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lammps/src/fix_ave_histo.cpp

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// 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.
------------------------------------------------------------------------- */
#include "fix_ave_histo.h"
#include "arg_info.h"
#include "atom.h"
#include "comm.h"
#include "compute.h"
#include "error.h"
#include "input.h"
#include "memory.h"
#include "modify.h"
#include "update.h"
#include "variable.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
enum { ONE, RUNNING };
enum { SCALAR, VECTOR, WINDOW };
enum { DEFAULT, GLOBAL, PERATOM, LOCAL };
enum { IGNORE, END, EXTRA };
static constexpr double BIG = 1.0e20;
/* ---------------------------------------------------------------------- */
FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), nvalues(0), fp(nullptr), stats_list(nullptr), bin(nullptr),
bin_total(nullptr), bin_all(nullptr), bin_list(nullptr), coord(nullptr), vector(nullptr)
{
auto mycmd = fmt::format("fix {}", style);
if (narg < 10) utils::missing_cmd_args(FLERR, mycmd, error);
nevery = utils::inumeric(FLERR, arg[3], false, lmp);
nrepeat = utils::inumeric(FLERR, arg[4], false, lmp);
nfreq = utils::inumeric(FLERR, arg[5], false, lmp);
global_freq = nfreq;
vector_flag = 1;
size_vector = 4;
extvector = 0;
array_flag = 1;
size_array_cols = 3;
extarray = 0;
dynamic_group_allow = 1;
time_depend = 1;
lo = utils::numeric(FLERR, arg[6], false, lmp);
hi = utils::numeric(FLERR, arg[7], false, lmp);
nbins = utils::inumeric(FLERR, arg[8], false, lmp);
// scan values to count them
// then read options so know mode = SCALAR/VECTOR before re-reading values
nvalues = 0;
int iarg = 9;
while (iarg < narg) {
if (strcmp(arg[iarg],"x") == 0 ||
strcmp(arg[iarg],"y") == 0 ||
strcmp(arg[iarg],"z") == 0 ||
strcmp(arg[iarg],"vx") == 0 ||
strcmp(arg[iarg],"vy") == 0 ||
strcmp(arg[iarg],"vz") == 0 ||
strcmp(arg[iarg],"fx") == 0 ||
strcmp(arg[iarg],"fy") == 0 ||
strcmp(arg[iarg],"fz") == 0 ||
strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
nvalues++;
iarg++;
} else break;
}
if (nvalues == 0) error->all(FLERR,"No values in {} command", mycmd);
options(iarg,narg,arg);
// expand args if any have wildcard character "*"
// this can reset nvalues
int expand = 0;
char **earg;
nvalues = utils::expand_args(FLERR, nvalues, &arg[9], mode, earg, lmp);
if (earg != &arg[9]) expand = 1;
arg = earg;
// parse values
values.clear();
for (int i = 0; i < nvalues; i++) {
value_t val;
val.id = "";
val.val.c = nullptr;
if (strcmp(arg[i],"x") == 0) {
val.which = ArgInfo::X;
val.argindex = 0;
} else if (strcmp(arg[i],"y") == 0) {
val.which = ArgInfo::X;
val.argindex = 1;
} else if (strcmp(arg[i],"z") == 0) {
val.which = ArgInfo::X;
val.argindex = 2;
} else if (strcmp(arg[i],"vx") == 0) {
val.which = ArgInfo::V;
val.argindex = 0;
} else if (strcmp(arg[i],"vy") == 0) {
val.which = ArgInfo::V;
val.argindex = 1;
} else if (strcmp(arg[i],"vz") == 0) {
val.which = ArgInfo::V;
val.argindex = 2;
} else if (strcmp(arg[i],"fx") == 0) {
val.which = ArgInfo::F;
val.argindex = 0;
} else if (strcmp(arg[i],"fy") == 0) {
val.which = ArgInfo::F;
val.argindex = 1;
} else if (strcmp(arg[i],"fz") == 0) {
val.which = ArgInfo::F;
val.argindex = 2;
} else {
ArgInfo argi(arg[i]);
if (argi.get_type() == ArgInfo::NONE) break;
if ((argi.get_type() == ArgInfo::UNKNOWN) || (argi.get_dim() > 1))
error->all(FLERR,"Invalid {} argument: {}", mycmd, arg[i]);
val.which = argi.get_type();
val.argindex = argi.get_index1();
val.id = argi.get_name();
}
values.push_back(val);
}
if (nvalues != (int)values.size())
error->all(FLERR, "Could not parse value data consistently for {}", mycmd);
// if wildcard expansion occurred, free earg memory from expand_args()
if (expand) {
for (int i = 0; i < nvalues; i++) delete[] earg[i];
memory->sfree(earg);
}
