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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14423 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2016-01-11 23:38:16 +00:00
parent 681ebfaf8f
commit 12c8aaf29d
6 changed files with 288 additions and 15 deletions
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91
src/compute_chunk_atom.cpp
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@ -191,6 +191,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
maxflag[1] = UPPER;
maxflag[2] = UPPER;
scaleflag = LATTICE;
pbcflag = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
@ -269,6 +270,12 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg+1],"reduced") == 0) scaleflag = REDUCED;
else error->all(FLERR,"Illegal compute chunk/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"pbc") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
if (strcmp(arg[iarg+1],"no") == 0) pbcflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) pbcflag = 1;
else error->all(FLERR,"Illegal compute chunk/atom command");
iarg += 2;
} else error->all(FLERR,"Illegal compute chunk/atom command");
}
@ -1265,7 +1272,7 @@ int ComputeChunkAtom::setup_xyz_bins()
int ComputeChunkAtom::setup_sphere_bins()
{
// convert sorigin_user to sorigin
// sorigin is always in box units, for orthogonal or triclinic domains
// sorigin,srad are always in box units, for orthogonal or triclinic domains
// lamda2x works for either orthogonal or triclinic
if (scaleflag == REDUCED) {
@ -1280,6 +1287,23 @@ int ComputeChunkAtom::setup_sphere_bins()
sradmax = sradmax_user;
}
// if pbcflag set, sradmax must be < 1/2 box in any periodic dim
// treat orthongonal and triclinic the same
// check every time bins are created
if (pbcflag) {
double *prd_half = domain->prd_half;
int *periodicity = domain->periodicity;
int flag = 0;
if (periodicity[0] && sradmax > prd_half[0]) flag = 1;
if (periodicity[1] && sradmax > prd_half[1]) flag = 1;
if (domain->dimension == 3 &&
periodicity[2] && sradmax > prd_half[2]) flag = 1;
if (flag)
error->all(FLERR,"Compute chunk/atom bin/sphere radius "
"is too large for periodic box");
}
sinvrad = nsbin / (sradmax-sradmin);
// allocate and set bin coordinates
@ -1328,6 +1352,21 @@ int ComputeChunkAtom::setup_cylinder_bins()
cradmax = cradmax_user;
}
// if pbcflag set, sradmax must be < 1/2 box in any periodic non-axis dim
// treat orthongonal and triclinic the same
// check every time bins are created
if (pbcflag) {
double *prd_half = domain->prd_half;
int *periodicity = domain->periodicity;
int flag = 0;
if (periodicity[cdim1] && sradmax > prd_half[cdim1]) flag = 1;
if (periodicity[cdim2] && sradmax > prd_half[cdim2]) flag = 1;
if (flag)
error->all(FLERR,"Compute chunk/atom bin/cylinder radius "
"is too large for periodic box");
}
cinvrad = ncbin / (cradmax-cradmin);
// allocate and set radial bin coordinates
@ -1743,6 +1782,7 @@ void ComputeChunkAtom::atom2binsphere()
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
double *prd = domain->prd;
double *prd_half = domain->prd_half;
int *periodicity = domain->periodicity;
// remap each atom's relevant coords back into box via PBC if necessary
@ -1773,6 +1813,33 @@ void ComputeChunkAtom::atom2binsphere()
dx = xremap - sorigin[0];
dy = yremap - sorigin[1];
dz = zremap - sorigin[2];
// if requested, apply PBC to distance from sphere center
// treat orthogonal and triclinic the same
// with dx,dy,dz = lengths independent of each other
// so do not use domain->minimum_image() which couples for triclinic
if (pbcflag) {
if (periodicity[0]) {
if (fabs(dx) > prd_half[0]) {
if (dx < 0.0) dx += prd[0];
else dx -= prd[0];
}
}
if (periodicity[1]) {
if (fabs(dy) > prd_half[1]) {
if (dy < 0.0) dy += prd[1];
else dy -= prd[1];
}
}
if (periodicity[2]) {
if (fabs(dz) > prd_half[2]) {
if (dz < 0.0) dz += prd[2];
else dz -= prd[2];
}
}
}
r = sqrt(dx*dx + dy*dy + dz*dz);
ibin = static_cast<int> ((r - sradmin) * sinvrad);
@ -1792,7 +1859,6 @@ void ComputeChunkAtom::atom2binsphere()
/* ----------------------------------------------------------------------
assign each atom to a cylindrical bin
------------------------------------------------------------------------- */
void ComputeChunkAtom::atom2bincylinder()
@ -1812,6 +1878,7 @@ void ComputeChunkAtom::atom2bincylinder()
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
double *prd = domain->prd;
double *prd_half = domain->prd_half;
int *periodicity = domain->periodicity;
// remap each atom's relevant coords back into box via PBC if necessary
@ -1837,6 +1904,26 @@ void ComputeChunkAtom::atom2bincylinder()
d1 = remap1 - corigin[cdim1];
d2 = remap2 - corigin[cdim2];
// if requested, apply PBC to distance from cylinder axis
// treat orthogonal and triclinic the same
// with d1,d2 = lengths independent of each other
if (pbcflag) {
if (periodicity[cdim1]) {
if (fabs(d1) > prd_half[cdim1]) {
if (d1 < 0.0) d1 += prd[cdim1];
else d1 -= prd[cdim1];
}
}
if (periodicity[cdim2]) {
if (fabs(d2) > prd_half[cdim2]) {
if (d2 < 0.0) d2 += prd[cdim2];
else d2 -= prd[cdim2];
}
}
}
r = sqrt(d1*d1 + d2*d2);
rbin = static_cast<int> ((r - cradmin) * cinvrad);