git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5064 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
336
src/compute_atom_molecule.cpp
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336
src/compute_atom_molecule.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "string.h"
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#include "stdlib.h"
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#include "compute_atom_molecule.h"
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "compute.h"
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#include "fix.h"
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#include "input.h"
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#include "variable.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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enum{COMPUTE,FIX,VARIABLE};
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#define INVOKED_PERATOM 8
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/* ---------------------------------------------------------------------- */
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ComputeAtomMolecule::
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ComputeAtomMolecule(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg < 4) error->all("Illegal compute atom/molecule command");
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if (atom->molecular == 0)
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error->all("Compute atom/molecule requires molecular atom style");
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// parse args
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which = new int[narg-3];
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argindex = new int[narg-3];
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ids = new char*[narg-3];
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value2index = new int[narg-3];
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nvalues = 0;
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int iarg = 3;
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while (iarg < narg) {
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if (strncmp(arg[iarg],"c_",2) == 0 ||
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strncmp(arg[iarg],"f_",2) == 0 ||
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strncmp(arg[iarg],"v_",2) == 0) {
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if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
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else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
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else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
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int n = strlen(arg[iarg]);
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char *suffix = new char[n];
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strcpy(suffix,&arg[iarg][2]);
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char *ptr = strchr(suffix,'[');
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if (ptr) {
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if (suffix[strlen(suffix)-1] != ']')
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error->all("Illegal compute reduce command");
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argindex[nvalues] = atoi(ptr+1);
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*ptr = '\0';
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} else argindex[nvalues] = 0;
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n = strlen(suffix) + 1;
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ids[nvalues] = new char[n];
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strcpy(ids[nvalues],suffix);
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nvalues++;
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delete [] suffix;
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} else error->all("Illegal compute atom/molecule command");
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iarg++;
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}
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// setup and error check
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for (int i = 0; i < nvalues; i++) {
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if (which[i] == COMPUTE) {
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int icompute = modify->find_compute(ids[i]);
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if (icompute < 0)
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error->all("Compute ID for compute atom/molecule does not exist");
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if (modify->compute[icompute]->peratom_flag == 0)
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error->all("Compute atom/molecule compute does not "
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"calculate per-atom values");
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if (argindex[i] == 0 &&
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modify->compute[icompute]->size_peratom_cols != 0)
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error->all("Compute atom/molecule compute does not "
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"calculate a per-atom vector");
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if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
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error->all("Compute atom/molecule compute does not "
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"calculate a per-atom array");
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if (argindex[i] &&
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argindex[i] > modify->compute[icompute]->size_peratom_cols)
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error->all("Compute atom/molecule compute array is "
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"accessed out-of-range");
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} else if (which[i] == FIX) {
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int ifix = modify->find_fix(ids[i]);
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if (ifix < 0)
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error->all("Fix ID for compute atom/molecule does not exist");
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if (modify->fix[ifix]->peratom_flag)
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error->all("Compute atom/molecule fix does not "
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"calculate per-atom values");
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if (argindex[i] == 0 &&
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modify->fix[ifix]->size_peratom_cols != 0)
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error->all("Compute atom/molecule fix does not "
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"calculate a per-atom vector");
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if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
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error->all("Compute atom/molecule fix does not "
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"calculate a per-atom array");
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if (argindex[i] &&
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argindex[i] > modify->fix[ifix]->size_peratom_cols)
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error->all("Compute atom/molecule fix array is accessed out-of-range");
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} else if (which[i] == VARIABLE) {
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int ivariable = input->variable->find(ids[i]);
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if (ivariable < 0)
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error->all("Variable name for compute atom/molecule does not exist");
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if (input->variable->atomstyle(ivariable) == 0)
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error->all("Compute atom/molecule variable is not "
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"atom-style variable");
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}
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}
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// setup molecule-based data
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nmolecules = molecules_in_group(idlo,idhi);
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vone = vector = NULL;
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aone = array = NULL;
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if (nvalues == 1) {
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vone = (double *) memory->smalloc(nmolecules*sizeof(double),
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"atom/molecule:vone");
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vector = (double *) memory->smalloc(nmolecules*sizeof(double),
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"atom/molecule:vector");
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vector_flag = 1;
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size_vector = nmolecules;
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extvector = 0;
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} else {
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aone = memory->create_2d_double_array(nmolecules,nvalues,
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"atom/molecule:aone");
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array = memory->create_2d_double_array(nmolecules,nvalues,
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"atom/molecule:array");
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array_flag = 1;
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size_array_rows = nmolecules;
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size_array_cols = nvalues;
