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lammps/src/USER-MISC/fix_ave_correlate_long.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:
Jorge Ramirez (jorge.ramirez@upm.es, Universidad Politecnica de Madrid),
Alexei Likhtman (University of Reading)
Structure and syntax of fix inspired by fix_ave_correlate
Scalar Correlator f(tau)=<A(t)A(t+tau)> and
Cross-correlator f(tau)=<A(t)B(t+tau)>
see J. Chem. Phys. 133, 154103 (2010)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include "fix_ave_correlate_long.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "citeme.h"
#include "memory.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{COMPUTE,FIX,VARIABLE};
enum{AUTO,UPPER,LOWER,AUTOUPPER,AUTOLOWER,FULL};
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
static const char cite_fix_ave_correlate_long[] =
"fix ave/correlate/long command:\n\n"
"@Article{Ramirez10,\n"
" author = {Jorge Rami{\'}rez and Sathish K. Sukumaran and Bart Vorselaars and Alexei E. Likhtman},\n"
" title = {Efficient on the fly calculation of time correlation functions in computer simulations},"
" journal = {J.~Chem.~Phys.},\n"
" year = 2010,\n"
" volume = 133,\n"
" pages = {154103}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
Fix (lmp, narg, arg)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_ave_correlate_long);
// At least nevery nfrez and one value are needed
if (narg < 6) error->all(FLERR,"Illegal fix ave/correlate/long command");
MPI_Comm_rank(world,&me);
nevery = force->inumeric(FLERR,arg[3]);
nfreq = force->inumeric(FLERR,arg[4]);
restart_global = 1;
global_freq = nfreq;
// parse values until one isn't recognized
which = new int[narg-5];
argindex = new int[narg-5];
ids = new char*[narg-5];
value2index = new int[narg-5];
nvalues = 0;
int iarg = 5;
while (iarg < narg) {
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/long 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;
startstep = 0;
fp = NULL;
overwrite = 0;
numcorrelators=20;
p = 16;
m = 2;
char *title1 = NULL;
char *title2 = NULL;
while (iarg < narg) {
if (strcmp(arg[iarg],"type") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long 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/long command");
iarg += 2;
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long command");
startstep = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"ncorr") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long command");
numcorrelators = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"nlen") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long command");
p = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"ncount") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long command");
m = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ave/correlate/long 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/long 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/long command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
title2 = new char[n];
strcpy(title2,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix ave/correlate/long command");
}
if (p % m != 0) error->all(FLERR,"fix_correlator: p mod m must be 0");
dmin = p/m;
length = numcorrelators*p;
npcorr = 0;
kmax = 0;
// setup and error check
// for fix inputs, check that fix frequency is acceptable
if (nevery <= 0 || nfreq <= 0)
error->all(FLERR,"Illegal fix ave/correlate/long command");
if (nfreq % nevery)
error->all(FLERR,"Illegal fix ave/correlate/long 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/long does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
error->all(FLERR,
"Fix ave/correlate/long compute does not calculate a scalar");
if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
error->all(FLERR,
"Fix ave/correlate/long compute does not calculate a vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
error->all(FLERR,"Fix ave/correlate/long 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/long does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
error->all(FLERR,"Fix ave/correlate/long fix does not calculate a scalar");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
