git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10394 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/VORONOI/README

@@ -28,6 +28,13 @@ compute the tesselation locally on each processor.
 
 5.  Compile LAMMPS (you should know how that works)
 
+== Run tests ==
+
+Run the includes test input file
+./lmp_serial < lammps/examples/voronoi/in.vorotest | grep '^TEST_'
+
+The output should conclude with 'TEST_DONE' and every line should 
+report an error of 0%. 
 
 == Credits and license ==
 

src/VORONOI/compute_voronoi_atom.cpp

@@ -20,15 +20,17 @@
 #include "stdlib.h"
 #include "compute_voronoi_atom.h"
 #include "atom.h"
+#include "group.h"
 #include "update.h"
 #include "modify.h"
 #include "domain.h"
 #include "memory.h"
 #include "error.h"
 #include "comm.h"
+#include "variable.h"
+#include "input.h"
 
 #include <vector>
-#include "voro++.hh"
 
 using namespace LAMMPS_NS;
 using namespace voro;
@@ -38,29 +40,88 @@ using namespace voro;
 ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg)
 {
-  if (narg != 3) error->all(FLERR,"Illegal compute voronoi/atom command");
-
-  peratom_flag = 1;
+  int sgroup;
+  
   size_peratom_cols = 2;
+  peratom_flag = 1;
 
-  nmax = 0;
+  surface = VOROSURF_NONE;
+  maxedge = 0;
+  fthresh = ethresh = 0.0;
+  radstr = NULL;
+  onlyGroup = false;
+
+  int iarg = 3;
+  while ( iarg<narg ) {
+    if (strcmp(arg[iarg], "only_group") == 0) {
+      onlyGroup = true;
+      iarg++;
+    } 
+    else if (strcmp(arg[iarg], "radius") == 0) {
+      if (iarg + 2 > narg || strstr(arg[iarg+1],"v_") != arg[iarg+1] ) error->all(FLERR,"Missing atom style variable for radical voronoi tesselation radius.");
+      int n = strlen(&arg[iarg+1][2]) + 1;
+      radstr = new char[n];
+      strcpy(radstr,&arg[iarg+1][2]);
+      iarg += 2;
+    } 
+    else if (strcmp(arg[iarg], "surface") == 0) {
+      if (iarg + 2 > narg) error->all(FLERR,"Missing group name after keyword 'surface'.");
+      // group all is a special case where we just skip group testing
+      if(strcmp(arg[iarg+1], "all") == 0) {
+        surface = VOROSURF_ALL;
+      } else {
+        sgroup = group->find(arg[iarg+1]);
+        if (sgroup == -1) error->all(FLERR,"Could not find compute/voronoi surface group ID");
+        sgroupbit = group->bitmask[sgroup]; 
+        surface = VOROSURF_GROUP;
+      }
+      size_peratom_cols = 3;
+      iarg += 2;
+    } else if (strcmp(arg[iarg], "edge_histo") == 0) {
+      if (iarg + 2 > narg) error->all(FLERR,"Missing maximum edge count after keyword 'edge_histo'.");
+      maxedge = atoi(arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg], "face_threshold") == 0) {
+      if (iarg + 2 > narg) error->all(FLERR,"Missing minimum face area after keyword 'face_threshold'.");
+      fthresh = atof(arg[iarg+1]);
+      iarg += 2;
+    } else if (strcmp(arg[iarg], "edge_threshold") == 0) {
+      if (iarg + 2 > narg) error->all(FLERR,"Missing minimum edge length after keyword 'edge_threshold'.");
+      ethresh = atof(arg[iarg+1]);
+      iarg += 2;
+    } 
+    else 
+      error->all(FLERR,"Illegal compute voronoi/atom command");
+  }
+
+  nmax = rmax = 0;
+  edge = rfield = sendvector = NULL;
   voro = NULL;
+
+  if ( maxedge > 0 ) {
+    vector_flag = 1;
+    size_vector = maxedge+1;
+    memory->create(edge,maxedge+1,"voronoi/atom:edge");
+    memory->create(sendvector,maxedge+1,"voronoi/atom:sendvector");
+    vector = edge;
+  }
 }
 
 /* ---------------------------------------------------------------------- */
 
 ComputeVoronoi::~ComputeVoronoi()
 {
+  memory->destroy(edge);
+  memory->destroy(rfield);
+  memory->destroy(sendvector);
   memory->destroy(voro);
+  delete[] radstr;
 }
 
