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lammps/src/fix_ave_chunk.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.
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include "fix_ave_chunk.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "compute.h"
#include "compute_chunk_atom.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{V,F,DENSITY_NUMBER,DENSITY_MASS,MASS,TEMPERATURE,COMPUTE,FIX,VARIABLE};
enum{SCALAR,VECTOR};
enum{SAMPLE,ALL};
enum{NOSCALE,ATOM};
enum{ONE,RUNNING,WINDOW};
#define INVOKED_PERATOM 8
/* ---------------------------------------------------------------------- */
FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
nvalues(0), nrepeat(0),
which(NULL), argindex(NULL), value2index(NULL), ids(NULL),
fp(NULL), idchunk(NULL), varatom(NULL),
count_one(NULL), count_many(NULL), count_sum(NULL),
values_one(NULL), values_many(NULL), values_sum(NULL),
count_total(NULL), count_list(NULL),
values_total(NULL), values_list(NULL)
{
if (narg < 7) error->all(FLERR,"Illegal fix ave/chunk command");
MPI_Comm_rank(world,&me);
nevery = force->inumeric(FLERR,arg[3]);
nrepeat = force->inumeric(FLERR,arg[4]);
nfreq = force->inumeric(FLERR,arg[5]);
int n = strlen(arg[6]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[6]);
global_freq = nfreq;
no_change_box = 1;
// expand args if any have wildcard character "*"
int expand = 0;
char **earg;
int nargnew = input->expand_args(narg-7,&arg[7],1,earg);
if (earg != &arg[7]) 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];
densityflag = 0;
int iarg = 0;
while (iarg < nargnew) {
ids[nvalues] = NULL;
if (strcmp(arg[iarg],"vx") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"vy") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"vz") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"fx") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"fy") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"fz") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"density/number") == 0) {
densityflag = 1;
which[nvalues] = DENSITY_NUMBER;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"density/mass") == 0) {
densityflag = 1;
which[nvalues] = DENSITY_MASS;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"mass") == 0) {
which[nvalues] = MASS;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"temp") == 0) {
which[nvalues] = TEMPERATURE;
argindex[nvalues++] = 0;
} else 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/chunk 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);
nvalues++;
delete [] suffix;
} else break;
iarg++;
}
if (nvalues == 0) error->all(FLERR,"No values in fix ave/chunk command");
// optional args
normflag = ALL;
scaleflag = ATOM;
ave = ONE;
nwindow = 0;
biasflag = 0;
id_bias = NULL;
adof = domain->dimension;
cdof = 0.0;
overwrite = 0;
format_user = NULL;
format = (char *) " %g";
char *title1 = NULL;
char *title2 = NULL;
char *title3 = NULL;
while (iarg < nargnew) {
if (strcmp(arg[iarg],"norm") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
if (strcmp(arg[iarg+1],"all") == 0) {
normflag = ALL;
scaleflag = ATOM;
} else if (strcmp(arg[iarg+1],"sample") == 0) {
normflag = SAMPLE;
scaleflag = ATOM;
} else if (strcmp(arg[iarg+1],"none") == 0) {
normflag = SAMPLE;
scaleflag = NOSCALE;
} else error->all(FLERR,"Illegal fix ave/chunk command");
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
else error->all(FLERR,"Illegal fix ave/chunk command");
if (ave == WINDOW) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
nwindow = force->inumeric(FLERR,arg[iarg+2]);
if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/chunk command");
}
iarg += 2;
if (ave == WINDOW) iarg++;
} else if (strcmp(arg[iarg],"bias") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/chunk command");
biasflag = 1;
int n = strlen(arg[iarg+1]) + 1;
id_bias = new char[n];
strcpy(id_bias,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"adof") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/chunk command");
