0xb301fc2,0x9302042,0x192fe042,0x1b2fdfc2,0x1b2f9f41,0x16fe0be,0x17020be,0x970603e,0x8705fbe,0xb701f3e,0x36fdf3e,0x1b6f9fbe,0x196fa03e,
	+ 11,0x10203f,0xfe040,0xfe03f,0x101fc0,0x101fbf,0xfdfc0,0xfdfbf,0xfe0bf,0x1020bf,0x1020c0,0xfe0c0,0x2fe041,0x302041,0x8106040,0x810603f,0x8105fbf,0x8105fc0,0x301fc1,0x2fdfc1,0x180fa040,0x180fa03f,0x6fe03e,0x70203e,0x701fbe,0x6fdfbe,0x180f9fbf,0x180f9fc0,0x30fdf40,0x3101f40,0x3101f3f,0x30fdf3f,0x81060bf,0x81060c0,0x3020c1,0x2fe0c1,0x180fa0c0,0x180fa0bf,0x6fe0be,0x7020be,0x8306041,0x8305fc1,0x182fa041,0x182f9fc1,0x870603e,0x8705fbe,0xb105f3f,0xb105f40,0xb301f41,0x32fdf41,0x186fa03e,0x186f9fbe,0x36fdf3e,0xb701f3e,0x1b6f9f3f,0x1b2f9f40,0x93060c1,0x97060be,0x192fa0c1,0x196fa0be,0x196fe13f,0x970213f,0x9302140,0x192fe140,
	+ 9,0xfe040,0x10203f,0x101fc0,0xfdfc0,0xfe03f,0xfdfbf,0x101fbf,0x102041,0xfe041,0x10fe0c0,0x11020c0,0x11020bf,0x10fe0bf,0xfdfc1,0x101fc1,0x8106040,0x810603f,0x8105fc0,0x8105fbf,0x180fa040,0x180f9fc0,0x180fa03f,0x180f9fbf,0x10fe0c1,0x11020c1,0x70203e,0x6fe03e,0x6fdfbe,0x701fbe,0x3101f3f,0x3101f40,0x30fdf40,0x30fdf3f,0x8106041,0x91060c0,0x91060bf,0x8305fc1,0x180fa041,0x190fa0c0,0x190fa0bf,0x180f9fc1,0x30fdf41,0x3301f41,0x17020be,0x16fe0be,0x93060c1,0x870603e,0x8705fbe,0xb105f3f,0xb105f40,0x192fa0c1,0x1b0f9f40,0x1b0f9f3f,0x186f9fbe,0x196fa03e,0x1b6fdf3e,0xb701f3e,0x97060be,0xb305f41,0x1b2f9f41,0x1b2fdfc2,0x192fe042,0xa302042,
	+ 11,0xfe040,0x101fc0,0xfdfc0,0xfe03f,0x10203f,0x101fbf,0xfdfbf,0xfe041,0x102041,0x101fc1,0xfdfc1,0x10fe0c0,0x11020c0,0x11020bf,0x10fe0bf,0x8106040,0x8105fc0,0x810603f,0x8105fbf,0x11020c1,0x10fe0c1,0x180fa040,0x180f9fc0,0x180fa03f,0x180f9fbf,0x30fdf40,0x3101f40,0x8106041,0x8105fc1,0x3101f3f,0x30fdf3f,0x91060c0,0x91060bf,0x180fa041,0x180f9fc1,0x6fe03e,0x70203e,0x701fbe,0x6fdfbe,0x190fa0c0,0x190fa0bf,0x30fdf41,0x3101f41,0x93060c1,0x192fa0c1,0xb105f40,0xb105f3f,0x17020be,0x16fe0be,0x970603e,0x8705fbe,0x1b0f9f40,0x1b0f9f3f,0x186f9fbe,0x196fa03e,0xb305f41,0xb301fc2,0x9302042,0x192fe042,0x1b2fdfc2,0x1b2f9f41,0x1b6fdf3e,0xb701f3e,
	+ 11,0xfe040,0x101fc0,0xfdfc0,0xfe03f,0x10203f,0x101fbf,0xfdfbf,0xfe041,0x102041,0x101fc1,0xfdfc1,0x10fe0c0,0x11020c0,0x11020bf,0x10fe0bf,0x8106040,0x8105fc0,0x11020c1,0x10fe0c1,0x810603f,0x8105fbf,0x180fa040,0x180f9fc0,0x8106041,0x8105fc1,0x3101f40,0x180fa03f,0x180f9fbf,0x30fdf40,0x180fa041,0x180f9fc1,0x91060c0,0x3101f3f,0x30fdf3f,0x30fdf41,0x3101f41,0x91060bf,0x190fa0c0,0x91060c1,0x190fa0bf,0x186fe03e,0x70203e,0x3701fbe,0x1b6fdfbe,0x190fa0c1,0x182fe042,0xb105f40,0xb105f3f,0x302042,0x3301fc2,0x1b2fdfc2,0x1b0f9f40,0x1b6f9f3f,0xb105f41,0x17020be,0x196fe0be,0x970603e,0xb705fbe,0x1b2f9f41,0x192fe0c2,0x13020c2,0x9306042,0xb305fc2,
	+ 11,0x10203f,0xfe040,0xfe03f,0xfdfbf,0x101fbf,0x101fc0,0xfdfc0,0xfe0c0,0x1020c0,0x1020bf,0xfe0bf,0x810603f,0x8106040,0x302041,0x2fe041,0x2fdfc1,0x301fc1,0x8105fc0,0x8105fbf,0x70203e,0x6fe03e,0x180fa03f,0x180fa040,0x180f9fc0,0x180f9fbf,0x6fdfbe,0x701fbe,0x81060bf,0x81060c0,0x3020c1,0x2fe0c1,0x180fa0c0,0x180fa0bf,0x6fe0be,0x7020be,0x3101f3f,0x3101f40,0x30fdf40,0x30fdf3f,0x8306041,0x8305fc1,0x870603e,0x8705fbe,0x182fa041,0x182f9fc1,0x93060c1,0x186fa03e,0x186f9fbe,0x97060be,0x192fa0c1,0x32fdf41,0x3301f41,0xb305f40,0xb105f3f,0xb701f3e,0x36fdf3e,0x196fa0be,0x196fe13f,0x192fe140,0x9302140,0x970213f,0x1b6f9f3f,0x1b2f9f40,
	+ 11,0xfe040,0x10203f,0xfe03f,0xfdfc0,0x101fc0,0x101fbf,0xfdfbf,0xfe0c0,0x1020c0,0x1020bf,0xfe0bf,0x2fe041,0x302041,0x301fc1,0x2fdfc1,0x8106040,0x810603f,0x8105fc0,0x8105fbf,0x3020c1,0x2fe0c1,0x180fa040,0x180fa03f,0x180f9fc0,0x180f9fbf,0x6fe03e,0x70203e,0x81060c0,0x81060bf,0x701fbe,0x6fdfbe,0x8306041,0x8305fc1,0x180fa0c0,0x180fa0bf,0x30fdf40,0x3101f40,0x3101f3f,0x30fdf3f,0x182fa041,0x182f9fc1,0x6fe0be,0x7020be,0x93060c1,0x192fa0c1,0x870603e,0x8705fbe,0x3301f41,0x32fdf41,0xb305f40,0xb105f3f,0x186fa03e,0x186f9fbe,0x1b0f9f3f,0x1b2f9f40,0x97060be,0x970213f,0x9302140,0x192fe140,0x196fe13f,0x196fa0be,0x1b6fdf3e,0xb701f3e,
	+ 15,0xfe040,0xfe03f,0x10203f,0x101fc0,0xfdfc0,0xfdfbf,0x101fbf,0x102041,0xfe041,0xfe0c0,0x1020c0,0x1020bf,0xfe0bf,0xfdfc1,0x101fc1,0x8106040,0x1020c1,0xfe0c1,0x810603f,0x8105fc0,0x8105fbf,0x180fa040,0x180fa03f,0x180f9fc0,0x180f9fbf,0x8106041,0x81060c0,0x81060bf,0x8105fc1,0x180fa041,0x180fa0c0,0x180fa0bf,0x6fe03e,0x70203e,0x3101f40,0x30fdf40,0x180f9fc1,0x30fdf3f,0x3101f3f,0x3701fbe,0x36fdfbe,0x93060c1,0x192fa0c1,0x6fe0be,0x7020be,0x3101f41,0x30fdf41,0xb305f40,0xb105f3f,0x970603e,0xb705fbe,0x196fa03e,0x186f9fbe,0x1b2f9f40,0x1b6f9f3f,0x192fe042,0x9302042,0xb301fc2,0x1b2fdfc2,0x192fe140,0x9302140,0x970213f,0x196fe13f,
	+ 15,0xfe040,0xfdfc0,0x101fc0,0x10203f,0xfe03f,0xfdfbf,0x101fbf,0x102041,0xfe041,0xfdfc1,0x101fc1,0x1020c0,0xfe0c0,0xfe0bf,0x1020bf,0x1020c1,0xfe0c1,0x8106040,0x8105fc0,0x810603f,0x8105fbf,0x180fa040,0x180f9fc0,0x8106041,0x8105fc1,0x81060c0,0x180fa03f,0x180f9fbf,0x180fa041,0x180f9fc1,0x180fa0c0,0x81060bf,0x91060c1,0x3101f40,0x30fdf40,0x30fdf3f,0x180fa0bf,0x190fa0c1,0x3101f3f,0x3101f41,0x30fdf41,0x186fe03e,0x70203e,0x3701fbe,0x1b6fdfbe,0x186fe0be,0x7020be,0x8302042,0x182fe042,0x1b2fdfc2,0xb301fc2,0xb105f40,0xb705f3f,0xb305f41,0x1b2f9f40,0x1b6f9f3f,0x192fe140,0x9302140,0x93020c2,0x192fe0c2,0x196fe13f,0x970213f,0xa70603e,
	+ 11,0x10203f,0xfe040,0xfe03f,0xfdfbf,0x101fbf,0x101fc0,0xfdfc0,0xfe0c0,0x1020c0,0x1020bf,0xfe0bf,0x810603f,0x8106040,0x302041,0x2fe041,0x2fdfc1,0x301fc1,0x8105fc0,0x8105fbf,0x70203e,0x6fe03e,0x180fa03f,0x180fa040,0x2fe0c1,0x3020c1,0x81060c0,0x81060bf,0x701fbe,0x6fdfbe,0x180f9fbf,0x180f9fc0,0x180fa0c0,0x180fa0bf,0x6fe0be,0x7020be,0x8306041,0x8305fc1,0x3101f40,0x3101f3f,0x30fdf3f,0x30fdf40,0x182fa041,0x870603e,0x8705fbe,0x93060c1,0x182f9fc1,0x192fa0c1,0x186fa03e,0x186f9fbe,0x97060be,0x970213f,0x9302140,0x192fe140,0x196fe13f,0x196fa0be,0x32fdf41,0x3301f41,0xb305f40,0xb105f3f,0xb701f3e,0x36fdf3e,0x1b6f9f3f,0x1b2f9f40,
	+ 11,0xfe040,0x10203f,0xfe03f,0xfdfc0,0x101fc0,0x101fbf,0xfdfbf,0xfe0c0,0x1020c0,0x1020bf,0xfe0bf,0x2fe041,0x302041,0x301fc1,0x2fdfc1,0x8106040,0x810603f,0x3020c1,0x2fe0c1,0x8105fc0,0x8105fbf,0x180fa040,0x180fa03f,0x81060c0,0x81060bf,0x70203e,0x180f9fc0,0x180f9fbf,0x6fe03e,0x180fa0c0,0x180fa0bf,0x8306041,0x701fbe,0x6fdfbe,0x6fe0be,0x7020be,0x8305fc1,0x182fa041,0x83060c1,0x182f9fc1,0x1b0fdf40,0x3101f40,0x3701f3f,0x1b6fdf3f,0x182fa0c1,0x190fe140,0x870603e,0x8705fbe,0x1102140,0x170213f,0x196fe13f,0x186fa03e,0x1b6f9fbe,0x87060be,0x3301f41,0x1b2fdf41,0xb305f40,0xb705f3f,0x196fa0be,0x192fe141,0x1302141,0x9306140,0x970613f,
	+ 15,0xfe040,0xfe03f,0x10203f,0x101fc0,0xfdfc0,0xfdfbf,0x101fbf,0x1020c0,0xfe0c0,0xfe0bf,0x1020bf,0x102041,0xfe041,0xfdfc1,0x101fc1,0x1020c1,0xfe0c1,0x8106040,0x810603f,0x8105fc0,0x8105fbf,0x180fa040,0x180fa03f,0x81060c0,0x81060bf,0x8106041,0x180f9fc0,0x180f9fbf,0x180fa0c0,0x180fa0bf,0x180fa041,0x8105fc1,0x83060c1,0x70203e,0x6fe03e,0x6fdfbe,0x180f9fc1,0x182fa0c1,0x701fbe,0x7020be,0x6fe0be,0x1b0fdf40,0x3101f40,0x3701f3f,0x1b6fdf3f,0x1b0fdf41,0x3101f41,0x9102140,0x190fe140,0x196fe13f,0x970213f,0x870603e,0xb705fbe,0x97060be,0x196fa03e,0x1b6f9fbe,0x192fe042,0x9302042,0x9302141,0x192fe141,0x1b2fdfc2,0xb301fc2,0xb505f40,
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	+ 11,0x10203f,0x101fc0,0x101fbf,0xfe040,0xfe03f,0xfdfc0,0xfdfbf,0x105fbf,0x10603f,0x106040,0x105fc0,0x301fc1,0x302041,0x11020c0,0x11020bf,0x10fe0bf,0x10fe0c0,0x2fe041,0x2fdfc1,0x3101f40,0x3101f3f,0x701fbe,0x70203e,0x6fe03e,0x6fdfbe,0x30fdf3f,0x30fdf40,0x180f9fc0,0x180fa040,0x180fa03f,0x180f9fbf,0x11060bf,0x11060c0,0x306041,0x305fc1,0x3105f40,0x3105f3f,0x705fbe,0x70603e,0x13020c1,0x12fe0c1,0x3301f41,0x32fdf41,0x17020be,0x16fe0be,0x190fa0bf,0x190fa0c0,0x192fa041,0x182f9fc1,0x3701f3e,0x36fdf3e,0x186f9fbe,0x196fa03e,0x1b6f9f3f,0x1b2f9f40,0x93060c1,0x97060be,0xb305f41,0xb705f3e,0xb709fbf,0x970a03f,0x930a040,0xb309fc0,
	+ 9,0x101fc0,0x10203f,0xfe040,0xfdfc0,0x101fbf,0xfdfbf,0xfe03f,0x102041,0x101fc1,0x8105fc0,0x8106040,0x810603f,0x8105fbf,0xfdfc1,0xfe041,0x11020c0,0x11020bf,0x10fe0c0,0x10fe0bf,0x3101f40,0x30fdf40,0x3101f3f,0x30fdf3f,0x8105fc1,0x8106041,0x70203e,0x701fbe,0x6fdfbe,0x6fe03e,0x180fa03f,0x180fa040,0x180f9fc0,0x180f9fbf,0x11020c1,0x91060c0,0x91060bf,0x12fe0c1,0x3101f41,0xb105f40,0xb105f3f,0x30fdf41,0x180f9fc1,0x182fa041,0x870603e,0x8705fbe,0x93060c1,0x17020be,0x16fe0be,0x190fa0bf,0x190fa0c0,0xb305f41,0x1b0f9f40,0x1b0f9f3f,0x36fdf3e,0xb701f3e,0x1b6f9fbe,0x196fa03e,0x97060be,0x192fa0c1,0x1b2f9f41,0x1b2fdfc2,0xb301fc2,0x11302042,
	+ 11,0x101fc0,0xfe040,0xfdfc0,0x101fbf,0x10203f,0xfe03f,0xfdfbf,0x101fc1,0x102041,0xfe041,0xfdfc1,0x8105fc0,0x8106040,0x810603f,0x8105fbf,0x11020c0,0x10fe0c0,0x11020bf,0x10fe0bf,0x8106041,0x8105fc1,0x3101f40,0x30fdf40,0x3101f3f,0x30fdf3f,0x180f9fc0,0x180fa040,0x11020c1,0x10fe0c1,0x180fa03f,0x180f9fbf,0x91060c0,0x91060bf,0x3101f41,0x30fdf41,0x701fbe,0x70203e,0x6fe03e,0x6fdfbe,0xb105f40,0xb105f3f,0x180f9fc1,0x180fa041,0x93060c1,0xb305f41,0x190fa0c0,0x190fa0bf,0x870603e,0x8705fbe,0x97020be,0x16fe0be,0x1b0f9f40,0x1b0f9f3f,0x36fdf3e,0xb701f3e,0x192fa0c1,0x192fe042,0x9302042,0xb301fc2,0x1b2fdfc2,0x1b2f9f41,0x1b6f9fbe,0x196fa03e,
	+ 11,0x101fc0,0xfe040,0xfdfc0,0x101fbf,0x10203f,0xfe03f,0xfdfbf,0x101fc1,0x102041,0xfe041,0xfdfc1,0x8105fc0,0x8106040,0x810603f,0x8105fbf,0x11020c0,0x10fe0c0,0x8106041,0x8105fc1,0x11020bf,0x10fe0bf,0x3101f40,0x30fdf40,0x11020c1,0x10fe0c1,0x180fa040,0x3101f3f,0x30fdf3f,0x180f9fc0,0x3101f41,0x30fdf41,0x91060c0,0x180fa03f,0x180f9fbf,0x180f9fc1,0x180fa041,0x91060bf,0xb105f40,0x91060c1,0xb105f3f,0x3701fbe,0x70203e,0x186fe03e,0x1b6fdfbe,0xb105f41,0x3301fc2,0x190fa0c0,0x190fa0bf,0x302042,0x182fe042,0x1b2fdfc2,0x1b0f9f40,0x1b6f9f3f,0x190fa0c1,0x870603e,0xb705fbe,0x97020be,0x196fe0be,0x1b2f9f41,0xb305fc2,0x8306042,0x93020c2,0x192fe0c2,
	+ 9,0x10203f,0x101fc0,0xfe040,0xfe03f,0x101fbf,0xfdfbf,0xfdfc0,0x1020c0,0x1020bf,0x810603f,0x8106040,0x8105fc0,0x8105fbf,0xfe0bf,0xfe0c0,0x302041,0x301fc1,0x2fe041,0x2fdfc1,0x70203e,0x6fe03e,0x701fbe,0x6fdfbe,0x81060bf,0x81060c0,0x3101f40,0x3101f3f,0x30fdf3f,0x30fdf40,0x180f9fc0,0x180fa040,0x180fa03f,0x180f9fbf,0x3020c1,0x8306041,0x8305fc1,0x12fe0c1,0x7020be,0x870603e,0x8705fbe,0x6fe0be,0x180fa0bf,0x190fa0c0,0xb105f40,0xb105f3f,0x93060c1,0x3301f41,0x32fdf41,0x182f9fc1,0x182fa041,0x97060be,0x186fa03e,0x186f9fbe,0x36fdf3e,0xb701f3e,0x1b6f9f3f,0x1b2f9f40,0xb305f41,0x192fa0c1,0x196fa0be,0x196fe13f,0x970213f,0x11302140,
	+ 7,0x10203f,0x101fc0,0xfe040,0xfe03f,0x101fbf,0xfdfc0,0xfdfbf,0x302041,0x1020c0,0x8106040,0x810603f,0x1020bf,0xfe0c0,0x2fe041,0x301fc1,0x8105fc0,0x8105fbf,0xfe0bf,0x2fdfc1,0x3020c1,0x8306041,0x81060c0,0x81060bf,0x2fe0c1,0x8305fc1,0x3101f40,0x3101f3f,0x701fbe,0x70203e,0x6fe03e,0x180fa03f,0x180fa040,0x180f9fc0,0x30fdf40,0x30fdf3f,0x6fdfbe,0x180f9fbf,0x180fa0c0,0x182fa041,0x93060c1,0x870603e,0x7020be,0x6fe0be,0x180fa0bf,0x182f9fc1,0x32fdf41,0x3301f41,0xb105f40,0xb105f3f,0x8705fbe,0x97060be,0x192fa0c1,0xb305f41,0xb701f3e,0x36fdf3e,0x1b0f9f3f,0x1b2f9f40,0x1b6f9fbe,0x196fa03e,0x196fe13f,0x9302140,0x970213f,0x192fe140,
	+ 11,0x101fc0,0xfe040,0xfdfc0,0x10203f,0x101fbf,0xfe03f,0xfdfbf,0x102041,0x101fc1,0xfe041,0xfdfc1,0x11020c0,0x8106040,0x8105fc0,0x10fe0c0,0x11020bf,0x810603f,0x8105fbf,0x10fe0bf,0x11020c1,0x8106041,0x8105fc1,0x10fe0c1,0x91060c0,0x91060bf,0x3101f40,0x30fdf40,0x180f9fc0,0x180fa040,0x180fa03f,0x180f9fbf,0x30fdf3f,0x3101f3f,0x701fbe,0x70203e,0x6fe03e,0x6fdfbe,0x93060c1,0x3101f41,0x30fdf41,0x180f9fc1,0x180fa041,0x190fa0c0,0x190fa0bf,0xb105f40,0xb105f3f,0x8705fbe,0x870603e,0x17020be,0x16fe0be,0x192fa0c1,0xb305f41,0xb301fc2,0x9302042,0x192fe042,0x1b2fdfc2,0x1b2f9f40,0x1b0f9f3f,0x186f9fbe,0x196fa03e,0x97060be,0xb701f3e,0x1b6fdf3e,
	+ 11,0x101fc0,0xfe040,0xfdfc0,0x10203f,0x101fbf,0xfe03f,0xfdfbf,0x102041,0x101fc1,0xfe041,0xfdfc1,0x11020c0,0x8106040,0x8105fc0,0x10fe0c0,0x11020bf,0x810603f,0x8105fbf,0x10fe0bf,0x11020c1,0x8106041,0x8105fc1,0x10fe0c1,0x91060c0,0x91060bf,0x3101f40,0x30fdf40,0x180f9fc0,0x180fa040,0x180fa03f,0x180f9fbf,0x30fdf3f,0x3101f3f,0x3101f41,0x91060c1,0x180fa041,0x180f9fc1,0x30fdf41,0xb105f40,0x70203e,0x3701fbe,0x186fe03e,0x1b6fdfbe,0x190fa0c0,0x190fa0bf,0x190fa0c1,0xb105f3f,0xb105f41,0x3301fc2,0x302042,0x182fe042,0x1b2fdfc2,0x1b0f9f40,0x17020be,0x970603e,0xb705fbe,0x196fe0be,0x1b6f9f3f,0x1b2f9f41,0x13020c2,0x9306042,0xb305fc2,0x192fe0c2,
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	+ 14,0x10203f,0x101fc0,0x101fbf,0xfe040,0xfe03f,0xfdfc0,0xfdfbf,0x106040,0x10603f,0x105fc0,0x105fbf,0x1020c0,0x1020bf,0xfe0c0,0x302041,0xfe0bf,0x301fc1,0x1060c0,0x1060bf,0x2fe041,0x2fdfc1,0x306041,0x305fc1,0x3020c1,0x2fe0c1,0x13060c1,0x70203e,0x701fbe,0x6fe03e,0x6fdfbe,0x70603e,0x705fbe,0x3701f3f,0x3101f40,0x30fdf40,0x36fdf3f,0x7020be,0x16fe0be,0x186fa03f,0x180fa040,0x1b0f9fc0,0x3105f40,0x3705f3f,0x1b6f9fbf,0x17060be,0x870a03f,0x810a040,0x3301f41,0x32fdf41,0xb109fc0,0xb709fbf,0x180fa0c0,0x196fa0bf,0x192fa041,0x1b2f9fc1,0x3305f41,0x9302140,0x970213f,0x910a0c0,0x970a0bf,0x930a041,0xb309fc1,0x194fe140,
	+ 15,0x10203f,0x101fc0,0x101fbf,0xfe040,0xfe03f,0xfdfc0,0x106040,0x10603f,0xfdfbf,0x105fc0,0x102041,0x1020c0,0x105fbf,0x1020bf,0x101fc1,0xfe041,0xfe0c0,0xfe0bf,0xfdfc1,0x106041,0x1060c0,0x1060bf,0x105fc1,0x1020c1,0x2fe0c1,0x13060c1,0x70203e,0x3101f40,0x3101f3f,0x3701fbe,0x6fe03e,0x6fdfbe,0x30fdf40,0x36fdf3f,0x3105f40,0x3105f3f,0x70603e,0x3705fbe,0x180fa040,0x186fa03f,0x1b0f9fc0,0x1b6f9fbf,0x7020be,0x16fe0be,0x3101f41,0x32fdf41,0xb305f41,0x810a040,0x870a03f,0x97060be,0xb109fc0,0xb709fbf,0x182fa041,0x182fa0c0,0x196fa0bf,0x1b2f9fc1,0x11302042,0x13301fc2,0xb30a041,0x950a0c0,0x9302140,0x970213f,0x194fe140,
	+ 17,0x101fc0,0x10203f,0xfe040,0xfdfc0,0x101fbf,0x106040,0x102041,0xfe03f,0x101fc1,0x105fc0,0x1020c0,0xfdfbf,0x10603f,0xfe041,0xfdfc1,0x105fbf,0x106041,0x1020bf,0xfe0c0,0x105fc1,0x1060c0,0x1020c1,0x10fe0bf,0x11060bf,0x10fe0c1,0x11060c1,0x3101f40,0x30fdf40,0x3101f3f,0x3105f40,0x3101f41,0x30fdf3f,0x70203e,0x3701fbe,0x180fa040,0x1b0f9fc0,0x30fdf41,0x3105f3f,0x6fe03e,0x186fa03f,0x1b0f9fbf,0x1b6fdfbe,0x70603e,0x3705fbe,0xb305f41,0x910a040,0xb109fc0,0x1302042,0x180fa041,0x1b0f9fc1,0x3301fc2,0x192fe042,0x192fa0c0,0x17020be,0x970a03f,0xb709fbf,0xa10a041,0xa306042,0x1b2fdfc2,0x190fa0bf,0x196fe0be,0x97060be,0x11502140,
	+ 17,0x10203f,0x101fbf,0x101fc0,0xfe040,0xfe03f,0x1020bf,0x1020c0,0x106040,0x10603f,0xfdfbf,0xfdfc0,0x105fc0,0x105fbf,0xfe0bf,0xfe0c0,0x1060c0,0x1060bf,0x302041,0x301fc1,0x2fe041,0x3020c1,0x306041,0x70203e,0x701fbe,0x6fe03e,0x2fdfc1,0x305fc1,0x2fe0c1,0x7020be,0x70603e,0x6fdfbe,0x3060c1,0x705fbe,0x6fe0be,0x7060be,0x3701f3f,0x3101f40,0x180fa040,0x186fa03f,0x186f9fbf,0x180f9fc0,0x1b0fdf40,0x1b6fdf3f,0x3705f3f,0x3105f40,0x830a040,0x870a03f,0x170213f,0x1302140,0x180fa0c0,0x186fa0bf,0x196fe13f,0x192fe140,0x1306140,0x170613f,0xb709fbf,0xb309fc0,0x930a0c0,0x970a0bf,0xb301f41,0x192fa041,0x182f9fc1,0x1b2fdf41,
	+ 17,0x10203f,0x101fc0,0xfe040,0xfe03f,0x101fbf,0x106040,0x1020c0,0x1020bf,0x10603f,0xfdfc0,0xfdfbf,0x105fc0,0x105fbf,0xfe0c0,0xfe0bf,0x1060c0,0x1060bf,0x302041,0x301fc1,0x2fe041,0x3020c1,0x306041,0x2fdfc1,0x305fc1,0x2fe0c1,0x3060c1,0x70203e,0x6fe03e,0x701fbe,0x70603e,0x7020be,0x6fdfbe,0x705fbe,0x6fe0be,0x7060be,0x3101f40,0x3701f3f,0x180fa040,0x186fa03f,0x180f9fc0,0x1b0fdf40,0x36fdf3f,0x1b6f9fbf,0x180fa0c0,0x186fa0bf,0x1302140,0x170213f,0x830a040,0x3105f40,0x3705f3f,0x870a03f,0xb309fc0,0xb709fbf,0x830a0c0,0x192fe140,0x196fe13f,0x9306140,0x170613f,0x970a0bf,0xb301f41,0x192fa041,0x182f9fc1,0x1b2fdf41,
	+ 17,0x10203f,0x101fc0,0xfe040,0xfe03f,0x101fbf,0x106040,0x1020c0,0xfdfc0,0x1020bf,0x10603f,0x102041,0xfdfbf,0x105fc0,0xfe0c0,0xfe0bf,0x105fbf,0x1060c0,0x101fc1,0xfe041,0x1060bf,0x106041,0x1020c1,0x2fdfc1,0x305fc1,0x2fe0c1,0x3060c1,0x70203e,0x6fe03e,0x701fbe,0x70603e,0x7020be,0x6fdfbe,0x3101f40,0x3701f3f,0x180fa040,0x186fa03f,0x6fe0be,0x705fbe,0x30fdf40,0x1b0f9fc0,0x186f9fbf,0x1b6fdf3f,0x3105f40,0x3705f3f,0x97060be,0x830a040,0x870a03f,0x1302140,0x180fa0c0,0x186fa0bf,0x170213f,0x192fe140,0x192fa041,0x3301f41,0xb309fc0,0xb709fbf,0x850a0c0,0x9506140,0x196fe13f,0x182f9fc1,0x1b2fdf41,0xb305f41,0x12302042,
	+ 16,0x10203f,0x101fc0,0xfe040,0x102041,0x1020c0,0x106040,0x101fbf,0xfe03f,0xfdfc0,0x101fc1,0x105fc0,0x10603f,0x1020bf,0xfe0c0,0xfe041,0xfdfbf,0x1020c1,0x106041,0x1060c0,0x105fbf,0xfe0bf,0xfdfc1,0x105fc1,0x1060bf,0xfe0c1,0x83060c1,0x70203e,0x3101f40,0x180fa040,0x180fa03f,0x186fe03e,0x701fbe,0x3701f3f,0x30fdf40,0x1b0f9fc0,0x180fa041,0x180fa0c0,0x7020be,0x70603e,0x3105f40,0xb101f41,0x9302042,0x1102140,0x930a040,0x6fdfbe,0x36fdf3f,0x1b6f9fbf,0x190fa0bf,0x196fe0be,0x170213f,0x196fe140,0x182f9fc1,0x1b2fdf41,0xb301fc2,0x1a2fe042,0x192fa0c1,0x8705fbe,0xb705f3f,0xb309fc0,0xa70a03f,0x97060be,0x9706140,0x11302141
	+};
	Index: extern/voro++/src/pre_container.hh
	===================================================================
	--- extern/voro++/src/pre_container.hh (revision 0)
	+++ extern/voro++/src/pre_container.hh (revision 0)
	@@ -0,0 +1,162 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file pre_container.hh
	+ * \brief Header file for the pre_container and related classes. */
	+
	+#ifndef VOROPP_PRE_CONTAINER_HH
	+#define VOROPP_PRE_CONTAINER_HH
	+
	+#include <cstdio>
	+
	+#include "c_loops.hh"
	+#include "container.hh"
	+
	+namespace voro {
	+
	+/** \brief A class for storing an arbitrary number of particles, prior to setting
	+ * up a container geometry.
	+ *
	+ * The pre_container_base class can dynamically import and store an arbitrary
	+ * number of particles. Once the particles have been read in, an appropriate
	+ * container class can be set up with the optimal grid size, and the particles
	+ * can be transferred.
	+ *
	+ * The pre_container_base class is not intended for direct use, but forms the
	+ * base of the pre_container and pre_container_poly classes, that add routines
	+ * depending on whether particle radii need to be tracked or not. */
	+class pre_container_base {
	+ public:
	+ /** The minimum x coordinate of the container. */
	+ const double ax;
	+ /** The maximum x coordinate of the container. */
	+ const double bx;
	+ /** The minimum y coordinate of the container. */
	+ const double ay;
	+ /** The maximum y coordinate of the container. */
	+ const double by;
	+ /** The minimum z coordinate of the container. */
	+ const double az;
	+ /** The maximum z coordinate of the container. */
	+ const double bz;
	+ /** A boolean value that determines if the x coordinate in
	+ * periodic or not. */
	+ const bool xperiodic;
	+ /** A boolean value that determines if the y coordinate in
	+ * periodic or not. */
	+ const bool yperiodic;
	+ /** A boolean value that determines if the z coordinate in
	+ * periodic or not. */
	+ const bool zperiodic;
	+ void guess_optimal(int &nx,int &ny,int &nz);
	+ pre_container_base(double ax_,double bx_,double ay_,double by_,double az_,double bz_,bool xperiodic_,bool yperiodic_,bool zperiodic_,int ps_);
	+ ~pre_container_base();
	+ /** Calculates and returns the total number of particles stored
	+ * within the class.
	+ * \return The number of particles. */
	+ inline int total_particles() {
	+ return (end_id-pre_id)pre_container_chunk_size+(ch_id-end_id);
	+ }
	+ protected:
	+ /** The number of doubles associated with a single particle
	+ * (three for the standard container, four when radius
	+ * information is stored). */
	+ const int ps;
	+ void new_chunk();
	+ void extend_chunk_index();
	+ /** The size of the chunk index. */
	+ int index_sz;
	+ /** A pointer to the chunk index to store the integer particle
	+ * IDs. */
	+ int **pre_id;
	+ /** A pointer to the last allocated integer ID chunk. */
	+ int **end_id;
	+ /** A pointer to the end of the integer ID chunk index, used to
	+ * determine when the chunk index is full. */
	+ int **l_id;
	+ /** A pointer to the next available slot on the current
	+ * particle ID chunk. */
	+ int *ch_id;
	+ /** A pointer to the end of the current integer chunk. */
	+ int *e_id;
	+ /** A pointer to the chunk index to store the floating point
	+ * information associated with particles. */
	+ double **pre_p;
	+ /** A pointer to the last allocated chunk of floating point
	+ * information. */
	+ double **end_p;
	+ /** A pointer to the next available slot on the current
	+ * floating point chunk. */
	+ double *ch_p;
	+};
	+
	+/** \brief A class for storing an arbitrary number of particles without radius
	+ * information, prior to setting up a container geometry.
	+ *
	+ * The pre_container class is an extension of the pre_container_base class for
	+ * cases when no particle radius information is available. */
	+class pre_container : public pre_container_base {
	+ public:
	+ /** The class constructor sets up the geometry of container,
	+ * initializing the minimum and maximum coordinates in each
	+ * direction.
	+ * \param[in] (ax_,bx_) the minimum and maximum x coordinates.
	+ * \param[in] (ay_,by_) the minimum and maximum y coordinates.
	+ * \param[in] (az_,bz_) the minimum and maximum z coordinates.
	+ * \param[in] (xperiodic_,yperiodic_,zperiodic_ ) flags setting whether the
	+ * container is periodic in
	+ * each coordinate direction. */
	+ pre_container(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
	+ bool xperiodic_,bool yperiodic_,bool zperiodic_)
	+ : pre_container_base(ax_,bx_,ay_,by_,az_,bz_,xperiodic_,yperiodic_,zperiodic_,3) {};
	+ void put(int n,double x,double y,double z);
	+ void import(FILE *fp=stdin);
	+ /** Imports particles from a file.
	+ * \param[in] filename the name of the file to read from. */
	+ inline void import(const char* filename) {
	+ FILE *fp=safe_fopen(filename,"r");
	+ import(fp);
	+ fclose(fp);
	+ }
	+ void setup(container &con);
	+ void setup(particle_order &vo,container &con);
	+};
	+
	+/** \brief A class for storing an arbitrary number of particles with radius
	+ * information, prior to setting up a container geometry.
	+ *
	+ * The pre_container_poly class is an extension of the pre_container_base class
	+ * for cases when particle radius information is available. */
	+class pre_container_poly : public pre_container_base {
	+ public:
	+ /** The class constructor sets up the geometry of container,
	+ * initializing the minimum and maximum coordinates in each
	+ * direction.
	+ * \param[in] (ax_,bx_) the minimum and maximum x coordinates.
	+ * \param[in] (ay_,by_) the minimum and maximum y coordinates.
	+ * \param[in] (az_,bz_) the minimum and maximum z coordinates.
	+ * \param[in] (xperiodic_,yperiodic_,zperiodic_ ) flags setting whether the
	+ * container is periodic in
	+ * each coordinate direction. */
	+ pre_container_poly(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
	+ bool xperiodic_,bool yperiodic_,bool zperiodic_)
	+ : pre_container_base(ax_,bx_,ay_,by_,az_,bz_,xperiodic_,yperiodic_,zperiodic_,4) {};
	+ void put(int n,double x,double y,double z,double r);
	+ void import(FILE *fp=stdin);
	+ /** Imports particles from a file.
	+ * \param[in] filename the name of the file to read from. */
	+ inline void import(const char* filename) {
	+ FILE *fp=safe_fopen(filename,"r");
	+ import(fp);
	+ fclose(fp);
	+ }
	+ void setup(container_poly &con);
	+ void setup(particle_order &vo,container_poly &con);
	+};
	+
	+}
	+
	+#endif
	Index: extern/voro++/src/c_interface.cc
	===================================================================
	--- extern/voro++/src/c_interface.cc (revision 0)
	+++ extern/voro++/src/c_interface.cc (revision 0)
	@@ -0,0 +1,42 @@
	+#include "c_interface.hh"
	+#include "voro++.hh"
	+
	+extern "C" {
	+
	+ container* container_new(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
	+ int nx_,int ny_,int nz_,int xperiodic_,int yperiodic_,int zperiodic_,int init_mem)
	+ {
	+
	+ return new voro::container(ax_, bx_, ay_, by_, az_, bz_, nx_, ny_, nz_,
	+ xperiodic_, yperiodic_, zperiodic_, init_mem);
	+ }
	+
	+ particle_order* particle_order_new(void)
	+ {
	+ return new voro::particle_order();
	+ }
	+
	+ void container_put(container* container, particle_order* p_order, int n,double x,double y,double z)
	+ {
	+ voro::container* c = (voro::container*)container;
	+ voro::particle_order* po = (voro::particle_order*)p_order;
	+
	+ if (po)
	+ {
	+ c->put(*po, n, x, y, z);
	+ }
	+ else
	+ {
	+ c->put(n, x, y, z);
	+ }
	+
	+ }
	+
	+ void container_print_custom(container* container, const char* format, FILE* fp)
	+ {
	+ voro::container* c = (voro::container*)container;
	+ c->print_custom(format, fp);
	+ }
	+
	+}
	+
	Index: extern/voro++/src/common.hh
	===================================================================
	--- extern/voro++/src/common.hh (revision 0)
	+++ extern/voro++/src/common.hh (revision 0)
	@@ -0,0 +1,67 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file common.hh
	+ * \brief Header file for the small helper functions. */
	+
	+#ifndef VOROPP_COMMON_HH
	+#define VOROPP_COMMON_HH
	+
	+#include <cstdio>
	+#include <cstdlib>
	+#include <vector>
	+
	+#include "config.hh"
	+
	+namespace voro {
	+
	+/** \brief Function for printing fatal error messages and exiting.
	+ *
	+ * Function for printing fatal error messages and exiting.
	+ * \param[in] p a pointer to the message to print.
	+ * \param[in] status the status code to return with. */
	+inline void voro_fatal_error(const char *p,int status) {
	+ fprintf(stderr,"voro++: %s\n",p);
	+ exit(status);
	+}
	+
	+/** \brief Prints a vector of positions.
	+ *
	+ * Prints a vector of positions as bracketed triplets.
	+ * \param[in] v the vector to print.
	+ * \param[in] fp the file stream to print to. */
	+inline void voro_print_positions(std::vector<double> &v,FILE *fp=stdout) {
	+ if(v.size()>0) {
	+ fprintf(fp,"(%g,%g,%g)",v[0],v[1],v[2]);
	+ for(int k=3;(unsigned int) k<v.size();k+=3) {
	+ fprintf(fp," (%g,%g,%g)",v[k],v[k+1],v[k+2]);
	+ }
	+ }
	+}
	+
	+/** \brief Opens a file and checks the operation was successful.
	+ *
	+ * Opens a file, and checks the return value to ensure that the operation
	+ * was successful.
	+ * \param[in] filename the file to open.
	+ * \param[in] mode the cstdio fopen mode to use.
	+ * \return The file handle. */
	+inline FILE* safe_fopen(const char filename,const char mode) {
	+ FILE *fp=fopen(filename,mode);
	+ if(fp==NULL) {
	+ fprintf(stderr,"voro++: Unable to open file '%s'\n",filename);
	+ exit(VOROPP_FILE_ERROR);
	+ }
	+ return fp;
	+}
	+
	+void voro_print_vector(std::vector<int> &v,FILE *fp=stdout);
	+void voro_print_vector(std::vector<double> &v,FILE *fp=stdout);
	+void voro_print_face_vertices(std::vector<int> &v,FILE *fp=stdout);
	+
	+}
	+
	+#endif
	Index: extern/voro++/src/rad_option.hh
	===================================================================
	--- extern/voro++/src/rad_option.hh (revision 0)
	+++ extern/voro++/src/rad_option.hh (revision 0)
	@@ -0,0 +1,158 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file rad_option.hh
	+ * \brief Header file for the classes encapsulating functionality for the
	+ * regular and radical Voronoi tessellations. */
	+
	+#ifndef VOROPP_RAD_OPTION_HH
	+#define VOROPP_RAD_OPTION_HH
	+
	+#include <cmath>
	+
	+namespace voro {
	+
	+/** \brief Class containing all of the routines that are specific to computing
	+ * the regular Voronoi tessellation.
	+ *
	+ * The container and container_periodic classes are derived from this class,
	+ * and during the Voronoi cell computation, these routines are used to create
	+ * the regular Voronoi tessellation. */
	+class radius_mono {
	+ protected:
	+ /** This is called prior to computing a Voronoi cell for a
	+ * given particle to initialize any required constants.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] s the index of the particle within the block. */
	+ inline void r_init(int ijk,int s) {}
	+ /** Sets a required constant to be used when carrying out a
	+ * plane bounds check. */
	+ inline void r_prime(double rv) {}
	+ /** Carries out a radius bounds check.
	+ * \param[in] crs the radius squared to be tested.
	+ * \param[in] mrs the current maximum distance to a Voronoi
	+ * vertex multiplied by two.
	+ * \return True if particles at this radius could not possibly
	+ * cut the cell, false otherwise. */
	+ inline bool r_ctest(double crs,double mrs) {return crs>mrs;}
	+ /** Scales a plane displacement during a plane bounds check.
	+ * \param[in] lrs the plane displacement.
	+ * \return The scaled value. */
	+ inline double r_cutoff(double lrs) {return lrs;}
	+ /** Adds the maximum radius squared to a given value.
	+ * \param[in] rs the value to consider.
	+ * \return The value with the radius squared added. */
	+ inline double r_max_add(double rs) {return rs;}
	+ /** Subtracts the radius squared of a particle from a given
	+ * value.
	+ * \param[in] rs the value to consider.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] q the index of the particle within the block.
	+ * \return The value with the radius squared subtracted. */
	+ inline double r_current_sub(double rs,int ijk,int q) {return rs;}
	+ /** Scales a plane displacement prior to use in the plane cutting
	+ * algorithm.
	+ * \param[in] rs the initial plane displacement.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] q the index of the particle within the block.
	+ * \return The scaled plane displacement. */
	+ inline double r_scale(double rs,int ijk,int q) {return rs;}
	+ /** Scales a plane displacement prior to use in the plane
	+ * cutting algorithm, and also checks if it could possibly cut
	+ * the cell.
	+ * \param[in,out] rs the plane displacement to be scaled.
	+ * \param[in] mrs the current maximum distance to a Voronoi
	+ * vertex multiplied by two.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] q the index of the particle within the block.
	+ * \return True if the cell could possibly cut the cell, false
	+ * otherwise. */
	+ inline bool r_scale_check(double &rs,double mrs,int ijk,int q) {return rs<mrs;}
	+};
	+
	+/** \brief Class containing all of the routines that are specific to computing
	+ * the radical Voronoi tessellation.
	+ *
	+ * The container_poly and container_periodic_poly classes are derived from this
	+ * class, and during the Voronoi cell computation, these routines are used to
	+ * create the radical Voronoi tessellation. */
	+class radius_poly {
	+ public:
	+ /** A two-dimensional array holding particle positions and radii. */
	+ double **ppr;
	+ /** The current maximum radius of any particle, used to
	+ * determine when to cut off the radical Voronoi computation.
	+ * */
	+ double max_radius;
	+ /** The class constructor sets the maximum particle radius to
	+ * be zero. */
	+ radius_poly() : max_radius(0) {}
	+ protected:
	+ /** This is called prior to computing a Voronoi cell for a
	+ * given particle to initialize any required constants.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] s the index of the particle within the block. */
	+ inline void r_init(int ijk,int s) {
	+ r_rad=ppr[ijk][4s+3]ppr[ijk][4*s+3];
	+ r_mul=r_rad-max_radius*max_radius;
	+ }
	+ /** Sets a required constant to be used when carrying out a
	+ * plane bounds check. */
	+ inline void r_prime(double rv) {r_val=1+r_mul/rv;}
	+ /** Carries out a radius bounds check.
	+ * \param[in] crs the radius squared to be tested.
	+ * \param[in] mrs the current maximum distance to a Voronoi
	+ * vertex multiplied by two.
	+ * \return True if particles at this radius could not possibly
	+ * cut the cell, false otherwise. */
	+ inline bool r_ctest(double crs,double mrs) {return crs+r_mul>sqrt(mrs*crs);}
	+ /** Scales a plane displacement during a plane bounds check.
	+ * \param[in] lrs the plane displacement.
	+ * \return The scaled value. */
	+ inline double r_cutoff(double lrs) {return lrs*r_val;}
	+ /** Adds the maximum radius squared to a given value.
	+ * \param[in] rs the value to consider.
	+ * \return The value with the radius squared added. */
	+ inline double r_max_add(double rs) {return rs+max_radius*max_radius;}
	+ /** Subtracts the radius squared of a particle from a given
	+ * value.
	+ * \param[in] rs the value to consider.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] q the index of the particle within the block.
	+ * \return The value with the radius squared subtracted. */
	+ inline double r_current_sub(double rs,int ijk,int q) {
	+ return rs-ppr[ijk][4q+3]ppr[ijk][4*q+3];
	+ }
	+ /** Scales a plane displacement prior to use in the plane cutting
	+ * algorithm.
	+ * \param[in] rs the initial plane displacement.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] q the index of the particle within the block.
	+ * \return The scaled plane displacement. */
	+ inline double r_scale(double rs,int ijk,int q) {
	+ return rs+r_rad-ppr[ijk][4q+3]ppr[ijk][4*q+3];
	+ }
	+ /** Scales a plane displacement prior to use in the plane
	+ * cutting algorithm, and also checks if it could possibly cut
	+ * the cell.
	+ * \param[in,out] rs the plane displacement to be scaled.
	+ * \param[in] mrs the current maximum distance to a Voronoi
	+ * vertex multiplied by two.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] q the index of the particle within the block.
	+ * \return True if the cell could possibly cut the cell, false
	+ * otherwise. */
	+ inline bool r_scale_check(double &rs,double mrs,int ijk,int q) {
	+ double trs=rs;
	+ rs+=r_rad-ppr[ijk][4q+3]ppr[ijk][4*q+3];
	+ return rs<sqrt(mrs*trs);
	+ }
	+ private:
	+ double r_rad,r_mul,r_val;
	+};
	+
	+}
	+#endif
	Index: extern/voro++/src/c_loops.hh
	===================================================================
	--- extern/voro++/src/c_loops.hh (revision 0)
	+++ extern/voro++/src/c_loops.hh (revision 0)
	@@ -0,0 +1,456 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file c_loops.hh
	+ * \brief Header file for the loop classes. */
	+
	+#ifndef VOROPP_C_LOOPS_HH
	+#define VOROPP_C_LOOPS_HH
	+
	+#include "config.hh"
	+
	+namespace voro {
	+
	+/** A type associated with a c_loop_subset class, determining what type of
	+ * geometrical region to loop over. */
	+enum c_loop_subset_mode {
	+ sphere,
	+ box,
	+ no_check
	+};
	+
	+/** \brief A class for storing ordering information when particles are added to
	+ * a container.
	+ *
	+ * When particles are added to a container class, they are sorted into an
	+ * internal computational grid of blocks. The particle_order class provides a
	+ * mechanism for remembering which block particles were sorted into. The import
	+ * and put routines in the container class have variants that also take a
	+ * particle_order class. Each time they are called, they will store the block
	+ * that the particle was sorted into, plus the position of the particle within
	+ * the block. The particle_order class can used by the c_loop_order class to
	+ * specifically loop over the particles that have their information stored
	+ * within it. */
	+class particle_order {
	+ public:
	+ /** A pointer to the array holding the ordering. */
	+ int *o;
	+ /** A pointer to the next position in the ordering array in
	+ * which to store an entry. */
	+ int *op;
	+ /** The current memory allocation for the class, set to the
	+ * number of entries which can be stored. */
	+ int size;
	+ /** The particle_order constructor allocates memory to store the
	+ * ordering information.
	+ * \param[in] init_size the initial amount of memory to
	+ * allocate. */
	+ particle_order(int init_size=init_ordering_size)
	+ : o(new int[init_size<<1]),op(o),size(init_size) {}
	+ /** The particle_order destructor frees the dynamically allocated
	+ * memory used to store the ordering information. */
	+ ~particle_order() {
	+ delete [] o;
	+ }
	+ /** Adds a record to the order, corresponding to the memory
	+ * address of where a particle was placed into the container.
	+ * \param[in] ijk the block into which the particle was placed.
	+ * \param[in] q the position within the block where the
	+ * particle was placed. */
	+ inline void add(int ijk,int q) {
	+ if(op==o+size) add_ordering_memory();
	+ (op++)=ijk;(op++)=q;
	+ }
	+ private:
	+ void add_ordering_memory();
	+};
	+
	+/** \brief Base class for looping over particles in a container.
	+ *
	+ * This class forms the base of all classes that can loop over a subset of
	+ * particles in a contaner in some order. When initialized, it stores constants
	+ * about the corresponding container geometry. It also contains a number of
	+ * routines for interrogating which particle currently being considered by the
	+ * loop, which are common between all of the derived classes. */
	+class c_loop_base {
	+ public:
	+ /** The number of blocks in the x direction. */
	+ const int nx;
	+ /** The number of blocks in the y direction. */
	+ const int ny;
	+ /** The number of blocks in the z direction. */
	+ const int nz;
	+ /** A constant, set to the value of nx multiplied by ny, which
	+ * is used in the routines that step through blocks in
	+ * sequence. */
	+ const int nxy;
	+ /** A constant, set to the value of nxnynz, which is used in
	+ * the routines that step through blocks in sequence. */
	+ const int nxyz;
	+ /** The number of floating point numbers per particle in the
	+ * associated container data structure. */
	+ const int ps;
	+ /** A pointer to the particle position information in the
	+ * associated container data structure. */
	+ double **p;
	+ /** A pointer to the particle ID information in the associated
	+ * container data structure. */
	+ int **id;
	+ /** A pointer to the particle counts in the associated
	+ * container data structure. */
	+ int *co;
	+ /** The current x-index of the block under consideration by the
	+ * loop. */
	+ int i;
	+ /** The current y-index of the block under consideration by the
	+ * loop. */
	+ int j;
	+ /** The current z-index of the block under consideration by the
	+ * loop. */
	+ int k;
	+ /** The current index of the block under consideration by the
	+ * loop. */
	+ int ijk;
	+ /** The index of the particle under consideration within the current
	+ * block. */
	+ int q;
	+ /** The constructor copies several necessary constants from the
	+ * base container class.
	+ * \param[in] con the container class to use. */
	+ template<class c_class>
	+ c_loop_base(c_class &con) : nx(con.nx), ny(con.ny), nz(con.nz),
	+ nxy(con.nxy), nxyz(con.nxyz), ps(con.ps),
	+ p(con.p), id(con.id), co(con.co) {}
	+ /** Returns the position vector of the particle currently being
	+ * considered by the loop.
	+ * \param[out] (x,y,z) the position vector of the particle. */
	+ inline void pos(double &x,double &y,double &z) {
	+ double pp=p[ijk]+psq;
	+ x=(pp++);y=(pp++);z=*pp;
	+ }
	+ /** Returns the ID, position vector, and radius of the particle
	+ * currently being considered by the loop.
	+ * \param[out] pid the particle ID.
	+ * \param[out] (x,y,z) the position vector of the particle.
	+ * \param[out] r the radius of the particle. If no radius
	+ * information is available the default radius
	+ * value is returned. */
	+ inline void pos(int &pid,double &x,double &y,double &z,double &r) {
	+ pid=id[ijk][q];
	+ double pp=p[ijk]+psq;
	+ x=(pp++);y=(pp++);z=*pp;
	+ r=ps==3?default_radius:*(++pp);
	+ }
	+ /** Returns the x position of the particle currently being
	+ * considered by the loop. */
	+ inline double x() {return p[ijk][ps*q];}
	+ /** Returns the y position of the particle currently being
	+ * considered by the loop. */
	+ inline double y() {return p[ijk][ps*q+1];}
	+ /** Returns the z position of the particle currently being
	+ * considered by the loop. */
	+ inline double z() {return p[ijk][ps*q+2];}
	+ /** Returns the ID of the particle currently being considered
	+ * by the loop. */
	+ inline int pid() {return id[ijk][q];}
	+};
	+
	+/** \brief Class for looping over all of the particles in a container.
	+ *
	+ * This is one of the simplest loop classes, that scans the computational
	+ * blocks in order, and scans all the particles within each block in order. */
	+class c_loop_all : public c_loop_base {
	+ public:
	+ /** The constructor copies several necessary constants from the
	+ * base container class.
	+ * \param[in] con the container class to use. */
	+ template<class c_class>
	+ c_loop_all(c_class &con) : c_loop_base(con) {}
	+ /** Sets the class to consider the first particle.
	+ * \return True if there is any particle to consider, false
	+ * otherwise. */
	+ inline bool start() {
	+ i=j=k=ijk=q=0;
	+ while(co[ijk]==0) if(!next_block()) return false;
	+ return true;
	+ }
	+ /** Finds the next particle to test.
	+ * \return True if there is another particle, false if no more
	+ * particles are available. */
	+ inline bool inc() {
	+ q++;
	+ if(q>=co[ijk]) {
	+ q=0;
	+ do {
	+ if(!next_block()) return false;
	+ } while(co[ijk]==0);
	+ }
	+ return true;
	+ }
	+ private:
	+ /** Updates the internal variables to find the next
	+ * computational block with any particles.
	+ * \return True if another block is found, false if there are
	+ * no more blocks. */
	+ inline bool next_block() {
	+ ijk++;
	+ i++;
	+ if(i==nx) {
	+ i=0;j++;
	+ if(j==ny) {
	+ j=0;k++;
	+ if(ijk==nxyz) return false;
	+ }
	+ }
	+ return true;
	+ }
	+};
	+
	+/** \brief Class for looping over a subset of particles in a container.
	+ *
	+ * This class can loop over a subset of particles in a certain geometrical
	+ * region within the container. The class can be set up to loop over a
	+ * rectangular box or sphere. It can also rectangular group of internal
	+ * computational blocks. */
	+class c_loop_subset : public c_loop_base {
	+ public:
	+ /** The current mode of operation, determining whether tests
	+ * should be applied to particles to ensure they are within a
	+ * certain geometrical object. */
	+ c_loop_subset_mode mode;
	+ /** The constructor copies several necessary constants from the
	+ * base container class.
	+ * \param[in] con the container class to use. */
	+ template<class c_class>
	+ c_loop_subset(c_class &con) : c_loop_base(con), ax(con.ax), ay(con.ay), az(con.az),
	+ sx(con.bx-ax), sy(con.by-ay), sz(con.bz-az), xsp(con.xsp), ysp(con.ysp), zsp(con.zsp),
	+ xperiodic(con.xperiodic), yperiodic(con.yperiodic), zperiodic(con.zperiodic) {}
	+ void setup_sphere(double vx,double vy,double vz,double r,bool bounds_test=true);
	+ void setup_box(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax,bool bounds_test=true);
	+ void setup_intbox(int ai_,int bi_,int aj_,int bj_,int ak_,int bk_);
	+ bool start();
	+ /** Finds the next particle to test.
	+ * \return True if there is another particle, false if no more
	+ * particles are available. */
	+ inline bool inc() {
	+ do {
	+ q++;
	+ while(q>=co[ijk]) {q=0;if(!next_block()) return false;}
	+ } while(mode!=no_check&&out_of_bounds());
	+ return true;
	+ }
	+ private:
	+ const double ax,ay,az,sx,sy,sz,xsp,ysp,zsp;
	+ const bool xperiodic,yperiodic,zperiodic;
	+ double px,py,pz,apx,apy,apz;
	+ double v0,v1,v2,v3,v4,v5;
	+ int ai,bi,aj,bj,ak,bk,s;
	+ int ci,cj,ck,di,dj,dk,inc1,inc2;
	+ inline int step_mod(int a,int b) {return a>=0?a%b:b-1-(b-1-a)%b;}
	+ inline int step_div(int a,int b) {return a>=0?a/b:-1+(a+1)/b;}
	+ inline int step_int(double a) {return a<0?int(a)-1:int(a);}
	+ void setup_common();
	+ bool next_block();
	+ bool out_of_bounds();
	+};
	+
	+/** \brief Class for looping over all of the particles specified in a
	+ * pre-assembled particle_order class.