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extarray = 0;
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}
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maxatom = 0;
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scratch = NULL;
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}
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/* ---------------------------------------------------------------------- */
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ComputeAtomMolecule::~ComputeAtomMolecule()
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{
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memory->sfree(vone);
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memory->sfree(vector);
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memory->sfree(aone);
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memory->destroy_2d_double_array(array);
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memory->sfree(scratch);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeAtomMolecule::init()
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{
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int ntmp = molecules_in_group(idlo,idhi);
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if (ntmp != nmolecules)
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error->all("Molecule count changed in compute atom/molecule");
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// set indices and check validity of all computes,fixes,variables
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for (int m = 0; m < nvalues; m++) {
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if (which[m] == COMPUTE) {
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int icompute = modify->find_compute(ids[m]);
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if (icompute < 0)
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error->all("Compute ID for compute atom/molecule does not exist");
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value2index[m] = icompute;
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} else if (which[m] == FIX) {
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int ifix = modify->find_fix(ids[m]);
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if (ifix < 0)
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error->all("Fix ID for compute atom/molecule does not exist");
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value2index[m] = ifix;
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} else if (which[m] == VARIABLE) {
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int ivariable = input->variable->find(ids[m]);
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if (ivariable < 0)
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error->all("Variable name for compute atom/molecule does not exist");
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value2index[m] = ivariable;
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} else value2index[m] = -1;
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeAtomMolecule::compute_vector()
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{
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int i,j,m,imol;
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invoked_vector = update->ntimestep;
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for (m = 0; m < nmolecules; m++) vone[m] = 0.0;
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compute_one(0);
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int *molecule = atom->molecule;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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j = 0;
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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vone[imol] = scratch[j];
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}
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j += nstride;
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}
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MPI_Allreduce(vone,vector,nmolecules,MPI_DOUBLE,MPI_SUM,world);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeAtomMolecule::compute_array()
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{
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int i,j,m,n,imol;
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invoked_array = update->ntimestep;
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int *molecule = atom->molecule;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (n = 0; n < nvalues; n++) {
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for (m = 0; m < nmolecules; m++) aone[n][m] = 0.0;
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compute_one(n);
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j = 0;
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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aone[n][imol] = scratch[j];
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}
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j += nstride;
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}
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}
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MPI_Allreduce(&aone[0][0],&array[0][0],nvalues*nmolecules,
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MPI_DOUBLE,MPI_SUM,world);
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}
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/* ----------------------------------------------------------------------
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calculate per-atom values for one input M
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invoke the appropriate compute,fix,variable
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reallocate scratch vector if necessary
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------------------------------------------------------------------------- */
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void ComputeAtomMolecule::compute_one(int m)
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{
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int vidx = value2index[m];
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int aidx = argindex[m];
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// invoke compute if not previously invoked
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if (which[m] == COMPUTE) {
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Compute *compute = modify->compute[vidx];
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if (!(compute->invoked_flag & INVOKED_PERATOM)) {
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compute->compute_peratom();
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compute->invoked_flag |= INVOKED_PERATOM;
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}
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if (aidx == 0) {
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scratch = compute->vector_atom;
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nstride = 1;
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} else {
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scratch = &compute->array_atom[0][aidx-1];
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nstride = compute->size_array_cols;
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}
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// access fix fields, check if fix frequency is a match
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} else if (which[m] == FIX) {
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if (update->ntimestep % modify->fix[vidx]->peratom_freq)
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error->all("Fix used in compute atom/molecule not computed "
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"at compatible time");
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Fix *fix = modify->fix[vidx];
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if (aidx == 0) {
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scratch = fix->vector_atom;
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nstride = 1;
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} else {
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scratch = &fix->array_atom[0][aidx-1];
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nstride = fix->size_array_cols;
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}
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// evaluate atom-style variable
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} else if (which[m] == VARIABLE) {
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if (atom->nlocal > maxatom) {
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maxatom = atom->nmax;
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memory->sfree(scratch);
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scratch = (double *)
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memory->smalloc(maxatom*sizeof(double),"atom/molecule:scratch");
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}
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input->variable->compute_atom(vidx,igroup,scratch,1,0);
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local data
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------------------------------------------------------------------------- */
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double ComputeAtomMolecule::memory_usage()
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{
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double bytes = 2*nmolecules*nvalues * sizeof(double);
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if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
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bytes += maxatom * sizeof(double);
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return bytes;
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}
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