adof = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"cdof") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/chunk command");
cdof = 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/chunk command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ave/chunk 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],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
delete [] format_user;
int n = strlen(arg[iarg+1]) + 2;
format_user = new char[n];
sprintf(format_user," %s",arg[iarg+1]);
format = format_user;
iarg += 2;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk 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/chunk 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/chunk 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/chunk command");
}
// setup and error check
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all(FLERR,"Illegal fix ave/chunk command");
if (nfreq % nevery || nrepeat*nevery > nfreq)
error->all(FLERR,"Illegal fix ave/chunk command");
if (ave != RUNNING && overwrite)
error->all(FLERR,"Illegal fix ave/chunk command");
if (biasflag) {
int i = modify->find_compute(id_bias);
if (i < 0)
error->all(FLERR,"Could not find compute ID for temperature bias");
tbias = modify->compute[i];
if (tbias->tempflag == 0)
error->all(FLERR,"Bias compute does not calculate temperature");
if (tbias->tempbias == 0)
error->all(FLERR,"Bias compute does not calculate a velocity bias");
}
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/chunk does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all(FLERR,"Fix ave/chunk compute does not "
"calculate per-atom values");
if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all(FLERR,"Fix ave/chunk compute does not "
"calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
error->all(FLERR,"Fix ave/chunk compute does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all(FLERR,
"Fix ave/chunk 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/chunk does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all(FLERR,
"Fix ave/chunk fix does not calculate per-atom values");
if (argindex[i] == 0 && modify->fix[ifix]->size_peratom_cols != 0)
error->all(FLERR,
"Fix ave/chunk fix does not calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
error->all(FLERR,
"Fix ave/chunk fix does not calculate a per-atom array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
error->all(FLERR,"Fix ave/chunk fix vector is accessed out-of-range");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix ave/chunk does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Fix ave/chunk variable is not atom-style variable");
}
}
// increment lock counter in compute chunk/atom
// only if nrepeat > 1 or ave = RUNNING/WINDOW,
// so that locking spans multiple timesteps
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for fix ave/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Fix ave/chunk does not use chunk/atom compute");
if (nrepeat > 1 || ave == RUNNING || ave == WINDOW) cchunk->lockcount++;
lockforever = 0;
// print file comment lines
if (fp && me == 0) {
clearerr(fp);
if (title1) fprintf(fp,"%s\n",title1);
else fprintf(fp,"# Chunk-averaged data for fix %s and group %s\n",
id,arg[1]);
if (title2) fprintf(fp,"%s\n",title2);
else fprintf(fp,"# Timestep Number-of-chunks Total-count\n");
if (title3) fprintf(fp,"%s\n",title3);
else {
int compress = cchunk->compress;
int ncoord = cchunk->ncoord;
if (!compress) {
if (ncoord == 0) fprintf(fp,"# Chunk Ncount");
else if (ncoord == 1) fprintf(fp,"# Chunk Coord1 Ncount");
else if (ncoord == 2) fprintf(fp,"# Chunk Coord1 Coord2 Ncount");
else if (ncoord == 3)
fprintf(fp,"# Chunk Coord1 Coord2 Coord3 Ncount");
} else {
if (ncoord == 0) fprintf(fp,"# Chunk OrigID Ncount");
else if (ncoord == 1) fprintf(fp,"# Chunk OrigID Coord1 Ncount");