	+ *
	+ * The particle_order class can be used to create a specific order of particles
	+ * within the container. This class can then loop over these particles in this
	+ * order. The class is particularly useful in cases where the ordering of the
	+ * output must match the ordering of particles as they were inserted into the
	+ * container. */
	+class c_loop_order : public c_loop_base {
	+ public:
	+ /** A reference to the ordering class to use. */
	+ particle_order &vo;
	+ /** A pointer to the current position in the ordering class. */
	+ int *cp;
	+ /** A pointer to the end position in the ordering class. */
	+ int *op;
	+ /** The constructor copies several necessary constants from the
	+ * base class, and sets up a reference to the ordering class to
	+ * use.
	+ * \param[in] con the container class to use.
	+ * \param[in] vo_ the ordering class to use. */
	+ template<class c_class>
	+ c_loop_order(c_class &con,particle_order &vo_)
	+ : c_loop_base(con), vo(vo_), nx(con.nx), nxy(con.nxy) {}
	+ /** Sets the class to consider the first particle.
	+ * \return True if there is any particle to consider, false
	+ * otherwise. */
	+ inline bool start() {
	+ cp=vo.o;op=vo.op;
	+ if(cp!=op) {
	+ ijk=*(cp++);decode();
	+ q=*(cp++);
	+ return true;
	+ } else return false;
	+ }
	+ /** Finds the next particle to test.
	+ * \return True if there is another particle, false if no more
	+ * particles are available. */
	+ inline bool inc() {
	+ if(cp==op) return false;
	+ ijk=*(cp++);decode();
	+ q=*(cp++);
	+ return true;
	+ }
	+ private:
	+ /** The number of computational blocks in the x direction. */
	+ const int nx;
	+ /** The number of computational blocks in a z-slice. */
	+ const int nxy;
	+ /** Takes the current block index and computes indices in the
	+ * x, y, and z directions. */
	+ inline void decode() {
	+ k=ijk/nxy;
	+ int ijkt=ijk-nxy*k;
	+ j=ijkt/nx;
	+ i=ijkt-j*nx;
	+ }
	+};
	+
	+/** \brief A class for looping over all particles in a container_periodic or
	+ * container_periodic_poly class.
	+ *
	+ * Since the container_periodic and container_periodic_poly classes have a
	+ * fundamentally different memory organization, the regular loop classes cannot
	+ * be used with them. */
	+class c_loop_all_periodic : public c_loop_base {
	+ public:
	+ /** The constructor copies several necessary constants from the
	+ * base periodic container class.
	+ * \param[in] con the periodic container class to use. */
	+ template<class c_class>
	+ c_loop_all_periodic(c_class &con) : c_loop_base(con), ey(con.ey), ez(con.ez), wy(con.wy), wz(con.wz),
	+ ijk0(nx(ey+con.oyez)), inc2(2nxcon.ey+1) {}
	+ /** Sets the class to consider the first particle.
	+ * \return True if there is any particle to consider, false
	+ * otherwise. */
	+ inline bool start() {
	+ i=0;
	+ j=ey;
	+ k=ez;
	+ ijk=ijk0;
	+ q=0;
	+ while(co[ijk]==0) if(!next_block()) return false;
	+ return true;
	+ }
	+ /** Finds the next particle to test.
	+ * \return True if there is another particle, false if no more
	+ * particles are available. */
	+ inline bool inc() {
	+ q++;
	+ if(q>=co[ijk]) {
	+ q=0;
	+ do {
	+ if(!next_block()) return false;
	+ } while(co[ijk]==0);
	+ }
	+ return true;
	+ }
	+ private:
	+ /** The lower y index (inclusive) of the primary domain within
	+ * the block structure. */
	+ int ey;
	+ /** The lower y index (inclusive) of the primary domain within
	+ * the block structure. */
	+ int ez;
	+ /** The upper y index (exclusive) of the primary domain within
	+ * the block structure. */
	+ int wy;
	+ /** The upper z index (exclusive) of the primary domain within
	+ * the block structure. */
	+ int wz;
	+ /** The index of the (0,0,0) block within the block structure.
	+ */
	+ int ijk0;
	+ /** A value to increase ijk by when the z index is increased.
	+ */
	+ int inc2;
	+ /** Updates the internal variables to find the next
	+ * computational block with any particles.
	+ * \return True if another block is found, false if there are
	+ * no more blocks. */
	+ inline bool next_block() {
	+ i++;
	+ if(i==nx) {
	+ i=0;j++;
	+ if(j==wy) {
	+ j=ey;k++;
	+ if(k==wz) return false;
	+ ijk+=inc2;
	+ } else ijk++;
	+ } else ijk++;
	+ return true;
	+ }
	+};
	+
	+/** \brief Class for looping over all of the particles specified in a
	+ * pre-assembled particle_order class, for use with container_periodic classes.
	+ *
	+ * The particle_order class can be used to create a specific order of particles
	+ * within the container. This class can then loop over these particles in this
	+ * order. The class is particularly useful in cases where the ordering of the
	+ * output must match the ordering of particles as they were inserted into the
	+ * container. */
	+class c_loop_order_periodic : public c_loop_base {
	+ public:
	+ /** A reference to the ordering class to use. */
	+ particle_order &vo;
	+ /** A pointer to the current position in the ordering class. */
	+ int *cp;
	+ /** A pointer to the end position in the ordering class. */
	+ int *op;
	+ /** The constructor copies several necessary constants from the
	+ * base class, and sets up a reference to the ordering class to
	+ * use.
	+ * \param[in] con the container class to use.
	+ * \param[in] vo_ the ordering class to use. */
	+ template<class c_class>
	+ c_loop_order_periodic(c_class &con,particle_order &vo_)
	+ : c_loop_base(con), vo(vo_), nx(con.nx), oxy(con.nx*con.oy) {}
	+ /** Sets the class to consider the first particle.
	+ * \return True if there is any particle to consider, false
	+ * otherwise. */
	+ inline bool start() {
	+ cp=vo.o;op=vo.op;
	+ if(cp!=op) {
	+ ijk=*(cp++);decode();
	+ q=*(cp++);
	+ return true;
	+ } else return false;
	+ }
	+ /** Finds the next particle to test.
	+ * \return True if there is another particle, false if no more
	+ * particles are available. */
	+ inline bool inc() {
	+ if(cp==op) return false;
	+ ijk=*(cp++);decode();
	+ q=*(cp++);
	+ return true;
	+ }
	+ private:
	+ /** The number of computational blocks in the x direction. */
	+ const int nx;
	+ /** The number of computational blocks in a z-slice. */
	+ const int oxy;
	+ /** Takes the current block index and computes indices in the
	+ * x, y, and z directions. */
	+ inline void decode() {
	+ k=ijk/oxy;
	+ int ijkt=ijk-oxy*k;
	+ j=ijkt/nx;
	+ i=ijkt-j*nx;
	+ }
	+};
	+
	+}
	+
	+#endif
	Index: extern/voro++/src/v_base.hh
	===================================================================
	--- extern/voro++/src/v_base.hh (revision 0)
	+++ extern/voro++/src/v_base.hh (revision 0)
	@@ -0,0 +1,88 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file v_base.hh
	+ * \brief Header file for the base Voronoi container class. */
	+
	+#ifndef VOROPP_V_BASE_HH
	+#define VOROPP_V_BASE_HH
	+
	+#include "worklist.hh"
	+
	+namespace voro {
	+
	+/** \brief Class containing data structures common across all particle container classes.
	+ *
	+ * This class contains constants and data structures that are common across all
	+ * particle container classes. It contains constants setting the size of the
	+ * underlying subgrid of blocks that forms the basis of the Voronoi cell
	+ * computations. It also constructs bound tables that are used in the Voronoi
	+ * cell computation, and contains a number of routines that are common across
	+ * all container classes. */
	+class voro_base {
	+ public:
	+ /** The number of blocks in the x direction. */
	+ const int nx;
	+ /** The number of blocks in the y direction. */
	+ const int ny;
	+ /** The number of blocks in the z direction. */
	+ const int nz;
	+ /** A constant, set to the value of nx multiplied by ny, which
	+ * is used in the routines that step through blocks in
	+ * sequence. */
	+ const int nxy;
	+ /** A constant, set to the value of nxnynz, which is used in
	+ * the routines that step through blocks in sequence. */
	+ const int nxyz;
	+ /** The size of a computational block in the x direction. */
	+ const double boxx;
	+ /** The size of a computational block in the y direction. */
	+ const double boxy;
	+ /** The size of a computational block in the z direction. */
	+ const double boxz;
	+ /** The inverse box length in the x direction. */
	+ const double xsp;
	+ /** The inverse box length in the y direction. */
	+ const double ysp;
	+ /** The inverse box length in the z direction. */
	+ const double zsp;
	+ /** An array to hold the minimum distances associated with the
	+ * worklists. This array is initialized during container
	+ * construction, by the initialize_radii() routine. */
	+ double *mrad;
	+ /** The pre-computed block worklists. */
	+ static const unsigned int wl[wl_seq_length*wl_hgridcu];
	+ bool contains_neighbor(const char* format);
	+ voro_base(int nx_,int ny_,int nz_,double boxx_,double boxy_,double boxz_);
	+ ~voro_base() {delete [] mrad;}
	+ protected:
	+ /** A custom int function that returns consistent stepping
	+ * for negative numbers, so that (-1.5, -0.5, 0.5, 1.5) maps
	+ * to (-2,-1,0,1).
	+ * \param[in] a the number to consider.
	+ * \return The value of the custom int operation. */
	+ inline int step_int(double a) {return a<0?int(a)-1:int(a);}
	+ /** A custom modulo function that returns consistent stepping
	+ * for negative numbers. For example, (-2,-1,0,1,2) step_mod 2
	+ * is (0,1,0,1,0).
	+ * \param[in] (a,b) the input integers.
	+ * \return The value of a modulo b, consistent for negative
	+ * numbers. */
	+ inline int step_mod(int a,int b) {return a>=0?a%b:b-1-(b-1-a)%b;}
	+ /** A custom integer division function that returns consistent
	+ * stepping for negative numbers. For example, (-2,-1,0,1,2)
	+ * step_div 2 is (-1,-1,0,0,1).
	+ * \param[in] (a,b) the input integers.
	+ * \return The value of a div b, consistent for negative
	+ * numbers. */
	+ inline int step_div(int a,int b) {return a>=0?a/b:-1+(a+1)/b;}
	+ private:
	+ void compute_minimum(double &minr,double &xlo,double &xhi,double &ylo,double &yhi,double &zlo,double &zhi,int ti,int tj,int tk);
	+};
	+
	+}
	+
	+#endif
	Index: extern/voro++/src/wall.hh
	===================================================================
	--- extern/voro++/src/wall.hh (revision 0)
	+++ extern/voro++/src/wall.hh (revision 0)
	@@ -0,0 +1,119 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file wall.hh
	+ * \brief Header file for the derived wall classes. */
	+
	+#ifndef VOROPP_WALL_HH
	+#define VOROPP_WALL_HH
	+
	+#include "cell.hh"
	+#include "container.hh"
	+
	+namespace voro {
	+
	+/** \brief A class representing a spherical wall object.
	+ *
	+ * This class represents a spherical wall object. */
	+struct wall_sphere : public wall {
	+ public:
	+ /** Constructs a spherical wall object.
	+ * \param[in] w_id_ an ID number to associate with the wall for
	+ * neighbor tracking.
	+ * \param[in] (xc_,yc_,zc_) a position vector for the sphere's
	+ * center.
	+ * \param[in] rc_ the radius of the sphere. */
	+ wall_sphere(double xc_,double yc_,double zc_,double rc_,int w_id_=-99)
	+ : w_id(w_id_), xc(xc_), yc(yc_), zc(zc_), rc(rc_) {}
	+ bool point_inside(double x,double y,double z);
	+ template<class v_cell>
	+ bool cut_cell_base(v_cell &c,double x,double y,double z);
	+ bool cut_cell(voronoicell &c,double x,double y,double z) {return cut_cell_base(c,x,y,z);}
	+ bool cut_cell(voronoicell_neighbor &c,double x,double y,double z) {return cut_cell_base(c,x,y,z);}
	+ private:
	+ const int w_id;
	+ const double xc,yc,zc,rc;
	+};
	+
	+/** \brief A class representing a plane wall object.
	+ *
	+ * This class represents a single plane wall object. */
	+struct wall_plane : public wall {
	+ public:
	+ /** Constructs a plane wall object.
	+ * \param[in] (xc_,yc_,zc_) a normal vector to the plane.
	+ * \param[in] ac_ a displacement along the normal vector.
	+ * \param[in] w_id_ an ID number to associate with the wall for
	+ * neighbor tracking. */
	+ wall_plane(double xc_,double yc_,double zc_,double ac_,int w_id_=-99)
	+ : w_id(w_id_), xc(xc_), yc(yc_), zc(zc_), ac(ac_) {}
	+ bool point_inside(double x,double y,double z);
	+ template<class v_cell>
	+ bool cut_cell_base(v_cell &c,double x,double y,double z);
	+ bool cut_cell(voronoicell &c,double x,double y,double z) {return cut_cell_base(c,x,y,z);}
	+ bool cut_cell(voronoicell_neighbor &c,double x,double y,double z) {return cut_cell_base(c,x,y,z);}
	+ private:
	+ const int w_id;
	+ const double xc,yc,zc,ac;
	+};
	+
	+/** \brief A class representing a cylindrical wall object.
	+ *
	+ * This class represents a open cylinder wall object. */
	+struct wall_cylinder : public wall {
	+ public:
	+ /** Constructs a cylinder wall object.
	+ * \param[in] (xc_,yc_,zc_) a point on the axis of the
	+ * cylinder.
	+ * \param[in] (xa_,ya_,za_) a vector pointing along the
	+ * direction of the cylinder.
	+ * \param[in] rc_ the radius of the cylinder
	+ * \param[in] w_id_ an ID number to associate with the wall for
	+ * neighbor tracking. */
	+ wall_cylinder(double xc_,double yc_,double zc_,double xa_,double ya_,double za_,double rc_,int w_id_=-99)
	+ : w_id(w_id_), xc(xc_), yc(yc_), zc(zc_), xa(xa_), ya(ya_), za(za_),
	+ asi(1/(xa_xa_+ya_ya_+za_*za_)), rc(rc_) {}
	+ bool point_inside(double x,double y,double z);
	+ template<class v_cell>
	+ bool cut_cell_base(v_cell &c,double x,double y,double z);
	+ bool cut_cell(voronoicell &c,double x,double y,double z) {return cut_cell_base(c,x,y,z);}
	+ bool cut_cell(voronoicell_neighbor &c,double x,double y,double z) {return cut_cell_base(c,x,y,z);}
	+ private:
	+ const int w_id;
	+ const double xc,yc,zc,xa,ya,za,asi,rc;
	+};
	+
	+
	+/** \brief A class representing a conical wall object.
	+ *
	+ * This class represents a cone wall object. */
	+struct wall_cone : public wall {
	+ public:
	+ /** Constructs a cone wall object.
	+ * \param[in] (xc_,yc_,zc_) the apex of the cone.
	+ * \param[in] (xa_,ya_,za_) a vector pointing along the axis of
	+ * the cone.
	+ * \param[in] ang the angle (in radians) of the cone, measured
	+ * from the axis.
	+ * \param[in] w_id_ an ID number to associate with the wall for
	+ * neighbor tracking. */
	+ wall_cone(double xc_,double yc_,double zc_,double xa_,double ya_,double za_,double ang,int w_id_=-99)
	+ : w_id(w_id_), xc(xc_), yc(yc_), zc(zc_), xa(xa_), ya(ya_), za(za_),
	+ asi(1/(xa_xa_+ya_ya_+za_*za_)),
	+ gra(tan(ang)), sang(sin(ang)), cang(cos(ang)) {}
	+ bool point_inside(double x,double y,double z);
	+ template<class v_cell>
	+ bool cut_cell_base(v_cell &c,double x,double y,double z);
	+ bool cut_cell(voronoicell &c,double x,double y,double z) {return cut_cell_base(c,x,y,z);}
	+ bool cut_cell(voronoicell_neighbor &c,double x,double y,double z) {return cut_cell_base(c,x,y,z);}
	+ private:
	+ const int w_id;
	+ const double xc,yc,zc,xa,ya,za,asi,gra,sang,cang;
	+};
	+
	+}
	+
	+#endif
	Index: extern/voro++/src/cmd_line.cc
	===================================================================
	--- extern/voro++/src/cmd_line.cc (revision 0)
	+++ extern/voro++/src/cmd_line.cc (revision 0)
	@@ -0,0 +1,498 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file cmd_line.cc
	+ * \brief Source code for the command-line utility. */
	+
	+#include <cstring>
	+
	+#include "voro++.hh"
	+using namespace voro;
	+
	+enum blocks_mode {
	+ none,
	+ length_scale,
	+ specified
	+};
	+
	+// A maximum allowed number of regions, to prevent enormous amounts of memory
	+// being allocated
	+const int max_regions=16777216;
	+
	+// This message gets displayed if the user requests the help flag
	+void help_message() {
	+ puts("Voro++ version 0.4.5, by Chris H. Rycroft (UC Berkeley/LBL)\n\n"
	+ "Syntax: voro++ [options] <x_min> <x_max> <y_min>\n"
	+ " <y_max> <z_min> <z_max> <filename>\n\n"
	+ "By default, the utility reads in the input file of particle IDs and positions,\n"
	+ "computes the Voronoi cell for each, and then creates <filename.vol> with an\n"
	+ "additional column containing the volume of each Voronoi cell.\n\n"
	+ "Available options:\n"
	+ " -c <str> : Specify a custom output string\n"
	+ " -g : Turn on the gnuplot output to <filename.gnu>\n"
	+ " -h/--help : Print this information\n"
	+ " -hc : Print information about custom output\n"
	+ " -l <len> : Manually specify a length scale to configure the internal\n"
	+ " computational grid\n"
	+ " -m <mem> : Manually choose the memory allocation per grid block\n"
	+ " (default 8)\n"
	+ " -n [3] : Manually specify the internal grid size\n"
	+ " -o : Ensure that the output file has the same order as the input\n"
	+ " file\n"
	+ " -p : Make container periodic in all three directions\n"
	+ " -px : Make container periodic in the x direction\n"
	+ " -py : Make container periodic in the y direction\n"
	+ " -pz : Make container periodic in the z direction\n"
	+ " -r : Assume the input file has an extra coordinate for radii\n"
	+ " -v : Verbose output\n"
	+ " --version : Print version information\n"
	+ " -wb [6] : Add six plane wall objects to make rectangular box containing\n"
	+ " the space x1<x<x2, x3<y<x4, x5<z<x6\n"
	+ " -wc [7] : Add a cylinder wall object, centered on (x1,x2,x3),\n"
	+ " pointing in (x4,x5,x6), radius x7\n"
	+ " -wo [7] : Add a conical wall object, apex at (x1,x2,x3), axis\n"
	+ " along (x4,x5,x6), angle x7 in radians\n"
	+ " -ws [4] : Add a sphere wall object, centered on (x1,x2,x3),\n"
	+ " with radius x4\n"
	+ " -wp [4] : Add a plane wall object, with normal (x1,x2,x3),\n"
	+ " and displacement x4\n"
	+ " -y : Save POV-Ray particles to <filename_p.pov> and POV-Ray Voronoi\n"
	+ " cells to <filename_v.pov>\n"
	+ " -yp : Save only POV-Ray particles to <filename_p.pov>\n"
	+ " -yv : Save only POV-Ray Voronoi cells to <filename_v.pov>");
	+}
	+
	+// This message gets displayed if the user requests information about doing
	+// custom output
	+void custom_output_message() {
	+ puts("The \"-c\" option allows a string to be specified that will customize the output\n"
	+ "file to contain a variety of statistics about each computed Voronoi cell. The\n"
	+ "string is similar to the standard C printf() function, made up of text with\n"
	+ "additional control sequences that begin with percentage signs that are expanded\n"
	+ "to different statistics. See http://math.lbl.gov/voro++/doc/custom.html for more\n"
	+ "information.\n"
	+ "\nParticle-related:\n"
	+ " %i The particle ID number\n"
	+ " %x The x coordinate of the particle\n"
	+ " %y The y coordinate of the particle\n"
	+ " %z The z coordinate of the particle\n"
	+ " %q The position vector of the particle, short for \"%x %y %z\"\n"
	+ " %r The radius of the particle (only printed if -p enabled)\n"
	+ "\nVertex-related:\n"
	+ " %w The number of vertices in the Voronoi cell\n"
	+ " %p A list of the vertices of the Voronoi cell in the format (x,y,z),\n"
	+ " relative to the particle center\n"
	+ " %P A list of the vertices of the Voronoi cell in the format (x,y,z),\n"
	+ " relative to the global coordinate system\n"
	+ " %o A list of the orders of each vertex\n"
	+ " %m The maximum radius squared of a vertex position, relative to the\n"
	+ " particle center\n"
	+ "\nEdge-related:\n"
	+ " %g The number of edges of the Voronoi cell\n"
	+ " %E The total edge distance\n"
	+ " %e A list of perimeters of each face\n"
	+ "\nFace-related:\n"
	+ " %s The number of faces of the Voronoi cell\n"
	+ " %F The total surface area of the Voronoi cell\n"
	+ " %A A frequency table of the number of edges for each face\n"
	+ " %a A list of the number of edges for each face\n"
	+ " %f A list of areas of each face\n"
	+ " %t A list of bracketed sequences of vertices that make up each face\n"
	+ " %l A list of normal vectors for each face\n"
	+ " %n A list of neighboring particle or wall IDs corresponding to each face\n"
	+ "\nVolume-related:\n"
	+ " %v The volume of the Voronoi cell\n"
	+ " %c The centroid of the Voronoi cell, relative to the particle center\n"
	+ " %C The centroid of the Voronoi cell, in the global coordinate system");
	+}
	+
	+// Ths message is displayed if the user requests version information
	+void version_message() {
	+ puts("Voro++ version 0.4.5 (July 27th 2012)");
	+}
	+
	+// Prints an error message. This is called when the program is unable to make
	+// sense of the command-line options.
	+void error_message() {
	+ fputs("voro++: Unrecognized command-line options; type \"voro++ -h\" for more\ninformation.\n",stderr);
	+}
	+
	+// Carries out the Voronoi computation and outputs the results to the requested
	+// files
	+template<class c_loop,class c_class>
	+void cmd_line_output(c_loop &vl,c_class &con,const char* format,FILE* outfile,FILE* gnu_file,FILE* povp_file,FILE* povv_file,bool verbose,double &vol,int &vcc,int &tp) {
	+ int pid,ps=con.ps;double x,y,z,r;
	+ if(con.contains_neighbor(format)) {
	+ voronoicell_neighbor c;
	+ if(vl.start()) do if(con.compute_cell(c,vl)) {
	+ vl.pos(pid,x,y,z,r);
	+ if(outfile!=NULL) c.output_custom(format,pid,x,y,z,r,outfile);
	+ if(gnu_file!=NULL) c.draw_gnuplot(x,y,z,gnu_file);
	+ if(povp_file!=NULL) {
	+ fprintf(povp_file,"// id %d\n",pid);
	+ if(ps==4) fprintf(povp_file,"sphere{<%g,%g,%g>,%g}\n",x,y,z,r);
	+ else fprintf(povp_file,"sphere{<%g,%g,%g>,s}\n",x,y,z);
	+ }
	+ if(povv_file!=NULL) {
	+ fprintf(povv_file,"// cell %d\n",pid);
	+ c.draw_pov(x,y,z,povv_file);
	+ }
	+ if(verbose) {vol+=c.volume();vcc++;}
	+ } while(vl.inc());
	+ } else {
	+ voronoicell c;
	+ if(vl.start()) do if(con.compute_cell(c,vl)) {
	+ vl.pos(pid,x,y,z,r);
	+ if(outfile!=NULL) c.output_custom(format,pid,x,y,z,r,outfile);
	+ if(gnu_file!=NULL) c.draw_gnuplot(x,y,z,gnu_file);
	+ if(povp_file!=NULL) {
	+ fprintf(povp_file,"// id %d\n",pid);
	+ if(ps==4) fprintf(povp_file,"sphere{<%g,%g,%g>,%g}\n",x,y,z,r);
	+ else fprintf(povp_file,"sphere{<%g,%g,%g>,s}\n",x,y,z);
	+ }
	+ if(povv_file!=NULL) {
	+ fprintf(povv_file,"// cell %d\n",pid);
	+ c.draw_pov(x,y,z,povv_file);
	+ }
	+ if(verbose) {vol+=c.volume();vcc++;}
	+ } while(vl.inc());
	+ }
	+ if(verbose) tp=con.total_particles();
	+}
	+
	+int main(int argc,char **argv) {
	+ int i=1,j=-7,custom_output=0,nx,ny,nz,init_mem(8);
	+ double ls=0;
	+ blocks_mode bm=none;
	+ bool gnuplot_output=false,povp_output=false,povv_output=false,polydisperse=false;
	+ bool xperiodic=false,yperiodic=false,zperiodic=false,ordered=false,verbose=false;
	+ pre_container pcon=NULL;pre_container_poly pconp=NULL;
	+ wall_list wl;
	+
	+ // If there's one argument, check to see if it's requesting help.
	+ // Otherwise, bail out with an error.
	+ if(argc==2) {
	+ if(strcmp(argv[1],"-h")==0\|\|strcmp(argv[1],"--help")==0) {
	+ help_message();return 0;
	+ } else if(strcmp(argv[1],"-hc")==0) {
	+ custom_output_message();return 0;
	+ } else if(strcmp(argv[1],"--version")==0) {
	+ version_message();return 0;
	+ } else {
	+ error_message();
	+ return VOROPP_CMD_LINE_ERROR;
	+ }
	+ }
	+
	+ // If there aren't enough command-line arguments, then bail out
	+ // with an error.
	+ if(argc<7) {
	+ error_message();
	+ return VOROPP_CMD_LINE_ERROR;
	+ }
	+
	+ // We have enough arguments. Now start searching for command-line
	+ // options.
	+ while(i<argc-7) {
	+ if(strcmp(argv[i],"-c")==0) {
	+ if(i>=argc-8) {error_message();wl.deallocate();return VOROPP_CMD_LINE_ERROR;}
	+ if(custom_output==0) {
	+ custom_output=++i;
	+ } else {
	+ fputs("voro++: multiple custom output strings detected\n",stderr);
	+ wl.deallocate();
	+ return VOROPP_CMD_LINE_ERROR;
	+ }
	+ } else if(strcmp(argv[i],"-g")==0) {
	+ gnuplot_output=true;
	+ } else if(strcmp(argv[i],"-h")==0\|\|strcmp(argv[i],"--help")==0) {
	+ help_message();wl.deallocate();return 0;
	+ } else if(strcmp(argv[i],"-hc")==0) {
	+ custom_output_message();wl.deallocate();return 0;
	+ } else if(strcmp(argv[i],"-l")==0) {
	+ if(i>=argc-8) {error_message();wl.deallocate();return VOROPP_CMD_LINE_ERROR;}
	+ if(bm!=none) {
	+ fputs("voro++: Conflicting options about grid setup (-l/-n)\n",stderr);
	+ wl.deallocate();
	+ return VOROPP_CMD_LINE_ERROR;
	+ }
	+ bm=length_scale;
	+ i++;ls=atof(argv[i]);
	+ } else if(strcmp(argv[i],"-m")==0) {
	+ i++;init_mem=atoi(argv[i]);
	+ } else if(strcmp(argv[i],"-n")==0) {
	+ if(i>=argc-10) {error_message();wl.deallocate();return VOROPP_CMD_LINE_ERROR;}
	+ if(bm!=none) {
	+ fputs("voro++: Conflicting options about grid setup (-l/-n)\n",stderr);
	+ wl.deallocate();
	+ return VOROPP_CMD_LINE_ERROR;
	+ }
	+ bm=specified;
	+ i++;
	+ nx=atoi(argv[i++]);
	+ ny=atoi(argv[i++]);
	+ nz=atoi(argv[i]);
	+ if(nx<=0\|\|ny<=0\|\|nz<=0) {
	+ fputs("voro++: Computational grid specified with -n must be greater than one\n"
	+ "in each direction\n",stderr);
	+ wl.deallocate();
	+ return VOROPP_CMD_LINE_ERROR;
	+ }
	+ } else if(strcmp(argv[i],"-o")==0) {
	+ ordered=true;
	+ } else if(strcmp(argv[i],"-p")==0) {
	+ xperiodic=yperiodic=zperiodic=true;
	+ } else if(strcmp(argv[i],"-px")==0) {
	+ xperiodic=true;
	+ } else if(strcmp(argv[i],"-py")==0) {
	+ yperiodic=true;
	+ } else if(strcmp(argv[i],"-pz")==0) {
	+ zperiodic=true;
	+ } else if(strcmp(argv[i],"-r")==0) {
	+ polydisperse=true;
	+ } else if(strcmp(argv[i],"-v")==0) {
	+ verbose=true;
	+ } else if(strcmp(argv[i],"--version")==0) {
	+ version_message();
	+ wl.deallocate();
	+ return 0;
	+ } else if(strcmp(argv[i],"-wb")==0) {
	+ if(i>=argc-13) {error_message();wl.deallocate();return VOROPP_CMD_LINE_ERROR;}
	+ i++;
	+ double w0=atof(argv[i++]),w1=atof(argv[i++]);
	+ double w2=atof(argv[i++]),w3=atof(argv[i++]);
	+ double w4=atof(argv[i++]),w5=atof(argv[i]);
	+ wl.add_wall(new wall_plane(-1,0,0,-w0,j));j--;
	+ wl.add_wall(new wall_plane(1,0,0,w1,j));j--;
	+ wl.add_wall(new wall_plane(0,-1,0,-w2,j));j--;
	+ wl.add_wall(new wall_plane(0,1,0,w3,j));j--;
	+ wl.add_wall(new wall_plane(0,0,-1,-w4,j));j--;
	+ wl.add_wall(new wall_plane(0,0,1,w5,j));j--;
	+ } else if(strcmp(argv[i],"-ws")==0) {
	+ if(i>=argc-11) {error_message();wl.deallocate();return VOROPP_CMD_LINE_ERROR;}
	+ i++;
	+ double w0=atof(argv[i++]),w1=atof(argv[i++]);
	+ double w2=atof(argv[i++]),w3=atof(argv[i]);
	+ wl.add_wall(new wall_sphere(w0,w1,w2,w3,j));
	+ j--;
	+ } else if(strcmp(argv[i],"-wp")==0) {
	+ if(i>=argc-11) {error_message();wl.deallocate();return VOROPP_CMD_LINE_ERROR;}
	+ i++;
	+ double w0=atof(argv[i++]),w1=atof(argv[i++]);
	+ double w2=atof(argv[i++]),w3=atof(argv[i]);
	+ wl.add_wall(new wall_plane(w0,w1,w2,w3,j));
	+ j--;
	+ } else if(strcmp(argv[i],"-wc")==0) {
	+ if(i>=argc-14) {error_message();wl.deallocate();return VOROPP_CMD_LINE_ERROR;}
	+ i++;
	+ double w0=atof(argv[i++]),w1=atof(argv[i++]);
	+ double w2=atof(argv[i++]),w3=atof(argv[i++]);
	+ double w4=atof(argv[i++]),w5=atof(argv[i++]);
	+ double w6=atof(argv[i]);
	+ wl.add_wall(new wall_cylinder(w0,w1,w2,w3,w4,w5,w6,j));
	+ j--;
	+ } else if(strcmp(argv[i],"-wo")==0) {
	+ if(i>=argc-14) {error_message();wl.deallocate();return VOROPP_CMD_LINE_ERROR;}
	+ i++;
	+ double w0=atof(argv[i++]),w1=atof(argv[i++]);
	+ double w2=atof(argv[i++]),w3=atof(argv[i++]);
	+ double w4=atof(argv[i++]),w5=atof(argv[i++]);
	+ double w6=atof(argv[i]);
	+ wl.add_wall(new wall_cone(w0,w1,w2,w3,w4,w5,w6,j));
	+ j--;
	+ } else if(strcmp(argv[i],"-y")==0) {
	+ povp_output=povv_output=true;
	+ } else if(strcmp(argv[i],"-yp")==0) {
	+ povp_output=true;
	+ } else if(strcmp(argv[i],"-yv")==0) {
	+ povv_output=true;
	+ } else {
	+ wl.deallocate();
	+ error_message();
	+ return VOROPP_CMD_LINE_ERROR;
	+ }
	+ i++;
	+ }
	+
	+ // Check the memory guess is positive
	+ if(init_mem<=0) {
	+ fputs("voro++: The memory allocation must be positive\n",stderr);
	+ wl.deallocate();
	+ return VOROPP_CMD_LINE_ERROR;
	+ }
	+
	+ // Read in the dimensions of the test box, and estimate the number of
	+ // boxes to divide the region up into
	+ double ax=atof(argv[i]),bx=atof(argv[i+1]);
	+ double ay=atof(argv[i+2]),by=atof(argv[i+3]);
	+ double az=atof(argv[i+4]),bz=atof(argv[i+5]);
	+
	+ // Check that for each coordinate, the minimum value is smaller
	+ // than the maximum value
	+ if(bx<ax) {
	+ fputs("voro++: Minimum x coordinate exceeds maximum x coordinate\n",stderr);
	+ wl.deallocate();
	+ return VOROPP_CMD_LINE_ERROR;
	+ }
	+ if(by<ay) {
	+ fputs("voro++: Minimum y coordinate exceeds maximum y coordinate\n",stderr);
	+ wl.deallocate();
	+ return VOROPP_CMD_LINE_ERROR;
	+ }
	+ if(bz<az) {
	+ fputs("voro++: Minimum z coordinate exceeds maximum z coordinate\n",stderr);
	+ wl.deallocate();
	+ return VOROPP_CMD_LINE_ERROR;
	+ }
	+
	+ if(bm==none) {
	+ if(polydisperse) {
	+ pconp=new pre_container_poly(ax,bx,ay,by,az,bz,xperiodic,yperiodic,zperiodic);
	+ pconp->import(argv[i+6]);
	+ pconp->guess_optimal(nx,ny,nz);
	+ } else {
	+ pcon=new pre_container(ax,bx,ay,by,az,bz,xperiodic,yperiodic,zperiodic);
	+ pcon->import(argv[i+6]);
	+ pcon->guess_optimal(nx,ny,nz);
	+ }
	+ } else {
	+ double nxf,nyf,nzf;
	+ if(bm==length_scale) {
	+
	+ // Check that the length scale is positive and
	+ // reasonably large
	+ if(ls<tolerance) {
	+ fputs("voro++: ",stderr);
	+ if(ls<0) {
	+ fputs("The length scale must be positive\n",stderr);
	+ } else {
	+ fprintf(stderr,"The length scale is smaller than the safe limit of %g. Either\nincrease the particle length scale, or recompile with a different limit.\n",tolerance);
	+ }
	+ wl.deallocate();
	+ return VOROPP_CMD_LINE_ERROR;
	+ }
	+ ls=0.6/ls;
	+ nxf=(bx-ax)*ls+1;
	+ nyf=(by-ay)*ls+1;
	+ nzf=(bz-az)*ls+1;
	+
	+ nx=int(nxf);ny=int(nyf);nz=int(nzf);
	+ } else {
	+ nxf=nx;nyf=ny;nzf=nz;
	+ }
	+
	+ // Compute the number regions based on the length scale
	+ // provided. If the total number exceeds a cutoff then bail
	+ // out, to prevent making a massive memory allocation. Do this
	+ // test using floating point numbers, since huge integers could
	+ // potentially wrap around to negative values.
	+ if(nxfnyfnzf>max_regions) {
	+ fprintf(stderr,"voro++: Number of computational blocks exceeds the maximum allowed of %d.\n"
	+ "Either increase the particle length scale, or recompile with an increased\nmaximum.",max_regions);
	+ wl.deallocate();
	+ return VOROPP_MEMORY_ERROR;
	+ }
	+ }
	+
	+ // Check that the output filename is a sensible length
	+ int flen=strlen(argv[i+6]);
	+ if(flen>4096) {
	+ fputs("voro++: Filename too long\n",stderr);
	+ wl.deallocate();
	+ return VOROPP_CMD_LINE_ERROR;
	+ }
	+
	+ // Open files for output
	+ char *buffer=new char[flen+7];
	+ sprintf(buffer,"%s.vol",argv[i+6]);
	+ FILE outfile=safe_fopen(buffer,"w"),gnu_file,povp_file,povv_file;
	+ if(gnuplot_output) {
	+ sprintf(buffer,"%s.gnu",argv[i+6]);
	+ gnu_file=safe_fopen(buffer,"w");
	+ } else gnu_file=NULL;
	+ if(povp_output) {
	+ sprintf(buffer,"%s_p.pov",argv[i+6]);
	+ povp_file=safe_fopen(buffer,"w");
	+ } else povp_file=NULL;
	+ if(povv_output) {
	+ sprintf(buffer,"%s_v.pov",argv[i+6]);
	+ povv_file=safe_fopen(buffer,"w");
	+ } else povv_file=NULL;
	+ delete [] buffer;
	+
	+ const char *c_str=(custom_output==0?(polydisperse?"%i %q %v %r":"%i %q %v"):argv[custom_output]);
	+
	+ // Now switch depending on whether polydispersity was enabled, and
	+ // whether output ordering is requested
	+ double vol=0;int tp=0,vcc=0;
	+ if(polydisperse) {
	+ if(ordered) {
	+ particle_order vo;
	+ container_poly con(ax,bx,ay,by,az,bz,nx,ny,nz,xperiodic,yperiodic,zperiodic,init_mem);
	+ con.add_wall(wl);
	+ if(bm==none) {
	+ pconp->setup(vo,con);delete pconp;
	+ } else con.import(vo,argv[i+6]);
	+
	+ c_loop_order vlo(con,vo);
	+ cmd_line_output(vlo,con,c_str,outfile,gnu_file,povp_file,povv_file,verbose,vol,vcc,tp);
	+ } else {
	+ container_poly con(ax,bx,ay,by,az,bz,nx,ny,nz,xperiodic,yperiodic,zperiodic,init_mem);
	+ con.add_wall(wl);
	+
	+ if(bm==none) {
	+ pconp->setup(con);delete pconp;
	+ } else con.import(argv[i+6]);
	+
	+ c_loop_all vla(con);
	+ cmd_line_output(vla,con,c_str,outfile,gnu_file,povp_file,povv_file,verbose,vol,vcc,tp);
	+ }
	+ } else {
	+ if(ordered) {
	+ particle_order vo;
	+ container con(ax,bx,ay,by,az,bz,nx,ny,nz,xperiodic,yperiodic,zperiodic,init_mem);
	+ con.add_wall(wl);
	+ if(bm==none) {
	+ pcon->setup(vo,con);delete pcon;
	+ } else con.import(vo,argv[i+6]);
	+
	+ c_loop_order vlo(con,vo);
	+ cmd_line_output(vlo,con,c_str,outfile,gnu_file,povp_file,povv_file,verbose,vol,vcc,tp);
	+ } else {
	+ container con(ax,bx,ay,by,az,bz,nx,ny,nz,xperiodic,yperiodic,zperiodic,init_mem);
	+ con.add_wall(wl);
	+ if(bm==none) {
	+ pcon->setup(con);delete pcon;
	+ } else con.import(argv[i+6]);
	+ c_loop_all vla(con);
	+ cmd_line_output(vla,con,c_str,outfile,gnu_file,povp_file,povv_file,verbose,vol,vcc,tp);
	+ }
	+ }
	+
	+ // Print information if verbose output requested
	+ if(verbose) {
	+ printf("Container geometry : [%g:%g] [%g:%g] [%g:%g]\n"
	+ "Computational grid size : %d by %d by %d (%s)\n"
	+ "Filename : %s\n"
	+ "Output string : %s%s\n",ax,bx,ay,by,az,bz,nx,ny,nz,
	+ bm==none?"estimated from file":(bm==length_scale?
	+ "estimated using length scale":"directly specified"),
	+ argv[i+6],c_str,custom_output==0?" (default)":"");
	+ printf("Total imported particles : %d (%.2g per grid block)\n"
	+ "Total V. cells computed : %d\n"
	+ "Total container volume : %g\n"
	+ "Total V. cell volume : %g\n",tp,((double) tp)/(nxnynz),
	+ vcc,(bx-ax)(by-ay)(bz-az),vol);
	+ }
	+
	+ // Close output files
	+ fclose(outfile);
	+ if(gnu_file!=NULL) fclose(gnu_file);
	+ if(povp_file!=NULL) fclose(povp_file);
	+ if(povv_file!=NULL) fclose(povv_file);
	+ return 0;
	+}
	+
	Index: extern/voro++/src/voro++.cc
	===================================================================
	--- extern/voro++/src/voro++.cc (revision 0)
	+++ extern/voro++/src/voro++.cc (revision 0)
	@@ -0,0 +1,19 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file voro++.cc
	+ * \brief A file that loads all of the function implementation files. */
	+
	+#include "cell.cc"
	+#include "common.cc"
	+#include "v_base.cc"
	+#include "container.cc"
	+#include "unitcell.cc"
	+#include "container_prd.cc"
	+#include "pre_container.cc"
	+#include "v_compute.cc"
	+#include "c_loops.cc"
	+#include "wall.cc"
	Index: extern/voro++/src/v_compute.hh
	===================================================================
	--- extern/voro++/src/v_compute.hh (revision 0)
	+++ extern/voro++/src/v_compute.hh (revision 0)
	@@ -0,0 +1,149 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file v_compute.hh
	+ * \brief Header file for the voro_compute template and related classes. */
	+
	+#ifndef VOROPP_V_COMPUTE_HH
	+#define VOROPP_V_COMPUTE_HH
	+
	+#include "config.hh"
	+#include "worklist.hh"
	+#include "cell.hh"
	+
	+namespace voro {
	+
	+/** \brief Structure for holding information about a particle.
	+ *
	+ * This small structure holds information about a single particle, and is used
	+ * by several of the routines in the voro_compute template for passing
	+ * information by reference between functions. */
	+struct particle_record {
	+ /** The index of the block that the particle is within. */
	+ int ijk;
	+ /** The number of particle within its block. */
	+ int l;
	+ /** The x-index of the block. */
	+ int di;
	+ /** The y-index of the block. */
	+ int dj;
	+ /** The z-index of the block. */
	+ int dk;
	+};
	+
	+/** \brief Template for carrying out Voronoi cell computations. */
	+template <class c_class>
	+class voro_compute {
	+ public:
	+ /** A reference to the container class on which to carry out*/
	+ c_class &con;
	+ /** The size of an internal computational block in the x
	+ * direction. */
	+ const double boxx;
	+ /** The size of an internal computational block in the y
	+ * direction. */
	+ const double boxy;
	+ /** The size of an internal computational block in the z
	+ * direction. */
	+ const double boxz;
	+ /** The inverse box length in the x direction, set to
	+ * nx/(bx-ax). */
	+ const double xsp;
	+ /** The inverse box length in the y direction, set to
	+ * ny/(by-ay). */
	+ const double ysp;
	+ /** The inverse box length in the z direction, set to
	+ * nz/(bz-az). */
	+ const double zsp;
	+ /** The number of boxes in the x direction for the searching mask. */
	+ const int hx;
	+ /** The number of boxes in the y direction for the searching mask. */
	+ const int hy;
	+ /** The number of boxes in the z direction for the searching mask. */
	+ const int hz;
	+ /** A constant, set to the value of hx multiplied by hy, which
	+ * is used in the routines which step through mask boxes in
	+ * sequence. */
	+ const int hxy;
	+ /** A constant, set to the value of hxhyhz, which is used in
	+ * the routines which step through mask boxes in sequence. */
	+ const int hxyz;
	+ /** The number of floating point entries to store for each
	+ * particle. */
	+ const int ps;
	+ /** This array holds the numerical IDs of each particle in each
	+ * computational box. */
	+ int **id;
	+ /** A two dimensional array holding particle positions. For the
	+ * derived container_poly class, this also holds particle
	+ * radii. */
	+ double **p;
	+ /** An array holding the number of particles within each
	+ * computational box of the container. */
	+ int *co;
	+ voro_compute(c_class &con_,int hx_,int hy_,int hz_);
	+ /** The class destructor frees the dynamically allocated memory
	+ * for the mask and queue. */
	+ ~voro_compute() {
	+ delete [] qu;
	+ delete [] mask;
	+ }
	+ template<class v_cell>
	+ bool compute_cell(v_cell &c,int ijk,int s,int ci,int cj,int ck);
	+ void find_voronoi_cell(double x,double y,double z,int ci,int cj,int ck,int ijk,particle_record &w,double &mrs);
	+ private:
	+ /** A constant set to boxxboxx+boxyboxy+boxz*boxz, which is
	+ * frequently used in the computation. */
	+ const double bxsq;
	+ /** This sets the current value being used to mark tested blocks
	+ * in the mask. */
	+ unsigned int mv;
	+ /** The current size of the search list. */
	+ int qu_size;
	+ /** A pointer to the array of worklists. */
	+ const unsigned int *wl;
	+ /** An pointer to the array holding the minimum distances
	+ * associated with the worklists. */
	+ double *mrad;
	+ /** This array is used during the cell computation to determine
	+ * which blocks have been considered. */
	+ unsigned int *mask;
	+ /** An array is used to store the queue of blocks to test
	+ * during the Voronoi cell computation. */
	+ int *qu;
	+ /** A pointer to the end of the queue array, used to determine
	+ * when the queue is full. */
	+ int *qu_l;
	+ template<class v_cell>
	+ bool corner_test(v_cell &c,double xl,double yl,double zl,double xh,double yh,double zh);
	+ template<class v_cell>
	+ inline bool edge_x_test(v_cell &c,double x0,double yl,double zl,double x1,double yh,double zh);
	+ template<class v_cell>
	+ inline bool edge_y_test(v_cell &c,double xl,double y0,double zl,double xh,double y1,double zh);
	+ template<class v_cell>
	+ inline bool edge_z_test(v_cell &c,double xl,double yl,double z0,double xh,double yh,double z1);
	+ template<class v_cell>
	+ inline bool face_x_test(v_cell &c,double xl,double y0,double z0,double y1,double z1);
	+ template<class v_cell>
	+ inline bool face_y_test(v_cell &c,double x0,double yl,double z0,double x1,double z1);
	+ template<class v_cell>
	+ inline bool face_z_test(v_cell &c,double x0,double y0,double zl,double x1,double y1);
	+ bool compute_min_max_radius(int di,int dj,int dk,double fx,double fy,double fz,double gx,double gy,double gz,double& crs,double mrs);
	+ bool compute_min_radius(int di,int dj,int dk,double fx,double fy,double fz,double mrs);
	+ inline void add_to_mask(int ei,int ej,int ek,int *&qu_e);
	+ inline void scan_bits_mask_add(unsigned int q,unsigned int mijk,int ei,int ej,int ek,int &qu_e);
	+ inline void scan_all(int ijk,double x,double y,double z,int di,int dj,int dk,particle_record &w,double &mrs);
	+ void add_list_memory(int& qu_s,int& qu_e);
	+ /** Resets the mask in cases where the mask counter wraps
	+ * around. */
	+ inline void reset_mask() {
	+ for(unsigned int mp(mask);mp<mask+hxyz;mp++) mp=0;
	+ }
	+};
	+
	+}
	+
	+#endif
	Index: extern/voro++/src/unitcell.cc
	===================================================================
	--- extern/voro++/src/unitcell.cc (revision 0)
	+++ extern/voro++/src/unitcell.cc (revision 0)
	@@ -0,0 +1,231 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file unitcell.cc
	+ * \brief Function implementations for the unitcell class. */
	+
	+#include <cmath>
	+#include <queue>
	+
	+#include "unitcell.hh"
	+#include "cell.hh"
	+
	+namespace voro {
	+
	+/** Initializes the unit cell class for a particular non-orthogonal periodic
	+ * geometry, corresponding to a parallelepiped with sides given by three
	+ * vectors. The class constructs the unit Voronoi cell corresponding to this
	+ * geometry.
	+ * \param[in] (bx_) The x coordinate of the first unit vector.
	+ * \param[in] (bxy_,by_) The x and y coordinates of the second unit vector.
	+ * \param[in] (bxz_,byz_,bz_) The x, y, and z coordinates of the third unit
	+ * vector. */
	+unitcell::unitcell(double bx_,double bxy_,double by_,double bxz_,double byz_,double bz_)
	+ : bx(bx_), bxy(bxy_), by(by_), bxz(bxz_), byz(byz_), bz(bz_) {
	+ int i,j,l=1;
	+
	+ // Initialize the Voronoi cell to be a very large rectangular box
	+ const double ucx=max_unit_voro_shellsbx,ucy=max_unit_voro_shellsby,ucz=max_unit_voro_shells*bz;
	+ unit_voro.init(-ucx,ucx,-ucy,ucy,-ucz,ucz);
	+
	+ // Repeatedly cut the cell by shells of periodic image particles
	+ while(l<2*max_unit_voro_shells) {
	+
	+ // Check to see if any of the planes from the current shell
	+ // will cut the cell
	+ if(unit_voro_intersect(l)) {
	+
	+ // If they do, apply the plane cuts from the current
	+ // shell
	+ unit_voro_apply(l,0,0);
	+ for(i=1;i<l;i++) {
	+ unit_voro_apply(l,i,0);
	+ unit_voro_apply(-l,i,0);
	+ }
	+ for(i=-l;i<=l;i++) unit_voro_apply(i,l,0);
	+ for(i=1;i<l;i++) for(j=-l+1;j<=l;j++) {
	+ unit_voro_apply(l,j,i);
	+ unit_voro_apply(-j,l,i);
	+ unit_voro_apply(-l,-j,i);
	+ unit_voro_apply(j,-l,i);
	+ }
	+ for(i=-l;i<=l;i++) for(j=-l;j<=l;j++) unit_voro_apply(i,j,l);
	+ } else {
	+
	+ // Calculate a bound on the maximum y and z coordinates
	+ // that could possibly cut the cell. This is based upon
	+ // a geometric result that particles with z>l can't cut
	+ // a cell lying within the paraboloid
	+ // z<=(ll-xx-yy)/(2l). It is always a tighter bound
	+ // than the one based on computing the maximum radius
	+ // of a Voronoi cell vertex.
	+ max_uv_y=max_uv_z=0;
	+ double y,z,q,pts=unit_voro.pts,pp=pts;
	+ while(pp<pts+3*unit_voro.p) {
	+ q=(pp++);y=(pp++);z=(pp++);q=sqrt(qq+yy+zz);
	+ if(y+q>max_uv_y) max_uv_y=y+q;
	+ if(z+q>max_uv_z) max_uv_z=z+q;
	+ }
	+ max_uv_z*=0.5;
	+ max_uv_y*=0.5;
	+ return;
	+ }
	+ l++;
	+ }
	+
	+ // If the routine makes it here, then the unit cell still hasn't been
	+ // completely bounded by the plane cuts. Give the memory error code,
	+ // because this is mainly a case of hitting a safe limit, than any
	+ // inherent problem.
	+ voro_fatal_error("Periodic cell computation failed",VOROPP_MEMORY_ERROR);
	+}
	+
	+/** Applies a pair of opposing plane cuts from a periodic image point
	+ * to the unit Voronoi cell.
	+ * \param[in] (i,j,k) the index of the periodic image to consider. */
	+inline void unitcell::unit_voro_apply(int i,int j,int k) {
	+ double x=ibx+jbxy+kbxz,y=jby+kbyz,z=kbz;
	+ unit_voro.plane(x,y,z);
	+ unit_voro.plane(-x,-y,-z);
	+}
	+
	+/** Calculates whether the unit Voronoi cell intersects a given periodic image
	+ * of the domain.
	+ * \param[in] (dx,dy,dz) the displacement of the periodic image.
	+ * \param[out] vol the proportion of the unit cell volume within this image,
	+ * only computed in the case that the two intersect.
	+ * \return True if they intersect, false otherwise. */
	+bool unitcell::intersects_image(double dx,double dy,double dz,double &vol) {
	+ const double bxinv=1/bx,byinv=1/by,bzinv=1/bz,ivol=bxinvbyinvbzinv;
	+ voronoicell c;
	+ c=unit_voro;
	+ dx=2;dy=2;dz*=2;
	+ if(!c.plane(0,0,bzinv,dz+1)) return false;
	+ if(!c.plane(0,0,-bzinv,-dz+1)) return false;
	+ if(!c.plane(0,byinv,-byzbyinvbzinv,dy+1)) return false;
	+ if(!c.plane(0,-byinv,byzbyinvbzinv,-dy+1)) return false;
	+ if(!c.plane(bxinv,-bxybxinvbyinv,(bxybyz-bybxz)*ivol,dx+1)) return false;
	+ if(!c.plane(-bxinv,bxybxinvbyinv,(-bxybyz+bybxz)*ivol,-dx+1)) return false;
	+ vol=c.volume()*ivol;
	+ return true;
	+}
	+
	+/** Computes a list of periodic domain images that intersect the unit Voronoi cell.
	+ * \param[out] vi a vector containing triplets (i,j,k) corresponding to domain
	+ * images that intersect the unit Voronoi cell, when it is
	+ * centered in the middle of the primary domain.
	+ * \param[out] vd a vector containing the fraction of the Voronoi cell volume
	+ * within each corresponding image listed in vi. */
	+void unitcell::images(std::vector<int> &vi,std::vector<double> &vd) {
	+ const int ms2=max_unit_voro_shells2+1,mss=ms2ms2*ms2;
	+ bool a=new bool[mss],ac=a+max_unit_voro_shells(1+ms2(1+ms2)),*ap=a;
	+ int i,j,k;
	+ double vol;
	+
	+ // Initialize mask
	+ while(ap<ac) *(ap++)=true;
	+ *(ap++)=false;
	+ while(ap<a+mss) *(ap++)=true;
	+
	+ // Set up the queue and add (0,0,0) image to it
	+ std::queue<int> q;
	+ q.push(0);q.push(0);q.push(0);
	+
	+ while(!q.empty()) {
	+
	+ // Read the next entry on the queue
	+ i=q.front();q.pop();
	+ j=q.front();q.pop();
	+ k=q.front();q.pop();
	+
	+ // Check intersection of this image
	+ if(intersects_image(i,j,k,vol)) {
	+
	+ // Add this entry to the output vectors
	+ vi.push_back(i);
	+ vi.push_back(j);
	+ vi.push_back(k);
	+ vd.push_back(vol);
	+
	+ // Add neighbors to the queue if they have not been
	+ // tested
	+ ap=ac+i+ms2(j+ms2k);
	+ if(k>-max_unit_voro_shells&&(ap-ms2ms2)) {q.push(i);q.push(j);q.push(k-1);(ap-ms2ms2)=false;}
	+ if(j>-max_unit_voro_shells&&(ap-ms2)) {q.push(i);q.push(j-1);q.push(k);(ap-ms2)=false;}
	+ if(i>-max_unit_voro_shells&&(ap-1)) {q.push(i-1);q.push(j);q.push(k);(ap-1)=false;}
	+ if(i<max_unit_voro_shells&&(ap+1)) {q.push(i+1);q.push(j);q.push(k);(ap+1)=false;}
	+ if(j<max_unit_voro_shells&&(ap+ms2)) {q.push(i);q.push(j+1);q.push(k);(ap+ms2)=false;}
	+ if(k<max_unit_voro_shells&&(ap+ms2ms2)) {q.push(i);q.push(j);q.push(k+1);(ap+ms2ms2)=false;}
	+ }
	+ }
	+
	+ // Remove mask memory
	+ delete [] a;
	+}
	+
	+/** Tests to see if a shell of periodic images could possibly cut the periodic
	+ * unit cell.
	+ * \param[in] l the index of the shell to consider.
	+ * \return True if a point in the shell cuts the cell, false otherwise. */
	+bool unitcell::unit_voro_intersect(int l) {
	+ int i,j;
	+ if(unit_voro_test(l,0,0)) return true;
	+ for(i=1;i<l;i++) {
	+ if(unit_voro_test(l,i,0)) return true;
	+ if(unit_voro_test(-l,i,0)) return true;
	+ }
	+ for(i=-l;i<=l;i++) if(unit_voro_test(i,l,0)) return true;
	+ for(i=1;i<l;i++) for(j=-l+1;j<=l;j++) {
	+ if(unit_voro_test(l,j,i)) return true;
	+ if(unit_voro_test(-j,l,i)) return true;
	+ if(unit_voro_test(-l,-j,i)) return true;
	+ if(unit_voro_test(j,-l,i)) return true;
	+ }
	+ for(i=-l;i<=l;i++) for(j=-l;j<=l;j++) if(unit_voro_test(i,j,l)) return true;
	+ return false;
	+}
	+
	+/** Tests to see if a plane cut from a particular periodic image will cut th
	+ * unit Voronoi cell.
	+ * \param[in] (i,j,k) the index of the periodic image to consider.
	+ * \return True if the image cuts the cell, false otherwise. */
	+inline bool unitcell::unit_voro_test(int i,int j,int k) {
	+ double x=ibx+jbxy+kbxz,y=jby+kbyz,z=kbz;
	+ double rsq=xx+yy+z*z;
	+ return unit_voro.plane_intersects(x,y,z,rsq);
	+}
	+
	+/** Draws the periodic domain in gnuplot format.
