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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13673 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-07-22 15:20:12 +00:00
parent b4a8019ee8
commit 60cd71620a
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562
src/fix_ave_histo_weight.cpp Normal file
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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.
------------------------------------------------------------------------- */
#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/weights: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)
bin_atoms_weights(&atom->x[0][j],3,weights,stride);
else if (which[i] == V)
bin_atoms_weights(&atom->v[0][j],3,weights,stride);
else if (which[i] == F)
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/weights: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) {
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);
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
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;
}
}

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src/fix_ave_histo_weight.h Normal file
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/* -*- c++ -*- ----------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(ave/histo/weight,FixAveHistoWeight)
#else
#ifndef LMP_FIX_AVE_HISTO_WEIGHT_H
#define LMP_FIX_AVE_HISTO_WEIGHT_H
#include "stdio.h"
#include "fix_ave_histo.h"
namespace LAMMPS_NS {
class FixAveHistoWeight : public FixAveHisto {
public:
FixAveHistoWeight(class LAMMPS *, int, char **);
~FixAveHistoWeight() {}
void end_of_step();
private:
void bin_one_weights(double, double);
void bin_vector_weights(int, double *, int, double *, int);
void bin_atoms_weights(double *, int, double *, int);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Compute ID for fix ave/histo does not exist
Self-explanatory.
E: Fix ID for fix ave/histo does not exist
Self-explanatory.
E: Fix ave/histo input is invalid compute
Self-explanatory.
E: Fix ave/histo input is invalid fix
Self-explanatory.
E: Fix ave/histo input is invalid variable
Self-explanatory.
E: Fix ave/histo inputs are not all global, peratom, or local
All inputs in a single fix ave/histo command must be of the
same style.
E: Fix ave/histo cannot input per-atom values in scalar mode
Self-explanatory.
E: Fix ave/histo cannot input local values in scalar mode
Self-explanatory.
E: Fix ave/histo compute does not calculate a global scalar
Self-explanatory.
E: Fix ave/histo compute does not calculate a global vector
Self-explanatory.
E: Fix ave/histo compute vector is accessed out-of-range
Self-explanatory.
E: Fix ave/histo compute does not calculate a global array
Self-explanatory.
E: Fix ave/histo compute array is accessed out-of-range
Self-explanatory.
E: Fix ave/histo compute does not calculate per-atom values
Self-explanatory.
E: Fix ave/histo compute does not calculate a per-atom vector
Self-explanatory.
E: Fix ave/histo compute does not calculate a per-atom array
Self-explanatory.
E: Fix ave/histo compute does not calculate local values
Self-explanatory.
E: Fix ave/histo compute does not calculate a local vector
Self-explanatory.
E: Fix ave/histo compute does not calculate a local array
Self-explanatory.
E: Fix ave/histo fix does not calculate a global scalar
Self-explanatory.
E: Fix ave/histo fix does not calculate a global vector
Self-explanatory.
E: Fix ave/histo fix vector is accessed out-of-range
Self-explanatory.
E: Fix for fix ave/histo not computed at compatible time
Fixes generate their values on specific timesteps. Fix ave/histo is
requesting a value on a non-allowed timestep.
E: Fix ave/histo fix does not calculate a global array
Self-explanatory.
E: Fix ave/histo fix array is accessed out-of-range
Self-explanatory.
E: Fix ave/histo fix does not calculate per-atom values
Self-explanatory.
E: Fix ave/histo fix does not calculate a per-atom vector
Self-explanatory.
E: Fix ave/histo fix does not calculate a per-atom array
Self-explanatory.
E: Fix ave/histo fix does not calculate local values
Self-explanatory.
E: Fix ave/histo fix does not calculate a local vector
Self-explanatory.
E: Fix ave/histo fix does not calculate a local array
Self-explanatory.
E: Variable name for fix ave/histo does not exist
Self-explanatory.
E: Invalid timestep reset for fix ave/histo
Resetting the timestep has invalidated the sequence of timesteps this
fix needs to process.
E: Cannot open fix ave/histo file %s
The specified file cannot be opened. Check that the path and name are
correct.
*/