 /* ---------------------------------------------------------------------- */
 
 void ComputeVoronoi::init()
 {
-  if (domain->triclinic != 0)
-    error->all(FLERR,"Compute voronoi/atom not allowed for triclinic boxes");
-
   int count = 0;
   for (int i = 0; i < modify->ncompute; i++)
     if (strcmp(modify->compute[i]->style,"voronoi/atom") == 0) count++;
@@ -74,7 +135,8 @@ void ComputeVoronoi::init()
 
 void ComputeVoronoi::compute_peratom()
 {
-  int i;
+  int i, j;
+  const double e = 0.01;
 
   invoked_peratom = update->ntimestep;
 
@@ -88,55 +150,240 @@ void ComputeVoronoi::compute_peratom()
     array_atom = voro;
   }
 
-  // n = # of voro++ spatial hash cells
-  // TODO: make square
-
-  int nall = nlocal + atom->nghost;
-  int n = int(floor( pow( double(nall)/8.0, 0.333333 ) ));
-  n = (n==0) ? 1 : n;
-
-  // initialize voro++ container
-  // preallocates 8 atoms per cell
-  // voro++ allocates more memory if needed
+  // in the onlyGroup mode we are not setting values for all atoms later in the voro loop
+  // initialize everything to zero here
+  if (onlyGroup) {
+    if (surface == VOROSURF_NONE) 
+      for (i = 0; i < nlocal; i++) voro[i][0] = voro[i][1] = 0.0;
+    else
+      for (i = 0; i < nlocal; i++) voro[i][0] = voro[i][1] = voro[i][2] = 0.0;
+  }
 
-  double *sublo = domain->sublo;
-  double *subhi = domain->subhi;
+  double *sublo = domain->sublo, *sublo_lamda = domain->sublo_lamda, *boxlo = domain->boxlo;
+  double *subhi = domain->subhi, *subhi_lamda = domain->subhi_lamda, *boxhi = domain->boxhi;
   double *cut = comm->cutghost;
-
-  container con(sublo[0]-cut[0],subhi[0]+cut[0],
-                sublo[1]-cut[1],subhi[1]+cut[1],
-                sublo[2]-cut[2],subhi[2]+cut[2],
-                n,n,n,false,false,false,8); 
-
-  // pass coordinates for local and ghost atoms to voro++
-
+  double sublo_bound[3], subhi_bound[3], cut_bound[3];
   double **x = atom->x;
-  for (i = 0; i < nall; i++)
-    con.put(i,x[i][0],x[i][1],x[i][2]);
+   
+  // setup bounds for voro++ domain for orthogonal and triclinic simulation boxes
+  if( domain->triclinic ) {
+    // triclinic box: embed parallelepiped into orthogonal voro++ domain
+    double mx, my, sxy,sxz,syz;
+    mx = (boxhi[0]-boxlo[0])/(subhi[0]-sublo[0]);
+    my = (boxhi[1]-boxlo[1])/(subhi[1]-sublo[1]);
+    sxy = domain->xy/mx;
+    sxz = domain->xz/mx;
+    syz = domain->yz/my;
+
+    // cutghost is in lamda coordinates for triclinic boxes, use subxx_lamda
+    double *h = domain->h, cuttri[3];
+    sublo_bound[0] = h[0]*sublo_lamda[0] + h[5]*sublo_lamda[1] + h[4]*sublo_lamda[2] + boxlo[0];
+    sublo_bound[1] = h[1]*sublo_lamda[1] + h[3]*sublo_lamda[2] + boxlo[1];
+    sublo_bound[2] = h[2]*sublo_lamda[2] + boxlo[2];
+    subhi_bound[0] = h[0]*subhi_lamda[0] + h[5]*subhi_lamda[1] + h[4]*subhi_lamda[2] + boxlo[0];
+    subhi_bound[1] = h[1]*subhi_lamda[1] + h[3]*subhi_lamda[2] + boxlo[1];
+    subhi_bound[2] = h[2]*subhi_lamda[2] + boxlo[2];
+    cut_bound[0] = h[0]*cut[0] + h[5]*cut[1] + h[4]*cut[2];
+    cut_bound[1] = h[1]*cut[1] + h[3]*cut[2];
+    cut_bound[2] = h[2]*cut[2];
+
+  } else {
+    // orthogonal box
+    for( i=0; i<3; ++i ) {
+      sublo_bound[i] = sublo[i];
+      subhi_bound[i] = subhi[i];
+      cut_bound[i] = cut[i];
+    }
+  }
 
-  // invoke voro++ and fetch results for owned atoms in group
+  // n = # of voro++ spatial hash cells (with approximately cubic cells)
+  int nall = nlocal + atom->nghost;
+  double n[3], V;
+  for( i=0; i<3; ++i ) n[i] = subhi_bound[i] - sublo_bound[i];
+  V = n[0]*n[1]*n[2];
+  for( i=0; i<3; ++i ) {
+    n[i] = round( n[i]*pow( double(nall)/(V*8.0), 0.333333 ) );
+    n[i] = n[i]==0 ? 1 : n[i];
+  } 
 
