mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12152 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
3b1a73c3bd
commit
635d42c51f
|
|
@ -42,7 +42,7 @@ ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
|
|||
Compute(lmp, narg, arg)
|
||||
{
|
||||
int sgroup;
|
||||
|
||||
|
||||
size_peratom_cols = 2;
|
||||
peratom_flag = 1;
|
||||
|
||||
|
|
@ -63,18 +63,18 @@ ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
|
|||
if (strcmp(arg[iarg], "occupation") == 0) {
|
||||
occupation = true;
|
||||
iarg++;
|
||||
}
|
||||
}
|
||||
else 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
|
||||
|
|
@ -83,7 +83,7 @@ ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
|
|||
} 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];
|
||||
sgroupbit = group->bitmask[sgroup];
|
||||
surface = VOROSURF_GROUP;
|
||||
}
|
||||
size_peratom_cols = 3;
|
||||
|
|
@ -100,12 +100,12 @@ ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
|
|||
if (iarg + 2 > narg) error->all(FLERR,"Missing minimum edge length after keyword 'edge_threshold'.");
|
||||
ethresh = force->numeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
}
|
||||
else
|
||||
}
|
||||
else
|
||||
error->all(FLERR,"Illegal compute voronoi/atom command");
|
||||
}
|
||||
|
||||
if (occupation && ( surface!=VOROSURF_NONE || maxedge>0 ) )
|
||||
if (occupation && ( surface!=VOROSURF_NONE || maxedge>0 ) )
|
||||
error->all(FLERR,"Illegal compute voronoi/atom command (occupation and (surface or edges))");
|
||||
|
||||
nmax = rmax = 0;
|
||||
|
|
@ -183,9 +183,9 @@ void ComputeVoronoi::compute_peratom()
|
|||
// linked list structure for cell occupation count on the atoms
|
||||
oldnall= nall;
|
||||
memory->create(lroot,nall,"voronoi/atom:lroot"); // point to first atom index in cell (or -1 for empty cell)
|
||||
lnext = NULL;
|
||||
lnext = NULL;
|
||||
lmax = 0;
|
||||
|
||||
|
||||
// build the occupation buffer
|
||||
oldnatoms = atom->natoms;
|
||||
memory->create(occvec,oldnatoms,"voronoi/atom:occvec");
|
||||
|
|
@ -208,11 +208,12 @@ void ComputeVoronoi::buildCells()
|
|||
int i;
|
||||
const double e = 0.01;
|
||||
int nlocal = atom->nlocal;
|
||||
int dim = domain->dimension;
|
||||
|
||||
// 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)
|
||||
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;
|
||||
|
|
@ -223,7 +224,7 @@ void ComputeVoronoi::buildCells()
|
|||
double *cut = comm->cutghost;
|
||||
double sublo_bound[3], subhi_bound[3], cut_bound[3];
|
||||
double **x = atom->x;
|
||||
|
||||
|
||||
// setup bounds for voro++ domain for orthogonal and triclinic simulation boxes
|
||||
if( domain->triclinic ) {
|
||||
// triclinic box: embed parallelepiped into orthogonal voro++ domain
|
||||
|
|
@ -257,7 +258,7 @@ void ComputeVoronoi::buildCells()
|
|||
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];
|
||||
}
|
||||
}
|
||||
|
||||
// clear edge statistics
|
||||
for (i = 0; i < maxedge; ++i) edge[i]=0;
|
||||
|
|
@ -289,8 +290,8 @@ void ComputeVoronoi::buildCells()
|
|||
delete con_poly;
|
||||
con_poly = new container_poly(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);
|
||||
sublo_bound[2]-(dim==3 ? cut_bound[2]-e : 0.0),subhi_bound[2]+(dim==3 ? cut_bound[2]+e : 0.0),
|
||||
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++)
|
||||
|
|
@ -301,8 +302,8 @@ void ComputeVoronoi::buildCells()
|
|||
delete con_mono;
|
