Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F69801999
fix_ave_histo_weight.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Jul 3, 14:16
Size
17 KB
Mime Type
text/x-c
Expires
Fri, Jul 5, 14:16 (2 d)
Engine
blob
Format
Raw Data
Handle
18755543
Attached To
rLAMMPS lammps
fix_ave_histo_weight.cpp
View Options
/* ----------------------------------------------------------------------
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: Shawn Coleman (ARL)
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include "fix_ave_histo_weight.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{X,V,F,COMPUTE,FIX,VARIABLE};
enum{ONE,RUNNING};
enum{SCALAR,VECTOR,WINDOW};
enum{GLOBAL,PERATOM,LOCAL};
enum{IGNORE,END,EXTRA};
enum{SINGLE,VALUE};
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
#define INVOKED_PERATOM 8
#define INVOKED_LOCAL 16
#define BIG 1.0e20
/* ---------------------------------------------------------------------- */
FixAveHistoWeight::FixAveHistoWeight(LAMMPS *lmp, int narg, char **arg) :
FixAveHisto(lmp, narg, arg)
{
// nvalues = 2 required for histo/weight
if (nvalues != 2) error->all(FLERR,"Illegal fix ave/histo/weight command");
// check that length of 2 values is the same
int size[2];
for (int i = 0; i < nvalues; i++) {
if (which[i] == X || which[i] == V || which[i] == F) {
size[i] = atom->nlocal;
} else if (which[i] == COMPUTE && kind == GLOBAL && mode == SCALAR) {
int icompute = modify->find_compute(ids[i]);
size[i] = modify->compute[icompute]->size_vector;
} else if (which[i] == COMPUTE && kind == GLOBAL && mode == VECTOR) {
int icompute = modify->find_compute(ids[i]);
size[i] = modify->compute[icompute]->size_array_rows;
} else if (which[i] == COMPUTE && kind == PERATOM) {
size[i] = atom->nlocal;
} else if (which[i] == COMPUTE && kind == LOCAL) {
int icompute = modify->find_compute(ids[i]);
size[i] = modify->compute[icompute]->size_local_rows;
} else if (which[i] == FIX && kind == GLOBAL && mode == SCALAR) {
int ifix = modify->find_fix(ids[i]);
size[i] = modify->fix[ifix]->size_vector;
} else if (which[i] == FIX && kind == GLOBAL && mode == VECTOR) {
int ifix = modify->find_fix(ids[i]);
size[i]= modify->fix[ifix]->size_array_rows;
} else if (which[i] == FIX && kind == PERATOM) {
size[i] = atom->nlocal;
} else if (which[i] == FIX && kind == LOCAL) {
int ifix = modify->find_fix(ids[i]);
size[i] = modify->fix[ifix]->size_local_rows;
} else if (which[i] == VARIABLE && kind == PERATOM) {
size[i] = atom->nlocal;
}
}
if (size[0] != size[1])
error->all(FLERR,"Fix ave/histo/weight value and weight vector "
"lengths do not match");
}
/* ---------------------------------------------------------------------- */
void FixAveHistoWeight::end_of_step()
{
int i,j,m;
// skip if not step which requires doing something
// error check if timestep was reset in an invalid manner
bigint ntimestep = update->ntimestep;
if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep reset for fix ave/histo");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
// zero if first step
if (irepeat == 0) {
stats[0] = stats[1] = 0.0;
stats[2] = BIG;
stats[3] = -BIG;
for (i = 0; i < nbins; i++) bin[i] = 0.0;
}
// first calculate weight factors, then bin single value
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
// calcualte weight factors which are 2nd value (i = 1)
double weight = 0.0;
double *weights = NULL;
int stride = 0;
i = 1;
m = value2index[i];
j = argindex[i];
// atom attributes
if (which[i] == X) {
weights = &atom->x[0][j];
stride = 3;
} else if (which[i] == V){
weights = &atom->v[0][j];
stride = 3;
bin_atoms(&atom->v[0][j],3);
} else if (which[i] == F) {
weights = &atom->f[0][j];
stride = 3;
}
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) {
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= INVOKED_SCALAR;
}
weight = compute->scalar;
} else {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
weight = compute->vector[j-1];
}
} else if (kind == GLOBAL && mode == VECTOR) {
if (j == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
weights = compute->vector;
stride = 1;
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
if (compute->array) weights = &compute->array[0][j-1];
stride = compute->size_array_cols;
}
} else if (kind == PERATOM) {
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
if (j == 0) {
weights = compute->vector_atom;
stride = 1;
} else if (compute->array_atom) {
weights = &compute->array_atom[0][j-1];
stride = compute->size_peratom_cols;
}
} else if (kind == LOCAL) {
