add support for loading run and min styles
This commit is contained in:
Axel Kohlmeyer
426
examples/plugins/verlet2.cpp
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426
examples/plugins/verlet2.cpp
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// 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 "verlet2.h"
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#include "angle.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "bond.h"
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#include "comm.h"
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#include "dihedral.h"
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#include "domain.h"
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#include "error.h"
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#include "fix.h"
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#include "force.h"
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#include "improper.h"
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#include "kspace.h"
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#include "modify.h"
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#include "neighbor.h"
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#include "output.h"
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#include "pair.h"
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#include "timer.h"
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#include "update.h"
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#include <cstring>
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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Verlet2::Verlet2(LAMMPS *lmp, int narg, char **arg) :
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Integrate(lmp, narg, arg) {}
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Verlet2::~Verlet2()
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{
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// do nothing
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}
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/* ----------------------------------------------------------------------
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initialization before run
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------------------------------------------------------------------------- */
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void Verlet2::init()
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{
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Integrate::init();
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// warn if no fixes doing time integration
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bool do_time_integrate = false;
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for (const auto &fix : modify->get_fix_list())
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if (fix->time_integrate) do_time_integrate = true;
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if (!do_time_integrate && (comm->me == 0))
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error->warning(FLERR,"No fixes with time integration, atoms won't move" + utils::errorurl(28));
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// virial_style:
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// VIRIAL_PAIR if computed explicitly in pair via sum over pair interactions
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// VIRIAL_FDOTR if computed implicitly in pair by
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// virial_fdotr_compute() via sum over ghosts
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if (force->newton_pair) virial_style = VIRIAL_FDOTR;
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else virial_style = VIRIAL_PAIR;
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// setup lists of computes for global and per-atom PE and pressure
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ev_setup();
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// detect if fix omp is present for clearing force arrays
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if (modify->get_fix_by_id("package_omp")) external_force_clear = 1;
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// set flags for arrays to clear in force_clear()
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torqueflag = extraflag = 0;
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if (atom->torque_flag) torqueflag = 1;
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if (atom->avec->forceclearflag) extraflag = 1;
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// orthogonal vs triclinic simulation box
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triclinic = domain->triclinic;
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}
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/* ----------------------------------------------------------------------
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setup before run
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------------------------------------------------------------------------- */
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void Verlet2::setup(int flag)
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{
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if (comm->me == 0 && screen) {
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fputs("Setting up Verlet2 run ...\n",screen);
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if (flag) {
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utils::print(screen," Unit style : {}\n"
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" Current step : {}\n"
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" Time step : {}\n",
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update->unit_style,update->ntimestep,update->dt);
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timer->print_timeout(screen);
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}
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}
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if (lmp->kokkos)
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error->all(FLERR,"KOKKOS package requires run_style verlet2/kk");
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update->setupflag = 1;
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// setup domain, communication and neighboring
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// acquire ghosts
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// build neighbor lists
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atom->setup();
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modify->setup_pre_exchange();
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if (triclinic) domain->x2lamda(atom->nlocal);
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domain->pbc();
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domain->reset_box();
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comm->setup();
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if (neighbor->style) neighbor->setup_bins();
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comm->exchange();
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if (atom->sortfreq > 0) atom->sort();
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comm->borders();
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if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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domain->image_check();
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domain->box_too_small_check();
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modify->setup_pre_neighbor();
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neighbor->build(1);
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modify->setup_post_neighbor();
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neighbor->ncalls = 0;
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// compute all forces
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force->setup();
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ev_set(update->ntimestep);
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force_clear();
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modify->setup_pre_force(vflag);
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if (pair_compute_flag) force->pair->compute(eflag,vflag);
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else if (force->pair) force->pair->compute_dummy(eflag,vflag);
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if (atom->molecular != Atom::ATOMIC) {
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if (force->bond) force->bond->compute(eflag,vflag);
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if (force->angle) force->angle->compute(eflag,vflag);
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if (force->dihedral) force->dihedral->compute(eflag,vflag);
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if (force->improper) force->improper->compute(eflag,vflag);
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}
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if (force->kspace) {
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force->kspace->setup();
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if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
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else force->kspace->compute_dummy(eflag,vflag);
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}
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modify->setup_pre_reverse(eflag,vflag);
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if (force->newton) comm->reverse_comm();
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modify->setup(vflag);
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output->setup(flag);
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update->setupflag = 0;
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}
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/* ----------------------------------------------------------------------
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setup without output
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flag = 0 = just force calculation
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flag = 1 = reneighbor and force calculation
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------------------------------------------------------------------------- */
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void Verlet2::setup_minimal(int flag)
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{
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update->setupflag = 1;
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// setup domain, communication and neighboring
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// acquire ghosts
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// build neighbor lists
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if (flag) {
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modify->setup_pre_exchange();
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if (triclinic) domain->x2lamda(atom->nlocal);
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domain->pbc();
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domain->reset_box();
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comm->setup();
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if (neighbor->style) neighbor->setup_bins();
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comm->exchange();
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comm->borders();
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if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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domain->image_check();
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domain->box_too_small_check();
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modify->setup_pre_neighbor();
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neighbor->build(1);
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modify->setup_post_neighbor();
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neighbor->ncalls = 0;
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}
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// compute all forces
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ev_set(update->ntimestep);
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force_clear();
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modify->setup_pre_force(vflag);
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if (pair_compute_flag) force->pair->compute(eflag,vflag);
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else if (force->pair) force->pair->compute_dummy(eflag,vflag);
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if (atom->molecular != Atom::ATOMIC) {
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if (force->bond) force->bond->compute(eflag,vflag);
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if (force->angle) force->angle->compute(eflag,vflag);
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if (force->dihedral) force->dihedral->compute(eflag,vflag);
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if (force->improper) force->improper->compute(eflag,vflag);
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}
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if (force->kspace) {
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force->kspace->setup();
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if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
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else force->kspace->compute_dummy(eflag,vflag);
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}
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modify->setup_pre_reverse(eflag,vflag);
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if (force->newton) comm->reverse_comm();
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modify->setup(vflag);
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update->setupflag = 0;
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}
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/* ----------------------------------------------------------------------
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run for N steps
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------------------------------------------------------------------------- */
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void Verlet2::run(int n)
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{
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bigint ntimestep;
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int nflag,sortflag;
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int n_post_integrate = modify->n_post_integrate;
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int n_pre_exchange = modify->n_pre_exchange;
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int n_pre_neighbor = modify->n_pre_neighbor;
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int n_post_neighbor = modify->n_post_neighbor;
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int n_pre_force = modify->n_pre_force;
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int n_pre_reverse = modify->n_pre_reverse;
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int n_post_force_any = modify->n_post_force_any;
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int n_end_of_step = modify->n_end_of_step;
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if (atom->sortfreq > 0) sortflag = 1;
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else sortflag = 0;
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for (int i = 0; i < n; i++) {
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if (timer->check_timeout(i)) {
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update->nsteps = i;
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break;
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}
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ntimestep = ++update->ntimestep;
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ev_set(ntimestep);
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// initial time integration
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timer->stamp();
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modify->initial_integrate(vflag);
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if (n_post_integrate) modify->post_integrate();
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timer->stamp(Timer::MODIFY);
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// regular communication vs neighbor list rebuild
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nflag = neighbor->decide();
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if (nflag == 0) {
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timer->stamp();
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comm->forward_comm();
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timer->stamp(Timer::COMM);
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} else {
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if (n_pre_exchange) {
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timer->stamp();
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modify->pre_exchange();
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timer->stamp(Timer::MODIFY);
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}
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if (triclinic) domain->x2lamda(atom->nlocal);
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domain->pbc();
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if (domain->box_change) {
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domain->reset_box();
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comm->setup();
