ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
905ceb98f1c63afba02f5f2abcf02d40dc080f99
lammps/src/EXTRA-FIX/fix_ave_correlate_long.cpp

800 lines
26 KiB
C++
Raw Blame History

// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
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 "fix_ave_correlate_long.h"
#include "arg_info.h"
#include "citeme.h"
#include "comm.h"
#include "compute.h"
#include "error.h"
#include "input.h"
#include "math_special.h"
#include "memory.h"
#include "modify.h"
#include "update.h"
#include "variable.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
using MathSpecial::powint;
enum { AUTO, UPPER, LOWER, AUTOUPPER, AUTOLOWER, FULL };
static const char cite_fix_ave_correlate_long[] =
"fix ave/correlate/long command: doi:10.1063/1.3491098\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"
" number = 15,\n"
" pages = {154103}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), shift(nullptr), shift2(nullptr), correlation(nullptr),
accumulator(nullptr), accumulator2(nullptr), ncorrelation(nullptr), naccumulator(nullptr),
insertindex(nullptr), fp(nullptr), cvalues(nullptr)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_ave_correlate_long);
// At least nevery nfreq and one value are needed
if (narg < 6) utils::missing_cmd_args(FLERR, "fix ave/correlate/long", error);
nevery = utils::inumeric(FLERR, arg[3], false, lmp);
nfreq = utils::inumeric(FLERR, arg[4], false, lmp);
restart_global = 1;
global_freq = nfreq;
time_depend = 1;
// expand args if any have wildcard character "*"
int expand = 0;
char **earg;
int nargnew = utils::expand_args(FLERR, narg - 5, &arg[5], 0, earg, lmp);
if (earg != &arg[5]) expand = 1;
arg = earg;
// parse values
int iarg = 0;
while (iarg < nargnew) {
ArgInfo argi(arg[iarg]);
value_t val;
if (argi.get_type() == ArgInfo::NONE) break;
if ((argi.get_type() == ArgInfo::UNKNOWN) || (argi.get_dim() > 1))
error->all(FLERR, "Unknown fix ave/correlate/long data type: {}", arg[iarg]);
val.which = argi.get_type();
val.argindex = argi.get_index1();
val.id = argi.get_name();
val.val.c = nullptr;
values.push_back(val);
iarg++;
}
nvalues = values.size();
// optional args
type = AUTO;
startstep = 0;
fp = nullptr;
overwrite = 0;
numcorrelators = 20;
p = 16;
m = 2;
char *title1 = nullptr;
char *title2 = nullptr;
while (iarg < nargnew) {
if (strcmp(arg[iarg], "type") == 0) {
if (iarg + 2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate/long type", error);
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, "Unknown fix ave/correlate/long type: {}");
iarg += 2;
} else if (strcmp(arg[iarg], "start") == 0) {
if (iarg + 2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate/long start", error);
startstep = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "ncorr") == 0) {
if (iarg + 2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate/long ncorr", error);
numcorrelators = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "nlen") == 0) {
if (iarg + 2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate/long nlen", error);
p = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "ncount") == 0) {
if (iarg + 2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate/long ncount", error);
m = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "file") == 0) {
if (iarg + 2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate/long file", error);
if (comm->me == 0) {
fp = fopen(arg[iarg + 1], "w");
if (fp == nullptr)
error->one(FLERR, "Cannot open fix ave/correlate/long file {}: {}", arg[iarg + 1],
utils::getsyserror());
}
iarg += 2;
} else if (strcmp(arg[iarg], "overwrite") == 0) {
overwrite = 1;
iarg += 1;
} else if (strcmp(arg[iarg], "title1") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate/long title1", error);
delete[] title1;
title1 = utils::strdup(arg[iarg + 1]);
iarg += 2;
} else if (strcmp(arg[iarg], "title2") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate/long title2", error);
delete[] title2;
title2 = utils::strdup(arg[iarg + 1]);
iarg += 2;
} else
error->all(FLERR, "Unknown fix ave/correlate/long keyword: {}", arg[iarg]);
}
