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fix_ave_spatial.cpp
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Wed, Nov 13, 01:27

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,COMPUTE,FIX};
enum{SAMPLE,ALL};
enum{BOX,LATTICE,REDUCED};
enum{ONE,RUNNING,WINDOW};
#define BIG 1000000000
/* ---------------------------------------------------------------------- */
FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 11) error->all("Illegal fix ave/spatial command");
MPI_Comm_rank(world,&me);
no_change_box = 1;
nevery = atoi(arg[3]);
nrepeat = atoi(arg[4]);
nfreq = atoi(arg[5]);
if (strcmp(arg[6],"x") == 0) dim = 0;
else if (strcmp(arg[6],"y") == 0) dim = 1;
else if (strcmp(arg[6],"z") == 0) dim = 2;
else error->all("Illegal fix ave/spatial command");
if (strcmp(arg[7],"lower") == 0) originflag = LOWER;
if (strcmp(arg[7],"center") == 0) originflag = CENTER;
if (strcmp(arg[7],"upper") == 0) originflag = UPPER;
else originflag = COORD;
if (originflag == COORD) origin = atof(arg[6]);
delta = atof(arg[8]);
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],"compute") == 0) {
which = COMPUTE;
int n = strlen(arg[10]) + 1;
id_compute = new char[n];
strcpy(id_compute,arg[10]);
} else if (strcmp(arg[9],"fix") == 0) {
which = FIX;
int n = strlen(arg[10]) + 1;
id_fix = new char[n];
strcpy(id_fix,arg[10]);
} else error->all("Illegal fix ave/spatial command");
// parse optional args
normflag = ALL;
scaleflag = BOX;
fp = NULL;
ave = ONE;
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 = 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 if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ave/spatial file %s",arg[iarg+1]);
error->one(str);
}
}
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
else error->all("Illegal fix ave/spatial command");
if (ave == WINDOW) {
if (iarg+3 > narg) error->all("Illegal fix ave/spatial command");
nwindow = atoi(arg[iarg+2]);
if (nwindow <= 0) error->all("Illegal fix ave/spatial command");
}
iarg += 2;
if (ave == WINDOW) iarg++;
} 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
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 == LATTICE) {
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 || (nrepeat-1)*nevery >= nfreq)
error->all("Illegal fix ave/spatial command");
if (delta <= 0.0) error->all("Illegal fix ave/spatial command");
invdelta = 1.0/delta;
// nvalues = # of quantites per line of output file
// for COMPUTE, setup list of computes to call, including pre-computes
nvalues = 1;
compute = NULL;
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 = size_peratom = modify->compute[icompute]->size_peratom;
if (nvalues == 0) nvalues = 1;
ncompute = 1 + modify->compute[icompute]->npre;
compute = new Compute*[ncompute];
}
if (which == FIX) {
int ifix = modify->find_fix(id_fix);
if (ifix < 0)
error->all("Fix ID for fix ave/spatial does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all("Fix ave/spatial fix does not calculate per-atom info");
nvalues = size_peratom = modify->fix[ifix]->size_peratom;
if (nvalues == 0) nvalues = 1;
}
// print header into file
if (fp && me == 0) {
fprintf(fp,"Spatial-averaged data for fix %s, group %s, and %s %s\n",
id,group->names[igroup],arg[10],arg[11]);
fprintf(fp,"TimeStep Number-of-layers (one per snapshot)\n");
fprintf(fp,"Layer Coord Atoms Value(s) (one per layer)\n");
}
// enable this fix to produce a global vector
// set size_vector to BIG since compute_vector() will check bounds
vector_flag = 1;
size_vector = BIG;
scalar_vector_freq = nfreq;
extensive = 0;
// initializations
irepeat = 0;
iwindow = window_limit = 0;
norm = 0;
nlayers = maxlayer = 0;
coord = NULL;
count_one = count_many = count_sum = count_total = NULL;
count_list = NULL;
values_one = values_many = values_sum = values_total = NULL;
values_list = NULL;
// nvalid = next step on which end_of_step does something
// can be this timestep if multiple of nfreq and nrepeat = 1
// else backup from next multiple of nfreq
nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
if (nvalid-nfreq == update->ntimestep && nrepeat == 1)
nvalid = update->ntimestep;
else
nvalid -= (nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += nfreq;
}
/* ---------------------------------------------------------------------- */
