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compute_sum.cpp
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Tue, Sep 10, 02:01

compute_sum.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_sum.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "force.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
#define INVOKED_PERATOM 4
enum{X,V,F,COMPUTE,FIX,VARIABLE};
/* ---------------------------------------------------------------------- */
ComputeSum::ComputeSum(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all("Illegal compute sum command");
// parse remaining values
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) {
ids[nvalues] = NULL;
if (strcmp(arg[iarg],"x") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"y") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"z") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 2;
} else 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 ((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("Illegal compute sum 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("Illegal compute sum 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("Compute ID for compute sum does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Compute sum compute does not calculate per-atom values");
if (argindex[i] == 0 && modify->compute[icompute]->size_peratom != 0)
error->all("Compute sum compute does not calculate a per-atom scalar");
if (argindex[i] && modify->compute[icompute]->size_peratom == 0)
error->all("Compute sum compute does not calculate a per-atom vector");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for compute sum does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all("Compute sum fix does not calculate per-atom values");
if (argindex[i] == 0 && modify->fix[ifix]->size_peratom != 0)
error->all("Compute sum fix does not calculate a per-atom scalar");
if (argindex[i] && modify->fix[ifix]->size_peratom == 0)
error->all("Compute sum fix does not calculate a per-atom vector");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for compute sum does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all("Compute sum variable is not atom-style variable");
}
}
// this compute produces either a scalar or vector
if (nvalues == 1) {
scalar_flag = 1;
extscalar = 1;
vector = NULL;
onevec = NULL;
} else {
vector_flag = 1;
size_vector = nvalues;
extvector = 1;
vector = new double[size_vector];
onevec = new double[size_vector];
}
maxatom = 0;
varatom = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSum::~ComputeSum()
{
delete [] which;
delete [] argindex;
for (int m = 0; m < nvalues; m++) delete [] ids[m];
delete [] ids;
delete [] value2index;
delete [] vector;
delete [] onevec;
memory->sfree(varatom);
}
/* ---------------------------------------------------------------------- */
void ComputeSum::init()
{
// 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("Compute ID for compute sum does not exist");
value2index[m] = icompute;
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all("Fix ID for compute sum does not exist");
value2index[m] = ifix;
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all("Variable name for compute sum does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
}
}
/* ---------------------------------------------------------------------- */
double ComputeSum::compute_scalar()
{
invoked |= INVOKED_SCALAR;
double one = compute_one(0);
MPI_Allreduce(&one,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeSum::compute_vector()
{
invoked |= INVOKED_VECTOR;
for (int m = 0; m < nvalues; m++) onevec[m] = compute_one(m);
MPI_Allreduce(onevec,vector,size_vector,MPI_DOUBLE,MPI_SUM,world);
}
/* ---------------------------------------------------------------------- */
double ComputeSum::compute_one(int m)
{
int i;
// invoke the appropriate attribute,compute,fix,variable
// compute scalar quantity by summing over atom scalars
// only include atoms in group
int *mask = atom->mask;
int nlocal = atom->nlocal;
int n = value2index[m];
int j = argindex[m];
double one = 0.0;
if (which[m] == X) {
double **x = atom->x;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += x[i][j];
} else if (which[m] == V) {
double **v = atom->v;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += v[i][j];
} else if (which[m] == F) {
double **f = atom->f;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += f[i][j];
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
if (!(modify->compute[n]->invoked & INVOKED_PERATOM))
modify->compute[n]->compute_peratom();
if (j == 0) {
double *compute_scalar = modify->compute[n]->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += compute_scalar[i];
} else {
double **compute_vector = modify->compute[n]->vector_atom;
int jm1 = j - 1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += compute_vector[i][jm1];
}
// access fix fields, check if frequency is a match
} else if (which[m] == FIX) {
if (update->ntimestep % modify->fix[n]->peratom_freq)
error->all("Fix used in compute sum not computed at compatible time");
if (j == 0) {
double *fix_scalar = modify->fix[n]->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += fix_scalar[i];
} else {
double **fix_vector = modify->fix[n]->vector_atom;
int jm1 = j - 1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += fix_vector[i][jm1];
}
// evaluate atom-style variable
} else if (which[m] == VARIABLE) {
if (nlocal > maxatom) {
maxatom = atom->nmax;
memory->sfree(varatom);
varatom = (double *)
memory->smalloc(maxatom*sizeof(double),"compute/sum:varatom");
}
input->variable->compute_atom(n,igroup,varatom,1,0);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += varatom[i];
}
return one;
}
/* ----------------------------------------------------------------------
memory usage of varatom
------------------------------------------------------------------------- */
double ComputeSum::memory_usage()
{
double bytes = maxatom * sizeof(double);
return bytes;
}

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