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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@679 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2007-06-26 21:47:46 +00:00
parent e9bbd83ca9
commit e361598ce7
4 changed files with 118 additions and 46 deletions
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63
src/fix_ave_spatial.cpp
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@ -33,6 +33,7 @@ using namespace LAMMPS_NS;
enum{LOWER,CENTER,UPPER,COORD};
enum{DENSITY_MASS,DENSITY_NUM,VX,VY,VZ,FX,FY,FZ,COMPUTE};
enum{SAMPLE,ALL};
enum{BOX,LATTICE,REDUCED};
/* ---------------------------------------------------------------------- */
@ -92,7 +93,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
// parse optional args
normflag = ALL;
int scaleflag = 1;
scaleflag = BOX;
int iarg = 11;
while (iarg < narg) {
@ -104,8 +105,9 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = BOX;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = LATTICE;
else if (strcmp(arg[iarg+1],"reduced") == 0) scaleflag = REDUCED;
else error->all("Illegal fix ave/spatial command");
iarg += 2;
} else error->all("Illegal fix ave/spatial command");
@ -119,10 +121,14 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
// setup scaling
if (scaleflag && domain->lattice == NULL)
int triclinic = domain->triclinic;
if (triclinic == 1 && scaleflag != REDUCED)
error->all("Fix ave/spatial for triclinic boxes requires units reduced");
if (scaleflag == LATTICE && domain->lattice == NULL)
error->all("Use of fix ave/spatial with undefined lattice");
if (scaleflag) {
if (scaleflag == LATTICE) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
@ -147,15 +153,6 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
if (delta <= 0.0) error->all("Illegal fix ave/spatial command");
invdelta = 1.0/delta;
if (domain->triclinic) {
if (dim == 0 && (domain->xy != 0.0 || domain->xz != 0.0))
error->all("Cannot (yet) use fix ave/spatial with triclinic box");
if (dim == 1 && (domain->xy != 0.0 || domain->yz != 0.0))
error->all("Cannot (yet) use fix ave/spatial with triclinic box");
if (dim == 2 && (domain->xz != 0.0 || domain->yz != 0.0))
error->all("Cannot (yet) use fix ave/spatial with triclinic box");
}
nvalues = 1;
if (which == COMPUTE) {
int icompute = modify->find_compute(id_compute);
@ -240,34 +237,42 @@ void FixAveSpatial::end_of_step()
// allocate and initialize arrays based on new layer count
if (nsum == 0) {
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
double *boxlo,*boxhi,*prd;
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 (originflag == LOWER) origin = boxlo[dim];
else if (originflag == UPPER) origin = boxhi[dim];
else if (originflag == CENTER)
origin = 0.5 * (boxlo[dim] + boxhi[dim]);
else if (originflag == CENTER) origin = 0.5 * (boxlo[dim] + boxhi[dim]);
if (origin < domain->boxlo[dim]) {
m = static_cast<int> ((domain->boxlo[dim] - origin) * invdelta);
if (origin < boxlo[dim]) {
m = static_cast<int> ((boxlo[dim] - origin) * invdelta);
lo = origin + m*delta;
} else {
m = static_cast<int> ((origin - domain->boxlo[dim]) * invdelta);
m = static_cast<int> ((origin - boxlo[dim]) * invdelta);
lo = origin - m*delta;
if (lo > domain->boxlo[dim]) lo -= delta;
if (lo > boxlo[dim]) lo -= delta;
}
if (origin < domain->boxhi[dim]) {
m = static_cast<int> ((domain->boxhi[dim] - origin) * invdelta);
if (origin < boxhi[dim]) {
m = static_cast<int> ((boxhi[dim] - origin) * invdelta);
hi = origin + m*delta;
if (hi < boxhi[dim]) hi += delta;
} else {
m = static_cast<int> ((origin - domain->boxhi[dim]) * invdelta);
m = static_cast<int> ((origin - boxhi[dim]) * invdelta);
hi = origin - m*delta;
}
offset = lo;
nlayers = static_cast<int> ((hi-lo) * invdelta + 0.5);
double volume = domain->xprd * domain->yprd * domain->zprd;
layer_volume = delta * volume/domain->prd[dim];
layer_volume = delta * volume/prd[dim];
if (nlayers > maxlayer) {
maxlayer = nlayers;
@ -307,6 +312,8 @@ void FixAveSpatial::end_of_step()
// perform the computation for one sample
// sum within each layer, only include atoms in fix group
// insure array index is within bounds (since atoms can be outside box)
// if scaleflag = REDUCED, convert box coords to lamda coords
// DENSITY_MASS adds mass to values
// DENSITY_NUM adds 1 to values
// ATOM adds atom vector to values
@ -316,6 +323,8 @@ void FixAveSpatial::end_of_step()
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
if (which == DENSITY_MASS) {
int *type = atom->type;
double *mass = atom->mass;
@ -386,6 +395,8 @@ void FixAveSpatial::end_of_step()
}
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
// average a single sample
if (normflag == ALL) {