error->all(FLERR,"Fix ave/correlate/long fix does not calculate a vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
error->all(FLERR,
"Fix ave/correlate/long fix vector is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all(FLERR,"Fix for fix ave/correlate/long "
"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/long does not exist");
if (input->variable->equalstyle(ivariable) == 0)
error->all(FLERR,
"Fix ave/correlate/long variable is not equal-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) {
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,"# Time");
if (type == AUTO)
for (int i = 0; i < nvalues; i++)
fprintf(fp," %s*%s",arg[5+i],arg[5+i]);
else if (type == UPPER)
for (int i = 0; i < nvalues; i++)
for (int j = i+1; j < nvalues; j++)
fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
else if (type == LOWER)
for (int i = 0; i < nvalues; i++)
for (int j = 0; j < i-1; j++)
fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
else if (type == AUTOUPPER)
for (int i = 0; i < nvalues; i++)
for (int j = i; j < nvalues; j++)
fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
else if (type == AUTOLOWER)
for (int i = 0; i < nvalues; i++)
for (int j = 0; j < i; j++)
fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
else if (type == FULL)
for (int i = 0; i < nvalues; i++)
for (int j = 0; j < nvalues; j++)
fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
fprintf(fp,"\n");
}
filepos = ftell(fp);
}
delete [] title1;
delete [] title2;
// allocate and initialize memory for calculated values and correlators
memory->create(values,nvalues,"correlator:values");
memory->create(shift,npair,numcorrelators,p,"correlator:shift");
memory->create(shift2,npair,numcorrelators,p,"correlator:shift2"); //NOT OPTMAL
memory->create(correlation,npair,numcorrelators,p,"correlator:correlation");
memory->create(accumulator,npair,numcorrelators,"correlator:accumulator");
memory->create(accumulator2,npair,numcorrelators,"correlator:accumulator2"); // NOT OPTIMAL
memory->create(ncorrelation,numcorrelators,p,"correlator:ncorrelation");
memory->create(naccumulator,numcorrelators,"correlator:naccumulator");
memory->create(insertindex,numcorrelators,"correlator:insertindex");
memory->create(t,length,"correlator:t");
memory->create(f,npair,length,"correlator:f");
for (int i=0;i<npair;i++)
for (int j=0;j<numcorrelators;j++) {
for (int k=0;k<p;k++) {
shift[i][j][k]=-2E10;
shift2[i][j][k]=0.0;
correlation[i][j][k]=0.0;
}
accumulator[i][j]=0.0;
accumulator2[i][j]=0.0;
}
for (int i=0;i<numcorrelators;i++) {
for (int j=0;j<p;j++) ncorrelation[i][j]=0;
naccumulator[i]=0;
insertindex[i]=0;
}
for (int i=0;i<length;i++) t[i]=0.0;
for (int i=0;i<npair;i++)
for (int j=0;j<length;j++) f[i][j]=0.0;
// 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
nvalid_last = -1;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
last_accumulated_step = -1;
}
/* ---------------------------------------------------------------------- */
FixAveCorrelateLong::~FixAveCorrelateLong()
{
delete [] which;
delete [] argindex;
delete [] value2index;
for (int i = 0; i < nvalues; i++) delete [] ids[i];
delete [] ids;
memory->destroy(values);
memory->destroy(shift);
memory->destroy(shift2);
memory->destroy(correlation);
memory->destroy(accumulator);
memory->destroy(accumulator2);
memory->destroy(ncorrelation);
memory->destroy(naccumulator);
memory->destroy(insertindex);
memory->destroy(t);
memory->destroy(f);
if (fp && me == 0) fclose(fp);
}
/* ---------------------------------------------------------------------- */
int FixAveCorrelateLong::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAveCorrelateLong::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/long 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/long 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/long does not exist");
value2index[i] = ivariable;
}
}
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveCorrelateLong::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveCorrelateLong::end_of_step()
{