else if (ncoord == 2) fprintf(fp,"# Chunk OrigID Coord1 Coord2 Ncount");
else if (ncoord == 3)
fprintf(fp,"# Chunk OrigID Coord1 Coord2 Coord3 Ncount");
}
for (int i = 0; i < nvalues; i++) fprintf(fp," %s",earg[i]);
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);
}
// this fix produces a global array
// size_array_rows is variable and set by allocate()
int compress = cchunk->compress;
int ncoord = cchunk->ncoord;
colextra = compress + ncoord;
array_flag = 1;
size_array_cols = colextra + 1 + nvalues;
size_array_rows_variable = 1;
extarray = 0;
// initializations
irepeat = 0;
iwindow = window_limit = 0;
normcount = 0;
maxvar = 0;
varatom = NULL;
count_one = count_many = count_sum = count_total = NULL;
count_list = NULL;
values_one = values_many = values_sum = values_total = NULL;
values_list = NULL;
maxchunk = 0;
nchunk = 1;
allocate();
// 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);
}
/* ---------------------------------------------------------------------- */
FixAveChunk::~FixAveChunk()
{
delete [] which;
delete [] argindex;
for (int i = 0; i < nvalues; i++) delete [] ids[i];
delete [] ids;
delete [] value2index;
if (fp && me == 0) fclose(fp);
memory->destroy(varatom);
memory->destroy(count_one);
memory->destroy(count_many);
memory->destroy(count_sum);
memory->destroy(count_total);
memory->destroy(count_list);
memory->destroy(values_one);
memory->destroy(values_many);
memory->destroy(values_sum);
memory->destroy(values_total);
memory->destroy(values_list);
// decrement lock counter in compute chunk/atom, it if still exists
if (nrepeat > 1 || ave == RUNNING || ave == WINDOW) {
int icompute = modify->find_compute(idchunk);
if (icompute >= 0) {
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (ave == RUNNING || ave == WINDOW) cchunk->unlock(this);
cchunk->lockcount--;
}
}
delete [] idchunk;
which = NULL;
argindex = NULL;
ids = NULL;
value2index = NULL;
fp = NULL;
varatom = NULL;
count_one = NULL;
count_many = NULL;
count_sum = NULL;
count_total = NULL;
count_list = NULL;
values_one = NULL;
values_many = NULL;
values_sum = NULL;
values_total = NULL;
values_list = NULL;
idchunk = NULL;
cchunk = NULL;
}
/* ---------------------------------------------------------------------- */
int FixAveChunk::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAveChunk::init()
{
// set indices and check validity of all computes,fixes,variables
// check that fix frequency is acceptable
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for fix ave/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (biasflag) {
int i = modify->find_compute(id_bias);
if (i < 0)
error->all(FLERR,"Could not find compute ID for temperature bias");
tbias = modify->compute[i];
}
for (int m = 0; m < nvalues; m++) {
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/chunk does not exist");
value2index[m] = icompute;
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/chunk does not exist");
value2index[m] = ifix;
if (nevery % modify->fix[ifix]->peratom_freq)
error->all(FLERR,
"Fix for fix ave/chunk not computed at compatible time");
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix ave/chunk does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
}
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
irepeat = 0;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
}
/* ----------------------------------------------------------------------
only does averaging if nvalid = current timestep
do not call setup_chunks(), even though fix ave/spatial called setup_bins()
b/c could cause nchunk to change if Nfreq epoch crosses 2 runs
does mean that if change_box is used between runs to change box size,
that nchunk may not track it
------------------------------------------------------------------------- */
void FixAveChunk::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveChunk::end_of_step()
{
int i,j,m,n,index;
