ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2141 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2008-10-01 23:34:10 +00:00
parent 820f667f2e
commit 96ec6bbbc8
1 changed files with 24 additions and 2 deletions
Download Patch File Download Diff File Expand all files Collapse all files

26
src/fix_ave_spatial.cpp
View File

@ -524,13 +524,14 @@ void FixAveSpatial::end_of_step()
} }
// assign each atom to a layer // assign each atom to a layer
// insure array index is within bounds (since atoms can be outside box) // remap each atom's relevant coord back into box via PBC if necessary
// if scaleflag = REDUCED, box coords -> lamda coords // if scaleflag = REDUCED, box coords -> lamda coords
double **x = atom->x; double **x = atom->x;
int *mask = atom->mask; int *mask = atom->mask;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
if (nlocal > maxatomlayer) { if (nlocal > maxatomlayer) {
maxatomlayer = atom->nmax; maxatomlayer = atom->nmax;
memory->sfree(layer); memory->sfree(layer);
@ -538,11 +539,32 @@ void FixAveSpatial::end_of_step()
memory->smalloc(maxatomlayer*sizeof(int),"ave/spatial:layer"); memory->smalloc(maxatomlayer*sizeof(int),"ave/spatial:layer");
} }
double *boxlo,*boxhi,*prd;
double xremap;
int periodicity = domain->periodicity[dim];
if (periodicity) {
if (scaleflag == REDUCED) {
boxlo = domain->boxlo_lamda;
boxhi = domain->boxhi_lamda;
prd = domain->prd_lamda;
} else {
boxlo = domain->boxlo;
boxhi = domain->boxhi;
prd = domain->prd;
}
}
if (scaleflag == REDUCED) domain->x2lamda(nlocal); if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++) for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[i][dim] - offset) * invdelta); xremap = x[i][dim];
if (periodicity) {
if (xremap < boxlo[dim]) xremap += prd[dim];
if (xremap >= boxhi[dim]) xremap -= prd[dim];
}
ilayer = static_cast<int> ((xremap - offset) * invdelta);
if (ilayer < 0) ilayer = 0; if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1; if (ilayer >= nlayers) ilayer = nlayers-1;
layer[i] = ilayer; layer[i] = ilayer;