-  int *mask = atom->mask;
-  std::vector<int> neigh;
+  // clear edge statistics
+  for (i = 0; i < maxedge; ++i) edge[i]=0;
 
+  // initialize voro++ container
+  // preallocates 8 atoms per cell
+  // voro++ allocates more memory if needed
   voronoicell_neighbor c;
-  c_loop_all cl(con);
-  if (cl.start()) do if (con.compute_cell(c,cl)) {
-    i = cl.pid();
-    if (i < nlocal && (mask[i] & groupbit)) {
-      voro[i][0] = c.volume();
-      c.neighbors(neigh);
-      voro[i][1] = neigh.size();
-    } else if (i < nlocal) voro[i][0] = voro[i][1] = 0.0;
-  } while (cl.inc());
+  int *mask = atom->mask;
+  if(radstr) {
+    // check and fetch atom style variable data
+    int radvar = input->variable->find(radstr);
+    if (radvar < 0)
+            error->all(FLERR,"Variable name for voronoi radius set does not exist");
+    if (!input->variable->atomstyle(radvar))
+            error->all(FLERR,"Variable for voronoi radius is not atom style");
+    // prepare destination buffer for variable evaluation
+    if (nlocal > rmax) {
+      memory->destroy(rfield);
+      rmax = atom->nmax;
+      memory->create(rfield,rmax,"voronoi/atom:rfield");
+    }
+    // compute atom style radius variable
+    input->variable->compute_atom(radvar,0,rfield,1,0);
+
+    // communicate values to ghost atoms of neighboring nodes
+    comm->forward_comm_compute(this);
+
+    // polydisperse voro++ container
+    container_poly con(sublo_bound[0]-cut_bound[0]-e,subhi_bound[0]+cut_bound[0]+e,
+                       sublo_bound[1]-cut_bound[1]-e,subhi_bound[1]+cut_bound[1]+e,
+                       sublo_bound[2]-cut_bound[2]-e,subhi_bound[2]+cut_bound[2]+e,
+                       int(n[0]),int(n[1]),int(n[2]),false,false,false,8); 
+
+    // pass coordinates for local and ghost atoms to voro++
+    for (i = 0; i < nall; i++)
+      if( !onlyGroup || (mask[i] & groupbit) )
+        con.put(i,x[i][0],x[i][1],x[i][2],rfield[i]);
+
+    // invoke voro++ and fetch results for owned atoms in group
+    c_loop_all cl(con);
+    if (cl.start()) do if (con.compute_cell(c,cl)) {
+      i = cl.pid();
+      processCell(c,i);
+    } while (cl.inc());
+  } else {
+    // monodisperse voro++ container
+    container con(sublo_bound[0]-cut_bound[0]-e,subhi_bound[0]+cut_bound[0]+e,
+                  sublo_bound[1]-cut_bound[1]-e,subhi_bound[1]+cut_bound[1]+e,
+                  sublo_bound[2]-cut_bound[2]-e,subhi_bound[2]+cut_bound[2]+e,
+                  int(n[0]),int(n[1]),int(n[2]),false,false,false,8); 
+
+    // pass coordinates for local and ghost atoms to voro++
+    for (i = 0; i < nall; i++)
+      if( !onlyGroup || (mask[i] & groupbit) )
+        con.put(i,x[i][0],x[i][1],x[i][2]);
+
+    // invoke voro++ and fetch results for owned atoms in group
+    c_loop_all cl(con);
+    if (cl.start()) do if (con.compute_cell(c,cl)) {
+      i = cl.pid();
+      processCell(c,i);
+    } while (cl.inc());
+  }
 }
 
