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sjplimp
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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_sum.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 "fix.h"
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#include "force.h"
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#include "comm.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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#define INVOKED_SCALAR 1
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#define INVOKED_VECTOR 2
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#define INVOKED_PERATOM 4
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enum{X,V,F,COMPUTE,FIX,VARIABLE};
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/* ---------------------------------------------------------------------- */
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ComputeSum::ComputeSum(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 sum command");
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// parse remaining values
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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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ids[nvalues] = NULL;
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if (strcmp(arg[iarg],"x") == 0) {
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which[nvalues] = X;
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argindex[nvalues++] = 0;
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} else if (strcmp(arg[iarg],"y") == 0) {
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which[nvalues] = X;
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argindex[nvalues++] = 1;
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} else if (strcmp(arg[iarg],"z") == 0) {
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which[nvalues] = X;
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argindex[nvalues++] = 2;
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} else if (strcmp(arg[iarg],"vx") == 0) {
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which[nvalues] = V;
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argindex[nvalues++] = 0;
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} else if (strcmp(arg[iarg],"vy") == 0) {
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which[nvalues] = V;
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argindex[nvalues++] = 1;
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} else if (strcmp(arg[iarg],"vz") == 0) {
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which[nvalues] = V;
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argindex[nvalues++] = 2;
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} else if (strcmp(arg[iarg],"fx") == 0) {
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which[nvalues] = F;
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argindex[nvalues++] = 0;
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} else if (strcmp(arg[iarg],"fy") == 0) {
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which[nvalues] = F;
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argindex[nvalues++] = 1;
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} else if (strcmp(arg[iarg],"fz") == 0) {
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which[nvalues] = F;
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argindex[nvalues++] = 2;
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} else 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 sum 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 sum 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 sum does not exist");
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if (modify->compute[icompute]->peratom_flag == 0)
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error->all("Compute sum compute does not calculate per-atom values");
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if (argindex[i] == 0 && modify->compute[icompute]->size_peratom != 0)
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error->all("Compute sum compute does not calculate a per-atom scalar");
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if (argindex[i] && modify->compute[icompute]->size_peratom == 0)
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error->all("Compute sum compute does not calculate a per-atom vector");
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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 sum does not exist");
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if (modify->fix[ifix]->peratom_flag == 0)
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error->all("Compute sum fix does not calculate per-atom values");
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if (argindex[i] == 0 && modify->fix[ifix]->size_peratom != 0)
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error->all("Compute sum fix does not calculate a per-atom scalar");
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if (argindex[i] && modify->fix[ifix]->size_peratom == 0)
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error->all("Compute sum fix does not calculate a per-atom vector");
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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 sum does not exist");
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if (input->variable->atomstyle(ivariable) == 0)
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error->all("Compute sum variable is not atom-style variable");
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}
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}
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// this compute produces either a scalar or vector
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if (nvalues == 1) {
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scalar_flag = 1;
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extscalar = 1;
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vector = NULL;
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onevec = NULL;
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} else {
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vector_flag = 1;
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size_vector = nvalues;
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extvector = 1;
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vector = new double[size_vector];
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onevec = new double[size_vector];
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}
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maxatom = 0;
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varatom = NULL;
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}
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/* ---------------------------------------------------------------------- */
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ComputeSum::~ComputeSum()
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{
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delete [] which;
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delete [] argindex;
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for (int m = 0; m < nvalues; m++) delete [] ids[m];
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delete [] ids;
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delete [] value2index;
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delete [] vector;
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delete [] onevec;
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memory->sfree(varatom);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSum::init()
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{
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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 sum 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 sum 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 sum 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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double ComputeSum::compute_scalar()
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{
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invoked |= INVOKED_SCALAR;
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double one = compute_one(0);
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MPI_Allreduce(&one,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
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return scalar;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSum::compute_vector()
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{
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invoked |= INVOKED_VECTOR;
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for (int m = 0; m < nvalues; m++) onevec[m] = compute_one(m);
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MPI_Allreduce(onevec,vector,size_vector,MPI_DOUBLE,MPI_SUM,world);
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}
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/* ---------------------------------------------------------------------- */
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double ComputeSum::compute_one(int m)
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{
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int i;
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// invoke the appropriate attribute,compute,fix,variable
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// compute scalar quantity by summing over atom scalars
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// only include atoms in group
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int n = value2index[m];
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int j = argindex[m];
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double one = 0.0;
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if (which[m] == X) {
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double **x = atom->x;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) one += x[i][j];
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} else if (which[m] == V) {
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double **v = atom->v;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) one += v[i][j];
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} else if (which[m] == F) {
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double **f = atom->f;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) one += f[i][j];
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// invoke compute if not previously invoked
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} else if (which[m] == COMPUTE) {
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if (!(modify->compute[n]->invoked & INVOKED_PERATOM))
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modify->compute[n]->compute_peratom();
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if (j == 0) {
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double *compute_scalar = modify->compute[n]->scalar_atom;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) one += compute_scalar[i];
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} else {
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double **compute_vector = modify->compute[n]->vector_atom;
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int jm1 = j - 1;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) one += compute_vector[i][jm1];
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}
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// access fix fields, check if frequency is a match
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} else if (which[m] == FIX) {
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if (update->ntimestep % modify->fix[n]->peratom_freq)
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error->all("Fix used in compute sum not computed at compatible time");
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if (j == 0) {
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double *fix_scalar = modify->fix[n]->scalar_atom;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) one += fix_scalar[i];
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} else {
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double **fix_vector = modify->fix[n]->vector_atom;
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int jm1 = j - 1;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) one += fix_vector[i][jm1];
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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 (nlocal > maxatom) {
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maxatom = atom->nmax;
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memory->sfree(varatom);
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varatom = (double *)
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memory->smalloc(maxatom*sizeof(double),"compute/sum:varatom");
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}
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input->variable->compute_atom(n,igroup,varatom,1,0);
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) one += varatom[i];
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}
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return one;
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}
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/* ----------------------------------------------------------------------
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memory usage of varatom
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------------------------------------------------------------------------- */
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double ComputeSum::memory_usage()
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{
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double bytes = maxatom * sizeof(double);
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return bytes;
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}
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@ -1,44 +0,0 @@
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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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#ifndef COMPUTE_SUM_H
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#define COMPUTE_SUM_H
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#include "compute.h"
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namespace LAMMPS_NS {
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class ComputeSum : public Compute {
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public:
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ComputeSum(class LAMMPS *, int, char **);
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~ComputeSum();
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void init();
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double compute_scalar();
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void compute_vector();
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double memory_usage();
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private:
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int nvalues;
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int *which,*argindex,*value2index;
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char **ids;
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double *onevec;
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int maxatom;
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double *varatom;
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double compute_one(int);
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};
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}
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#endif
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