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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6319 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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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 "stdlib.h"
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#include "string.h"
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#include "compute_slice.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 "group.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};
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#define INVOKED_VECTOR 2
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#define INVOKED_ARRAY 4
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/* ---------------------------------------------------------------------- */
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ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg < 7) error->all("Illegal compute slice command");
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MPI_Comm_rank(world,&me);
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nstart = atoi(arg[3]);
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nstop = atoi(arg[4]);
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nskip = atoi(arg[5]);
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if (nstart < 1 || nstop < nstart || nskip < 1)
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error->all("Illegal compute slice command");
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// parse remaining values until one isn't recognized
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which = new int[narg-6];
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argindex = new int[narg-6];
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ids = new char*[narg-6];
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value2index = new int[narg-6];
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nvalues = 0;
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for (int iarg = 6; iarg < narg; iarg++) {
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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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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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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 slice 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 slice command");
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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 slice does not exist");
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if (modify->compute[icompute]->vector_flag) {
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if (argindex[i])
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error->all("Compute slice compute does not calculate a global array");
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if (nstop > modify->compute[icompute]->size_vector)
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error->all("Compute slice compute vector is accessed out-of-range");
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} else if (modify->compute[icompute]->array_flag) {
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if (argindex[i] == 0)
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error->all("Compute slice compute does not calculate a global vector");
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if (argindex[i] > modify->compute[icompute]->size_array_cols)
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error->all("Compute slice compute array is accessed out-of-range");
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if (nstop > modify->compute[icompute]->size_array_rows)
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error->all("Compute slice compute array is accessed out-of-range");
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} else error->all("Compute slice compute does not calculate "
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"global vector or array");
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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 slice does not exist");
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if (modify->fix[ifix]->vector_flag) {
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if (argindex[i])
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error->all("Compute slice fix does not calculate a global array");
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if (nstop > modify->fix[ifix]->size_vector)
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error->all("Compute slice fix vector is accessed out-of-range");
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} else if (modify->fix[ifix]->array_flag) {
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if (argindex[i] == 0)
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error->all("Compute slice fix does not calculate a global vector");
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if (argindex[i] > modify->fix[ifix]->size_array_cols)
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error->all("Compute slice fix array is accessed out-of-range");
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if (nstop > modify->fix[ifix]->size_array_rows)
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error->all("Compute slice fix array is accessed out-of-range");
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} else error->all("Compute slice fix does not calculate "
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"global vector or array");
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}
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}
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// this compute produces either a vector or array
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// for vector, set intensive/extensive to mirror input values
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// for array, set intensive if all input values are intensive, else extensive
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vector = NULL;
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array = NULL;
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extlist = NULL;
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if (nvalues == 1) {
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vector_flag = 1;
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size_vector = (nstop-nstart) / nskip;
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memory->create(vector,size_vector,"slice:vector");
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if (which[0] == COMPUTE) {
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int icompute = modify->find_compute(ids[0]);
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if (argindex[0] == 0) {
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extvector = modify->compute[icompute]->extvector;
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if (modify->compute[icompute]->extvector == -1) {
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extlist = new int[size_vector];
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int j = 0;
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for (int i = nstart; i < nstop; i += nskip)
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extlist[j++] = modify->compute[icompute]->extlist[i-1];
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}
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} else extvector = modify->compute[icompute]->extarray;
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} else if (which[0] = FIX) {
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int ifix = modify->find_fix(ids[0]);
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if (argindex[0] == 0) {
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extvector = modify->fix[ifix]->extvector;
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if (modify->fix[ifix]->extvector == -1) {
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extlist = new int[size_vector];
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int j = 0;
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for (int i = nstart; i < nstop; i += nskip)
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extlist[j++] = modify->fix[ifix]->extlist[i-1];
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}
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} else extvector = modify->fix[ifix]->extarray;
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}
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} else {
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array_flag = 1;
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size_array_rows = (nstop-nstart) / nskip;
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size_array_cols = nvalues;
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memory->create(array,size_array_rows,size_array_cols,"slice:array");
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extarray = 0;
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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 (argindex[i] == 0) {
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if (modify->compute[icompute]->extvector == 1) extarray = 1;