if (p % m != 0) error->all(FLERR, "Fix ave/correlate/long: nlen must be divisible by ncount");
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) error->all(FLERR, "Illegal fix ave/correlate/long nevery value: {}", nevery);
if (nfreq <= 0) error->all(FLERR, "Illegal fix ave/correlate/long nfreq value: {}", nfreq);
if (nfreq % nevery) error->all(FLERR, "Inconsistent fix ave/correlate/long nevery/nfreq values");
for (auto &val : values) {
if (val.which == ArgInfo::COMPUTE) {
val.val.c = modify->get_compute_by_id(val.id);
if (!val.val.c)
error->all(FLERR, "Compute ID {} for fix ave/correlate/long does not exist", val.id);
if (val.argindex == 0 && val.val.c->scalar_flag == 0)
error->all(FLERR, "Fix ave/correlate/long compute {} does not calculate a scalar", val.id);
if (val.argindex && val.val.c->vector_flag == 0)
error->all(FLERR, "Fix ave/correlate/long compute {} does not calculate a vector", val.id);
if (val.argindex && val.argindex > val.val.c->size_vector)
error->all(FLERR, "Fix ave/correlate/long compute {} vector is accessed out-of-range",
val.id);
} else if (val.which == ArgInfo::FIX) {
val.val.f = modify->get_fix_by_id(val.id);
if (!val.val.f)
error->all(FLERR, "Fix ID {} for fix ave/correlate/long does not exist", val.id);
if (val.argindex == 0 && val.val.f->scalar_flag == 0)
error->all(FLERR, "Fix ave/correlate/long fix {} does not calculate a scalar", val.id);
if (val.argindex && val.val.f->vector_flag == 0)
error->all(FLERR, "Fix ave/correlate/long fix {} does not calculate a vector", val.id);
if (val.argindex && val.argindex > val.val.f->size_vector)
error->all(FLERR, "Fix ave/correlate/long fix {} vector is accessed out-of-range", val.id);
if (nevery % val.val.f->global_freq)
error->all(FLERR, "Fix {} for fix ave/correlate/long not computed at compatible time",
val.id);
} else if (val.which == ArgInfo::VARIABLE) {
val.val.v = input->variable->find(val.id.c_str());
if (val.val.v < 0)
error->all(FLERR, "Variable name {} for fix ave/correlate/long does not exist", val.id);
if (val.argindex == 0 && input->variable->equalstyle(val.val.v) == 0)
error->all(FLERR, "Fix ave/correlate/long variable {} is not equal-style variable", val.id);
if (val.argindex && input->variable->vectorstyle(val.val.v) == 0)
error->all(FLERR, "Fix ave/correlate/long variable {} is not vector-style variable",
val.id);
}
}
// 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 && comm->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,"# Time");
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 ave/correlate/long header: {}", utils::getsyserror());
filepos = platform::ftell(fp);
}
delete[] title1;
delete[] title2;
// 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 calculated values and correlators
memory->create(cvalues,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 (unsigned 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 (unsigned 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()
{
memory->destroy(cvalues);
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 && comm->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 (auto &val : values) {
if (val.which == ArgInfo::COMPUTE) {
val.val.c = modify->get_compute_by_id(val.id);
if (!val.val.c)
error->all(FLERR, "Compute ID {} for fix ave/correlate/long does not exist", val.id);
} else if (val.which == ArgInfo::FIX) {
val.val.f = modify->get_fix_by_id(val.id);
if (!val.val.f)
error->all(FLERR,"Fix ID {} for fix ave/correlate/long does not exist", val.id);
} else if (val.which == ArgInfo::VARIABLE) {
val.val.v = input->variable->find(val.id.c_str());
if (val.val.v < 0)
error->all(FLERR,"Variable name {} for fix ave/correlate/long does not exist", val.id);
}
}
// 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()
{
// skip if not step which requires doing something
bigint ntimestep = update->ntimestep;
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();
int i = 0;
for (auto &val : values) {
double scalar = 0.0;
// invoke compute if not previously invoked
if (val.which == ArgInfo::COMPUTE) {
if (val.argindex == 0) {
