Added faces as local compute (005f9d5a) · Commits · 郑智淋 / lammps

src/VORONOI/compute_voronoi_atom.cpp

+60 −7

Original line number	Diff line number	Diff line
		@@ -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;
		}

src/VORONOI/compute_voronoi_atom.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -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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