// check input args for kind consistency
// inputs must all be all either global, per-atom, or local
if (nevery <= 0)
error->all(FLERR,"Illegal {} nevery value: {}", mycmd, nevery);
if (nrepeat <= 0)
error->all(FLERR,"Illegal {} nrepeat value: {}", mycmd, nrepeat);
if (nfreq <= 0)
error->all(FLERR,"Illegal {} nfreq value: {}", mycmd, nfreq);
if (nfreq % nevery || nrepeat*nevery > nfreq)
error->all(FLERR,"Inconsistent {} nevery/nrepeat/nfreq values", mycmd);
if (ave != RUNNING && overwrite)
error->all(FLERR,"{} overwrite keyword requires ave running setting", mycmd);
int kindglobal,kindperatom,kindlocal;
for (auto &val : values) {
kindglobal = kindperatom = kindlocal = 0;
if ((val.which == ArgInfo::X) || (val.which == ArgInfo::V) || (val.which == ArgInfo::F)) {
kindperatom = 1;
} else 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 {} does not exist", val.id, mycmd);
// computes can produce multiple kinds of output
if (val.val.c->scalar_flag || val.val.c->vector_flag || val.val.c->array_flag)
kindglobal = 1;
if (val.val.c->peratom_flag) kindperatom = 1;
if (val.val.c->local_flag) kindlocal = 1;
} 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 {} does not exist", val.id, mycmd);
// fixes can produce multiple kinds of output
if (val.val.f->scalar_flag || val.val.f->vector_flag || val.val.f->array_flag)
kindglobal = 1;
if (val.val.f->peratom_flag) kindperatom = 1;
if (val.val.f->local_flag) kindlocal = 1;
} 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 {} does not exist", val.id, mycmd);
// variables only produce one kind of output
if (input->variable->equalstyle(val.val.v) || input->variable->vectorstyle(val.val.v))
kindglobal = 1;
else if (input->variable->atomstyle(val.val.v)) kindperatom = 1;
else error->all(FLERR,"{} variable {} is incompatible style", mycmd, val.id);
}
if (kind == DEFAULT) {
if (kindglobal + kindperatom + kindlocal > 1)
error->all(FLERR,"{} input kind is ambiguous", mycmd);
if (kindglobal) kind = GLOBAL;
if (kindperatom) kind = PERATOM;
if (kindlocal) kind = LOCAL;
} else if (kind == GLOBAL) {
if (!kindglobal)
error->all(FLERR,"{} input kind is not global", mycmd);
} else if (kind == PERATOM) {
if (!kindperatom)
error->all(FLERR,"{} input kind is not peratom", mycmd);
} else if (kind == LOCAL) {
if (!kindlocal)
error->all(FLERR,"{} input kind is not local", mycmd);
}
}
// more error checks
// for fix inputs, check that fix frequency is acceptable
if (kind == PERATOM && mode == SCALAR)
error->all(FLERR, "{} cannot process per-atom values in scalar mode", mycmd);
if (kind == LOCAL && mode == SCALAR)
error->all(FLERR,"{} cannot process local values in scalar mode", mycmd);
for (auto &val : values) {
if (val.which == ArgInfo::COMPUTE && kind == GLOBAL && mode == SCALAR) {
if (val.argindex == 0 && val.val.c->scalar_flag == 0)
error->all(FLERR, "{} compute {} does not calculate a global scalar", mycmd, val.id);
if (val.argindex && val.val.c->vector_flag == 0)
error->all(FLERR, "{} compute {} does not calculate a global vector", mycmd, val.id);
if (val.argindex && val.argindex > val.val.c->size_vector)
error->all(FLERR, "{} compute {} vector is accessed out-of-range", mycmd, val.id);
} else if (val.which == ArgInfo::COMPUTE && kind == GLOBAL && mode == VECTOR) {
if (val.argindex == 0 && val.val.c->vector_flag == 0)
error->all(FLERR, "{} compute {} does not calculate a global vector", mycmd, val.id);
if (val.argindex && val.val.c->array_flag == 0)
error->all(FLERR, "{} compute {} does not calculate a global array", mycmd, val.id);
if (val.argindex && val.argindex > val.val.c->size_array_cols)
error->all(FLERR, "{} compute {} array is accessed out-of-range", mycmd, val.id);
} else if (val.which == ArgInfo::COMPUTE && kind == PERATOM) {
if (val.val.c->peratom_flag == 0)
error->all(FLERR, "{} compute {} does not calculate per-atom values", mycmd, val.id);
