From 005f9d5ac5e8575e37e25f78cb52f66959839485 Mon Sep 17 00:00:00 2001
From: athomps <athomps@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 21 Jan 2016 01:58:43 +0000
Subject: [PATCH] Added faces as local compute
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14463 f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/VORONOI/compute_voronoi_atom.cpp | 67 +++++++++++++++++++++++++---
src/VORONOI/compute_voronoi_atom.h | 2 +
2 files changed, 62 insertions(+), 7 deletions(-)
diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp
index 052260895c..305a98716d 100644
--- a/src/VORONOI/compute_voronoi_atom.cpp
+++ b/src/VORONOI/compute_voronoi_atom.cpp
@@ -37,6 +37,8 @@
using namespace LAMMPS_NS;
using namespace voro;
+#define FACESDELTA 10000
+
/* ---------------------------------------------------------------------- */
ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
@@ -47,6 +49,7 @@ ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
size_peratom_cols = 2;
peratom_flag = 1;
comm_forward = 1;
+ faces_flag = 0;
surface = VOROSURF_NONE;
maxedge = 0;
@@ -59,6 +62,7 @@ ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
con_poly = NULL;
tags = NULL;
occvec = sendocc = lroot = lnext = NULL;
+ faces = NULL;
int iarg = 3;
while ( iarg<narg ) {
@@ -103,6 +107,12 @@ ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
if (iarg + 2 > narg) error->all(FLERR,"Illegal compute voronoi/atom command");
ethresh = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
+ } else if (strcmp(arg[iarg], "neighbors") == 0) {
+ if (iarg + 2 > narg) error->all(FLERR,"Illegal compute voronoi/atom command");
+ if (strcmp(arg[iarg+1],"yes") == 0) faces_flag = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) faces_flag = 0;
+ else error->all(FLERR,"Illegal compute voronoi/atom command");
+ iarg += 2;
}
else error->all(FLERR,"Illegal compute voronoi/atom command");
}
@@ -121,6 +131,14 @@ ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
memory->create(sendvector,maxedge+1,"voronoi/atom:sendvector");
vector = edge;
}
+
+ // store local face data: i, j, area
+
+ if (faces_flag) {
+ local_flag = 1;
+ size_local_cols = 3;
+ nfacesmax = 0;
+ }
}
/* ---------------------------------------------------------------------- */
@@ -145,6 +163,7 @@ ComputeVoronoi::~ComputeVoronoi()
memory->destroy(sendocc);
#endif
memory->destroy(tags);
+ memory->destroy(faces);
}
/* ---------------------------------------------------------------------- */
@@ -423,6 +442,7 @@ void ComputeVoronoi::loopCells()
// invoke voro++ and fetch results for owned atoms in group
voronoicell_neighbor c;
int i;
+ if (faces_flag) nfaces = 0;
if (radstr) {
c_loop_all cl(*con_poly);
if (cl.start()) do if (con_poly->compute_cell(c,cl)) {
@@ -436,6 +456,8 @@ void ComputeVoronoi::loopCells()
processCell(c,i);
} while (cl.inc());
}
+ if (faces_flag) size_local_rows = nfaces;
+
}
/* ----------------------------------------------------------------------
@@ -459,12 +481,6 @@ void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
c.neighbors(neigh);
int neighs = neigh.size();
-// // DEBUG CODE!!
-// // loop over all faces (neighbors)
-// for (j=0; j<neighs; ++j)
-// printf("neighbors %d %d %d\n",i,j,neigh[j]);
-// // END DEBUG CODE!!
-
if (fthresh > 0) {
// count only faces above area threshold
c.face_areas(narea);
@@ -486,7 +502,7 @@ void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
// each entry in neigh should correspond to an entry in narea
if (neighs != narea.size())
- error->all(FLERR,"Voro++ error: narea and neigh have a different size");
+ error->one(FLERR,"Voro++ error: narea and neigh have a different size");
// loop over all faces (neighbors) and check if they are in the surface group
for (j=0; j<neighs; ++j)
@@ -495,6 +511,7 @@ void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
}
// histogram of number of face edges
+
if (maxedge>0) {
if (ethresh > 0) {
// count only edges above length threshold
@@ -533,12 +550,48 @@ void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
}
}
}
+
+ // store info for local faces
+
+ if (faces_flag) {
+ if (nfaces+voro[i][1] > nfacesmax) {
+ while (nfacesmax < nfaces+voro[i][1]) nfacesmax += FACESDELTA;
+ memory->grow(faces,nfacesmax,size_local_cols,"compute/voronoi/atom:faces");
+ array_local = faces;
+ }
+
+ if (!have_narea) c.face_areas(narea);
+
+ if (neighs != narea.size())
+ error->one(FLERR,"Voro++ error: narea and neigh have a different size");
+ tagint itag, jtag;
+ tagint *tag = atom->tag;
+ itag = tag[i];
+ for (j=0; j<neighs; ++j)
+ if (narea[j] > fthresh) {
+
+ // external faces assigned the tag 0
+
+ int jj = neigh[j];
+ if (jj >= 0) jtag = tag[jj];
+ else jtag = 0;
+
+ faces[nfaces][0] = itag;
+ faces[nfaces][1] = jtag;
+ faces[nfaces][2] = narea[j];
+ nfaces++;
+ }
+ }
+
+
} 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);
+ // estimate based on average coordination of 12
+ if (faces_flag) bytes += 12 * size_local_cols * nmax * sizeof(double);
return bytes;
}
diff --git a/src/VORONOI/compute_voronoi_atom.h b/src/VORONOI/compute_voronoi_atom.h
index ca58eca574..086b0e2936 100644
--- a/src/VORONOI/compute_voronoi_atom.h
+++ b/src/VORONOI/compute_voronoi_atom.h
@@ -56,6 +56,8 @@ class ComputeVoronoi : public Compute {
tagint *tags;
int *occvec, *sendocc, *lroot, *lnext, lmax, oldnatoms, oldnall;
+ int faces_flag, nfaces, nfacesmax;
+ double **faces;
};
}
--
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