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lammps/src/fix_ave_spatial.cpp

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "fix_ave_spatial.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "lattice.h"
#include "modify.h"
#include "compute.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{LOWER,CENTER,UPPER,COORD};
enum{DENSITY_MASS,DENSITY_NUM,VX,VY,VZ,FX,FY,FZ,COMPUTE};
enum{SAMPLE,ALL};
/* ---------------------------------------------------------------------- */
FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 11) error->all("Illegal fix ave/spatial command");
nevery = atoi(arg[3]);
nfreq = atoi(arg[4]);
if (strcmp(arg[5],"x") == 0) dim = 0;
else if (strcmp(arg[5],"y") == 0) dim = 1;
else if (strcmp(arg[5],"z") == 0) dim = 2;
else error->all("Illegal fix ave/spatial command");
if (strcmp(arg[6],"lower") == 0) originflag = LOWER;
if (strcmp(arg[6],"center") == 0) originflag = CENTER;
if (strcmp(arg[6],"upper") == 0) originflag = UPPER;
else originflag = COORD;
if (originflag == COORD) origin = atof(arg[6]);
delta = atof(arg[7]);
MPI_Comm_rank(world,&me);
if (me == 0) {
fp = fopen(arg[8],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ave/spatial file %s",arg[8]);
error->one(str);
}
}
if (strcmp(arg[9],"density") == 0) {
if (strcmp(arg[10],"mass") == 0) which = DENSITY_MASS;
else if (strcmp(arg[10],"number") == 0) which = DENSITY_NUM;
else error->all("Illegal fix ave/spatial command");
} else if (strcmp(arg[9],"atom") == 0) {
if (strcmp(arg[10],"vx") == 0) which = VX;
else if (strcmp(arg[10],"vy") == 0) which = VY;
else if (strcmp(arg[10],"vz") == 0) which = VZ;
else if (strcmp(arg[10],"fx") == 0) which = FX;
else if (strcmp(arg[10],"fy") == 0) which = FY;
else if (strcmp(arg[10],"fz") == 0) which = FZ;
else error->all("Illegal fix ave/spatial command");
} else if (strcmp(arg[9],"compute") == 0) {
which = COMPUTE;
int n = strlen(arg[10]) + 1;
id_compute = new char[n];
strcpy(id_compute,arg[10]);
} else error->all("Illegal fix ave/spatial command");
// parse optional args
normflag = ALL;
int scaleflag = 1;
int iarg = 11;
while (iarg < narg) {
if (strcmp(arg[iarg],"norm") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (strcmp(arg[iarg+1],"all") == 0) normflag = ALL;
else if (strcmp(arg[iarg+1],"sample") == 0) normflag = SAMPLE;
else error->all("Illegal fix ave/spatial command");
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;
else error->all("Illegal fix ave/spatial command");
iarg += 2;
} else error->all("Illegal fix ave/spatial command");
}
// if density, no normalization by atom count should be done
// thus ALL and SAMPLE should give same answer, but code does normalize
// thus only ALL is computed correctly, so force norm to be ALL
if (which == DENSITY_MASS || which == DENSITY_NUM) normflag = ALL;
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all("Use of fix ave/spatial with undefined lattice");
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// apply scaling factors
double scale;
if (dim == 0) scale = xscale;
if (dim == 1) scale = yscale;
if (dim == 2) scale = zscale;
delta *= scale;
if (originflag == COORD) origin *= scale;
// setup and error check
if (nevery <= 0) error->all("Illegal fix ave/spatial command");
if (nfreq < nevery || nfreq % nevery)
error->all("Illegal fix ave/spatial command");
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);
if (icompute < 0)
error->all("Compute ID for fix ave/spatial does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Fix ave/spatial compute does not calculate per-atom info");
nvalues = compute_size_peratom = modify->compute[icompute]->size_peratom;
if (nvalues == 0) nvalues = 1;
}
if (me == 0) {
fprintf(fp,"Spatial-averaged data for fix %s, group %s, and %s %s\n",
id,group->names[igroup],arg[9],arg[10]);
fprintf(fp,"TimeStep Number-of-layers (one per snapshot)\n");
fprintf(fp,"Layer Coord Atoms Value(s) (one per layer)\n");
}
nsum = nlayers = maxlayer = 0;
coord = NULL;
count_one = count_many = count_total = NULL;
values_one = values_many = values_total = NULL;
}
/* ---------------------------------------------------------------------- */
FixAveSpatial::~FixAveSpatial()
{
if (which == COMPUTE) delete [] id_compute;
if (me == 0) fclose(fp);
memory->sfree(coord);
memory->sfree(count_one);
memory->sfree(count_many);
memory->sfree(count_total);
memory->destroy_2d_double_array(values_one);
memory->destroy_2d_double_array(values_many);
memory->destroy_2d_double_array(values_total);
}
/* ---------------------------------------------------------------------- */
int FixAveSpatial::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAveSpatial::init()
{
// set ptrs to current compute and precompute
if (which == COMPUTE) {
int icompute = modify->find_compute(id_compute);
if (icompute < 0)
error->all("Compute ID for fix ave/spatial does not exist");
compute = modify->compute[icompute];
if (compute->id_pre) {
icompute = modify->find_compute(compute->id_pre);
if (icompute < 0)
error->all("Precompute ID for fix ave/spatial does not exist");
precompute = modify->compute[icompute];
} else precompute = NULL;
}
}
/* ---------------------------------------------------------------------- */
void FixAveSpatial::end_of_step()
{
int i,j,m,ilayer,nstide;
double lo,hi;
// if computing the first sample, setup layers
// compute current origin = boundary for some layer
