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lammps/src/fix_ave_correlate.cpp
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fix_ave_correlate.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 authors:
Benoit Leblanc, Dave Rigby, Paul Saxe (Materials Design)
Reese Jones (Sandia)
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include "fix_ave_correlate.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{COMPUTE,FIX,VARIABLE};
enum{ONE,RUNNING};
enum{AUTO,UPPER,LOWER,AUTOUPPER,AUTOLOWER,FULL};
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
/* ---------------------------------------------------------------------- */
FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
Fix (lmp, narg, arg)
{
if (narg < 7) error->all(FLERR,"Illegal fix ave/correlate command");
MPI_Comm_rank(world,&me);
nevery = force->inumeric(FLERR,arg[3]);
nrepeat = force->inumeric(FLERR,arg[4]);
nfreq = force->inumeric(FLERR,arg[5]);
global_freq = nfreq;
// expand args if any have wildcard character "*"
int expand = 0;
char **earg;
int nargnew = input->expand_args(narg-6,&arg[6],0,earg);
if (earg != &arg[6]) expand = 1;
arg = earg;
// parse values until one isn't recognized
which = new int[nargnew];
argindex = new int[nargnew];
ids = new char*[nargnew];
value2index = new int[nargnew];
nvalues = 0;
int iarg = 0;
while (iarg < nargnew) {
if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal fix ave/correlate command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
delete [] suffix;
nvalues++;
iarg++;
} else break;
}
// optional args
type = AUTO;
ave = ONE;
startstep = 0;
prefactor = 1.0;
fp = NULL;
overwrite = 0;
char *title1 = NULL;
char *title2 = NULL;
char *title3 = NULL;
while (iarg < nargnew) {
if (strcmp(arg[iarg],"type") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command");
if (strcmp(arg[iarg+1],"auto") == 0) type = AUTO;
else if (strcmp(arg[iarg+1],"upper") == 0) type = UPPER;
else if (strcmp(arg[iarg+1],"lower") == 0) type = LOWER;
else if (strcmp(arg[iarg+1],"auto/upper") == 0) type = AUTOUPPER;
else if (strcmp(arg[iarg+1],"auto/lower") == 0) type = AUTOLOWER;
else if (strcmp(arg[iarg+1],"full") == 0) type = FULL;
else error->all(FLERR,"Illegal fix ave/correlate command");
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command");
if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
else error->all(FLERR,"Illegal fix ave/correlate command");
iarg += 2;
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command");
startstep = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"prefactor") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command");
prefactor = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ave/correlate file %s",arg[iarg+1]);
error->one(FLERR,str);
}
}
iarg += 2;
} else if (strcmp(arg[iarg],"overwrite") == 0) {
overwrite = 1;
iarg += 1;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command");
delete [] title1;
int n = strlen(arg[iarg+1]) + 1;
title1 = new char[n];
strcpy(title1,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
title2 = new char[n];
strcpy(title2,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command");
delete [] title3;
int n = strlen(arg[iarg+1]) + 1;
title3 = new char[n];
strcpy(title3,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix ave/correlate command");
}
// setup and error check
// for fix inputs, check that fix frequency is acceptable
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all(FLERR,"Illegal fix ave/correlate command");
if (nfreq % nevery)
error->all(FLERR,"Illegal fix ave/correlate command");
if (ave == ONE && nfreq < (nrepeat-1)*nevery)
error->all(FLERR,"Illegal fix ave/correlate command");
if (ave != RUNNING && overwrite)
error->all(FLERR,"Illegal fix ave/correlate command");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/correlate does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
error->all(FLERR,
"Fix ave/correlate compute does not calculate a scalar");
if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
error->all(FLERR,
"Fix ave/correlate compute does not calculate a vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
error->all(FLERR,"Fix ave/correlate compute vector "
"is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/correlate does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
error->all(FLERR,"Fix ave/correlate fix does not calculate a scalar");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
error->all(FLERR,"Fix ave/correlate fix does not calculate a vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
error->all(FLERR,
"Fix ave/correlate fix vector is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all(FLERR,"Fix for fix ave/correlate "