||||
con_mono = new container(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);
|
||||
sublo_bound[2]-(dim==3 ? cut_bound[2]-e : 0.0),subhi_bound[2]+(dim==3 ? cut_bound[2]+e : 0.0),
|
||||
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++)
|
||||
|
|
@ -346,12 +347,12 @@ void ComputeVoronoi::checkOccupation()
|
|||
if (i<nlocal) occvec[tags[k]-1]++;
|
||||
|
||||
// add this atom to the linked list of cell j
|
||||
if (lroot[k]<0)
|
||||
if (lroot[k]<0)
|
||||
lroot[k]=i;
|
||||
else {
|
||||
j = lroot[k];
|
||||
while (lnext[j]>=0) j=lnext[j];
|
||||
lnext[j] = i;
|
||||
lnext[j] = i;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -382,7 +383,7 @@ void ComputeVoronoi::checkOccupation()
|
|||
}
|
||||
}
|
||||
|
||||
// cherry pick currently owned atoms
|
||||
// cherry pick currently owned atoms
|
||||
for (i=0; i<nlocal; i++) {
|
||||
// set the new atom count in the atom's first frame voronoi cell
|
||||
voro[i][0] = occvec[atom->tag[i]-1];
|
||||
|
|
@ -412,7 +413,7 @@ void ComputeVoronoi::loopCells()
|
|||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
|
||||
void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
|
||||
{
|
||||
int j,k, *mask = atom->mask;
|
||||
std::vector<int> neigh, norder, vlist;
|
||||
|
|
@ -428,16 +429,18 @@ void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
|
|||
|
||||
// number of cell faces
|
||||
c.neighbors(neigh);
|
||||
int neighs = neigh.size();
|
||||
|
||||
if (fthresh > 0) {
|
||||
// count only faces above area threshold
|
||||
c.face_areas(narea);
|
||||
have_narea = true;
|
||||
voro[i][1] = 0.0;
|
||||
for (j=0; j<narea.size(); ++j)
|
||||
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();
|
||||
voro[i][1] = neighs;
|
||||
}
|
||||
|
||||
// cell surface area
|
||||
|
|
@ -446,23 +449,29 @@ void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
|
|||
} else if (surface == VOROSURF_GROUP) {
|
||||
if (!have_narea) c.face_areas(narea);
|
||||
voro[i][2] = 0.0;
|
||||
|
||||
// each entry in neigh should correspond to amn entry in narea
|
||||
if (neighs != narea.size())
|
||||
error->all(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<voro[i][1]; ++j)
|
||||
if (mask[neigh[j]] & sgroupbit) voro[i][2] += narea[j];
|
||||
for (j=0; j<neighs; ++j)
|
||||
if (neigh[j] >= 0 && 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
|
||||
// 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 ) {
|
||||
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
|
||||
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];
|
||||
|
|
@ -472,7 +481,7 @@ void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
|
|||
}
|
||||
// counted edges above threshold, now put into the correct bin
|
||||
if (nedge>0) {
|
||||
if (nedge<=maxedge)
|
||||
if (nedge<=maxedge)
|
||||
edge[nedge-1]++;
|
||||
else
|
||||
edge[maxedge]++;
|
||||
|
|
@ -483,7 +492,7 @@ void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
|
|||
c.face_orders(norder);
|
||||
for (j=0; j<voro[i][1]; ++j)
|
||||
if (norder[j]>0) {
|
||||
if (norder[j]<=maxedge)
|
||||
if (norder[j]<=maxedge)
|
||||
edge[norder[j]-1]++;
|
||||
else
|
||||
edge[maxedge]++;
|
||||
|
|
@ -526,4 +535,3 @@ void ComputeVoronoi::unpack_comm(int n, int first, double *buf)
|
|||
last = first + n;
|
||||
for (i = first; i < last; i++) rfield[i] = buf[m++];
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue