492 lines
16 KiB
C++
492 lines
16 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://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 "compute_global_atom.h"
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#include "arg_info.h"
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#include "atom.h"
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#include "error.h"
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#include "fix.h"
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#include "input.h"
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#include "memory.h"
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#include "modify.h"
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#include "update.h"
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#include "variable.h"
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using namespace LAMMPS_NS;
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enum{VECTOR,ARRAY};
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#define BIG 1.0e20
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/* ---------------------------------------------------------------------- */
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ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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idref(nullptr), which(nullptr), argindex(nullptr), value2index(nullptr), ids(nullptr),
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indices(nullptr), varatom(nullptr), vecglobal(nullptr)
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{
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if (narg < 5) error->all(FLERR,"Illegal compute global/atom command");
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peratom_flag = 1;
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// process index arg
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int iarg = 3;
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ArgInfo argi(arg[iarg]);
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whichref = argi.get_type();
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indexref = argi.get_index1();
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idref = argi.copy_name();
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if ((whichref == ArgInfo::UNKNOWN) || (whichref == ArgInfo::NONE)
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|| (argi.get_dim() > 1))
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error->all(FLERR,"Illegal compute global/atom command");
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iarg++;
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// expand args if any have wildcard character "*"
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int expand = 0;
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char **earg;
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int nargnew = utils::expand_args(FLERR,narg-iarg,&arg[iarg],1,earg,lmp);
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if (earg != &arg[iarg]) expand = 1;
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arg = earg;
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// parse values until one isn't recognized
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which = new int[nargnew];
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argindex = new int[nargnew];
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ids = new char*[nargnew];
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value2index = new int[nargnew];
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nvalues = 0;
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for (iarg = 0; iarg < nargnew; iarg++) {
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ArgInfo argi(arg[iarg]);
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which[nvalues] = argi.get_type();
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argindex[nvalues] = argi.get_index1();
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ids[nvalues] = argi.copy_name();
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if ((which[nvalues] == ArgInfo::UNKNOWN) || (which[nvalues] == ArgInfo::NONE)
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|| (argi.get_dim() > 1))
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error->all(FLERR,"Illegal compute slice command");
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nvalues++;
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}
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// if wildcard expansion occurred, free earg memory from expand_args()
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if (expand) {
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for (int i = 0; i < nargnew; i++) delete [] earg[i];
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memory->sfree(earg);
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}
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// setup and error check both index arg and values
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if (whichref == ArgInfo::COMPUTE) {
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int icompute = modify->find_compute(idref);
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if (icompute < 0)
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error->all(FLERR,"Compute ID for compute global/atom does not exist");
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if (!modify->compute[icompute]->peratom_flag)
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error->all(FLERR,"Compute global/atom compute does not "
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"calculate a per-atom vector or array");
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if (indexref == 0 &&
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modify->compute[icompute]->size_peratom_cols != 0)
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error->all(FLERR,"Compute global/atom compute does not "
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"calculate a per-atom vector");
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if (indexref && modify->compute[icompute]->size_peratom_cols == 0)
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error->all(FLERR,"Compute global/atom compute does not "
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"calculate a per-atom array");
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if (indexref && indexref > modify->compute[icompute]->size_peratom_cols)
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error->all(FLERR,
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"Compute global/atom compute array is accessed out-of-range");
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} else if (whichref == ArgInfo::FIX) {
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int ifix = modify->find_fix(idref);
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if (ifix < 0)
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error->all(FLERR,"Fix ID for compute global/atom does not exist");
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if (!modify->fix[ifix]->peratom_flag)
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error->all(FLERR,"Compute global/atom fix does not "
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"calculate a per-atom vector or array");
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if (indexref == 0 &&
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modify->fix[ifix]->size_peratom_cols != 0)
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error->all(FLERR,"Compute global/atom fix does not "
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"calculate a per-atom vector");
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if (indexref && modify->fix[ifix]->size_peratom_cols == 0)
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error->all(FLERR,"Compute global/atom fix does not "
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"calculate a per-atom array");
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if (indexref && indexref > modify->fix[ifix]->size_peratom_cols)
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error->all(FLERR,
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"Compute global/atom fix array is accessed out-of-range");
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} else if (whichref == ArgInfo::VARIABLE) {
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int ivariable = input->variable->find(idref);
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if (ivariable < 0)
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error->all(FLERR,"Variable name for compute global/atom does not exist");
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if (input->variable->atomstyle(ivariable) == 0)
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error->all(FLERR,"Compute global/atom variable is not "
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"atom-style variable");
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}
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for (int i = 0; i < nvalues; i++) {
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if (which[i] == ArgInfo::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(FLERR,"Compute ID for compute global/atom does not exist");
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if (argindex[i] == 0) {
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if (!modify->compute[icompute]->vector_flag)
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error->all(FLERR,"Compute global/atom compute does not "
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"calculate a global vector");
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} else {
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if (!modify->compute[icompute]->array_flag)
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error->all(FLERR,"Compute global/atom compute does not "
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"calculate a global array");
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if (argindex[i] > modify->compute[icompute]->size_array_cols)
