457 lines
16 KiB
C++
457 lines
16 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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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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/* ---------------------------------------------------------------------- */
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ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg), indices(nullptr), varatom(nullptr), vecglobal(nullptr)
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{
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if (narg < 5) utils::missing_cmd_args(FLERR,"compute global/atom", error);
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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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reference.which = argi.get_type();
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reference.argindex = argi.get_index1();
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reference.id = argi.get_name();
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if ((reference.which == ArgInfo::UNKNOWN) || (reference.which == ArgInfo::NONE)
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|| (argi.get_dim() > 1))
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error->all(FLERR,"Illegal compute global/atom index property: {}", arg[iarg]);
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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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values.clear();
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for (iarg = 0; iarg < nargnew; iarg++) {
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ArgInfo argi2(arg[iarg]);
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value_t val;
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val.which = argi2.get_type();
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val.argindex = argi2.get_index1();
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val.id = argi2.get_name();
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val.val.c = nullptr;
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if ((val.which == ArgInfo::UNKNOWN) || (val.which == ArgInfo::NONE)
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|| (argi2.get_dim() > 1))
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error->all(FLERR,"Illegal compute global/atom global property: {}", arg[iarg]);
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values.push_back(val);
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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 for both, index arg and values
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if (reference.which == ArgInfo::COMPUTE) {
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reference.val.c = modify->get_compute_by_id(reference.id);
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if (!reference.val.c)
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error->all(FLERR,"Compute ID {} for compute global/atom index", reference.id);
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if (!reference.val.c->peratom_flag)
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error->all(FLERR,"Compute global/atom compute {} does not calculate a per-atom "
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"vector or array", reference.id);
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if ((reference.argindex == 0) && (reference.val.c->size_peratom_cols != 0))
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error->all(FLERR,"Compute global/atom compute {} does not calculate a per-atom "
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"vector", reference.id);
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if (reference.argindex && (reference.val.c->size_peratom_cols == 0))
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error->all(FLERR,"Compute global/atom compute does not calculate a per-atom "
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"array", reference.id);
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if (reference.argindex && (reference.argindex > reference.val.c->size_peratom_cols))
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error->all(FLERR, "Compute global/atom compute array {} is accessed out-of-range",
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reference.id);
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} else if (reference.which == ArgInfo::FIX) {
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reference.val.f =modify->get_fix_by_id(reference.id);
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if (!reference.val.f)
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error->all(FLERR,"Fix ID {} for compute global/atom does not exist", reference.id);
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if (!reference.val.f->peratom_flag)
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error->all(FLERR,"Compute global/atom fix {} does not calculate a per-atom vector "
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"or array", reference.id);
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if (reference.argindex == 0 && (reference.val.f->size_peratom_cols != 0))
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error->all(FLERR,"Compute global/atom fix {} does not calculate a per-atom vector",
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reference.id);
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if (reference.argindex && (reference.val.f->size_peratom_cols == 0))
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error->all(FLERR,"Compute global/atom fix {} does not calculate a per-atom array",
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reference.id);
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if (reference.argindex && (reference.argindex > reference.val.f->size_peratom_cols))
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error->all(FLERR, "Compute global/atom fix {} array is accessed out-of-range", reference.id);
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} else if (reference.which == ArgInfo::VARIABLE) {
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reference.val.v = input->variable->find(reference.id.c_str());
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if (reference.val.v < 0)
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error->all(FLERR,"Variable name {} for compute global/atom index does not exist",
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reference.id);
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if (input->variable->atomstyle(reference.val.v) == 0)
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error->all(FLERR,"Compute global/atom index variable {} is not atom-style variable",
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reference.id);
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}
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for (auto &val : values) {
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if (val.which == ArgInfo::COMPUTE) {
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val.val.c = modify->get_compute_by_id(val.id);
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if (!val.val.c)
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error->all(FLERR,"Compute ID {} for compute global/atom does not exist", val.id);
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if (val.argindex == 0) {
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if (!val.val.c->vector_flag)
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error->all(FLERR,"Compute ID {} for global/atom compute does not calculate "
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"a global vector", val.id);
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} else {
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if (!val.val.c->array_flag)
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error->all(FLERR,"Compute ID {} for global/atom compute does not calculate "
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"a global array", val.id);
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if (val.argindex > val.val.c->size_array_cols)
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error->all(FLERR,"Compute global/atom compute {} array is accessed out-of-range", val.id);
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}
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} else if (val.which == ArgInfo::FIX) {
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val.val.f = modify->get_fix_by_id(val.id);
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if (!val.val.f) error->all(FLERR,"Fix ID {} for compute global/atom does not exist", val.id);
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if (val.argindex == 0) {
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if (!val.val.f->vector_flag)
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error->all(FLERR,"Fix ID {} for compute global/atom compute does not calculate "
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"a global vector", val.id);
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} else {
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if (!val.val.f->array_flag)
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error->all(FLERR,"Fix ID {} for compute global/atom compute does not calculate "
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"a global array", val.id);
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if (val.argindex > val.val.f->size_array_cols)
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error->all(FLERR,"Compute global/atom fix {} array is accessed out-of-range", val.id);
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}
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} else if (val.which == ArgInfo::VARIABLE) {
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val.val.v = input->variable->find(val.id.c_str());
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if (val.val.v < 0)
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error->all(FLERR,"Variable name {} for compute global/atom does not exist", val.id);
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if (input->variable->vectorstyle(val.val.v) == 0)
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error->all(FLERR,"Compute global/atom variable {} is not vector-style variable", val.id);
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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 (values.size() == 1) size_peratom_cols = 0;
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else size_peratom_cols = values.size();
