Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/src/compute_global_atom.cpp
3653f4012013lammm-devel

Last Change
Raw File

compute_global_atom.cpp
View Options

/* ----------------------------------------------------------------------
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_global_atom.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "force.h"
#include "comm.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{COMPUTE,FIX,VARIABLE};
enum{VECTOR,ARRAY};
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
#define INVOKED_PERATOM 8
#define BIG 1.0e20
/* ---------------------------------------------------------------------- */
ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
idref(NULL), which(NULL), argindex(NULL), value2index(NULL), ids(NULL),
indices(NULL), varatom(NULL), vecglobal(NULL)
{
if (narg < 5) error->all(FLERR,"Illegal compute global/atom command");
peratom_flag = 1;
// process index arg
int iarg = 3;
if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') whichref = COMPUTE;
else if (arg[iarg][0] == 'f') whichref = FIX;
else if (arg[iarg][0] == 'v') whichref = 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 global/atom command");
indexref = atoi(ptr+1);
*ptr = '\0';
} else indexref = 0;
n = strlen(suffix) + 1;
idref = new char[n];
strcpy(idref,suffix);
delete [] suffix;
} else error->all(FLERR,"Illegal compute global/atom command");
iarg++;
// expand args if any have wildcard character "*"
int expand = 0;
char **earg;
int nargnew = input->expand_args(narg-iarg,&arg[iarg],1,earg);
if (earg != &arg[iarg]) 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];
nvalues = 0;
iarg = 0;
while (iarg < nargnew) {
ids[nvalues] = NULL;
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 global/atom 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 global/atom command");
iarg++;
}
// if wildcard expansion occurred, free earg memory from expand_args()
if (expand) {
for (int i = 0; i < nargnew; i++) delete [] earg[i];
memory->sfree(earg);
}
// setup and error check both index arg and values
if (whichref == COMPUTE) {
int icompute = modify->find_compute(idref);
if (icompute < 0)
error->all(FLERR,"Compute ID for compute global/atom does not exist");
if (!modify->compute[icompute]->peratom_flag)
error->all(FLERR,"Compute global/atom compute does not "
"calculate a per-atom vector or array");
if (indexref == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all(FLERR,"Compute global/atom compute does not "
"calculate a per-atom vector");
if (indexref && modify->compute[icompute]->size_peratom_cols == 0)
error->all(FLERR,"Compute global/atom compute does not "
"calculate a per-atom array");
if (indexref && indexref > modify->compute[icompute]->size_peratom_cols)
error->all(FLERR,
"Compute global/atom compute array is accessed out-of-range");
} else if (whichref == FIX) {
int ifix = modify->find_fix(idref);
if (ifix < 0)
error->all(FLERR,"Fix ID for compute global/atom does not exist");
if (!modify->fix[ifix]->peratom_flag)
error->all(FLERR,"Compute global/atom fix does not "
"calculate a per-atom vector or array");
if (indexref == 0 &&
modify->fix[ifix]->size_peratom_cols != 0)
error->all(FLERR,"Compute global/atom fix does not "
"calculate a per-atom vector");
if (indexref && modify->fix[ifix]->size_peratom_cols == 0)
error->all(FLERR,"Compute global/atom fix does not "
"calculate a per-atom array");
if (indexref && indexref > modify->fix[ifix]->size_peratom_cols)
error->all(FLERR,
"Compute global/atom fix array is accessed out-of-range");
} else if (whichref == VARIABLE) {
int ivariable = input->variable->find(idref);
if (ivariable < 0)
error->all(FLERR,"Variable name for compute global/atom does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Compute global/atom variable is not "
"atom-style variable");
}
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 global/atom does not exist");
