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bug fix for compute voronoi with triclinic simulation boxes #3702

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Mar 23, 2023
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bug fix for compute voronoi with triclinic simulation boxes #3702

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82 changes: 55 additions & 27 deletions src/VORONOI/compute_voronoi_atom.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -234,15 +234,18 @@ void ComputeVoronoi::compute_peratom()
}
}

/* ---------------------------------------------------------------------- */

void ComputeVoronoi::buildCells()
{
int i;
const double e = 0.01;
const double EPS = 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)
for (i = 0; i < nlocal; i++) voro[i][0] = voro[i][1] = 0.0;
Expand All @@ -256,36 +259,37 @@ void ComputeVoronoi::buildCells()
double sublo_bound[3], subhi_bound[3];
double **x = atom->x;

// setup bounds for voro++ domain for orthogonal and triclinic simulation boxes
// setup bounds for each processor's Voro++ domain

// triclinic box
// embed parallelepiped into orthogonal voro++ domain
// cutghost is in lamda coordinates for triclinic boxes, use sub*_lamda

if (domain->triclinic) {
// triclinic box: embed parallelepiped into orthogonal voro++ domain

// cutghost is in lamda coordinates for triclinic boxes, use subxx_lamda
double *h = domain->h;
for (i=0; i<3; ++i) {
sublo_bound[i] = sublo_lamda[i]-cut[i]-e;
subhi_bound[i] = subhi_lamda[i]+cut[i]+e;
if (domain->periodicity[i]==0) {
sublo_bound[i] = MAX(sublo_bound[i],0.0);
subhi_bound[i] = MIN(subhi_bound[i],1.0);

double sublo_bound_lamda[3], subhi_bound_lamda[3];
for (i = 0; i < 3; ++i) {
sublo_bound_lamda[i] = sublo_lamda[i] - cut[i] - EPS;
subhi_bound_lamda[i] = subhi_lamda[i] + cut[i] + EPS;
if (domain->periodicity[i] == 0) {
sublo_bound_lamda[i] = MAX(sublo_bound_lamda[i], 0.0);
subhi_bound_lamda[i] = MIN(subhi_bound_lamda[i], 1.0);
}
}
if (dim == 2) {
sublo_bound[2] = 0.0;
subhi_bound[2] = 1.0;
sublo_bound_lamda[2] = 0.0;
subhi_bound_lamda[2] = 1.0;
}
sublo_bound[0] = h[0]*sublo_bound[0] + h[5]*sublo_bound[1] + h[4]*sublo_bound[2] + boxlo[0];
sublo_bound[1] = h[1]*sublo_bound[1] + h[3]*sublo_bound[2] + boxlo[1];
sublo_bound[2] = h[2]*sublo_bound[2] + boxlo[2];
subhi_bound[0] = h[0]*subhi_bound[0] + h[5]*subhi_bound[1] + h[4]*subhi_bound[2] + boxlo[0];
subhi_bound[1] = h[1]*subhi_bound[1] + h[3]*subhi_bound[2] + boxlo[1];
subhi_bound[2] = h[2]*subhi_bound[2] + boxlo[2];

domain->bbox(sublo_bound_lamda,subhi_bound_lamda,sublo_bound,subhi_bound);

// orthogonal box

} else {
// orthogonal box
for (i=0; i<3; ++i) {
sublo_bound[i] = sublo[i]-cut[i]-e;
subhi_bound[i] = subhi[i]+cut[i]+e;
sublo_bound[i] = sublo[i]-cut[i] - EPS;
subhi_bound[i] = subhi[i]+cut[i] + EPS;
if (domain->periodicity[i]==0) {
sublo_bound[i] = MAX(sublo_bound[i],domain->boxlo[i]);
subhi_bound[i] = MIN(subhi_bound[i],domain->boxhi[i]);
Expand All @@ -298,6 +302,7 @@ void ComputeVoronoi::buildCells()
}

// 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];
Expand All @@ -308,33 +313,43 @@ void ComputeVoronoi::buildCells()
}

// clear edge statistics

if (maxedge > 0)
for (i = 0; i <= maxedge; ++i) edge[i]=0;

// initialize voro++ container
// preallocates 8 atoms per cell
// voro++ allocates more memory if needed
// Voro++ allocates more memory if needed

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 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 (atom->nmax > 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(this);

// polydisperse voro++ container
// polydisperse Voro++ container

delete con_poly;
con_poly = new container_poly(sublo_bound[0],
subhi_bound[0],
Expand All @@ -345,13 +360,16 @@ void ComputeVoronoi::buildCells()
int(n[0]),int(n[1]),int(n[2]),
false,false,false,8);

// pass coordinates for local and ghost atoms to voro++
// pass coordinates for local and ghost atoms to Voro++

for (i = 0; i < nall; i++) {
if (!onlyGroup || (mask[i] & groupbit))
con_poly->put(i,x[i][0],x[i][1],x[i][2],rfield[i]);
}

// monodisperse Voro++ container

} else {
// monodisperse voro++ container
delete con_mono;

con_mono = new container(sublo_bound[0],
Expand All @@ -363,13 +381,16 @@ void ComputeVoronoi::buildCells()
int(n[0]),int(n[1]),int(n[2]),
false,false,false,8);

// pass coordinates for local and ghost atoms to voro++
// pass coordinates for local and ghost atoms to Voro++

for (i = 0; i < nall; i++)
if (!onlyGroup || (mask[i] & groupbit))
con_mono->put(i,x[i][0],x[i][1],x[i][2]);
}
}

/* ---------------------------------------------------------------------- */

void ComputeVoronoi::checkOccupation()
{
// clear occupation vector
Expand Down Expand Up @@ -455,6 +476,8 @@ void ComputeVoronoi::checkOccupation()
}
}

/* ---------------------------------------------------------------------- */

void ComputeVoronoi::loopCells()
{
// invoke voro++ and fetch results for owned atoms in group
Expand All @@ -481,6 +504,7 @@ void ComputeVoronoi::loopCells()
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */

void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
{
int j,k, *mask = atom->mask;
Expand Down Expand Up @@ -605,6 +629,8 @@ void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
} else if (i < atom->nlocal) voro[i][0] = voro[i][1] = 0.0;
}

/* ---------------------------------------------------------------------- */

double ComputeVoronoi::memory_usage()
{
double bytes = (double)size_peratom_cols * nmax * sizeof(double);
Expand All @@ -613,6 +639,8 @@ double ComputeVoronoi::memory_usage()
return bytes;
}

/* ---------------------------------------------------------------------- */

void ComputeVoronoi::compute_vector()
{
invoked_vector = update->ntimestep;
Expand Down