if (val.argindex == 0 && val.val.c->size_peratom_cols != 0)
error->all(FLERR, "{} compute {} does not calculate a per-atom vector", mycmd, val.id);
if (val.argindex && val.val.c->size_peratom_cols == 0)
error->all(FLERR, "{} compute {} does not calculate a per-atom array", mycmd, val.id);
if (val.argindex && val.argindex > val.val.c->size_peratom_cols)
error->all(FLERR, "{} compute {} array is accessed out-of-range", mycmd, val.id);
} else if (val.which == ArgInfo::COMPUTE && kind == LOCAL) {
if (val.val.c->local_flag == 0)
error->all(FLERR, "{} compute {} does not calculate local values", mycmd, val.id);
if (val.argindex == 0 && val.val.c->size_local_cols != 0)
error->all(FLERR, "{} compute {} does not calculate a local vector", mycmd, val.id);
if (val.argindex && val.val.c->size_local_cols == 0)
error->all(FLERR, "{} compute {} does not calculate a local array", mycmd, val.id);
if (val.argindex && val.argindex > val.val.c->size_local_cols)
error->all(FLERR, "{} compute {} array is accessed out-of-range", mycmd, val.id);
} else if (val.which == ArgInfo::FIX && kind == GLOBAL && mode == SCALAR) {
if (val.argindex == 0 && val.val.f->scalar_flag == 0)
error->all(FLERR, "{} fix {} does not calculate a global scalar", mycmd, val.id);
if (val.argindex && val.val.f->vector_flag == 0)
error->all(FLERR, "{} fix {} does not calculate a global vector", mycmd, val.id);
if (val.argindex && val.argindex > val.val.f->size_vector)
error->all(FLERR, "{} fix {} vector is accessed out-of-range", mycmd, val.id);
if (nevery % val.val.f->global_freq)
error->all(FLERR, "Fix {} for {} not computed at compatible time", val.id, mycmd);
} else if (val.which == ArgInfo::FIX && kind == GLOBAL && mode == VECTOR) {
if (val.argindex == 0 && val.val.f->vector_flag == 0)
error->all(FLERR, "{} fix {} does not calculate a global vector", mycmd, val.id);
if (val.argindex && val.val.f->array_flag == 0)
error->all(FLERR, "{} fix {} does not calculate a global array", mycmd, val.id);
if (val.argindex && val.argindex > val.val.f->size_array_cols)
error->all(FLERR, "{} fix {} array is accessed out-of-range", mycmd, val.id);
if (nevery % val.val.f->global_freq)
error->all(FLERR, "Fix {} for {} not computed at compatible time", val.id, mycmd);
} else if (val.which == ArgInfo::FIX && kind == PERATOM) {
if (val.val.f->peratom_flag == 0)
error->all(FLERR, "{} fix {} does not calculate per-atom values", mycmd, val.id);
if (val.argindex == 0 && val.val.f->size_peratom_cols != 0)
error->all(FLERR," {} fix {} does not calculate a per-atom vector", mycmd, val.id);
if (val.argindex && val.val.f->size_peratom_cols == 0)
error->all(FLERR, "{} fix {} does not ""calculate a per-atom array", mycmd, val.id);
if (val.argindex && val.argindex > val.val.f->size_peratom_cols)
error->all(FLERR, "{} fix {} array is accessed out-of-range", mycmd, val.id);
if (nevery % val.val.f->global_freq)
error->all(FLERR, "Fix {} for {} not computed at compatible time", val.id, mycmd);
} else if (val.which == ArgInfo::FIX && kind == LOCAL) {
if (val.val.f->local_flag == 0)
error->all(FLERR, "{} fix {} does not calculate local values", mycmd, val.id);
if (val.argindex == 0 && val.val.f->size_local_cols != 0)
error->all(FLERR, "{} fix {} does not calculate a local vector", mycmd, val.id);
if (val.argindex && val.val.f->size_local_cols == 0)
error->all(FLERR, "{} fix does not calculate a local array", mycmd, val.id);
if (val.argindex && val.argindex > val.val.f->size_local_cols)
error->all(FLERR, "{} fix {} array is accessed out-of-range", mycmd, val.id);
if (nevery % val.val.f->global_freq)
error->all(FLERR, "Fix {} for {} not computed at compatible time", val.id, mycmd);
} else if (val.which == ArgInfo::VARIABLE && kind == GLOBAL && mode == SCALAR) {
if (val.argindex == 0 && input->variable->equalstyle(val.val.v) == 0)
error->all(FLERR,"{} variable {} is not equal-style variable", mycmd, val.id);