// 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/chunk");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
// first sample within single Nfreq epoch
// zero out arrays that accumulate over many samples, but not across epochs
// invoke setup_chunks() to determine current nchunk
// re-allocate per-chunk arrays if needed
// invoke lock() in two cases:
// if nrepeat > 1: so nchunk cannot change until Nfreq epoch is over,
// will be unlocked on last repeat of this Nfreq
// if ave = RUNNING/WINDOW and not yet locked:
// set forever, will be unlocked in fix destructor
// wrap setup_chunks in clearstep/addstep b/c it may invoke computes
// both nevery and nfreq are future steps,
// since call below to cchunk->ichunk()
// does not re-invoke internal cchunk compute on this same step
if (irepeat == 0) {
if (cchunk->computeflag) modify->clearstep_compute();
nchunk = cchunk->setup_chunks();
if (cchunk->computeflag) {
modify->addstep_compute(ntimestep+nevery);
modify->addstep_compute(ntimestep+nfreq);
}
allocate();
if (nrepeat > 1 && ave == ONE)
cchunk->lock(this,ntimestep,ntimestep+(nrepeat-1)*nevery);
else if ((ave == RUNNING || ave == WINDOW) && !lockforever) {
cchunk->lock(this,update->ntimestep,-1);
lockforever = 1;
}
for (m = 0; m < nchunk; m++) {
count_many[m] = count_sum[m] = 0.0;
for (i = 0; i < nvalues; i++) values_many[m][i] = 0.0;
}
// if any DENSITY requested, invoke setup_chunks() on each sampling step
// nchunk will not change but bin volumes might, e.g. for NPT simulation
} else if (densityflag) {
cchunk->setup_chunks();
}
// zero out arrays for one sample
for (m = 0; m < nchunk; m++) {
count_one[m] = 0.0;
for (i = 0; i < nvalues; i++) values_one[m][i] = 0.0;
}
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
// wrap compute_ichunk in clearstep/addstep b/c it may invoke computes
if (cchunk->computeflag) modify->clearstep_compute();
cchunk->compute_ichunk();
int *ichunk = cchunk->ichunk;
if (cchunk->computeflag) modify->addstep_compute(ntimestep+nevery);
// perform the computation for one sample
// count # of atoms in each bin
// accumulate results of attributes,computes,fixes,variables to local copy
// sum within each chunk, only include atoms in fix group
// compute/fix/variable may invoke computes so wrap with clear/add
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0)
count_one[ichunk[i]-1]++;
modify->clearstep_compute();
for (m = 0; m < nvalues; m++) {
n = value2index[m];
j = argindex[m];
// V,F adds velocities,forces to values
if (which[m] == V || which[m] == F) {
double **attribute;
if (which[m] == V) attribute = atom->v;
else attribute = atom->f;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0) {
index = ichunk[i]-1;
values_one[index][m] += attribute[i][j];
}
// DENSITY_NUMBER adds 1 to values
} else if (which[m] == DENSITY_NUMBER) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0) {
index = ichunk[i]-1;
values_one[index][m] += 1.0;
}
// DENSITY_MASS or MASS adds mass to values
} else if (which[m] == DENSITY_MASS || which[m] == MASS) {
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
if (rmass) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0) {
index = ichunk[i]-1;
values_one[index][m] += rmass[i];
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0) {
index = ichunk[i]-1;
values_one[index][m] += mass[type[i]];
}
}
// TEMPERATURE adds KE to values
// subtract and restore velocity bias if requested
} else if (which[m] == TEMPERATURE) {
if (biasflag) {
if (tbias->invoked_scalar != ntimestep) tbias->compute_scalar();
tbias->remove_bias_all();
}
double **v = atom->v;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
if (rmass) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0) {
index = ichunk[i]-1;
values_one[index][m] +=
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0) {
index = ichunk[i]-1;
values_one[index][m] +=
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
}
}
if (biasflag) tbias->restore_bias_all();