if (!(val.val.c->invoked_flag & Compute::INVOKED_SCALAR)) {
val.val.c->compute_scalar();
val.val.c->invoked_flag |= Compute::INVOKED_SCALAR;
}
scalar = val.val.c->scalar;
} else {
if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) {
val.val.c->compute_vector();
val.val.c->invoked_flag |= Compute::INVOKED_VECTOR;
}
scalar = val.val.c->vector[val.argindex-1];
}
// access fix fields, guaranteed to be ready
} else if (val.which == ArgInfo::FIX) {
if (val.argindex == 0)
scalar = val.val.f->compute_scalar();
else
scalar = val.val.f->compute_vector(val.argindex-1);
// evaluate equal-style or vector-style variable
// if index exceeds vector length, use a zero value
// this can be useful if vector length is not known a priori
} else if (val.which == ArgInfo::VARIABLE) {
if (val.argindex == 0)
scalar = input->variable->compute_equal(val.val.v);
else {
double *varvec;
int nvec = input->variable->compute_vector(val.val.v,&varvec);
int index = val.argindex;
if (index > nvec) scalar = 0.0;
else scalar = varvec[index-1];
}
}
cvalues[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 && comm->me == 0) {
clearerr(fp);
if (overwrite) platform::fseek(fp,filepos);
fmt::print(fp,"# Timestep: {}\n", ntimestep);
for (unsigned int i=0; i < npcorr; ++i) {
fprintf(fp, "%lg ", t[i]*update->dt*nevery);
for (int j=0; j < npair; ++j) {
fprintf(fp, "%lg ", f[j][i]);
}
fprintf(fp, "\n");
}
if (ferror(fp))
error->one(FLERR,"Error writing out fix ave/correlate/long data: {}", utils::getsyserror());
fflush(fp);
if (overwrite) {
bigint fileend = platform::ftell(fp);
if ((fileend > 0) && (platform::ftruncate(fp,fileend)))
error->warning(FLERR,"Error while truncating output: {}", utils::getsyserror());
}
}
}
void FixAveCorrelateLong::evaluate() {
unsigned int jm=0;
// First correlator
for (unsigned 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 (unsigned int j=dmin; j < p; ++j) {
if (ncorrelation[k][j]>0) {
t[jm] = j * powint((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,cvalues[i]);
} else if (type == UPPER) {
ipair = 0;
for (i=0; i < nvalues; i++)
for (j=i+1; j < nvalues; j++) add(ipair++,cvalues[i],cvalues[j]);
} else if (type == LOWER) {
ipair = 0;
for (i=0; i < nvalues; i++)
for (j=0; j < i; j++) add(ipair++,cvalues[i],cvalues[j]);
} else if (type == AUTOUPPER) {
ipair = 0;
for (i=0; i < nvalues; i++)
for (j=i; j < nvalues; j++) {
if (i == j) add(ipair++,cvalues[i]);
else add(ipair++,cvalues[i],cvalues[j]);
}
} else if (type == AUTOLOWER) {
ipair = 0;
for (i=0; i < nvalues; i++)
for (j=0; j <=i; j++) {
if (i==j) add(ipair++,cvalues[i]);
else add(ipair++,cvalues[i],cvalues[j]);
}
} else if (type == FULL) {
ipair = 0;
for (i=0; i < nvalues; i++)
for (j=0; j < nvalues; j++) {
if (i == j) add(ipair++,cvalues[i]);
else add(ipair++,cvalues[i],cvalues[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 (unsigned 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 (unsigned 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 (unsigned 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 (unsigned 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)
+ (double)numcorrelators*p*sizeof(unsigned long int)
+ 2.0*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 (comm->me == 0) {
int nsize = 3*npair*numcorrelators*p + 2*npair*numcorrelators
+ numcorrelators*p + 2*numcorrelators + 7;
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++] = kmax;
list[n++] = last_accumulated_step;
for (int i=0; i < npair; i++)
for (int j=0; j < numcorrelators; j++) {
for (unsigned 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 (unsigned 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;
auto 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++]);
kmax = static_cast<int>(list[n++]);
last_accumulated_step = static_cast<int>(list[n++]);
if ((npairin!=npair) || (numcorrelatorsin!=numcorrelators) || (pin!=(int)p) || (min!=(int)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 (unsigned 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 (unsigned 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++]);
}
}
Reference in New Issue View Git Blame Copy Permalink