if (argindex[i] == 0) {
if (!modify->compute[icompute]->vector_flag)
error->all(FLERR,"Compute global/atom compute does not "
"calculate a global vector");
} else {
if (!modify->compute[icompute]->array_flag)
error->all(FLERR,"Compute global/atom compute does not "
"calculate a global array");
if (argindex[i] > modify->compute[icompute]->size_array_cols)
error->all(FLERR,"Compute global/atom 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 global/atom does not exist");
if (argindex[i] == 0) {
if (!modify->fix[ifix]->vector_flag)
error->all(FLERR,"Compute global/atom fix does not "
"calculate a global vector");
} else {
if (!modify->fix[ifix]->array_flag)
error->all(FLERR,"Compute global/atom fix does not "
"calculate a global array");
if (argindex[i] > modify->fix[ifix]->size_array_cols)
error->all(FLERR,"Compute global/atom 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 global/atom "
"does not exist");
if (input->variable->vectorstyle(ivariable) == 0)
error->all(FLERR,"Compute global/atom variable is not "
"vector-style variable");
}
}
// this compute produces either a peratom vector or array
if (nvalues == 1) size_peratom_cols = 0;
else size_peratom_cols = nvalues;
nmax = maxvector = 0;
indices = NULL;
varatom = NULL;
vecglobal = NULL;
vector_atom = NULL;
array_atom = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeGlobalAtom::~ComputeGlobalAtom()
{
delete [] idref;
delete [] which;
delete [] argindex;
for (int m = 0; m < nvalues; m++) delete [] ids[m];
delete [] ids;
delete [] value2index;
memory->destroy(indices);
memory->destroy(varatom);
memory->destroy(vecglobal);
memory->destroy(vector_atom);
memory->destroy(array_atom);
}
/* ---------------------------------------------------------------------- */
void ComputeGlobalAtom::init()
{
// set indices of all computes,fixes,variables
if (whichref == COMPUTE) {
int icompute = modify->find_compute(idref);
if (icompute < 0)
error->all(FLERR,"Compute ID for compute global/atom does not exist");
ref2index = icompute;
} else if (whichref == FIX) {
int ifix = modify->find_fix(idref);
if (ifix < 0)
error->all(FLERR,"Fix ID for compute global/atom does not exist");
ref2index = ifix;
} else if (whichref == VARIABLE) {
int ivariable = input->variable->find(idref);
if (ivariable < 0)
error->all(FLERR,"Variable name for compute global/atom does not exist");
ref2index = ivariable;
}
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 global/atom 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 global/atom 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 global/atom "
"does not exist");
value2index[m] = ivariable;
}
}
}
/* ---------------------------------------------------------------------- */
void ComputeGlobalAtom::compute_peratom()
{
int i,j;
invoked_peratom = update->ntimestep;
// grow indices and output vector or array if necessary
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->destroy(indices);
memory->create(indices,nmax,"global/atom:indices");
if (nvalues == 1) {
memory->destroy(vector_atom);
memory->create(vector_atom,nmax,"global/atom:vector_atom");
} else {
memory->destroy(array_atom);
memory->create(array_atom,nmax,nvalues,"global/atom:array_atom");
}
}
// setup current peratom indices
// integer indices are rounded down from double values
// indices are decremented from 1 to N -> 0 to N-1
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (whichref == COMPUTE) {
Compute *compute = modify->compute[ref2index];
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
if (indexref == 0) {
double *compute_vector = compute->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
indices[i] = static_cast<int> (compute_vector[i]) - 1;
} else {
double **compute_array = compute->array_atom;
int im1 = indexref - 1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
indices[i] = static_cast<int> (compute_array[i][im1]) - 1;