// lo = layer boundary immediately below boxlo
// hi = layer boundary immediately above boxhi
// allocate and initialize arrays based on new layer count
if (nsum == 0) {
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
if (originflag == LOWER) origin = boxlo[dim];
else if (originflag == UPPER) origin = 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);
lo = origin + m*delta;
} else {
m = static_cast<int> ((origin - domain->boxlo[dim]) * invdelta);
lo = origin - m*delta;
if (lo > domain->boxlo[dim]) lo -= delta;
}
if (origin < domain->boxhi[dim]) {
m = static_cast<int> ((domain->boxhi[dim] - origin) * invdelta);
hi = origin + m*delta;
if (hi < boxhi[dim]) hi += delta;
} else {
m = static_cast<int> ((origin - domain->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];
if (nlayers > maxlayer) {
maxlayer = nlayers;
coord = (double *) memory->srealloc(coord,nlayers*sizeof(double),
"ave/spatial:coord");
count_one = (double *)
memory->srealloc(count_one,nlayers*sizeof(double),
"ave/spatial:count_one");
count_many = (double *)
memory->srealloc(count_many,nlayers*sizeof(double),
"ave/spatial:count_many");
count_total = (double *)
memory->srealloc(count_total,nlayers*sizeof(double),
"ave/spatial:count_total");
values_one = memory->grow_2d_double_array(values_one,nlayers,nvalues,
"ave/spatial:values_one");
values_many = memory->grow_2d_double_array(values_many,nlayers,nvalues,
"ave/spatial:values_many");
values_total = memory->grow_2d_double_array(values_total,nlayers,nvalues,
"ave/spatial:values_total");
}
for (m = 0; m < nlayers; m++) {
coord[m] = offset + (m+0.5)*delta;
count_many[m] = count_total[m] = 0.0;
for (i = 0; i < nvalues; i++) values_many[m][i] = 0.0;
}
}
// zero out arrays for one sample
nsum++;
for (m = 0; m < nlayers; m++) {
count_one[m] = 0.0;
for (i = 0; i < nvalues; i++) values_one[m][i] = 0.0;
}
// perform the computation for one sample
// sum within each layer, only include atoms in fix group
// DENSITY_MASS adds mass
// DENSITY_NUM adds 1 to values
// ATOM adds atom vector to values
// COMPUTE adds its vector to values
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (which == DENSITY_MASS) {
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[dim][i] - offset) * invdelta);
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
count_one[ilayer] += 1.0;
if (mass) values_one[ilayer][0] += mass[type[i]];
else values_one[ilayer][0] += rmass[i];
}
}
} else if (which == DENSITY_NUM) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[dim][i] - offset) * invdelta);
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
count_one[ilayer] += 1.0;
values_one[ilayer][0] += 1.0;
}
}
} else if (which != COMPUTE) {
double *vector;
int nstride = 3;
if (which == VX) vector = &atom->v[0][0];
else if (which == VY) vector = &atom->v[0][1];
else if (which == VZ) vector = &atom->v[0][2];
else if (which == FX) vector = &atom->f[0][0];
else if (which == FY) vector = &atom->f[0][1];
else if (which == FZ) vector = &atom->f[0][2];
m = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[dim][i] - offset) * invdelta);
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
count_one[ilayer] += 1.0;
values_one[ilayer][0] += vector[m];
}
m += nstride;
}
} else {
if (precompute) precompute->compute_peratom();
compute->compute_peratom();
double *scalar = compute->scalar_atom;
double **vector = compute->vector_atom;
m = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[dim][i] - offset) * invdelta);
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
count_one[ilayer] += 1.0;
if (compute_size_peratom == 0) values_one[ilayer][0] += scalar[i];
else
for (j = 0; j < nvalues; j++)
values_one[ilayer][j] += vector[i][j];
}
}
}
// average a single sample
if (normflag == ALL) {
for (m = 0; m < nlayers; m++) {
count_many[m] += count_one[m];
for (j = 0; j < nvalues; j++)
values_many[m][j] += values_one[m][j];
}
} else {
MPI_Allreduce(count_one,count_many,nlayers,MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nlayers; m++) {
if (count_many[m] > 0.0)
for (j = 0; j < nvalues; j++)
values_many[m][j] += values_one[m][j]/count_many[m];
count_total[m] += count_many[m];
}
}
// output the results
// time average across samples
// if density, also normalize by volume
if (update->ntimestep % nfreq == 0) {
if (normflag == ALL) {
MPI_Allreduce(count_many,count_total,nlayers,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&values_many[0][0],&values_total[0][0],nlayers*nvalues,
MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nlayers; m++) {
if (count_total[m] > 0.0)
for (j = 0; j < nvalues; j++)
values_total[m][j] /= count_total[m];
count_total[m] /= nsum;
}
} else {
MPI_Allreduce(&values_many[0][0],&values_total[0][0],nlayers*nvalues,
MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nlayers; m++) {
for (j = 0; j < nvalues; j++)
values_total[m][j] /= nsum;
count_total[m] /= nsum;
}
}
if (which == DENSITY_MASS || which == DENSITY_NUM) {
for (m = 0; m < nlayers; m++)
values_total[m][0] *= count_total[m] / layer_volume;
}
if (me == 0) {
fprintf(fp,"%d %d\n",update->ntimestep,nlayers);
for (m = 0; m < nlayers; m++) {
fprintf(fp," %d %g %g",m+1,coord[m],count_total[m]);
for (i = 0; i < nvalues; i++) fprintf(fp," %g",values_total[m][i]);
fprintf(fp,"\n");
}
}
nsum = 0;
}
}
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