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error->all(FLERR,"Compute global/atom compute array is "
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"accessed out-of-range");
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}
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} else if (which[i] == ArgInfo::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(FLERR,"Fix ID for compute global/atom does not exist");
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if (argindex[i] == 0) {
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if (!modify->fix[ifix]->vector_flag)
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error->all(FLERR,"Compute global/atom fix does not "
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"calculate a global vector");
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} else {
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if (!modify->fix[ifix]->array_flag)
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error->all(FLERR,"Compute global/atom fix does not "
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"calculate a global array");
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if (argindex[i] > modify->fix[ifix]->size_array_cols)
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error->all(FLERR,"Compute global/atom fix array is "
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"accessed out-of-range");
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}
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} else if (which[i] == ArgInfo::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(FLERR,"Variable name for compute global/atom "
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"does not exist");
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if (input->variable->vectorstyle(ivariable) == 0)
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error->all(FLERR,"Compute global/atom variable is not "
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"vector-style variable");
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}
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}
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// this compute produces either a peratom vector or array
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if (nvalues == 1) size_peratom_cols = 0;
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else size_peratom_cols = nvalues;
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nmax = maxvector = 0;
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vector_atom = nullptr;
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array_atom = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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ComputeGlobalAtom::~ComputeGlobalAtom()
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{
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delete [] idref;
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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(indices);
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memory->destroy(varatom);
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memory->destroy(vecglobal);
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memory->destroy(vector_atom);
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memory->destroy(array_atom);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeGlobalAtom::init()
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{
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// set indices of all computes,fixes,variables
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if (whichref == ArgInfo::COMPUTE) {
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int icompute = modify->find_compute(idref);
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if (icompute < 0)
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error->all(FLERR,"Compute ID for compute global/atom does not exist");
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ref2index = icompute;
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} else if (whichref == ArgInfo::FIX) {
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int ifix = modify->find_fix(idref);
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if (ifix < 0)
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error->all(FLERR,"Fix ID for compute global/atom does not exist");
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ref2index = ifix;
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} else if (whichref == ArgInfo::VARIABLE) {
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int ivariable = input->variable->find(idref);
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if (ivariable < 0)
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error->all(FLERR,"Variable name for compute global/atom does not exist");
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ref2index = ivariable;
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}
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for (int m = 0; m < nvalues; m++) {
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if (which[m] == ArgInfo::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(FLERR,"Compute ID for compute global/atom does not exist");
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value2index[m] = icompute;
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} else if (which[m] == ArgInfo::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(FLERR,"Fix ID for compute global/atom does not exist");
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value2index[m] = ifix;
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} else if (which[m] == ArgInfo::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(FLERR,"Variable name for compute global/atom "
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"does not exist");
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value2index[m] = ivariable;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeGlobalAtom::compute_peratom()
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{
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int i,j;
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invoked_peratom = update->ntimestep;
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// grow indices and output vector or array if necessary
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if (atom->nmax > nmax) {
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nmax = atom->nmax;
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memory->destroy(indices);
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memory->create(indices,nmax,"global/atom:indices");
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if (whichref == ArgInfo::VARIABLE) {
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memory->destroy(varatom);
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memory->create(varatom,nmax,"global/atom:varatom");
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}
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if (nvalues == 1) {
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memory->destroy(vector_atom);
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memory->create(vector_atom,nmax,"global/atom:vector_atom");
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} else {
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memory->destroy(array_atom);
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memory->create(array_atom,nmax,nvalues,"global/atom:array_atom");
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}
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}
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// setup current peratom indices
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// integer indices are rounded down from double values
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// indices are decremented from 1 to N -> 0 to N-1
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (whichref == ArgInfo::COMPUTE) {
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Compute *compute = modify->compute[ref2index];
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if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
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compute->compute_peratom();
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compute->invoked_flag |= Compute::INVOKED_PERATOM;
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}
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if (indexref == 0) {
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double *compute_vector = compute->vector_atom;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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indices[i] = static_cast<int> (compute_vector[i]) - 1;
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} else {
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double **compute_array = compute->array_atom;
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int im1 = indexref - 1;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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indices[i] = static_cast<int> (compute_array[i][im1]) - 1;
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}
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} else if (whichref == ArgInfo::FIX) {
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if (update->ntimestep % modify->fix[ref2index]->peratom_freq)
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error->all(FLERR,"Fix used in compute global/atom not "
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"computed at compatible time");
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Fix *fix = modify->fix[ref2index];
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if (indexref == 0) {
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double *fix_vector = fix->vector_atom;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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indices[i] = static_cast<int> (fix_vector[i]) - 1;
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} else {