// COMPUTE adds its scalar or vector component to values
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[n];
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
double *vector = compute->vector_atom;
double **array = compute->array_atom;
int jm1 = j - 1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0) {
index = ichunk[i]-1;
if (j == 0) values_one[index][m] += vector[i];
else values_one[index][m] += array[i][jm1];
}
// FIX adds its scalar or vector component to values
// access fix fields, guaranteed to be ready
} else if (which[m] == FIX) {
double *vector = modify->fix[n]->vector_atom;
double **array = modify->fix[n]->array_atom;
int jm1 = j - 1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0) {
index = ichunk[i]-1;
if (j == 0) values_one[index][m] += vector[i];
else values_one[index][m] += array[i][jm1];
}
// VARIABLE adds its per-atom quantities to values
// evaluate atom-style variable
} else if (which[m] == VARIABLE) {
if (atom->nmax > maxvar) {
maxvar = atom->nmax;
memory->destroy(varatom);
memory->create(varatom,maxvar,"ave/chunk:varatom");
}
input->variable->compute_atom(n,igroup,varatom,1,0);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0) {
index = ichunk[i]-1;
values_one[index][m] += varatom[i];
}
}
}
// process the current sample
// if normflag = ALL, accumulate values,count separately to many
// if normflag = SAMPLE, one = value/count, accumulate one to many
// count is MPI summed here, value is MPI summed below across samples
// exception is TEMPERATURE: normalize by DOF
// exception is DENSITY_NUMBER:
// normalize by bin volume, not by atom count
// exception is DENSITY_MASS:
// scale by mv2d, normalize by bin volume, not by atom count
// exception is scaleflag = NOSCALE (norm = NONE):
// no normalize by atom count
// check last so other options can take precedence
double mvv2e = force->mvv2e;
double mv2d = force->mv2d;
double boltz = force->boltz;
if (normflag == ALL) {
for (m = 0; m < nchunk; m++) {
count_many[m] += count_one[m];
for (j = 0; j < nvalues; j++)
values_many[m][j] += values_one[m][j];
}
} else if (normflag == SAMPLE) {
MPI_Allreduce(count_one,count_many,nchunk,MPI_DOUBLE,MPI_SUM,world);
if (cchunk->chunk_volume_vec) {
volflag = VECTOR;
chunk_volume_vec = cchunk->chunk_volume_vec;
} else {
volflag = SCALAR;
chunk_volume_scalar = cchunk->chunk_volume_scalar;
}
for (m = 0; m < nchunk; m++) {
if (count_many[m] > 0.0)
for (j = 0; j < nvalues; j++) {
if (which[j] == TEMPERATURE) {
values_many[m][j] += mvv2e*values_one[m][j] /
((cdof + adof*count_many[m]) * boltz);
} else if (which[j] == DENSITY_NUMBER) {
if (volflag == SCALAR) values_one[m][j] /= chunk_volume_scalar;
else values_one[m][j] /= chunk_volume_vec[m];
values_many[m][j] += values_one[m][j];
} else if (which[j] == DENSITY_MASS) {
if (volflag == SCALAR) values_one[m][j] /= chunk_volume_scalar;
else values_one[m][j] /= chunk_volume_vec[m];
values_many[m][j] += mv2d*values_one[m][j];
} else if (scaleflag == NOSCALE) {
values_many[m][j] += values_one[m][j];
} else {
values_many[m][j] += values_one[m][j]/count_many[m];
}
}
count_sum[m] += count_many[m];
}
}
// 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);
// unlock compute chunk/atom at end of Nfreq epoch
// do not unlock if ave = RUNNING or WINDOW
if (nrepeat > 1 && ave == ONE) cchunk->unlock(this);
// time average across samples
// if normflag = ALL, final is total value / total count
// exception is TEMPERATURE: normalize by DOF for total count
// exception is DENSITY_NUMBER:
// normalize by final bin_volume and repeat, not by total count
// exception is DENSITY_MASS:
// scale by mv2d, normalize by bin volume and repeat, not by total count
// exception is scaleflag == NOSCALE:
// normalize by repeat, not by total count
// check last so other options can take precedence
// if normflag = SAMPLE, final is sum of ave / repeat
double repeat = nrepeat;