int i,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/long");
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();
for (i = 0; i < nvalues; i++) {
m = value2index[i];
scalar = 0.0;
// 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 variable
} else if (which[i] == VARIABLE)
scalar = input->variable->compute_equal(m);
values[i] = scalar;
}
// fistindex = index in values ring of earliest time sample
nvalid += nevery;
modify->addstep_compute(nvalid);
// calculate all Cij() enabled by latest values
accumulate();
if (ntimestep % nfreq) return;
// output result to file
evaluate();
if (fp && me == 0) {
if(overwrite) fseek(fp,filepos,SEEK_SET);
fprintf(fp,"# Timestep: " BIGINT_FORMAT "\n", ntimestep);
for (unsigned int i=0;i<npcorr;++i) {
fprintf(fp, "%lg ", t[i]*update->dt);
for (int j=0;j<npair;++j) {
fprintf(fp, "%lg ", f[j][i]);
}
fprintf(fp, "\n");
}
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
if (fileend > 0) ftruncate(fileno(fp),fileend);
}
}
return;
}
void FixAveCorrelateLong::evaluate() {
unsigned int jm=0;
// First correlator
for (int j=0;j<p;++j) {
if (ncorrelation[0][j] > 0) {
t[jm] = j;
for (int i=0;i<npair;++i)
f[i][jm] = correlation[i][0][j]/ncorrelation[0][j];
++jm;
}
}
// Subsequent correlators
for (int k=1;k<kmax;++k) {
for (int j=dmin;j<p;++j) {
if (ncorrelation[k][j]>0) {
t[jm] = j * pow((double)m, k);
for (int i=0;i<npair;++i)
f[i][jm] = correlation[i][k][j] / ncorrelation[k][j];
++jm;
}
}
}
npcorr = jm;
}
/* ----------------------------------------------------------------------
accumulate correlation data using more recently added values
------------------------------------------------------------------------- */
void FixAveCorrelateLong::accumulate()
{
int i,j,ipair;
if (update->ntimestep <= last_accumulated_step) return;
if (type == AUTO) {
for (i=0; i<nvalues;i++) add(i,values[i]);
} else if (type == UPPER) {
ipair = 0;
for (i=0;i<nvalues;i++)
for (j=i+1;j<nvalues;j++) add(ipair++,values[i],values[j]);
} else if (type == LOWER) {
ipair = 0;
for (i=0;i<nvalues;i++)
for (j=0;j<i;j++) add(ipair++,values[i],values[j]);
} else if (type == AUTOUPPER) {
ipair = 0;
for (i=0;i<nvalues;i++)
for (j=i;j<nvalues;j++) {
if (i==j) add(ipair++,values[i]);
else add(ipair++,values[i],values[j]);
}
} else if (type == AUTOLOWER) {
ipair = 0;
for (i=0;i<nvalues;i++)
for (j=0;j<=i;j++) {
if (i==j) add(ipair++,values[i]);
else add(ipair++,values[i],values[j]);
}
} else if (type == FULL) {
ipair = 0;
for (i=0;i<nvalues;i++)
for (j=0;j<nvalues;j++) {
if (i==j) add(ipair++,values[i]);
else add(ipair++,values[i],values[j]);
}
}
last_accumulated_step = update->ntimestep;
}
/* ----------------------------------------------------------------------
Add a scalar value to the autocorrelator k of pair i
------------------------------------------------------------------------- */
void FixAveCorrelateLong::add(const int i, const double w, const int k){
// If we exceed the correlator side, the value is discarded
if (k == numcorrelators) return;
if (k > kmax) kmax=k;
// Insert new value in shift array
shift[i][k][insertindex[k]] = w;
// Add to accumulator and, if needed, add to next correlator
accumulator[i][k] += w;
if (i==0) ++naccumulator[k];
if (naccumulator[k]==m) {
add(i,accumulator[i][k]/m, k+1);
accumulator[i][k]=0;
if (i==npair-1) naccumulator[k]=0;
}
// Calculate correlation function
unsigned int ind1=insertindex[k];
if (k==0) { // First correlator is different
int ind2=ind1;
for (int j=0;j<p;++j) {
if (shift[i][k][ind2] > -1e10) {
correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2];
if (i==0) ++ncorrelation[k][j];
}
--ind2;
if (ind2<0) ind2+=p;
}
} else {
int ind2=ind1-dmin;
for (int j=dmin;j<p;++j) {
if (ind2<0) ind2+=p;
if (shift[i][k][ind2] > -1e10) {
correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2];
if (i==0) ++ncorrelation[k][j];
}
--ind2;
}
}
if (i==npair-1) {
++insertindex[k];
if (insertindex[k]==p) insertindex[k]=0;
}
}
/* ----------------------------------------------------------------------
Add 2 scalar values to the cross-correlator k of pair i
------------------------------------------------------------------------- */