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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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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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// store references of all computes, fixes, or variables
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if (reference.which == ArgInfo::COMPUTE) {
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reference.val.c = modify->get_compute_by_id(reference.id);
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if (!reference.val.c)
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error->all(FLERR,"Compute ID {} for compute global/atom index does not exist", reference.id);
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} else if (reference.which == ArgInfo::FIX) {
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reference.val.f = modify->get_fix_by_id(reference.id);
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if (reference.val.f)
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error->all(FLERR,"Fix ID {} for compute global/atom index does not exist", reference.id);
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} else if (reference.which == ArgInfo::VARIABLE) {
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reference.val.v = input->variable->find(reference.id.c_str());
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if (reference.val.v < 0)
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error->all(FLERR,"Variable name {} for compute global/atom index does not exist",
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reference.id);
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}
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for (auto &val : values) {
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if (val.which == ArgInfo::COMPUTE) {
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val.val.c = modify->get_compute_by_id(val.id);
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if (!val.val.c)
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error->all(FLERR,"Compute ID {} for compute global/atom does not exist", val.id);
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} else if (val.which == ArgInfo::FIX) {
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val.val.f = modify->get_fix_by_id(val.id);
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if (!val.val.f)
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error->all(FLERR,"Fix ID {} for compute global/atom does not exist", val.id);
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} else if (val.which == ArgInfo::VARIABLE) {
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val.val.v = input->variable->find(val.id.c_str());
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if (val.val.v < 0)
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error->all(FLERR,"Variable name {} for compute global/atom does not exist", val.id);
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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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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 (reference.which == 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 (values.size() == 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,values.size(),"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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const int nlocal = atom->nlocal;
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if (reference.which == ArgInfo::COMPUTE) {
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if (!(reference.val.c->invoked_flag & Compute::INVOKED_PERATOM)) {
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reference.val.c->compute_peratom();
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reference.val.c->invoked_flag |= Compute::INVOKED_PERATOM;
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}
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if (reference.argindex == 0) {
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double *compute_vector = reference.val.c->vector_atom;
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for (int 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 = reference.val.c->array_atom;
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int im1 = reference.argindex - 1;
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for (int 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 (reference.which == ArgInfo::FIX) {
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if (update->ntimestep % reference.val.f->peratom_freq)
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error->all(FLERR,"Fix {} used in compute global/atom not computed at compatible time",
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reference.id);
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if (reference.argindex == 0) {
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double *fix_vector = reference.val.f->vector_atom;
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for (int 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 = reference.val.f->array_atom;
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int im1 = reference.argindex - 1;
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for (int 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 (reference.which == ArgInfo::VARIABLE) {
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input->variable->compute_atom(reference.val.v, igroup, varatom, 1, 0);
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for (int 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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int m = 0;
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for (auto &val : values) {
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// output = vector
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if (val.argindex == 0) {
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int vmax;
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double *source;
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if (val.which == ArgInfo::COMPUTE) {
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if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) {
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val.val.c->compute_vector();
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val.val.c->invoked_flag |= Compute::INVOKED_VECTOR;
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}
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source = val.val.c->vector;
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vmax = val.val.c->size_vector;
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} else if (val.which == ArgInfo::FIX) {
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if (update->ntimestep % val.val.f->peratom_freq)
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error->all(FLERR,"Fix {} used in compute global/atom not computed at compatible time",
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val.id);
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vmax = reference.val.f->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 (int i = 0; i < vmax; i++)
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vecglobal[i] = val.val.f->compute_vector(i);
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source = vecglobal;
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} else if (val.which == ArgInfo::VARIABLE) {
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vmax = input->variable->compute_vector(val.val.v, &source);
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}
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if (values.size() == 1) {
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for (int 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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int 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 (int 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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int 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 = val.argindex - 1;
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if (val.which == ArgInfo::COMPUTE) {
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if (!(val.val.c->invoked_flag & Compute::INVOKED_ARRAY)) {
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val.val.c->compute_array();
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val.val.c->invoked_flag |= Compute::INVOKED_ARRAY;
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}
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double **compute_array = val.val.c->array;
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vmax = val.val.c->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 (int 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 (val.which == ArgInfo::FIX) {
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if (update->ntimestep % val.val.f->peratom_freq)
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error->all(FLERR,"Fix {} used in compute global/atom not computed at compatible time",
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val.id);
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vmax = val.val.f->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 (int i = 0; i < vmax; i++)
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vecglobal[i] = val.val.f->compute_array(i,col);
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source = vecglobal;
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} else if (val.which == ArgInfo::VARIABLE) {
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vmax = input->variable->compute_vector(val.val.v, &source);
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}
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if (values.size() == 1) {
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for (int 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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int 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 (int 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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int 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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++m;
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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*values.size() * 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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