FixAveSpatial::~FixAveSpatial()
{
if (which == COMPUTE) delete [] id_compute;
if (which == FIX) delete [] id_fix;
if (fp && me == 0) fclose(fp);
delete [] compute;
memory->sfree(coord);
memory->sfree(count_one);
memory->sfree(count_many);
memory->sfree(count_sum);
memory->sfree(count_total);
memory->destroy_2d_double_array(count_list);
memory->destroy_2d_double_array(values_one);
memory->destroy_2d_double_array(values_many);
memory->destroy_2d_double_array(values_sum);
memory->destroy_2d_double_array(values_total);
memory->destroy_3d_double_array(values_list);
}
/* ---------------------------------------------------------------------- */
int FixAveSpatial::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAveSpatial::init()
{
// # of layers cannot vary for ave = RUNNING or WINDOW
if (ave == RUNNING || ave == WINDOW) {
if (scaleflag != REDUCED && domain->box_change)
error->all("Fix ave/spatial settings invalid with changing box");
}
// set ptrs to compute and its pre-computes called each end-of-step
// put pre-computes in list before compute
if (which == COMPUTE) {
int icompute = modify->find_compute(id_compute);
if (icompute < 0)
error->all("Compute ID for fix ave/spatial does not exist");
ncompute = 0;
if (modify->compute[icompute]->npre)
for (int i = 0; i < modify->compute[icompute]->npre; i++) {
int ic = modify->find_compute(modify->compute[icompute]->id_pre[i]);
if (ic < 0)
error->all("Precompute ID for fix ave/spatial does not exist");
compute[ncompute++] = modify->compute[ic];
}
compute[ncompute++] = modify->compute[icompute];
}
// set ptr to fix ID
// check that fix frequency is acceptable
if (which == FIX) {
int ifix = modify->find_fix(id_fix);
if (ifix < 0)
error->all("Fix ID for fix ave/spatial does not exist");
fix = modify->fix[ifix];
if (nevery % fix->peratom_freq)
error->all("Fix ave/spatial and fix not computed at compatible times");
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveSpatial::setup()
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveSpatial::end_of_step()
{
int i,j,m,ilayer;
double lo,hi;
// skip if not step which requires doing something
if (update->ntimestep != nvalid) return;
// 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 (irepeat == 0) {
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]);
if (origin < boxlo[dim]) {
m = static_cast<int> ((boxlo[dim] - origin) * invdelta);
lo = origin + m*delta;
} else {
m = static_cast<int> ((origin - boxlo[dim]) * invdelta);
lo = origin - m*delta;
if (lo > boxlo[dim]) lo -= delta;
}
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 - 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/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_sum = (double *)
memory->srealloc(count_sum,nlayers*sizeof(double),
"ave/spatial:count_sum");
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_sum = memory->grow_2d_double_array(values_sum,nlayers,nvalues,
"ave/spatial:values_sum");
values_total = memory->grow_2d_double_array(values_total,nlayers,nvalues,
"ave/spatial:values_total");
// initialize count and values total to zero since they accumulate
for (m = 0; m < nlayers; m++) {
for (i = 0; i < nvalues; i++) values_total[m][i] = 0.0;
count_total[m] = 0.0;
}
// only allocate count and values list for ave = WINDOW
// only happens once since nlayers never changes for these ave settings
if (ave == WINDOW) {
count_list =
memory->create_2d_double_array(nwindow,nlayers,
"ave/spatial:count_list");
values_list =
memory->create_3d_double_array(nwindow,nlayers,nvalues,
"ave/spatial:values_list");
}
}
for (m = 0; m < nlayers; m++) {
coord[m] = offset + (m+0.5)*delta;
count_many[m] = count_sum[m] = 0.0;
for (i = 0; i < nvalues; i++) values_many[m][i] = 0.0;
}
}
// zero out arrays for one sample
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
// insure array index is within bounds (since atoms can be outside box)
// if scaleflag = REDUCED, box coords -> lamda coords before computing layer
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// DENSITY_MASS adds mass to values
if (which == DENSITY_MASS) {
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[i][dim] - 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];
}
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
