apply clang-format
This commit is contained in:
Axel Kohlmeyer
@ -22,21 +22,21 @@
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Version 1.0
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------------------------------------------------------------------------- */
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#include <cmath>
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#include <cstring>
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#include <cstdlib>
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#include <chrono>
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#include <fstream>
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#include "fix_pimdb_langevin.h"
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#include "universe.h"
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#include "comm.h"
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#include "force.h"
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#include "atom.h"
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#include "comm.h"
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#include "domain.h"
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#include "update.h"
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#include "memory.h"
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#include "error.h"
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#include <algorithm>
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#include "force.h"
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#include "memory.h"
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#include "universe.h"
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#include "update.h"
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#include <cmath>
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#include <cstdlib>
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#include <cstring>
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using namespace LAMMPS_NS;
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using namespace FixConst;
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@ -46,44 +46,46 @@ FixPIMDBLangevin::FixPIMDBLangevin(LAMMPS *lmp, int narg, char **arg) :
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FixPIMDLangevin(lmp, narg, filtered_args = filter_args(narg, arg)), filtered_narg(narg),
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nbosons(atom->nlocal), bosonic_exchange(lmp, atom->nlocal, np, universe->me, true, false)
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{
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synch_energies = true;
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// Loop over the arguments with i++ instead of i+=2 like the parent,
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// because the parent's loop has i++ inside some if blocks.
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for (int i = 3; i < narg - 1; i++) {
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if ((strcmp(arg[i], "method") == 0) && (strcmp(arg[i+1], "pimd") != 0)) {
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error->universe_all(FLERR, "Method not supported in fix pimdb/langevin; only method PIMD");
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}
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else if (strcmp(arg[i], "scale") == 0) {
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error->universe_all(FLERR, "The scale parameter of the PILE_L thermostat is not supported for pimdb, and should be removed.");
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}
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else if ((strcmp(arg[i], "iso") == 0) || (strcmp(arg[i], "aniso") == 0) || (strcmp(arg[i], "barostat") == 0) || (strcmp(arg[i], "taup") == 0)) {
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error->universe_all(FLERR, "Barostat parameters are not available for pimdb.");
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}
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else if (strcmp(arg[i], "esynch") == 0) {
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if (strcmp(arg[i + 1], "yes") == 0) {
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synch_energies = true;
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}
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else if (strcmp(arg[i + 1], "no") == 0) {
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synch_energies = false;
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}
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else {
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error->universe_all(FLERR, "The esynch parameter can only receive yes or no!");
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}
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}
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synch_energies = true;
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// Loop over the arguments with i++ instead of i+=2 like the parent,
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// because the parent's loop has i++ inside some if blocks.
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for (int i = 3; i < narg - 1; i++) {
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if ((strcmp(arg[i], "method") == 0) && (strcmp(arg[i + 1], "pimd") != 0)) {
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error->universe_all(FLERR, "Method not supported in fix pimdb/langevin; only method PIMD");
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} else if (strcmp(arg[i], "scale") == 0) {
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error->universe_all(FLERR,
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"The scale parameter of the PILE_L thermostat is not supported for "
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"pimdb, and should be removed.");
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} else if ((strcmp(arg[i], "iso") == 0) || (strcmp(arg[i], "aniso") == 0) ||
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(strcmp(arg[i], "barostat") == 0) || (strcmp(arg[i], "taup") == 0)) {
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error->universe_all(FLERR, "Barostat parameters are not available for pimdb.");
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} else if (strcmp(arg[i], "esynch") == 0) {
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if (strcmp(arg[i + 1], "yes") == 0) {
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synch_energies = true;
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} else if (strcmp(arg[i + 1], "no") == 0) {
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synch_energies = false;
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} else {
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error->universe_all(FLERR, "The esynch parameter can only receive yes or no!");
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}
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}
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}
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if (fmmode != PHYSICAL) {
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error->universe_all(FLERR, "The only available fmmode for pimdb is physical, please remove the fmmode keyword.");
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}
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if (ensemble != NVE && ensemble != NVT) {
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error->universe_all(FLERR, "The only available ensembles for pimdb are nve and nvt, please choose one of these ensembles.");
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}
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if (fmmode != PHYSICAL) {
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error->universe_all(
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FLERR,
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"The only available fmmode for pimdb is physical, please remove the fmmode keyword.");
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}
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if (ensemble != NVE && ensemble != NVT) {
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error->universe_all(FLERR,
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"The only available ensembles for pimdb are nve and nvt, please choose one "
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"of these ensembles.");
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}
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method = PIMD;
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method = PIMD;
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size_vector = 6;
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size_vector = 6;
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memory->create(f_tag_order, nbosons, 3, "FixPIMDBLangevin:f_tag_order");