}
} else if (whichref == FIX) {
if (update->ntimestep % modify->fix[ref2index]->peratom_freq)
error->all(FLERR,"Fix used in compute global/atom not "
"computed at compatible time");
Fix *fix = modify->fix[ref2index];
if (indexref == 0) {
double *fix_vector = fix->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
indices[i] = static_cast<int> (fix_vector[i]) - 1;
} else {
double **fix_array = fix->array_atom;
int im1 = indexref - 1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
indices[i] = static_cast<int> (fix_array[i][im1]) - 1;
}
} else if (whichref == VARIABLE) {
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->destroy(varatom);
memory->create(varatom,nmax,"global/atom:varatom");
}
input->variable->compute_atom(ref2index,igroup,varatom,1,0);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
indices[i] = static_cast<int> (varatom[i]) - 1;
}
// loop over values to fill output vector or array
for (int m = 0; m < nvalues; m++) {
// output = vector
if (argindex[m] == 0) {
int vmax;
double *source;
if (which[m] == COMPUTE) {
Compute *compute = modify->compute[value2index[m]];
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
source = compute->vector;
vmax = compute->size_vector;
} else if (which[m] == FIX) {
if (update->ntimestep % modify->fix[value2index[m]]->peratom_freq)
error->all(FLERR,"Fix used in compute global/atom not "
"computed at compatible time");
Fix *fix = modify->fix[value2index[m]];
vmax = fix->size_vector;
if (vmax > maxvector) {
maxvector = vmax;
memory->destroy(vecglobal);
memory->create(vecglobal,maxvector,"global/atom:vecglobal");
}
for (i = 0; i < vmax; i++)
vecglobal[i] = fix->compute_vector(i);
source = vecglobal;
} else if (which[m] == VARIABLE) {
vmax = input->variable->compute_vector(value2index[m],&source);
}
if (nvalues == 1) {
for (i = 0; i < nlocal; i++) {
vector_atom[i] = 0.0;
if (mask[i] & groupbit) {
j = indices[i];
if (j >= 0 && j < vmax) vector_atom[i] = source[j];
}
}
} else {
for (i = 0; i < nlocal; i++) {
array_atom[i][m] = 0.0;
if (mask[i] & groupbit) {
j = indices[i];
if (j >= 0 && j < vmax) array_atom[i][m] = source[j];
}
}
}
// output = array
} else {
int vmax;
double *source;
int col = argindex[m] - 1;
if (which[m] == COMPUTE) {
Compute *compute = modify->compute[value2index[m]];
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
double **compute_array = compute->array;
vmax = compute->size_array_rows;
if (vmax > maxvector) {
maxvector = vmax;
memory->destroy(vecglobal);
memory->create(vecglobal,maxvector,"global/atom:vecglobal");
}
for (i = 0; i < vmax; i++)
vecglobal[i] = compute_array[i][col];
source = vecglobal;
} else if (which[m] == FIX) {
if (update->ntimestep % modify->fix[value2index[m]]->peratom_freq)
error->all(FLERR,"Fix used in compute global/atom not "
"computed at compatible time");
Fix *fix = modify->fix[value2index[m]];
vmax = fix->size_array_rows;
if (vmax > maxvector) {
maxvector = vmax;
memory->destroy(vecglobal);
memory->create(vecglobal,maxvector,"global/atom:vecglobal");
}
for (i = 0; i < vmax; i++)
vecglobal[i] = fix->compute_array(i,col);
source = vecglobal;
} else if (which[m] == VARIABLE) {
vmax = input->variable->compute_vector(value2index[m],&source);
}
if (nvalues == 1) {
for (i = 0; i < nlocal; i++) {
vector_atom[i] = 0.0;
if (mask[i] & groupbit) {
j = indices[i];
if (j >= 0 && j < vmax) vector_atom[i] = source[j];
}
}
} else {
for (i = 0; i < nlocal; i++) {
array_atom[i][m] = 0.0;
if (mask[i] & groupbit) {
j = indices[i];
if (j >= 0 && j < vmax) array_atom[i][m] = source[j];
}
}
}
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeGlobalAtom::memory_usage()
{
double bytes = nmax*nvalues * sizeof(double);
bytes += nmax * sizeof(int); // indices
if (varatom) bytes += nmax * sizeof(double); // varatom
bytes += maxvector * sizeof(double); // vecglobal
return bytes;
}
c4science · Help