	+ * \param[in] fp the file handle to write to. */
	+void unitcell::draw_domain_gnuplot(FILE *fp) {
	+ fprintf(fp,"0 0 0\n%g 0 0\n%g %g 0\n%g %g 0\n",bx,bx+bxy,by,bxy,by);
	+ fprintf(fp,"%g %g %g\n%g %g %g\n%g %g %g\n%g %g %g\n",bxy+bxz,by+byz,bz,bx+bxy+bxz,by+byz,bz,bx+bxz,byz,bz,bxz,byz,bz);
	+ fprintf(fp,"0 0 0\n%g %g 0\n\n%g %g %g\n%g %g %g\n\n",bxy,by,bxz,byz,bz,bxy+bxz,by+byz,bz);
	+ fprintf(fp,"%g 0 0\n%g %g %g\n\n%g %g 0\n%g %g %g\n\n",bx,bx+bxz,byz,bz,bx+bxy,by,bx+bxy+bxz,by+byz,bz);
	+}
	+
	+/** Draws the periodic domain in POV-Ray format.
	+ * \param[in] fp the file handle to write to. */
	+void unitcell::draw_domain_pov(FILE *fp) {
	+ fprintf(fp,"cylinder{0,0,0>,<%g,0,0>,rr}\n"
	+ "cylinder{<%g,%g,0>,<%g,%g,0>,rr}\n",bx,bxy,by,bx+bxy,by);
	+ fprintf(fp,"cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n"
	+ "cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n",bxz,byz,bz,bx+bxz,byz,bz,bxy+bxz,by+byz,bz,bx+bxy+bxz,by+byz,bz);
	+ fprintf(fp,"cylinder{<0,0,0>,<%g,%g,0>,rr}\n"
	+ "cylinder{<%g,0,0>,<%g,%g,0>,rr}\n",bxy,by,bx,bx+bxy,by);
	+ fprintf(fp,"cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n"
	+ "cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n",bxz,byz,bz,bxy+bxz,by+byz,bz,bx+bxz,byz,bz,bx+bxy+bxz,by+byz,bz);
	+ fprintf(fp,"cylinder{<0,0,0>,<%g,%g,%g>,rr}\n"
	+ "cylinder{<%g,0,0>,<%g,%g,%g>,rr}\n",bxz,byz,bz,bx,bx+bxz,byz,bz);
	+ fprintf(fp,"cylinder{<%g,%g,0>,<%g,%g,%g>,rr}\n"
	+ "cylinder{<%g,%g,0>,<%g,%g,%g>,rr}\n",bxy,by,bxy+bxz,by+byz,bz,bx+bxy,by,bx+bxy+bxz,by+byz,bz);
	+ fprintf(fp,"sphere{<0,0,0>,rr}\nsphere{<%g,0,0>,rr}\n"
	+ "sphere{<%g,%g,0>,rr}\nsphere{<%g,%g,0>,rr}\n",bx,bxy,by,bx+bxy,by);
	+ fprintf(fp,"sphere{<%g,%g,%g>,rr}\nsphere{<%g,%g,%g>,rr}\n"
	+ "sphere{<%g,%g,%g>,rr}\nsphere{<%g,%g,%g>,rr}\n",bxz,byz,bz,bx+bxz,byz,bz,bxy+bxz,by+byz,bz,bx+bxy+bxz,by+byz,bz);
	+}
	+
	+}
	Index: extern/voro++/src/cell.cc
	===================================================================
	--- extern/voro++/src/cell.cc (revision 0)
	+++ extern/voro++/src/cell.cc (revision 0)
	@@ -0,0 +1,2252 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file cell.cc
	+ * \brief Function implementations for the voronoicell and related classes. */
	+
	+#include <cmath>
	+#include <cstring>
	+
	+#include "config.hh"
	+#include "common.hh"
	+#include "cell.hh"
	+
	+namespace voro {
	+
	+/** Constructs a Voronoi cell and sets up the initial memory. */
	+voronoicell_base::voronoicell_base() :
	+ current_vertices(init_vertices), current_vertex_order(init_vertex_order),
	+ current_delete_size(init_delete_size), current_delete2_size(init_delete2_size),
	+ ed(new int*[current_vertices]), nu(new int[current_vertices]),
	+ pts(new double[3*current_vertices]), mem(new int[current_vertex_order]),
	+ mec(new int[current_vertex_order]), mep(new int*[current_vertex_order]),
	+ ds(new int[current_delete_size]), stacke(ds+current_delete_size),
	+ ds2(new int[current_delete2_size]), stacke2(ds2+current_delete_size),
	+ current_marginal(init_marginal), marg(new int[current_marginal]) {
	+ int i;
	+ for(i=0;i<3;i++) {
	+ mem[i]=init_n_vertices;mec[i]=0;
	+ mep[i]=new int[init_n_vertices*((i<<1)+1)];
	+ }
	+ mem[3]=init_3_vertices;mec[3]=0;
	+ mep[3]=new int[init_3_vertices*7];
	+ for(i=4;i<current_vertex_order;i++) {
	+ mem[i]=init_n_vertices;mec[i]=0;
	+ mep[i]=new int[init_n_vertices*((i<<1)+1)];
	+ }
	+}
	+
	+/** The voronoicell destructor deallocates all the dynamic memory. */
	+voronoicell_base::~voronoicell_base() {
	+ for(int i=current_vertex_order-1;i>=0;i--) if(mem[i]>0) delete [] mep[i];
	+ delete [] marg;
	+ delete [] ds2;delete [] ds;
	+ delete [] mep;delete [] mec;
	+ delete [] mem;delete [] pts;
	+ delete [] nu;delete [] ed;
	+}
	+
	+/** Ensures that enough memory is allocated prior to carrying out a copy.
	+ * \param[in] vc a reference to the specialized version of the calling class.
	+ * \param[in] vb a pointered to the class to be copied. */
	+template<class vc_class>
	+void voronoicell_base::check_memory_for_copy(vc_class &vc,voronoicell_base* vb) {
	+ while(current_vertex_order<vb->current_vertex_order) add_memory_vorder(vc);
	+ for(int i=0;i<current_vertex_order;i++) while(mem[i]<vb->mec[i]) add_memory(vc,i,ds2);
	+ while(current_vertices<vb->p) add_memory_vertices(vc);
	+}
	+
	+/** Copies the vertex and edge information from another class. The routine
	+ * assumes that enough memory is available for the copy.
	+ * \param[in] vb a pointer to the class to copy. */
	+void voronoicell_base::copy(voronoicell_base* vb) {
	+ int i,j;
	+ p=vb->p;up=0;
	+ for(i=0;i<current_vertex_order;i++) {
	+ mec[i]=vb->mec[i];
	+ for(j=0;j<mec[i](2i+1);j++) mep[i][j]=vb->mep[i][j];
	+ for(j=0;j<mec[i](2i+1);j+=2i+1) ed[mep[i][j+2i]]=mep[i]+j;
	+ }
	+ for(i=0;i<p;i++) nu[i]=vb->nu[i];
	+ for(i=0;i<3*p;i++) pts[i]=vb->pts[i];
	+}
	+
	+/** Copies the information from another voronoicell class into this
	+ * class, extending memory allocation if necessary.
	+ * \param[in] c the class to copy. */
	+void voronoicell_neighbor::operator=(voronoicell &c) {
	+ voronoicell_base vb=((voronoicell_base) &c);
	+ check_memory_for_copy(*this,vb);copy(vb);
	+ int i,j;
	+ for(i=0;i<c.current_vertex_order;i++) {
	+ for(j=0;j<c.mec[i]*i;j++) mne[i][j]=0;
	+ for(j=0;j<c.mec[i];j++) ne[c.mep[i][(2i+1)j+2i]]=mne[i]+(ji);
	+ }
	+}
	+
	+/** Copies the information from another voronoicell_neighbor class into this
	+ * class, extending memory allocation if necessary.
	+ * \param[in] c the class to copy. */
	+void voronoicell_neighbor::operator=(voronoicell_neighbor &c) {
	+ voronoicell_base vb=((voronoicell_base) &c);
	+ check_memory_for_copy(*this,vb);copy(vb);
	+ int i,j;
	+ for(i=0;i<c.current_vertex_order;i++) {
	+ for(j=0;j<c.mec[i]*i;j++) mne[i][j]=c.mne[i][j];
	+ for(j=0;j<c.mec[i];j++) ne[c.mep[i][(2i+1)j+2i]]=mne[i]+(ji);
	+ }
	+}
	+
	+/** Translates the vertices of the Voronoi cell by a given vector.
	+ * \param[in] (x,y,z) the coordinates of the vector. */
	+void voronoicell_base::translate(double x,double y,double z) {
	+ x=2;y=2;z*=2;
	+ double *ptsp=pts;
	+ while(ptsp<pts+3*p) {
	+ (ptsp++)=x;(ptsp++)=y;*(ptsp++)=z;
	+ }
	+}
	+
	+/** Increases the memory storage for a particular vertex order, by increasing
	+ * the size of the of the corresponding mep array. If the arrays already exist,
	+ * their size is doubled; if they don't exist, then new ones of size
	+ * init_n_vertices are allocated. The routine also ensures that the pointers in
	+ * the ed array are updated, by making use of the back pointers. For the cases
	+ * where the back pointer has been temporarily overwritten in the marginal
	+ * vertex code, the auxiliary delete stack is scanned to find out how to update
	+ * the ed value. If the template has been instantiated with the neighbor
	+ * tracking turned on, then the routine also reallocates the corresponding mne
	+ * array.
	+ * \param[in] i the order of the vertex memory to be increased. */
	+template<class vc_class>
	+void voronoicell_base::add_memory(vc_class &vc,int i,int *stackp2) {
	+ int s=(i<<1)+1;
	+ if(mem[i]==0) {
	+ vc.n_allocate(i,init_n_vertices);
	+ mep[i]=new int[init_n_vertices*s];
	+ mem[i]=init_n_vertices;
	+#if VOROPP_VERBOSE >=2
	+ fprintf(stderr,"Order %d vertex memory created\n",i);
	+#endif
	+ } else {
	+ int j=0,k,*l;
	+ mem[i]<<=1;
	+ if(mem[i]>max_n_vertices) voro_fatal_error("Point memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
	+#if VOROPP_VERBOSE >=2
	+ fprintf(stderr,"Order %d vertex memory scaled up to %d\n",i,mem[i]);
	+#endif
	+ l=new int[s*mem[i]];
	+ int m=0;
	+ vc.n_allocate_aux1(i);
	+ while(j<s*mec[i]) {
	+ k=mep[i][j+(i<<1)];
	+ if(k>=0) {
	+ ed[k]=l+j;
	+ vc.n_set_to_aux1_offset(k,m);
	+ } else {
	+ int *dsp;
	+ for(dsp=ds2;dsp<stackp2;dsp++) {
	+ if(ed[*dsp]==mep[i]+j) {
	+ ed[*dsp]=l+j;
	+ vc.n_set_to_aux1_offset(*dsp,m);
	+ break;
	+ }
	+ }
	+ if(dsp==stackp2) voro_fatal_error("Couldn't relocate dangling pointer",VOROPP_INTERNAL_ERROR);
	+#if VOROPP_VERBOSE >=3
	+ fputs("Relocated dangling pointer",stderr);
	+#endif
	+ }
	+ for(k=0;k<s;k++,j++) l[j]=mep[i][j];
	+ for(k=0;k<i;k++,m++) vc.n_copy_to_aux1(i,m);
	+ }
	+ delete [] mep[i];
	+ mep[i]=l;
	+ vc.n_switch_to_aux1(i);
	+ }
	+}
	+
	+/** Doubles the maximum number of vertices allowed, by reallocating the ed, nu,
	+ * and pts arrays. If the allocation exceeds the absolute maximum set in
	+ * max_vertices, then the routine exits with a fatal error. If the template has
	+ * been instantiated with the neighbor tracking turned on, then the routine
	+ * also reallocates the ne array. */
	+template<class vc_class>
	+void voronoicell_base::add_memory_vertices(vc_class &vc) {
	+ int i=(current_vertices<<1),j,*pp,pnu;
	+ if(i>max_vertices) voro_fatal_error("Vertex memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
	+#if VOROPP_VERBOSE >=2
	+ fprintf(stderr,"Vertex memory scaled up to %d\n",i);
	+#endif
	+ double *ppts;
	+ pp=new int*[i];
	+ for(j=0;j<current_vertices;j++) pp[j]=ed[j];
	+ delete [] ed;ed=pp;
	+ vc.n_add_memory_vertices(i);
	+ pnu=new int[i];
	+ for(j=0;j<current_vertices;j++) pnu[j]=nu[j];
	+ delete [] nu;nu=pnu;
	+ ppts=new double[3*i];
	+ for(j=0;j<3*current_vertices;j++) ppts[j]=pts[j];
	+ delete [] pts;pts=ppts;
	+ current_vertices=i;
	+}
	+
	+/** Doubles the maximum allowed vertex order, by reallocating mem, mep, and mec
	+ * arrays. If the allocation exceeds the absolute maximum set in
	+ * max_vertex_order, then the routine causes a fatal error. If the template has
	+ * been instantiated with the neighbor tracking turned on, then the routine
	+ * also reallocates the mne array. */
	+template<class vc_class>
	+void voronoicell_base::add_memory_vorder(vc_class &vc) {
	+ int i=(current_vertex_order<<1),j,p1,*p2;
	+ if(i>max_vertex_order) voro_fatal_error("Vertex order memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
	+#if VOROPP_VERBOSE >=2
	+ fprintf(stderr,"Vertex order memory scaled up to %d\n",i);
	+#endif
	+ p1=new int[i];
	+ for(j=0;j<current_vertex_order;j++) p1[j]=mem[j];while(j<i) p1[j++]=0;
	+ delete [] mem;mem=p1;
	+ p2=new int*[i];
	+ for(j=0;j<current_vertex_order;j++) p2[j]=mep[j];
	+ delete [] mep;mep=p2;
	+ p1=new int[i];
	+ for(j=0;j<current_vertex_order;j++) p1[j]=mec[j];while(j<i) p1[j++]=0;
	+ delete [] mec;mec=p1;
	+ vc.n_add_memory_vorder(i);
	+ current_vertex_order=i;
	+}
	+
	+/** Doubles the size allocation of the main delete stack. If the allocation
	+ * exceeds the absolute maximum set in max_delete_size, then routine causes a
	+ * fatal error. */
	+void voronoicell_base::add_memory_ds(int *&stackp) {
	+ current_delete_size<<=1;
	+ if(current_delete_size>max_delete_size) voro_fatal_error("Delete stack 1 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
	+#if VOROPP_VERBOSE >=2
	+ fprintf(stderr,"Delete stack 1 memory scaled up to %d\n",current_delete_size);
	+#endif
	+ int dsn=new int[current_delete_size],dsnp=dsn,*dsp=ds;
	+ while(dsp<stackp) (dsnp++)=(dsp++);
	+ delete [] ds;ds=dsn;stackp=dsnp;
	+ stacke=ds+current_delete_size;
	+}
	+
	+/** Doubles the size allocation of the auxiliary delete stack. If the
	+ * allocation exceeds the absolute maximum set in max_delete2_size, then the
	+ * routine causes a fatal error. */
	+void voronoicell_base::add_memory_ds2(int *&stackp2) {
	+ current_delete2_size<<=1;
	+ if(current_delete2_size>max_delete2_size) voro_fatal_error("Delete stack 2 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
	+#if VOROPP_VERBOSE >=2
	+ fprintf(stderr,"Delete stack 2 memory scaled up to %d\n",current_delete2_size);
	+#endif
	+ int dsn=new int[current_delete2_size],dsnp=dsn,*dsp=ds2;
	+ while(dsp<stackp2) (dsnp++)=(dsp++);
	+ delete [] ds2;ds2=dsn;stackp2=dsnp;
	+ stacke2=ds2+current_delete2_size;
	+}
	+
	+/** Initializes a Voronoi cell as a rectangular box with the given dimensions.
	+ * \param[in] (xmin,xmax) the minimum and maximum x coordinates.
	+ * \param[in] (ymin,ymax) the minimum and maximum y coordinates.
	+ * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */
	+void voronoicell_base::init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) {
	+ for(int i=0;i<current_vertex_order;i++) mec[i]=0;up=0;
	+ mec[3]=p=8;xmin=2;xmax=2;ymin=2;ymax=2;zmin=2;zmax=2;
	+ *pts=xmin;pts[1]=ymin;pts[2]=zmin;
	+ pts[3]=xmax;pts[4]=ymin;pts[5]=zmin;
	+ pts[6]=xmin;pts[7]=ymax;pts[8]=zmin;
	+ pts[9]=xmax;pts[10]=ymax;pts[11]=zmin;
	+ pts[12]=xmin;pts[13]=ymin;pts[14]=zmax;
	+ pts[15]=xmax;pts[16]=ymin;pts[17]=zmax;
	+ pts[18]=xmin;pts[19]=ymax;pts[20]=zmax;
	+ pts[21]=xmax;pts[22]=ymax;pts[23]=zmax;
	+ int *q=mep[3];
	+ *q=1;q[1]=4;q[2]=2;q[3]=2;q[4]=1;q[5]=0;q[6]=0;
	+ q[7]=3;q[8]=5;q[9]=0;q[10]=2;q[11]=1;q[12]=0;q[13]=1;
	+ q[14]=0;q[15]=6;q[16]=3;q[17]=2;q[18]=1;q[19]=0;q[20]=2;
	+ q[21]=2;q[22]=7;q[23]=1;q[24]=2;q[25]=1;q[26]=0;q[27]=3;
	+ q[28]=6;q[29]=0;q[30]=5;q[31]=2;q[32]=1;q[33]=0;q[34]=4;
	+ q[35]=4;q[36]=1;q[37]=7;q[38]=2;q[39]=1;q[40]=0;q[41]=5;
	+ q[42]=7;q[43]=2;q[44]=4;q[45]=2;q[46]=1;q[47]=0;q[48]=6;
	+ q[49]=5;q[50]=3;q[51]=6;q[52]=2;q[53]=1;q[54]=0;q[55]=7;
	+ *ed=q;ed[1]=q+7;ed[2]=q+14;ed[3]=q+21;
	+ ed[4]=q+28;ed[5]=q+35;ed[6]=q+42;ed[7]=q+49;
	+ *nu=nu[1]=nu[2]=nu[3]=nu[4]=nu[5]=nu[6]=nu[7]=3;
	+}
	+
	+/** Initializes a Voronoi cell as a regular octahedron.
	+ * \param[in] l The distance from the octahedron center to a vertex. Six
	+ * vertices are initialized at (-l,0,0), (l,0,0), (0,-l,0),
	+ * (0,l,0), (0,0,-l), and (0,0,l). */
	+void voronoicell_base::init_octahedron_base(double l) {
	+ for(int i=0;i<current_vertex_order;i++) mec[i]=0;up=0;
	+ mec[4]=p=6;l*=2;
	+ *pts=-l;pts[1]=0;pts[2]=0;
	+ pts[3]=l;pts[4]=0;pts[5]=0;
	+ pts[6]=0;pts[7]=-l;pts[8]=0;
	+ pts[9]=0;pts[10]=l;pts[11]=0;
	+ pts[12]=0;pts[13]=0;pts[14]=-l;
	+ pts[15]=0;pts[16]=0;pts[17]=l;
	+ int *q=mep[4];
	+ *q=2;q[1]=5;q[2]=3;q[3]=4;q[4]=0;q[5]=0;q[6]=0;q[7]=0;q[8]=0;
	+ q[9]=2;q[10]=4;q[11]=3;q[12]=5;q[13]=2;q[14]=2;q[15]=2;q[16]=2;q[17]=1;
	+ q[18]=0;q[19]=4;q[20]=1;q[21]=5;q[22]=0;q[23]=3;q[24]=0;q[25]=1;q[26]=2;
	+ q[27]=0;q[28]=5;q[29]=1;q[30]=4;q[31]=2;q[32]=3;q[33]=2;q[34]=1;q[35]=3;
	+ q[36]=0;q[37]=3;q[38]=1;q[39]=2;q[40]=3;q[41]=3;q[42]=1;q[43]=1;q[44]=4;
	+ q[45]=0;q[46]=2;q[47]=1;q[48]=3;q[49]=1;q[50]=3;q[51]=3;q[52]=1;q[53]=5;
	+ *ed=q;ed[1]=q+9;ed[2]=q+18;ed[3]=q+27;ed[4]=q+36;ed[5]=q+45;
	+ *nu=nu[1]=nu[2]=nu[3]=nu[4]=nu[5]=4;
	+}
	+
	+/** Initializes a Voronoi cell as a tetrahedron. It assumes that the normal to
	+ * the face for the first three vertices points inside.
	+ * \param (x0,y0,z0) a position vector for the first vertex.
	+ * \param (x1,y1,z1) a position vector for the second vertex.
	+ * \param (x2,y2,z2) a position vector for the third vertex.
	+ * \param (x3,y3,z3) a position vector for the fourth vertex. */
	+void voronoicell_base::init_tetrahedron_base(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3) {
	+ for(int i=0;i<current_vertex_order;i++) mec[i]=0;up=0;
	+ mec[3]=p=4;
	+ pts=x02;pts[1]=y02;pts[2]=z02;
	+ pts[3]=x12;pts[4]=y12;pts[5]=z1*2;
	+ pts[6]=x22;pts[7]=y22;pts[8]=z2*2;
	+ pts[9]=x32;pts[10]=y32;pts[11]=z3*2;
	+ int *q=mep[3];
	+ *q=1;q[1]=3;q[2]=2;q[3]=0;q[4]=0;q[5]=0;q[6]=0;
	+ q[7]=0;q[8]=2;q[9]=3;q[10]=0;q[11]=2;q[12]=1;q[13]=1;
	+ q[14]=0;q[15]=3;q[16]=1;q[17]=2;q[18]=2;q[19]=1;q[20]=2;
	+ q[21]=0;q[22]=1;q[23]=2;q[24]=1;q[25]=2;q[26]=1;q[27]=3;
	+ *ed=q;ed[1]=q+7;ed[2]=q+14;ed[3]=q+21;
	+ *nu=nu[1]=nu[2]=nu[3]=3;
	+}
	+
	+/** Checks that the relational table of the Voronoi cell is accurate, and
	+ * prints out any errors. This algorithm is O(p), so running it every time the
	+ * plane routine is called will result in a significant slowdown. */
	+void voronoicell_base::check_relations() {
	+ int i,j;
	+ for(i=0;i<p;i++) for(j=0;j<nu[i];j++) if(ed[ed[i][j]][ed[i][nu[i]+j]]!=i)
	+ printf("Relational error at point %d, edge %d.\n",i,j);
	+}
	+
	+/** This routine checks for any two vertices that are connected by more than
	+ * one edge. The plane algorithm is designed so that this should not happen, so
	+ * any occurrences are most likely errors. Note that the routine is O(p), so
	+ * running it every time the plane routine is called will result in a
	+ * significant slowdown. */
	+void voronoicell_base::check_duplicates() {
	+ int i,j,k;
	+ for(i=0;i<p;i++) for(j=1;j<nu[i];j++) for(k=0;k<j;k++) if(ed[i][j]==ed[i][k])
	+ printf("Duplicate edges: (%d,%d) and (%d,%d) [%d]\n",i,j,i,k,ed[i][j]);
	+}
	+
	+/** Constructs the relational table if the edges have been specified. */
	+void voronoicell_base::construct_relations() {
	+ int i,j,k,l;
	+ for(i=0;i<p;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ l=0;
	+ while(ed[k][l]!=i) {
	+ l++;
	+ if(l==nu[k]) voro_fatal_error("Relation table construction failed",VOROPP_INTERNAL_ERROR);
	+ }
	+ ed[i][nu[i]+j]=l;
	+ }
	+}
	+
	+/** Starting from a point within the current cutting plane, this routine attempts
	+ * to find an edge to a point outside the cutting plane. This prevents the plane
	+ * routine from .
	+ * \param[in] vc a reference to the specialized version of the calling class.
	+ * \param[in,out] up */
	+template<class vc_class>
	+inline bool voronoicell_base::search_for_outside_edge(vc_class &vc,int &up) {
	+ int i,lp,lw,j(ds2),stackp2(ds2);
	+ double l;
	+ *(stackp2++)=up;
	+ while(j<stackp2) {
	+ up=*(j++);
	+ for(i=0;i<nu[up];i++) {
	+ lp=ed[up][i];
	+ lw=m_test(lp,l);
	+ if(lw==-1) return true;
	+ else if(lw==0) add_to_stack(vc,lp,stackp2);
	+ }
	+ }
	+ return false;
	+}
	+
	+/** Adds a point to the auxiliary delete stack if it is not already there.
	+ * \param[in] vc a reference to the specialized version of the calling class.
	+ * \param[in] lp the index of the point to add.
	+ * \param[in,out] stackp2 a pointer to the end of the stack entries. */
	+template<class vc_class>
	+inline void voronoicell_base::add_to_stack(vc_class &vc,int lp,int *&stackp2) {
	+ for(int k(ds2);k<stackp2;k++) if(k==lp) return;
	+ if(stackp2==stacke2) add_memory_ds2(stackp2);
	+ *(stackp2++)=lp;
	+}
	+
	+/** Cuts the Voronoi cell by a particle whose center is at a separation of
	+ * (x,y,z) from the cell center. The value of rsq should be initially set to
	+ * \f$x^2+y^2+z^2\f$.
	+ * \param[in] vc a reference to the specialized version of the calling class.
	+ * \param[in] (x,y,z) the normal vector to the plane.
	+ * \param[in] rsq the distance along this vector of the plane.
	+ * \param[in] p_id the plane ID (for neighbor tracking only).
	+ * \return False if the plane cut deleted the cell entirely, true otherwise. */
	+template<class vc_class>
	+bool voronoicell_base::nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id) {
	+ int count=0,i,j,k,lp=up,cp,qp,rp,stackp(ds),stackp2(ds2),*dsp;
	+ int us=0,ls=0,qs,iqs,cs,uw,qw,lw;
	+ int edp,edd;
	+ double u,l,r,q;bool complicated_setup=false,new_double_edge=false,double_edge=false;
	+
	+ // Initialize the safe testing routine
	+ n_marg=0;px=x;py=y;pz=z;prsq=rsq;
	+
	+ // Test approximately sqrt(n)/4 points for their proximity to the plane
	+ // and keep the one which is closest
	+ uw=m_test(up,u);
	+
	+ // Starting from an initial guess, we now move from vertex to vertex,
	+ // to try and find an edge which intersects the cutting plane,
	+ // or a vertex which is on the plane
	+ try {
	+ if(uw==1) {
	+
	+ // The test point is inside the cutting plane.
	+ us=0;
	+ do {
	+ lp=ed[up][us];
	+ lw=m_test(lp,l);
	+ if(l<u) break;
	+ us++;
	+ } while (us<nu[up]);
	+
	+ if(us==nu[up]) {
	+ return false;
	+ }
	+
	+ ls=ed[up][nu[up]+us];
	+ while(lw==1) {
	+ if(++count>=p) throw true;
	+ u=l;up=lp;
	+ for(us=0;us<ls;us++) {
	+ lp=ed[up][us];
	+ lw=m_test(lp,l);
	+ if(l<u) break;
	+ }
	+ if(us==ls) {
	+ us++;
	+ while(us<nu[up]) {
	+ lp=ed[up][us];
	+ lw=m_test(lp,l);
	+ if(l<u) break;
	+ us++;
	+ }
	+ if(us==nu[up]) {
	+ return false;
	+ }
	+ }
	+ ls=ed[up][nu[up]+us];
	+ }
	+
	+ // If the last point in the iteration is within the
	+ // plane, we need to do the complicated setup
	+ // routine. Otherwise, we use the regular iteration.
	+ if(lw==0) {
	+ up=lp;
	+ complicated_setup=true;
	+ } else complicated_setup=false;
	+ } else if(uw==-1) {
	+ us=0;
	+ do {
	+ qp=ed[up][us];
	+ qw=m_test(qp,q);
	+ if(u<q) break;
	+ us++;
	+ } while (us<nu[up]);
	+ if(us==nu[up]) return true;
	+
	+ while(qw==-1) {
	+ qs=ed[up][nu[up]+us];
	+ if(++count>=p) throw true;
	+ u=q;up=qp;
	+ for(us=0;us<qs;us++) {
	+ qp=ed[up][us];
	+ qw=m_test(qp,q);
	+ if(u<q) break;
	+ }
	+ if(us==qs) {
	+ us++;
	+ while(us<nu[up]) {
	+ qp=ed[up][us];
	+ qw=m_test(qp,q);
	+ if(u<q) break;
	+ us++;
	+ }
	+ if(us==nu[up]) return true;
	+ }
	+ }
	+ if(qw==1) {
	+ lp=up;ls=us;l=u;
	+ up=qp;us=ed[lp][nu[lp]+ls];u=q;
	+ complicated_setup=false;
	+ } else {
	+ up=qp;
	+ complicated_setup=true;
	+ }
	+ } else {
	+
	+ // Our original test point was on the plane, so we
	+ // automatically head for the complicated setup
	+ // routine
	+ complicated_setup=true;
	+ }
	+ }
	+ catch(bool except) {
	+ // This routine is a fall-back, in case floating point errors
	+ // cause the usual search routine to fail. In the fall-back
	+ // routine, we just test every edge to find one straddling
	+ // the plane.
	+#if VOROPP_VERBOSE >=1
	+ fputs("Bailed out of convex calculation\n",stderr);
	+#endif
	+ qw=1;lw=0;
	+ for(qp=0;qp<p;qp++) {
	+ qw=m_test(qp,q);
	+ if(qw==1) {
	+
	+ // The point is inside the cutting space. Now
	+ // see if we can find a neighbor which isn't.
	+ for(us=0;us<nu[qp];us++) {
	+ lp=ed[qp][us];
	+ if(lp<qp) {
	+ lw=m_test(lp,l);
	+ if(lw!=1) break;
	+ }
	+ }
	+ if(us<nu[qp]) {
	+ up=qp;
	+ if(lw==0) {
	+ complicated_setup=true;
	+ } else {
	+ complicated_setup=false;
	+ u=q;
	+ ls=ed[up][nu[up]+us];
	+ }
	+ break;
	+ }
	+ } else if(qw==-1) {
	+
	+ // The point is outside the cutting space. See
	+ // if we can find a neighbor which isn't.
	+ for(ls=0;ls<nu[qp];ls++) {
	+ up=ed[qp][ls];
	+ if(up<qp) {
	+ uw=m_test(up,u);
	+ if(uw!=-1) break;
	+ }
	+ }
	+ if(ls<nu[qp]) {
	+ if(uw==0) {
	+ up=qp;
	+ complicated_setup=true;
	+ } else {
	+ complicated_setup=false;
	+ lp=qp;l=q;
	+ us=ed[lp][nu[lp]+ls];
	+ }
	+ break;
	+ }
	+ } else {
	+
	+ // The point is in the plane, so we just
	+ // proceed with the complicated setup routine
	+ up=qp;
	+ complicated_setup=true;
	+ break;
	+ }
	+ }
	+ if(qp==p) return qw==-1?true:false;
	+ }
	+
	+ // We're about to add the first point of the new facet. In either
	+ // routine, we have to add a point, so first check there's space for
	+ // it.
	+ if(p==current_vertices) add_memory_vertices(vc);
	+
	+ if(complicated_setup) {
	+
	+ // We want to be strict about reaching the conclusion that the
	+ // cell is entirely within the cutting plane. It's not enough
	+ // to find a vertex that has edges which are all inside or on
	+ // the plane. If the vertex has neighbors that are also on the
	+ // plane, we should check those too.
	+ if(!search_for_outside_edge(vc,up)) return false;
	+
	+ // The search algorithm found a point which is on the cutting
	+ // plane. We leave that point in place, and create a new one at
	+ // the same location.
	+ pts[3p]=pts[3up];
	+ pts[3p+1]=pts[3up+1];
	+ pts[3p+2]=pts[3up+2];
	+
	+ // Search for a collection of edges of the test vertex which
	+ // are outside of the cutting space. Begin by testing the
	+ // zeroth edge.
	+ i=0;
	+ lp=*ed[up];
	+ lw=m_test(lp,l);
	+ if(lw!=-1) {
	+
	+ // The first edge is either inside the cutting space,
	+ // or lies within the cutting plane. Test the edges
	+ // sequentially until we find one that is outside.
	+ rp=lw;
	+ do {
	+ i++;
	+
	+ // If we reached the last edge with no luck
	+ // then all of the vertices are inside
	+ // or on the plane, so the cell is completely
	+ // deleted
	+ if(i==nu[up]) return false;
	+ lp=ed[up][i];
	+ lw=m_test(lp,l);
	+ } while (lw!=-1);
	+ j=i+1;
	+
	+ // We found an edge outside the cutting space. Keep
	+ // moving through these edges until we find one that's
	+ // inside or on the plane.
	+ while(j<nu[up]) {
	+ lp=ed[up][j];
	+ lw=m_test(lp,l);
	+ if(lw!=-1) break;
	+ j++;
	+ }
	+
	+ // Compute the number of edges for the new vertex. In
	+ // general it will be the number of outside edges
	+ // found, plus two. But we need to recognize the
	+ // special case when all but one edge is outside, and
	+ // the remaining one is on the plane. For that case we
	+ // have to reduce the edge count by one to prevent
	+ // doubling up.
	+ if(j==nu[up]&&i==1&&rp==0) {
	+ nu[p]=nu[up];
	+ double_edge=true;
	+ } else nu[p]=j-i+2;
	+ k=1;
	+
	+ // Add memory for the new vertex if needed, and
	+ // initialize
	+ while (nu[p]>=current_vertex_order) add_memory_vorder(vc);
	+ if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2);
	+ vc.n_set_pointer(p,nu[p]);
	+ ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++;
	+ ed[p][nu[p]<<1]=p;
	+
	+ // Copy the edges of the original vertex into the new
	+ // one. Delete the edges of the original vertex, and
	+ // update the relational table.
	+ us=cycle_down(i,up);
	+ while(i<j) {
	+ qp=ed[up][i];
	+ qs=ed[up][nu[up]+i];
	+ vc.n_copy(p,k,up,i);
	+ ed[p][k]=qp;
	+ ed[p][nu[p]+k]=qs;
	+ ed[qp][qs]=p;
	+ ed[qp][nu[qp]+qs]=k;
	+ ed[up][i]=-1;
	+ i++;k++;
	+ }
	+ qs=i==nu[up]?0:i;
	+ } else {
	+
	+ // In this case, the zeroth edge is outside the cutting
	+ // plane. Begin by searching backwards from the last
	+ // edge until we find an edge which isn't outside.
	+ i=nu[up]-1;
	+ lp=ed[up][i];
	+ lw=m_test(lp,l);
	+ while(lw==-1) {
	+ i--;
	+
	+ // If i reaches zero, then we have a point in
	+ // the plane all of whose edges are outside
	+ // the cutting space, so we just exit
	+ if(i==0) return true;
	+ lp=ed[up][i];
	+ lw=m_test(lp,l);
	+ }
	+
	+ // Now search forwards from zero
	+ j=1;
	+ qp=ed[up][j];
	+ qw=m_test(qp,q);
	+ while(qw==-1) {
	+ j++;
	+ qp=ed[up][j];
	+ qw=m_test(qp,l);
	+ }
	+
	+ // Compute the number of edges for the new vertex. In
	+ // general it will be the number of outside edges
	+ // found, plus two. But we need to recognize the
	+ // special case when all but one edge is outside, and
	+ // the remaining one is on the plane. For that case we
	+ // have to reduce the edge count by one to prevent
	+ // doubling up.
	+ if(i==j&&qw==0) {
	+ double_edge=true;
	+ nu[p]=nu[up];
	+ } else {
	+ nu[p]=nu[up]-i+j+1;
	+ }
	+
	+ // Add memory to store the vertex if it doesn't exist
	+ // already
	+ k=1;
	+ while(nu[p]>=current_vertex_order) add_memory_vorder(vc);
	+ if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2);
	+
	+ // Copy the edges of the original vertex into the new
	+ // one. Delete the edges of the original vertex, and
	+ // update the relational table.
	+ vc.n_set_pointer(p,nu[p]);
	+ ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++;
	+ ed[p][nu[p]<<1]=p;
	+ us=i++;
	+ while(i<nu[up]) {
	+ qp=ed[up][i];
	+ qs=ed[up][nu[up]+i];
	+ vc.n_copy(p,k,up,i);
	+ ed[p][k]=qp;
	+ ed[p][nu[p]+k]=qs;
	+ ed[qp][qs]=p;
	+ ed[qp][nu[qp]+qs]=k;
	+ ed[up][i]=-1;
	+ i++;k++;
	+ }
	+ i=0;
	+ while(i<j) {
	+ qp=ed[up][i];
	+ qs=ed[up][nu[up]+i];
	+ vc.n_copy(p,k,up,i);
	+ ed[p][k]=qp;
	+ ed[p][nu[p]+k]=qs;
	+ ed[qp][qs]=p;
	+ ed[qp][nu[qp]+qs]=k;
	+ ed[up][i]=-1;
	+ i++;k++;
	+ }
	+ qs=j;
	+ }
	+ if(!double_edge) {
	+ vc.n_copy(p,k,up,qs);
	+ vc.n_set(p,0,p_id);
	+ } else vc.n_copy(p,0,up,qs);
	+
	+ // Add this point to the auxiliary delete stack
	+ if(stackp2==stacke2) add_memory_ds2(stackp2);
	+ *(stackp2++)=up;
	+
	+ // Look at the edges on either side of the group that was
	+ // detected. We're going to commence facet computation by
	+ // moving along one of them. We are going to end up coming back
	+ // along the other one.
	+ cs=k;
	+ qp=up;q=u;
	+ i=ed[up][us];
	+ us=ed[up][nu[up]+us];
	+ up=i;
	+ ed[qp][nu[qp]<<1]=-p;
	+
	+ } else {
	+
	+ // The search algorithm found an intersected edge between the
	+ // points lp and up. Create a new vertex between them which
	+ // lies on the cutting plane. Since u and l differ by at least
	+ // the tolerance, this division should never screw up.
	+ if(stackp==stacke) add_memory_ds(stackp);
	+ *(stackp++)=up;
	+ r=u/(u-l);l=1-r;
	+ pts[3p]=pts[3lp]r+pts[3up]*l;
	+ pts[3p+1]=pts[3lp+1]r+pts[3up+1]*l;
	+ pts[3p+2]=pts[3lp+2]r+pts[3up+2]*l;
	+
	+ // This point will always have three edges. Connect one of them
	+ // to lp.
	+ nu[p]=3;
	+ if(mec[3]==mem[3]) add_memory(vc,3,stackp2);
	+ vc.n_set_pointer(p,3);
	+ vc.n_set(p,0,p_id);
	+ vc.n_copy(p,1,up,us);
	+ vc.n_copy(p,2,lp,ls);
	+ ed[p]=mep[3]+7*mec[3]++;
	+ ed[p][6]=p;
	+ ed[up][us]=-1;
	+ ed[lp][ls]=p;
	+ ed[lp][nu[lp]+ls]=1;
	+ ed[p][1]=lp;
	+ ed[p][nu[p]+1]=ls;
	+ cs=2;
	+
	+ // Set the direction to move in
	+ qs=cycle_up(us,up);
	+ qp=up;q=u;
	+ }
	+
	+ // When the code reaches here, we have initialized the first point, and
	+ // we have a direction for moving it to construct the rest of the facet
	+ cp=p;rp=p;p++;
	+ while(qp!=up\|\|qs!=us) {
	+
	+ // We're currently tracing round an intersected facet. Keep
	+ // moving around it until we find a point or edge which
	+ // intersects the plane.
	+ lp=ed[qp][qs];
	+ lw=m_test(lp,l);
	+
	+ if(lw==1) {
	+
	+ // The point is still in the cutting space. Just add it
	+ // to the delete stack and keep moving.
	+ qs=cycle_up(ed[qp][nu[qp]+qs],lp);
	+ qp=lp;
	+ q=l;
	+ if(stackp==stacke) add_memory_ds(stackp);
	+ *(stackp++)=qp;
	+
	+ } else if(lw==-1) {
	+
	+ // The point is outside of the cutting space, so we've
	+ // found an intersected edge. Introduce a regular point
	+ // at the point of intersection. Connect it to the
	+ // point we just tested. Also connect it to the previous
	+ // new point in the facet we're constructing.
	+ if(p==current_vertices) add_memory_vertices(vc);
	+ r=q/(q-l);l=1-r;
	+ pts[3p]=pts[3lp]r+pts[3qp]*l;
	+ pts[3p+1]=pts[3lp+1]r+pts[3qp+1]*l;
	+ pts[3p+2]=pts[3lp+2]r+pts[3qp+2]*l;
	+ nu[p]=3;
	+ if(mec[3]==mem[3]) add_memory(vc,3,stackp2);
	+ ls=ed[qp][qs+nu[qp]];
	+ vc.n_set_pointer(p,3);
	+ vc.n_set(p,0,p_id);
	+ vc.n_copy(p,1,qp,qs);
	+ vc.n_copy(p,2,lp,ls);
	+ ed[p]=mep[3]+7*mec[3]++;
	+ *ed[p]=cp;
	+ ed[p][1]=lp;
	+ ed[p][3]=cs;
	+ ed[p][4]=ls;
	+ ed[p][6]=p;
	+ ed[lp][ls]=p;
	+ ed[lp][nu[lp]+ls]=1;
	+ ed[cp][cs]=p;
	+ ed[cp][nu[cp]+cs]=0;
	+ ed[qp][qs]=-1;
	+ qs=cycle_up(qs,qp);
	+ cp=p++;
	+ cs=2;
	+ } else {
	+
	+ // We've found a point which is on the cutting plane.
	+ // We're going to introduce a new point right here, but
	+ // first we need to figure out the number of edges it
	+ // has.
	+ if(p==current_vertices) add_memory_vertices(vc);
	+
	+ // If the previous vertex detected a double edge, our
	+ // new vertex will have one less edge.
	+ k=double_edge?0:1;
	+ qs=ed[qp][nu[qp]+qs];
	+ qp=lp;
	+ iqs=qs;
	+
	+ // Start testing the edges of the current point until
	+ // we find one which isn't outside the cutting space
	+ do {
	+ k++;
	+ qs=cycle_up(qs,qp);
	+ lp=ed[qp][qs];
	+ lw=m_test(lp,l);
	+ } while (lw==-1);
	+
	+ // Now we need to find out whether this marginal vertex
	+ // we are on has been visited before, because if that's
	+ // the case, we need to add vertices to the existing
	+ // new vertex, rather than creating a fresh one. We also
	+ // need to figure out whether we're in a case where we
	+ // might be creating a duplicate edge.
	+ j=-ed[qp][nu[qp]<<1];
	+ if(qp==up&&qs==us) {
	+
	+ // If we're heading into the final part of the
	+ // new facet, then we never worry about the
	+ // duplicate edge calculation.
	+ new_double_edge=false;
	+ if(j>0) k+=nu[j];
	+ } else {
	+ if(j>0) {
	+
	+ // This vertex was visited before, so
	+ // count those vertices to the ones we
	+ // already have.
	+ k+=nu[j];
	+
	+ // The only time when we might make a
	+ // duplicate edge is if the point we're
	+ // going to move to next is also a
	+ // marginal point, so test for that
	+ // first.
	+ if(lw==0) {
	+
	+ // Now see whether this marginal point
	+ // has been visited before.
	+ i=-ed[lp][nu[lp]<<1];
	+ if(i>0) {
	+
	+ // Now see if the last edge of that other
	+ // marginal point actually ends up here.
	+ if(ed[i][nu[i]-1]==j) {
	+ new_double_edge=true;
	+ k-=1;
	+ } else new_double_edge=false;
	+ } else {
	+
	+ // That marginal point hasn't been visited
	+ // before, so we probably don't have to worry
	+ // about duplicate edges, except in the
	+ // case when that's the way into the end
	+ // of the facet, because that way always creates
	+ // an edge.
	+ if(j==rp&&lp==up&&ed[qp][nu[qp]+qs]==us) {
	+ new_double_edge=true;
	+ k-=1;
	+ } else new_double_edge=false;
	+ }
	+ } else new_double_edge=false;
	+ } else {
	+
	+ // The vertex hasn't been visited
	+ // before, but let's see if it's
	+ // marginal
	+ if(lw==0) {
	+
	+ // If it is, we need to check
	+ // for the case that it's a
	+ // small branch, and that we're
	+ // heading right back to where
	+ // we came from
	+ i=-ed[lp][nu[lp]<<1];
	+ if(i==cp) {
	+ new_double_edge=true;
	+ k-=1;
	+ } else new_double_edge=false;
	+ } else new_double_edge=false;
	+ }
	+ }
	+
	+ // k now holds the number of edges of the new vertex
	+ // we are forming. Add memory for it if it doesn't exist
	+ // already.
	+ while(k>=current_vertex_order) add_memory_vorder(vc);
	+ if(mec[k]==mem[k]) add_memory(vc,k,stackp2);
	+
	+ // Now create a new vertex with order k, or augment
	+ // the existing one
	+ if(j>0) {
	+
	+ // If we're augmenting a vertex but we don't
	+ // actually need any more edges, just skip this
	+ // routine to avoid memory confusion
	+ if(nu[j]!=k) {
	+ // Allocate memory and copy the edges
	+ // of the previous instance into it
	+ vc.n_set_aux1(k);
	+ edp=mep[k]+((k<<1)+1)*mec[k]++;
	+ i=0;
	+ while(i<nu[j]) {
	+ vc.n_copy_aux1(j,i);
	+ edp[i]=ed[j][i];
	+ edp[k+i]=ed[j][nu[j]+i];
	+ i++;
	+ }
	+ edp[k<<1]=j;
	+
	+ // Remove the previous instance with
	+ // fewer vertices from the memory
	+ // structure
	+ edd=mep[nu[j]]+((nu[j]<<1)+1)*--mec[nu[j]];
	+ if(edd!=ed[j]) {
	+ for(lw=0;lw<=(nu[j]<<1);lw++) ed[j][lw]=edd[lw];
	+ vc.n_set_aux2_copy(j,nu[j]);
	+ vc.n_copy_pointer(edd[nu[j]<<1],j);
	+ ed[edd[nu[j]<<1]]=ed[j];
	+ }
	+ vc.n_set_to_aux1(j);
	+ ed[j]=edp;
	+ } else i=nu[j];
	+ } else {
	+
	+ // Allocate a new vertex of order k
	+ vc.n_set_pointer(p,k);
	+ ed[p]=mep[k]+((k<<1)+1)*mec[k]++;
	+ ed[p][k<<1]=p;
	+ if(stackp2==stacke2) add_memory_ds2(stackp2);
	+ *(stackp2++)=qp;
	+ pts[3p]=pts[3qp];
	+ pts[3p+1]=pts[3qp+1];
	+ pts[3p+2]=pts[3qp+2];
	+ ed[qp][nu[qp]<<1]=-p;
	+ j=p++;
	+ i=0;
	+ }
	+ nu[j]=k;
	+
	+ // Unless the previous case was a double edge, connect
	+ // the first available edge of the new vertex to the
	+ // last one in the facet
	+ if(!double_edge) {
	+ ed[j][i]=cp;
	+ ed[j][nu[j]+i]=cs;
	+ vc.n_set(j,i,p_id);
	+ ed[cp][cs]=j;
	+ ed[cp][nu[cp]+cs]=i;
	+ i++;
	+ }
	+
	+ // Copy in the edges of the underlying vertex,
	+ // and do one less if this was a double edge
	+ qs=iqs;
	+ while(i<(new_double_edge?k:k-1)) {
	+ qs=cycle_up(qs,qp);
	+ lp=ed[qp][qs];ls=ed[qp][nu[qp]+qs];
	+ vc.n_copy(j,i,qp,qs);
	+ ed[j][i]=lp;
	+ ed[j][nu[j]+i]=ls;
	+ ed[lp][ls]=j;
	+ ed[lp][nu[lp]+ls]=i;
	+ ed[qp][qs]=-1;
	+ i++;
	+ }
	+ qs=cycle_up(qs,qp);
	+ cs=i;
	+ cp=j;
	+ vc.n_copy(j,new_double_edge?0:cs,qp,qs);
	+
	+ // Update the double_edge flag, to pass it
	+ // to the next instance of this routine
	+ double_edge=new_double_edge;
	+ }
	+ }
	+
	+ // Connect the final created vertex to the initial one
	+ ed[cp][cs]=rp;
	+ *ed[rp]=cp;
	+ ed[cp][nu[cp]+cs]=0;
	+ ed[rp][nu[rp]]=cs;
	+
	+ // Delete points: first, remove any duplicates
	+ dsp=ds;
	+ while(dsp<stackp) {
	+ j=*dsp;
	+ if(ed[j][nu[j]]!=-1) {
	+ ed[j][nu[j]]=-1;
	+ dsp++;
	+ } else dsp=(--stackp);
	+ }
	+
	+ // Add the points in the auxiliary delete stack,
	+ // and reset their back pointers
	+ for(dsp=ds2;dsp<stackp2;dsp++) {
	+ j=*dsp;
	+ ed[j][nu[j]<<1]=j;
	+ if(ed[j][nu[j]]!=-1) {
	+ ed[j][nu[j]]=-1;
	+ if(stackp==stacke) add_memory_ds(stackp);
	+ *(stackp++)=j;
	+ }
	+ }
	+
	+ // Scan connections and add in extras
	+ for(dsp=ds;dsp<stackp;dsp++) {
	+ cp=*dsp;
	+ for(edp=ed[cp];edp<ed[cp]+nu[cp];edp++) {
	+ qp=*edp;
	+ if(qp!=-1&&ed[qp][nu[qp]]!=-1) {
	+ if(stackp==stacke) {
	+ int dis=stackp-dsp;
	+ add_memory_ds(stackp);
	+ dsp=ds+dis;
	+ }
	+ *(stackp++)=qp;
	+ ed[qp][nu[qp]]=-1;
	+ }
	+ }
	+ }
	+ up=0;
	+
	+ // Delete them from the array structure
	+ while(stackp>ds) {
	+ --p;
	+ while(ed[p][nu[p]]==-1) {
	+ j=nu[p];
	+ edp=ed[p];edd=(mep[j]+((j<<1)+1)*--mec[j]);
	+ while(edp<ed[p]+(j<<1)+1) (edp++)=(edd++);
	+ vc.n_set_aux2_copy(p,j);
	+ vc.n_copy_pointer(ed[p][(j<<1)],p);
	+ ed[ed[p][(j<<1)]]=ed[p];
	+ --p;
	+ }
	+ up=*(--stackp);
	+ if(up<p) {
	+
	+ // Vertex management
	+ pts[3up]=pts[3p];
	+ pts[3up+1]=pts[3p+1];
	+ pts[3up+2]=pts[3p+2];
	+
	+ // Memory management
	+ j=nu[up];
	+ edp=ed[up];edd=(mep[j]+((j<<1)+1)*--mec[j]);
	+ while(edp<ed[up]+(j<<1)+1) (edp++)=(edd++);
	+ vc.n_set_aux2_copy(up,j);
	+ vc.n_copy_pointer(ed[up][j<<1],up);
	+ vc.n_copy_pointer(up,p);
	+ ed[ed[up][j<<1]]=ed[up];
	+
	+ // Edge management
	+ ed[up]=ed[p];
	+ nu[up]=nu[p];
	+ for(i=0;i<nu[up];i++) ed[ed[up][i]][ed[up][nu[up]+i]]=up;
	+ ed[up][nu[up]<<1]=up;
	+ } else up=p++;
	+ }
	+
	+ // Check for any vertices of zero order
	+ if(*mec>0) voro_fatal_error("Zero order vertex formed",VOROPP_INTERNAL_ERROR);
	+
	+ // Collapse any order 2 vertices and exit
	+ return collapse_order2(vc);
	+}
	+
	+/** During the creation of a new facet in the plane routine, it is possible
	+ * that some order two vertices may arise. This routine removes them.
	+ * Suppose an order two vertex joins c and d. If there's a edge between
	+ * c and d already, then the order two vertex is just removed; otherwise,
	+ * the order two vertex is removed and c and d are joined together directly.
	+ * It is possible this process will create order two or order one vertices,
	+ * and the routine is continually run until all of them are removed.
	+ * \return False if the vertex removal was unsuccessful, indicative of the cell
	+ * reducing to zero volume and disappearing; true if the vertex removal
	+ * was successful. */
	+template<class vc_class>
	+inline bool voronoicell_base::collapse_order2(vc_class &vc) {
	+ if(!collapse_order1(vc)) return false;
	+ int a,b,i,j,k,l;
	+ while(mec[2]>0) {
	+
	+ // Pick a order 2 vertex and read in its edges
	+ i=--mec[2];
	+ j=mep[2][5i];k=mep[2][5i+1];
	+ if(j==k) {
	+#if VOROPP_VERBOSE >=1
	+ fputs("Order two vertex joins itself",stderr);
	+#endif
	+ return false;
	+ }
	+
	+ // Scan the edges of j to see if joins k
	+ for(l=0;l<nu[j];l++) {
	+ if(ed[j][l]==k) break;
	+ }
	+
	+ // If j doesn't already join k, join them together.
	+ // Otherwise delete the connection to the current
	+ // vertex from j and k.
	+ a=mep[2][5i+2];b=mep[2][5i+3];i=mep[2][5*i+4];
	+ if(l==nu[j]) {
	+ ed[j][a]=k;
	+ ed[k][b]=j;
	+ ed[j][nu[j]+a]=b;
	+ ed[k][nu[k]+b]=a;
	+ } else {
	+ if(!delete_connection(vc,j,a,false)) return false;
	+ if(!delete_connection(vc,k,b,true)) return false;
	+ }
	+
	+ // Compact the memory
	+ --p;
	+ if(up==i) up=0;
	+ if(p!=i) {
	+ if(up==p) up=i;
	+ pts[3i]=pts[3p];
	+ pts[3i+1]=pts[3p+1];
	+ pts[3i+2]=pts[3p+2];
	+ for(k=0;k<nu[p];k++) ed[ed[p][k]][ed[p][nu[p]+k]]=i;
	+ vc.n_copy_pointer(i,p);
	+ ed[i]=ed[p];
	+ nu[i]=nu[p];
	+ ed[i][nu[i]<<1]=i;
	+ }
	+
	+ // Collapse any order 1 vertices if they were created
	+ if(!collapse_order1(vc)) return false;
	+ }
	+ return true;
	+}
	+
	+/** Order one vertices can potentially be created during the order two collapse
	+ * routine. This routine keeps removing them until there are none left.
	+ * \return False if the vertex removal was unsuccessful, indicative of the cell
	+ * having zero volume and disappearing; true if the vertex removal was
	+ * successful. */
	+template<class vc_class>
	+inline bool voronoicell_base::collapse_order1(vc_class &vc) {
	+ int i,j,k;
	+ while(mec[1]>0) {
	+ up=0;
	+#if VOROPP_VERBOSE >=1
	+ fputs("Order one collapse\n",stderr);
	+#endif
	+ i=--mec[1];
	+ j=mep[1][3i];k=mep[1][3i+1];
	+ i=mep[1][3*i+2];
	+ if(!delete_connection(vc,j,k,false)) return false;
	+ --p;
	+ if(up==i) up=0;
	+ if(p!=i) {
	+ if(up==p) up=i;
	+ pts[3i]=pts[3p];
	+ pts[3i+1]=pts[3p+1];
	+ pts[3i+2]=pts[3p+2];
	+ for(k=0;k<nu[p];k++) ed[ed[p][k]][ed[p][nu[p]+k]]=i;
	+ vc.n_copy_pointer(i,p);
	+ ed[i]=ed[p];
	+ nu[i]=nu[p];
	+ ed[i][nu[i]<<1]=i;
	+ }
	+ }
	+ return true;
	+}
	+
	+/** This routine deletes the kth edge of vertex j and reorganizes the memory.
	+ * If the neighbor computation is enabled, we also have to supply an handedness
	+ * flag to decide whether to preserve the plane on the left or right of the
	+ * connection.
	+ * \return False if a zero order vertex was formed, indicative of the cell
	+ * disappearing; true if the vertex removal was successful. */
	+template<class vc_class>
	+inline bool voronoicell_base::delete_connection(vc_class &vc,int j,int k,bool hand) {
	+ int q=hand?k:cycle_up(k,j);
	+ int i=nu[j]-1,l,edp,edd,m;
	+#if VOROPP_VERBOSE >=1
	+ if(i<1) {
	+ fputs("Zero order vertex formed\n",stderr);
	+ return false;
	+ }
	+#endif
	+ if(mec[i]==mem[i]) add_memory(vc,i,ds2);
	+ vc.n_set_aux1(i);
	+ for(l=0;l<q;l++) vc.n_copy_aux1(j,l);
	+ while(l<i) {
	+ vc.n_copy_aux1_shift(j,l);
	+ l++;
	+ }
	+ edp=mep[i]+((i<<1)+1)*mec[i]++;
	+ edp[i<<1]=j;
	+ for(l=0;l<k;l++) {
	+ edp[l]=ed[j][l];
	+ edp[l+i]=ed[j][l+nu[j]];
	+ }
	+ while(l<i) {
	+ m=ed[j][l+1];
	+ edp[l]=m;
	+ k=ed[j][l+nu[j]+1];
	+ edp[l+i]=k;
	+ ed[m][nu[m]+k]--;
	+ l++;
	+ }
	+
	+ edd=mep[nu[j]]+((nu[j]<<1)+1)*--mec[nu[j]];
	+ for(l=0;l<=(nu[j]<<1);l++) ed[j][l]=edd[l];
	+ vc.n_set_aux2_copy(j,nu[j]);
	+ vc.n_set_to_aux2(edd[nu[j]<<1]);
	+ vc.n_set_to_aux1(j);
	+ ed[edd[nu[j]<<1]]=edd;
	+ ed[j]=edp;
	+ nu[j]=i;
	+ return true;
	+}
	+
	+/** Calculates the volume of the Voronoi cell, by decomposing the cell into
	+ * tetrahedra extending outward from the zeroth vertex, whose volumes are
	+ * evaluated using a scalar triple product.