// DENSITY_NUM adds 1 to values
} else if (which == DENSITY_NUM) {
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[i][dim] - offset) * invdelta);
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
count_one[ilayer] += 1.0;
values_one[ilayer][0] += 1.0;
}
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
// COMPUTE adds its scalar or vector quantity to values
} else if (which == COMPUTE) {
for (i = 0; i < ncompute; i++) compute[i]->compute_peratom();
double *scalar = compute[ncompute-1]->scalar_atom;
double **vector = compute[ncompute-1]->vector_atom;
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
m = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[i][dim] - offset) * invdelta);
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
count_one[ilayer] += 1.0;
if (size_peratom == 0) values_one[ilayer][0] += scalar[i];
else
for (j = 0; j < nvalues; j++)
values_one[ilayer][j] += vector[i][j];
}
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
// FIX adds its scalar or vector quantity to values
} else if (which == FIX) {
double *scalar = fix->scalar_atom;
double **vector = fix->vector_atom;
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
m = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ilayer = static_cast<int> ((x[i][dim] - offset) * invdelta);
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
count_one[ilayer] += 1.0;
if (size_peratom == 0) values_one[ilayer][0] += scalar[i];
else
for (j = 0; j < nvalues; j++)
values_one[ilayer][j] += vector[i][j];
}
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
}
// 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_sum[m] += count_many[m];
}
}
// done if irepeat < nrepeat
irepeat++;
nvalid += nevery;
if (irepeat < nrepeat) return;
// time average across samples
// if density, also normalize by volume
double repeat = nrepeat;
if (normflag == ALL) {
MPI_Allreduce(count_many,count_sum,nlayers,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nlayers*nvalues,
MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nlayers; m++) {
if (count_sum[m] > 0.0)
for (j = 0; j < nvalues; j++)
values_sum[m][j] /= count_sum[m];
count_sum[m] /= repeat;
}
} else {
MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nlayers*nvalues,
MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nlayers; m++) {
for (j = 0; j < nvalues; j++)
values_sum[m][j] /= repeat;
count_sum[m] /= repeat;
}
}
if (which == DENSITY_MASS || which == DENSITY_NUM) {
for (m = 0; m < nlayers; m++)
values_sum[m][0] *= count_sum[m] / layer_volume;
}
// reset irepeat and nvalid
irepeat = 0;
nvalid = update->ntimestep+nfreq - (nrepeat-1)*nevery;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, comine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
for (m = 0; m < nlayers; m++) {
for (i = 0; i < nvalues; i++)
values_total[m][i] = values_sum[m][i];
count_total[m] = count_sum[m];
}
norm = 1;
} else if (ave == RUNNING) {
for (m = 0; m < nlayers; m++) {
for (i = 0; i < nvalues; i++)
values_total[m][i] += values_sum[m][i];
count_total[m] += count_sum[m];
}
norm++;
} else if (ave == WINDOW) {
for (m = 0; m < nlayers; m++) {
for (i = 0; i < nvalues; i++) {
values_total[m][i] += values_sum[m][i];
if (window_limit) values_total[m][i] -= values_list[iwindow][m][i];
values_list[iwindow][m][i] = values_sum[m][i];
}
count_total[m] += count_sum[m];
if (window_limit) count_total[m] -= count_list[iwindow][m];
count_list[iwindow][m] = count_sum[m];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
// output result to file
if (fp && 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]/norm);
for (i = 0; i < nvalues; i++) fprintf(fp," %g",values_total[m][i]/norm);
fprintf(fp,"\n");
}
fflush(fp);
}
}
/* ----------------------------------------------------------------------
return Nth vector value
since values_sum is 2d array, map N into ilayer and ivalue
if ilayer >= nlayers, just return 0, since nlayers can vary with time
------------------------------------------------------------------------- */
double FixAveSpatial::compute_vector(int n)
{
int ivalue = n % nvalues;
int ilayer = n / nvalues;
if (ilayer < nlayers && norm) return values_total[ilayer][ivalue]/norm;
return 0.0;
}

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