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lammps/src/compute_atom_molecule.cpp
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compute_atom_molecule.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 "string.h"
#include "stdlib.h"
#include "compute_atom_molecule.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "fix.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{COMPUTE,FIX,VARIABLE};
#define INVOKED_PERATOM 8
/* ---------------------------------------------------------------------- */
ComputeAtomMolecule::
ComputeAtomMolecule(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal compute atom/molecule command");
if (atom->molecular == 0)
error->all(FLERR,"Compute atom/molecule requires molecular atom style");
// parse args
which = new int[narg-3];
argindex = new int[narg-3];
ids = new char*[narg-3];
value2index = new int[narg-3];
nvalues = 0;
int iarg = 3;
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 compute reduce 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 error->all(FLERR,"Illegal compute atom/molecule command");
iarg++;
}
// setup and error check
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 compute atom/molecule does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all(FLERR,"Compute atom/molecule compute does not "
"calculate per-atom values");
if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all(FLERR,"Compute atom/molecule compute does not "
"calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
error->all(FLERR,"Compute atom/molecule compute does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all(FLERR,"Compute atom/molecule compute array 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 compute atom/molecule does not exist");
if (modify->fix[ifix]->peratom_flag)
error->all(FLERR,"Compute atom/molecule fix does not "
"calculate per-atom values");
if (argindex[i] == 0 &&
modify->fix[ifix]->size_peratom_cols != 0)
error->all(FLERR,"Compute atom/molecule fix does not "
"calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
error->all(FLERR,"Compute atom/molecule fix does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->fix[ifix]->size_peratom_cols)
error->all(FLERR,
"Compute atom/molecule fix array 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 compute atom/molecule does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Compute atom/molecule variable is not "
"atom-style variable");
}
}
// setup molecule-based data
nmolecules = molecules_in_group(idlo,idhi);
vone = vector = NULL;
aone = array = NULL;
if (nvalues == 1) {
memory->create(vone,nmolecules,"atom/molecule:vone");
memory->create(vector,nmolecules,"atom/molecule:vector");
vector_flag = 1;
size_vector = nmolecules;
extvector = 0;
} else {
memory->create(aone,nmolecules,nvalues,"atom/molecule:aone");
memory->create(array,nmolecules,nvalues,"atom/molecule:array");
array_flag = 1;
size_array_rows = nmolecules;
size_array_cols = nvalues;
extarray = 0;
}
maxatom = 0;
scratch = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeAtomMolecule::~ComputeAtomMolecule()
{
delete [] which;
delete [] argindex;
for (int m = 0; m < nvalues; m++) delete [] ids[m];
delete [] ids;
delete [] value2index;
memory->destroy(vone);
memory->destroy(vector);
memory->destroy(aone);
memory->destroy(array);
memory->destroy(scratch);
}
/* ---------------------------------------------------------------------- */
void ComputeAtomMolecule::init()
{
int ntmp = molecules_in_group(idlo,idhi);
if (ntmp != nmolecules)
error->all(FLERR,"Molecule count changed in compute atom/molecule");
// set indices and check validity of all computes,fixes,variables
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 compute atom/molecule 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 compute atom/molecule does not exist");
value2index[m] = ifix;
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all(FLERR,
"Variable name for compute atom/molecule does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
}
}
/* ---------------------------------------------------------------------- */
void ComputeAtomMolecule::compute_vector()
{
int i,j,n,imol;
invoked_vector = update->ntimestep;
for (n = 0; n < nmolecules; n++) vone[n] = 0.0;
compute_one(0);
int *molecule = atom->molecule;
int *mask = atom->mask;
int nlocal = atom->nlocal;
j = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
else imol--;
vone[imol] += peratom[j];
}
j += nstride;
}
int me;
MPI_Comm_rank(world,&me);
MPI_Allreduce(vone,vector,nmolecules,MPI_DOUBLE,MPI_SUM,world);
}
/* ---------------------------------------------------------------------- */
void ComputeAtomMolecule::compute_array()
{
int i,j,m,n,imol;
invoked_array = update->ntimestep;
int *molecule = atom->molecule;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (m = 0; m < nvalues; m++) {
for (n = 0; n < nmolecules; n++) aone[n][m] = 0.0;
compute_one(m);
j = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
else imol--;
aone[imol][m] += peratom[j];
}
j += nstride;
}
}
if (array)
MPI_Allreduce(&aone[0][0],&array[0][0],nvalues*nmolecules,
MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
calculate per-atom values for one input M
invoke the appropriate compute,fix,variable
reallocate scratch if necessary for per-atom variable scratch space
------------------------------------------------------------------------- */
void ComputeAtomMolecule::compute_one(int m)
{
int vidx = value2index[m];
int aidx = argindex[m];
// invoke compute if not previously invoked
if (which[m] == COMPUTE) {
Compute *compute = modify->compute[vidx];
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
if (aidx == 0) {
peratom = compute->vector_atom;
nstride = 1;
} else {
if (compute->array_atom) peratom = &compute->array_atom[0][aidx-1];
else peratom = NULL;
nstride = compute->size_array_cols;
}
// access fix fields, check if fix frequency is a match
} else if (which[m] == FIX) {
if (update->ntimestep % modify->fix[vidx]->peratom_freq)
error->all(FLERR,"Fix used in compute atom/molecule not computed "
"at compatible time");
Fix *fix = modify->fix[vidx];
if (aidx == 0) {
peratom = fix->vector_atom;
nstride = 1;
} else {
peratom = &fix->array_atom[0][aidx-1];
nstride = fix->size_array_cols;
}
// evaluate atom-style variable
} else if (which[m] == VARIABLE) {
if (atom->nlocal > maxatom) {
maxatom = atom->nmax;
memory->destroy(scratch);
memory->create(scratch,maxatom,"atom/molecule:scratch");
peratom = scratch;
}
input->variable->compute_atom(vidx,igroup,peratom,1,0);
nstride = 1;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeAtomMolecule::memory_usage()
{
double bytes = 2*nmolecules*nvalues * sizeof(double);
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
bytes += maxatom * sizeof(double);
return bytes;
}
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