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double **fix_array = fix->array_atom;
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int im1 = indexref - 1;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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indices[i] = static_cast<int> (fix_array[i][im1]) - 1;
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}
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} else if (whichref == ArgInfo::VARIABLE) {
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input->variable->compute_atom(ref2index,igroup,varatom,1,0);
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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indices[i] = static_cast<int> (varatom[i]) - 1;
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}
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// loop over values to fill output vector or array
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for (int m = 0; m < nvalues; m++) {
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// output = vector
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if (argindex[m] == 0) {
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int vmax;
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double *source;
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if (which[m] == ArgInfo::COMPUTE) {
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Compute *compute = modify->compute[value2index[m]];
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if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) {
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compute->compute_vector();
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compute->invoked_flag |= Compute::INVOKED_VECTOR;
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}
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source = compute->vector;
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vmax = compute->size_vector;
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} else if (which[m] == ArgInfo::FIX) {
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if (update->ntimestep % modify->fix[value2index[m]]->peratom_freq)
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error->all(FLERR,"Fix used in compute global/atom not "
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"computed at compatible time");
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Fix *fix = modify->fix[value2index[m]];
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vmax = fix->size_vector;
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if (vmax > maxvector) {
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maxvector = vmax;
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memory->destroy(vecglobal);
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memory->create(vecglobal,maxvector,"global/atom:vecglobal");
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}
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for (i = 0; i < vmax; i++)
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vecglobal[i] = fix->compute_vector(i);
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source = vecglobal;
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} else if (which[m] == ArgInfo::VARIABLE) {
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vmax = input->variable->compute_vector(value2index[m],&source);
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}
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if (nvalues == 1) {
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for (i = 0; i < nlocal; i++) {
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vector_atom[i] = 0.0;
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if (mask[i] & groupbit) {
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j = indices[i];
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if (j >= 0 && j < vmax) vector_atom[i] = source[j];
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}
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}
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} else {
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for (i = 0; i < nlocal; i++) {
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array_atom[i][m] = 0.0;
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if (mask[i] & groupbit) {
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j = indices[i];
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if (j >= 0 && j < vmax) array_atom[i][m] = source[j];
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}
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}
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}
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// output = array
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} else {
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int vmax;
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double *source;
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int col = argindex[m] - 1;
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if (which[m] == ArgInfo::COMPUTE) {
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Compute *compute = modify->compute[value2index[m]];
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if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) {
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compute->compute_array();
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compute->invoked_flag |= Compute::INVOKED_ARRAY;
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}
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double **compute_array = compute->array;
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vmax = compute->size_array_rows;
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if (vmax > maxvector) {
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maxvector = vmax;
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memory->destroy(vecglobal);
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memory->create(vecglobal,maxvector,"global/atom:vecglobal");
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}
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for (i = 0; i < vmax; i++)
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vecglobal[i] = compute_array[i][col];
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source = vecglobal;
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} else if (which[m] == ArgInfo::FIX) {
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if (update->ntimestep % modify->fix[value2index[m]]->peratom_freq)
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error->all(FLERR,"Fix used in compute global/atom not "
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"computed at compatible time");
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Fix *fix = modify->fix[value2index[m]];
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vmax = fix->size_array_rows;
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if (vmax > maxvector) {
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maxvector = vmax;
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memory->destroy(vecglobal);
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memory->create(vecglobal,maxvector,"global/atom:vecglobal");
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}
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for (i = 0; i < vmax; i++)
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vecglobal[i] = fix->compute_array(i,col);
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source = vecglobal;
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} else if (which[m] == ArgInfo::VARIABLE) {
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vmax = input->variable->compute_vector(value2index[m],&source);
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}
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if (nvalues == 1) {
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for (i = 0; i < nlocal; i++) {
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vector_atom[i] = 0.0;
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if (mask[i] & groupbit) {
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j = indices[i];
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if (j >= 0 && j < vmax) vector_atom[i] = source[j];
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}
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}
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} else {
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for (i = 0; i < nlocal; i++) {
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array_atom[i][m] = 0.0;
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if (mask[i] & groupbit) {
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j = indices[i];
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if (j >= 0 && j < vmax) array_atom[i][m] = source[j];
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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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/* ----------------------------------------------------------------------
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memory usage of local atom-based array
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------------------------------------------------------------------------- */
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double ComputeGlobalAtom::memory_usage()
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{
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double bytes = (double)nmax*nvalues * sizeof(double);
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bytes += (double)nmax * sizeof(int); // indices
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if (varatom) bytes += (double)nmax * sizeof(double); // varatom
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bytes += (double)maxvector * sizeof(double); // vecglobal
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return bytes;
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}
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