if (!(compute->invoked_flag & INVOKED_LOCAL)) {
compute->compute_local();
compute->invoked_flag |= INVOKED_LOCAL;
}
if (j == 0) {
weights = compute->vector_local;
stride = 1;
} else if (compute->array_local) {
weights = &compute->array_local[0][j-1];
stride = compute->size_local_cols;
}
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
Fix *fix = modify->fix[m];
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) weight = fix->compute_scalar();
else weight = fix->compute_vector(j-1);
} else if (kind == GLOBAL && mode == VECTOR) {
error->all(FLERR,"Illegal fix ave/spatial command");
if (j == 0) {
int n = fix->size_vector;
for (i = 0; i < n; i++) weights[n] = fix->compute_vector(i);
} else {
int n = fix->size_vector;
for (i = 0; i < n; i++) weights[n] = fix->compute_array(i,j-1);
}
} else if (kind == PERATOM) {
if (j == 0) {
weights = fix->vector_atom;
stride = 1;
} else if (fix->array_atom) {
weights = fix->array_atom[j-1];
stride = fix->size_peratom_cols;
}
} else if (kind == LOCAL) {
if (j == 0) {
weights = fix->vector_local;
stride = 1;
} else if (fix->array_local) {
weights = &fix->array_local[0][j-1];
stride = fix->size_local_cols;
}
}
// evaluate equal-style variable
} else if (which[i] == VARIABLE && kind == GLOBAL) {
weight = input->variable->compute_equal(m);
} else if (which[i] == VARIABLE && kind == PERATOM) {
if (atom->nlocal > maxatom) {
memory->destroy(vector);
maxatom = atom->nmax;
memory->create(vector,maxatom,"ave/histo/weight:vector");
}
input->variable->compute_atom(m,igroup,vector,1,0);
weights = vector;
stride = 1;
}
// bin values using weights, values are 1st value (i = 0)
i = 0;
m = value2index[i];
j = argindex[i];
// atom attributes
if (which[i] == X && weights != NULL)
bin_atoms_weights(&atom->x[0][j],3,weights,stride);
else if (which[i] == V && weights != NULL)
bin_atoms_weights(&atom->v[0][j],3,weights,stride);
else if (which[i] == F && weights != NULL)
bin_atoms_weights(&atom->f[0][j],3,weights,stride);
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) {
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= INVOKED_SCALAR;
}
bin_one_weights(compute->scalar,weight);
} else {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
bin_one_weights(compute->vector[j-1],weight);
}
} else if (kind == GLOBAL && mode == VECTOR) {
if (j == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
bin_vector_weights(compute->size_vector,compute->vector,1,
weights,stride);
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
if (compute->array)
bin_vector_weights(compute->size_array_rows,&compute->array[0][j-1],
compute->size_array_cols,weights,stride);
}
} else if (kind == PERATOM) {
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
if (j == 0)
bin_atoms_weights(compute->vector_atom,1,weights, stride);
else if (compute->array_atom)
bin_atoms_weights(&compute->array_atom[0][j-1],
compute->size_peratom_cols,weights,stride);
} else if (kind == LOCAL) {
if (!(compute->invoked_flag & INVOKED_LOCAL)) {
compute->compute_local();
compute->invoked_flag |= INVOKED_LOCAL;
}
if (j == 0)
bin_vector_weights(compute->size_local_rows,
compute->vector_local,1,weights,stride);
else if (compute->array_local)
bin_vector_weights(compute->size_local_rows,
&compute->array_local[0][j-1],
compute->size_local_cols,weights,stride);
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
Fix *fix = modify->fix[m];
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) bin_one_weights(fix->compute_scalar(),weight);
else bin_one_weights(fix->compute_vector(j-1),weight);
} else if (kind == GLOBAL && mode == VECTOR) {
if (j == 0) {
int n = fix->size_vector;
for (i = 0; i < n; i++)
bin_one_weights(fix->compute_vector(i),weights[i*stride]);
} else {
int n = fix->size_vector;
for (i = 0; i < n; i++)
bin_one_weights(fix->compute_array(i,j-1),weights[i*stride]);
}
} else if (kind == PERATOM) {
if (j == 0)
bin_atoms_weights(fix->vector_atom,1,weights,stride);
else if (fix->array_atom)
bin_atoms_weights(fix->array_atom[j-1],fix->size_peratom_cols,
weights,stride);
} else if (kind == LOCAL) {
if (j == 0) bin_vector_weights(fix->size_local_rows,fix->vector_local,1,
weights,stride);
else if (fix->array_local)
bin_vector_weights(fix->size_local_rows,&fix->array_local[0][j-1],
fix->size_local_cols,weights,stride);
}
// evaluate equal-style variable
} else if (which[i] == VARIABLE && kind == GLOBAL) {
bin_one_weights(input->variable->compute_equal(m),weight);
} else if (which[i] == VARIABLE && kind == PERATOM) {
if (atom->nlocal > maxatom) {
memory->destroy(vector);