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if (modify->compute[icompute]->extvector == -1) {
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for (int j = 0; j < modify->compute[icompute]->size_vector; j++)
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if (modify->compute[icompute]->extlist[j]) extarray = 1;
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}
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} else {
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if (modify->compute[icompute]->extarray) extarray = 1;
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}
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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 (argindex[i] == 0) {
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if (modify->fix[ifix]->extvector == 1) extarray = 1;
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if (modify->fix[ifix]->extvector == -1) {
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for (int j = 0; j < modify->fix[ifix]->size_vector; j++)
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if (modify->fix[ifix]->extlist[j]) extarray = 1;
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}
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} else {
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if (modify->fix[ifix]->extarray) extarray = 1;
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}
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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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ComputeSlice::~ComputeSlice()
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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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memory->destroy(vector);
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memory->destroy(array);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSlice::init()
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{
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// set indices and check validity of all computes,fixes
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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 slice 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 slice does not exist");
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value2index[m] = ifix;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSlice::compute_vector()
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{
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invoked_vector = update->ntimestep;
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extract_one(0,vector,1);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSlice::compute_array()
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{
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invoked_array = update->ntimestep;
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for (int m = 0; m < nvalues; m++)
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extract_one(0,&array[m][0],nvalues);
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}
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/* ----------------------------------------------------------------------
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calculate sliced value for one input M and return it in vec
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vec may be array so that returned values are with stride
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------------------------------------------------------------------------- */
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void ComputeSlice::extract_one(int m, double *vec, int stride)
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{
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int i,j;
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// invoke the appropriate compute if needed
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if (which[m] == COMPUTE) {
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Compute *compute = modify->compute[value2index[m]];
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if (argindex[m] == 0) {
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if (!(compute->invoked_flag & INVOKED_VECTOR)) {
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compute->compute_vector();
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compute->invoked_flag |= INVOKED_VECTOR;
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}
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double *cvector = compute->vector;
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j = 0;
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for (i = nstart; i < nstop; i += nskip) {
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vec[j] = cvector[i-1];
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j += stride;
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}
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} else {
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if (!(compute->invoked_flag & INVOKED_ARRAY)) {
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compute->compute_array();
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compute->invoked_flag |= INVOKED_ARRAY;
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}
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double **carray = compute->array;
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int icol = argindex[m]-1;
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j = 0;
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for (i = nstart; i < nstop; i += nskip) {
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vec[j] = carray[i-1][icol];
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j += stride;
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}
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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[value2index[m]]->global_freq)
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error->all("Fix used in compute slice not computed at compatible time");
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Fix *fix = modify->fix[value2index[m]];
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if (argindex[m] == 0) {
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j = 0;
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for (i = nstart; i < nstop; i += nskip) {
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vec[j] = fix->compute_vector(i-1);
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j += stride;
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}
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} else {
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int icol = argindex[m]-1;
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j = 0;
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for (i = nstart; i < nstop; i += nskip) {
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vec[j] = fix->compute_array(i-1,icol);
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j += stride;
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}
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}
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}
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}
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@ -0,0 +1,47 @@
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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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#ifdef COMPUTE_CLASS
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ComputeStyle(slice,ComputeSlice)
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#else
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#ifndef LMP_COMPUTE_SLICE_H
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#define LMP_COMPUTE_SLICE_H
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#include "compute.h"
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namespace LAMMPS_NS {
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class ComputeSlice : public Compute {
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public:
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ComputeSlice(class LAMMPS *, int, char **);
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virtual ~ComputeSlice();
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void init();
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void compute_vector();
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void compute_array();
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private:
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int me;
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int nstart,nstop,nskip,nvalues;
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int *which,*argindex,*value2index;
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char **ids;
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void extract_one(int, double *, int);
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};
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}
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#endif
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#endif
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