"not computed at compatible time");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix ave/correlate does not exist");
if (argindex[i] == 0 && input->variable->equalstyle(ivariable) == 0)
error->all(FLERR,
"Fix ave/correlate variable is not equal-style variable");
if (argindex[i] && input->variable->vectorstyle(ivariable) == 0)
error->all(FLERR,
"Fix ave/correlate variable is not vector-style variable");
}
}
// npair = # of correlation pairs to calculate
if (type == AUTO) npair = nvalues;
if (type == UPPER || type == LOWER) npair = nvalues*(nvalues-1)/2;
if (type == AUTOUPPER || type == AUTOLOWER) npair = nvalues*(nvalues+1)/2;
if (type == FULL) npair = nvalues*nvalues;
// print file comment lines
if (fp && me == 0) {
clearerr(fp);
if (title1) fprintf(fp,"%s\n",title1);
else fprintf(fp,"# Time-correlated data for fix %s\n",id);
if (title2) fprintf(fp,"%s\n",title2);
else fprintf(fp,"# Timestep Number-of-time-windows\n");
if (title3) fprintf(fp,"%s\n",title3);
else {
fprintf(fp,"# Index TimeDelta Ncount");
if (type == AUTO)
for (int i = 0; i < nvalues; i++)
fprintf(fp," %s*%s",earg[i],earg[i]);
else if (type == UPPER)
for (int i = 0; i < nvalues; i++)
for (int j = i+1; j < nvalues; j++)
fprintf(fp," %s*%s",earg[i],earg[j]);
else if (type == LOWER)
for (int i = 0; i < nvalues; i++)
for (int j = 0; j < i-1; j++)
fprintf(fp," %s*%s",earg[i],earg[j]);
else if (type == AUTOUPPER)
for (int i = 0; i < nvalues; i++)
for (int j = i; j < nvalues; j++)
fprintf(fp," %s*%s",earg[i],earg[j]);
else if (type == AUTOLOWER)
for (int i = 0; i < nvalues; i++)
for (int j = 0; j < i; j++)
fprintf(fp," %s*%s",earg[i],earg[j]);
else if (type == FULL)
for (int i = 0; i < nvalues; i++)
for (int j = 0; j < nvalues; j++)
fprintf(fp," %s*%s",earg[i],earg[j]);
fprintf(fp,"\n");
}
if (ferror(fp))
error->one(FLERR,"Error writing file header");
filepos = ftell(fp);
}
delete [] title1;
delete [] title2;
delete [] title3;
// if wildcard expansion occurred, free earg memory from expand_args()
// wait to do this until after file comment lines are printed
if (expand) {
for (int i = 0; i < nargnew; i++) delete [] earg[i];
memory->sfree(earg);
}
// allocate and initialize memory for averaging
// set count and corr to zero since they accumulate
// also set save versions to zero in case accessed via compute_array()
memory->create(values,nrepeat,nvalues,"ave/correlate:values");
memory->create(count,nrepeat,"ave/correlate:count");
memory->create(save_count,nrepeat,"ave/correlate:save_count");
memory->create(corr,nrepeat,npair,"ave/correlate:corr");
memory->create(save_corr,nrepeat,npair,"ave/correlate:save_corr");
int i,j;
for (i = 0; i < nrepeat; i++) {
save_count[i] = count[i] = 0;
for (j = 0; j < npair; j++)
save_corr[i][j] = corr[i][j] = 0.0;
}
// this fix produces a global array
array_flag = 1;
size_array_rows = nrepeat;
size_array_cols = npair+2;
extarray = 0;
// nvalid = next step on which end_of_step does something
// add nvalid to all computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can set timestep for ones actually invoked
lastindex = -1;
firstindex = 0;
nsample = 0;
nvalid_last = -1;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
/* ---------------------------------------------------------------------- */
FixAveCorrelate::~FixAveCorrelate()
{
delete [] which;
delete [] argindex;
delete [] value2index;
for (int i = 0; i < nvalues; i++) delete [] ids[i];
delete [] ids;
memory->destroy(values);
memory->destroy(count);
memory->destroy(save_count);
memory->destroy(corr);
memory->destroy(save_corr);
if (fp && me == 0) fclose(fp);
}
/* ---------------------------------------------------------------------- */
int FixAveCorrelate::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAveCorrelate::init()
{
// set current indices for all computes,fixes,variables
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/correlate does not exist");
value2index[i] = icompute;
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/correlate does not exist");
value2index[i] = ifix;
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix ave/correlate does not exist");
value2index[i] = ivariable;
}
}
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
lastindex = -1;
firstindex = 0;
nsample = 0;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveCorrelate::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveCorrelate::end_of_step()
{
int i,j,m;
double scalar;
// 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/correlate");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
// accumulate results of computes,fixes,variables to origin
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