	+ * \return A floating point number holding the calculated volume. */
	+double voronoicell_base::volume() {
	+ const double fe=1/48.0;
	+ double vol=0;
	+ int i,j,k,l,m,n;
	+ double ux,uy,uz,vx,vy,vz,wx,wy,wz;
	+ for(i=1;i<p;i++) {
	+ ux=pts-pts[3i];
	+ uy=pts[1]-pts[3*i+1];
	+ uz=pts[2]-pts[3*i+2];
	+ for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) {
	+ ed[i][j]=-1-k;
	+ l=cycle_up(ed[i][nu[i]+j],k);
	+ vx=pts[3k]-pts;
	+ vy=pts[3*k+1]-pts[1];
	+ vz=pts[3*k+2]-pts[2];
	+ m=ed[k][l];ed[k][l]=-1-m;
	+ while(m!=i) {
	+ n=cycle_up(ed[k][nu[k]+l],m);
	+ wx=pts[3m]-pts;
	+ wy=pts[3*m+1]-pts[1];
	+ wz=pts[3*m+2]-pts[2];
	+ vol+=uxvywz+uyvzwx+uzvxwy-uzvywx-uyvxwz-uxvzwy;
	+ k=m;l=n;vx=wx;vy=wy;vz=wz;
	+ m=ed[k][l];ed[k][l]=-1-m;
	+ }
	+ }
	+ }
	+ }
	+ reset_edges();
	+ return vol*fe;
	+}
	+
	+/** Calculates the areas of each face of the Voronoi cell and prints the
	+ * results to an output stream.
	+ * \param[out] v the vector to store the results in. */
	+void voronoicell_base::face_areas(std::vector<double> &v) {
	+ double area;
	+ v.clear();
	+ int i,j,k,l,m,n;
	+ double ux,uy,uz,vx,vy,vz,wx,wy,wz;
	+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) {
	+ area=0;
	+ ed[i][j]=-1-k;
	+ l=cycle_up(ed[i][nu[i]+j],k);
	+ m=ed[k][l];ed[k][l]=-1-m;
	+ while(m!=i) {
	+ n=cycle_up(ed[k][nu[k]+l],m);
	+ ux=pts[3k]-pts[3i];
	+ uy=pts[3k+1]-pts[3i+1];
	+ uz=pts[3k+2]-pts[3i+2];
	+ vx=pts[3m]-pts[3i];
	+ vy=pts[3m+1]-pts[3i+1];
	+ vz=pts[3m+2]-pts[3i+2];
	+ wx=uyvz-uzvy;
	+ wy=uzvx-uxvz;
	+ wz=uxvy-uyvx;
	+ area+=sqrt(wxwx+wywy+wz*wz);
	+ k=m;l=n;
	+ m=ed[k][l];ed[k][l]=-1-m;
	+ }
	+ v.push_back(0.125*area);
	+ }
	+ }
	+ reset_edges();
	+}
	+
	+
	+/** Calculates the total surface area of the Voronoi cell.
	+ * \return The computed area. */
	+double voronoicell_base::surface_area() {
	+ double area=0;
	+ int i,j,k,l,m,n;
	+ double ux,uy,uz,vx,vy,vz,wx,wy,wz;
	+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) {
	+ ed[i][j]=-1-k;
	+ l=cycle_up(ed[i][nu[i]+j],k);
	+ m=ed[k][l];ed[k][l]=-1-m;
	+ while(m!=i) {
	+ n=cycle_up(ed[k][nu[k]+l],m);
	+ ux=pts[3k]-pts[3i];
	+ uy=pts[3k+1]-pts[3i+1];
	+ uz=pts[3k+2]-pts[3i+2];
	+ vx=pts[3m]-pts[3i];
	+ vy=pts[3m+1]-pts[3i+1];
	+ vz=pts[3m+2]-pts[3i+2];
	+ wx=uyvz-uzvy;
	+ wy=uzvx-uxvz;
	+ wz=uxvy-uyvx;
	+ area+=sqrt(wxwx+wywy+wz*wz);
	+ k=m;l=n;
	+ m=ed[k][l];ed[k][l]=-1-m;
	+ }
	+ }
	+ }
	+ reset_edges();
	+ return 0.125*area;
	+}
	+
	+
	+/** Calculates the centroid of the Voronoi cell, by decomposing the cell into
	+ * tetrahedra extending outward from the zeroth vertex.
	+ * \param[out] (cx,cy,cz) references to floating point numbers in which to
	+ * pass back the centroid vector. */
	+void voronoicell_base::centroid(double &cx,double &cy,double &cz) {
	+ double tvol,vol=0;cx=cy=cz=0;
	+ int i,j,k,l,m,n;
	+ double ux,uy,uz,vx,vy,vz,wx,wy,wz;
	+ for(i=1;i<p;i++) {
	+ ux=pts-pts[3i];
	+ uy=pts[1]-pts[3*i+1];
	+ uz=pts[2]-pts[3*i+2];
	+ for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) {
	+ ed[i][j]=-1-k;
	+ l=cycle_up(ed[i][nu[i]+j],k);
	+ vx=pts[3k]-pts;
	+ vy=pts[3*k+1]-pts[1];
	+ vz=pts[3*k+2]-pts[2];
	+ m=ed[k][l];ed[k][l]=-1-m;
	+ while(m!=i) {
	+ n=cycle_up(ed[k][nu[k]+l],m);
	+ wx=pts[3m]-pts;
	+ wy=pts[3*m+1]-pts[1];
	+ wz=pts[3*m+2]-pts[2];
	+ tvol=uxvywz+uyvzwx+uzvxwy-uzvywx-uyvxwz-uxvzwy;
	+ vol+=tvol;
	+ cx+=(wx+vx-ux)*tvol;
	+ cy+=(wy+vy-uy)*tvol;
	+ cz+=(wz+vz-uz)*tvol;
	+ k=m;l=n;vx=wx;vy=wy;vz=wz;
	+ m=ed[k][l];ed[k][l]=-1-m;
	+ }
	+ }
	+ }
	+ }
	+ reset_edges();
	+ if(vol>tolerance_sq) {
	+ vol=0.125/vol;
	+ cx=cxvol+0.5(*pts);
	+ cy=cyvol+0.5pts[1];
	+ cz=czvol+0.5pts[2];
	+ } else cx=cy=cz=0;
	+}
	+
	+/** Computes the maximum radius squared of a vertex from the center of the
	+ * cell. It can be used to determine when enough particles have been testing an
	+ * all planes that could cut the cell have been considered.
	+ * \return The maximum radius squared of a vertex.*/
	+double voronoicell_base::max_radius_squared() {
	+ double r,s,ptsp=pts+3,ptse=pts+3*p;
	+ r=pts(pts)+pts[1]pts[1]+pts[2]*pts[2];
	+ while(ptsp<ptse) {
	+ s=ptsp(*ptsp);ptsp++;
	+ s+=ptsp(*ptsp);ptsp++;
	+ s+=ptsp(*ptsp);ptsp++;
	+ if(s>r) r=s;
	+ }
	+ return r;
	+}
	+
	+/** Calculates the total edge distance of the Voronoi cell.
	+ * \return A floating point number holding the calculated distance. */
	+double voronoicell_base::total_edge_distance() {
	+ int i,j,k;
	+ double dis=0,dx,dy,dz;
	+ for(i=0;i<p-1;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>i) {
	+ dx=pts[3k]-pts[3i];
	+ dy=pts[3k+1]-pts[3i+1];
	+ dz=pts[3k+2]-pts[3i+2];
	+ dis+=sqrt(dxdx+dydy+dz*dz);
	+ }
	+ }
	+ return 0.5*dis;
	+}
	+
	+/** Outputs the edges of the Voronoi cell in POV-Ray format to an open file
	+ * stream, displacing the cell by given vector.
	+ * \param[in] (x,y,z) a displacement vector to be added to the cell's position.
	+ * \param[in] fp a file handle to write to. */
	+void voronoicell_base::draw_pov(double x,double y,double z,FILE* fp) {
	+ int i,j,k;double ptsp=pts,pt2;
	+ char posbuf1[128],posbuf2[128];
	+ for(i=0;i<p;i++,ptsp+=3) {
	+ sprintf(posbuf1,"%g,%g,%g",x+ptsp0.5,y+ptsp[1]0.5,z+ptsp[2]0.5);
	+ fprintf(fp,"sphere{<%s>,r}\n",posbuf1);
	+ for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k<i) {
	+ pt2=pts+3*k;
	+ sprintf(posbuf2,"%g,%g,%g",x+pt20.5,y+0.5pt2[1],z+0.5pt2[2]);
	+ if(strcmp(posbuf1,posbuf2)!=0) fprintf(fp,"cylinder{<%s>,<%s>,r}\n",posbuf1,posbuf2);
	+ }
	+ }
	+ }
	+}
	+
	+/** Outputs the edges of the Voronoi cell in gnuplot format to an output stream.
	+ * \param[in] (x,y,z) a displacement vector to be added to the cell's position.
	+ * \param[in] fp a file handle to write to. */
	+void voronoicell_base::draw_gnuplot(double x,double y,double z,FILE *fp) {
	+ int i,j,k,l,m;
	+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) {
	+ fprintf(fp,"%g %g %g\n",x+0.5pts[3i],y+0.5pts[3i+1],z+0.5pts[3i+2]);
	+ l=i;m=j;
	+ do {
	+ ed[k][ed[l][nu[l]+m]]=-1-l;
	+ ed[l][m]=-1-k;
	+ l=k;
	+ fprintf(fp,"%g %g %g\n",x+0.5pts[3k],y+0.5pts[3k+1],z+0.5pts[3k+2]);
	+ } while (search_edge(l,m,k));
	+ fputs("\n\n",fp);
	+ }
	+ }
	+ reset_edges();
	+}
	+
	+inline bool voronoicell_base::search_edge(int l,int &m,int &k) {
	+ for(m=0;m<nu[l];m++) {
	+ k=ed[l][m];
	+ if(k>=0) return true;
	+ }
	+ return false;
	+}
	+
	+/** Outputs the Voronoi cell in the POV mesh2 format, described in section
	+ * 1.3.2.2 of the POV-Ray documentation. The mesh2 output consists of a list of
	+ * vertex vectors, followed by a list of triangular faces. The routine also
	+ * makes use of the optional inside_vector specification, which makes the mesh
	+ * object solid, so the the POV-Ray Constructive Solid Geometry (CSG) can be
	+ * applied.
	+ * \param[in] (x,y,z) a displacement vector to be added to the cell's position.
	+ * \param[in] fp a file handle to write to. */
	+void voronoicell_base::draw_pov_mesh(double x,double y,double z,FILE *fp) {
	+ int i,j,k,l,m,n;
	+ double *ptsp=pts;
	+ fprintf(fp,"mesh2 {\nvertex_vectors {\n%d\n",p);
	+ for(i=0;i<p;i++,ptsp+=3) fprintf(fp,",<%g,%g,%g>\n",x+ptsp0.5,y+ptsp[1]0.5,z+ptsp[2]0.5);
	+ fprintf(fp,"}\nface_indices {\n%d\n",(p-2)<<1);
	+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) {
	+ ed[i][j]=-1-k;
	+ l=cycle_up(ed[i][nu[i]+j],k);
	+ m=ed[k][l];ed[k][l]=-1-m;
	+ while(m!=i) {
	+ n=cycle_up(ed[k][nu[k]+l],m);
	+ fprintf(fp,",<%d,%d,%d>\n",i,k,m);
	+ k=m;l=n;
	+ m=ed[k][l];ed[k][l]=-1-m;
	+ }
	+ }
	+ }
	+ fputs("}\ninside_vector <0,0,1>\n}\n",fp);
	+ reset_edges();
	+}
	+
	+/** Several routines in the class that gather cell-based statistics internally
	+ * track their progress by flipping edges to negative so that they know what
	+ * parts of the cell have already been tested. This function resets them back
	+ * to positive. When it is called, it assumes that every edge in the routine
	+ * should have already been flipped to negative, and it bails out with an
	+ * internal error if it encounters a positive edge. */
	+inline void voronoicell_base::reset_edges() {
	+ int i,j;
	+ for(i=0;i<p;i++) for(j=0;j<nu[i];j++) {
	+ if(ed[i][j]>=0) voro_fatal_error("Edge reset routine found a previously untested edge",VOROPP_INTERNAL_ERROR);
	+ ed[i][j]=-1-ed[i][j];
	+ }
	+}
	+
	+/** Checks to see if a given vertex is inside, outside or within the test
	+ * plane. If the point is far away from the test plane, the routine immediately
	+ * returns whether it is inside or outside. If the routine is close the the
	+ * plane and within the specified tolerance, then the special check_marginal()
	+ * routine is called.
	+ * \param[in] n the vertex to test.
	+ * \param[out] ans the result of the scalar product used in evaluating the
	+ * location of the point.
	+ * \return -1 if the point is inside the plane, 1 if the point is outside the
	+ * plane, or 0 if the point is within the plane. */
	+inline int voronoicell_base::m_test(int n,double &ans) {
	+ double *pp=pts+n+(n<<1);
	+ ans=(pp++)px;
	+ ans+=(pp++)py;
	+ ans+=pppz-prsq;
	+ if(ans<-tolerance2) {
	+ return -1;
	+ } else if(ans>tolerance2) {
	+ return 1;
	+ }
	+ return check_marginal(n,ans);
	+}
	+
	+/** Checks to see if a given vertex is inside, outside or within the test
	+ * plane, for the case when the point has been detected to be very close to the
	+ * plane. The routine ensures that the returned results are always consistent
	+ * with previous tests, by keeping a table of any marginal results. The routine
	+ * first sees if the vertex is in the table, and if it finds a previously
	+ * computed result it uses that. Otherwise, it computes a result for this
	+ * vertex and adds it the table.
	+ * \param[in] n the vertex to test.
	+ * \param[in] ans the result of the scalar product used in evaluating
	+ * the location of the point.
	+ * \return -1 if the point is inside the plane, 1 if the point is outside the
	+ * plane, or 0 if the point is within the plane. */
	+int voronoicell_base::check_marginal(int n,double &ans) {
	+ int i;
	+ for(i=0;i<n_marg;i+=2) if(marg[i]==n) return marg[i+1];
	+ if(n_marg==current_marginal) {
	+ current_marginal<<=1;
	+ if(current_marginal>max_marginal)
	+ voro_fatal_error("Marginal case buffer allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
	+#if VOROPP_VERBOSE >=2
	+ fprintf(stderr,"Marginal cases buffer scaled up to %d\n",i);
	+#endif
	+ int *pmarg=new int[current_marginal];
	+ for(int j=0;j<n_marg;j++) pmarg[j]=marg[j];
	+ delete [] marg;
	+ marg=pmarg;
	+ }
	+ marg[n_marg++]=n;
	+ marg[n_marg++]=ans>tolerance?1:(ans<-tolerance?-1:0);
	+ return marg[n_marg-1];
	+}
	+
	+/** For each face of the Voronoi cell, this routine prints the out the normal
	+ * vector of the face, and scales it to the distance from the cell center to
	+ * that plane.
	+ * \param[out] v the vector to store the results in. */
	+void voronoicell_base::normals(std::vector<double> &v) {
	+ int i,j,k;
	+ v.clear();
	+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) normals_search(v,i,j,k);
	+ }
	+ reset_edges();
	+}
	+
	+/** This inline routine is called by normals(). It attempts to construct a
	+ * single normal vector that is associated with a particular face. It first
	+ * traces around the face, trying to find two vectors along the face edges
	+ * whose vector product is above the numerical tolerance. It then constructs
	+ * the normal vector using this product. If the face is too small, and none of
	+ * the vector products are large enough, the routine may return (0,0,0) as the
	+ * normal vector.
	+ * \param[in] v the vector to store the results in.
	+ * \param[in] i the initial vertex of the face to test.
	+ * \param[in] j the index of an edge of the vertex.
	+ * \param[in] k the neighboring vertex of i, set to ed[i][j]. */
	+inline void voronoicell_base::normals_search(std::vector<double> &v,int i,int j,int k) {
	+ ed[i][j]=-1-k;
	+ int l=cycle_up(ed[i][nu[i]+j],k),m;
	+ double ux,uy,uz,vx,vy,vz,wx,wy,wz,wmag;
	+ do {
	+ m=ed[k][l];ed[k][l]=-1-m;
	+ ux=pts[3m]-pts[3k];
	+ uy=pts[3m+1]-pts[3k+1];
	+ uz=pts[3m+2]-pts[3k+2];
	+
	+ // Test to see if the length of this edge is above the tolerance
	+ if(uxux+uyuy+uz*uz>tolerance_sq) {
	+ while(m!=i) {
	+ l=cycle_up(ed[k][nu[k]+l],m);
	+ k=m;m=ed[k][l];ed[k][l]=-1-m;
	+ vx=pts[3m]-pts[3k];
	+ vy=pts[3m+1]-pts[3k+1];
	+ vz=pts[3m+2]-pts[3k+2];
	+
	+ // Construct the vector product of this edge with
	+ // the previous one
	+ wx=uzvy-uyvz;
	+ wy=uxvz-uzvx;
	+ wz=uyvx-uxvy;
	+ wmag=wxwx+wywy+wz*wz;
	+
	+ // Test to see if this vector product of the
	+ // two edges is above the tolerance
	+ if(wmag>tolerance_sq) {
	+
	+ // Construct the normal vector and print it
	+ wmag=1/sqrt(wmag);
	+ v.push_back(wx*wmag);
	+ v.push_back(wy*wmag);
	+ v.push_back(wz*wmag);
	+
	+ // Mark all of the remaining edges of this
	+ // face and exit
	+ while(m!=i) {
	+ l=cycle_up(ed[k][nu[k]+l],m);
	+ k=m;m=ed[k][l];ed[k][l]=-1-m;
	+ }
	+ return;
	+ }
	+ }
	+ v.push_back(0);
	+ v.push_back(0);
	+ v.push_back(0);
	+ return;
	+ }
	+ l=cycle_up(ed[k][nu[k]+l],m);
	+ k=m;
	+ } while (k!=i);
	+ v.push_back(0);
	+ v.push_back(0);
	+ v.push_back(0);
	+}
	+
	+
	+/** Returns the number of faces of a computed Voronoi cell.
	+ * \return The number of faces. */
	+int voronoicell_base::number_of_faces() {
	+ int i,j,k,l,m,s=0;
	+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) {
	+ s++;
	+ ed[i][j]=-1-k;
	+ l=cycle_up(ed[i][nu[i]+j],k);
	+ do {
	+ m=ed[k][l];
	+ ed[k][l]=-1-m;
	+ l=cycle_up(ed[k][nu[k]+l],m);
	+ k=m;
	+ } while (k!=i);
	+
	+ }
	+ }
	+ reset_edges();
	+ return s;
	+}
	+
	+/** Returns a vector of the vertex orders.
	+ * \param[out] v the vector to store the results in. */
	+void voronoicell_base::vertex_orders(std::vector<int> &v) {
	+ v.resize(p);
	+ for(int i=0;i<p;i++) v[i]=nu[i];
	+}
	+
	+/** Outputs the vertex orders.
	+ * \param[out] fp the file handle to write to. */
	+void voronoicell_base::output_vertex_orders(FILE *fp) {
	+ if(p>0) {
	+ fprintf(fp,"%d",*nu);
	+ for(int nup=nu+1;nup<nu+p;nup++) fprintf(fp," %d",nup);
	+ }
	+}
	+
	+/** Returns a vector of the vertex vectors using the local coordinate system.
	+ * \param[out] v the vector to store the results in. */
	+void voronoicell_base::vertices(std::vector<double> &v) {
	+ v.resize(3*p);
	+ double *ptsp=pts;
	+ for(int i=0;i<3*p;i+=3) {
	+ v[i]=(ptsp++)0.5;
	+ v[i+1]=(ptsp++)0.5;
	+ v[i+2]=(ptsp++)0.5;
	+ }
	+}
	+
	+/** Outputs the vertex vectors using the local coordinate system.
	+ * \param[out] fp the file handle to write to. */
	+void voronoicell_base::output_vertices(FILE *fp) {
	+ if(p>0) {
	+ fprintf(fp,"(%g,%g,%g)",pts0.5,pts[1]0.5,pts[2]0.5);
	+ for(double ptsp=pts+3;ptsp<pts+3p;ptsp+=3) fprintf(fp," (%g,%g,%g)",ptsp0.5,ptsp[1]0.5,ptsp[2]0.5);
	+ }
	+}
	+
	+
	+/** Returns a vector of the vertex vectors in the global coordinate system.
	+ * \param[out] v the vector to store the results in.
	+ * \param[in] (x,y,z) the position vector of the particle in the global
	+ * coordinate system. */
	+void voronoicell_base::vertices(double x,double y,double z,std::vector<double> &v) {
	+ v.resize(3*p);
	+ double *ptsp=pts;
	+ for(int i=0;i<3*p;i+=3) {
	+ v[i]=x+(ptsp++)0.5;
	+ v[i+1]=y+(ptsp++)0.5;
	+ v[i+2]=z+(ptsp++)0.5;
	+ }
	+}
	+
	+/** Outputs the vertex vectors using the global coordinate system.
	+ * \param[out] fp the file handle to write to.
	+ * \param[in] (x,y,z) the position vector of the particle in the global
	+ * coordinate system. */
	+void voronoicell_base::output_vertices(double x,double y,double z,FILE *fp) {
	+ if(p>0) {
	+ fprintf(fp,"(%g,%g,%g)",x+pts0.5,y+pts[1]0.5,z+pts[2]0.5);
	+ for(double ptsp=pts+3;ptsp<pts+3p;ptsp+=3) fprintf(fp," (%g,%g,%g)",x+ptsp0.5,y+ptsp[1]0.5,z+ptsp[2]0.5);
	+ }
	+}
	+
	+/** This routine returns the perimeters of each face.
	+ * \param[out] v the vector to store the results in. */
	+void voronoicell_base::face_perimeters(std::vector<double> &v) {
	+ v.clear();
	+ int i,j,k,l,m;
	+ double dx,dy,dz,perim;
	+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) {
	+ dx=pts[3k]-pts[3i];
	+ dy=pts[3k+1]-pts[3i+1];
	+ dz=pts[3k+2]-pts[3i+2];
	+ perim=sqrt(dxdx+dydy+dz*dz);
	+ ed[i][j]=-1-k;
	+ l=cycle_up(ed[i][nu[i]+j],k);
	+ do {
	+ m=ed[k][l];
	+ dx=pts[3m]-pts[3k];
	+ dy=pts[3m+1]-pts[3k+1];
	+ dz=pts[3m+2]-pts[3k+2];
	+ perim+=sqrt(dxdx+dydy+dz*dz);
	+ ed[k][l]=-1-m;
	+ l=cycle_up(ed[k][nu[k]+l],m);
	+ k=m;
	+ } while (k!=i);
	+ v.push_back(0.5*perim);
	+ }
	+ }
	+ reset_edges();
	+}
	+
	+/** For each face, this routine outputs a bracketed sequence of numbers
	+ * containing a list of all the vertices that make up that face.
	+ * \param[out] v the vector to store the results in. */
	+void voronoicell_base::face_vertices(std::vector<int> &v) {
	+ int i,j,k,l,m,vp(0),vn;
	+ v.clear();
	+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) {
	+ v.push_back(0);
	+ v.push_back(i);
	+ ed[i][j]=-1-k;
	+ l=cycle_up(ed[i][nu[i]+j],k);
	+ do {
	+ v.push_back(k);
	+ m=ed[k][l];
	+ ed[k][l]=-1-m;
	+ l=cycle_up(ed[k][nu[k]+l],m);
	+ k=m;
	+ } while (k!=i);
	+ vn=v.size();
	+ v[vp]=vn-vp-1;
	+ vp=vn;
	+ }
	+ }
	+ reset_edges();
	+}
	+
	+/** Outputs a list of the number of edges in each face.
	+ * \param[out] v the vector to store the results in. */
	+void voronoicell_base::face_orders(std::vector<int> &v) {
	+ int i,j,k,l,m,q;
	+ v.clear();
	+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) {
	+ q=1;
	+ ed[i][j]=-1-k;
	+ l=cycle_up(ed[i][nu[i]+j],k);
	+ do {
	+ q++;
	+ m=ed[k][l];
	+ ed[k][l]=-1-m;
	+ l=cycle_up(ed[k][nu[k]+l],m);
	+ k=m;
	+ } while (k!=i);
	+ v.push_back(q);;
	+ }
	+ }
	+ reset_edges();
	+}
	+
	+/** Computes the number of edges that each face has and outputs a frequency
	+ * table of the results.
	+ * \param[out] v the vector to store the results in. */
	+void voronoicell_base::face_freq_table(std::vector<int> &v) {
	+ int i,j,k,l,m,q;
	+ v.clear();
	+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) {
	+ q=1;
	+ ed[i][j]=-1-k;
	+ l=cycle_up(ed[i][nu[i]+j],k);
	+ do {
	+ q++;
	+ m=ed[k][l];
	+ ed[k][l]=-1-m;
	+ l=cycle_up(ed[k][nu[k]+l],m);
	+ k=m;
	+ } while (k!=i);
	+ if((unsigned int) q>=v.size()) v.resize(q+1,0);
	+ v[q]++;
	+ }
	+ }
	+ reset_edges();
	+}
	+
	+/** This routine tests to see whether the cell intersects a plane by starting
	+ * from the guess point up. If up intersects, then it immediately returns true.
	+ * Otherwise, it calls the plane_intersects_track() routine.
	+ * \param[in] (x,y,z) the normal vector to the plane.
	+ * \param[in] rsq the distance along this vector of the plane.
	+ * \return False if the plane does not intersect the plane, true if it does. */
	+bool voronoicell_base::plane_intersects(double x,double y,double z,double rsq) {
	+ double g=xpts[3up]+ypts[3up+1]+zpts[3up+2];
	+ if(g<rsq) return plane_intersects_track(x,y,z,rsq,g);
	+ return true;
	+}
	+
	+/** This routine tests to see if a cell intersects a plane. It first tests a
	+ * random sample of approximately sqrt(p)/4 points. If any of those are
	+ * intersect, then it immediately returns true. Otherwise, it takes the closest
	+ * point and passes that to plane_intersect_track() routine.
	+ * \param[in] (x,y,z) the normal vector to the plane.
	+ * \param[in] rsq the distance along this vector of the plane.
	+ * \return False if the plane does not intersect the plane, true if it does. */
	+bool voronoicell_base::plane_intersects_guess(double x,double y,double z,double rsq) {
	+ up=0;
	+ double g=xpts[3up]+ypts[3up+1]+zpts[3up+2];
	+ if(g<rsq) {
	+ int ca=1,cc=p>>3,mp=1;
	+ double m;
	+ while(ca<cc) {
	+ m=xpts[3mp]+ypts[3mp+1]+zpts[3mp+2];
	+ if(m>g) {
	+ if(m>rsq) return true;
	+ g=m;up=mp;
	+ }
	+ ca+=mp++;
	+ }
	+ return plane_intersects_track(x,y,z,rsq,g);
	+ }
	+ return true;
	+}
	+
	+/* This routine tests to see if a cell intersects a plane, by tracing over the cell from
	+ * vertex to vertex, starting at up. It is meant to be called either by plane_intersects()
	+ * or plane_intersects_track(), when those routines cannot immediately resolve the case.
	+ * \param[in] (x,y,z) the normal vector to the plane.
	+ * \param[in] rsq the distance along this vector of the plane.
	+ * \param[in] g the distance of up from the plane.
	+ * \return False if the plane does not intersect the plane, true if it does. */
	+inline bool voronoicell_base::plane_intersects_track(double x,double y,double z,double rsq,double g) {
	+ int count=0,ls,us,tp;
	+ double t;
	+
	+ // The test point is outside of the cutting space
	+ for(us=0;us<nu[up];us++) {
	+ tp=ed[up][us];
	+ t=xpts[3tp]+ypts[3tp+1]+zpts[3tp+2];
	+ if(t>g) {
	+ ls=ed[up][nu[up]+us];
	+ up=tp;
	+ while (t<rsq) {
	+ if(++count>=p) {
	+#if VOROPP_VERBOSE >=1
	+ fputs("Bailed out of convex calculation",stderr);
	+#endif
	+ for(tp=0;tp<p;tp++) if(xpts[3tp]+ypts[3tp+1]+zpts[3tp+2]>rsq) return true;
	+ return false;
	+ }
	+
	+ // Test all the neighbors of the current point
	+ // and find the one which is closest to the
	+ // plane
	+ for(us=0;us<ls;us++) {
	+ tp=ed[up][us];
	+ g=xpts[3tp]+ypts[3tp+1]+zpts[3tp+2];
	+ if(g>t) break;
	+ }
	+ if(us==ls) {
	+ us++;
	+ while(us<nu[up]) {
	+ tp=ed[up][us];
	+ g=xpts[3tp]+ypts[3tp+1]+zpts[3tp+2];
	+ if(g>t) break;
	+ us++;
	+ }
	+ if(us==nu[up]) return false;
	+ }
	+ ls=ed[up][nu[up]+us];up=tp;t=g;
	+ }
	+ return true;
	+ }
	+ }
	+ return false;
	+}
	+
	+/** Counts the number of edges of the Voronoi cell.
	+ * \return the number of edges. */
	+int voronoicell_base::number_of_edges() {
	+ int edges=0,*nup=nu;
	+ while(nup<nu+p) edges+=*(nup++);
	+ return edges>>1;
	+}
	+
	+/** Outputs a custom string of information about the Voronoi cell. The string
	+ * of information follows a similar style as the C printf command, and detailed
	+ * information about its format is available at
	+ * http://math.lbl.gov/voro++/doc/custom.html.
	+ * \param[in] format the custom string to print.
	+ * \param[in] i the ID of the particle associated with this Voronoi cell.
	+ * \param[in] (x,y,z) the position of the particle associated with this Voronoi
	+ * cell.
	+ * \param[in] r a radius associated with the particle.
	+ * \param[in] fp the file handle to write to. */
	+void voronoicell_base::output_custom(const char format,int i,double x,double y,double z,double r,FILE fp) {
	+ char fmp=(const_cast<char>(format));
	+ std::vector<int> vi;
	+ std::vector<double> vd;
	+ while(*fmp!=0) {
	+ if(*fmp=='%') {
	+ fmp++;
	+ switch(*fmp) {
	+
	+ // Particle-related output
	+ case 'i': fprintf(fp,"%d",i);break;
	+ case 'x': fprintf(fp,"%g",x);break;
	+ case 'y': fprintf(fp,"%g",y);break;
	+ case 'z': fprintf(fp,"%g",z);break;
	+ case 'q': fprintf(fp,"%g %g %g",x,y,z);break;
	+ case 'r': fprintf(fp,"%g",r);break;
	+
	+ // Vertex-related output
	+ case 'w': fprintf(fp,"%d",p);break;
	+ case 'p': output_vertices(fp);break;
	+ case 'P': output_vertices(x,y,z,fp);break;
	+ case 'o': output_vertex_orders(fp);break;
	+ case 'm': fprintf(fp,"%g",0.25*max_radius_squared());break;
	+
	+ // Edge-related output
	+ case 'g': fprintf(fp,"%d",number_of_edges());break;
	+ case 'E': fprintf(fp,"%g",total_edge_distance());break;
	+ case 'e': face_perimeters(vd);voro_print_vector(vd,fp);break;
	+
	+ // Face-related output
	+ case 's': fprintf(fp,"%d",number_of_faces());break;
	+ case 'F': fprintf(fp,"%g",surface_area());break;
	+ case 'A': {
	+ face_freq_table(vi);
	+ voro_print_vector(vi,fp);
	+ } break;
	+ case 'a': face_orders(vi);voro_print_vector(vi,fp);break;
	+ case 'f': face_areas(vd);voro_print_vector(vd,fp);break;
	+ case 't': {
	+ face_vertices(vi);
	+ voro_print_face_vertices(vi,fp);
	+ } break;
	+ case 'l': normals(vd);
	+ voro_print_positions(vd,fp);
	+ break;
	+ case 'n': neighbors(vi);
	+ voro_print_vector(vi,fp);
	+ break;
	+
	+ // Volume-related output
	+ case 'v': fprintf(fp,"%g",volume());break;
	+ case 'c': {
	+ double cx,cy,cz;
	+ centroid(cx,cy,cz);
	+ fprintf(fp,"%g %g %g",cx,cy,cz);
	+ } break;
	+ case 'C': {
	+ double cx,cy,cz;
	+ centroid(cx,cy,cz);
	+ fprintf(fp,"%g %g %g",x+cx,y+cy,z+cz);
	+ } break;
	+
	+ // End-of-string reached
	+ case 0: fmp--;break;
	+
	+ // The percent sign is not part of a
	+ // control sequence
	+ default: putc('%',fp);putc(*fmp,fp);
	+ }
	+ } else putc(*fmp,fp);
	+ fmp++;
	+ }
	+ fputs("\n",fp);
	+}
	+
	+/** This initializes the class to be a rectangular box. It calls the base class
	+ * initialization routine to set up the edge and vertex information, and then
	+ * sets up the neighbor information, with initial faces being assigned ID
	+ * numbers from -1 to -6.
	+ * \param[in] (xmin,xmax) the minimum and maximum x coordinates.
	+ * \param[in] (ymin,ymax) the minimum and maximum y coordinates.
	+ * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */
	+void voronoicell_neighbor::init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) {
	+ init_base(xmin,xmax,ymin,ymax,zmin,zmax);
	+ int *q=mne[3];
	+ *q=-5;q[1]=-3;q[2]=-1;
	+ q[3]=-5;q[4]=-2;q[5]=-3;
	+ q[6]=-5;q[7]=-1;q[8]=-4;
	+ q[9]=-5;q[10]=-4;q[11]=-2;
	+ q[12]=-6;q[13]=-1;q[14]=-3;
	+ q[15]=-6;q[16]=-3;q[17]=-2;
	+ q[18]=-6;q[19]=-4;q[20]=-1;
	+ q[21]=-6;q[22]=-2;q[23]=-4;
	+ *ne=q;ne[1]=q+3;ne[2]=q+6;ne[3]=q+9;
	+ ne[4]=q+12;ne[5]=q+15;ne[6]=q+18;ne[7]=q+21;
	+}
	+
	+/** This initializes the class to be an octahedron. It calls the base class
	+ * initialization routine to set up the edge and vertex information, and then
	+ * sets up the neighbor information, with the initial faces being assigned ID
	+ * numbers from -1 to -8.
	+ * \param[in] l The distance from the octahedron center to a vertex. Six
	+ * vertices are initialized at (-l,0,0), (l,0,0), (0,-l,0),
	+ * (0,l,0), (0,0,-l), and (0,0,l). */
	+void voronoicell_neighbor::init_octahedron(double l) {
	+ init_octahedron_base(l);
	+ int *q=mne[4];
	+ *q=-5;q[1]=-6;q[2]=-7;q[3]=-8;
	+ q[4]=-1;q[5]=-2;q[6]=-3;q[7]=-4;
	+ q[8]=-6;q[9]=-5;q[10]=-2;q[11]=-1;
	+ q[12]=-8;q[13]=-7;q[14]=-4;q[15]=-3;
	+ q[16]=-5;q[17]=-8;q[18]=-3;q[19]=-2;
	+ q[20]=-7;q[21]=-6;q[22]=-1;q[23]=-4;
	+ *ne=q;ne[1]=q+4;ne[2]=q+8;ne[3]=q+12;ne[4]=q+16;ne[5]=q+20;
	+}
	+
	+/** This initializes the class to be a tetrahedron. It calls the base class
	+ * initialization routine to set up the edge and vertex information, and then
	+ * sets up the neighbor information, with the initial faces being assigned ID
	+ * numbers from -1 to -4.
	+ * \param (x0,y0,z0) a position vector for the first vertex.
	+ * \param (x1,y1,z1) a position vector for the second vertex.
	+ * \param (x2,y2,z2) a position vector for the third vertex.
	+ * \param (x3,y3,z3) a position vector for the fourth vertex. */
	+void voronoicell_neighbor::init_tetrahedron(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3) {
	+ init_tetrahedron_base(x0,y0,z0,x1,y1,z1,x2,y2,z2,x3,y3,z3);
	+ int *q=mne[3];
	+ *q=-4;q[1]=-3;q[2]=-2;
	+ q[3]=-3;q[4]=-4;q[5]=-1;
	+ q[6]=-4;q[7]=-2;q[8]=-1;
	+ q[9]=-2;q[10]=-3;q[11]=-1;
	+ *ne=q;ne[1]=q+3;ne[2]=q+6;ne[3]=q+9;
	+}
	+
	+/** This routine checks to make sure the neighbor information of each face is
	+ * consistent. */
	+void voronoicell_neighbor::check_facets() {
	+ int i,j,k,l,m,q;
	+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) {
	+ ed[i][j]=-1-k;
	+ q=ne[i][j];
	+ l=cycle_up(ed[i][nu[i]+j],k);
	+ do {
	+ m=ed[k][l];
	+ ed[k][l]=-1-m;
	+ if(ne[k][l]!=q) fprintf(stderr,"Facet error at (%d,%d)=%d, started from (%d,%d)=%d\n",k,l,ne[k][l],i,j,q);
	+ l=cycle_up(ed[k][nu[k]+l],m);
	+ k=m;
	+ } while (k!=i);
	+ }
	+ }
	+ reset_edges();
	+}
	+
	+/** The class constructor allocates memory for storing neighbor information. */
	+voronoicell_neighbor::voronoicell_neighbor() {
	+ int i;
	+ mne=new int*[current_vertex_order];
	+ ne=new int*[current_vertices];
	+ for(i=0;i<3;i++) mne[i]=new int[init_n_vertices*i];
	+ mne[3]=new int[init_3_vertices*3];
	+ for(i=4;i<current_vertex_order;i++) mne[i]=new int[init_n_vertices*i];
	+}
	+
	+/** The class destructor frees the dynamically allocated memory for storing
	+ * neighbor information. */
	+voronoicell_neighbor::~voronoicell_neighbor() {
	+ for(int i=current_vertex_order-1;i>=0;i--) if(mem[i]>0) delete [] mne[i];
	+ delete [] mne;
	+ delete [] ne;
	+}
	+
	+/** Computes a vector list of neighbors. */
	+void voronoicell_neighbor::neighbors(std::vector<int> &v) {
	+ v.clear();
	+ int i,j,k,l,m;
	+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
	+ k=ed[i][j];
	+ if(k>=0) {
	+ v.push_back(ne[i][j]);
	+ ed[i][j]=-1-k;
	+ l=cycle_up(ed[i][nu[i]+j],k);
	+ do {
	+ m=ed[k][l];
	+ ed[k][l]=-1-m;
	+ l=cycle_up(ed[k][nu[k]+l],m);
	+ k=m;
	+ } while (k!=i);
	+ }
	+ }
	+ reset_edges();
	+}
	+
	+/** Prints the vertices, their edges, the relation table, and also notifies if
	+ * any memory errors are visible. */
	+void voronoicell_base::print_edges() {
	+ int j;
	+ double *ptsp=pts;
	+ for(int i=0;i<p;i++,ptsp+=3) {
	+ printf("%d %d ",i,nu[i]);
	+ for(j=0;j<nu[i];j++) printf(" %d",ed[i][j]);
	+ printf(" ");
	+ while(j<(nu[i]<<1)) printf(" %d",ed[i][j]);
	+ printf(" %d",ed[i][j]);
	+ print_edges_neighbors(i);
	+ printf(" %g %g %g %p",ptsp,ptsp[1],ptsp[2],(void) ed[i]);
	+ if(ed[i]>=mep[nu[i]]+mec[nu[i]]*((nu[i]<<1)+1)) puts(" Memory error");
	+ else puts("");
	+ }
	+}
	+
	+/** This prints out the neighbor information for vertex i. */
	+void voronoicell_neighbor::print_edges_neighbors(int i) {
	+ if(nu[i]>0) {
	+ int j=0;
	+ printf(" (");
	+ while(j<nu[i]-1) printf("%d,",ne[i][j++]);
	+ printf("%d)",ne[i][j]);
	+ } else printf(" ()");
	+}
	+
	+// Explicit instantiation
	+template bool voronoicell_base::nplane(voronoicell&,double,double,double,double,int);
	+template bool voronoicell_base::nplane(voronoicell_neighbor&,double,double,double,double,int);
	+template void voronoicell_base::check_memory_for_copy(voronoicell&,voronoicell_base*);
	+template void voronoicell_base::check_memory_for_copy(voronoicell_neighbor&,voronoicell_base*);
	+
	+}
	Index: extern/voro++/src/container.cc
	===================================================================
	--- extern/voro++/src/container.cc (revision 0)
	+++ extern/voro++/src/container.cc (revision 0)
	@@ -0,0 +1,549 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file container.cc
	+ * \brief Function implementations for the container and related classes. */
	+
	+#include "container.hh"
	+
	+namespace voro {
	+
	+/** The class constructor sets up the geometry of container, initializing the
	+ * minimum and maximum coordinates in each direction, and setting whether each
	+ * direction is periodic or not. It divides the container into a rectangular
	+ * grid of blocks, and allocates memory for each of these for storing particle
	+ * positions and IDs.
	+ * \param[in] (ax_,bx_) the minimum and maximum x coordinates.
	+ * \param[in] (ay_,by_) the minimum and maximum y coordinates.
	+ * \param[in] (az_,bz_) the minimum and maximum z coordinates.
	+ * \param[in] (nx_,ny_,nz_) the number of grid blocks in each of the three
	+ * coordinate directions.
	+ * \param[in] (xperiodic_,yperiodic_,zperiodic_) flags setting whether the
	+ * container is periodic in each
	+ * coordinate direction.
	+ * \param[in] init_mem the initial memory allocation for each block.
	+ * \param[in] ps_ the number of floating point entries to store for each
	+ * particle. */
	+container_base::container_base(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
	+ int nx_,int ny_,int nz_,bool xperiodic_,bool yperiodic_,bool zperiodic_,int init_mem,int ps_)
	+ : voro_base(nx_,ny_,nz_,(bx_-ax_)/nx_,(by_-ay_)/ny_,(bz_-az_)/nz_),
	+ ax(ax_), bx(bx_), ay(ay_), by(by_), az(az_), bz(bz_),
	+ xperiodic(xperiodic_), yperiodic(yperiodic_), zperiodic(zperiodic_),
	+ id(new int[nxyz]), p(new double[nxyz]), co(new int[nxyz]), mem(new int[nxyz]), ps(ps_) {
	+ int l;
	+ for(l=0;l<nxyz;l++) co[l]=0;
	+ for(l=0;l<nxyz;l++) mem[l]=init_mem;
	+ for(l=0;l<nxyz;l++) id[l]=new int[init_mem];
	+ for(l=0;l<nxyz;l++) p[l]=new double[ps*init_mem];
	+}
	+
	+/** The container destructor frees the dynamically allocated memory. */
	+container_base::~container_base() {
	+ int l;
	+ for(l=0;l<nxyz;l++) delete [] p[l];
	+ for(l=0;l<nxyz;l++) delete [] id[l];
	+ delete [] id;
	+ delete [] p;
	+ delete [] co;
	+ delete [] mem;
	+}
	+
	+/** The class constructor sets up the geometry of container.
	+ * \param[in] (ax_,bx_) the minimum and maximum x coordinates.
	+ * \param[in] (ay_,by_) the minimum and maximum y coordinates.
	+ * \param[in] (az_,bz_) the minimum and maximum z coordinates.
	+ * \param[in] (nx_,ny_,nz_) the number of grid blocks in each of the three
	+ * coordinate directions.
	+ * \param[in] (xperiodic_,yperiodic_,zperiodic_) flags setting whether the
	+ * container is periodic in each
	+ * coordinate direction.
	+ * \param[in] init_mem the initial memory allocation for each block. */
	+container::container(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
	+ int nx_,int ny_,int nz_,bool xperiodic_,bool yperiodic_,bool zperiodic_,int init_mem)
	+ : container_base(ax_,bx_,ay_,by_,az_,bz_,nx_,ny_,nz_,xperiodic_,yperiodic_,zperiodic_,init_mem,3),
	+ vc(this,xperiodic_?2nx_+1:nx_,yperiodic_?2ny_+1:ny_,zperiodic_?2nz_+1:nz_) {}
	+
	+/** The class constructor sets up the geometry of container.
	+ * \param[in] (ax_,bx_) the minimum and maximum x coordinates.
	+ * \param[in] (ay_,by_) the minimum and maximum y coordinates.
	+ * \param[in] (az_,bz_) the minimum and maximum z coordinates.
	+ * \param[in] (nx_,ny_,nz_) the number of grid blocks in each of the three
	+ * coordinate directions.
	+ * \param[in] (xperiodic_,yperiodic_,zperiodic_) flags setting whether the
	+ * container is periodic in each
	+ * coordinate direction.
	+ * \param[in] init_mem the initial memory allocation for each block. */
	+container_poly::container_poly(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
	+ int nx_,int ny_,int nz_,bool xperiodic_,bool yperiodic_,bool zperiodic_,int init_mem)
	+ : container_base(ax_,bx_,ay_,by_,az_,bz_,nx_,ny_,nz_,xperiodic_,yperiodic_,zperiodic_,init_mem,4),
	+ vc(this,xperiodic_?2nx_+1:nx_,yperiodic_?2ny_+1:ny_,zperiodic_?2nz_+1:nz_) {ppr=p;}
	+
	+/** Put a particle into the correct region of the container.
	+ * \param[in] n the numerical ID of the inserted particle.
	+ * \param[in] (x,y,z) the position vector of the inserted particle. */
	+void container::put(int n,double x,double y,double z) {
	+ int ijk;
	+ if(put_locate_block(ijk,x,y,z)) {
	+ id[ijk][co[ijk]]=n;
	+ double pp=p[ijk]+3co[ijk]++;
	+ (pp++)=x;(pp++)=y;*pp=z;
	+ }
	+}
	+
	+/** Put a particle into the correct region of the container.
	+ * \param[in] n the numerical ID of the inserted particle.
	+ * \param[in] (x,y,z) the position vector of the inserted particle.
	+ * \param[in] r the radius of the particle. */
	+void container_poly::put(int n,double x,double y,double z,double r) {
	+ int ijk;
	+ if(put_locate_block(ijk,x,y,z)) {
	+ id[ijk][co[ijk]]=n;
	+ double pp=p[ijk]+4co[ijk]++;
	+ (pp++)=x;(pp++)=y;(pp++)=z;pp=r;
	+ if(max_radius<r) max_radius=r;
	+ }
	+}
	+
	+/** Put a particle into the correct region of the container, also recording
	+ * into which region it was stored.
	+ * \param[in] vo the ordering class in which to record the region.
	+ * \param[in] n the numerical ID of the inserted particle.
	+ * \param[in] (x,y,z) the position vector of the inserted particle. */
	+void container::put(particle_order &vo,int n,double x,double y,double z) {
	+ int ijk;
	+ if(put_locate_block(ijk,x,y,z)) {
	+ id[ijk][co[ijk]]=n;
	+ vo.add(ijk,co[ijk]);
	+ double pp=p[ijk]+3co[ijk]++;
	+ (pp++)=x;(pp++)=y;*pp=z;
	+ }
	+}
	+
	+/** Put a particle into the correct region of the container, also recording
	+ * into which region it was stored.
	+ * \param[in] vo the ordering class in which to record the region.
	+ * \param[in] n the numerical ID of the inserted particle.
	+ * \param[in] (x,y,z) the position vector of the inserted particle.
	+ * \param[in] r the radius of the particle. */
	+void container_poly::put(particle_order &vo,int n,double x,double y,double z,double r) {
	+ int ijk;
	+ if(put_locate_block(ijk,x,y,z)) {
	+ id[ijk][co[ijk]]=n;
	+ vo.add(ijk,co[ijk]);
	+ double pp=p[ijk]+4co[ijk]++;
	+ (pp++)=x;(pp++)=y;(pp++)=z;pp=r;
	+ if(max_radius<r) max_radius=r;
	+ }
	+}
	+
	+/** This routine takes a particle position vector, tries to remap it into the
	+ * primary domain. If successful, it computes the region into which it can be
	+ * stored and checks that there is enough memory within this region to store
	+ * it.
	+ * \param[out] ijk the region index.
	+ * \param[in,out] (x,y,z) the particle position, remapped into the primary
	+ * domain if necessary.
	+ * \return True if the particle can be successfully placed into the container,
	+ * false otherwise. */
	+inline bool container_base::put_locate_block(int &ijk,double &x,double &y,double &z) {
	+ if(put_remap(ijk,x,y,z)) {
	+ if(co[ijk]==mem[ijk]) add_particle_memory(ijk);
	+ return true;
	+ }
	+#if VOROPP_REPORT_OUT_OF_BOUNDS ==1
	+ fprintf(stderr,"Out of bounds: (x,y,z)=(%g,%g,%g)\n",x,y,z);
	+#endif
	+ return false;
	+}
	+
	+/** Takes a particle position vector and computes the region index into which
	+ * it should be stored. If the container is periodic, then the routine also
	+ * maps the particle position to ensure it is in the primary domain. If the
	+ * container is not periodic, the routine bails out.
	+ * \param[out] ijk the region index.
	+ * \param[in,out] (x,y,z) the particle position, remapped into the primary
	+ * domain if necessary.
	+ * \return True if the particle can be successfully placed into the container,
	+ * false otherwise. */
	+inline bool container_base::put_remap(int &ijk,double &x,double &y,double &z) {
	+ int l;
	+
	+ ijk=step_int((x-ax)*xsp);
	+ if(xperiodic) {l=step_mod(ijk,nx);x+=boxx*(l-ijk);ijk=l;}
	+ else if(ijk<0\|\|ijk>=nx) return false;
	+
	+ int j=step_int((y-ay)*ysp);
	+ if(yperiodic) {l=step_mod(j,ny);y+=boxy*(l-j);j=l;}
	+ else if(j<0\|\|j>=ny) return false;
	+
	+ int k=step_int((z-az)*zsp);
	+ if(zperiodic) {l=step_mod(k,nz);z+=boxz*(l-k);k=l;}
	+ else if(k<0\|\|k>=nz) return false;
	+
	+ ijk+=nxj+nxyk;
	+ return true;
	+}
	+
	+/** Takes a position vector and attempts to remap it into the primary domain.
	+ * \param[out] (ai,aj,ak) the periodic image displacement that the vector is in,
	+ * with (0,0,0) corresponding to the primary domain.
	+ * \param[out] (ci,cj,ck) the index of the block that the position vector is
	+ * within, once it has been remapped.
	+ * \param[in,out] (x,y,z) the position vector to consider, which is remapped
	+ * into the primary domain during the routine.
	+ * \param[out] ijk the block index that the vector is within.
	+ * \return True if the particle is within the container or can be remapped into
	+ * it, false if it lies outside of the container bounds. */
	+inline bool container_base::remap(int &ai,int &aj,int &ak,int &ci,int &cj,int &ck,double &x,double &y,double &z,int &ijk) {
	+ ci=step_int((x-ax)*xsp);
	+ if(ci<0\|\|ci>=nx) {
	+ if(xperiodic) {ai=step_div(ci,nx);x-=ai(bx-ax);ci-=ainx;}
	+ else return false;
	+ } else ai=0;
	+
	+ cj=step_int((y-ay)*ysp);
	+ if(cj<0\|\|cj>=ny) {
	+ if(yperiodic) {aj=step_div(cj,ny);y-=aj(by-ay);cj-=ajny;}
	+ else return false;
	+ } else aj=0;
	+
	+ ck=step_int((z-az)*zsp);
	+ if(ck<0\|\|ck>=nz) {
	+ if(zperiodic) {ak=step_div(ck,nz);z-=ak(bz-az);ck-=aknz;}
	+ else return false;
	+ } else ak=0;
	+
	+ ijk=ci+nxcj+nxyck;
	+ return true;
	+}
	+
	+/** Takes a vector and finds the particle whose Voronoi cell contains that
	+ * vector. This is equivalent to finding the particle which is nearest to the
	+ * vector. Additional wall classes are not considered by this routine.
	+ * \param[in] (x,y,z) the vector to test.
	+ * \param[out] (rx,ry,rz) the position of the particle whose Voronoi cell
	+ * contains the vector. If the container is periodic,
	+ * this may point to a particle in a periodic image of
	+ * the primary domain.
	+ * \param[out] pid the ID of the particle.
	+ * \return True if a particle was found. If the container has no particles,
	+ * then the search will not find a Voronoi cell and false is returned. */
	+bool container::find_voronoi_cell(double x,double y,double z,double &rx,double &ry,double &rz,int &pid) {
	+ int ai,aj,ak,ci,cj,ck,ijk;
	+ particle_record w;
	+ double mrs;
	+
	+ // If the given vector lies outside the domain, but the container
	+ // is periodic, then remap it back into the domain
	+ if(!remap(ai,aj,ak,ci,cj,ck,x,y,z,ijk)) return false;
	+ vc.find_voronoi_cell(x,y,z,ci,cj,ck,ijk,w,mrs);
	+
	+ if(w.ijk!=-1) {
	+
	+ // Assemble the position vector of the particle to be returned,
	+ // applying a periodic remapping if necessary
	+ if(xperiodic) {ci+=w.di;if(ci<0\|\|ci>=nx) ai+=step_div(ci,nx);}
	+ if(yperiodic) {cj+=w.dj;if(cj<0\|\|cj>=ny) aj+=step_div(cj,ny);}
	+ if(zperiodic) {ck+=w.dk;if(ck<0\|\|ck>=nz) ak+=step_div(ck,nz);}
	+ rx=p[w.ijk][3w.l]+ai(bx-ax);
	+ ry=p[w.ijk][3w.l+1]+aj(by-ay);
	+ rz=p[w.ijk][3w.l+2]+ak(bz-az);
	+ pid=id[w.ijk][w.l];
	+ return true;
	+ }
	+
	+ // If no particle if found then just return false
	+ return false;
	+}
	+
	+/** Takes a vector and finds the particle whose Voronoi cell contains that
	+ * vector. Additional wall classes are not considered by this routine.
	+ * \param[in] (x,y,z) the vector to test.
	+ * \param[out] (rx,ry,rz) the position of the particle whose Voronoi cell
	+ * contains the vector. If the container is periodic,
	+ * this may point to a particle in a periodic image of
	+ * the primary domain.
	+ * \param[out] pid the ID of the particle.
	+ * \return True if a particle was found. If the container has no particles,
	+ * then the search will not find a Voronoi cell and false is returned. */
	+bool container_poly::find_voronoi_cell(double x,double y,double z,double &rx,double &ry,double &rz,int &pid) {
	+ int ai,aj,ak,ci,cj,ck,ijk;
	+ particle_record w;
	+ double mrs;
	+
	+ // If the given vector lies outside the domain, but the container
	+ // is periodic, then remap it back into the domain
	+ if(!remap(ai,aj,ak,ci,cj,ck,x,y,z,ijk)) return false;
	+ vc.find_voronoi_cell(x,y,z,ci,cj,ck,ijk,w,mrs);
	+
	+ if(w.ijk!=-1) {
	+
	+ // Assemble the position vector of the particle to be returned,
	+ // applying a periodic remapping if necessary
	+ if(xperiodic) {ci+=w.di;if(ci<0\|\|ci>=nx) ai+=step_div(ci,nx);}
	+ if(yperiodic) {cj+=w.dj;if(cj<0\|\|cj>=ny) aj+=step_div(cj,ny);}
	+ if(zperiodic) {ck+=w.dk;if(ck<0\|\|ck>=nz) ak+=step_div(ck,nz);}
	+ rx=p[w.ijk][4w.l]+ai(bx-ax);
	+ ry=p[w.ijk][4w.l+1]+aj(by-ay);
	+ rz=p[w.ijk][4w.l+2]+ak(bz-az);
	+ pid=id[w.ijk][w.l];
	+ return true;
	+ }
	+
	+ // If no particle if found then just return false
	+ return false;
	+}
	+
	+/** Increase memory for a particular region.
	+ * \param[in] i the index of the region to reallocate. */
	+void container_base::add_particle_memory(int i) {
	+ int l,nmem=mem[i]<<1;
	+
	+ // Carry out a check on the memory allocation size, and
	+ // print a status message if requested
	+ if(nmem>max_particle_memory)
	+ voro_fatal_error("Absolute maximum memory allocation exceeded",VOROPP_MEMORY_ERROR);
	+#if VOROPP_VERBOSE >=3
	+ fprintf(stderr,"Particle memory in region %d scaled up to %d\n",i,nmem);
	+#endif
	+
	+ // Allocate new memory and copy in the contents of the old arrays
	+ int *idp=new int[nmem];
	+ for(l=0;l<co[i];l++) idp[l]=id[i][l];
	+ double pp=new double[psnmem];
	+ for(l=0;l<ps*co[i];l++) pp[l]=p[i][l];
	+
	+ // Update pointers and delete old arrays
	+ mem[i]=nmem;
	+ delete [] id[i];id[i]=idp;
	+ delete [] p[i];p[i]=pp;
	+}
	+
	+/** Import a list of particles from an open file stream into the container.