if (val.argindex && input->variable->vectorstyle(val.val.v) == 0)
error->all(FLERR,"{} variable {} is not vector-style variable" , mycmd, val.id);
} else if (val.which == ArgInfo::VARIABLE && kind == GLOBAL && mode == VECTOR) {
if (val.argindex == 0 && input->variable->vectorstyle(val.val.v) == 0)
error->all(FLERR,"{} variable {} is not vector-style variable", mycmd, val.id);
if (val.argindex) error->all(FLERR,"{} variable {} cannot be indexed", mycmd, val.id);
} else if (val.which == ArgInfo::VARIABLE && kind == PERATOM) {
if (val.argindex == 0 && input->variable->atomstyle(val.val.v) == 0)
error->all(FLERR,"{} variable {} is not atom-style variable", mycmd, val.id);
if (val.argindex) error->all(FLERR,"{} variable {} cannot be indexed", mycmd, val.id);
}
}
// print file comment lines
if (fp && comm->me == 0) {
clearerr(fp);
if (title1) fprintf(fp,"%s\n",title1);
else fprintf(fp,"# Histogrammed data for fix %s\n",id);
if (title2) fprintf(fp,"%s\n",title2);
else fprintf(fp,"# TimeStep Number-of-bins "
"Total-counts Missing-counts Min-value Max-value\n");
if (title3) fprintf(fp,"%s\n",title3);
else fprintf(fp,"# Bin Coord Count Count/Total\n");
if (ferror(fp)) error->one(FLERR,"Error writing file header: {}", utils::getsyserror());
filepos = platform::ftell(fp);
}
delete[] title1;
delete[] title2;
delete[] title3;
// allocate and initialize memory for averaging
if (beyond == EXTRA) nbins += 2;
size_array_rows = nbins;
bin = new double[nbins];
bin_total = new double[nbins];
bin_all = new double[nbins];
coord = new double[nbins];
stats_list = nullptr;
bin_list = nullptr;
vector = nullptr;
maxatom = 0;
if (ave == WINDOW) {
memory->create(stats_list,nwindow,4,"ave/histo:stats_list");
memory->create(bin_list,nwindow,nbins,"ave/histo:bin_list");
}
// initializations
// set coord to bin centers
if (beyond == EXTRA) {
binsize = (hi-lo)/(nbins-2);
bininv = 1.0/binsize;
} else {
binsize = (hi-lo)/nbins;
bininv = 1.0/binsize;
}
if (beyond == EXTRA) {
coord[0] = lo;
coord[nbins-1] = hi;
for (int i = 1; i < nbins-1; i++)
coord[i] = lo + (i-1+0.5)*binsize;
} else {
for (int i = 0; i < nbins; i++)
coord[i] = lo + (i+0.5)*binsize;
}
irepeat = 0;
iwindow = window_limit = 0;
stats_total[0] = stats_total[1] = stats_total[2] = stats_total[3] = 0.0;
for (int i = 0; i < nbins; i++) bin_total[i] = 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);
}
/* ---------------------------------------------------------------------- */
FixAveHisto::~FixAveHisto()
{
if (fp && comm->me == 0) fclose(fp);
delete[] bin;
delete[] bin_total;
delete[] bin_all;
delete[] coord;
memory->destroy(stats_list);
memory->destroy(bin_list);
memory->destroy(vector);
}
/* ---------------------------------------------------------------------- */
int FixAveHisto::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAveHisto::init()
{
auto mycmd = fmt::format("fix {}", style);
// update indices/pointers 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 {} does not exist", val.id, mycmd);
} 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 {} does not exist", val.id, mycmd);
} 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 {} does not exist", val.id, mycmd);
}
}
// 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 something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveHisto::setup(int /*vflag*/)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveHisto::end_of_step()
{
// skip if not step which requires doing something
bigint ntimestep = update->ntimestep;
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
// zero if first step
if (irepeat == 0) {
stats[0] = stats[1] = 0.0;
stats[2] = BIG;
stats[3] = -BIG;
for (int i = 0; i < nbins; i++) bin[i] = 0.0;
}
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (auto &val : values) {
int j = val.argindex;
// atom attributes
if (val.which == ArgInfo::X)