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memory->create(f_tag_order, nbosons, 3, "FixPIMDBLangevin:f_tag_order");
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}
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/* ---------------------------------------------------------------------- */
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@ -115,74 +117,72 @@ char **FixPIMDBLangevin::filter_args(int narg, char **arg)
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void FixPIMDBLangevin::prepare_coordinates()
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{
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inter_replica_comm(atom->x);
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double ff = fbond * atom->mass[atom->type[0]];
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int nlocal = atom->nlocal;
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double* me_bead_positions = *(atom->x);
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double* last_bead_positions = &bufsortedall[x_last * nlocal][0];
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double* next_bead_positions = &bufsortedall[x_next * nlocal][0];
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inter_replica_comm(atom->x);
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double ff = fbond * atom->mass[atom->type[0]];
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int nlocal = atom->nlocal;
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double *me_bead_positions = *(atom->x);
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double *last_bead_positions = &bufsortedall[x_last * nlocal][0];
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double *next_bead_positions = &bufsortedall[x_next * nlocal][0];
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bosonic_exchange.prepare_with_coordinates(me_bead_positions,
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last_bead_positions, next_bead_positions,
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beta_np, ff);
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bosonic_exchange.prepare_with_coordinates(me_bead_positions, last_bead_positions,
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next_bead_positions, beta_np, ff);
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}
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/* ---------------------------------------------------------------------- */
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void FixPIMDBLangevin::spring_force() {
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void FixPIMDBLangevin::spring_force()
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{
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for (int i = 0; i < nbosons; i++) {
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f_tag_order[i][0] = 0.0;
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f_tag_order[i][1] = 0.0;
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f_tag_order[i][2] = 0.0;
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}
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bosonic_exchange.spring_force(f_tag_order);
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for (int i = 0; i < nbosons; i++) {
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f_tag_order[i][0] = 0.0;
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f_tag_order[i][1] = 0.0;
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f_tag_order[i][2] = 0.0;
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}
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bosonic_exchange.spring_force(f_tag_order);
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double** f = atom->f;
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tagint* tag = atom->tag;
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for (int i = 0; i < nbosons; i++) {
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f[i][0] += f_tag_order[tag[i] - 1][0];
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f[i][1] += f_tag_order[tag[i] - 1][1];
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f[i][2] += f_tag_order[tag[i] - 1][2];
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}
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double **f = atom->f;
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tagint *tag = atom->tag;
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for (int i = 0; i < nbosons; i++) {
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f[i][0] += f_tag_order[tag[i] - 1][0];
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f[i][1] += f_tag_order[tag[i] - 1][1];
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f[i][2] += f_tag_order[tag[i] - 1][2];
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixPIMDBLangevin::compute_spring_energy() {
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se_bead = bosonic_exchange.get_bead_spring_energy();
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void FixPIMDBLangevin::compute_spring_energy()
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{
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se_bead = bosonic_exchange.get_bead_spring_energy();
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if (synch_energies) {
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MPI_Allreduce(&se_bead, &total_spring_energy, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
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total_spring_energy /= universe->procs_per_world[universe->iworld];
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}
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else {
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total_spring_energy = 0;
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}
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if (synch_energies) {
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MPI_Allreduce(&se_bead, &total_spring_energy, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
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total_spring_energy /= universe->procs_per_world[universe->iworld];
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} else {
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total_spring_energy = 0;
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixPIMDBLangevin::compute_t_prim()
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{
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if (synch_energies) {
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double prim = bosonic_exchange.prim_estimator();
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MPI_Allreduce(&prim, &t_prim, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
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}
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else {
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t_prim = bosonic_exchange.prim_estimator();
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}
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if (synch_energies) {
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double prim = bosonic_exchange.prim_estimator();
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MPI_Allreduce(&prim, &t_prim, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
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} else {
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t_prim = bosonic_exchange.prim_estimator();
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}
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}
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/* ---------------------------------------------------------------------- */
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double FixPIMDBLangevin::compute_vector(int n)
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{
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if (0 <= n && n < 6) {
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return FixPIMDLangevin::compute_vector(n);
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}
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else {
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error->universe_all(FLERR, "Fix only has 6 outputs!");
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}
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return 0.0;
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if (0 <= n && n < 6) {
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return FixPIMDLangevin::compute_vector(n);
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} else {
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error->universe_all(FLERR, "Fix only has 6 outputs!");
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}
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return 0.0;
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}
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