	+ * Entries of four numbers (Particle ID, x position, y position, z position)
	+ * are searched for. If the file cannot be successfully read, then the routine
	+ * causes a fatal error.
	+ * \param[in] fp the file handle to read from. */
	+void container::import(FILE *fp) {
	+ int i,j;
	+ double x,y,z;
	+ while((j=fscanf(fp,"%d %lg %lg %lg",&i,&x,&y,&z))==4) put(i,x,y,z);
	+ if(j!=EOF) voro_fatal_error("File import error",VOROPP_FILE_ERROR);
	+}
	+
	+/** Import a list of particles from an open file stream, also storing the order
	+ * of that the particles are read. Entries of four numbers (Particle ID, x
	+ * position, y position, z position) are searched for. If the file cannot be
	+ * successfully read, then the routine causes a fatal error.
	+ * \param[in,out] vo a reference to an ordering class to use.
	+ * \param[in] fp the file handle to read from. */
	+void container::import(particle_order &vo,FILE *fp) {
	+ int i,j;
	+ double x,y,z;
	+ while((j=fscanf(fp,"%d %lg %lg %lg",&i,&x,&y,&z))==4) put(vo,i,x,y,z);
	+ if(j!=EOF) voro_fatal_error("File import error",VOROPP_FILE_ERROR);
	+}
	+
	+/** Import a list of particles from an open file stream into the container.
	+ * Entries of five numbers (Particle ID, x position, y position, z position,
	+ * radius) are searched for. If the file cannot be successfully read, then the
	+ * routine causes a fatal error.
	+ * \param[in] fp the file handle to read from. */
	+void container_poly::import(FILE *fp) {
	+ int i,j;
	+ double x,y,z,r;
	+ while((j=fscanf(fp,"%d %lg %lg %lg %lg",&i,&x,&y,&z,&r))==5) put(i,x,y,z,r);
	+ if(j!=EOF) voro_fatal_error("File import error",VOROPP_FILE_ERROR);
	+}
	+
	+/** Import a list of particles from an open file stream, also storing the order
	+ * of that the particles are read. Entries of four numbers (Particle ID, x
	+ * position, y position, z position, radius) are searched for. If the file
	+ * cannot be successfully read, then the routine causes a fatal error.
	+ * \param[in,out] vo a reference to an ordering class to use.
	+ * \param[in] fp the file handle to read from. */
	+void container_poly::import(particle_order &vo,FILE *fp) {
	+ int i,j;
	+ double x,y,z,r;
	+ while((j=fscanf(fp,"%d %lg %lg %lg %lg",&i,&x,&y,&z,&r))==5) put(vo,i,x,y,z,r);
	+ if(j!=EOF) voro_fatal_error("File import error",VOROPP_FILE_ERROR);
	+}
	+
	+/** Outputs the a list of all the container regions along with the number of
	+ * particles stored within each. */
	+void container_base::region_count() {
	+ int i,j,k,*cop=co;
	+ for(k=0;k<nz;k++) for(j=0;j<ny;j++) for(i=0;i<nx;i++)
	+ printf("Region (%d,%d,%d): %d particles\n",i,j,k,*(cop++));
	+}
	+
	+/** Clears a container of particles. */
	+void container::clear() {
	+ for(int cop=co;cop<co+nxyz;cop++) cop=0;
	+}
	+
	+/** Clears a container of particles, also clearing resetting the maximum radius
	+ * to zero. */
	+void container_poly::clear() {
	+ for(int cop=co;cop<co+nxyz;cop++) cop=0;
	+ max_radius=0;
	+}
	+
	+/** Computes all the Voronoi cells and saves customized information about them.
	+ * \param[in] format the custom output string to use.
	+ * \param[in] fp a file handle to write to. */
	+void container::print_custom(const char format,FILE fp) {
	+ c_loop_all vl(*this);
	+ print_custom(vl,format,fp);
	+}
	+
	+/** Computes all the Voronoi cells and saves customized
	+ * information about them.
	+ * \param[in] format the custom output string to use.
	+ * \param[in] fp a file handle to write to. */
	+void container_poly::print_custom(const char format,FILE fp) {
	+ c_loop_all vl(*this);
	+ print_custom(vl,format,fp);
	+}
	+
	+/** Computes all the Voronoi cells and saves customized information about them.
	+ * \param[in] format the custom output string to use.
	+ * \param[in] filename the name of the file to write to. */
	+void container::print_custom(const char format,const char filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ print_custom(format,fp);
	+ fclose(fp);
	+}
	+
	+/** Computes all the Voronoi cells and saves customized
	+ * information about them
	+ * \param[in] format the custom output string to use.
	+ * \param[in] filename the name of the file to write to. */
	+void container_poly::print_custom(const char format,const char filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ print_custom(format,fp);
	+ fclose(fp);
	+}
	+
	+/** Computes all of the Voronoi cells in the container, but does nothing
	+ * with the output. It is useful for measuring the pure computation time
	+ * of the Voronoi algorithm, without any additional calculations such as
	+ * volume evaluation or cell output. */
	+void container::compute_all_cells() {
	+ voronoicell c;
	+ c_loop_all vl(*this);
	+ if(vl.start()) do compute_cell(c,vl);
	+ while(vl.inc());
	+}
	+
	+/** Computes all of the Voronoi cells in the container, but does nothing
	+ * with the output. It is useful for measuring the pure computation time
	+ * of the Voronoi algorithm, without any additional calculations such as
	+ * volume evaluation or cell output. */
	+void container_poly::compute_all_cells() {
	+ voronoicell c;
	+ c_loop_all vl(*this);
	+ if(vl.start()) do compute_cell(c,vl);while(vl.inc());
	+}
	+
	+/** Calculates all of the Voronoi cells and sums their volumes. In most cases
	+ * without walls, the sum of the Voronoi cell volumes should equal the volume
	+ * of the container to numerical precision.
	+ * \return The sum of all of the computed Voronoi volumes. */
	+double container::sum_cell_volumes() {
	+ voronoicell c;
	+ double vol=0;
	+ c_loop_all vl(*this);
	+ if(vl.start()) do if(compute_cell(c,vl)) vol+=c.volume();while(vl.inc());
	+ return vol;
	+}
	+
	+/** Calculates all of the Voronoi cells and sums their volumes. In most cases
	+ * without walls, the sum of the Voronoi cell volumes should equal the volume
	+ * of the container to numerical precision.
	+ * \return The sum of all of the computed Voronoi volumes. */
	+double container_poly::sum_cell_volumes() {
	+ voronoicell c;
	+ double vol=0;
	+ c_loop_all vl(*this);
	+ if(vl.start()) do if(compute_cell(c,vl)) vol+=c.volume();while(vl.inc());
	+ return vol;
	+}
	+
	+/** This function tests to see if a given vector lies within the container
	+ * bounds and any walls.
	+ * \param[in] (x,y,z) the position vector to be tested.
	+ * \return True if the point is inside the container, false if the point is
	+ * outside. */
	+bool container_base::point_inside(double x,double y,double z) {
	+ if(x<ax\|\|x>bx\|\|y<ay\|\|y>by\|\|z<az\|\|z>bz) return false;
	+ return point_inside_walls(x,y,z);
	+}
	+
	+/** Draws an outline of the domain in gnuplot format.
	+ * \param[in] fp the file handle to write to. */
	+void container_base::draw_domain_gnuplot(FILE *fp) {
	+ fprintf(fp,"%g %g %g\n%g %g %g\n%g %g %g\n%g %g %g\n",ax,ay,az,bx,ay,az,bx,by,az,ax,by,az);
	+ fprintf(fp,"%g %g %g\n%g %g %g\n%g %g %g\n%g %g %g\n",ax,by,bz,bx,by,bz,bx,ay,bz,ax,ay,bz);
	+ fprintf(fp,"%g %g %g\n\n%g %g %g\n%g %g %g\n\n",ax,by,bz,ax,ay,az,ax,ay,bz);
	+ fprintf(fp,"%g %g %g\n%g %g %g\n\n%g %g %g\n%g %g %g\n\n",bx,ay,az,bx,ay,bz,bx,by,az,bx,by,bz);
	+}
	+
	+/** Draws an outline of the domain in POV-Ray format.
	+ * \param[in] fp the file handle to write to. */
	+void container_base::draw_domain_pov(FILE *fp) {
	+ fprintf(fp,"cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n"
	+ "cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n",ax,ay,az,bx,ay,az,ax,by,az,bx,by,az);
	+ fprintf(fp,"cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n"
	+ "cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n",ax,by,bz,bx,by,bz,ax,ay,bz,bx,ay,bz);
	+ fprintf(fp,"cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n"
	+ "cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n",ax,ay,az,ax,by,az,bx,ay,az,bx,by,az);
	+ fprintf(fp,"cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n"
	+ "cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n",bx,ay,bz,bx,by,bz,ax,ay,bz,ax,by,bz);
	+ fprintf(fp,"cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n"
	+ "cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n",ax,ay,az,ax,ay,bz,bx,ay,az,bx,ay,bz);
	+ fprintf(fp,"cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n"
	+ "cylinder{<%g,%g,%g>,<%g,%g,%g>,rr}\n",bx,by,az,bx,by,bz,ax,by,az,ax,by,bz);
	+ fprintf(fp,"sphere{<%g,%g,%g>,rr}\nsphere{<%g,%g,%g>,rr}\n"
	+ "sphere{<%g,%g,%g>,rr}\nsphere{<%g,%g,%g>,rr}\n",ax,ay,az,bx,ay,az,ax,by,az,bx,by,az);
	+ fprintf(fp,"sphere{<%g,%g,%g>,rr}\nsphere{<%g,%g,%g>,rr}\n"
	+ "sphere{<%g,%g,%g>,rr}\nsphere{<%g,%g,%g>,rr}\n",ax,ay,bz,bx,ay,bz,ax,by,bz,bx,by,bz);
	+}
	+
	+
	+/** The wall_list constructor sets up an array of pointers to wall classes. */
	+wall_list::wall_list() : walls(new wall*[init_wall_size]), wep(walls), wel(walls+init_wall_size),
	+ current_wall_size(init_wall_size) {}
	+
	+/** The wall_list destructor frees the array of pointers to the wall classes.
	+ */
	+wall_list::~wall_list() {
	+ delete [] walls;
	+}
	+
	+/** Adds all of the walls on another wall_list to this class.
	+ * \param[in] wl a reference to the wall class. */
	+void wall_list::add_wall(wall_list &wl) {
	+ for(wall *wp=wl.walls;wp<wl.wep;wp++) add_wall(wp);
	+}
	+
	+/** Deallocates all of the wall classes pointed to by the wall_list. */
	+void wall_list::deallocate() {
	+ for(wall *wp=walls;wp<wep;wp++) delete wp;
	+}
	+
	+/** Increases the memory allocation for the walls array. */
	+void wall_list::increase_wall_memory() {
	+ current_wall_size<<=1;
	+ if(current_wall_size>max_wall_size)
	+ voro_fatal_error("Wall memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
	+ wall *nwalls=new wall[current_wall_size],nwp=nwalls,wp=walls;
	+ while(wp<wep) (nwp++)=(wp++);
	+ delete [] walls;
	+ walls=nwalls;wel=walls+current_wall_size;wep=nwp;
	+}
	+
	+}
	Index: extern/voro++/src/worklist.hh
	===================================================================
	--- extern/voro++/src/worklist.hh (revision 0)
	+++ extern/voro++/src/worklist.hh (revision 0)
	@@ -0,0 +1,32 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file worklist.hh
	+ * \brief Header file for setting constants used in the block worklists that are
	+ * used during cell computation.
	+ *
	+ * This file is automatically generated by worklist_gen.pl and it is not
	+ * intended to be edited by hand. */
	+
	+#ifndef VOROPP_WORKLIST_HH
	+#define VOROPP_WORKLIST_HH
	+
	+namespace voro {
	+
	+/** Each region is divided into a grid of subregions, and a worklist is
	+# constructed for each. This parameter sets is set to half the number of
	+# subregions that the block is divided into. */
	+const int wl_hgrid=4;
	+/** The number of subregions that a block is subdivided into, which is twice
	+the value of hgrid. */
	+const int wl_fgrid=8;
	+/** The total number of worklists, set to the cube of hgrid. */
	+const int wl_hgridcu=64;
	+/** The number of elements in each worklist. */
	+const int wl_seq_length=64;
	+
	+}
	+#endif
	Index: extern/voro++/src/common.cc
	===================================================================
	--- extern/voro++/src/common.cc (revision 0)
	+++ extern/voro++/src/common.cc (revision 0)
	@@ -0,0 +1,90 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file common.cc
	+ * \brief Implementations of the small helper functions. */
	+
	+#include "common.hh"
	+
	+namespace voro {
	+
	+/** \brief Prints a vector of integers.
	+ *
	+ * Prints a vector of integers.
	+ * \param[in] v the vector to print.
	+ * \param[in] fp the file stream to print to. */
	+void voro_print_vector(std::vector<int> &v,FILE *fp) {
	+ int k=0,s=v.size();
	+ while(k+4<s) {
	+ fprintf(fp,"%d %d %d %d ",v[k],v[k+1],v[k+2],v[k+3]);
	+ k+=4;
	+ }
	+ if(k+3<=s) {
	+ if(k+4==s) fprintf(fp,"%d %d %d %d",v[k],v[k+1],v[k+2],v[k+3]);
	+ else fprintf(fp,"%d %d %d",v[k],v[k+1],v[k+2]);
	+ } else {
	+ if(k+2==s) fprintf(fp,"%d %d",v[k],v[k+1]);
	+ else fprintf(fp,"%d",v[k]);
	+ }
	+}
	+
	+/** \brief Prints a vector of doubles.
	+ *
	+ * Prints a vector of doubles.
	+ * \param[in] v the vector to print.
	+ * \param[in] fp the file stream to print to. */
	+void voro_print_vector(std::vector<double> &v,FILE *fp) {
	+ int k=0,s=v.size();
	+ while(k+4<s) {
	+ fprintf(fp,"%g %g %g %g ",v[k],v[k+1],v[k+2],v[k+3]);
	+ k+=4;
	+ }
	+ if(k+3<=s) {
	+ if(k+4==s) fprintf(fp,"%g %g %g %g",v[k],v[k+1],v[k+2],v[k+3]);
	+ else fprintf(fp,"%g %g %g",v[k],v[k+1],v[k+2]);
	+ } else {
	+ if(k+2==s) fprintf(fp,"%g %g",v[k],v[k+1]);
	+ else fprintf(fp,"%g",v[k]);
	+ }
	+}
	+
	+/** \brief Prints a vector a face vertex information.
	+ *
	+ * Prints a vector of face vertex information. A value is read, which
	+ * corresponds to the number of vertices in the next face. The routine reads
	+ * this number of values and prints them as a bracked list. This is repeated
	+ * until the end of the vector is reached.
	+ * \param[in] v the vector to interpret and print.
	+ * \param[in] fp the file stream to print to. */
	+void voro_print_face_vertices(std::vector<int> &v,FILE *fp) {
	+ int j,k=0,l;
	+ if(v.size()>0) {
	+ l=v[k++];
	+ if(l<=1) {
	+ if(l==1) fprintf(fp,"(%d)",v[k++]);
	+ else fputs("()",fp);
	+ } else {
	+ j=k+l;
	+ fprintf(fp,"(%d",v[k++]);
	+ while(k<j) fprintf(fp,",%d",v[k++]);
	+ fputs(")",fp);
	+ }
	+ while((unsigned int) k<v.size()) {
	+ l=v[k++];
	+ if(l<=1) {
	+ if(l==1) fprintf(fp," (%d)",v[k++]);
	+ else fputs(" ()",fp);
	+ } else {
	+ j=k+l;
	+ fprintf(fp," (%d",v[k++]);
	+ while(k<j) fprintf(fp,",%d",v[k++]);
	+ fputs(")",fp);
	+ }
	+ }
	+ }
	+}
	+
	+}
	Index: extern/voro++/src/pre_container.cc
	===================================================================
	--- extern/voro++/src/pre_container.cc (revision 0)
	+++ extern/voro++/src/pre_container.cc (revision 0)
	@@ -0,0 +1,236 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file pre_container.cc
	+ * \brief Function implementations for the pre_container and related classes.
	+ */
	+
	+#include <cmath>
	+
	+#include "config.hh"
	+#include "pre_container.hh"
	+
	+namespace voro {
	+
	+/** The class constructor sets up the geometry of container, initializing the
	+ * minimum and maximum coordinates in each direction. It allocates an initial
	+ * chunk into which to store particle information.
	+ * \param[in] (ax_,bx_) the minimum and maximum x coordinates.
	+ * \param[in] (ay_,by_) the minimum and maximum y coordinates.
	+ * \param[in] (az_,bz_) the minimum and maximum z coordinates.
	+ * \param[in] (xperiodic_,yperiodic_,zperiodic_ ) flags setting whether the
	+ * container is periodic in each
	+ * coordinate direction.
	+ * \param[in] ps_ the number of floating point entries to store for each
	+ * particle. */
	+pre_container_base::pre_container_base(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
	+ bool xperiodic_,bool yperiodic_,bool zperiodic_,int ps_) :
	+ ax(ax_), bx(bx_), ay(ay_), by(by_), az(az_), bz(bz_),
	+ xperiodic(xperiodic_), yperiodic(yperiodic_), zperiodic(zperiodic_), ps(ps_),
	+ index_sz(init_chunk_size), pre_id(new int*[index_sz]), end_id(pre_id),
	+ pre_p(new double*[index_sz]), end_p(pre_p) {
	+ ch_id=*end_id=new int[pre_container_chunk_size];
	+ l_id=end_id+index_sz;e_id=ch_id+pre_container_chunk_size;
	+ ch_p=end_p=new double[pspre_container_chunk_size];
	+}
	+
	+/** The destructor frees the dynamically allocated memory. */
	+pre_container_base::~pre_container_base() {
	+ delete [] *end_p;
	+ delete [] *end_id;
	+ while (end_id!=pre_id) {
	+ end_p--;
	+ delete [] *end_p;
	+ end_id--;
	+ delete [] *end_id;
	+ }
	+ delete [] pre_p;
	+ delete [] pre_id;
	+}
	+
	+/** Makes a guess at the optimal grid of blocks to use, computing in
	+ * a way that
	+ * \param[out] (nx,ny,nz) the number of blocks to use. */
	+void pre_container_base::guess_optimal(int &nx,int &ny,int &nz) {
	+ double dx=bx-ax,dy=by-ay,dz=bz-az;
	+ double ilscale=pow(total_particles()/(optimal_particlesdxdy*dz),1/3.0);
	+ nx=int(dx*ilscale+1);
	+ ny=int(dy*ilscale+1);
	+ nz=int(dz*ilscale+1);
	+}
	+
	+/** Stores a particle ID and position, allocating a new memory chunk if
	+ * necessary. For coordinate directions in which the container is not periodic,
	+ * the routine checks to make sure that the particle is within the container
	+ * bounds. If the particle is out of bounds, it is not stored.
	+ * \param[in] n the numerical ID of the inserted particle.
	+ * \param[in] (x,y,z) the position vector of the inserted particle. */
	+void pre_container::put(int n,double x,double y,double z) {
	+ if((xperiodic\|\|(x>=ax&&x<=bx))&&(yperiodic\|\|(y>=ay&&y<=by))&&(zperiodic\|\|(z>=az&&z<=bz))) {
	+ if(ch_id==e_id) new_chunk();
	+ *(ch_id++)=n;
	+ (ch_p++)=x;(ch_p++)=y;*(ch_p++)=z;
	+ }
	+#if VOROPP_REPORT_OUT_OF_BOUNDS ==1
	+ else fprintf(stderr,"Out of bounds: (x,y,z)=(%g,%g,%g)\n",x,y,z);
	+#endif
	+}
	+
	+/** Stores a particle ID and position, allocating a new memory chunk if necessary.
	+ * \param[in] n the numerical ID of the inserted particle.
	+ * \param[in] (x,y,z) the position vector of the inserted particle.
	+ * \param[in] r the radius of the particle. */
	+void pre_container_poly::put(int n,double x,double y,double z,double r) {
	+ if((xperiodic\|\|(x>=ax&&x<=bx))&&(yperiodic\|\|(y>=ay&&y<=by))&&(zperiodic\|\|(z>=az&&z<=bz))) {
	+ if(ch_id==e_id) new_chunk();
	+ *(ch_id++)=n;
	+ (ch_p++)=x;(ch_p++)=y;(ch_p++)=z;(ch_p++)=r;
	+ }
	+#if VOROPP_REPORT_OUT_OF_BOUNDS ==1
	+ else fprintf(stderr,"Out of bounds: (x,y,z)=(%g,%g,%g)\n",x,y,z);
	+#endif
	+}
	+
	+/** Transfers the particles stored within the class to a container class.
	+ * \param[in] con the container class to transfer to. */
	+void pre_container::setup(container &con) {
	+ int *c_id=pre_id,idp,*ide,n;
	+ double *c_p=pre_p,pp,x,y,z;
	+ while(c_id<end_id) {
	+ idp=*(c_id++);ide=idp+pre_container_chunk_size;
	+ pp=*(c_p++);
	+ while(idp<ide) {
	+ n=(idp++);x=(pp++);y=(pp++);z=(pp++);
	+ con.put(n,x,y,z);
	+ }
	+ }
	+ idp=*c_id;
	+ pp=*c_p;
	+ while(idp<ch_id) {
	+ n=(idp++);x=(pp++);y=(pp++);z=(pp++);
	+ con.put(n,x,y,z);
	+ }
	+}
	+
	+/** Transfers the particles stored within the class to a container_poly class.
	+ * \param[in] con the container_poly class to transfer to. */
	+void pre_container_poly::setup(container_poly &con) {
	+ int *c_id=pre_id,idp,*ide,n;
	+ double *c_p=pre_p,pp,x,y,z,r;
	+ while(c_id<end_id) {
	+ idp=*(c_id++);ide=idp+pre_container_chunk_size;
	+ pp=*(c_p++);
	+ while(idp<ide) {
	+ n=(idp++);x=(pp++);y=(pp++);z=(pp++);r=*(pp++);
	+ con.put(n,x,y,z,r);
	+ }
	+ }
	+ idp=*c_id;
	+ pp=*c_p;
	+ while(idp<ch_id) {
	+ n=(idp++);x=(pp++);y=(pp++);z=(pp++);r=*(pp++);
	+ con.put(n,x,y,z,r);
	+ }
	+}
	+
	+/** Transfers the particles stored within the class to a container class, also
	+ * recording the order in which particles were stored.
	+ * \param[in] vo the ordering class to use.
	+ * \param[in] con the container class to transfer to. */
	+void pre_container::setup(particle_order &vo,container &con) {
	+ int *c_id=pre_id,idp,*ide,n;
	+ double *c_p=pre_p,pp,x,y,z;
	+ while(c_id<end_id) {
	+ idp=*(c_id++);ide=idp+pre_container_chunk_size;
	+ pp=*(c_p++);
	+ while(idp<ide) {
	+ n=(idp++);x=(pp++);y=(pp++);z=(pp++);
	+ con.put(vo,n,x,y,z);
	+ }
	+ }
	+ idp=*c_id;
	+ pp=*c_p;
	+ while(idp<ch_id) {
	+ n=(idp++);x=(pp++);y=(pp++);z=(pp++);
	+ con.put(vo,n,x,y,z);
	+ }
	+}
	+
	+/** Transfers the particles stored within the class to a container_poly class,
	+ * also recording the order in which particles were stored.
	+ * \param[in] vo the ordering class to use.
	+ * \param[in] con the container_poly class to transfer to. */
	+void pre_container_poly::setup(particle_order &vo,container_poly &con) {
	+ int *c_id=pre_id,idp,*ide,n;
	+ double *c_p=pre_p,pp,x,y,z,r;
	+ while(c_id<end_id) {
	+ idp=*(c_id++);ide=idp+pre_container_chunk_size;
	+ pp=*(c_p++);
	+ while(idp<ide) {
	+ n=(idp++);x=(pp++);y=(pp++);z=(pp++);r=*(pp++);
	+ con.put(vo,n,x,y,z,r);
	+ }
	+ }
	+ idp=*c_id;
	+ pp=*c_p;
	+ while(idp<ch_id) {
	+ n=(idp++);x=(pp++);y=(pp++);z=(pp++);r=*(pp++);
	+ con.put(vo,n,x,y,z,r);
	+ }
	+}
	+
	+/** Import a list of particles from an open file stream into the container.
	+ * Entries of four numbers (Particle ID, x position, y position, z position)
	+ * are searched for. If the file cannot be successfully read, then the routine
	+ * causes a fatal error.
	+ * \param[in] fp the file handle to read from. */
	+void pre_container::import(FILE *fp) {
	+ int i,j;
	+ double x,y,z;
	+ while((j=fscanf(fp,"%d %lg %lg %lg",&i,&x,&y,&z))==4) put(i,x,y,z);
	+ if(j!=EOF) voro_fatal_error("File import error",VOROPP_FILE_ERROR);
	+}
	+
	+/** Import a list of particles from an open file stream, also storing the order
	+ * of that the particles are read. Entries of four numbers (Particle ID, x
	+ * position, y position, z position) are searched for. If the file cannot be
	+ * successfully read, then the routine causes a fatal error.
	+ * \param[in] fp the file handle to read from. */
	+void pre_container_poly::import(FILE *fp) {
	+ int i,j;
	+ double x,y,z,r;
	+ while((j=fscanf(fp,"%d %lg %lg %lg %lg",&i,&x,&y,&z,&r))==5) put(i,x,y,z,r);
	+ if(j!=EOF) voro_fatal_error("File import error",VOROPP_FILE_ERROR);
	+}
	+
	+/** Allocates a new chunk of memory for storing particles. */
	+void pre_container_base::new_chunk() {
	+ end_id++;end_p++;
	+ if(end_id==l_id) extend_chunk_index();
	+ ch_id=*end_id=new int[pre_container_chunk_size];
	+ e_id=ch_id+pre_container_chunk_size;
	+ ch_p=end_p=new double[pspre_container_chunk_size];
	+}
	+
	+/** Extends the index of chunks. */
	+void pre_container_base::extend_chunk_index() {
	+ index_sz<<=1;
	+ if(index_sz>max_chunk_size)
	+ voro_fatal_error("Absolute memory limit on chunk index reached",VOROPP_MEMORY_ERROR);
	+#if VOROPP_VERBOSE >=2
	+ fprintf(stderr,"Pre-container chunk index scaled up to %d\n",index_sz);
	+#endif
	+ int *n_id=new int[index_sz],p_id=n_id,c_id=pre_id;
	+ double *n_p=new double[index_sz],p_p=n_p,c_p=pre_p;
	+ while(c_id<end_id) {
	+ (p_id++)=(c_id++);
	+ (p_p++)=(c_p++);
	+ }
	+ delete [] pre_id;pre_id=n_id;end_id=p_id;l_id=pre_id+index_sz;
	+ delete [] pre_p;pre_p=n_p;end_p=p_p;
	+}
	+
	+}
	Index: extern/voro++/src/Makefile
	===================================================================
	--- extern/voro++/src/Makefile (revision 0)
	+++ extern/voro++/src/Makefile (revision 0)
	@@ -0,0 +1,39 @@
	+# Voro++ makefile
	+#
	+# Author : Chris H. Rycroft (LBL / UC Berkeley)
	+# Email : chr@alum.mit.edu
	+# Date : August 30th 2011
	+
	+# Load the common configuration file
	+include ../config.mk
	+
	+# List of the common source files
	+objs=cell.o common.o container.o unitcell.o v_compute.o c_loops.o \
	+ v_base.o wall.o pre_container.o container_prd.o
	+src=$(patsubst %.o,%.cc,$(objs))
	+
	+# Makefile rules
	+all: libvoro++.a voro++
	+
	+depend:
	+ $(CXX) -MM $(src) >Makefile.dep
	+
	+include Makefile.dep
	+
	+libvoro++.a: $(objs)
	+ rm -f libvoro++.a
	+ ar rs libvoro++.a $^
	+
	+voro++: libvoro++.a cmd_line.cc
	+ $(CXX) $(CFLAGS) -L. -o voro++ cmd_line.cc -lvoro++
	+
	+%.o: %.cc
	+ $(CXX) $(CFLAGS) -c $<
	+
	+help: Doxyfile $(SOURCE)
	+ doxygen Doxyfile
	+
	+clean:
	+ rm -f $(objs) voro++ libvoro++.a
	+
	+.PHONY: all help execs depend
	Index: extern/voro++/src/worklist_gen.pl
	===================================================================
	--- extern/voro++/src/worklist_gen.pl (revision 0)
	+++ extern/voro++/src/worklist_gen.pl (revision 0)
	@@ -0,0 +1,236 @@
	+#!/usr/bin/perl
	+# Voro++, a 3D cell-based Voronoi library
	+#
	+# Author : Chris H. Rycroft (LBL / UC Berkeley)
	+# Email : chr@alum.mit.edu
	+# Date : August 30th 2011
	+#
	+# worklist_gen.pl - this perl script is used to automatically generate the
	+# worklists of blocks that are stored in worklist.cc, that are used by the
	+# compute_cell() routine to ensure maximum efficiency
	+
	+# Each region is divided into a grid of subregions, and a worklist is
	+# constructed for each. This parameter sets is set to half the number of
	+# subregions that the block is divided into.
	+$hr=4;
	+
	+# This parameter is automatically set to the the number of subregions that the
	+# block is divided into
	+$r=$hr*2;
	+
	+# This parameter sets the total number of block entries in each worklist
	+$ls=63;
	+
	+# When the worklists are being constructed, a mask array is made use of. To
	+# prevent the creation of array elements with negative indices, this parameter
	+# sets an arbitrary displacement.
	+$dis=8;
	+
	+# Constants used mask indexing
	+$d=2$dis+1;$dd=$d$d;$d0=(1+$d+$dd)*$dis;
	+
	+use Math::Trig;
	+
	+# Construct the worklist header file, based on the parameters above
	+open W,">worklist.hh";
	+print W <<EOF;
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr\@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \\file worklist.hh
	+ * \\brief Header file for setting constants used in the block worklists that are
	+ * used during cell computation.
	+ *
	+ * This file is automatically generated by worklist_gen.pl and it is not
	+ * intended to be edited by hand. */
	+
	+#ifndef VOROPP_WORKLIST_HH
	+#define VOROPP_WORKLIST_HH
	+
	+namespace voro {
	+
	+/** Each region is divided into a grid of subregions, and a worklist is
	+# constructed for each. This parameter sets is set to half the number of
	+# subregions that the block is divided into. */
	+EOF
	+print W "const int wl_hgrid=$hr;\n";
	+print W <<EOF;
	+/** The number of subregions that a block is subdivided into, which is twice
	+the value of hgrid. */
	+EOF
	+print W "const int wl_fgrid=$r;\n";
	+print W <<EOF;
	+/** The total number of worklists, set to the cube of hgrid. */
	+EOF
	+printf W "const int wl_hgridcu=%d;\n",$hr$hr$hr;
	+print W <<EOF;
	+/** The number of elements in each worklist. */
	+EOF
	+printf W "const int wl_seq_length=%d;\n",$ls+1;
	+print W <<EOF;
	+
	+}
	+#endif
	+EOF
	+close W;
	+
	+# Construct the preamble to the worklist.cc file
	+open W,">v_base_wl.cc";
	+print W <<EOF;
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr\@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \\file v_base_wl.cc
	+ * \\brief The table of block worklists that are used during the cell
	+ * computation, which is part of the voro_base class.
	+ *
	+ * This file is automatically generated by worklist_gen.pl and it is not
	+ * intended to be edited by hand. */
	+
	+EOF
	+printf W "const unsigned int voro_base::wl[wl_seq_length*wl_hgridcu]={\n";
	+
	+# Now create a worklist for each subregion
	+for($kk=0;$kk<$hr;$kk++) {
	+ for($jj=0;$jj<$hr;$jj++) {
	+ for($ii=0;$ii<$hr;$ii++) {
	+ worklist($ii,$jj,$kk);
	+ }
	+ }
	+}
	+
	+# Finish the file and close it
	+print W "};\n";
	+close W;
	+
	+# A subroutine
	+sub worklist {
	+# print "@_[0] @_[1] @_[2]\n";
	+ $ind=@_[0]+$hr(@_[1]+$hr@_[2]);
	+ $ac=0;$v+=2;
	+ $xp=$yp=$zp=0;
	+ $x=(@_[0]+0.5)/$r;
	+ $y=(@_[1]+0.5)/$r;
	+ $z=(@_[2]+0.5)/$r;
	+ $m[$d0]=$v;
	+ add(1,0,0);add(0,1,0);add(0,0,1);
	+ add(-1,0,0);add(0,-1,0);add(0,0,-1);
	+ foreach $l (1..$ls) {
	+ $minwei=1e9;
	+ foreach (0..$ac-1) {
	+ $xt=@a[3$_];$yt=@a[3$_+1];$zt=@a[3*$_+2];
	+# $wei=dis($x,$y,$z,$xt,$yt,$zt)+1acos(($xt$xp+$yt$yp+$zt$zp)/($xt$xt+$yt$yt+$zt$zt)($xp$xp+$yp$yp+$zp*$zp));
	+ $wei=adis($x,$y,$z,$xt,$yt,$zt)+0.02sqrt(($xt-$xp)2+($yt-$yp)2+($zt-$zp)*2);
	+ $nx=$_,$minwei=$wei if $wei<$minwei;
	+ }
	+ $xp=@a[3$nx];$yp=@a[3$nx+1];$zp=@a[3*$nx+2];
	+ add($xp+1,$yp,$zp);add($xp,$yp+1,$zp);add($xp,$yp,$zp+1);
	+ add($xp-1,$yp,$zp);add($xp,$yp-1,$zp);add($xp,$yp,$zp-1);
	+# print "=> $l $xp $yp $zp\n" if $l<4;
	+ push @b,(splice @a,3*$nx,3);$ac--;
	+ }
	+
	+ # Mark all blocks that are on this worklist entry
	+ $m[$d0]=++$v;
	+ for($i=0;$i<$#b;$i+=3) {
	+ $xt=$b[$i];$yt=$b[$i+1];$zt=$b[$i+2];
	+ $m[$d0+$xt+$d$yt+$dd$zt]=$v;
	+ }
	+
	+ # Find which neighboring outside blocks need to be marked when
	+ # considering this block, being as conservative as possible by
	+ # overwriting the marks, so that the last possible entry that can reach
	+ # a block is used
	+ for($i=$j=0;$i<$#b;$i+=3,$j++) {
	+ $xt=$b[$i];$yt=$b[$i+1];$zt=$b[$i+2];
	+ $k=$d0+$xt+$yt$d+$zt$dd;
	+ $la[$k+1]=$j, $m[$k+1]=$v+1 if $xt>=0 && $m[$k+1]!=$v;
	+ $la[$k+$d]=$j, $m[$k+$d]=$v+1 if $yt>=0 && $m[$k+$d]!=$v;
	+ $la[$k+$dd]=$j, $m[$k+$dd]=$v+1 if $zt>=0 && $m[$k+$dd]!=$v;
	+ $la[$k-1]=$j, $m[$k-1]=$v+1 if $xt<=0 && $m[$k-1]!=$v;
	+ $la[$k-$d]=$j, $m[$k-$d]=$v+1 if $yt<=0 && $m[$k-$d]!=$v;
	+ $la[$k-$dd]=$j, $m[$k-$dd]=$v+1 if $zt<=0 && $m[$k-$dd]!=$v;
	+ }
	+
	+ # Scan to ensure that no neighboring blocks have been missed by the
	+ # outwards-looking logic in the above section
	+ for($i=0;$i<$#b;$i+=3) {
	+ wl_check($d0+$b[$i]+$b[$i+1]$d+$b[$i+2]$dd);
	+ }
	+
	+ # Compute the number of entries where outside blocks do not need to be
	+ # consider
	+ for($i=$j=0;$i<$#b;$i+=3,$j++) {
	+ $k=$d0+$b[$i]+$b[$i+1]$d+$b[$i+2]$dd;
	+ last if $m[$k+1]!=$v;
	+ last if $m[$k+$d]!=$v;
	+ last if $m[$k+$dd]!=$v;
	+ last if $m[$k-1]!=$v;
	+ last if $m[$k-$d]!=$v;
	+ last if $m[$k-$dd]!=$v;
	+ }
	+ print W "\t$j";
	+
	+ # Create worklist entry and save to file
	+ $j=0;
	+ while ($#b>0) {
	+ $xt=shift @b;$yt=shift @b;$zt=shift @b;
	+ $k=$d0+$xt+$yt$d+$zt$dd;
	+ $o=0;
	+ $o\|=1 if $m[$k+1]!=$v && $la[$k+1]==$j;
	+ $o^=3 if $m[$k-1]!=$v && $la[$k-1]==$j;
	+ $o\|=8 if $m[$k+$d]!=$v && $la[$k+$d]==$j;
	+ $o^=24 if $m[$k-$d]!=$v && $la[$k-$d]==$j;
	+ $o\|=64 if $m[$k+$dd]!=$v && $la[$k+$dd]==$j;
	+ $o^=192 if $m[$k-$dd]!=$v && $la[$k-$dd]==$j;
	+ printf W ",%#x",(($xt+64)\|($yt+64)<<7\|($zt+64)<<14\|$o<<21);
	+ $j++;
	+ }
	+ print W "," unless $ind==$hr$hr$hr-1;
	+ print W "\n";
	+
	+ # Remove list memory
	+ undef @a;
	+ undef @b;
	+}
	+
	+sub add {
	+ if ($m[$d0+@_[0]+$d@_[1]+$dd@_[2]]!=$v) {
	+ $ac++;
	+ push @a,@_[0],@_[1],@_[2];
	+ $m[$d0+@_[0]+$d@_[1]+$dd@_[2]]=$v;
	+ }
	+}
	+
	+sub dis {
	+ $xl=@_[3]+0.3-@_[0];$xh=@_[3]+0.7-@_[0];
	+ $yl=@_[4]+0.3-@_[1];$yh=@_[4]+0.7-@_[1];
	+ $zl=@_[5]+0.3-@_[2];$zh=@_[5]+0.7-@_[2];
	+ $dis=(abs($xl)<abs($xh)?$xl:$xh)**2
	+ +(abs($yl)<abs($yh)?$yl:$yh)**2
	+ +(abs($zl)<abs($zh)?$zl:$zh)**2;
	+ return sqrt $dis;
	+}
	+
	+sub adis {
	+ $xco=$yco=$zco=0;
	+ $xco=@_[0]-@_[3] if @_[3]>0;
	+ $xco=@_[0]-@_[3]-1 if @_[3]<0;
	+ $yco=@_[1]-@_[4] if @_[4]>0;
	+ $yco=@_[1]-@_[4]-1 if @_[4]<0;
	+ $zco=@_[2]-@_[5] if @_[5]>0;
	+ $zco=@_[2]-@_[5]-1 if @_[5]<0;
	+ return sqrt $xco$xco+$yco$yco+$zco*$zco;
	+}
	+
	+sub wl_check {
	+ die "Failure in worklist construction\n" if $m[@_[0]+1]<$v\|\|$m[@_[0]-1]<$v
	+ \|\|$m[@_[0]+$d]<$v\|\|$m[@_[0]-$d]<$v
	+ \|\|$m[@_[0]+$dd]<$v\|\|$m[@_[0]-$dd]<$v;
	+}
	Index: extern/voro++/src/c_loops.cc
	===================================================================
	--- extern/voro++/src/c_loops.cc (revision 0)
	+++ extern/voro++/src/c_loops.cc (revision 0)
	@@ -0,0 +1,150 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file c_loops.cc
	+ * \brief Function implementations for the loop classes. */
	+
	+#include "c_loops.hh"
	+
	+namespace voro {
	+
	+/** Initializes a c_loop_subset object to scan over all particles within a
	+ * given sphere.
	+ * \param[in] (vx,vy,vz) the position vector of the center of the sphere.
	+ * \param[in] r the radius of the sphere.
	+ * \param[in] bounds_test whether to do detailed bounds checking. If this is
	+ * false then the class will loop over all particles in
	+ * blocks that overlap the given sphere. If it is true,
	+ * the particle will only loop over the particles which
	+ * actually lie within the sphere.
	+ * \return True if there is any valid point to loop over, false otherwise. */
	+void c_loop_subset::setup_sphere(double vx,double vy,double vz,double r,bool bounds_test) {
	+ if(bounds_test) {mode=sphere;v0=vx;v1=vy;v2=vz;v3=r*r;} else mode=no_check;
	+ ai=step_int((vx-ax-r)*xsp);
	+ bi=step_int((vx-ax+r)*xsp);
	+ aj=step_int((vy-ay-r)*ysp);
	+ bj=step_int((vy-ay+r)*ysp);
	+ ak=step_int((vz-az-r)*zsp);
	+ bk=step_int((vz-az+r)*zsp);
	+ setup_common();
	+}
	+
	+/** Initializes the class to loop over all particles in a rectangular subgrid
	+ * of blocks.
	+ * \param[in] (ai_,bi_) the subgrid range in the x-direction, inclusive of both
	+ * ends.
	+ * \param[in] (aj_,bj_) the subgrid range in the y-direction, inclusive of both
	+ * ends.
	+ * \param[in] (ak_,bk_) the subgrid range in the z-direction, inclusive of both
	+ * ends.
	+ * \return True if there is any valid point to loop over, false otherwise. */
	+void c_loop_subset::setup_intbox(int ai_,int bi_,int aj_,int bj_,int ak_,int bk_) {
	+ ai=ai_;bi=bi_;aj=aj_;bj=bj_;ak=ak_;bk=bk_;
	+ mode=no_check;
	+ setup_common();
	+}
	+
	+/** Sets up all of the common constants used for the loop.
	+ * \return True if there is any valid point to loop over, false otherwise. */
	+void c_loop_subset::setup_common() {
	+ if(!xperiodic) {
	+ if(ai<0) {ai=0;if(bi<0) bi=0;}
	+ if(bi>=nx) {bi=nx-1;if(ai>=nx) ai=nx-1;}
	+ }
	+ if(!yperiodic) {
	+ if(aj<0) {aj=0;if(bj<0) bj=0;}
	+ if(bj>=ny) {bj=ny-1;if(aj>=ny) aj=ny-1;}
	+ }
	+ if(!zperiodic) {
	+ if(ak<0) {ak=0;if(bk<0) bk=0;}
	+ if(bk>=nz) {bk=nz-1;if(ak>=nz) ak=nz-1;}
	+ }
	+ ci=ai;cj=aj;ck=ak;
	+ di=i=step_mod(ci,nx);apx=px=step_div(ci,nx)*sx;
	+ dj=j=step_mod(cj,ny);apy=py=step_div(cj,ny)*sy;
	+ dk=k=step_mod(ck,nz);apz=pz=step_div(ck,nz)*sz;
	+ inc1=di-step_mod(bi,nx);
	+ inc2=nx*(ny+dj-step_mod(bj,ny))+inc1;
	+ inc1+=nx;
	+ ijk=di+nx(dj+nydk);
	+ q=0;
	+}
	+
	+/** Starts the loop by finding the first particle within the container to
	+ * consider.
	+ * \return True if there is any particle to consider, false otherwise. */
	+bool c_loop_subset::start() {
	+ while(co[ijk]==0) {if(!next_block()) return false;}
	+ while(mode!=no_check&&out_of_bounds()) {
	+ q++;
	+ while(q>=co[ijk]) {q=0;if(!next_block()) return false;}
	+ }
	+ return true;
	+}
	+
	+/** Initializes the class to loop over all particles in a rectangular box.
	+ * \param[in] (xmin,xmax) the minimum and maximum x coordinates of the box.
	+ * \param[in] (ymin,ymax) the minimum and maximum y coordinates of the box.
	+ * \param[in] (zmin,zmax) the minimum and maximum z coordinates of the box.
	+ * \param[in] bounds_test whether to do detailed bounds checking. If this is
	+ * false then the class will loop over all particles in
	+ * blocks that overlap the given box. If it is true, the
	+ * particle will only loop over the particles which
	+ * actually lie within the box.
	+ * \return True if there is any valid point to loop over, false otherwise. */
	+void c_loop_subset::setup_box(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax,bool bounds_test) {
	+ if(bounds_test) {mode=box;v0=xmin;v1=xmax;v2=ymin;v3=ymax;v4=zmin;v5=zmax;} else mode=no_check;
	+ ai=step_int((xmin-ax)*xsp);
	+ bi=step_int((xmax-ax)*xsp);
	+ aj=step_int((ymin-ay)*ysp);
	+ bj=step_int((ymax-ay)*ysp);
	+ ak=step_int((zmin-az)*zsp);
	+ bk=step_int((zmax-az)*zsp);
	+ setup_common();
	+}
	+
	+/** Computes whether the current point is out of bounds, relative to the
	+ * current loop setup.
	+ * \return True if the point is out of bounds, false otherwise. */
	+bool c_loop_subset::out_of_bounds() {
	+ double pp=p[ijk]+psq;
	+ if(mode==sphere) {
	+ double fx(*pp+px-v0),fy(pp[1]+py-v1),fz(pp[2]+pz-v2);
	+ return fxfx+fyfy+fz*fz>v3;
	+ } else {
	+ double f(*pp+px);if(f<v0\|\|f>v1) return true;
	+ f=pp[1]+py;if(f<v2\|\|f>v3) return true;
	+ f=pp[2]+pz;return f<v4\|\|f>v5;
	+ }
	+}
	+
	+/** Returns the next block to be tested in a loop, and updates the periodicity
	+ * vector if necessary. */
	+bool c_loop_subset::next_block() {
	+ if(i<bi) {
	+ i++;
	+ if(ci<nx-1) {ci++;ijk++;} else {ci=0;ijk+=1-nx;px+=sx;}
	+ return true;
	+ } else if(j<bj) {
	+ i=ai;ci=di;px=apx;j++;
	+ if(cj<ny-1) {cj++;ijk+=inc1;} else {cj=0;ijk+=inc1-nxy;py+=sy;}
	+ return true;
	+ } else if(k<bk) {
	+ i=ai;ci=di;j=aj;cj=dj;px=apx;py=apy;k++;
	+ if(ck<nz-1) {ck++;ijk+=inc2;} else {ck=0;ijk+=inc2-nxyz;pz+=sz;}
	+ return true;
	+ } else return false;
	+}
	+
	+/** Extends the memory available for storing the ordering. */
	+void particle_order::add_ordering_memory() {
	+ int no=new int[size<<2],nop=no,*opp=o;
	+ while(opp<op) (nop++)=(opp++);
	+ delete [] o;
	+ size<<=1;o=no;op=nop;
	+}
	+
	+}
	Index: extern/voro++/src/v_base.cc
	===================================================================
	--- extern/voro++/src/v_base.cc (revision 0)
	+++ extern/voro++/src/v_base.cc (revision 0)
	@@ -0,0 +1,118 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file v_base.cc
	+ * \brief Function implementations for the base Voronoi container class. */
	+
	+#include "v_base.hh"
	+#include "config.hh"
	+
	+namespace voro {
	+
	+/** This function is called during container construction. The routine scans
	+ * all of the worklists in the wl[] array. For a given worklist of blocks
	+ * labeled \f$w_1\f$ to \f$w_n\f$, it computes a sequence \f$r_0\f$ to
	+ * \f$r_n\f$ so that $r_i$ is the minimum distance to all the blocks
	+ * \f$w_{j}\f$ where \f$j>i\f$ and all blocks outside the worklist. The values
	+ * of \f$r_n\f$ is calculated first, as the minimum distance to any block in
	+ * the shell surrounding the worklist. The \f$r_i\f$ are then computed in
	+ * reverse order by considering the distance to \f$w_{i+1}\f$. */
	+voro_base::voro_base(int nx_,int ny_,int nz_,double boxx_,double boxy_,double boxz_) :
	+ nx(nx_), ny(ny_), nz(nz_), nxy(nx_ny_), nxyz(nxynz_), boxx(boxx_), boxy(boxy_), boxz(boxz_),
	+ xsp(1/boxx_), ysp(1/boxy_), zsp(1/boxz_), mrad(new double[wl_hgridcu*wl_seq_length]) {
	+ const unsigned int b1=1<<21,b2=1<<22,b3=1<<24,b4=1<<25,b5=1<<27,b6=1<<28;
	+ const double xstep=boxx/wl_fgrid,ystep=boxy/wl_fgrid,zstep=boxz/wl_fgrid;
	+ int i,j,k,lx,ly,lz,q;
	+ unsigned int f,e=const_cast<unsigned int> (wl);
	+ double xlo,ylo,zlo,xhi,yhi,zhi,minr,*radp=mrad;
	+ for(zlo=0,zhi=zstep,lz=0;lz<wl_hgrid;zlo=zhi,zhi+=zstep,lz++) {
	+ for(ylo=0,yhi=ystep,ly=0;ly<wl_hgrid;ylo=yhi,yhi+=ystep,ly++) {
	+ for(xlo=0,xhi=xstep,lx=0;lx<wl_hgrid;xlo=xhi,xhi+=xstep,lx++) {
	+ minr=large_number;
	+ for(q=e[0]+1;q<wl_seq_length;q++) {
	+ f=e[q];
	+ i=(f&127)-64;
	+ j=(f>>7&127)-64;
	+ k=(f>>14&127)-64;
	+ if((f&b2)==b2) {
	+ compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i-1,j,k);
	+ if((f&b1)==0) compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i+1,j,k);
	+ } else if((f&b1)==b1) compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i+1,j,k);
	+ if((f&b4)==b4) {
	+ compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j-1,k);
	+ if((f&b3)==0) compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j+1,k);
	+ } else if((f&b3)==b3) compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j+1,k);
	+ if((f&b6)==b6) {
	+ compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j,k-1);
	+ if((f&b5)==0) compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j,k+1);
	+ } else if((f&b5)==b5) compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j,k+1);
	+ }
	+ q--;
	+ while(q>0) {
	+ radp[q]=minr;
	+ f=e[q];
	+ i=(f&127)-64;
	+ j=(f>>7&127)-64;
	+ k=(f>>14&127)-64;
	+ compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j,k);
	+ q--;
	+ }
	+ *radp=minr;
	+ e+=wl_seq_length;
	+ radp+=wl_seq_length;
	+ }
	+ }
	+ }
	+}
	+
	+/** Computes the minimum distance from a subregion to a given block. If this distance
	+ * is smaller than the value of minr, then it passes
	+ * \param[in,out] minr a pointer to the current minimum distance. If the distance
	+ * computed in this function is smaller, then this distance is
	+ * set to the new one.
	+ * \param[out] (xlo,ylo,zlo) the lower coordinates of the subregion being
	+ * considered.
	+ * \param[out] (xhi,yhi,zhi) the upper coordinates of the subregion being
	+ * considered.
	+ * \param[in] (ti,tj,tk) the coordinates of the block. */
	+void voro_base::compute_minimum(double &minr,double &xlo,double &xhi,double &ylo,double &yhi,double &zlo,double &zhi,int ti,int tj,int tk) {
	+ double radsq,temp;
	+ if(ti>0) {temp=boxxti-xhi;radsq=temptemp;}
	+ else if(ti<0) {temp=xlo-boxx(1+ti);radsq=temptemp;}
	+ else radsq=0;
	+
	+ if(tj>0) {temp=boxytj-yhi;radsq+=temptemp;}
	+ else if(tj<0) {temp=ylo-boxy(1+tj);radsq+=temptemp;}
	+
	+ if(tk>0) {temp=boxztk-zhi;radsq+=temptemp;}
	+ else if(tk<0) {temp=zlo-boxz(1+tk);radsq+=temptemp;}
	+
	+ if(radsq<minr) minr=radsq;
	+}
	+
	+/** Checks to see whether "%n" appears in a format sequence to determine
	+ * whether neighbor information is required or not.
	+ * \param[in] format the format string to check.
	+ * \return True if a "%n" is found, false otherwise. */
	+bool voro_base::contains_neighbor(const char *format) {
	+ char fmp=(const_cast<char>(format));
	+
	+ // Check to see if "%n" appears in the format sequence
	+ while(*fmp!=0) {
	+ if(*fmp=='%') {
	+ fmp++;
	+ if(*fmp=='n') return true;
	+ else if(*fmp==0) return false;
	+ }
	+ fmp++;
	+ }
	+
	+ return false;
	+}
	+
	+#include "v_base_wl.cc"
	+
	+}
	Index: extern/voro++/src/wall.cc
	===================================================================
	--- extern/voro++/src/wall.cc (revision 0)
	+++ extern/voro++/src/wall.cc (revision 0)
	@@ -0,0 +1,122 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file wall.cc
	+ * \brief Function implementations for the derived wall classes. */
	+
	+#include "wall.hh"
	+
	+namespace voro {
	+
	+/** Tests to see whether a point is inside the sphere wall object.
	+ * \param[in,out] (x,y,z) the vector to test.
	+ * \return True if the point is inside, false if the point is outside. */
	+bool wall_sphere::point_inside(double x,double y,double z) {
	+ return (x-xc)(x-xc)+(y-yc)(y-yc)+(z-zc)(z-zc)<rcrc;
	+}
	+
	+/** Cuts a cell by the sphere wall object. The spherical wall is approximated by
	+ * a single plane applied at the point on the sphere which is closest to the center
	+ * of the cell. This works well for particle arrangements that are packed against
	+ * the wall, but loses accuracy for sparse particle distributions.
	+ * \param[in,out] c the Voronoi cell to be cut.
	+ * \param[in] (x,y,z) the location of the Voronoi cell.
	+ * \return True if the cell still exists, false if the cell is deleted. */
	+template<class v_cell>
	+bool wall_sphere::cut_cell_base(v_cell &c,double x,double y,double z) {
	+ double xd=x-xc,yd=y-yc,zd=z-zc,dq=xdxd+ydyd+zd*zd;
	+ if (dq>1e-5) {
	+ dq=2(sqrt(dq)rc-dq);
	+ return c.nplane(xd,yd,zd,dq,w_id);
	+ }
	+ return true;
	+}
	+
	+/** Tests to see whether a point is inside the plane wall object.
	+ * \param[in] (x,y,z) the vector to test.
	+ * \return True if the point is inside, false if the point is outside. */
	+bool wall_plane::point_inside(double x,double y,double z) {
	+ return xxc+yyc+z*zc<ac;
	+}
	+
	+/** Cuts a cell by the plane wall object.
	+ * \param[in,out] c the Voronoi cell to be cut.
	+ * \param[in] (x,y,z) the location of the Voronoi cell.
	+ * \return True if the cell still exists, false if the cell is deleted. */
	+template<class v_cell>
	+bool wall_plane::cut_cell_base(v_cell &c,double x,double y,double z) {
	+ double dq=2(ac-xxc-yyc-zzc);
	+ return c.nplane(xc,yc,zc,dq,w_id);
	+}
	+
	+/** Tests to see whether a point is inside the cylindrical wall object.
	+ * \param[in] (x,y,z) the vector to test.
	+ * \return True if the point is inside, false if the point is outside. */
	+bool wall_cylinder::point_inside(double x,double y,double z) {
	+ double xd=x-xc,yd=y-yc,zd=z-zc;
	+ double pa=(xdxa+ydya+zdza)asi;
	+ xd-=xapa;yd-=yapa;zd-=za*pa;
	+ return xdxd+ydyd+zdzd<rcrc;
	+}
	+
	+/** Cuts a cell by the cylindrical wall object. The cylindrical wall is
	+ * approximated by a single plane applied at the point on the cylinder which is
	+ * closest to the center of the cell. This works well for particle arrangements
	+ * that are packed against the wall, but loses accuracy for sparse particle
	+ * distributions.
	+ * \param[in,out] c the Voronoi cell to be cut.
	+ * \param[in] (x,y,z) the location of the Voronoi cell.
	+ * \return True if the cell still exists, false if the cell is deleted. */
	+template<class v_cell>
	+bool wall_cylinder::cut_cell_base(v_cell &c,double x,double y,double z) {
	+ double xd=x-xc,yd=y-yc,zd=z-zc,pa=(xdxa+ydya+zdza)asi;
	+ xd-=xapa;yd-=yapa;zd-=za*pa;
	+ pa=xdxd+ydyd+zd*zd;
	+ if(pa>1e-5) {
	+ pa=2(sqrt(pa)rc-pa);
	+ return c.nplane(xd,yd,zd,pa,w_id);
	+ }
	+ return true;
	+}
	+
	+/** Tests to see whether a point is inside the cone wall object.
	+ * \param[in] (x,y,z) the vector to test.
	+ * \return True if the point is inside, false if the point is outside. */
	+bool wall_cone::point_inside(double x,double y,double z) {
	+ double xd=x-xc,yd=y-yc,zd=z-zc,pa=(xdxa+ydya+zdza)asi;
	+ xd-=xapa;yd-=yapa;zd-=za*pa;
	+ pa*=gra;
	+ if (pa<0) return false;
	+ pa*=pa;
	+ return xdxd+ydyd+zd*zd<pa;
	+}
	+
	+/** Cuts a cell by the cone wall object. The conical wall is
	+ * approximated by a single plane applied at the point on the cone which is
	+ * closest to the center of the cell. This works well for particle arrangements
	+ * that are packed against the wall, but loses accuracy for sparse particle
	+ * distributions.
	+ * \param[in,out] c the Voronoi cell to be cut.
	+ * \param[in] (x,y,z) the location of the Voronoi cell.