bin_atoms(&atom->x[0][j],3);
else if (val.which == ArgInfo::V)
bin_atoms(&atom->v[0][j],3);
else if (val.which == ArgInfo::F)
bin_atoms(&atom->f[0][j],3);
// invoke compute if not previously invoked
if (val.which == ArgInfo::COMPUTE) {
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) {
if (!(val.val.c->invoked_flag & Compute::INVOKED_SCALAR)) {
val.val.c->compute_scalar();
val.val.c->invoked_flag |= Compute::INVOKED_SCALAR;
}
bin_one(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;
}
bin_one(val.val.c->vector[j-1]);
}
} else if (kind == GLOBAL && mode == VECTOR) {
if (j == 0) {
if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) {
val.val.c->compute_vector();
val.val.c->invoked_flag |= Compute::INVOKED_VECTOR;
}
bin_vector(val.val.c->size_vector,val.val.c->vector,1);
} else {
if (!(val.val.c->invoked_flag & Compute::INVOKED_ARRAY)) {
val.val.c->compute_array();
val.val.c->invoked_flag |= Compute::INVOKED_ARRAY;
}
if (val.val.c->array)
bin_vector(val.val.c->size_array_rows,&val.val.c->array[0][j-1],
val.val.c->size_array_cols);
}
} else if (kind == PERATOM) {
if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) {
val.val.c->compute_peratom();
val.val.c->invoked_flag |= Compute::INVOKED_PERATOM;
}
if (j == 0)
bin_atoms(val.val.c->vector_atom,1);
else if (val.val.c->array_atom)
bin_atoms(&val.val.c->array_atom[0][j-1],val.val.c->size_peratom_cols);
} else if (kind == LOCAL) {
if (!(val.val.c->invoked_flag & Compute::INVOKED_LOCAL)) {
val.val.c->compute_local();
val.val.c->invoked_flag |= Compute::INVOKED_LOCAL;
}
if (j == 0)
bin_vector(val.val.c->size_local_rows,val.val.c->vector_local,1);
else if (val.val.c->array_local)
bin_vector(val.val.c->size_local_rows,&val.val.c->array_local[0][j-1],
val.val.c->size_local_cols);
}
// access fix fields, guaranteed to be ready
} else if (val.which == ArgInfo::FIX) {
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) bin_one(val.val.f->compute_scalar());
else bin_one(val.val.f->compute_vector(j-1));
} else if (kind == GLOBAL && mode == VECTOR) {
if (j == 0) {
int n = val.val.f->size_vector;
for (int i = 0; i < n; i++) bin_one(val.val.f->compute_vector(i));
} else {
int n = val.val.f->size_vector;
for (int i = 0; i < n; i++) bin_one(val.val.f->compute_array(i,j-1));
}
} else if (kind == PERATOM) {
if (j == 0) bin_atoms(val.val.f->vector_atom,1);
else if (val.val.f->array_atom)
bin_atoms(&val.val.f->array_atom[0][j-1],val.val.f->size_peratom_cols);
} else if (kind == LOCAL) {
if (j == 0) bin_vector(val.val.f->size_local_rows,val.val.f->vector_local,1);
else if (val.val.f->array_local)
bin_vector(val.val.f->size_local_rows,&val.val.f->array_local[0][j-1],
val.val.f->size_local_cols);
}
// evaluate equal-style or vector-style or atom-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 (kind == GLOBAL && mode == SCALAR) {
if (j == 0) bin_one(input->variable->compute_equal(val.val.v));
else {
double *varvec;
int nvec = input->variable->compute_vector(val.val.v,&varvec);
if (j > nvec) bin_one(0.0);
else bin_one(varvec[j-1]);
}
} else if (kind == GLOBAL && mode == VECTOR) {
double *varvec;
int nvec = input->variable->compute_vector(val.val.v,&varvec);
bin_vector(nvec,varvec,1);
} else if (val.which == ArgInfo::VARIABLE && kind == PERATOM) {
if (atom->nmax > maxatom) {
memory->destroy(vector);
maxatom = atom->nmax;
memory->create(vector,maxatom,"ave/histo:vector");
}
input->variable->compute_atom(val.val.v,igroup,vector,1,0);
bin_atoms(vector,1);
}
}
}
// 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 - static_cast<bigint>(nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// merge histogram stats across procs if necessary
if (kind == PERATOM || kind == LOCAL) {
MPI_Allreduce(stats,stats_all,2,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&stats[2],&stats_all[2],1,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(&stats[3],&stats_all[3],1,MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(bin,bin_all,nbins,MPI_DOUBLE,MPI_SUM,world);