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if (neighbor->style) neighbor->setup_bins();
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}
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timer->stamp();
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comm->exchange();
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if (sortflag && ntimestep >= atom->nextsort) atom->sort();
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comm->borders();
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if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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timer->stamp(Timer::COMM);
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if (n_pre_neighbor) {
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modify->pre_neighbor();
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timer->stamp(Timer::MODIFY);
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}
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neighbor->build(1);
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timer->stamp(Timer::NEIGH);
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if (n_post_neighbor) {
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modify->post_neighbor();
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timer->stamp(Timer::MODIFY);
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}
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}
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// force computations
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// important for pair to come before bonded contributions
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// since some bonded potentials tally pairwise energy/virial
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// and Pair:ev_tally() needs to be called before any tallying
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force_clear();
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timer->stamp();
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if (n_pre_force) {
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modify->pre_force(vflag);
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timer->stamp(Timer::MODIFY);
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}
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if (pair_compute_flag) {
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force->pair->compute(eflag,vflag);
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timer->stamp(Timer::PAIR);
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}
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if (atom->molecular != Atom::ATOMIC) {
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if (force->bond) force->bond->compute(eflag,vflag);
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if (force->angle) force->angle->compute(eflag,vflag);
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if (force->dihedral) force->dihedral->compute(eflag,vflag);
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if (force->improper) force->improper->compute(eflag,vflag);
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timer->stamp(Timer::BOND);
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}
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if (kspace_compute_flag) {
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force->kspace->compute(eflag,vflag);
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timer->stamp(Timer::KSPACE);
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}
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if (n_pre_reverse) {
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modify->pre_reverse(eflag,vflag);
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timer->stamp(Timer::MODIFY);
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}
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// reverse communication of forces
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if (force->newton) {
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comm->reverse_comm();
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timer->stamp(Timer::COMM);
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}
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// force modifications, final time integration, diagnostics
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if (n_post_force_any) modify->post_force(vflag);
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modify->final_integrate();
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if (n_end_of_step) modify->end_of_step();
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timer->stamp(Timer::MODIFY);
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// all output
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if (ntimestep == output->next) {
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timer->stamp();
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output->write(ntimestep);
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timer->stamp(Timer::OUTPUT);
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void Verlet2::cleanup()
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{
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modify->post_run();
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domain->box_too_small_check();
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update->update_time();
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}
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/* ----------------------------------------------------------------------
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clear force on own & ghost atoms
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clear other arrays as needed
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------------------------------------------------------------------------- */
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void Verlet2::force_clear()
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{
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size_t nbytes;
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if (external_force_clear) return;
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// clear force on all particles
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// if either newton flag is set, also include ghosts
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// when using threads always clear all forces.
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int nlocal = atom->nlocal;
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if (neighbor->includegroup == 0) {
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nbytes = sizeof(double) * nlocal;
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if (force->newton) nbytes += sizeof(double) * atom->nghost;
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if (nbytes) {
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memset(&atom->f[0][0],0,3*nbytes);
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if (torqueflag) memset(&atom->torque[0][0],0,3*nbytes);
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if (extraflag) atom->avec->force_clear(0,nbytes);
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}
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// neighbor includegroup flag is set
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// clear force only on initial nfirst particles
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// if either newton flag is set, also include ghosts
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} else {
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nbytes = sizeof(double) * atom->nfirst;
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if (nbytes) {
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memset(&atom->f[0][0],0,3*nbytes);
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if (torqueflag) memset(&atom->torque[0][0],0,3*nbytes);
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if (extraflag) atom->avec->force_clear(0,nbytes);
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}
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if (force->newton) {
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nbytes = sizeof(double) * atom->nghost;
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if (nbytes) {
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memset(&atom->f[nlocal][0],0,3*nbytes);
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if (torqueflag) memset(&atom->torque[nlocal][0],0,3*nbytes);
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if (extraflag) atom->avec->force_clear(nlocal,nbytes);
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}
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}
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}
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}
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Block a user