	+ * \return True if the cell still exists, false if the cell is deleted. */
	+template<class v_cell>
	+bool wall_cone::cut_cell_base(v_cell &c,double x,double y,double z) {
	+ double xd=x-xc,yd=y-yc,zd=z-zc,xf,yf,zf,q,pa=(xdxa+ydya+zdza)asi;
	+ xd-=xapa;yd-=yapa;zd-=za*pa;
	+ pa=xdxd+ydyd+zd*zd;
	+ if(pa>1e-5) {
	+ pa=1/sqrt(pa);
	+ q=sqrt(asi);
	+ xf=-sangqxa+cangpaxd;
	+ yf=-sangqya+cangpayd;
	+ zf=-sangqza+cangpazd;
	+ pa=2(xf(xc-x)+yf(yc-y)+zf(zc-z));
	+ return c.nplane(xf,yf,zf,pa,w_id);
	+ }
	+ return true;
	+}
	+
	+}
	Index: extern/voro++/src/Makefile.dep
	===================================================================
	--- extern/voro++/src/Makefile.dep (revision 0)
	+++ extern/voro++/src/Makefile.dep (revision 0)
	@@ -0,0 +1,18 @@
	+cell.o: cell.cc config.hh common.hh cell.hh
	+common.o: common.cc common.hh config.hh
	+container.o: container.cc container.hh config.hh common.hh v_base.hh \
	+ worklist.hh cell.hh c_loops.hh v_compute.hh rad_option.hh
	+unitcell.o: unitcell.cc unitcell.hh config.hh cell.hh common.hh
	+v_compute.o: v_compute.cc worklist.hh v_compute.hh config.hh cell.hh \
	+ common.hh rad_option.hh container.hh v_base.hh c_loops.hh \
	+ container_prd.hh unitcell.hh
	+c_loops.o: c_loops.cc c_loops.hh config.hh
	+v_base.o: v_base.cc v_base.hh worklist.hh config.hh v_base_wl.cc
	+wall.o: wall.cc wall.hh cell.hh config.hh common.hh container.hh \
	+ v_base.hh worklist.hh c_loops.hh v_compute.hh rad_option.hh
	+pre_container.o: pre_container.cc config.hh pre_container.hh c_loops.hh \
	+ container.hh common.hh v_base.hh worklist.hh cell.hh v_compute.hh \
	+ rad_option.hh
	+container_prd.o: container_prd.cc container_prd.hh config.hh common.hh \
	+ v_base.hh worklist.hh cell.hh c_loops.hh v_compute.hh unitcell.hh \
	+ rad_option.hh
	Index: extern/voro++/src/container_prd.hh
	===================================================================
	--- extern/voro++/src/container_prd.hh (revision 0)
	+++ extern/voro++/src/container_prd.hh (revision 0)
	@@ -0,0 +1,616 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file container_prd.hh
	+ * \brief Header file for the container_periodic_base and related classes. */
	+
	+#ifndef VOROPP_CONTAINER_PRD_HH
	+#define VOROPP_CONTAINER_PRD_HH
	+
	+#include <cstdio>
	+#include <vector>
	+
	+#include "config.hh"
	+#include "common.hh"
	+#include "v_base.hh"
	+#include "cell.hh"
	+#include "c_loops.hh"
	+#include "v_compute.hh"
	+#include "unitcell.hh"
	+#include "rad_option.hh"
	+
	+namespace voro {
	+
	+/** \brief Class for representing a particle system in a 3D periodic
	+ * non-orthogonal periodic domain.
	+ *
	+ * This class represents a particle system in a three-dimensional
	+ * non-orthogonal periodic domain. The domain is defined by three periodicity
	+ * vectors (bx,0,0), (bxy,by,0), and (bxz,byz,bz) that represent a
	+ * parallelepiped. Internally, the class stores particles in the box 0<x<bx,
	+ * 0<y<by, 0<z<bz, and constructs periodic images of particles that displaced
	+ * by the three periodicity vectors when they are necessary for the
	+ * computation. The internal memory structure for this class is significantly
	+ * different from the container_base class in order to handle the dynamic
	+ * construction of these periodic images.
	+ *
	+ * The class is derived from the unitcell class, which encapsulates information
	+ * about the domain geometry, and the voro_base class, which encapsulates
	+ * information about the underlying computational grid. */
	+class container_periodic_base : public unitcell, public voro_base {
	+ public:
	+ /** The lower y index (inclusive) of the primary domain within
	+ * the block structure. */
	+ int ey;
	+ /** The lower z index (inclusive) of the primary domain within
	+ * the block structure. */
	+ int ez;
	+ /** The upper y index (exclusive) of the primary domain within
	+ * the block structure. */
	+ int wy;
	+ /** The upper z index (exclusive) of the primary domain within
	+ * the block structure. */
	+ int wz;
	+ /** The total size of the block structure (including images) in
	+ * the y direction. */
	+ int oy;
	+ /** The total size of the block structure (including images) in
	+ * the z direction. */
	+ int oz;
	+ /** The total number of blocks. */
	+ int oxyz;
	+ /** This array holds the numerical IDs of each particle in each
	+ * computational box. */
	+ int **id;
	+ /** A two dimensional array holding particle positions. For the
	+ * derived container_poly class, this also holds particle
	+ * radii. */
	+ double **p;
	+ /** This array holds the number of particles within each
	+ * computational box of the container. */
	+ int *co;
	+ /** This array holds the maximum amount of particle memory for
	+ * each computational box of the container. If the number of
	+ * particles in a particular box ever approaches this limit,
	+ * more is allocated using the add_particle_memory() function.
	+ */
	+ int *mem;
	+ /** An array holding information about periodic image
	+ * construction at a given location. */
	+ char *img;
	+ /** The initial amount of memory to allocate for particles
	+ * for each block. */
	+ const int init_mem;
	+ /** The amount of memory in the array structure for each
	+ * particle. This is set to 3 when the basic class is
	+ * initialized, so that the array holds (x,y,z) positions. If
	+ * the container class is initialized as part of the derived
	+ * class container_poly, then this is set to 4, to also hold
	+ * the particle radii. */
	+ const int ps;
	+ container_periodic_base(double bx_,double bxy_,double by_,double bxz_,double byz_,double bz_,
	+ int nx_,int ny_,int nz_,int init_mem_,int ps);
	+ ~container_periodic_base();
	+ /** Prints all particles in the container, including those that
	+ * have been constructed in image blocks. */
	+ inline void print_all_particles() {
	+ int ijk,q;
	+ for(ijk=0;ijk<oxyz;ijk++) for(q=0;q<co[ijk];q++)
	+ printf("%d %g %g %g\n",id[ijk][q],p[ijk][psq],p[ijk][psq+1],p[ijk][ps*q+2]);
	+ }
	+ void region_count();
	+ /** Initializes the Voronoi cell prior to a compute_cell
	+ * operation for a specific particle being carried out by a
	+ * voro_compute class. The cell is initialized to be the
	+ * pre-computed unit Voronoi cell based on planes formed by
	+ * periodic images of the particle.
	+ * \param[in,out] c a reference to a voronoicell object.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] q the index of the particle within its block.
	+ * \param[in] (ci,cj,ck) the coordinates of the block in the
	+ * container coordinate system.
	+ * \param[out] (i,j,k) the coordinates of the test block
	+ * relative to the voro_compute
	+ * coordinate system.
	+ * \param[out] (x,y,z) the position of the particle.
	+ * \param[out] disp a block displacement used internally by the
	+ * compute_cell routine.
	+ * \return False if the plane cuts applied by walls completely
	+ * removed the cell, true otherwise. */
	+ template<class v_cell>
	+ inline bool initialize_voronoicell(v_cell &c,int ijk,int q,int ci,int cj,int ck,int &i,int &j,int &k,double &x,double &y,double &z,int &disp) {
	+ c=unit_voro;
	+ double pp=p[ijk]+psq;
	+ x=(pp++);y=(pp++);z=*pp;
	+ i=nx;j=ey;k=ez;
	+ return true;
	+ }
	+ /** Initializes parameters for a find_voronoi_cell call within
	+ * the voro_compute template.
	+ * \param[in] (ci,cj,ck) the coordinates of the test block in
	+ * the container coordinate system.
	+ * \param[in] ijk the index of the test block
	+ * \param[out] (i,j,k) the coordinates of the test block
	+ * relative to the voro_compute
	+ * coordinate system.
	+ * \param[out] disp a block displacement used internally by the
	+ * find_voronoi_cell routine (but not needed
	+ * in this instance.) */
	+ inline void initialize_search(int ci,int cj,int ck,int ijk,int &i,int &j,int &k,int &disp) {
	+ i=nx;j=ey;k=ez;
	+ }
	+ /** Returns the position of a particle currently being computed
	+ * relative to the computational block that it is within. It is
	+ * used to select the optimal worklist entry to use.
	+ * \param[in] (x,y,z) the position of the particle.
	+ * \param[in] (ci,cj,ck) the block that the particle is within.
	+ * \param[out] (fx,fy,fz) the position relative to the block.
	+ */
	+ inline void frac_pos(double x,double y,double z,double ci,double cj,double ck,double &fx,double &fy,double &fz) {
	+ fx=x-boxx*ci;
	+ fy=y-boxy*(cj-ey);
	+ fz=z-boxz*(ck-ez);
	+ }
	+ /** Calculates the index of block in the container structure
	+ * corresponding to given coordinates.
	+ * \param[in] (ci,cj,ck) the coordinates of the original block
	+ * in the current computation, relative
	+ * to the container coordinate system.
	+ * \param[in] (ei,ej,ek) the displacement of the current block
	+ * from the original block.
	+ * \param[in,out] (qx,qy,qz) the periodic displacement that
	+ * must be added to the particles
	+ * within the computed block.
	+ * \param[in] disp a block displacement used internally by the
	+ * find_voronoi_cell and compute_cell routines
	+ * (but not needed in this instance.)
	+ * \return The block index. */
	+ inline int region_index(int ci,int cj,int ck,int ei,int ej,int ek,double &qx,double &qy,double &qz,int &disp) {
	+ int qi=ci+(ei-nx),qj=cj+(ej-ey),qk=ck+(ek-ez);
	+ int iv(step_div(qi,nx));if(iv!=0) {qx=ivbx;qi-=nxiv;} else qx=0;
	+ create_periodic_image(qi,qj,qk);
	+ return qi+nx(qj+oyqk);
	+ }
	+ void create_all_images();
	+ void check_compartmentalized();
	+ protected:
	+ void add_particle_memory(int i);
	+ void put_locate_block(int &ijk,double &x,double &y,double &z);
	+ void put_locate_block(int &ijk,double &x,double &y,double &z,int &ai,int &aj,int &ak);
	+ /** Creates particles within an image block by copying them
	+ * from the primary domain and shifting them. If the given
	+ * block is aligned with the primary domain in the z-direction,
	+ * the routine calls the simpler create_side_image routine
	+ * where the image block may comprise of particles from up to
	+ * two primary blocks. Otherwise is calls the more complex
	+ * create_vertical_image where the image block may comprise of
	+ * particles from up to four primary blocks.
	+ * \param[in] (di,dj,dk) the coordinates of the image block to
	+ * create. */
	+ inline void create_periodic_image(int di,int dj,int dk) {
	+ if(di<0\|\|di>=nx\|\|dj<0\|\|dj>=oy\|\|dk<0\|\|dk>=oz)
	+ voro_fatal_error("Constructing periodic image for nonexistent point",VOROPP_INTERNAL_ERROR);
	+ if(dk>=ez&&dk<wz) {
	+ if(dj<ey\|\|dj>=wy) create_side_image(di,dj,dk);
	+ } else create_vertical_image(di,dj,dk);
	+ }
	+ void create_side_image(int di,int dj,int dk);
	+ void create_vertical_image(int di,int dj,int dk);
	+ void put_image(int reg,int fijk,int l,double dx,double dy,double dz);
	+ inline void remap(int &ai,int &aj,int &ak,int &ci,int &cj,int &ck,double &x,double &y,double &z,int &ijk);
	+};
	+
	+/** \brief Extension of the container_periodic_base class for computing regular
	+ * Voronoi tessellations.
	+ *
	+ * This class is an extension of the container_periodic_base that has routines
	+ * specifically for computing the regular Voronoi tessellation with no
	+ * dependence on particle radii. */
	+class container_periodic : public container_periodic_base, public radius_mono {
	+ public:
	+ container_periodic(double bx_,double bxy_,double by_,double bxz_,double byz_,double bz_,
	+ int nx_,int ny_,int nz_,int init_mem_);
	+ void clear();
	+ void put(int n,double x,double y,double z);
	+ void put(int n,double x,double y,double z,int &ai,int &aj,int &ak);
	+ void put(particle_order &vo,int n,double x,double y,double z);
	+ void import(FILE *fp=stdin);
	+ void import(particle_order &vo,FILE *fp=stdin);
	+ /** Imports a list of particles from an open file stream into
	+ * the container. Entries of four numbers (Particle ID, x
	+ * position, y position, z position) are searched for. If the
	+ * file cannot be successfully read, then the routine causes a
	+ * fatal error.
	+ * \param[in] filename the name of the file to open and read
	+ * from. */
	+ inline void import(const char* filename) {
	+ FILE *fp=safe_fopen(filename,"r");
	+ import(fp);
	+ fclose(fp);
	+ }
	+ /** Imports a list of particles from an open file stream into
	+ * the container. Entries of four numbers (Particle ID, x
	+ * position, y position, z position) are searched for. In
	+ * addition, the order in which particles are read is saved
	+ * into an ordering class. If the file cannot be successfully
	+ * read, then the routine causes a fatal error.
	+ * \param[in,out] vo the ordering class to use.
	+ * \param[in] filename the name of the file to open and read
	+ * from. */
	+ inline void import(particle_order &vo,const char* filename) {
	+ FILE *fp=safe_fopen(filename,"r");
	+ import(vo,fp);
	+ fclose(fp);
	+ }
	+ void compute_all_cells();
	+ double sum_cell_volumes();
	+ /** Dumps particle IDs and positions to a file.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_particles(c_loop &vl,FILE *fp) {
	+ double *pp;
	+ if(vl.start()) do {
	+ pp=p[vl.ijk]+3*vl.q;
	+ fprintf(fp,"%d %g %g %g\n",id[vl.ijk][vl.q],*pp,pp[1],pp[2]);
	+ } while(vl.inc());
	+ }
	+ /** Dumps all of the particle IDs and positions to a file.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_particles(FILE *fp=stdout) {
	+ c_loop_all_periodic vl(*this);
	+ draw_particles(vl,fp);
	+ }
	+ /** Dumps all of the particle IDs and positions to a file.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_particles(const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_particles(fp);
	+ fclose(fp);
	+ }
	+ /** Dumps particle positions in POV-Ray format.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_particles_pov(c_loop &vl,FILE *fp) {
	+ double *pp;
	+ if(vl.start()) do {
	+ pp=p[vl.ijk]+3*vl.q;
	+ fprintf(fp,"// id %d\nsphere{<%g,%g,%g>,s}\n",
	+ id[vl.ijk][vl.q],*pp,pp[1],pp[2]);
	+ } while(vl.inc());
	+ }
	+ /** Dumps all particle positions in POV-Ray format.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_particles_pov(FILE *fp=stdout) {
	+ c_loop_all_periodic vl(*this);
	+ draw_particles_pov(vl,fp);
	+ }
	+ /** Dumps all particle positions in POV-Ray format.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_particles_pov(const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_particles_pov(fp);
	+ fclose(fp);
	+ }
	+ /** Computes Voronoi cells and saves the output in gnuplot
	+ * format.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_cells_gnuplot(c_loop &vl,FILE *fp) {
	+ voronoicell c;double *pp;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ pp=p[vl.ijk]+ps*vl.q;
	+ c.draw_gnuplot(*pp,pp[1],pp[2],fp);
	+ } while(vl.inc());
	+ }
	+ /** Computes all Voronoi cells and saves the output in gnuplot
	+ * format.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_cells_gnuplot(FILE *fp=stdout) {
	+ c_loop_all_periodic vl(*this);
	+ draw_cells_gnuplot(vl,fp);
	+ }
	+ /** Compute all Voronoi cells and saves the output in gnuplot
	+ * format.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_cells_gnuplot(const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_cells_gnuplot(fp);
	+ fclose(fp);
	+ }
	+ /** Computes Voronoi cells and saves the output in POV-Ray
	+ * format.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_cells_pov(c_loop &vl,FILE *fp) {
	+ voronoicell c;double *pp;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ fprintf(fp,"// cell %d\n",id[vl.ijk][vl.q]);
	+ pp=p[vl.ijk]+ps*vl.q;
	+ c.draw_pov(*pp,pp[1],pp[2],fp);
	+ } while(vl.inc());
	+ }
	+ /** Computes all Voronoi cells and saves the output in POV-Ray
	+ * format.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_cells_pov(FILE *fp=stdout) {
	+ c_loop_all_periodic vl(*this);
	+ draw_cells_pov(vl,fp);
	+ }
	+ /** Computes all Voronoi cells and saves the output in POV-Ray
	+ * format.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_cells_pov(const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_cells_pov(fp);
	+ fclose(fp);
	+ }
	+ /** Computes the Voronoi cells and saves customized information
	+ * about them.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] format the custom output string to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void print_custom(c_loop &vl,const char format,FILE fp) {
	+ int ijk,q;double *pp;
	+ if(contains_neighbor(format)) {
	+ voronoicell_neighbor c;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
	+ c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],default_radius,fp);
	+ } while(vl.inc());
	+ } else {
	+ voronoicell c;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
	+ c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],default_radius,fp);
	+ } while(vl.inc());
	+ }
	+ }
	+ void print_custom(const char format,FILE fp=stdout);
	+ void print_custom(const char format,const char filename);
	+ bool find_voronoi_cell(double x,double y,double z,double &rx,double &ry,double &rz,int &pid);
	+ /** Computes the Voronoi cell for a particle currently being
	+ * referenced by a loop class.
	+ * \param[out] c a Voronoi cell class in which to store the
	+ * computed cell.
	+ * \param[in] vl the loop class to use.
	+ * \return True if the cell was computed. If the cell cannot be
	+ * computed because it was removed entirely for some reason,
	+ * then the routine returns false. */
	+ template<class v_cell,class c_loop>
	+ inline bool compute_cell(v_cell &c,c_loop &vl) {
	+ return vc.compute_cell(c,vl.ijk,vl.q,vl.i,vl.j,vl.k);
	+ }
	+ /** Computes the Voronoi cell for given particle.
	+ * \param[out] c a Voronoi cell class in which to store the
	+ * computed cell.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] q the index of the particle within the block.
	+ * \return True if the cell was computed. If the cell cannot be
	+ * computed because it was removed entirely for some reason,
	+ * then the routine returns false. */
	+ template<class v_cell>
	+ inline bool compute_cell(v_cell &c,int ijk,int q) {
	+ int k(ijk/(nxoy)),ijkt(ijk-(nxoy)k),j(ijkt/nx),i(ijkt-jnx);
	+ return vc.compute_cell(c,ijk,q,i,j,k);
	+ }
	+ private:
	+ voro_compute<container_periodic> vc;
	+ friend class voro_compute<container_periodic>;
	+};
	+
	+/** \brief Extension of the container_periodic_base class for computing radical
	+ * Voronoi tessellations.
	+ *
	+ * This class is an extension of container_periodic_base that has routines
	+ * specifically for computing the radical Voronoi tessellation that depends
	+ * on the particle radii. */
	+class container_periodic_poly : public container_periodic_base, public radius_poly {
	+ public:
	+ container_periodic_poly(double bx_,double bxy_,double by_,double bxz_,double byz_,double bz_,
	+ int nx_,int ny_,int nz_,int init_mem_);
	+ void clear();
	+ void put(int n,double x,double y,double z,double r);
	+ void put(int n,double x,double y,double z,double r,int &ai,int &aj,int &ak);
	+ void put(particle_order &vo,int n,double x,double y,double z,double r);
	+ void import(FILE *fp=stdin);
	+ void import(particle_order &vo,FILE *fp=stdin);
	+ /** Imports a list of particles from an open file stream into
	+ * the container_poly class. Entries of five numbers (Particle
	+ * ID, x position, y position, z position, radius) are searched
	+ * for. If the file cannot be successfully read, then the
	+ * routine causes a fatal error.
	+ * \param[in] filename the name of the file to open and read
	+ * from. */
	+ inline void import(const char* filename) {
	+ FILE *fp=safe_fopen(filename,"r");
	+ import(fp);
	+ fclose(fp);
	+ }
	+ /** Imports a list of particles from an open file stream into
	+ * the container_poly class. Entries of five numbers (Particle
	+ * ID, x position, y position, z position, radius) are searched
	+ * for. In addition, the order in which particles are read is
	+ * saved into an ordering class. If the file cannot be
	+ * successfully read, then the routine causes a fatal error.
	+ * \param[in,out] vo the ordering class to use.
	+ * \param[in] filename the name of the file to open and read
	+ * from. */
	+ inline void import(particle_order &vo,const char* filename) {
	+ FILE *fp=safe_fopen(filename,"r");
	+ import(vo,fp);
	+ fclose(fp);
	+ }
	+ void compute_all_cells();
	+ double sum_cell_volumes();
	+ /** Dumps particle IDs, positions and radii to a file.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_particles(c_loop &vl,FILE *fp) {
	+ double *pp;
	+ if(vl.start()) do {
	+ pp=p[vl.ijk]+4*vl.q;
	+ fprintf(fp,"%d %g %g %g %g\n",id[vl.ijk][vl.q],*pp,pp[1],pp[2],pp[3]);
	+ } while(vl.inc());
	+ }
	+ /** Dumps all of the particle IDs, positions and radii to a
	+ * file.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_particles(FILE *fp=stdout) {
	+ c_loop_all_periodic vl(*this);
	+ draw_particles(vl,fp);
	+ }
	+ /** Dumps all of the particle IDs, positions and radii to a
	+ * file.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_particles(const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_particles(fp);
	+ fclose(fp);
	+ }
	+ /** Dumps particle positions in POV-Ray format.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_particles_pov(c_loop &vl,FILE *fp) {
	+ double *pp;
	+ if(vl.start()) do {
	+ pp=p[vl.ijk]+4*vl.q;
	+ fprintf(fp,"// id %d\nsphere{<%g,%g,%g>,%g}\n",
	+ id[vl.ijk][vl.q],*pp,pp[1],pp[2],pp[3]);
	+ } while(vl.inc());
	+ }
	+ /** Dumps all the particle positions in POV-Ray format.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_particles_pov(FILE *fp=stdout) {
	+ c_loop_all_periodic vl(*this);
	+ draw_particles_pov(vl,fp);
	+ }
	+ /** Dumps all the particle positions in POV-Ray format.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_particles_pov(const char *filename) {
	+ FILE *fp(safe_fopen(filename,"w"));
	+ draw_particles_pov(fp);
	+ fclose(fp);
	+ }
	+ /** Computes Voronoi cells and saves the output in gnuplot
	+ * format.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_cells_gnuplot(c_loop &vl,FILE *fp) {
	+ voronoicell c;double *pp;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ pp=p[vl.ijk]+ps*vl.q;
	+ c.draw_gnuplot(*pp,pp[1],pp[2],fp);
	+ } while(vl.inc());
	+ }
	+ /** Compute all Voronoi cells and saves the output in gnuplot
	+ * format.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_cells_gnuplot(FILE *fp=stdout) {
	+ c_loop_all_periodic vl(*this);
	+ draw_cells_gnuplot(vl,fp);
	+ }
	+ /** Compute all Voronoi cells and saves the output in gnuplot
	+ * format.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_cells_gnuplot(const char *filename) {
	+ FILE *fp(safe_fopen(filename,"w"));
	+ draw_cells_gnuplot(fp);
	+ fclose(fp);
	+ }
	+ /** Computes Voronoi cells and saves the output in POV-Ray
	+ * format.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void draw_cells_pov(c_loop &vl,FILE *fp) {
	+ voronoicell c;double *pp;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ fprintf(fp,"// cell %d\n",id[vl.ijk][vl.q]);
	+ pp=p[vl.ijk]+ps*vl.q;
	+ c.draw_pov(*pp,pp[1],pp[2],fp);
	+ } while(vl.inc());
	+ }
	+ /** Computes all Voronoi cells and saves the output in POV-Ray
	+ * format.
	+ * \param[in] fp a file handle to write to. */
	+ inline void draw_cells_pov(FILE *fp=stdout) {
	+ c_loop_all_periodic vl(*this);
	+ draw_cells_pov(vl,fp);
	+ }
	+ /** Computes all Voronoi cells and saves the output in POV-Ray
	+ * format.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_cells_pov(const char *filename) {
	+ FILE *fp(safe_fopen(filename,"w"));
	+ draw_cells_pov(fp);
	+ fclose(fp);
	+ }
	+ /** Computes the Voronoi cells and saves customized information
	+ * about them.
	+ * \param[in] vl the loop class to use.
	+ * \param[in] format the custom output string to use.
	+ * \param[in] fp a file handle to write to. */
	+ template<class c_loop>
	+ void print_custom(c_loop &vl,const char format,FILE fp) {
	+ int ijk,q;double *pp;
	+ if(contains_neighbor(format)) {
	+ voronoicell_neighbor c;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
	+ c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],pp[3],fp);
	+ } while(vl.inc());
	+ } else {
	+ voronoicell c;
	+ if(vl.start()) do if(compute_cell(c,vl)) {
	+ ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
	+ c.output_custom(format,id[ijk][q],*pp,pp[1],pp[2],pp[3],fp);
	+ } while(vl.inc());
	+ }
	+ }
	+ /** Computes the Voronoi cell for a particle currently being
	+ * referenced by a loop class.
	+ * \param[out] c a Voronoi cell class in which to store the
	+ * computed cell.
	+ * \param[in] vl the loop class to use.
	+ * \return True if the cell was computed. If the cell cannot be
	+ * computed because it was removed entirely for some reason,
	+ * then the routine returns false. */
	+ template<class v_cell,class c_loop>
	+ inline bool compute_cell(v_cell &c,c_loop &vl) {
	+ return vc.compute_cell(c,vl.ijk,vl.q,vl.i,vl.j,vl.k);
	+ }
	+ /** Computes the Voronoi cell for given particle.
	+ * \param[out] c a Voronoi cell class in which to store the
	+ * computed cell.
	+ * \param[in] ijk the block that the particle is within.
	+ * \param[in] q the index of the particle within the block.
	+ * \return True if the cell was computed. If the cell cannot be
	+ * computed because it was removed entirely for some reason,
	+ * then the routine returns false. */
	+ template<class v_cell>
	+ inline bool compute_cell(v_cell &c,int ijk,int q) {
	+ int k(ijk/(nxoy)),ijkt(ijk-(nxoy)k),j(ijkt/nx),i(ijkt-jnx);
	+ return vc.compute_cell(c,ijk,q,i,j,k);
	+ }
	+ void print_custom(const char format,FILE fp=stdout);
	+ void print_custom(const char format,const char filename);
	+ bool find_voronoi_cell(double x,double y,double z,double &rx,double &ry,double &rz,int &pid);
	+ private:
	+ voro_compute<container_periodic_poly> vc;
	+ friend class voro_compute<container_periodic_poly>;
	+};
	+
	+}
	+
	+#endif
	Index: extern/voro++/src/v_compute.cc
	===================================================================
	--- extern/voro++/src/v_compute.cc (revision 0)
	+++ extern/voro++/src/v_compute.cc (revision 0)
	@@ -0,0 +1,1006 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file v_compute.cc
	+ * \brief Function implementantions for the voro_compute template. */
	+
	+#include "worklist.hh"
	+#include "v_compute.hh"
	+#include "rad_option.hh"
	+#include "container.hh"
	+#include "container_prd.hh"
	+
	+namespace voro {
	+
	+/** The class constructor initializes constants from the container class, and
	+ * sets up the mask and queue used for Voronoi computations.
	+ * \param[in] con_ a reference to the container class to use.
	+ * \param[in] (hx_,hy_,hz_) the size of the mask to use. */
	+template<class c_class>
	+voro_compute<c_class>::voro_compute(c_class &con_,int hx_,int hy_,int hz_) :
	+ con(con_), boxx(con_.boxx), boxy(con_.boxy), boxz(con_.boxz),
	+ xsp(con_.xsp), ysp(con_.ysp), zsp(con_.zsp),
	+ hx(hx_), hy(hy_), hz(hz_), hxy(hx_hy_), hxyz(hxyhz_), ps(con_.ps),
	+ id(con_.id), p(con_.p), co(con_.co), bxsq(boxxboxx+boxyboxy+boxz*boxz),
	+ mv(0), qu_size(3(3+hxy+hz(hx+hy))), wl(con_.wl), mrad(con_.mrad),
	+ mask(new unsigned int[hxyz]), qu(new int[qu_size]), qu_l(qu+qu_size) {
	+ reset_mask();
	+}
	+
	+/** Scans all of the particles within a block to see if any of them have a
	+ * smaller distance to the given test vector. If one is found, the routine
	+ * updates the minimum distance and store information about this particle.
	+ * \param[in] ijk the index of the block.
	+ * \param[in] (x,y,z) the test vector to consider (which may have already had a
	+ * periodic displacement applied to it).
	+ * \param[in] (di,dj,dk) the coordinates of the current block, to store if the
	+ * particle record is updated.
	+ * \param[in,out] w a reference to a particle record in which to store
	+ * information about the particle whose Voronoi cell the
	+ * vector is within.
	+ * \param[in,out] mrs the current minimum distance, that may be updated if a
	+ * closer particle is found. */
	+template<class c_class>
	+inline void voro_compute<c_class>::scan_all(int ijk,double x,double y,double z,int di,int dj,int dk,particle_record &w,double &mrs) {
	+ double x1,y1,z1,rs;bool in_block=false;
	+ for(int l=0;l<co[ijk];l++) {
	+ x1=p[ijk][ps*l]-x;
	+ y1=p[ijk][ps*l+1]-y;
	+ z1=p[ijk][ps*l+2]-z;
	+ rs=con.r_current_sub(x1x1+y1y1+z1*z1,ijk,l);
	+ if(rs<mrs) {mrs=rs;w.l=l;in_block=true;}
	+ }
	+ if(in_block) {w.ijk=ijk;w.di=di;w.dj=dj,w.dk=dk;}
	+}
	+
	+/** Finds the Voronoi cell that given vector is within. For containers that are
	+ * not radially dependent, this corresponds to findig the particle that is
	+ * closest to the vector; for the radical tessellation containers, this
	+ * corresponds to a finding the minimum weighted distance.
	+ * \param[in] (x,y,z) the vector to consider.
	+ * \param[in] (ci,cj,ck) the coordinates of the block that the test particle is
	+ * in relative to the container data structure.
	+ * \param[in] ijk the index of the block that the test particle is in.
	+ * \param[out] w a reference to a particle record in which to store information
	+ * about the particle whose Voronoi cell the vector is within.
	+ * \param[out] mrs the minimum computed distance. */
	+template<class c_class>
	+void voro_compute<c_class>::find_voronoi_cell(double x,double y,double z,int ci,int cj,int ck,int ijk,particle_record &w,double &mrs) {
	+ double qx=0,qy=0,qz=0,rs;
	+ int i,j,k,di,dj,dk,ei,ej,ek,f,g,disp;
	+ double fx,fy,fz,mxs,mys,mzs,*radp;
	+ unsigned int q,e,mijk;
	+
	+ // Init setup for parameters to return
	+ w.ijk=-1;mrs=large_number;
	+
	+ con.initialize_search(ci,cj,ck,ijk,i,j,k,disp);
	+
	+ // Test all particles in the particle's local region first
	+ scan_all(ijk,x,y,z,0,0,0,w,mrs);
	+
	+ // Now compute the fractional position of the particle within its
	+ // region and store it in (fx,fy,fz). We use this to compute an index
	+ // (di,dj,dk) of which subregion the particle is within.
	+ unsigned int m1,m2;
	+ con.frac_pos(x,y,z,ci,cj,ck,fx,fy,fz);
	+ di=int(fxxspwl_fgrid);dj=int(fyyspwl_fgrid);dk=int(fzzspwl_fgrid);
	+
	+ // The indices (di,dj,dk) tell us which worklist to use, to test the
	+ // blocks in the optimal order. But we only store worklists for the
	+ // eighth of the region where di, dj, and dk are all less than half the
	+ // full grid. The rest of the cases are handled by symmetry. In this
	+ // section, we detect for these cases, by reflecting high values of di,
	+ // dj, and dk. For these cases, a mask is constructed in m1 and m2
	+ // which is used to flip the worklist information when it is loaded.
	+ if(di>=wl_hgrid) {
	+ mxs=boxx-fx;
	+ m1=127+(3<<21);m2=1+(1<<21);di=wl_fgrid-1-di;if(di<0) di=0;
	+ } else {m1=m2=0;mxs=fx;}
	+ if(dj>=wl_hgrid) {
	+ mys=boxy-fy;
	+ m1\|=(127<<7)+(3<<24);m2\|=(1<<7)+(1<<24);dj=wl_fgrid-1-dj;if(dj<0) dj=0;
	+ } else mys=fy;
	+ if(dk>=wl_hgrid) {
	+ mzs=boxz-fz;
	+ m1\|=(127<<14)+(3<<27);m2\|=(1<<14)+(1<<27);dk=wl_fgrid-1-dk;if(dk<0) dk=0;
	+ } else mzs=fz;
	+
	+ // Do a quick test to account for the case when the minimum radius is
	+ // small enought that no other blocks need to be considered
	+ rs=con.r_max_add(mrs);
	+ if(mxsmxs>rs&&mysmys>rs&&mzs*mzs>rs) return;
	+
	+ // Now compute which worklist we are going to use, and set radp and e to
	+ // point at the right offsets
	+ ijk=di+wl_hgrid(dj+wl_hgriddk);
	+ radp=mrad+ijk*wl_seq_length;
	+ e=(const_cast<unsigned int> (wl))+ijkwl_seq_length;
	+
	+ // Read in how many items in the worklist can be tested without having to
	+ // worry about writing to the mask
	+ f=e[0];g=0;
	+ do {
	+
	+ // If mrs is less than the minimum distance to any untested
	+ // block, then we are done
	+ if(con.r_max_add(mrs)<radp[g]) return;
	+ g++;
	+
	+ // Load in a block off the worklist, permute it with the
	+ // symmetry mask, and decode its position. These are all
	+ // integer bit operations so they should run very fast.
	+ q=e[g];q^=m1;q+=m2;
	+ di=q&127;di-=64;
	+ dj=(q>>7)&127;dj-=64;
	+ dk=(q>>14)&127;dk-=64;
	+
	+ // Check that the worklist position is in range
	+ ei=di+i;if(ei<0\|\|ei>=hx) continue;
	+ ej=dj+j;if(ej<0\|\|ej>=hy) continue;
	+ ek=dk+k;if(ek<0\|\|ek>=hz) continue;
	+
	+ // Call the compute_min_max_radius() function. This returns
	+ // true if the minimum distance to the block is bigger than the
	+ // current mrs, in which case we skip this block and move on.
	+ // Otherwise, it computes the maximum distance to the block and
	+ // returns it in crs.
	+ if(compute_min_radius(di,dj,dk,fx,fy,fz,mrs)) continue;
	+
	+ // Now compute which region we are going to loop over, adding a
	+ // displacement for the periodic cases
	+ ijk=con.region_index(ci,cj,ck,ei,ej,ek,qx,qy,qz,disp);
	+
	+ // If mrs is bigger than the maximum distance to the block,
	+ // then we have to test all particles in the block for
	+ // intersections. Otherwise, we do additional checks and skip
	+ // those particles which can't possibly intersect the block.
	+ scan_all(ijk,x-qx,y-qy,z-qz,di,dj,dk,w,mrs);
	+ } while(g<f);
	+
	+ // Update mask value and initialize queue
	+ mv++;
	+ if(mv==0) {reset_mask();mv=1;}
	+ int qu_s=qu,qu_e=qu;
	+
	+ while(g<wl_seq_length-1) {
	+
	+ // If mrs is less than the minimum distance to any untested
	+ // block, then we are done
	+ if(con.r_max_add(mrs)<radp[g]) return;
	+ g++;
	+
	+ // Load in a block off the worklist, permute it with the
	+ // symmetry mask, and decode its position. These are all
	+ // integer bit operations so they should run very fast.
	+ q=e[g];q^=m1;q+=m2;
	+ di=q&127;di-=64;
	+ dj=(q>>7)&127;dj-=64;
	+ dk=(q>>14)&127;dk-=64;
	+
	+ // Compute the position in the mask of the current block. If
	+ // this lies outside the mask, then skip it. Otherwise, mark
	+ // it.
	+ ei=di+i;if(ei<0\|\|ei>=hx) continue;
	+ ej=dj+j;if(ej<0\|\|ej>=hy) continue;
	+ ek=dk+k;if(ek<0\|\|ek>=hz) continue;
	+ mijk=mask+ei+hx(ej+hyek);
	+ *mijk=mv;
	+
	+ // Skip this block if it is further away than the current
	+ // minimum radius
	+ if(compute_min_radius(di,dj,dk,fx,fy,fz,mrs)) continue;
	+
	+ // Now compute which region we are going to loop over, adding a
	+ // displacement for the periodic cases
	+ ijk=con.region_index(ci,cj,ck,ei,ej,ek,qx,qy,qz,disp);
	+ scan_all(ijk,x-qx,y-qy,z-qz,di,dj,dk,w,mrs);
	+
	+ if(qu_e>qu_l-18) add_list_memory(qu_s,qu_e);
	+ scan_bits_mask_add(q,mijk,ei,ej,ek,qu_e);
	+ }
	+
	+ // Do a check to see if we've reached the radius cutoff
	+ if(con.r_max_add(mrs)<radp[g]) return;
	+
	+ // We were unable to completely compute the cell based on the blocks in
	+ // the worklist, so now we have to go block by block, reading in items
	+ // off the list
	+ while(qu_s!=qu_e) {
	+
	+ // Read the next entry of the queue
	+ if(qu_s==qu_l) qu_s=qu;
	+ ei=(qu_s++);ej=(qu_s++);ek=*(qu_s++);
	+ di=ei-i;dj=ej-j;dk=ek-k;
	+ if(compute_min_radius(di,dj,dk,fx,fy,fz,mrs)) continue;
	+
	+ ijk=con.region_index(ci,cj,ck,ei,ej,ek,qx,qy,qz,disp);
	+ scan_all(ijk,x-qx,y-qy,z-qz,di,dj,dk,w,mrs);
	+
	+ // Test the neighbors of the current block, and add them to the
	+ // block list if they haven't already been tested
	+ if((qu_s<=qu_e?(qu_l-qu_e)+(qu_s-qu):qu_s-qu_e)<18) add_list_memory(qu_s,qu_e);
	+ add_to_mask(ei,ej,ek,qu_e);
	+ }
	+}
	+
	+/** Scans the six orthogonal neighbors of a given block and adds them to the
	+ * queue if they haven't been considered already. It assumes that the queue
	+ * will definitely have enough memory to add six entries at the end.
	+ * \param[in] (ei,ej,ek) the block to consider.
	+ * \param[in,out] qu_e a pointer to the end of the queue. */
	+template<class c_class>
	+inline void voro_compute<c_class>::add_to_mask(int ei,int ej,int ek,int *&qu_e) {
	+ unsigned int mijk=mask+ei+hx(ej+hy*ek);
	+ if(ek>0) if((mijk-hxy)!=mv) {if(qu_e==qu_l) qu_e=qu;(mijk-hxy)=mv;(qu_e++)=ei;(qu_e++)=ej;*(qu_e++)=ek-1;}
	+ if(ej>0) if((mijk-hx)!=mv) {if(qu_e==qu_l) qu_e=qu;(mijk-hx)=mv;(qu_e++)=ei;(qu_e++)=ej-1;*(qu_e++)=ek;}
	+ if(ei>0) if((mijk-1)!=mv) {if(qu_e==qu_l) qu_e=qu;(mijk-1)=mv;(qu_e++)=ei-1;(qu_e++)=ej;*(qu_e++)=ek;}
	+ if(ei<hx-1) if((mijk+1)!=mv) {if(qu_e==qu_l) qu_e=qu;(mijk+1)=mv;(qu_e++)=ei+1;(qu_e++)=ej;*(qu_e++)=ek;}
	+ if(ej<hy-1) if((mijk+hx)!=mv) {if(qu_e==qu_l) qu_e=qu;(mijk+hx)=mv;(qu_e++)=ei;(qu_e++)=ej+1;*(qu_e++)=ek;}
	+ if(ek<hz-1) if((mijk+hxy)!=mv) {if(qu_e==qu_l) qu_e=qu;(mijk+hxy)=mv;(qu_e++)=ei;(qu_e++)=ej;*(qu_e++)=ek+1;}
	+}
	+
	+/** Scans a worklist entry and adds any blocks to the queue
	+ * \param[in] (ei,ej,ek) the block to consider.
	+ * \param[in,out] qu_e a pointer to the end of the queue. */
	+template<class c_class>
	+inline void voro_compute<c_class>::scan_bits_mask_add(unsigned int q,unsigned int mijk,int ei,int ej,int ek,int &qu_e) {
	+ const unsigned int b1=1<<21,b2=1<<22,b3=1<<24,b4=1<<25,b5=1<<27,b6=1<<28;
	+ if((q&b2)==b2) {
	+ if(ei>0) {(mijk-1)=mv;(qu_e++)=ei-1;(qu_e++)=ej;(qu_e++)=ek;}
	+ if((q&b1)==0&&ei<hx-1) {(mijk+1)=mv;(qu_e++)=ei+1;(qu_e++)=ej;(qu_e++)=ek;}
	+ } else if((q&b1)==b1&&ei<hx-1) {(mijk+1)=mv;(qu_e++)=ei+1;(qu_e++)=ej;(qu_e++)=ek;}
	+ if((q&b4)==b4) {
	+ if(ej>0) {(mijk-hx)=mv;(qu_e++)=ei;(qu_e++)=ej-1;(qu_e++)=ek;}
	+ if((q&b3)==0&&ej<hy-1) {(mijk+hx)=mv;(qu_e++)=ei;(qu_e++)=ej+1;(qu_e++)=ek;}
	+ } else if((q&b3)==b3&&ej<hy-1) {(mijk+hx)=mv;(qu_e++)=ei;(qu_e++)=ej+1;(qu_e++)=ek;}
	+ if((q&b6)==b6) {
	+ if(ek>0) {(mijk-hxy)=mv;(qu_e++)=ei;(qu_e++)=ej;(qu_e++)=ek-1;}
	+ if((q&b5)==0&&ek<hz-1) {(mijk+hxy)=mv;(qu_e++)=ei;(qu_e++)=ej;(qu_e++)=ek+1;}
	+ } else if((q&b5)==b5&&ek<hz-1) {(mijk+hxy)=mv;(qu_e++)=ei;(qu_e++)=ej;(qu_e++)=ek+1;}
	+}
	+
	+/** This routine computes a Voronoi cell for a single particle in the
	+ * container. It can be called by the user, but is also forms the core part of
	+ * several of the main functions, such as store_cell_volumes(), print_all(),
	+ * and the drawing routines. The algorithm constructs the cell by testing over
	+ * the neighbors of the particle, working outwards until it reaches those
	+ * particles which could not possibly intersect the cell. For maximum
	+ * efficiency, this algorithm is divided into three parts. In the first
	+ * section, the algorithm tests over the blocks which are in the immediate
	+ * vicinity of the particle, by making use of one of the precomputed worklists.
	+ * The code then continues to test blocks on the worklist, but also begins to
	+ * construct a list of neighboring blocks outside the worklist which may need
	+ * to be test. In the third section, the routine starts testing these
	+ * neighboring blocks, evaluating whether or not a particle in them could
	+ * possibly intersect the cell. For blocks that intersect the cell, it tests
	+ * the particles in that block, and then adds the block neighbors to the list
	+ * of potential places to consider.
	+ * \param[in,out] c a reference to a voronoicell object.
	+ * \param[in] ijk the index of the block that the test particle is in.
	+ * \param[in] s the index of the particle within the test block.
	+ * \param[in] (ci,cj,ck) the coordinates of the block that the test particle is
	+ * in relative to the container data structure.
	+ * \return False if the Voronoi cell was completely removed during the
	+ * computation and has zero volume, true otherwise. */
	+template<class c_class>
	+template<class v_cell>
	+bool voro_compute<c_class>::compute_cell(v_cell &c,int ijk,int s,int ci,int cj,int ck) {
	+ static const int count_list[8]={7,11,15,19,26,35,45,59},*count_e=count_list+8;
	+ double x,y,z,x1,y1,z1,qx=0,qy=0,qz=0;
	+ double xlo,ylo,zlo,xhi,yhi,zhi,x2,y2,z2,rs;
	+ int i,j,k,di,dj,dk,ei,ej,ek,f,g,l,disp;
	+ double fx,fy,fz,gxs,gys,gzs,*radp;
	+ unsigned int q,e,mijk;
	+
	+ if(!con.initialize_voronoicell(c,ijk,s,ci,cj,ck,i,j,k,x,y,z,disp)) return false;
	+ con.r_init(ijk,s);
	+
	+ // Initialize the Voronoi cell to fill the entire container
	+ double crs,mrs;
	+
	+ int next_count=3,count_p=(const_cast<int> (count_list));
	+
	+ // Test all particles in the particle's local region first
	+ for(l=0;l<s;l++) {
	+ x1=p[ijk][ps*l]-x;
	+ y1=p[ijk][ps*l+1]-y;
	+ z1=p[ijk][ps*l+2]-z;
	+ rs=con.r_scale(x1x1+y1y1+z1*z1,ijk,l);
	+ if(!c.nplane(x1,y1,z1,rs,id[ijk][l])) return false;
	+ }
	+ l++;
	+ while(l<co[ijk]) {
	+ x1=p[ijk][ps*l]-x;
	+ y1=p[ijk][ps*l+1]-y;
	+ z1=p[ijk][ps*l+2]-z;
	+ rs=con.r_scale(x1x1+y1y1+z1*z1,ijk,l);
	+ if(!c.nplane(x1,y1,z1,rs,id[ijk][l])) return false;
	+ l++;
	+ }
	+
	+ // Now compute the maximum distance squared from the cell center to a
	+ // vertex. This is used to cut off the calculation since we only need
	+ // to test out to twice this range.
	+ mrs=c.max_radius_squared();
	+
	+ // Now compute the fractional position of the particle within its
	+ // region and store it in (fx,fy,fz). We use this to compute an index
	+ // (di,dj,dk) of which subregion the particle is within.
	+ unsigned int m1,m2;
	+ con.frac_pos(x,y,z,ci,cj,ck,fx,fy,fz);
	+ di=int(fxxspwl_fgrid);dj=int(fyyspwl_fgrid);dk=int(fzzspwl_fgrid);
	+
	+ // The indices (di,dj,dk) tell us which worklist to use, to test the
	+ // blocks in the optimal order. But we only store worklists for the
	+ // eighth of the region where di, dj, and dk are all less than half the
	+ // full grid. The rest of the cases are handled by symmetry. In this
	+ // section, we detect for these cases, by reflecting high values of di,
	+ // dj, and dk. For these cases, a mask is constructed in m1 and m2
	+ // which is used to flip the worklist information when it is loaded.
	+ if(di>=wl_hgrid) {
	+ gxs=fx;
	+ m1=127+(3<<21);m2=1+(1<<21);di=wl_fgrid-1-di;if(di<0) di=0;
	+ } else {m1=m2=0;gxs=boxx-fx;}
	+ if(dj>=wl_hgrid) {
	+ gys=fy;
	+ m1\|=(127<<7)+(3<<24);m2\|=(1<<7)+(1<<24);dj=wl_fgrid-1-dj;if(dj<0) dj=0;
	+ } else gys=boxy-fy;
	+ if(dk>=wl_hgrid) {
	+ gzs=fz;
	+ m1\|=(127<<14)+(3<<27);m2\|=(1<<14)+(1<<27);dk=wl_fgrid-1-dk;if(dk<0) dk=0;
	+ } else gzs=boxz-fz;
	+ gxs=gxs;gys=gys;gzs*=gzs;
	+
	+ // Now compute which worklist we are going to use, and set radp and e to
	+ // point at the right offsets
	+ ijk=di+wl_hgrid(dj+wl_hgriddk);
	+ radp=mrad+ijk*wl_seq_length;
	+ e=(const_cast<unsigned int> (wl))+ijkwl_seq_length;
	+
	+ // Read in how many items in the worklist can be tested without having to
	+ // worry about writing to the mask
	+ f=e[0];g=0;
	+ do {
	+
	+ // At the intervals specified by count_list, we recompute the
	+ // maximum radius squared
	+ if(g==next_count) {
	+ mrs=c.max_radius_squared();
	+ if(count_p!=count_e) next_count=*(count_p++);
	+ }
	+
	+ // If mrs is less than the minimum distance to any untested
	+ // block, then we are done
	+ if(con.r_ctest(radp[g],mrs)) return true;
	+ g++;
	+
	+ // Load in a block off the worklist, permute it with the
	+ // symmetry mask, and decode its position. These are all
	+ // integer bit operations so they should run very fast.
	+ q=e[g];q^=m1;q+=m2;
	+ di=q&127;di-=64;
	+ dj=(q>>7)&127;dj-=64;
	+ dk=(q>>14)&127;dk-=64;
	+
	+ // Check that the worklist position is in range
	+ ei=di+i;if(ei<0\|\|ei>=hx) continue;
	+ ej=dj+j;if(ej<0\|\|ej>=hy) continue;
	+ ek=dk+k;if(ek<0\|\|ek>=hz) continue;
	+
	+ // Call the compute_min_max_radius() function. This returns
	+ // true if the minimum distance to the block is bigger than the
	+ // current mrs, in which case we skip this block and move on.
	+ // Otherwise, it computes the maximum distance to the block and
	+ // returns it in crs.
	+ if(compute_min_max_radius(di,dj,dk,fx,fy,fz,gxs,gys,gzs,crs,mrs)) continue;
	+
	+ // Now compute which region we are going to loop over, adding a
	+ // displacement for the periodic cases
	+ ijk=con.region_index(ci,cj,ck,ei,ej,ek,qx,qy,qz,disp);
	+
	+ // If mrs is bigger than the maximum distance to the block,
	+ // then we have to test all particles in the block for
	+ // intersections. Otherwise, we do additional checks and skip
	+ // those particles which can't possibly intersect the block.
	+ if(co[ijk]>0) {
	+ l=0;x2=x-qx;y2=y-qy;z2=z-qz;
	+ if(!con.r_ctest(crs,mrs)) {
	+ do {
	+ x1=p[ijk][ps*l]-x2;
	+ y1=p[ijk][ps*l+1]-y2;
	+ z1=p[ijk][ps*l+2]-z2;
	+ rs=con.r_scale(x1x1+y1y1+z1*z1,ijk,l);
	+ if(!c.nplane(x1,y1,z1,rs,id[ijk][l])) return false;
	+ l++;
	+ } while (l<co[ijk]);
	+ } else {
	+ do {
	+ x1=p[ijk][ps*l]-x2;
	+ y1=p[ijk][ps*l+1]-y2;
	+ z1=p[ijk][ps*l+2]-z2;
	+ rs=x1x1+y1y1+z1*z1;
	+ if(con.r_scale_check(rs,mrs,ijk,l)&&!c.nplane(x1,y1,z1,rs,id[ijk][l])) return false;
	+ l++;
	+ } while (l<co[ijk]);
	+ }
	+ }
	+ } while(g<f);
	+
	+ // If we reach here, we were unable to compute the entire cell using
	+ // the first part of the worklist. This section of the algorithm
	+ // continues the worklist, but it now starts preparing the mask that we
	+ // need if we end up going block by block. We do the same as before,
	+ // but we put a mark down on the mask for every block that's tested.
	+ // The worklist also contains information about which neighbors of each
	+ // block are not also on the worklist, and we start storing those
	+ // points in a list in case we have to go block by block. Update the
	+ // mask counter, and if it wraps around then reset the whole mask; that
	+ // will only happen once every 2^32 tries.
	+ mv++;
	+ if(mv==0) {reset_mask();mv=1;}
	+
	+ // Set the queue pointers
	+ int qu_s=qu,qu_e=qu;
	+
	+ while(g<wl_seq_length-1) {
	+
	+ // At the intervals specified by count_list, we recompute the
	+ // maximum radius squared
	+ if(g==next_count) {
	+ mrs=c.max_radius_squared();
	+ if(count_p!=count_e) next_count=*(count_p++);
	+ }
	+
	+ // If mrs is less than the minimum distance to any untested
	+ // block, then we are done
	+ if(con.r_ctest(radp[g],mrs)) return true;
	+ g++;
	+
	+ // Load in a block off the worklist, permute it with the
	+ // symmetry mask, and decode its position. These are all
	+ // integer bit operations so they should run very fast.
	+ q=e[g];q^=m1;q+=m2;
	+ di=q&127;di-=64;
	+ dj=(q>>7)&127;dj-=64;
	+ dk=(q>>14)&127;dk-=64;
	+
	+ // Compute the position in the mask of the current block. If
	+ // this lies outside the mask, then skip it. Otherwise, mark
	+ // it.
	+ ei=di+i;if(ei<0\|\|ei>=hx) continue;
	+ ej=dj+j;if(ej<0\|\|ej>=hy) continue;
	+ ek=dk+k;if(ek<0\|\|ek>=hz) continue;
	+ mijk=mask+ei+hx(ej+hyek);
	+ *mijk=mv;
	+
	+ // Call the compute_min_max_radius() function. This returns
	+ // true if the minimum distance to the block is bigger than the
	+ // current mrs, in which case we skip this block and move on.
	+ // Otherwise, it computes the maximum distance to the block and
	+ // returns it in crs.
	+ if(compute_min_max_radius(di,dj,dk,fx,fy,fz,gxs,gys,gzs,crs,mrs)) continue;
	+
	+ // Now compute which region we are going to loop over, adding a
	+ // displacement for the periodic cases
	+ ijk=con.region_index(ci,cj,ck,ei,ej,ek,qx,qy,qz,disp);
	+
	+ // If mrs is bigger than the maximum distance to the block,
	+ // then we have to test all particles in the block for
	+ // intersections. Otherwise, we do additional checks and skip
	+ // those particles which can't possibly intersect the block.
	+ if(co[ijk]>0) {
	+ l=0;x2=x-qx;y2=y-qy;z2=z-qz;
	+ if(!con.r_ctest(crs,mrs)) {
	+ do {
	+ x1=p[ijk][ps*l]-x2;
	+ y1=p[ijk][ps*l+1]-y2;
	+ z1=p[ijk][ps*l+2]-z2;
	+ rs=con.r_scale(x1x1+y1y1+z1*z1,ijk,l);
	+ if(!c.nplane(x1,y1,z1,rs,id[ijk][l])) return false;
	+ l++;
	+ } while (l<co[ijk]);
	+ } else {
	+ do {
	+ x1=p[ijk][ps*l]-x2;
	+ y1=p[ijk][ps*l+1]-y2;
	+ z1=p[ijk][ps*l+2]-z2;
	+ rs=x1x1+y1y1+z1*z1;
	+ if(con.r_scale_check(rs,mrs,ijk,l)&&!c.nplane(x1,y1,z1,rs,id[ijk][l])) return false;
	+ l++;
	+ } while (l<co[ijk]);
	+ }
	+ }
	+
	+ // If there might not be enough memory on the list for these
	+ // additions, then add more
	+ if(qu_e>qu_l-18) add_list_memory(qu_s,qu_e);
	+
	+ // Test the parts of the worklist element which tell us what
	+ // neighbors of this block are not on the worklist. Store them
	+ // on the block list, and mark the mask.