maxatom = atom->nmax;
memory->create(vector,maxatom,"ave/histo/weight:vector");
}
input->variable->compute_atom(m,igroup,vector,1,0);
bin_atoms_weights(vector,1,weights,stride);
}
// code beyond this point is identical to FixAveHisto
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep + nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// merge histogram stats across procs if necessary
if (kind == PERATOM || kind == LOCAL) {
MPI_Allreduce(stats,stats_all,2,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&stats[2],&stats_all[2],1,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(&stats[3],&stats_all[3],1,MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(bin,bin_all,nbins,MPI_DOUBLE,MPI_SUM,world);
stats[0] = stats_all[0];
stats[1] = stats_all[1];
stats[2] = stats_all[2];
stats[3] = stats_all[3];
for (i = 0; i < nbins; i++) bin[i] = bin_all[i];
}
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
stats_total[0] = stats[0];
stats_total[1] = stats[1];
stats_total[2] = stats[2];
stats_total[3] = stats[3];
for (i = 0; i < nbins; i++) bin_total[i] = bin[i];
} else if (ave == RUNNING) {
stats_total[0] += stats[0];
stats_total[1] += stats[1];
stats_total[2] = MIN(stats_total[2],stats[2]);
stats_total[3] = MAX(stats_total[3],stats[3]);
for (i = 0; i < nbins; i++) bin_total[i] += bin[i];
} else if (ave == WINDOW) {
stats_total[0] += stats[0];
if (window_limit) stats_total[0] -= stats_list[iwindow][0];
stats_list[iwindow][0] = stats[0];
stats_total[1] += stats[1];
if (window_limit) stats_total[1] -= stats_list[iwindow][1];
stats_list[iwindow][1] = stats[1];
if (window_limit) m = nwindow;
else m = iwindow+1;
stats_list[iwindow][2] = stats[2];
stats_total[2] = stats_list[0][2];
for (i = 1; i < m; i++)
stats_total[2] = MIN(stats_total[2],stats_list[i][2]);
stats_list[iwindow][3] = stats[3];
stats_total[3] = stats_list[0][3];
for (i = 1; i < m; i++)
stats_total[3] = MAX(stats_total[3],stats_list[i][3]);
for (i = 0; i < nbins; i++) {
bin_total[i] += bin[i];
if (window_limit) bin_total[i] -= bin_list[iwindow][i];
bin_list[iwindow][i] = bin[i];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
}
// output result to file
if (fp && me == 0) {
clearerr(fp);
if (overwrite) fseek(fp,filepos,SEEK_SET);
fprintf(fp,BIGINT_FORMAT " %d %g %g %g %g\n",ntimestep,nbins,
stats_total[0],stats_total[1],stats_total[2],stats_total[3]);
if (stats_total[0] != 0.0)
for (i = 0; i < nbins; i++)
fprintf(fp,"%d %g %g %g\n",
i+1,coord[i],bin_total[i],bin_total[i]/stats_total[0]);
else
for (i = 0; i < nbins; i++)
fprintf(fp,"%d %g %g %g\n",i+1,coord[i],0.0,0.0);
if (ferror(fp))
error->one(FLERR,"Error writing out histogram data");
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
if (fileend > 0) ftruncate(fileno(fp),fileend);
}
}
}
/* ----------------------------------------------------------------------
bin a single value with weight)
------------------------------------------------------------------------- */
void FixAveHistoWeight::bin_one_weights(double value, double weight)
{
stats[2] = MIN(stats[2],value);
stats[3] = MAX(stats[3],value);
if (value < lo) {
if (beyond == IGNORE) {
stats[1] += weight;
return;
} else bin[0] += weight;
} else if (value > hi) {
if (beyond == IGNORE) {
stats[1] += weight;
return;
} else bin[nbins-1] += weight;
} else {
int ibin = static_cast<int> ((value-lo)*bininv);
ibin = MIN(ibin,nbins-1);
if (beyond == EXTRA) ibin++;
bin[ibin] += weight;
}
stats[0] += weight;
}
/* ----------------------------------------------------------------------
bin a vector of values with weights
values and weights each have a stride
------------------------------------------------------------------------- */
void FixAveHistoWeight::bin_vector_weights(int n, double *values,
int stride, double *weights,
int stridewt)
{
int m = 0;
int m2 = 0;
for (int i = 0; i < n; i++) {
bin_one_weights(values[m],weights[m2]);
m += stride;
m2 += stridewt;
}
}
/* ----------------------------------------------------------------------
bin a per-atom vector of values with weights
values and weights each have a stride
only bin if atom is in group
------------------------------------------------------------------------- */
void FixAveHistoWeight::bin_atoms_weights(double *values, int stride,
double *weights, int stridewt)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m = 0;
int m2 = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) bin_one_weights(values[m],weights[m2]);
m += stride;
m2 += stridewt;
}
}
Event Timeline
Log In to Comment