if (normflag == ALL) {
MPI_Allreduce(count_many,count_sum,nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nchunk*nvalues,
MPI_DOUBLE,MPI_SUM,world);
if (cchunk->chunk_volume_vec) {
volflag = VECTOR;
chunk_volume_vec = cchunk->chunk_volume_vec;
} else {
volflag = SCALAR;
chunk_volume_scalar = cchunk->chunk_volume_scalar;
}
for (m = 0; m < nchunk; m++) {
if (count_sum[m] > 0.0)
for (j = 0; j < nvalues; j++) {
if (which[j] == TEMPERATURE) {
values_sum[m][j] *= mvv2e / ((cdof + adof*count_sum[m]) * boltz);
} else if (which[j] == DENSITY_NUMBER) {
if (volflag == SCALAR) values_sum[m][j] /= chunk_volume_scalar;
else values_sum[m][j] /= chunk_volume_vec[m];
values_sum[m][j] /= repeat;
} else if (which[j] == DENSITY_MASS) {
if (volflag == SCALAR) values_sum[m][j] /= chunk_volume_scalar;
else values_sum[m][j] /= chunk_volume_vec[m];
values_sum[m][j] *= mv2d/repeat;
} else if (scaleflag == NOSCALE) {
values_sum[m][j] /= repeat;
} else {
values_sum[m][j] /= count_sum[m];
}
}
count_sum[m] /= repeat;
}
} else if (normflag == SAMPLE) {
MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nchunk*nvalues,
MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nchunk; m++) {
for (j = 0; j < nvalues; j++) values_sum[m][j] /= repeat;
count_sum[m] /= repeat;
}
}
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, comine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
for (m = 0; m < nchunk; m++) {
for (i = 0; i < nvalues; i++)
values_total[m][i] = values_sum[m][i];
count_total[m] = count_sum[m];
}
normcount = 1;
} else if (ave == RUNNING) {
for (m = 0; m < nchunk; m++) {
for (i = 0; i < nvalues; i++)
values_total[m][i] += values_sum[m][i];
count_total[m] += count_sum[m];
}
normcount++;
} else if (ave == WINDOW) {
for (m = 0; m < nchunk; m++) {
for (i = 0; i < nvalues; i++) {
values_total[m][i] += values_sum[m][i];
if (window_limit) values_total[m][i] -= values_list[iwindow][m][i];
values_list[iwindow][m][i] = values_sum[m][i];
}
count_total[m] += count_sum[m];
if (window_limit) count_total[m] -= count_list[iwindow][m];
count_list[iwindow][m] = count_sum[m];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) normcount = nwindow;
else normcount = iwindow;
}
// output result to file
if (fp && me == 0) {
clearerr(fp);
if (overwrite) fseek(fp,filepos,SEEK_SET);
double count = 0.0;
for (m = 0; m < nchunk; m++) count += count_total[m];
fprintf(fp,BIGINT_FORMAT " %d %g\n",ntimestep,nchunk,count);
int compress = cchunk->compress;
int *chunkID = cchunk->chunkID;
int ncoord = cchunk->ncoord;
double **coord = cchunk->coord;
if (!compress) {
if (ncoord == 0) {
for (m = 0; m < nchunk; m++) {
fprintf(fp," %d %g",m+1,count_total[m]/normcount);
for (i = 0; i < nvalues; i++)
fprintf(fp,format,values_total[m][i]/normcount);
fprintf(fp,"\n");
}
} else if (ncoord == 1) {
for (m = 0; m < nchunk; m++) {
fprintf(fp," %d %g %g",m+1,coord[m][0],
count_total[m]/normcount);
for (i = 0; i < nvalues; i++)
fprintf(fp,format,values_total[m][i]/normcount);
fprintf(fp,"\n");
}
} else if (ncoord == 2) {
for (m = 0; m < nchunk; m++) {
fprintf(fp," %d %g %g %g",m+1,coord[m][0],coord[m][1],
count_total[m]/normcount);
for (i = 0; i < nvalues; i++)
fprintf(fp,format,values_total[m][i]/normcount);
fprintf(fp,"\n");
}
} else if (ncoord == 3) {
for (m = 0; m < nchunk; m++) {
fprintf(fp," %d %g %g %g %g",m+1,
coord[m][0],coord[m][1],coord[m][2],count_total[m]/normcount);
for (i = 0; i < nvalues; i++)
fprintf(fp,format,values_total[m][i]/normcount);
fprintf(fp,"\n");
}
}
} else {
int j;
if (ncoord == 0) {
for (m = 0; m < nchunk; m++) {
fprintf(fp," %d %d %g",m+1,chunkID[m],count_total[m]/normcount);
for (i = 0; i < nvalues; i++)
fprintf(fp,format,values_total[m][i]/normcount);
fprintf(fp,"\n");
}
} else if (ncoord == 1) {
for (m = 0; m < nchunk; m++) {
j = chunkID[m];
fprintf(fp," %d %d %g %g",m+1,j,coord[j-1][0],
count_total[m]/normcount);
for (i = 0; i < nvalues; i++)