stats[0] = stats_all[0];
stats[1] = stats_all[1];
stats[2] = stats_all[2];
stats[3] = stats_all[3];
for (int i = 0; i < nbins; i++) bin[i] = bin_all[i];
}
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
stats_total[0] = stats[0];
stats_total[1] = stats[1];
stats_total[2] = stats[2];
stats_total[3] = stats[3];
for (int i = 0; i < nbins; i++) bin_total[i] = bin[i];
} else if (ave == RUNNING) {
stats_total[0] += stats[0];
stats_total[1] += stats[1];
stats_total[2] = MIN(stats_total[2],stats[2]);
stats_total[3] = MAX(stats_total[3],stats[3]);
for (int i = 0; i < nbins; i++) bin_total[i] += bin[i];
} else if (ave == WINDOW) {
int m;
stats_total[0] += stats[0];
if (window_limit) stats_total[0] -= stats_list[iwindow][0];
stats_list[iwindow][0] = stats[0];
stats_total[1] += stats[1];
if (window_limit) stats_total[1] -= stats_list[iwindow][1];
stats_list[iwindow][1] = stats[1];
if (window_limit) m = nwindow;
else m = iwindow+1;
stats_list[iwindow][2] = stats[2];
stats_total[2] = stats_list[0][2];
for (int i = 1; i < m; i++)
stats_total[2] = MIN(stats_total[2],stats_list[i][2]);
stats_list[iwindow][3] = stats[3];
stats_total[3] = stats_list[0][3];
for (int i = 1; i < m; i++)
stats_total[3] = MAX(stats_total[3],stats_list[i][3]);
for (int i = 0; i < nbins; i++) {
bin_total[i] += bin[i];
if (window_limit) bin_total[i] -= bin_list[iwindow][i];
bin_list[iwindow][i] = bin[i];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
}
// output result to file
if (fp && comm->me == 0) {
clearerr(fp);
if (overwrite) (void) platform::fseek(fp,filepos);
fmt::print(fp,"{} {} {} {} {} {}\n",ntimestep,nbins,
stats_total[0],stats_total[1],stats_total[2],stats_total[3]);
if (stats_total[0] != 0.0)
for (int i = 0; i < nbins; i++)
fprintf(fp,"%d %g %g %g\n",
i+1,coord[i],bin_total[i],bin_total[i]/stats_total[0]);
else
for (int i = 0; i < nbins; i++)
fprintf(fp,"%d %g %g %g\n",i+1,coord[i],0.0,0.0);
if (ferror(fp))
error->one(FLERR,"Error writing out histogram data");
fflush(fp);
if (overwrite) {
bigint fileend = platform::ftell(fp);
if ((fileend > 0) && (platform::ftruncate(fp,fileend)))
error->warning(FLERR,"Error while tuncating output: {}",utils::getsyserror());
}
}
}
/* ----------------------------------------------------------------------
return Ith vector value
------------------------------------------------------------------------- */
double FixAveHisto::compute_vector(int i)
{
return stats_total[i];
}
/* ----------------------------------------------------------------------
return I,J array value
------------------------------------------------------------------------- */
double FixAveHisto::compute_array(int i, int j)
{
if (j == 0) return coord[i];
else if (j == 1) return bin_total[i];
else if (stats_total[0] != 0.0) return bin_total[i]/stats_total[0];
return 0.0;
}
/* ----------------------------------------------------------------------
bin a single value
------------------------------------------------------------------------- */
void FixAveHisto::bin_one(double value)
{
stats[2] = MIN(stats[2],value);
stats[3] = MAX(stats[3],value);
if (value < lo) {
if (beyond == IGNORE) {
stats[1] += 1.0;
return;
} else bin[0] += 1.0;
} else if (value > hi) {
if (beyond == IGNORE) {
stats[1] += 1.0;
return;
} else bin[nbins-1] += 1.0;
} else {
int ibin = static_cast<int> ((value-lo)*bininv);
ibin = MIN(ibin,nbins-1);
if (beyond == EXTRA) ibin++;
bin[ibin] += 1.0;
}
stats[0] += 1.0;
}
/* ----------------------------------------------------------------------
bin a vector of values with stride
------------------------------------------------------------------------- */
void FixAveHisto::bin_vector(int n, double *values, int stride)
{
int m = 0;
for (int i = 0; i < n; i++) {