void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
const int k) {
if (k == numcorrelators) return;
if (k > kmax) kmax=k;
shift[i][k][insertindex[k]] = wA;
shift2[i][k][insertindex[k]] = wB;
accumulator[i][k] += wA;
accumulator2[i][k] += wB;
if (i==0) ++naccumulator[k];
if (naccumulator[k]==m) {
add(i,accumulator[i][k]/m, accumulator2[i][k]/m,k+1);
accumulator[i][k]=0;
accumulator2[i][k]=0;
if (i==npair-1) naccumulator[k]=0;
}
unsigned int ind1=insertindex[k];
if (k==0) {
int ind2=ind1;
for (int j=0;j<p;++j) {
if (shift[i][k][ind2] > -1e10) {
correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2];
if (i==0) ++ncorrelation[k][j];
}
--ind2;
if (ind2<0) ind2+=p;
}
}
else {
int ind2=ind1-dmin;
for (int j=dmin;j<p;++j) {
if (ind2<0) ind2+=p;
if (shift[i][k][ind2] > -1e10) {
correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2];
if (i==0) ++ncorrelation[k][j];
}
--ind2;
}
}
if (i==npair-1) {
++insertindex[k];
if (insertindex[k]==p) insertindex[k]=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 FixAveCorrelateLong::nextvalid()
{
bigint nvalid = update->ntimestep;
if (startstep > nvalid) nvalid = startstep;
if (nvalid % nevery) nvalid = (nvalid/nevery)*nevery + nevery;
return nvalid;
}
/* ----------------------------------------------------------------------
memory_usage
------------------------------------------------------------------------- */
double FixAveCorrelateLong::memory_usage() {
// shift: npair x numcorrelators x p
// shift2: npair x numcorrelators x p
// correlation: npair x numcorrelators x p
// accumulator: npair x numcorrelators
// accumulator2: npair x numcorrelators
// ncorrelation: numcorrelators x p
// naccumulator: numcorrelators
// insertindex: numcorrelators
// t: numcorrelators x p
// f: npair x numcorrelators x p
double bytes = (4*npair*numcorrelators*p + 2*npair*numcorrelators
+ numcorrelators*p)*sizeof(double)
+ numcorrelators*p*sizeof(unsigned long int)
+ 2*numcorrelators*sizeof(unsigned int);
return bytes;
}
/* ----------------------------------------------------------------------
Write Restart data to restart file
------------------------------------------------------------------------- */
// Save everything except t and f
void FixAveCorrelateLong::write_restart(FILE *fp) {
if (me == 0) {
int nsize = 3*npair*numcorrelators*p + 2*npair*numcorrelators
+ numcorrelators*p + 2*numcorrelators + 6;
int n=0;
double *list;
memory->create(list,nsize,"correlator:list");
list[n++]=npair;
list[n++]=numcorrelators;
list[n++]=p;
list[n++]=m;
list[n++] = last_accumulated_step;
for (int i=0;i<npair;i++)
for (int j=0;j<numcorrelators;j++) {
for (int k=0;k<p;k++) {
list[n++]=shift[i][j][k];
list[n++]=shift2[i][j][k];
list[n++]=correlation[i][j][k];
}
list[n++]=accumulator[i][j];
list[n++]=accumulator2[i][j];
}
for (int i=0;i<numcorrelators;i++) {
for (int j=0;j<p;j++) list[n++]=ncorrelation[i][j];
list[n++]=naccumulator[i];
list[n++]=insertindex[i];
}
int size = n*sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
memory->destroy(list);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixAveCorrelateLong::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
int npairin = static_cast<int> (list[n++]);
int numcorrelatorsin = static_cast<int> (list[n++]);
int pin = static_cast<int> (list[n++]);
int min = static_cast<int> (list[n++]);
last_accumulated_step = static_cast<int> (list[n++]);
if ((npairin!=npair) || (numcorrelatorsin!=numcorrelators)
|| (pin!=p) || (min!=m))
error->all(FLERR,"Fix ave/correlate/long: restart and input data are different");
for (int i=0;i<npair;i++)
for (int j=0;j<numcorrelators;j++) {
for (int k=0;k<p;k++) {
shift[i][j][k] = list[n++];
shift2[i][j][k] = list[n++];
correlation[i][j][k] = list[n++];
}
accumulator[i][j] = list[n++];
accumulator2[i][j] = list[n++];
}
for (int i=0;i<numcorrelators;i++) {
for (int j=0;j<p;j++)
ncorrelation[i][j] = static_cast<unsigned long int>(list[n++]);
naccumulator[i] = static_cast<unsigned int> (list[n++]);
insertindex[i] = static_cast<unsigned int> (list[n++]);
}
}
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