	+ scan_bits_mask_add(q,mijk,ei,ej,ek,qu_e);
	+ }
	+
	+ // Do a check to see if we've reached the radius cutoff
	+ if(con.r_ctest(radp[g],mrs)) return true;
	+
	+ // We were unable to completely compute the cell based on the blocks in
	+ // the worklist, so now we have to go block by block, reading in items
	+ // off the list
	+ while(qu_s!=qu_e) {
	+
	+ // If we reached the end of the list memory loop back to the
	+ // start
	+ if(qu_s==qu_l) qu_s=qu;
	+
	+ // Read in a block off the list, and compute the upper and lower
	+ // coordinates in each of the three dimensions
	+ ei=(qu_s++);ej=(qu_s++);ek=*(qu_s++);
	+ xlo=(ei-i)*boxx-fx;xhi=xlo+boxx;
	+ ylo=(ej-j)*boxy-fy;yhi=ylo+boxy;
	+ zlo=(ek-k)*boxz-fz;zhi=zlo+boxz;
	+
	+ // Carry out plane tests to see if any particle in this block
	+ // could possibly intersect the cell
	+ if(ei>i) {
	+ if(ej>j) {
	+ if(ek>k) {if(corner_test(c,xlo,ylo,zlo,xhi,yhi,zhi)) continue;}
	+ else if(ek<k) {if(corner_test(c,xlo,ylo,zhi,xhi,yhi,zlo)) continue;}
	+ else {if(edge_z_test(c,xlo,ylo,zlo,xhi,yhi,zhi)) continue;}
	+ } else if(ej<j) {
	+ if(ek>k) {if(corner_test(c,xlo,yhi,zlo,xhi,ylo,zhi)) continue;}
	+ else if(ek<k) {if(corner_test(c,xlo,yhi,zhi,xhi,ylo,zlo)) continue;}
	+ else {if(edge_z_test(c,xlo,yhi,zlo,xhi,ylo,zhi)) continue;}
	+ } else {
	+ if(ek>k) {if(edge_y_test(c,xlo,ylo,zlo,xhi,yhi,zhi)) continue;}
	+ else if(ek<k) {if(edge_y_test(c,xlo,ylo,zhi,xhi,yhi,zlo)) continue;}
	+ else {if(face_x_test(c,xlo,ylo,zlo,yhi,zhi)) continue;}
	+ }
	+ } else if(ei<i) {
	+ if(ej>j) {
	+ if(ek>k) {if(corner_test(c,xhi,ylo,zlo,xlo,yhi,zhi)) continue;}
	+ else if(ek<k) {if(corner_test(c,xhi,ylo,zhi,xlo,yhi,zlo)) continue;}
	+ else {if(edge_z_test(c,xhi,ylo,zlo,xlo,yhi,zhi)) continue;}
	+ } else if(ej<j) {
	+ if(ek>k) {if(corner_test(c,xhi,yhi,zlo,xlo,ylo,zhi)) continue;}
	+ else if(ek<k) {if(corner_test(c,xhi,yhi,zhi,xlo,ylo,zlo)) continue;}
	+ else {if(edge_z_test(c,xhi,yhi,zlo,xlo,ylo,zhi)) continue;}
	+ } else {
	+ if(ek>k) {if(edge_y_test(c,xhi,ylo,zlo,xlo,yhi,zhi)) continue;}
	+ else if(ek<k) {if(edge_y_test(c,xhi,ylo,zhi,xlo,yhi,zlo)) continue;}
	+ else {if(face_x_test(c,xhi,ylo,zlo,yhi,zhi)) continue;}
	+ }
	+ } else {
	+ if(ej>j) {
	+ if(ek>k) {if(edge_x_test(c,xlo,ylo,zlo,xhi,yhi,zhi)) continue;}
	+ else if(ek<k) {if(edge_x_test(c,xlo,ylo,zhi,xhi,yhi,zlo)) continue;}
	+ else {if(face_y_test(c,xlo,ylo,zlo,xhi,zhi)) continue;}
	+ } else if(ej<j) {
	+ if(ek>k) {if(edge_x_test(c,xlo,yhi,zlo,xhi,ylo,zhi)) continue;}
	+ else if(ek<k) {if(edge_x_test(c,xlo,yhi,zhi,xhi,ylo,zlo)) continue;}
	+ else {if(face_y_test(c,xlo,yhi,zlo,xhi,zhi)) continue;}
	+ } else {
	+ if(ek>k) {if(face_z_test(c,xlo,ylo,zlo,xhi,yhi)) continue;}
	+ else if(ek<k) {if(face_z_test(c,xlo,ylo,zhi,xhi,yhi)) continue;}
	+ else voro_fatal_error("Compute cell routine revisiting central block, which should never\nhappen.",VOROPP_INTERNAL_ERROR);
	+ }
	+ }
	+
	+ // Now compute the region that we are going to test over, and
	+ // set a displacement vector for the periodic cases
	+ ijk=con.region_index(ci,cj,ck,ei,ej,ek,qx,qy,qz,disp);
	+
	+ // Loop over all the elements in the block to test for cuts. It
	+ // would be possible to exclude some of these cases by testing
	+ // against mrs, but this will probably not save time.
	+ if(co[ijk]>0) {
	+ l=0;x2=x-qx;y2=y-qy;z2=z-qz;
	+ do {
	+ x1=p[ijk][ps*l]-x2;
	+ y1=p[ijk][ps*l+1]-y2;
	+ z1=p[ijk][ps*l+2]-z2;
	+ rs=con.r_scale(x1x1+y1y1+z1*z1,ijk,l);
	+ if(!c.nplane(x1,y1,z1,rs,id[ijk][l])) return false;
	+ l++;
	+ } while (l<co[ijk]);
	+ }
	+
	+ // If there's not much memory on the block list then add more
	+ if((qu_s<=qu_e?(qu_l-qu_e)+(qu_s-qu):qu_s-qu_e)<18) add_list_memory(qu_s,qu_e);
	+
	+ // Test the neighbors of the current block, and add them to the
	+ // block list if they haven't already been tested
	+ add_to_mask(ei,ej,ek,qu_e);
	+ }
	+
	+ return true;
	+}
	+
	+/** This function checks to see whether a particular block can possibly have
	+ * any intersection with a Voronoi cell, for the case when the closest point
	+ * from the cell center to the block is at a corner.
	+ * \param[in,out] c a reference to a Voronoi cell.
	+ * \param[in] (xl,yl,zl) the relative coordinates of the corner of the block
	+ * closest to the cell center.
	+ * \param[in] (xh,yh,zh) the relative coordinates of the corner of the block
	+ * furthest away from the cell center.
	+ * \return False if the block may intersect, true if does not. */
	+template<class c_class>
	+template<class v_cell>
	+bool voro_compute<c_class>::corner_test(v_cell &c,double xl,double yl,double zl,double xh,double yh,double zh) {
	+ con.r_prime(xlxl+ylyl+zl*zl);
	+ if(c.plane_intersects_guess(xh,yl,zl,con.r_cutoff(xlxh+ylyl+zl*zl))) return false;
	+ if(c.plane_intersects(xh,yh,zl,con.r_cutoff(xlxh+ylyh+zl*zl))) return false;
	+ if(c.plane_intersects(xl,yh,zl,con.r_cutoff(xlxl+ylyh+zl*zl))) return false;
	+ if(c.plane_intersects(xl,yh,zh,con.r_cutoff(xlxl+ylyh+zl*zh))) return false;
	+ if(c.plane_intersects(xl,yl,zh,con.r_cutoff(xlxl+ylyl+zl*zh))) return false;
	+ if(c.plane_intersects(xh,yl,zh,con.r_cutoff(xlxh+ylyl+zl*zh))) return false;
	+ return true;
	+}
	+
	+/** This function checks to see whether a particular block can possibly have
	+ * any intersection with a Voronoi cell, for the case when the closest point
	+ * from the cell center to the block is on an edge which points along the x
	+ * direction.
	+ * \param[in,out] c a reference to a Voronoi cell.
	+ * \param[in] (x0,x1) the minimum and maximum relative x coordinates of the
	+ * block.
	+ * \param[in] (yl,zl) the relative y and z coordinates of the corner of the
	+ * block closest to the cell center.
	+ * \param[in] (yh,zh) the relative y and z coordinates of the corner of the
	+ * block furthest away from the cell center.
	+ * \return False if the block may intersect, true if does not. */
	+template<class c_class>
	+template<class v_cell>
	+inline bool voro_compute<c_class>::edge_x_test(v_cell &c,double x0,double yl,double zl,double x1,double yh,double zh) {
	+ con.r_prime(ylyl+zlzl);
	+ if(c.plane_intersects_guess(x0,yl,zh,con.r_cutoff(ylyl+zlzh))) return false;
	+ if(c.plane_intersects(x1,yl,zh,con.r_cutoff(ylyl+zlzh))) return false;
	+ if(c.plane_intersects(x1,yl,zl,con.r_cutoff(ylyl+zlzl))) return false;
	+ if(c.plane_intersects(x0,yl,zl,con.r_cutoff(ylyl+zlzl))) return false;
	+ if(c.plane_intersects(x0,yh,zl,con.r_cutoff(ylyh+zlzl))) return false;
	+ if(c.plane_intersects(x1,yh,zl,con.r_cutoff(ylyh+zlzl))) return false;
	+ return true;
	+}
	+
	+/** This function checks to see whether a particular block can possibly have
	+ * any intersection with a Voronoi cell, for the case when the closest point
	+ * from the cell center to the block is on an edge which points along the y
	+ * direction.
	+ * \param[in,out] c a reference to a Voronoi cell.
	+ * \param[in] (y0,y1) the minimum and maximum relative y coordinates of the
	+ * block.
	+ * \param[in] (xl,zl) the relative x and z coordinates of the corner of the
	+ * block closest to the cell center.
	+ * \param[in] (xh,zh) the relative x and z coordinates of the corner of the
	+ * block furthest away from the cell center.
	+ * \return False if the block may intersect, true if does not. */
	+template<class c_class>
	+template<class v_cell>
	+inline bool voro_compute<c_class>::edge_y_test(v_cell &c,double xl,double y0,double zl,double xh,double y1,double zh) {
	+ con.r_prime(xlxl+zlzl);
	+ if(c.plane_intersects_guess(xl,y0,zh,con.r_cutoff(xlxl+zlzh))) return false;
	+ if(c.plane_intersects(xl,y1,zh,con.r_cutoff(xlxl+zlzh))) return false;
	+ if(c.plane_intersects(xl,y1,zl,con.r_cutoff(xlxl+zlzl))) return false;
	+ if(c.plane_intersects(xl,y0,zl,con.r_cutoff(xlxl+zlzl))) return false;
	+ if(c.plane_intersects(xh,y0,zl,con.r_cutoff(xlxh+zlzl))) return false;
	+ if(c.plane_intersects(xh,y1,zl,con.r_cutoff(xlxh+zlzl))) return false;
	+ return true;
	+}
	+
	+/** This function checks to see whether a particular block can possibly have
	+ * any intersection with a Voronoi cell, for the case when the closest point
	+ * from the cell center to the block is on an edge which points along the z
	+ * direction.
	+ * \param[in,out] c a reference to a Voronoi cell.
	+ * \param[in] (z0,z1) the minimum and maximum relative z coordinates of the block.
	+ * \param[in] (xl,yl) the relative x and y coordinates of the corner of the
	+ * block closest to the cell center.
	+ * \param[in] (xh,yh) the relative x and y coordinates of the corner of the
	+ * block furthest away from the cell center.
	+ * \return False if the block may intersect, true if does not. */
	+template<class c_class>
	+template<class v_cell>
	+inline bool voro_compute<c_class>::edge_z_test(v_cell &c,double xl,double yl,double z0,double xh,double yh,double z1) {
	+ con.r_prime(xlxl+ylyl);
	+ if(c.plane_intersects_guess(xl,yh,z0,con.r_cutoff(xlxl+ylyh))) return false;
	+ if(c.plane_intersects(xl,yh,z1,con.r_cutoff(xlxl+ylyh))) return false;
	+ if(c.plane_intersects(xl,yl,z1,con.r_cutoff(xlxl+ylyl))) return false;
	+ if(c.plane_intersects(xl,yl,z0,con.r_cutoff(xlxl+ylyl))) return false;
	+ if(c.plane_intersects(xh,yl,z0,con.r_cutoff(xlxh+ylyl))) return false;
	+ if(c.plane_intersects(xh,yl,z1,con.r_cutoff(xlxh+ylyl))) return false;
	+ return true;
	+}
	+
	+/** This function checks to see whether a particular block can possibly have
	+ * any intersection with a Voronoi cell, for the case when the closest point
	+ * from the cell center to the block is on a face aligned with the x direction.
	+ * \param[in,out] c a reference to a Voronoi cell.
	+ * \param[in] xl the minimum distance from the cell center to the face.
	+ * \param[in] (y0,y1) the minimum and maximum relative y coordinates of the
	+ * block.
	+ * \param[in] (z0,z1) the minimum and maximum relative z coordinates of the
	+ * block.
	+ * \return False if the block may intersect, true if does not. */
	+template<class c_class>
	+template<class v_cell>
	+inline bool voro_compute<c_class>::face_x_test(v_cell &c,double xl,double y0,double z0,double y1,double z1) {
	+ con.r_prime(xl*xl);
	+ if(c.plane_intersects_guess(xl,y0,z0,con.r_cutoff(xl*xl))) return false;
	+ if(c.plane_intersects(xl,y0,z1,con.r_cutoff(xl*xl))) return false;
	+ if(c.plane_intersects(xl,y1,z1,con.r_cutoff(xl*xl))) return false;
	+ if(c.plane_intersects(xl,y1,z0,con.r_cutoff(xl*xl))) return false;
	+ return true;
	+}
	+
	+/** This function checks to see whether a particular block can possibly have
	+ * any intersection with a Voronoi cell, for the case when the closest point
	+ * from the cell center to the block is on a face aligned with the y direction.
	+ * \param[in,out] c a reference to a Voronoi cell.
	+ * \param[in] yl the minimum distance from the cell center to the face.
	+ * \param[in] (x0,x1) the minimum and maximum relative x coordinates of the
	+ * block.
	+ * \param[in] (z0,z1) the minimum and maximum relative z coordinates of the
	+ * block.
	+ * \return False if the block may intersect, true if does not. */
	+template<class c_class>
	+template<class v_cell>
	+inline bool voro_compute<c_class>::face_y_test(v_cell &c,double x0,double yl,double z0,double x1,double z1) {
	+ con.r_prime(yl*yl);
	+ if(c.plane_intersects_guess(x0,yl,z0,con.r_cutoff(yl*yl))) return false;
	+ if(c.plane_intersects(x0,yl,z1,con.r_cutoff(yl*yl))) return false;
	+ if(c.plane_intersects(x1,yl,z1,con.r_cutoff(yl*yl))) return false;
	+ if(c.plane_intersects(x1,yl,z0,con.r_cutoff(yl*yl))) return false;
	+ return true;
	+}
	+
	+/** This function checks to see whether a particular block can possibly have
	+ * any intersection with a Voronoi cell, for the case when the closest point
	+ * from the cell center to the block is on a face aligned with the z direction.
	+ * \param[in,out] c a reference to a Voronoi cell.
	+ * \param[in] zl the minimum distance from the cell center to the face.
	+ * \param[in] (x0,x1) the minimum and maximum relative x coordinates of the
	+ * block.
	+ * \param[in] (y0,y1) the minimum and maximum relative y coordinates of the
	+ * block.
	+ * \return False if the block may intersect, true if does not. */
	+template<class c_class>
	+template<class v_cell>
	+inline bool voro_compute<c_class>::face_z_test(v_cell &c,double x0,double y0,double zl,double x1,double y1) {
	+ con.r_prime(zl*zl);
	+ if(c.plane_intersects_guess(x0,y0,zl,con.r_cutoff(zl*zl))) return false;
	+ if(c.plane_intersects(x0,y1,zl,con.r_cutoff(zl*zl))) return false;
	+ if(c.plane_intersects(x1,y1,zl,con.r_cutoff(zl*zl))) return false;
	+ if(c.plane_intersects(x1,y0,zl,con.r_cutoff(zl*zl))) return false;
	+ return true;
	+}
	+
	+
	+/** This routine checks to see whether a point is within a particular distance
	+ * of a nearby region. If the point is within the distance of the region, then
	+ * the routine returns true, and computes the maximum distance from the point
	+ * to the region. Otherwise, the routine returns false.
	+ * \param[in] (di,dj,dk) the position of the nearby region to be tested,
	+ * relative to the region that the point is in.
	+ * \param[in] (fx,fy,fz) the displacement of the point within its region.
	+ * \param[in] (gxs,gys,gzs) the maximum squared distances from the point to the
	+ * sides of its region.
	+ * \param[out] crs a reference in which to return the maximum distance to the
	+ * region (only computed if the routine returns false).
	+ * \param[in] mrs the distance to be tested.
	+ * \return True if the region is further away than mrs, false if the region in
	+ * within mrs. */
	+template<class c_class>
	+bool voro_compute<c_class>::compute_min_max_radius(int di,int dj,int dk,double fx,double fy,double fz,double gxs,double gys,double gzs,double &crs,double mrs) {
	+ double xlo,ylo,zlo;
	+ if(di>0) {
	+ xlo=di*boxx-fx;
	+ crs=xlo*xlo;
	+ if(dj>0) {
	+ ylo=dj*boxy-fy;
	+ crs+=ylo*ylo;
	+ if(dk>0) {
	+ zlo=dk*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=bxsq+2(boxxxlo+boxyylo+boxzzlo);
	+ } else if(dk<0) {
	+ zlo=(dk+1)*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=bxsq+2(boxxxlo+boxyylo-boxzzlo);
	+ } else {
	+ if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxx(2xlo+boxx)+boxy(2ylo+boxy)+gzs;
	+ }
	+ } else if(dj<0) {
	+ ylo=(dj+1)*boxy-fy;
	+ crs+=ylo*ylo;
	+ if(dk>0) {
	+ zlo=dk*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=bxsq+2(boxxxlo-boxyylo+boxzzlo);
	+ } else if(dk<0) {
	+ zlo=(dk+1)*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=bxsq+2(boxxxlo-boxyylo-boxzzlo);
	+ } else {
	+ if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxx(2xlo+boxx)+boxy(-2ylo+boxy)+gzs;
	+ }
	+ } else {
	+ if(dk>0) {
	+ zlo=dk*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxz(2zlo+boxz);
	+ } else if(dk<0) {
	+ zlo=(dk+1)*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxz(-2zlo+boxz);
	+ } else {
	+ if(con.r_ctest(crs,mrs)) return true;
	+ crs+=gzs;
	+ }
	+ crs+=gys+boxx(2xlo+boxx);
	+ }
	+ } else if(di<0) {
	+ xlo=(di+1)*boxx-fx;
	+ crs=xlo*xlo;
	+ if(dj>0) {
	+ ylo=dj*boxy-fy;
	+ crs+=ylo*ylo;
	+ if(dk>0) {
	+ zlo=dk*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=bxsq+2(-boxxxlo+boxyylo+boxzzlo);
	+ } else if(dk<0) {
	+ zlo=(dk+1)*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=bxsq+2(-boxxxlo+boxyylo-boxzzlo);
	+ } else {
	+ if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxx(-2xlo+boxx)+boxy(2ylo+boxy)+gzs;
	+ }
	+ } else if(dj<0) {
	+ ylo=(dj+1)*boxy-fy;
	+ crs+=ylo*ylo;
	+ if(dk>0) {
	+ zlo=dk*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=bxsq+2(-boxxxlo-boxyylo+boxzzlo);
	+ } else if(dk<0) {
	+ zlo=(dk+1)*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=bxsq+2(-boxxxlo-boxyylo-boxzzlo);
	+ } else {
	+ if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxx(-2xlo+boxx)+boxy(-2ylo+boxy)+gzs;
	+ }
	+ } else {
	+ if(dk>0) {
	+ zlo=dk*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxz(2zlo+boxz);
	+ } else if(dk<0) {
	+ zlo=(dk+1)*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxz(-2zlo+boxz);
	+ } else {
	+ if(con.r_ctest(crs,mrs)) return true;
	+ crs+=gzs;
	+ }
	+ crs+=gys+boxx(-2xlo+boxx);
	+ }
	+ } else {
	+ if(dj>0) {
	+ ylo=dj*boxy-fy;
	+ crs=ylo*ylo;
	+ if(dk>0) {
	+ zlo=dk*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxz(2zlo+boxz);
	+ } else if(dk<0) {
	+ zlo=(dk+1)*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxz(-2zlo+boxz);
	+ } else {
	+ if(con.r_ctest(crs,mrs)) return true;
	+ crs+=gzs;
	+ }
	+ crs+=boxy(2ylo+boxy);
	+ } else if(dj<0) {
	+ ylo=(dj+1)*boxy-fy;
	+ crs=ylo*ylo;
	+ if(dk>0) {
	+ zlo=dk*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxz(2zlo+boxz);
	+ } else if(dk<0) {
	+ zlo=(dk+1)*boxz-fz;
	+ crs+=zlo*zlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxz(-2zlo+boxz);
	+ } else {
	+ if(con.r_ctest(crs,mrs)) return true;
	+ crs+=gzs;
	+ }
	+ crs+=boxy(-2ylo+boxy);
	+ } else {
	+ if(dk>0) {
	+ zlo=dkboxz-fz;crs=zlozlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxz(2zlo+boxz);
	+ } else if(dk<0) {
	+ zlo=(dk+1)boxz-fz;crs=zlozlo;if(con.r_ctest(crs,mrs)) return true;
	+ crs+=boxz(-2zlo+boxz);
	+ } else {
	+ crs=0;
	+ voro_fatal_error("Min/max radius function called for central block, which should never\nhappen.",VOROPP_INTERNAL_ERROR);
	+ }
	+ crs+=gys;
	+ }
	+ crs+=gxs;
	+ }
	+ return false;
	+}
	+
	+template<class c_class>
	+bool voro_compute<c_class>::compute_min_radius(int di,int dj,int dk,double fx,double fy,double fz,double mrs) {
	+ double t,crs;
	+
	+ if(di>0) {t=diboxx-fx;crs=tt;}
	+ else if(di<0) {t=(di+1)boxx-fx;crs=tt;}
	+ else crs=0;
	+
	+ if(dj>0) {t=djboxy-fy;crs+=tt;}
	+ else if(dj<0) {t=(dj+1)boxy-fy;crs+=tt;}
	+
	+ if(dk>0) {t=dkboxz-fz;crs+=tt;}
	+ else if(dk<0) {t=(dk+1)boxz-fz;crs+=tt;}
	+
	+ return crs>con.r_max_add(mrs);
	+}
	+
	+/** Adds memory to the queue.
	+ * \param[in,out] qu_s a reference to the queue start pointer.
	+ * \param[in,out] qu_e a reference to the queue end pointer. */
	+template<class c_class>
	+inline void voro_compute<c_class>::add_list_memory(int& qu_s,int& qu_e) {
	+ qu_size<<=1;
	+ int qu_n=new int[qu_size],qu_c=qu_n;
	+#if VOROPP_VERBOSE >=2
	+ fprintf(stderr,"List memory scaled up to %d\n",qu_size);
	+#endif
	+ if(qu_s<=qu_e) {
	+ while(qu_s<qu_e) (qu_c++)=(qu_s++);
	+ } else {
	+ while(qu_s<qu_l) (qu_c++)=(qu_s++);qu_s=qu;
	+ while(qu_s<qu_e) (qu_c++)=(qu_s++);
	+ }
	+ delete [] qu;
	+ qu_s=qu=qu_n;
	+ qu_l=qu+qu_size;
	+ qu_e=qu_c;
	+}
	+
	+// Explicit template instantiation
	+template voro_compute<container>::voro_compute(container&,int,int,int);
	+template voro_compute<container_poly>::voro_compute(container_poly&,int,int,int);
	+template bool voro_compute<container>::compute_cell(voronoicell&,int,int,int,int,int);
	+template bool voro_compute<container>::compute_cell(voronoicell_neighbor&,int,int,int,int,int);
	+template void voro_compute<container>::find_voronoi_cell(double,double,double,int,int,int,int,particle_record&,double&);
	+template bool voro_compute<container_poly>::compute_cell(voronoicell&,int,int,int,int,int);
	+template bool voro_compute<container_poly>::compute_cell(voronoicell_neighbor&,int,int,int,int,int);
	+template void voro_compute<container_poly>::find_voronoi_cell(double,double,double,int,int,int,int,particle_record&,double&);
	+
	+// Explicit template instantiation
	+template voro_compute<container_periodic>::voro_compute(container_periodic&,int,int,int);
	+template voro_compute<container_periodic_poly>::voro_compute(container_periodic_poly&,int,int,int);
	+template bool voro_compute<container_periodic>::compute_cell(voronoicell&,int,int,int,int,int);
	+template bool voro_compute<container_periodic>::compute_cell(voronoicell_neighbor&,int,int,int,int,int);
	+template void voro_compute<container_periodic>::find_voronoi_cell(double,double,double,int,int,int,int,particle_record&,double&);
	+template bool voro_compute<container_periodic_poly>::compute_cell(voronoicell&,int,int,int,int,int);
	+template bool voro_compute<container_periodic_poly>::compute_cell(voronoicell_neighbor&,int,int,int,int,int);
	+template void voro_compute<container_periodic_poly>::find_voronoi_cell(double,double,double,int,int,int,int,particle_record&,double&);
	+
	+}
	Index: extern/voro++/src/README
	===================================================================
	--- extern/voro++/src/README (revision 0)
	+++ extern/voro++/src/README (revision 0)
	@@ -0,0 +1,21 @@
	+Voro++ library source files
	+===========================
	+This directory contains the source code for the library. For full details of
	+each file, see the files section of the online reference manual at
	+http://math.lbl.gov/voro++/doc/refman/
	+
	+Several other files are present:
	+
	+Makefile - the GNU Makefile controlling the compilation.
	+
	+Makefile.dep - a file containing all the dependencies of the source files,
	+automatically generated by the GNU compiler.
	+
	+cmd_line.cc - source file for creating the command-line utility that makes use
	+of the library.
	+
	+Doxyfile - configuration file for Doxygen, used to automatically generate
	+documentation based on the source code comments.
	+
	+worklist_gen.pl - perl script for automatically generating the worklist.hh and
	+v_base_wl.cc files.
	Index: extern/voro++/src/c_interface.hh
	===================================================================
	--- extern/voro++/src/c_interface.hh (revision 0)
	+++ extern/voro++/src/c_interface.hh (revision 0)
	@@ -0,0 +1,19 @@
	+typedef void container;
	+typedef void particle_order;
	+#include <stdio.h>
	+
	+#ifdef __cplusplus
	+extern "C" {
	+#endif
	+
	+ container* container_new(double ax_,double bx_,double ay_,double by_,double az_,double bz_,
	+ int nx_,int ny_,int nz_,int xperiodic_,int yperiodic_,int zperiodic_,int init_mem);
	+ particle_order* particle_order_new();
	+
	+ void container_put(container* container, particle_order* po, int n, double x, double y, double z);
	+ void container_print_custom(container* container, const char* format, FILE* fp);
	+
	+#ifdef __cplusplus
	+}
	+#endif
	+
	Index: extern/voro++/src/config.hh
	===================================================================
	--- extern/voro++/src/config.hh (revision 0)
	+++ extern/voro++/src/config.hh (revision 0)
	@@ -0,0 +1,127 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file config.hh
	+ * \brief Master configuration file for setting various compile-time options. */
	+
	+#ifndef VOROPP_CONFIG_HH
	+#define VOROPP_CONFIG_HH
	+
	+namespace voro {
	+
	+// These constants set the initial memory allocation for the Voronoi cell
	+/** The initial memory allocation for the number of vertices. */
	+const int init_vertices=256;
	+/** The initial memory allocation for the maximum vertex order. */
	+const int init_vertex_order=64;
	+/** The initial memory allocation for the number of regular vertices of order
	+ * 3. */
	+const int init_3_vertices=256;
	+/** The initial memory allocation for the number of vertices of higher order.
	+ */
	+const int init_n_vertices=8;
	+/** The initial buffer size for marginal cases used by the suretest class. */
	+const int init_marginal=64;
	+/** The initial size for the delete stack. */
	+const int init_delete_size=256;
	+/** The initial size for the auxiliary delete stack. */
	+const int init_delete2_size=256;
	+/** The initial size for the wall pointer array. */
	+const int init_wall_size=32;
	+/** The default initial size for the ordering class. */
	+const int init_ordering_size=4096;
	+/** The initial size of the pre_container chunk index. */
	+const int init_chunk_size=256;
	+
	+// If the initial memory is too small, the program dynamically allocates more.
	+// However, if the limits below are reached, then the program bails out.
	+/** The maximum memory allocation for the number of vertices. */
	+const int max_vertices=16777216;
	+/** The maximum memory allocation for the maximum vertex order. */
	+const int max_vertex_order=2048;
	+/** The maximum memory allocation for the any particular order of vertex. */
	+const int max_n_vertices=16777216;
	+/** The maximum buffer size for marginal cases used by the suretest class. */
	+const int max_marginal=16777216;
	+/** The maximum size for the delete stack. */
	+const int max_delete_size=16777216;
	+/** The maximum size for the auxiliary delete stack. */
	+const int max_delete2_size=16777216;
	+/** The maximum amount of particle memory allocated for a single region. */
	+const int max_particle_memory=16777216;
	+/** The maximum size for the wall pointer array. */
	+const int max_wall_size=2048;
	+/** The maximum size for the ordering class. */
	+const int max_ordering_size=67108864;
	+/** The maximum size for the pre_container chunk index. */
	+const int max_chunk_size=65536;
	+
	+/** The chunk size in the pre_container classes. */
	+const int pre_container_chunk_size=1024;
	+
	+#ifndef VOROPP_VERBOSE
	+/** Voro++ can print a number of different status and debugging messages to
	+ * notify the user of special behavior, and this macro sets the amount which
	+ * are displayed. At level 0, no messages are printed. At level 1, messages
	+ * about unusual cases during cell construction are printed, such as when the
	+ * plane routine bails out due to floating point problems. At level 2, general
	+ * messages about memory expansion are printed. At level 3, technical details
	+ * about memory management are printed. */
	+#define VOROPP_VERBOSE 0
	+#endif
	+
	+/** If a point is within this distance of a cutting plane, then the code
	+ * assumes that point exactly lies on the plane. */
	+const double tolerance=1e-11;
	+
	+/** If a point is within this distance of a cutting plane, then the code stores
	+ * whether this point is inside, outside, or exactly on the cutting plane in
	+ * the marginal cases buffer, to prevent the test giving a different result on
	+ * a subsequent evaluation due to floating point rounding errors. */
	+const double tolerance2=2e-11;
	+
	+/** The square of the tolerance, used when deciding whether some squared
	+ * quantities are large enough to be used. */
	+const double tolerance_sq=tolerance*tolerance;
	+
	+/** A large number that is used in the computation. */
	+const double large_number=1e30;
	+
	+/** A radius to use as a placeholder when no other information is available. */
	+const double default_radius=0.5;
	+
	+/** The maximum number of shells of periodic images to test over. */
	+const int max_unit_voro_shells=10;
	+
	+/** A guess for the optimal number of particles per block, used to set up the
	+ * container grid. */
	+const double optimal_particles=5.6;
	+
	+/** If this is set to 1, then the code reports any instances of particles being
	+ * put outside of the container geometry. */
	+#define VOROPP_REPORT_OUT_OF_BOUNDS 0
	+
	+/** Voro++ returns this status code if there is a file-related error, such as
	+ * not being able to open file. */
	+#define VOROPP_FILE_ERROR 1
	+
	+/** Voro++ returns this status code if there is a memory allocation error, if
	+ * one of the safe memory limits is exceeded. */
	+#define VOROPP_MEMORY_ERROR 2
	+
	+/** Voro++ returns this status code if there is any type of internal error, if
	+ * it detects that representation of the Voronoi cell is inconsistent. This
	+ * status code will generally indicate a bug, and the developer should be
	+ * contacted. */
	+#define VOROPP_INTERNAL_ERROR 3
	+
	+/** Voro++ returns this status code if it could not interpret the command line
	+ * arguments passed to the command line utility. */
	+#define VOROPP_CMD_LINE_ERROR 4
	+
	+}
	+
	+#endif
	Index: extern/voro++/src/voro++.hh
	===================================================================
	--- extern/voro++/src/voro++.hh (revision 0)
	+++ extern/voro++/src/voro++.hh (revision 0)
	@@ -0,0 +1,333 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file voro++.hh
	+ * \brief A file that loads all of the Voro++ header files. */
	+
	+/** \mainpage Voro++ class reference manual
	+ * \section intro Introduction
	+ * Voro++ is a software library for carrying out three-dimensional computations
	+ * of the Voronoi tessellation. A distinguishing feature of the Voro++ library
	+ * is that it carries out cell-based calculations, computing the Voronoi cell
	+ * for each particle individually, rather than computing the Voronoi
	+ * tessellation as a global network of vertices and edges. It is particularly
	+ * well-suited for applications that rely on cell-based statistics, where
	+ * features of Voronoi cells (eg. volume, centroid, number of faces) can be
	+ * used to analyze a system of particles.
	+ *
	+ * Voro++ is written in C++ and can be built as a static library that can be
	+ * linked to. This manual provides a reference for every function in the class
	+ * structure. For a general overview of the program, see the Voro++ website at
	+ * http://math.lbl.gov/voro++/ and in particular the example programs at
	+ * http://math.lbl.gov/voro++/examples/ that demonstrate many of the library's
	+ * features.
	+ *
	+ * \section class C++ class structure
	+ * The code is structured around several C++ classes. The voronoicell_base
	+ * class contains all of the routines for constructing a single Voronoi cell.
	+ * It represents the cell as a collection of vertices that are connected by
	+ * edges, and there are routines for initializing, making, and outputting the
	+ * cell. The voronoicell_base class form the base of the voronoicell and
	+ * voronoicell_neighbor classes, which add specialized routines depending on
	+ * whether neighboring particle ID information for each face must be tracked or
	+ * not. Collectively, these classes are referred to as "voronoicell classes"
	+ * within the documentation.
	+ *
	+ * There is a hierarchy of classes that represent three-dimensional particle
	+ * systems. All of these are derived from the voro_base class, which contains
	+ * constants that divide a three-dimensional system into a rectangular grid of
	+ * equally-sized rectangular blocks; this grid is used for computational
	+ * efficiency during the Voronoi calculations.
	+ *
	+ * The container_base, container, and container_poly are then derived from the
	+ * voro_base class to represent a particle system in a specific
	+ * three-dimensional rectangular box using both periodic and non-periodic
	+ * boundary conditions. In addition, the container_periodic_base,
	+ * container_periodic, and container_periodic_poly classes represent
	+ * a particle system in a three-dimensional non-orthogonal periodic domain,
	+ * defined by three periodicity vectors that represent a parallelepiped.
	+ * Collectively, these classes are referred to as "container classes" within
	+ * the documentation.
	+ *
	+ * The voro_compute template encapsulates all of the routines for computing
	+ * Voronoi cells. Each container class has a voro_compute template within
	+ * it, that accesses the container's particle system, and computes the Voronoi
	+ * cells.
	+ *
	+ * There are several wall classes that can be used to apply certain boundary
	+ * conditions using additional plane cuts during the Voronoi cell compution.
	+ * The code also contains a number of small loop classes, c_loop_all,
	+ * c_loop_subset, c_loop_all_periodic, and c_loop_order that can be used to
	+ * iterate over a certain subset of particles in a container. The latter class
	+ * makes use of a special particle_order class that stores a specific order of
	+ * particles within the container. The library also contains the classes
	+ * pre_container_base, pre_container, and pre_container_poly, that can be used
	+ * as temporary storage when importing data of unknown size.
	+ *
	+ * \section voronoicell The voronoicell classes
	+ * The voronoicell class represents a single Voronoi cell as a convex
	+ * polyhedron, with a set of vertices that are connected by edges. The class
	+ * contains a variety of functions that can be used to compute and output the
	+ * Voronoi cell corresponding to a particular particle. The command init()
	+ * can be used to initialize a cell as a large rectangular box. The Voronoi cell
	+ * can then be computed by repeatedly cutting it with planes that correspond to
	+ * the perpendicular bisectors between that particle and its neighbors.
	+ *
	+ * This is achieved by using the plane() routine, which will recompute the
	+ * cell's vertices and edges after cutting it with a single plane. This is the
	+ * key routine in voronoicell class. It begins by exploiting the convexity
	+ * of the underlying cell, tracing between edges to work out if the cell
	+ * intersects the cutting plane. If it does not intersect, then the routine
	+ * immediately exits. Otherwise, it finds an edge or vertex that intersects
	+ * the plane, and from there, traces out a new face on the cell, recomputing
	+ * the edge and vertex structure accordingly.
	+ *
	+ * Once the cell is computed, there are many routines for computing features of
	+ * the the Voronoi cell, such as its volume, surface area, or centroid. There
	+ * are also many routines for outputting features of the Voronoi cell, or
	+ * writing its shape in formats that can be read by Gnuplot or POV-Ray.
	+ *
	+ * \subsection internal Internal data representation
	+ * The voronoicell class has a public member p representing the
	+ * number of vertices. The polyhedral structure of the cell is stored
	+ * in the following arrays:
	+ *
	+ * - pts: a one-dimensional array of floating point numbers, that represent the
	+ * position vectors x_0, x_1, ..., x_{p-1} of the polyhedron vertices.
	+ * - nu: the order of each vertex n_0, n_1, ..., n_{p-1}, corresponding to
	+ * the number of other vertices to which each is connected.
	+ * - ed: a two-dimensional table of edges and relations. For the ith vertex,
	+ * ed[i] has 2n_i+1 elements. The first n_i elements are the edges e(j,i),
	+ * where e(j,i) is the jth neighbor of vertex i. The edges are ordered
	+ * according to a right-hand rule with respect to an outward-pointing normal.
	+ * The next n_i elements are the relations l(j,i) which satisfy the property
	+ * e(l(j,i),e(j,i)) = i. The final element of the ed[i] list is a back
	+ * pointer used in memory allocation.
	+ *
	+ * In a very large number of cases, the values of n_i will be 3. This is because
	+ * the only way that a higher-order vertex can be created in the plane()
	+ * routine is if the cutting plane perfectly intersects an existing vertex. For
	+ * random particle arrangements with position vectors specified to double
	+ * precision this should happen very rarely. A preliminary version of this code
	+ * was quite successful with only making use of vertices of order 3. However,
	+ * when calculating millions of cells, it was found that this approach is not
	+ * robust, since a single floating point error can invalidate the computation.
	+ * This can also be a problem for cases featuring crystalline arrangements of
	+ * particles where the corresponding Voronoi cells may have high-order vertices
	+ * by construction.
	+ *
	+ * Because of this, Voro++ takes the approach that it if an existing vertex is
	+ * within a small numerical tolerance of the cutting plane, it is treated as
	+ * being exactly on the plane, and the polyhedral topology is recomputed
	+ * accordingly. However, while this improves robustness, it also adds the
	+ * complexity that n_i may no longer always be 3. This causes memory management
	+ * to be significantly more complicated, as different vertices require a
	+ * different number of elements in the ed[][] array. To accommodate this, the
	+ * voronoicell class allocated edge memory in a different array called mep[][],
	+ * in such a way that all vertices of order k are held in mep[k]. If vertex
	+ * i has order k, then ed[i] points to memory within mep[k]. The array ed[][]
	+ * is never directly initialized as a two-dimensional array itself, but points
	+ * at allocations within mep[][]. To the user, it appears as though each row of
	+ * ed[][] has a different number of elements. When vertices are added or
	+ * deleted, care must be taken to reorder and reassign elements in these
	+ * arrays.
	+ *
	+ * During the plane() routine, the code traces around the vertices of the cell,
	+ * and adds new vertices along edges which intersect the cutting plane to
	+ * create a new face. The values of l(j,i) are used in this computation, as
	+ * when the code is traversing from one vertex on the cell to another, this
	+ * information allows the code to immediately work out which edge of a vertex
	+ * points back to the one it came from. As new vertices are created, the l(j,i)
	+ * are also updated to ensure consistency. To ensure robustness, the plane
	+ * cutting algorithm should work with any possible combination of vertices
	+ * which are inside, outside, or exactly on the cutting plane.
	+ *
	+ * Vertices exactly on the cutting plane create some additional computational
	+ * difficulties. If there are two marginal vertices connected by an existing
	+ * edge, then it would be possible for duplicate edges to be created between
	+ * those two vertices, if the plane routine traces along both sides of this
	+ * edge while constructing the new face. The code recognizes these cases and
	+ * prevents the double edge from being formed. Another possibility is the
	+ * formation of vertices of order two or one. At the end of the plane cutting
	+ * routine, the code checks to see if any of these are present, removing the
	+ * order one vertices by just deleting them, and removing the order two
	+ * vertices by connecting the two neighbors of each vertex together. It is
	+ * possible that the removal of a single low-order vertex could result in the
	+ * creation of additional low-order vertices, so the process is applied
	+ * recursively until no more are left.
	+ *
	+ * \section container The container classes
	+ * There are four container classes available for general usage: container,
	+ * container_poly, container_periodic, and container_periodic_poly. Each of
	+ * these represent a system of particles in a specific three-dimensional
	+ * geometry. They contain routines for importing particles from a text file,
	+ * and adding particles individually. They also contain a large number of
	+ * analyzing and outputting the particle system. Internally, the routines that
	+ * compute Voronoi cells do so by making use of the voro_compute template.
	+ * Each container class contains routines that tell the voro_compute template
	+ * about the specific geometry of this container.
	+ *
	+ * \section voro_compute The voro_compute template
	+ * The voro_compute template encapsulates the routines for carrying out the
	+ * Voronoi cell computations. It contains data structures suchs as a mask and a
	+ * queue that are used in the computations. The voro_compute template is
	+ * associated with a specific container class, and during the computation, it
	+ * calls routines in the container class to access the particle positions that
	+ * are stored there.
	+ *
	+ * The key routine in this class is compute_cell(), which makes use of a
	+ * voronoicell class to construct a Voronoi cell for a specific particle in the
	+ * container. The basic approach that this function takes is to repeatedly cut
	+ * the Voronoi cell by planes corresponding neighboring particles, and stop
	+ * when it recognizes that all the remaining particles in the container are too
	+ * far away to possibly influence cell's shape. The code makes use of two
	+ * possible methods for working out when a cell computation is complete:
	+ *
	+ * - Radius test: if the maximum distance of a Voronoi cell
	+ * vertex from the cell center is R, then no particles more than a distance
	+ * 2R away can possibly influence the cell. This a very fast computation to
	+ * do, but it has no directionality: if the cell extends a long way in one
	+ * direction then particles a long distance in other directions will still
	+ * need to be tested.
	+ * - Region test: it is possible to test whether a specific region can
	+ * possibly influence the cell by applying a series of plane tests at the
	+ * point on the region which is closest to the Voronoi cell center. This is a
	+ * slower computation to do, but it has directionality.
	+ *
	+ * Another useful observation is that the regions that need to be tested are
	+ * simply connected, meaning that if a particular region does not need to be
	+ * tested, then neighboring regions which are further away do not need to be
	+ * tested.
	+ *
	+ * For maximum efficiency, it was found that a hybrid approach making use of
	+ * both of the above tests worked well in practice. Radius tests work well for
	+ * the first few blocks, but switching to region tests after then prevent the
	+ * code from becoming extremely slow, due to testing over very large spherical
	+ * shells of particles. The compute_cell() routine therefore takes the
	+ * following approach:
	+ *
	+ * - Initialize the voronoicell class to fill the entire computational domain.
	+ * - Cut the cell by any wall objects that have been added to the container.
	+ * - Apply plane cuts to the cell corresponding to the other particles which
	+ * are within the current particle's region.
	+ * - Test over a pre-computed worklist of neighboring regions, that have been
	+ * ordered according to the minimum distance away from the particle's
	+ * position. Apply radius tests after every few regions to see if the
	+ * calculation can terminate.
	+ * - If the code reaches the end of the worklist, add all the neighboring
	+ * regions to a new list.
	+ * - Carry out a region test on the first item of the list. If the region needs
	+ * to be tested, apply the plane() routine for all of its particles, and then
	+ * add any neighboring regions to the end of the list that need to be tested.
	+ * Continue until the list has no elements left.
	+ *
	+ * The compute_cell() routine forms the basis of many other routines, such as
	+ * store_cell_volumes() and draw_cells_gnuplot() that can be used to calculate
	+ * and draw the cells in a container.
	+ *
	+ * \section walls Wall computation
	+ * Wall computations are handled by making use of a pure virtual wall class.
	+ * Specific wall types are derived from this class, and require the
	+ * specification of two routines: point_inside() that tests to see if a point
	+ * is inside a wall or not, and cut_cell() that cuts a cell according to the
	+ * wall's position. The walls can be added to the container using the
	+ * add_wall() command, and these are called each time a compute_cell() command
	+ * is carried out. At present, wall types for planes, spheres, cylinders, and
	+ * cones are provided, although custom walls can be added by creating new
	+ * classes derived from the pure virtual class. Currently all wall types
	+ * approximate the wall surface with a single plane, which produces some small
	+ * errors, but generally gives good results for dense particle packings in
	+ * direct contact with a wall surface. It would be possible to create more
	+ * accurate walls by making cut_cell() routines that approximate the curved
	+ * surface with multiple plane cuts.
	+ *
	+ * The wall objects can used for periodic calculations, although to obtain
	+ * valid results, the walls should also be periodic as well. For example, in a
	+ * domain that is periodic in the x direction, a cylinder aligned along the x
	+ * axis could be added. At present, the interior of all wall objects are convex
	+ * domains, and consequently any superposition of them will be a convex domain
	+ * also. Carrying out computations in non-convex domains poses some problems,
	+ * since this could theoretically lead to non-convex Voronoi cells, which the
	+ * internal data representation of the voronoicell class does not support. For
	+ * non-convex cases where the wall surfaces feature just a small amount of
	+ * negative curvature (eg. a torus) approximating the curved surface with a
	+ * single plane cut may give an acceptable level of accuracy. For non-convex
	+ * cases that feature internal angles, the best strategy may be to decompose
	+ * the domain into several convex subdomains, carry out a calculation in each,
	+ * and then add the results together. The voronoicell class cannot be easily
	+ * modified to handle non-convex cells as this would fundamentally alter the
	+ * algorithms that it uses, and cases could arise where a single plane cut
	+ * could create several new faces as opposed to just one.
	+ *
	+ * \section loops Loop classes
	+ * The container classes have a number of simple routines for calculating
	+ * Voronoi cells for all particles within them. However, in some situations it
	+ * is desirable to iterate over a specific subset of particles. This can be
	+ * achieved with the c_loop classes that are all derived from the c_loop_base
	+ * class. Each class can iterate over a specific subset of particles in a
	+ * container. There are three loop classes for use with the container and
	+ * container_poly classes:
	+ *
	+ * - c_loop_all will loop over all of the particles in a container.
	+ * - c_loop_subset will loop over a subset of particles in a container that lie
	+ * within some geometrical region. It can loop over particles in a
	+ * rectangular box, particles in a sphere, or particles that lie within
	+ * specific internal computational blocks.
	+ * - c_loop_order will loop over a specific list of particles that were
	+ * previously stored in a particle_order class.
	+ *
	+ * Several of the key routines within the container classes (such as
	+ * draw_cells_gnuplot and print_custom) have versions where they can be passed
	+ * a loop class to use. Loop classes can also be used directly and there are
	+ * some examples on the library website that demonstrate this. It is also
	+ * possible to write custom loop classes.
	+ *
	+ * In addition to the loop classes mentioned above, there is also a
	+ * c_loop_all_periodic class, that is specifically for use with the
	+ * container_periodic and container_periodic_poly classes. Since the data
	+ * structures of these containers differ considerably, it requires a different
	+ * loop class that is not interoperable with the others.
	+ *
	+ * \section pre_container The pre_container classes
	+ * Voro++ makes use of internal computational grid of blocks that are used to
	+ * configure the code for maximum efficiency. As discussed on the library
	+ * website, the best performance is achieved for around 5 particles per block,
	+ * with anything in the range from 3 to 12 giving good performance. Usually
	+ * the size of the grid can be chosen by ensuring that the number of blocks is
	+ * equal to the number of particles divided by 5.
	+ *
	+ * However, this can be difficult to choose in cases when the number of
	+ * particles is not known a priori, and in thes cases the pre_container classes
	+ * can be used. They can import an arbitrary number of particle positions from
	+ * a file, dynamically allocating memory in chunks as necessary. Once particles
	+ * are imported, they can guess an optimal block arrangement to use for the
	+ * container class, and then transfer the particles to the container. By
	+ * default, this procedure is used by the command-line utility to enable it to
	+ * work well with arbitrary sizes of input data.
	+ *
	+ * The pre_container class can be used when no particle radius information is
	+ * available, and the pre_container_poly class can be used when radius
	+ * information is available. At present, the pre_container classes can only be
	+ * used with the container and container_poly classes. They do not support
	+ * the container_periodic and container_periodic_poly classes. */
	+
	+#ifndef VOROPP_HH
	+#define VOROPP_HH
	+
	+#include "config.hh"
	+#include "common.hh"
	+#include "cell.hh"
	+#include "v_base.hh"
	+#include "rad_option.hh"
	+#include "container.hh"
	+#include "unitcell.hh"
	+#include "container_prd.hh"
	+#include "pre_container.hh"
	+#include "v_compute.hh"
	+#include "c_loops.hh"
	+#include "wall.hh"
	+
	+#endif
	Index: extern/voro++/src/container_prd.cc
	===================================================================
	--- extern/voro++/src/container_prd.cc (revision 0)
	+++ extern/voro++/src/container_prd.cc (revision 0)
	@@ -0,0 +1,768 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file container_prd.cc
	+ * \brief Function implementations for the container_periodic_base and
	+ * related classes. */
	+
	+#include "container_prd.hh"
	+
	+namespace voro {
	+
	+/** The class constructor sets up the geometry of container, initializing the
	+ * minimum and maximum coordinates in each direction, and setting whether each
	+ * direction is periodic or not. It divides the container into a rectangular
	+ * grid of blocks, and allocates memory for each of these for storing particle
	+ * positions and IDs.
	+ * \param[in] (bx_) The x coordinate of the first unit vector.
	+ * \param[in] (bxy_,by_) The x and y coordinates of the second unit vector.
	+ * \param[in] (bxz_,byz_,bz_) The x, y, and z coordinates of the third unit
	+ * vector.
	+ * \param[in] (nx_,ny_,nz_) the number of grid blocks in each of the three
	+ * coordinate directions.
	+ * \param[in] init_mem_ the initial memory allocation for each block.
	+ * \param[in] ps_ the number of floating point entries to store for each
	+ * particle. */
	+container_periodic_base::container_periodic_base(double bx_,double bxy_,double by_,
	+ double bxz_,double byz_,double bz_,int nx_,int ny_,int nz_,int init_mem_,int ps_)
	+ : unitcell(bx_,bxy_,by_,bxz_,byz_,bz_), voro_base(nx_,ny_,nz_,bx_/nx_,by_/ny_,bz_/nz_),
	+ ey(int(max_uv_yysp+1)), ez(int(max_uv_zzsp+1)), wy(ny+ey), wz(nz+ez),
	+ oy(ny+2ey), oz(nz+2ez), oxyz(nxoyoz), id(new int[oxyz]), p(new double[oxyz]),
	+ co(new int[oxyz]), mem(new int[oxyz]), img(new char[oxyz]), init_mem(init_mem_), ps(ps_) {
	+ int i,j,k,l;
	+
	+ // Clear the global arrays
	+ int pp=co;while(pp<co+oxyz) (pp++)=0;
	+ pp=mem;while(pp<mem+oxyz) *(pp++)=0;
	+ char cp=img;while(cp<img+oxyz) (cp++)=0;
	+
	+ // Set up memory for the blocks in the primary domain
	+ for(k=ez;k<wz;k++) for(j=ey;j<wy;j++) for(i=0;i<nx;i++) {
	+ l=i+nx(j+oyk);
	+ mem[l]=init_mem;
	+ id[l]=new int[init_mem];
	+ p[l]=new double[ps*init_mem];
	+ }
	+}
	+
	+/** The container destructor frees the dynamically allocated memory. */
	+container_periodic_base::~container_periodic_base() {
	+ for(int l=oxyz-1;l>=0;l--) if(mem[l]>0) {
	+ delete [] p[l];
	+ delete [] id[l];
	+ }
	+ delete [] img;
	+ delete [] mem;
	+ delete [] co;
	+ delete [] id;
	+ delete [] p;
	+}
	+
	+/** The class constructor sets up the geometry of container.
	+ * \param[in] (bx_) The x coordinate of the first unit vector.
	+ * \param[in] (bxy_,by_) The x and y coordinates of the second unit vector.
	+ * \param[in] (bxz_,byz_,bz_) The x, y, and z coordinates of the third unit
	+ * vector.
	+ * \param[in] (nx_,ny_,nz_) the number of grid blocks in each of the three
	+ * coordinate directions.
	+ * \param[in] init_mem_ the initial memory allocation for each block. */
	+container_periodic::container_periodic(double bx_,double bxy_,double by_,double bxz_,double byz_,double bz_,
	+ int nx_,int ny_,int nz_,int init_mem_)
	+ : container_periodic_base(bx_,bxy_,by_,bxz_,byz_,bz_,nx_,ny_,nz_,init_mem_,3),
	+ vc(this,2nx_+1,2ey+1,2ez+1) {}
	+
	+/** The class constructor sets up the geometry of container.
	+ * \param[in] (bx_) The x coordinate of the first unit vector.
	+ * \param[in] (bxy_,by_) The x and y coordinates of the second unit vector.
	+ * \param[in] (bxz_,byz_,bz_) The x, y, and z coordinates of the third unit
	+ * vector.
	+ * \param[in] (nx_,ny_,nz_) the number of grid blocks in each of the three
	+ * coordinate directions.
	+ * \param[in] init_mem_ the initial memory allocation for each block. */
	+container_periodic_poly::container_periodic_poly(double bx_,double bxy_,double by_,double bxz_,double byz_,double bz_,
	+ int nx_,int ny_,int nz_,int init_mem_)
	+ : container_periodic_base(bx_,bxy_,by_,bxz_,byz_,bz_,nx_,ny_,nz_,init_mem_,4),
	+ vc(this,2nx_+1,2ey+1,2ez+1) {ppr=p;}
	+
	+/** Put a particle into the correct region of the container.
	+ * \param[in] n the numerical ID of the inserted particle.
	+ * \param[in] (x,y,z) the position vector of the inserted particle. */
	+void container_periodic::put(int n,double x,double y,double z) {
	+ int ijk;
	+ put_locate_block(ijk,x,y,z);
	+ id[ijk][co[ijk]]=n;
	+ double pp=p[ijk]+3co[ijk]++;
	+ (pp++)=x;(pp++)=y;*pp=z;
	+}
	+
	+/** Put a particle into the correct region of the container.
	+ * \param[in] n the numerical ID of the inserted particle.
	+ * \param[in] (x,y,z) the position vector of the inserted particle.
	+ * \param[in] r the radius of the particle. */
	+void container_periodic_poly::put(int n,double x,double y,double z,double r) {
	+ int ijk;
	+ put_locate_block(ijk,x,y,z);
	+ id[ijk][co[ijk]]=n;
	+ double pp=p[ijk]+4co[ijk]++;
	+ (pp++)=x;(pp++)=y;(pp++)=z;pp=r;
	+ if(max_radius<r) max_radius=r;
	+}
	+
	+/** Put a particle into the correct region of the container.
	+ * \param[in] n the numerical ID of the inserted particle.
	+ * \param[in] (x,y,z) the position vector of the inserted particle.
	+ * \param[out] (ai,aj,ak) the periodic image displacement that the particle is
	+ * in, with (0,0,0) corresponding to the primary domain.
	+ */
	+void container_periodic::put(int n,double x,double y,double z,int &ai,int &aj,int &ak) {
	+ int ijk;
	+ put_locate_block(ijk,x,y,z,ai,aj,ak);
	+ id[ijk][co[ijk]]=n;
	+ double pp=p[ijk]+3co[ijk]++;
	+ (pp++)=x;(pp++)=y;*pp=z;
	+}
	+
	+/** Put a particle into the correct region of the container.
	+ * \param[in] n the numerical ID of the inserted particle.
	+ * \param[in] (x,y,z) the position vector of the inserted particle.
	+ * \param[in] r the radius of the particle.
	+ * \param[out] (ai,aj,ak) the periodic image displacement that the particle is
	+ * in, with (0,0,0) corresponding to the primary domain.
	+ */
	+void container_periodic_poly::put(int n,double x,double y,double z,double r,int &ai,int &aj,int &ak) {
	+ int ijk;
	+ put_locate_block(ijk,x,y,z,ai,aj,ak);
	+ id[ijk][co[ijk]]=n;
	+ double pp=p[ijk]+4co[ijk]++;
	+ (pp++)=x;(pp++)=y;(pp++)=z;pp=r;
	+ if(max_radius<r) max_radius=r;
	+}
	+
	+/** Put a particle into the correct region of the container, also recording
	+ * into which region it was stored.
	+ * \param[in] vo the ordering class in which to record the region.
	+ * \param[in] n the numerical ID of the inserted particle.
	+ * \param[in] (x,y,z) the position vector of the inserted particle. */
	+void container_periodic::put(particle_order &vo,int n,double x,double y,double z) {
	+ int ijk;
	+ put_locate_block(ijk,x,y,z);
	+ id[ijk][co[ijk]]=n;
	+ vo.add(ijk,co[ijk]);
	+ double pp=p[ijk]+3co[ijk]++;
	+ (pp++)=x;(pp++)=y;*pp=z;
	+}
	+
	+/** Put a particle into the correct region of the container, also recording
	+ * into which region it was stored.
	+ * \param[in] vo the ordering class in which to record the region.
	+ * \param[in] n the numerical ID of the inserted particle.
	+ * \param[in] (x,y,z) the position vector of the inserted particle.
	+ * \param[in] r the radius of the particle. */
	+void container_periodic_poly::put(particle_order &vo,int n,double x,double y,double z,double r) {
	+ int ijk;
	+ put_locate_block(ijk,x,y,z);
	+ id[ijk][co[ijk]]=n;
	+ vo.add(ijk,co[ijk]);
	+ double pp=p[ijk]+4co[ijk]++;
	+ (pp++)=x;(pp++)=y;(pp++)=z;pp=r;
	+ if(max_radius<r) max_radius=r;
	+}
	+
	+/** Takes a particle position vector and computes the region index into which
	+ * it should be stored. If the container is periodic, then the routine also
	+ * maps the particle position to ensure it is in the primary domain. If the
	+ * container is not periodic, the routine bails out.
	+ * \param[out] ijk the region index.
	+ * \param[in,out] (x,y,z) the particle position, remapped into the primary
	+ * domain if necessary.