bin_one(values[m]);
m += stride;
}
}
/* ----------------------------------------------------------------------
bin a per-atom vector of values with stride
only bin if atom is in group
------------------------------------------------------------------------- */
void FixAveHisto::bin_atoms(double *values, int stride)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) bin_one(values[m]);
m += stride;
}
}
/* ----------------------------------------------------------------------
parse optional args
------------------------------------------------------------------------- */
void FixAveHisto::options(int iarg, int narg, char **arg)
{
// option defaults
fp = nullptr;
kind = DEFAULT;
ave = ONE;
startstep = 0;
mode = SCALAR;
beyond = IGNORE;
overwrite = 0;
title1 = nullptr;
title2 = nullptr;
title3 = nullptr;
// optional args
auto mycmd = fmt::format("fix {}", style);
while (iarg < narg) {
if ((strcmp(arg[iarg],"file") == 0) || (strcmp(arg[iarg],"append") == 0)) {
if (iarg+2 > narg)
utils::missing_cmd_args(FLERR, std::string("fix ave/histo ")+arg[iarg], error);
if (comm->me == 0) {
if (strcmp(arg[iarg],"file") == 0) fp = fopen(arg[iarg+1],"w");
else fp = fopen(arg[iarg+1],"a");
if (fp == nullptr)
error->one(FLERR, "Cannot open fix ave/histo file {}: {}",
arg[iarg+1], utils::getsyserror());
}
iarg += 2;
} else if (strcmp(arg[iarg],"kind") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " kind", error);
if (strcmp(arg[iarg+1],"global") == 0) kind = GLOBAL;
else if (strcmp(arg[iarg+1],"peratom") == 0) kind = PERATOM;
else if (strcmp(arg[iarg+1],"local") == 0) kind = LOCAL;
else error->all(FLERR,"Unknown fix ave/histo kind option: {}", arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " ave", error);
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,"Unknown fix ave/histo ave option: {}", arg[iarg+1]);
if (ave == WINDOW) {
if (iarg+3 > narg) utils::missing_cmd_args(FLERR, mycmd + " ave window", error);
nwindow = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/histo ave window size: {}", nwindow);
}
iarg += 2;
if (ave == WINDOW) iarg++;
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " start", error);
startstep = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"mode") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " mode", error);
if (strcmp(arg[iarg+1],"scalar") == 0) mode = SCALAR;
else if (strcmp(arg[iarg+1],"vector") == 0) mode = VECTOR;
else error->all(FLERR,"Unknown fix ave/histo mode option: {}", arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"beyond") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " beyond", error);
if (strcmp(arg[iarg+1],"ignore") == 0) beyond = IGNORE;
else if (strcmp(arg[iarg+1],"end") == 0) beyond = END;
else if (strcmp(arg[iarg+1],"extra") == 0) beyond = EXTRA;
else error->all(FLERR,"Unknown fix ave/histo beyond option: {}", arg[iarg+1]);
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, mycmd + " 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, mycmd + " title2", error);
delete[] title2;
title2 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " title3", error);
delete[] title3;
title3 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Unknown {} option: {}", mycmd, arg[iarg]);
}
}
/* ----------------------------------------------------------------------
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
startstep is lower bound on nfreq multiple
------------------------------------------------------------------------- */
bigint FixAveHisto::nextvalid()
{
bigint nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
while (nvalid < startstep) nvalid += nfreq;
if (nvalid-nfreq == update->ntimestep && nrepeat == 1)
nvalid = update->ntimestep;
else
nvalid -= static_cast<bigint>(nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += nfreq;
return nvalid;
}
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