 /* ----------------------------------------------------------------------
    memory usage of local atom-based array
 ------------------------------------------------------------------------- */
+void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i) 
+{
+  int j,k, *mask = atom->mask;
+  std::vector<int> neigh, norder, vlist;
+  std::vector<double> narea, vcell;
+  bool have_narea = false;
+
+  // zero out surface area if surface computation was requested
+  if (surface != VOROSURF_NONE && !onlyGroup) voro[i][2] = 0.0;
+
+  if (i < atom->nlocal && (mask[i] & groupbit)) {
+    // cell volume
+    voro[i][0] = c.volume();
+
+    // number of cell faces
+    c.neighbors(neigh);
+    if (fthresh > 0) {
+      // count only faces above area threshold
+      c.face_areas(narea);
+      have_narea = true;
+      for (j=0; j<narea.size(); ++j)  
+        if (narea[j] > fthresh) voro[i][1] += 1.0;
+    } else {
+      // unthresholded face count
+      voro[i][1] = neigh.size();
+    }
+
+    // cell surface area
+    if (surface == VOROSURF_ALL) {
+      voro[i][2] = c.surface_area();
+    } else if (surface == VOROSURF_GROUP) {
+      if (!have_narea) c.face_areas(narea);
+      // loop over all faces (neighbors) and check if they are in the surface group
+      for (j=0; j<voro[i][1]; ++j)  
+        if (mask[neigh[j]] & sgroupbit) voro[i][2] += narea[j];
+    }
+
+    // histogram of number of face edges
+    if (maxedge>0) {
+      if (ethresh > 0) {
+        // count only edges above length threshold 
+        c.vertices(vcell);
+        c.face_vertices(vlist); // for each face: vertex count followed list of vertex indices (n_1,v1_1,v2_1,v3_1,..,vn_1,n_2,v2_1,...)
+        double dx, dy, dz, r2, t2 = ethresh*ethresh;
+        for( j=0; j<vlist.size(); j+=vlist[j]+1 ) { 
+          int a, b, nedge = 0;
+          // vlist[j] contains number of vertex indices for the current face
+          for( k=0; k<vlist[j]; ++k ) { 
+            a = vlist[j+1+k];              // first vertex in edge 
+            b = vlist[j+1+(k+1)%vlist[j]]; // second vertex in edge (possible wrap around to first vertex in list)
+            dx = vcell[a*3]   - vcell[b*3];
+            dy = vcell[a*3+1] - vcell[b*3+1];
+            dz = vcell[a*3+2] - vcell[b*3+2];
+            r2 = dx*dx+dy*dy+dz*dz;
+            if (r2 > t2) nedge++;
+          }
+          // counted edges above threshold, now put into the correct bin
+          if (nedge>0) {
+            if (nedge<=maxedge) 
+              edge[nedge-1]++;
+            else
+              edge[maxedge]++;
+          }
+        }
+      } else {
+        // unthresholded edge counts
+        c.face_orders(norder);
+        for (j=0; j<voro[i][1]; ++j)
+          if (norder[j]>0) {
+            if (norder[j]<=maxedge) 
+              edge[norder[j]-1]++;
+            else
+              edge[maxedge]++;
+          }
+      }
+    }
+  } else if (i < atom->nlocal) voro[i][0] = voro[i][1] = 0.0;
+}
 
 double ComputeVoronoi::memory_usage()
 {
   double bytes = size_peratom_cols * nmax * sizeof(double);
   return bytes;
 }
+
+void ComputeVoronoi::compute_vector()
+{
+  invoked_vector = update->ntimestep;
+  if( invoked_peratom < invoked_vector ) compute_peratom();
+
+  for( int i=0; i<size_vector; ++i ) sendvector[i] = edge[i];
+  MPI_Allreduce(sendvector,edge,size_vector,MPI_DOUBLE,MPI_SUM,world);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int ComputeVoronoi::pack_comm(int n, int *list, double *buf,
+                                  int pbc_flag, int *pbc)
+{
+  int i,m=0;
+  for (i = 0; i < n; i++) buf[m++] = rfield[list[i]];
+  return 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeVoronoi::unpack_comm(int n, int first, double *buf)
+{
+  int i,last,m=0;
+  last = first + n;
+  for (i = first; i < last; i++) rfield[i] = buf[m++];
+}
+

src/VORONOI/compute_voronoi_atom.h

@@ -21,6 +21,7 @@ ComputeStyle(voronoi/atom,ComputeVoronoi)
 #define LMP_COMPUTE_VORONOI_H
 
 #include "compute.h"
+#include "voro++.hh"
 
 namespace LAMMPS_NS {
 
@@ -30,11 +31,22 @@ class ComputeVoronoi : public Compute {
   ~ComputeVoronoi();
   void init();
   void compute_peratom();
+  void compute_vector();
   double memory_usage();
 
+  int pack_comm(int, int *, double *, int, int *);
+  void unpack_comm(int, int, double *);
+
  private:
-  int nmax;
+  void processCell(voro::voronoicell_neighbor&, int);
+
+  int nmax, rmax, maxedge, sgroupbit;
+  char *radstr;
+  double fthresh, ethresh;
   double **voro;
+  double *edge, *sendvector, *rfield;
+  enum { VOROSURF_NONE, VOROSURF_ALL, VOROSURF_GROUP } surface;
+  bool onlyGroup;
 };
 
 }