	+ * \return True if the particle can be successfully placed into the container,
	+ * false otherwise. */
	+void container_periodic_base::put_locate_block(int &ijk,double &x,double &y,double &z) {
	+
	+ // Remap particle in the z direction if necessary
	+ int k=step_int(z*zsp);
	+ if(k<0\|\|k>=nz) {
	+ int ak=step_div(k,nz);
	+ z-=akbz;y-=akbyz;x-=akbxz;k-=aknz;
	+ }
	+
	+ // Remap particle in the y direction if necessary
	+ int j=step_int(y*ysp);
	+ if(j<0\|\|j>=ny) {
	+ int aj=step_div(j,ny);
	+ y-=ajby;x-=ajbxy;j-=aj*ny;
	+ }
	+
	+ // Remap particle in the x direction if necessary
	+ ijk=step_int(x*xsp);
	+ if(ijk<0\|\|ijk>=nx) {
	+ int ai=step_div(ijk,nx);
	+ x-=aibx;ijk-=ainx;
	+ }
	+
	+ // Compute the block index and check memory allocation
	+ j+=ey;k+=ez;
	+ ijk+=nx(j+oyk);
	+ if(co[ijk]==mem[ijk]) add_particle_memory(ijk);
	+}
	+
	+/** Takes a particle position vector and computes the region index into which
	+ * it should be stored. If the container is periodic, then the routine also
	+ * maps the particle position to ensure it is in the primary domain. If the
	+ * container is not periodic, the routine bails out.
	+ * \param[out] ijk the region index.
	+ * \param[in,out] (x,y,z) the particle position, remapped into the primary
	+ * domain if necessary.
	+ * \param[out] (ai,aj,ak) the periodic image displacement that the particle is
	+ * in, with (0,0,0) corresponding to the primary domain.
	+ * \return True if the particle can be successfully placed into the container,
	+ * false otherwise. */
	+void container_periodic_base::put_locate_block(int &ijk,double &x,double &y,double &z,int &ai,int &aj,int &ak) {
	+
	+ // Remap particle in the z direction if necessary
	+ int k=step_int(z*zsp);
	+ if(k<0\|\|k>=nz) {
	+ ak=step_div(k,nz);
	+ z-=akbz;y-=akbyz;x-=akbxz;k-=aknz;
	+ } else ak=0;
	+
	+ // Remap particle in the y direction if necessary
	+ int j=step_int(y*ysp);
	+ if(j<0\|\|j>=ny) {
	+ aj=step_div(j,ny);
	+ y-=ajby;x-=ajbxy;j-=aj*ny;
	+ } else aj=0;
	+
	+ // Remap particle in the x direction if necessary
	+ ijk=step_int(x*xsp);
	+ if(ijk<0\|\|ijk>=nx) {
	+ ai=step_div(ijk,nx);
	+ x-=aibx;ijk-=ainx;
	+ } else ai=0;
	+
	+ // Compute the block index and check memory allocation
	+ j+=ey;k+=ez;
	+ ijk+=nx(j+oyk);
	+ if(co[ijk]==mem[ijk]) add_particle_memory(ijk);
	+}
	+
	+/** Takes a position vector and remaps it into the primary domain.
	+ * \param[out] (ai,aj,ak) the periodic image displacement that the vector is in,
	+ * with (0,0,0) corresponding to the primary domain.
	+ * \param[out] (ci,cj,ck) the index of the block that the position vector is
	+ * within, once it has been remapped.
	+ * \param[in,out] (x,y,z) the position vector to consider, which is remapped
	+ * into the primary domain during the routine.
	+ * \param[out] ijk the block index that the vector is within. */
	+inline void container_periodic_base::remap(int &ai,int &aj,int &ak,int &ci,int &cj,int &ck,double &x,double &y,double &z,int &ijk) {
	+
	+ // Remap particle in the z direction if necessary
	+ ck=step_int(z*zsp);
	+ if(ck<0\|\|ck>=nz) {
	+ ak=step_div(ck,nz);
	+ z-=akbz;y-=akbyz;x-=akbxz;ck-=aknz;
	+ } else ak=0;
	+
	+ // Remap particle in the y direction if necessary
	+ cj=step_int(y*ysp);
	+ if(cj<0\|\|cj>=ny) {
	+ aj=step_div(cj,ny);
	+ y-=ajby;x-=ajbxy;cj-=aj*ny;
	+ } else aj=0;
	+
	+ // Remap particle in the x direction if necessary
	+ ci=step_int(x*xsp);
	+ if(ci<0\|\|ci>=nx) {
	+ ai=step_div(ci,nx);
	+ x-=aibx;ci-=ainx;
	+ } else ai=0;
	+
	+ cj+=ey;ck+=ez;
	+ ijk=ci+nx(cj+oyck);
	+}
	+
	+/** Takes a vector and finds the particle whose Voronoi cell contains that
	+ * vector. This is equivalent to finding the particle which is nearest to the
	+ * vector.
	+ * \param[in] (x,y,z) the vector to test.
	+ * \param[out] (rx,ry,rz) the position of the particle whose Voronoi cell
	+ * contains the vector. This may point to a particle in
	+ * a periodic image of the primary domain.
	+ * \param[out] pid the ID of the particle.
	+ * \return True if a particle was found. If the container has no particles,
	+ * then the search will not find a Voronoi cell and false is returned. */
	+bool container_periodic::find_voronoi_cell(double x,double y,double z,double &rx,double &ry,double &rz,int &pid) {
	+ int ai,aj,ak,ci,cj,ck,ijk;
	+ particle_record w;
	+ double mrs;
	+
	+ // Remap the vector into the primary domain and then search for the
	+ // Voronoi cell that it is within
	+ remap(ai,aj,ak,ci,cj,ck,x,y,z,ijk);
	+ vc.find_voronoi_cell(x,y,z,ci,cj,ck,ijk,w,mrs);
	+
	+ if(w.ijk!=-1) {
	+
	+ // Assemble the position vector of the particle to be returned,
	+ // applying a periodic remapping if necessary
	+ ci+=w.di;if(ci<0\|\|ci>=nx) ai+=step_div(ci,nx);
	+ rx=p[w.ijk][3w.l]+akbxz+ajbxy+aibx;
	+ ry=p[w.ijk][3w.l+1]+akbyz+aj*by;
	+ rz=p[w.ijk][3w.l+2]+akbz;
	+ pid=id[w.ijk][w.l];
	+ return true;
	+ }
	+ return false;
	+}
	+
	+/** Takes a vector and finds the particle whose Voronoi cell contains that
	+ * vector. Additional wall classes are not considered by this routine.
	+ * \param[in] (x,y,z) the vector to test.
	+ * \param[out] (rx,ry,rz) the position of the particle whose Voronoi cell
	+ * contains the vector. If the container is periodic,
	+ * this may point to a particle in a periodic image of
	+ * the primary domain.
	+ * \param[out] pid the ID of the particle.
	+ * \return True if a particle was found. If the container has no particles,
	+ * then the search will not find a Voronoi cell and false is returned. */
	+bool container_periodic_poly::find_voronoi_cell(double x,double y,double z,double &rx,double &ry,double &rz,int &pid) {
	+ int ai,aj,ak,ci,cj,ck,ijk;
	+ particle_record w;
	+ double mrs;
	+
	+ // Remap the vector into the primary domain and then search for the
	+ // Voronoi cell that it is within
	+ remap(ai,aj,ak,ci,cj,ck,x,y,z,ijk);
	+ vc.find_voronoi_cell(x,y,z,ci,cj,ck,ijk,w,mrs);
	+
	+ if(w.ijk!=-1) {
	+
	+ // Assemble the position vector of the particle to be returned,
	+ // applying a periodic remapping if necessary
	+ ci+=w.di;if(ci<0\|\|ci>=nx) ai+=step_div(ci,nx);
	+ rx=p[w.ijk][4w.l]+akbxz+ajbxy+aibx;
	+ ry=p[w.ijk][4w.l+1]+akbyz+aj*by;
	+ rz=p[w.ijk][4w.l+2]+akbz;
	+ pid=id[w.ijk][w.l];
	+ return true;
	+ }
	+ return false;
	+}
	+
	+/** Increase memory for a particular region.
	+ * \param[in] i the index of the region to reallocate. */
	+void container_periodic_base::add_particle_memory(int i) {
	+
	+ // Handle the case when no memory has been allocated for this block
	+ if(mem[i]==0) {
	+ mem[i]=init_mem;
	+ id[i]=new int[init_mem];
	+ p[i]=new double[ps*init_mem];
	+ return;
	+ }
	+
	+ // Otherwise, double the memory allocation for this block. Carry out a
	+ // check on the memory allocation size, and print a status message if
	+ // requested.
	+ int l,nmem(mem[i]<<1);
	+ if(nmem>max_particle_memory)
	+ voro_fatal_error("Absolute maximum memory allocation exceeded",VOROPP_MEMORY_ERROR);
	+#if VOROPP_VERBOSE >=3
	+ fprintf(stderr,"Particle memory in region %d scaled up to %d\n",i,nmem);
	+#endif
	+
	+ // Allocate new memory and copy in the contents of the old arrays
	+ int *idp=new int[nmem];
	+ for(l=0;l<co[i];l++) idp[l]=id[i][l];
	+ double pp=new double[psnmem];
	+ for(l=0;l<ps*co[i];l++) pp[l]=p[i][l];
	+
	+ // Update pointers and delete old arrays
	+ mem[i]=nmem;
	+ delete [] id[i];id[i]=idp;
	+ delete [] p[i];p[i]=pp;
	+}
	+
	+/** Import a list of particles from an open file stream into the container.
	+ * Entries of four numbers (Particle ID, x position, y position, z position)
	+ * are searched for. If the file cannot be successfully read, then the routine
	+ * causes a fatal error.
	+ * \param[in] fp the file handle to read from. */
	+void container_periodic::import(FILE *fp) {
	+ int i,j;
	+ double x,y,z;
	+ while((j=fscanf(fp,"%d %lg %lg %lg",&i,&x,&y,&z))==4) put(i,x,y,z);
	+ if(j!=EOF) voro_fatal_error("File import error",VOROPP_FILE_ERROR);
	+}
	+
	+/** Import a list of particles from an open file stream, also storing the order
	+ * of that the particles are read. Entries of four numbers (Particle ID, x
	+ * position, y position, z position) are searched for. If the file cannot be
	+ * successfully read, then the routine causes a fatal error.
	+ * \param[in,out] vo a reference to an ordering class to use.
	+ * \param[in] fp the file handle to read from. */
	+void container_periodic::import(particle_order &vo,FILE *fp) {
	+ int i,j;
	+ double x,y,z;
	+ while((j=fscanf(fp,"%d %lg %lg %lg",&i,&x,&y,&z))==4) put(vo,i,x,y,z);
	+ if(j!=EOF) voro_fatal_error("File import error",VOROPP_FILE_ERROR);
	+}
	+
	+/** Import a list of particles from an open file stream into the container.
	+ * Entries of five numbers (Particle ID, x position, y position, z position,
	+ * radius) are searched for. If the file cannot be successfully read, then the
	+ * routine causes a fatal error.
	+ * \param[in] fp the file handle to read from. */
	+void container_periodic_poly::import(FILE *fp) {
	+ int i,j;
	+ double x,y,z,r;
	+ while((j=fscanf(fp,"%d %lg %lg %lg %lg",&i,&x,&y,&z,&r))==5) put(i,x,y,z,r);
	+ if(j!=EOF) voro_fatal_error("File import error",VOROPP_FILE_ERROR);
	+}
	+
	+/** Import a list of particles from an open file stream, also storing the order
	+ * of that the particles are read. Entries of four numbers (Particle ID, x
	+ * position, y position, z position, radius) are searched for. If the file
	+ * cannot be successfully read, then the routine causes a fatal error.
	+ * \param[in,out] vo a reference to an ordering class to use.
	+ * \param[in] fp the file handle to read from. */
	+void container_periodic_poly::import(particle_order &vo,FILE *fp) {
	+ int i,j;
	+ double x,y,z,r;
	+ while((j=fscanf(fp,"%d %lg %lg %lg %lg",&i,&x,&y,&z,&r))==5) put(vo,i,x,y,z,r);
	+ if(j!=EOF) voro_fatal_error("File import error",VOROPP_FILE_ERROR);
	+}
	+
	+/** Outputs the a list of all the container regions along with the number of
	+ * particles stored within each. */
	+void container_periodic_base::region_count() {
	+ int i,j,k,*cop=co;
	+ for(k=0;k<nz;k++) for(j=0;j<ny;j++) for(i=0;i<nx;i++)
	+ printf("Region (%d,%d,%d): %d particles\n",i,j,k,*(cop++));
	+}
	+
	+/** Clears a container of particles. */
	+void container_periodic::clear() {
	+ for(int cop=co;cop<co+nxyz;cop++) cop=0;
	+}
	+
	+/** Clears a container of particles, also clearing resetting the maximum radius
	+ * to zero. */
	+void container_periodic_poly::clear() {
	+ for(int cop=co;cop<co+nxyz;cop++) cop=0;
	+ max_radius=0;
	+}
	+
	+/** Computes all the Voronoi cells and saves customized information about them.
	+ * \param[in] format the custom output string to use.
	+ * \param[in] fp a file handle to write to. */
	+void container_periodic::print_custom(const char format,FILE fp) {
	+ c_loop_all_periodic vl(*this);
	+ print_custom(vl,format,fp);
	+}
	+
	+/** Computes all the Voronoi cells and saves customized
	+ * information about them.
	+ * \param[in] format the custom output string to use.
	+ * \param[in] fp a file handle to write to. */
	+void container_periodic_poly::print_custom(const char format,FILE fp) {
	+ c_loop_all_periodic vl(*this);
	+ print_custom(vl,format,fp);
	+}
	+
	+/** Computes all the Voronoi cells and saves customized information about them.
	+ * \param[in] format the custom output string to use.
	+ * \param[in] filename the name of the file to write to. */
	+void container_periodic::print_custom(const char format,const char filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ print_custom(format,fp);
	+ fclose(fp);
	+}
	+
	+/** Computes all the Voronoi cells and saves customized
	+ * information about them
	+ * \param[in] format the custom output string to use.
	+ * \param[in] filename the name of the file to write to. */
	+void container_periodic_poly::print_custom(const char format,const char filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ print_custom(format,fp);
	+ fclose(fp);
	+}
	+
	+/** Computes all of the Voronoi cells in the container, but does nothing
	+ * with the output. It is useful for measuring the pure computation time
	+ * of the Voronoi algorithm, without any additional calculations such as
	+ * volume evaluation or cell output. */
	+void container_periodic::compute_all_cells() {
	+ voronoicell c;
	+ c_loop_all_periodic vl(*this);
	+ if(vl.start()) do compute_cell(c,vl);
	+ while(vl.inc());
	+}
	+
	+/** Computes all of the Voronoi cells in the container, but does nothing
	+ * with the output. It is useful for measuring the pure computation time
	+ * of the Voronoi algorithm, without any additional calculations such as
	+ * volume evaluation or cell output. */
	+void container_periodic_poly::compute_all_cells() {
	+ voronoicell c;
	+ c_loop_all_periodic vl(*this);
	+ if(vl.start()) do compute_cell(c,vl);while(vl.inc());
	+}
	+
	+/** Calculates all of the Voronoi cells and sums their volumes. In most cases
	+ * without walls, the sum of the Voronoi cell volumes should equal the volume
	+ * of the container to numerical precision.
	+ * \return The sum of all of the computed Voronoi volumes. */
	+double container_periodic::sum_cell_volumes() {
	+ voronoicell c;
	+ double vol=0;
	+ c_loop_all_periodic vl(*this);
	+ if(vl.start()) do if(compute_cell(c,vl)) vol+=c.volume();while(vl.inc());
	+ return vol;
	+}
	+
	+/** Calculates all of the Voronoi cells and sums their volumes. In most cases
	+ * without walls, the sum of the Voronoi cell volumes should equal the volume
	+ * of the container to numerical precision.
	+ * \return The sum of all of the computed Voronoi volumes. */
	+double container_periodic_poly::sum_cell_volumes() {
	+ voronoicell c;
	+ double vol=0;
	+ c_loop_all_periodic vl(*this);
	+ if(vl.start()) do if(compute_cell(c,vl)) vol+=c.volume();while(vl.inc());
	+ return vol;
	+}
	+
	+/** This routine creates all periodic images of the particles. It is meant for
	+ * diagnostic purposes only, since usually periodic images are dynamically
	+ * created in when they are referenced. */
	+void container_periodic_base::create_all_images() {
	+ int i,j,k;
	+ for(k=0;k<oz;k++) for(j=0;j<oy;j++) for(i=0;i<nx;i++) create_periodic_image(i,j,k);
	+}
	+
	+/** Checks that the particles within each block lie within that block's bounds.
	+ * This is useful for diagnosing problems with periodic image computation. */
	+void container_periodic_base::check_compartmentalized() {
	+ int c,l,i,j,k;
	+ double mix,miy,miz,max,may,maz,*pp;
	+ for(k=l=0;k<oz;k++) for(j=0;j<oy;j++) for(i=0;i<nx;i++,l++) if(mem[l]>0) {
	+
	+ // Compute the block's bounds, adding in a small tolerance
	+ mix=i*boxx-tolerance;max=mix+boxx+tolerance;
	+ miy=(j-ey)*boxy-tolerance;may=miy+boxy+tolerance;
	+ miz=(k-ez)*boxz-tolerance;maz=miz+boxz+tolerance;
	+
	+ // Print entries for any particles that lie outside the block's
	+ // bounds
	+ for(pp=p[l],c=0;c<co[l];c++,pp+=ps) if(pp<mix\|\|pp>max\|\|pp[1]<miy\|\|pp[1]>may\|\|pp[2]<miz\|\|pp[2]>maz)
	+ printf("%d %d %d %d %f %f %f %f %f %f %f %f %f\n",
	+ id[l][c],i,j,k,*pp,pp[1],pp[2],mix,max,miy,may,miz,maz);
	+ }
	+}
	+
	+/** Creates particles within an image block that is aligned with the primary
	+ * domain in the z axis. In this case, the image block may be comprised of
	+ * particles from two primary blocks. The routine considers these two primary
	+ * blocks, and adds the needed particles to the image. The remaining particles
	+ * from the primary blocks are also filled into the neighboring images.
	+ * \param[in] (di,dj,dk) the index of the block to consider. The z index must
	+ * satisfy ez<=dk<wz. */
	+void container_periodic_base::create_side_image(int di,int dj,int dk) {
	+ int l,dijk=di+nx(dj+oydk),odijk,ima=step_div(dj-ey,ny);
	+ int qua=di+step_int(-imabxyxsp),quadiv=step_div(qua,nx);
	+ int fi=qua-quadivnx,fijk=fi+nx(dj-imany+oydk);
	+ double dis=imabxy+quadivbx,switchx=diboxx-imabxy-quadiv*bx,adis;
	+
	+ // Left image computation
	+ if((img[dijk]&1)==0) {
	+ if(di>0) {
	+ odijk=dijk-1;adis=dis;
	+ } else {
	+ odijk=dijk+nx-1;adis=dis+bx;
	+ }
	+ img[odijk]\|=2;
	+ for(l=0;l<co[fijk];l++) {
	+ if(p[fijk][psl]>switchx) put_image(dijk,fijk,l,dis,byima,0);
	+ else put_image(odijk,fijk,l,adis,by*ima,0);
	+ }
	+ }
	+
	+ // Right image computation
	+ if((img[dijk]&2)==0) {
	+ if(fi==nx-1) {
	+ fijk+=1-nx;switchx+=(1-nx)*boxx;dis+=bx;
	+ } else {
	+ fijk++;switchx+=boxx;
	+ }
	+ if(di==nx-1) {
	+ odijk=dijk-nx+1;adis=dis-bx;
	+ } else {
	+ odijk=dijk+1;adis=dis;
	+ }
	+ img[odijk]\|=1;
	+ for(l=0;l<co[fijk];l++) {
	+ if(p[fijk][psl]<switchx) put_image(dijk,fijk,l,dis,byima,0);
	+ else put_image(odijk,fijk,l,adis,by*ima,0);
	+ }
	+ }
	+
	+ // All contributions to the block now added, so set both two bits of
	+ // the image information
	+ img[dijk]=3;
	+}
	+
	+/** Creates particles within an image block that is not aligned with the
	+ * primary domain in the z axis. In this case, the image block may be comprised
	+ * of particles from four primary blocks. The routine considers these four
	+ * primary blocks, and adds the needed particles to the image. The remaining
	+ * particles from the primary blocks are also filled into the neighboring
	+ * images.
	+ * \param[in] (di,dj,dk) the index of the block to consider. The z index must
	+ * satisfy dk<ez or dk>=wz. */
	+void container_periodic_base::create_vertical_image(int di,int dj,int dk) {
	+ int l,dijk=di+nx(dj+oydk),dijkl,dijkr,ima=step_div(dk-ez,nz);
	+ int qj=dj+step_int(-imabyzysp),qjdiv=step_div(qj-ey,ny);
	+ int qi=di+step_int((-imabxz-qjdivbxy)*xsp),qidiv=step_div(qi,nx);
	+ int fi=qi-qidivnx,fj=qj-qjdivny,fijk=fi+nx(fj+oy(dk-ima*nz)),fijk2;
	+ double disy=imabyz+qjdivby,switchy=(dj-ey)boxy-imabyz-qjdiv*by;
	+ double disx=imabxz+qjdivbxy+qidivbx,switchx=diboxx-imabxz-qjdivbxy-qidiv*bx;
	+ double switchx2,disxl,disxr,disx2,disxr2;
	+
	+ if(di==0) {dijkl=dijk+nx-1;disxl=disx+bx;}
	+ else {dijkl=dijk-1;disxl=disx;}
	+
	+ if(di==nx-1) {dijkr=dijk-nx+1;disxr=disx-bx;}
	+ else {dijkr=dijk+1;disxr=disx;}
	+
	+ // Down-left image computation
	+ bool y_exist=dj!=0;
	+ if((img[dijk]&1)==0) {
	+ img[dijkl]\|=2;
	+ if(y_exist) {
	+ img[dijkl-nx]\|=8;
	+ img[dijk-nx]\|=4;
	+ }
	+ for(l=0;l<co[fijk];l++) {
	+ if(p[fijk][ps*l+1]>switchy) {
	+ if(p[fijk][psl]>switchx) put_image(dijk,fijk,l,disx,disy,bzima);
	+ else put_image(dijkl,fijk,l,disxl,disy,bz*ima);
	+ } else {
	+ if(!y_exist) continue;
	+ if(p[fijk][psl]>switchx) put_image(dijk-nx,fijk,l,disx,disy,bzima);
	+ else put_image(dijkl-nx,fijk,l,disxl,disy,bz*ima);
	+ }
	+ }
	+ }
	+
	+ // Down-right image computation
	+ if((img[dijk]&2)==0) {
	+ if(fi==nx-1) {
	+ fijk2=fijk+1-nx;switchx2=switchx+(1-nx)*boxx;disx2=disx+bx;disxr2=disxr+bx;
	+ } else {
	+ fijk2=fijk+1;switchx2=switchx+boxx;disx2=disx;disxr2=disxr;
	+ }
	+ img[dijkr]\|=1;
	+ if(y_exist) {
	+ img[dijkr-nx]\|=4;
	+ img[dijk-nx]\|=8;
	+ }
	+ for(l=0;l<co[fijk2];l++) {
	+ if(p[fijk2][ps*l+1]>switchy) {
	+ if(p[fijk2][psl]>switchx2) put_image(dijkr,fijk2,l,disxr2,disy,bzima);
	+ else put_image(dijk,fijk2,l,disx2,disy,bz*ima);
	+ } else {
	+ if(!y_exist) continue;
	+ if(p[fijk2][psl]>switchx2) put_image(dijkr-nx,fijk2,l,disxr2,disy,bzima);
	+ else put_image(dijk-nx,fijk2,l,disx2,disy,bz*ima);
	+ }
	+ }
	+ }
	+
	+ // Recomputation of some intermediate quantities for boundary cases
	+ if(fj==wy-1) {
	+ fijk+=nx*(1-ny)-fi;
	+ switchy+=(1-ny)*boxy;
	+ disy+=by;
	+ qi=di+step_int(-(imabxz+(qjdiv+1)bxy)*xsp);
	+ int dqidiv=step_div(qi,nx)-qidiv;qidiv+=dqidiv;
	+ fi=qi-qidiv*nx;
	+ fijk+=fi;
	+ disx+=bxy+bx*dqidiv;
	+ disxl+=bxy+bx*dqidiv;
	+ disxr+=bxy+bx*dqidiv;
	+ switchx-=bxy+bx*dqidiv;
	+ } else {
	+ fijk+=nx;switchy+=boxy;
	+ }
	+
	+ // Up-left image computation
	+ y_exist=dj!=oy-1;
	+ if((img[dijk]&4)==0) {
	+ img[dijkl]\|=8;
	+ if(y_exist) {
	+ img[dijkl+nx]\|=2;
	+ img[dijk+nx]\|=1;
	+ }
	+ for(l=0;l<co[fijk];l++) {
	+ if(p[fijk][ps*l+1]>switchy) {
	+ if(!y_exist) continue;
	+ if(p[fijk][psl]>switchx) put_image(dijk+nx,fijk,l,disx,disy,bzima);
	+ else put_image(dijkl+nx,fijk,l,disxl,disy,bz*ima);
	+ } else {
	+ if(p[fijk][psl]>switchx) put_image(dijk,fijk,l,disx,disy,bzima);
	+ else put_image(dijkl,fijk,l,disxl,disy,bz*ima);
	+ }
	+ }
	+ }
	+
	+ // Up-right image computation
	+ if((img[dijk]&8)==0) {
	+ if(fi==nx-1) {
	+ fijk2=fijk+1-nx;switchx2=switchx+(1-nx)*boxx;disx2=disx+bx;disxr2=disxr+bx;
	+ } else {
	+ fijk2=fijk+1;switchx2=switchx+boxx;disx2=disx;disxr2=disxr;
	+ }
	+ img[dijkr]\|=4;
	+ if(y_exist) {
	+ img[dijkr+nx]\|=1;
	+ img[dijk+nx]\|=2;
	+ }
	+ for(l=0;l<co[fijk2];l++) {
	+ if(p[fijk2][ps*l+1]>switchy) {
	+ if(!y_exist) continue;
	+ if(p[fijk2][psl]>switchx2) put_image(dijkr+nx,fijk2,l,disxr2,disy,bzima);
	+ else put_image(dijk+nx,fijk2,l,disx2,disy,bz*ima);
	+ } else {
	+ if(p[fijk2][psl]>switchx2) put_image(dijkr,fijk2,l,disxr2,disy,bzima);
	+ else put_image(dijk,fijk2,l,disx2,disy,bz*ima);
	+ }
	+ }
	+ }
	+
	+ // All contributions to the block now added, so set all four bits of
	+ // the image information
	+ img[dijk]=15;
	+}
	+
	+/** Copies a particle position from the primary domain into an image block.
	+ * \param[in] reg the block index within the primary domain that the particle
	+ * is within.
	+ * \param[in] fijk the index of the image block.
	+ * \param[in] l the index of the particle entry within the primary block.
	+ * \param[in] (dx,dy,dz) the displacement vector to add to the particle. */
	+void container_periodic_base::put_image(int reg,int fijk,int l,double dx,double dy,double dz) {
	+ if(co[reg]==mem[reg]) add_particle_memory(reg);
	+ double p1=p[reg]+psco[reg],p2=p[fijk]+psl;
	+ (p1++)=(p2++)+dx;
	+ (p1++)=(p2++)+dy;
	+ p1=p2+dz;
	+ if(ps==4) (++p1)=(++p2);
	+ id[reg][co[reg]++]=id[fijk][l];
	+}
	+
	+}
	Index: extern/voro++/src/unitcell.hh
	===================================================================
	--- extern/voro++/src/unitcell.hh (revision 0)
	+++ extern/voro++/src/unitcell.hh (revision 0)
	@@ -0,0 +1,79 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file unitcell.hh
	+ * \brief Header file for the unitcell class. */
	+
	+#ifndef VOROPP_UNITCELL_HH
	+#define VOROPP_UNITCELL_HH
	+
	+#include <vector>
	+
	+#include "config.hh"
	+#include "cell.hh"
	+
	+namespace voro {
	+
	+/** \brief Class for computation of the unit Voronoi cell associated with
	+ * a 3D non-rectangular periodic domain. */
	+class unitcell {
	+ public:
	+ /** The x coordinate of the first vector defining the periodic
	+ * domain. */
	+ const double bx;
	+ /** The x coordinate of the second vector defining the periodic
	+ * domain. */
	+ const double bxy;
	+ /** The y coordinate of the second vector defining the periodic
	+ * domain. */
	+ const double by;
	+ /** The x coordinate of the third vector defining the periodic
	+ * domain. */
	+ const double bxz;
	+ /** The y coordinate of the third vector defining the periodic
	+ * domain. */
	+ const double byz;
	+ /** The z coordinate of the third vector defining the periodic
	+ * domain. */
	+ const double bz;
	+ /** The computed unit Voronoi cell corresponding the given
	+ * 3D non-rectangular periodic domain geometry. */
	+ voronoicell unit_voro;
	+ unitcell(double bx_,double bxy_,double by_,double bxz_,double byz_,double bz_);
	+ /** Draws an outline of the domain in Gnuplot format.
	+ * \param[in] filename the filename to write to. */
	+ inline void draw_domain_gnuplot(const char* filename) {
	+ FILE *fp(safe_fopen(filename,"w"));
	+ draw_domain_gnuplot(fp);
	+ fclose(fp);
	+ }
	+ void draw_domain_gnuplot(FILE *fp=stdout);
	+ /** Draws an outline of the domain in Gnuplot format.
	+ * \param[in] filename the filename to write to. */
	+ inline void draw_domain_pov(const char* filename) {
	+ FILE *fp(safe_fopen(filename,"w"));
	+ draw_domain_pov(fp);
	+ fclose(fp);
	+ }
	+ void draw_domain_pov(FILE *fp=stdout);
	+ bool intersects_image(double dx,double dy,double dz,double &vol);
	+ void images(std::vector<int> &vi,std::vector<double> &vd);
	+ protected:
	+ /** The maximum y-coordinate that could possibly cut the
	+ * computed unit Voronoi cell. */
	+ double max_uv_y;
	+ /** The maximum z-coordinate that could possibly cut the
	+ * computed unit Voronoi cell. */
	+ double max_uv_z;
	+ private:
	+ inline void unit_voro_apply(int i,int j,int k);
	+ bool unit_voro_intersect(int l);
	+ inline bool unit_voro_test(int i,int j,int k);
	+};
	+
	+}
	+
	+#endif
	Index: extern/voro++/src/cell.hh
	===================================================================
	--- extern/voro++/src/cell.hh (revision 0)
	+++ extern/voro++/src/cell.hh (revision 0)
	@@ -0,0 +1,514 @@
	+// Voro++, a 3D cell-based Voronoi library
	+//
	+// Author : Chris H. Rycroft (LBL / UC Berkeley)
	+// Email : chr@alum.mit.edu
	+// Date : August 30th 2011
	+
	+/** \file cell.hh
	+ * \brief Header file for the voronoicell and related classes. */
	+
	+#ifndef VOROPP_CELL_HH
	+#define VOROPP_CELL_HH
	+
	+#include <vector>
	+
	+#include "config.hh"
	+#include "common.hh"
	+
	+namespace voro {
	+
	+/** \brief A class representing a single Voronoi cell.
	+ *
	+ * This class represents a single Voronoi cell, as a collection of vertices
	+ * that are connected by edges. The class contains routines for initializing
	+ * the Voronoi cell to be simple shapes such as a box, tetrahedron, or octahedron.
	+ * It the contains routines for recomputing the cell based on cutting it
	+ * by a plane, which forms the key routine for the Voronoi cell computation.
	+ * It contains numerous routine for computing statistics about the Voronoi cell,
	+ * and it can output the cell in several formats.
	+ *
	+ * This class is not intended for direct use, but forms the base of the
	+ * voronoicell and voronoicell_neighbor classes, which extend it based on
	+ * whether neighboring particle ID information needs to be tracked. */
	+class voronoicell_base {
	+ public:
	+ /** This holds the current size of the arrays ed and nu, which
	+ * hold the vertex information. If more vertices are created
	+ * than can fit in this array, then it is dynamically extended
	+ * using the add_memory_vertices routine. */
	+ int current_vertices;
	+ /** This holds the current maximum allowed order of a vertex,
	+ * which sets the size of the mem, mep, and mec arrays. If a
	+ * vertex is created with more vertices than this, the arrays
	+ * are dynamically extended using the add_memory_vorder routine.
	+ */
	+ int current_vertex_order;
	+ /** This sets the size of the main delete stack. */
	+ int current_delete_size;
	+ /** This sets the size of the auxiliary delete stack. */
	+ int current_delete2_size;
	+ /** This sets the total number of vertices in the current cell.
	+ */
	+ int p;
	+ /** This is the index of particular point in the cell, which is
	+ * used to start the tracing routines for plane intersection
	+ * and cutting. These routines will work starting from any
	+ * point, but it's often most efficient to start from the last
	+ * point considered, since in many cases, the cell construction
	+ * algorithm may consider many planes with similar vectors
	+ * concurrently. */
	+ int up;
	+ /** This is a two dimensional array that holds information
	+ * about the edge connections of the vertices that make up the
	+ * cell. The two dimensional array is not allocated in the
	+ * usual method. To account for the fact the different vertices
	+ * have different orders, and thus require different amounts of
	+ * storage, the elements of ed[i] point to one-dimensional
	+ * arrays in the mep[] array of different sizes.
	+ *
	+ * More specifically, if vertex i has order m, then ed[i]
	+ * points to a one-dimensional array in mep[m] that has 2*m+1
	+ * entries. The first m elements hold the neighboring edges, so
	+ * that the jth edge of vertex i is held in ed[i][j]. The next
	+ * m elements hold a table of relations which is redundant but
	+ * helps speed up the computation. It satisfies the relation
	+ * ed[ed[i][j]][ed[i][m+j]]=i. The final entry holds a back
	+ * pointer, so that ed[i+2*m]=i. The back pointers are used
	+ * when rearranging the memory. */
	+ int **ed;
	+ /** This array holds the order of the vertices in the Voronoi
	+ * cell. This array is dynamically allocated, with its current
	+ * size held by current_vertices. */
	+ int *nu;
	+ /** This in an array with size 3*current_vertices for holding
	+ * the positions of the vertices. */
	+ double *pts;
	+ voronoicell_base();
	+ ~voronoicell_base();
	+ void init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
	+ void init_octahedron_base(double l);
	+ void init_tetrahedron_base(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3);
	+ void translate(double x,double y,double z);
	+ void draw_pov(double x,double y,double z,FILE *fp=stdout);
	+ /** Outputs the cell in POV-Ray format, using cylinders for edges
	+ * and spheres for vertices, to a given file.
	+ * \param[in] (x,y,z) a displacement to add to the cell's
	+ * position.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_pov(double x,double y,double z,const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_pov(x,y,z,fp);
	+ fclose(fp);
	+ };
	+ void draw_pov_mesh(double x,double y,double z,FILE *fp=stdout);
	+ /** Outputs the cell in POV-Ray format as a mesh2 object to a
	+ * given file.
	+ * \param[in] (x,y,z) a displacement to add to the cell's
	+ * position.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_pov_mesh(double x,double y,double z,const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_pov_mesh(x,y,z,fp);
	+ fclose(fp);
	+ }
	+ void draw_gnuplot(double x,double y,double z,FILE *fp=stdout);
	+ /** Outputs the cell in Gnuplot format a given file.
	+ * \param[in] (x,y,z) a displacement to add to the cell's
	+ * position.
	+ * \param[in] filename the name of the file to write to. */
	+ inline void draw_gnuplot(double x,double y,double z,const char *filename) {
	+ FILE *fp=safe_fopen(filename,"w");
	+ draw_gnuplot(x,y,z,fp);
	+ fclose(fp);
	+ }
	+ double volume();
	+ double max_radius_squared();
	+ double total_edge_distance();
	+ double surface_area();
	+ void centroid(double &cx,double &cy,double &cz);
	+ int number_of_faces();
	+ int number_of_edges();
	+ void vertex_orders(std::vector<int> &v);
	+ void output_vertex_orders(FILE *fp=stdout);
	+ void vertices(std::vector<double> &v);
	+ void output_vertices(FILE *fp=stdout);
	+ void vertices(double x,double y,double z,std::vector<double> &v);
	+ void output_vertices(double x,double y,double z,FILE *fp=stdout);
	+ void face_areas(std::vector<double> &v);
	+ /** Outputs the areas of the faces.
	+ * \param[in] fp the file handle to write to. */
	+ inline void output_face_areas(FILE *fp=stdout) {
	+ std::vector<double> v;face_areas(v);
	+ voro_print_vector(v,fp);
	+ }
	+ void face_orders(std::vector<int> &v);
	+ /** Outputs a list of the number of sides of each face.
	+ * \param[in] fp the file handle to write to. */
	+ inline void output_face_orders(FILE *fp=stdout) {
	+ std::vector<int> v;face_orders(v);
	+ voro_print_vector(v,fp);
	+ }
	+ void face_freq_table(std::vector<int> &v);
	+ /** Outputs a */
	+ inline void output_face_freq_table(FILE *fp=stdout) {
	+ std::vector<int> v;face_freq_table(v);
	+ voro_print_vector(v,fp);
	+ }
	+ void face_vertices(std::vector<int> &v);
	+ /** Outputs the */
	+ inline void output_face_vertices(FILE *fp=stdout) {
	+ std::vector<int> v;face_vertices(v);
	+ voro_print_face_vertices(v,fp);
	+ }
	+ void face_perimeters(std::vector<double> &v);
	+ /** Outputs a list of the perimeters of each face.
	+ * \param[in] fp the file handle to write to. */
	+ inline void output_face_perimeters(FILE *fp=stdout) {
	+ std::vector<double> v;face_perimeters(v);
	+ voro_print_vector(v,fp);
	+ }
	+ void normals(std::vector<double> &v);
	+ /** Outputs a list of the perimeters of each face.
	+ * \param[in] fp the file handle to write to. */
	+ inline void output_normals(FILE *fp=stdout) {
	+ std::vector<double> v;normals(v);
	+ voro_print_positions(v,fp);
	+ }
	+ /** Outputs a custom string of information about the Voronoi
	+ * cell to a file. It assumes the cell is at (0,0,0) and has a
	+ * the default_radius associated with it.
	+ * \param[in] format the custom format string to use.
	+ * \param[in] fp the file handle to write to. */
	+ inline void output_custom(const char format,FILE fp=stdout) {output_custom(format,0,0,0,0,default_radius,fp);}
	+ void output_custom(const char format,int i,double x,double y,double z,double r,FILE fp=stdout);
	+ template<class vc_class>
	+ bool nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id);
	+ bool plane_intersects(double x,double y,double z,double rsq);
	+ bool plane_intersects_guess(double x,double y,double z,double rsq);
	+ void construct_relations();
	+ void check_relations();
	+ void check_duplicates();
	+ void print_edges();
	+ /** Returns a list of IDs of neighboring particles
	+ * corresponding to each face.
	+ * \param[out] v a reference to a vector in which to return the
	+ * results. If no neighbor information is
	+ * available, a blank vector is returned. */
	+ virtual void neighbors(std::vector<int> &v) {v.clear();}
	+ /** This is a virtual function that is overridden by a routine
	+ * to print a list of IDs of neighboring particles
	+ * corresponding to each face. By default, when no neighbor
	+ * information is available, the routine does nothing.
	+ * \param[in] fp the file handle to write to. */
	+ virtual void output_neighbors(FILE *fp=stdout) {}
	+ /** This a virtual function that is overridden by a routine to
	+ * print the neighboring particle IDs for a given vertex. By
	+ * default, when no neighbor information is available, the
	+ * routine does nothing.
	+ * \param[in] i the vertex to consider. */
	+ virtual void print_edges_neighbors(int i) {};
	+ /** This is a simple inline function for picking out the index
	+ * of the next edge counterclockwise at the current vertex.
	+ * \param[in] a the index of an edge of the current vertex.
	+ * \param[in] p the number of the vertex.
	+ * \return 0 if a=nu[p]-1, or a+1 otherwise. */
	+ inline int cycle_up(int a,int p) {return a==nu[p]-1?0:a+1;}
	+ /** This is a simple inline function for picking out the index
	+ * of the next edge clockwise from the current vertex.
	+ * \param[in] a the index of an edge of the current vertex.
	+ * \param[in] p the number of the vertex.
	+ * \return nu[p]-1 if a=0, or a-1 otherwise. */
	+ inline int cycle_down(int a,int p) {return a==0?nu[p]-1:a-1;}
	+ protected:
	+ /** This a one dimensional array that holds the current sizes
	+ * of the memory allocations for them mep array.*/
	+ int *mem;
	+ /** This is a one dimensional array that holds the current
	+ * number of vertices of order p that are stored in the mep[p]
	+ * array. */
	+ int *mec;
	+ /** This is a two dimensional array for holding the information
	+ * about the edges of the Voronoi cell. mep[p] is a
	+ * one-dimensional array for holding the edge information about
	+ * all vertices of order p, with each vertex holding 2*p+1
	+ * integers of information. The total number of vertices held
	+ * on mep[p] is stored in mem[p]. If the space runs out, the
	+ * code allocates more using the add_memory() routine. */
	+ int **mep;
	+ inline void reset_edges();
	+ template<class vc_class>
	+ void check_memory_for_copy(vc_class &vc,voronoicell_base* vb);
	+ void copy(voronoicell_base* vb);
	+ private:
	+ /** This is the delete stack, used to store the vertices which
	+ * are going to be deleted during the plane cutting procedure.
	+ */
	+ int ds,stacke;
	+ /** This is the auxiliary delete stack, which has size set by
	+ * current_delete2_size. */
	+ int ds2,stacke2;
	+ /** This stores the current memory allocation for the marginal
	+ * cases. */
	+ int current_marginal;
	+ /** This stores the total number of marginal points which are
	+ * currently in the buffer. */
	+ int n_marg;
	+ /** This array contains a list of the marginal points, and also
	+ * the outcomes of the marginal tests. */
	+ int *marg;
	+ /** The x coordinate of the normal vector to the test plane. */
	+ double px;
	+ /** The y coordinate of the normal vector to the test plane. */
	+ double py;
	+ /** The z coordinate of the normal vector to the test plane. */
	+ double pz;
	+ /** The magnitude of the normal vector to the test plane. */
	+ double prsq;
	+ template<class vc_class>
	+ void add_memory(vc_class &vc,int i,int *stackp2);
	+ template<class vc_class>
	+ void add_memory_vertices(vc_class &vc);
	+ template<class vc_class>
	+ void add_memory_vorder(vc_class &vc);
	+ void add_memory_ds(int *&stackp);
	+ void add_memory_ds2(int *&stackp2);
	+ template<class vc_class>
	+ inline bool collapse_order1(vc_class &vc);
	+ template<class vc_class>
	+ inline bool collapse_order2(vc_class &vc);
	+ template<class vc_class>
	+ inline bool delete_connection(vc_class &vc,int j,int k,bool hand);
	+ template<class vc_class>
	+ inline bool search_for_outside_edge(vc_class &vc,int &up);
	+ template<class vc_class>
	+ inline void add_to_stack(vc_class &vc,int lp,int *&stackp2);
	+ inline bool plane_intersects_track(double x,double y,double z,double rs,double g);
	+ inline void normals_search(std::vector<double> &v,int i,int j,int k);
	+ inline bool search_edge(int l,int &m,int &k);
	+ inline int m_test(int n,double &ans);
	+ int check_marginal(int n,double &ans);
	+ friend class voronoicell;
	+ friend class voronoicell_neighbor;
	+};
	+
	+/** \brief Extension of the voronoicell_base class to represent a Voronoi
	+ * cell without neighbor information.
	+ *
	+ * This class is an extension of the voronoicell_base class, in cases when
	+ * is not necessary to track the IDs of neighboring particles associated
	+ * with each face of the Voronoi cell. */
	+class voronoicell : public voronoicell_base {
	+ public:
	+ using voronoicell_base::nplane;
	+ /** Copies the information from another voronoicell class into
	+ * this class, extending memory allocation if necessary.
	+ * \param[in] c the class to copy. */
	+ inline void operator=(voronoicell &c) {
	+ voronoicell_base* vb((voronoicell_base*) &c);
	+ check_memory_for_copy(*this,vb);copy(vb);
	+ }
	+ /** Cuts a Voronoi cell using by the plane corresponding to the
	+ * perpendicular bisector of a particle.
	+ * \param[in] (x,y,z) the position of the particle.
	+ * \param[in] rsq the modulus squared of the vector.
	+ * \param[in] p_id the plane ID, ignored for this case where no
	+ * neighbor tracking is enabled.
	+ * \return False if the plane cut deleted the cell entirely,
	+ * true otherwise. */
	+ inline bool nplane(double x,double y,double z,double rsq,int p_id) {
	+ return nplane(*this,x,y,z,rsq,0);
	+ }
	+ /** Cuts a Voronoi cell using by the plane corresponding to the
	+ * perpendicular bisector of a particle.
	+ * \param[in] (x,y,z) the position of the particle.
	+ * \param[in] p_id the plane ID, ignored for this case where no
	+ * neighbor tracking is enabled.
	+ * \return False if the plane cut deleted the cell entirely,
	+ * true otherwise. */
	+ inline bool nplane(double x,double y,double z,int p_id) {
	+ double rsq=xx+yy+z*z;
	+ return nplane(*this,x,y,z,rsq,0);
	+ }
	+ /** Cuts a Voronoi cell using by the plane corresponding to the
	+ * perpendicular bisector of a particle.
	+ * \param[in] (x,y,z) the position of the particle.
	+ * \param[in] rsq the modulus squared of the vector.
	+ * \return False if the plane cut deleted the cell entirely,
	+ * true otherwise. */
	+ inline bool plane(double x,double y,double z,double rsq) {
	+ return nplane(*this,x,y,z,rsq,0);
	+ }
	+ /** Cuts a Voronoi cell using by the plane corresponding to the
	+ * perpendicular bisector of a particle.
	+ * \param[in] (x,y,z) the position of the particle.
	+ * \return False if the plane cut deleted the cell entirely,
	+ * true otherwise. */
	+ inline bool plane(double x,double y,double z) {
	+ double rsq=xx+yy+z*z;
	+ return nplane(*this,x,y,z,rsq,0);
	+ }
	+ /** Initializes the Voronoi cell to be rectangular box with the
	+ * given dimensions.
	+ * \param[in] (xmin,xmax) the minimum and maximum x coordinates.
	+ * \param[in] (ymin,ymax) the minimum and maximum y coordinates.
	+ * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */
	+ inline void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) {
	+ init_base(xmin,xmax,ymin,ymax,zmin,zmax);
	+ }
	+ /** Initializes the cell to be an octahedron with vertices at
	+ * (l,0,0), (-l,0,0), (0,l,0), (0,-l,0), (0,0,l), and (0,0,-l).
	+ * \param[in] l a parameter setting the size of the octahedron.
	+ */
	+ inline void init_octahedron(double l) {
	+ init_octahedron_base(l);
	+ }
	+ /** Initializes the cell to be a tetrahedron.
	+ * \param[in] (x0,y0,z0) the coordinates of the first vertex.
	+ * \param[in] (x1,y1,z1) the coordinates of the second vertex.
	+ * \param[in] (x2,y2,z2) the coordinates of the third vertex.
	+ * \param[in] (x3,y3,z3) the coordinates of the fourth vertex.
	+ */
	+ inline void init_tetrahedron(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3) {
	+ init_tetrahedron_base(x0,y0,z0,x1,y1,z1,x2,y2,z2,x3,y3,z3);
	+ }
	+ private:
	+ inline void n_allocate(int i,int m) {};
	+ inline void n_add_memory_vertices(int i) {};
	+ inline void n_add_memory_vorder(int i) {};
	+ inline void n_set_pointer(int p,int n) {};
	+ inline void n_copy(int a,int b,int c,int d) {};
	+ inline void n_set(int a,int b,int c) {};
	+ inline void n_set_aux1(int k) {};
	+ inline void n_copy_aux1(int a,int b) {};
	+ inline void n_copy_aux1_shift(int a,int b) {};
	+ inline void n_set_aux2_copy(int a,int b) {};
	+ inline void n_copy_pointer(int a,int b) {};
	+ inline void n_set_to_aux1(int j) {};
	+ inline void n_set_to_aux2(int j) {};
	+ inline void n_allocate_aux1(int i) {};
	+ inline void n_switch_to_aux1(int i) {};
	+ inline void n_copy_to_aux1(int i,int m) {};
	+ inline void n_set_to_aux1_offset(int k,int m) {};
	+ inline void n_neighbors(std::vector<int> &v) {v.clear();};
	+ friend class voronoicell_base;
	+};
	+
	+/** \brief Extension of the voronoicell_base class to represent a Voronoi cell
	+ * with neighbor information.
	+ *
	+ * This class is an extension of the voronoicell_base class, in cases when the
	+ * IDs of neighboring particles associated with each face of the Voronoi cell.
	+ * It contains additional data structures mne and ne for storing this
	+ * information. */
	+class voronoicell_neighbor : public voronoicell_base {
	+ public:
	+ using voronoicell_base::nplane;
	+ /** This two dimensional array holds the neighbor information
	+ * associated with each vertex. mne[p] is a one dimensional
	+ * array which holds all of the neighbor information for
	+ * vertices of order p. */
	+ int **mne;
	+ /** This is a two dimensional array that holds the neighbor
	+ * information associated with each vertex. ne[i] points to a
	+ * one-dimensional array in mne[nu[i]]. ne[i][j] holds the
	+ * neighbor information associated with the jth edge of vertex
	+ * i. It is set to the ID number of the plane that made the
	+ * face that is clockwise from the jth edge. */
	+ int **ne;
	+ voronoicell_neighbor();
	+ ~voronoicell_neighbor();
	+ void operator=(voronoicell &c);
	+ void operator=(voronoicell_neighbor &c);
	+ /** Cuts the Voronoi cell by a particle whose center is at a
	+ * separation of (x,y,z) from the cell center. The value of rsq
	+ * should be initially set to \f$x^2+y^2+z^2\f$.
	+ * \param[in] (x,y,z) the normal vector to the plane.
	+ * \param[in] rsq the distance along this vector of the plane.
	+ * \param[in] p_id the plane ID (for neighbor tracking only).
	+ * \return False if the plane cut deleted the cell entirely,
	+ * true otherwise. */
	+ inline bool nplane(double x,double y,double z,double rsq,int p_id) {
	+ return nplane(*this,x,y,z,rsq,p_id);
	+ }
	+ /** This routine calculates the modulus squared of the vector
	+ * before passing it to the main nplane() routine with full
	+ * arguments.
	+ * \param[in] (x,y,z) the vector to cut the cell by.
	+ * \param[in] p_id the plane ID (for neighbor tracking only).
	+ * \return False if the plane cut deleted the cell entirely,
	+ * true otherwise. */
	+ inline bool nplane(double x,double y,double z,int p_id) {
	+ double rsq=xx+yy+z*z;
	+ return nplane(*this,x,y,z,rsq,p_id);
	+ }
	+ /** This version of the plane routine just makes up the plane
	+ * ID to be zero. It will only be referenced if neighbor
	+ * tracking is enabled.
	+ * \param[in] (x,y,z) the vector to cut the cell by.
	+ * \param[in] rsq the modulus squared of the vector.
	+ * \return False if the plane cut deleted the cell entirely,
	+ * true otherwise. */
	+ inline bool plane(double x,double y,double z,double rsq) {
	+ return nplane(*this,x,y,z,rsq,0);
	+ }
	+ /** Cuts a Voronoi cell using the influence of a particle at
	+ * (x,y,z), first calculating the modulus squared of this
	+ * vector before passing it to the main nplane() routine. Zero
	+ * is supplied as the plane ID, which will be ignored unless
	+ * neighbor tracking is enabled.
	+ * \param[in] (x,y,z) the vector to cut the cell by.
	+ * \return False if the plane cut deleted the cell entirely,
	+ * true otherwise. */
	+ inline bool plane(double x,double y,double z) {
	+ double rsq=xx+yy+z*z;
	+ return nplane(*this,x,y,z,rsq,0);
	+ }
	+ void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
	+ void init_octahedron(double l);
	+ void init_tetrahedron(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3);
	+ void check_facets();
	+ virtual void neighbors(std::vector<int> &v);
	+ virtual void print_edges_neighbors(int i);
	+ virtual void output_neighbors(FILE *fp=stdout) {
	+ std::vector<int> v;neighbors(v);
	+ voro_print_vector(v,fp);
	+ }
	+ private:
	+ int *paux1;
	+ int *paux2;
	+ inline void n_allocate(int i,int m) {mne[i]=new int[m*i];}
	+ inline void n_add_memory_vertices(int i) {
	+ int *pp=new int[i];
	+ for(int j=0;j<current_vertices;j++) pp[j]=ne[j];
	+ delete [] ne;ne=pp;
	+ }
	+ inline void n_add_memory_vorder(int i) {
	+ int *p2=new int[i];
	+ for(int j=0;j<current_vertex_order;j++) p2[j]=mne[j];
	+ delete [] mne;mne=p2;
	+ }
	+ inline void n_set_pointer(int p,int n) {
	+ ne[p]=mne[n]+n*mec[n];
	+ }
	+ inline void n_copy(int a,int b,int c,int d) {ne[a][b]=ne[c][d];}
	+ inline void n_set(int a,int b,int c) {ne[a][b]=c;}
	+ inline void n_set_aux1(int k) {paux1=mne[k]+k*mec[k];}
	+ inline void n_copy_aux1(int a,int b) {paux1[b]=ne[a][b];}
	+ inline void n_copy_aux1_shift(int a,int b) {paux1[b]=ne[a][b+1];}
	+ inline void n_set_aux2_copy(int a,int b) {
	+ paux2=mne[b]+b*mec[b];
	+ for(int i=0;i<b;i++) ne[a][i]=paux2[i];
	+ }
	+ inline void n_copy_pointer(int a,int b) {ne[a]=ne[b];}
	+ inline void n_set_to_aux1(int j) {ne[j]=paux1;}
	+ inline void n_set_to_aux2(int j) {ne[j]=paux2;}
	+ inline void n_allocate_aux1(int i) {paux1=new int[i*mem[i]];}
	+ inline void n_switch_to_aux1(int i) {delete [] mne[i];mne[i]=paux1;}
	+ inline void n_copy_to_aux1(int i,int m) {paux1[m]=mne[i][m];}
	+ inline void n_set_to_aux1_offset(int k,int m) {ne[k]=paux1+m;}
	+ friend class voronoicell_base;
	+};
	+
	+}
	+
	+#endif
	Index: extern/voro++/CMakeLists.txt
	===================================================================
	--- extern/voro++/CMakeLists.txt (revision 0)
	+++ extern/voro++/CMakeLists.txt (revision 0)
	@@ -0,0 +1,40 @@
	+set (INC
	+ src
	+)
	+
	+set (INC_SYS
	+)
	+
	+set (SRC
	+ src/c_loops.cc
	+ src/cell.cc
	+ src/cmd_line.cc
	+ src/common.cc
	+ src/container_prd.cc
	+ src/container.cc
	+ src/pre_container.cc
	+ src/unitcell.cc
	+ src/v_base.cc
	+ src/v_compute.cc
	+ src/voro++.cc
	+ src/wall.cc
	+ src/c_interface.cc
	+
	+ src/c_loops.hh
	+ src/cell.hh
	+ src/common.hh
	+ src/config.hh
	+ src/container_prd.hh
	+ src/container.hh
	+ src/pre_container.hh
	+ src/rad_option.hh
	+ src/unitcell.hh
	+ src/v_base.hh
	+ src/v_compute.hh
	+ src/voro++.hh
	+ src/wall.hh
	+ src/worklist.hh
	+ src/c_interface.hh
	+)
	+
	+blender_add_lib(extern_voro++ "${SRC}" "${INC}" "${INC_SYS}")
	\ No newline at end of file
	Index: extern/CMakeLists.txt
	===================================================================
	--- extern/CMakeLists.txt (revision 53656)
	+++ extern/CMakeLists.txt (working copy)
	@@ -81,3 +81,5 @@
	add_subdirectory(xdnd)
	endif()
	endif()
	+
	+add_subdirectory(voro++)
	Index: SConstruct
	===================================================================
	--- SConstruct (revision 53656)
	+++ SConstruct (working copy)
	@@ -266,6 +266,7 @@
	target_env_defs['WITH_BF_SMOKE'] = False
	target_env_defs['WITH_BF_BOOLEAN'] = False
	target_env_defs['WITH_BF_REMESH'] = False
	+ target_env_defs['WITH_BF_VORONOI'] = False
	target_env_defs['WITH_BF_PYTHON'] = False
	target_env_defs['WITH_BF_3DMOUSE'] = False
	target_env_defs['WITH_BF_LIBMV'] = False
	Index: CMakeLists.txt
	===================================================================
	--- CMakeLists.txt (revision 53656)
	+++ CMakeLists.txt (working copy)
	@@ -198,6 +198,7 @@
	# option(WITH_MOD_CLOTH_ELTOPO "Enable Experimental cloth solver" OFF) # this is now only available in a branch
	# mark_as_advanced(WITH_MOD_CLOTH_ELTOPO)
	option(WITH_MOD_OCEANSIM "Enable Ocean Modifier" OFF)
	+option(WITH_MOD_VORONOI "Enable Voronoi Cells in Explode Modifier" ON)

	# Image format support
	option(WITH_IMAGE_OPENEXR "Enable OpenEXR Support (http://www.openexr.com)" ON)
	@@ -2159,6 +2160,7 @@
	info_cfg_option(WITH_MOD_REMESH)
	info_cfg_option(WITH_MOD_FLUID)
	info_cfg_option(WITH_MOD_OCEANSIM)
	+ info_cfg_option(WITH_MOD_VORONOI)

	info_cfg_text("")

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