// lastindex = index in values ring of latest time sample
lastindex++;
if (lastindex == nrepeat) lastindex = 0;
for (i = 0; i < nvalues; i++) {
m = value2index[i];
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[i] == 0) {
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= INVOKED_SCALAR;
}
scalar = compute->scalar;
} else {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
scalar = compute->vector[argindex[i]-1];
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
if (argindex[i] == 0)
scalar = modify->fix[m]->compute_scalar();
else
scalar = modify->fix[m]->compute_vector(argindex[i]-1);
// evaluate equal-style or vector-style variable
} else if (which[i] == VARIABLE) {
if (argindex[i] == 0)
scalar = input->variable->compute_equal(m);
else {
double *varvec;
int nvec = input->variable->compute_vector(m,&varvec);
int index = argindex[i];
if (nvec < index) scalar = 0.0;
else scalar = varvec[index-1];
}
}
values[lastindex][i] = scalar;
}
// fistindex = index in values ring of earliest time sample
// nsample = number of time samples in values ring
if (nsample < nrepeat) nsample++;
else {
firstindex++;
if (firstindex == nrepeat) firstindex = 0;
}
nvalid += nevery;
modify->addstep_compute(nvalid);
// calculate all Cij() enabled by latest values
accumulate();
if (ntimestep % nfreq) return;
// save results in save_count and save_corr
for (i = 0; i < nrepeat; i++) {
save_count[i] = count[i];
if (count[i])
for (j = 0; j < npair; j++)
save_corr[i][j] = prefactor*corr[i][j]/count[i];
else
for (j = 0; j < npair; j++)
save_corr[i][j] = 0.0;
}
// output result to file
if (fp && me == 0) {
clearerr(fp);
if (overwrite) fseek(fp,filepos,SEEK_SET);
fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nrepeat);
for (i = 0; i < nrepeat; i++) {
fprintf(fp,"%d %d %d",i+1,i*nevery,count[i]);
if (count[i])
for (j = 0; j < npair; j++)
fprintf(fp," %g",prefactor*corr[i][j]/count[i]);
else
for (j = 0; j < npair; j++)
fprintf(fp," 0.0");
fprintf(fp,"\n");
}
if (ferror(fp))
error->one(FLERR,"Error writing out correlation data");
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
if (fileend > 0) ftruncate(fileno(fp),fileend);
}
}
// zero accumulation if requested
// recalculate Cij(0)
if (ave == ONE) {
for (i = 0; i < nrepeat; i++) {
count[i] = 0;
for (j = 0; j < npair; j++)
corr[i][j] = 0.0;
}
nsample = 1;
accumulate();
}
}
/* ----------------------------------------------------------------------
accumulate correlation data using more recently added values
------------------------------------------------------------------------- */
void FixAveCorrelate::accumulate()
{
int i,j,k,m,n,ipair;
for (k = 0; k < nsample; k++) count[k]++;
if (type == AUTO) {
m = n = lastindex;
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++) {
corr[k][ipair++] += values[m][i]*values[n][i];
}
m--;
if (m < 0) m = nrepeat-1;
}
} else if (type == UPPER) {
m = n = lastindex;
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
for (j = i+1; j < nvalues; j++)
corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
} else if (type == LOWER) {
m = n = lastindex;
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
for (j = 0; j < i; j++)
corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
} else if (type == AUTOUPPER) {
m = n = lastindex;
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
for (j = i; j < nvalues; j++)
corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
} else if (type == AUTOLOWER) {
m = n = lastindex;
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
for (j = 0; j <= i; j++)
corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
} else if (type == FULL) {
m = n = lastindex;
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
for (j = 0; j < nvalues; j++)
corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
}
}
/* ----------------------------------------------------------------------
return I,J array value
------------------------------------------------------------------------- */
double FixAveCorrelate::compute_array(int i, int j)
{
if (j == 0) return 1.0*i*nevery;
else if (j == 1) return 1.0*save_count[i];
else if (save_count[i]) return save_corr[i][j-2];
return 0.0;
}
/* ----------------------------------------------------------------------
nvalid = next step on which end_of_step does something
this step if multiple of nevery, else next multiple
startstep is lower bound
------------------------------------------------------------------------- */
bigint FixAveCorrelate::nextvalid()
{
bigint nvalid = update->ntimestep;
if (startstep > nvalid) nvalid = startstep;
if (nvalid % nevery) nvalid = (nvalid/nevery)*nevery + nevery;
return nvalid;
}
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