fprintf(fp,format,values_total[m][i]/normcount);
fprintf(fp,"\n");
}
} else if (ncoord == 2) {
for (m = 0; m < nchunk; m++) {
j = chunkID[m];
fprintf(fp," %d %d %g %g %g",m+1,j,coord[j-1][0],coord[j-1][1],
count_total[m]/normcount);
for (i = 0; i < nvalues; i++)
fprintf(fp,format,values_total[m][i]/normcount);
fprintf(fp,"\n");
}
} else if (ncoord == 3) {
for (m = 0; m < nchunk; m++) {
j = chunkID[m];
fprintf(fp," %d %d %g %g %g %g",m+1,j,coord[j-1][0],
coord[j-1][1],coord[j-1][2],count_total[m]/normcount);
for (i = 0; i < nvalues; i++)
fprintf(fp,format,values_total[m][i]/normcount);
fprintf(fp,"\n");
}
}
}
if (ferror(fp))
error->one(FLERR,"Error writing averaged chunk data");
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
if (fileend > 0) ftruncate(fileno(fp),fileend);
}
}
}
/* ----------------------------------------------------------------------
allocate all per-chunk vectors
------------------------------------------------------------------------- */
void FixAveChunk::allocate()
{
size_array_rows = nchunk;
// reallocate chunk arrays if needed
if (nchunk > maxchunk) {
maxchunk = nchunk;
memory->grow(count_one,nchunk,"ave/chunk:count_one");
memory->grow(count_many,nchunk,"ave/chunk:count_many");
memory->grow(count_sum,nchunk,"ave/chunk:count_sum");
memory->grow(count_total,nchunk,"ave/chunk:count_total");
memory->grow(values_one,nchunk,nvalues,"ave/chunk:values_one");
memory->grow(values_many,nchunk,nvalues,"ave/chunk:values_many");
memory->grow(values_sum,nchunk,nvalues,"ave/chunk:values_sum");
memory->grow(values_total,nchunk,nvalues,"ave/chunk:values_total");
// only allocate count and values list for ave = WINDOW
if (ave == WINDOW) {
memory->create(count_list,nwindow,nchunk,"ave/chunk:count_list");
memory->create(values_list,nwindow,nchunk,nvalues,
"ave/chunk:values_list");
}
// reinitialize regrown count/values total since they accumulate
int i,m;
for (m = 0; m < nchunk; m++) {
for (i = 0; i < nvalues; i++) values_total[m][i] = 0.0;
count_total[m] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
return I,J array value
if I exceeds current nchunks, return 0.0 instead of generating an error
columns 1 to colextra = chunkID + ncoord
next column = count, remaining columns = Nvalues
------------------------------------------------------------------------- */
double FixAveChunk::compute_array(int i, int j)
{
if (values_total == NULL) return 0.0;
if (i >= nchunk) return 0.0;
if (j < colextra) {
if (cchunk->compress) {
if (j == 0) return (double) cchunk->chunkID[i];
return cchunk->coord[i][j-1];
} else return cchunk->coord[i][j];
}
j -= colextra + 1;
if (!normcount) return 0.0;
if (j < 0) return count_total[i]/normcount;
return values_total[i][j]/normcount;
}
/* ----------------------------------------------------------------------
calculate nvalid = next step on which end_of_step does something
can be this timestep if multiple of nfreq and nrepeat = 1
else backup from next multiple of nfreq
------------------------------------------------------------------------- */
bigint FixAveChunk::nextvalid()
{
bigint nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
if (nvalid-nfreq == update->ntimestep && nrepeat == 1)
nvalid = update->ntimestep;
else
nvalid -= (nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += nfreq;
return nvalid;
}
/* ----------------------------------------------------------------------
memory usage of varatom and bins
------------------------------------------------------------------------- */
double FixAveChunk::memory_usage()
{
double bytes = maxvar * sizeof(double); // varatom
bytes += 4*maxchunk * sizeof(double); // count one,many,sum,total
bytes += nvalues*maxchunk * sizeof(double); // values one,many,sum,total
bytes += nwindow*maxchunk * sizeof(double); // count_list
bytes += nwindow*maxchunk*nvalues * sizeof(double); // values_list
return bytes;
}
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