129 lines
4.3 KiB
C++
129 lines
4.3 KiB
C++
// clang-format off
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/*----------------------------------------------------------------------
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PuReMD - Purdue ReaxFF Molecular Dynamics Program
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Copyright (2010) Purdue University
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Hasan Metin Aktulga, hmaktulga@lbl.gov
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Joseph Fogarty, jcfogart@mail.usf.edu
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Sagar Pandit, pandit@usf.edu
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Ananth Y Grama, ayg@cs.purdue.edu
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Please cite the related publication:
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H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
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"Parallel Reactive Molecular Dynamics: Numerical Methods and
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Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259.
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This program is free software; you can redistribute it and/or
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modify it under the terms of the GNU General Public License as
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published by the Free Software Foundation; either version 2 of
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the License, or (at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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See the GNU General Public License for more details:
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<https://www.gnu.org/licenses/>.
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----------------------------------------------------------------------*/
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#include "reaxff_api.h"
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#include "error.h"
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#include <cstring>
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namespace ReaxFF {
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static void Reset_Atoms(reax_system* system, control_params *control)
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{
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int i;
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reax_atom *atom;
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system->numH = 0;
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if (control->hbond_cut > 0)
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for (i = 0; i < system->n; ++i) {
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atom = &(system->my_atoms[i]);
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if (atom->type < 0) continue;
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if (system->reax_param.sbp[atom->type].p_hbond == 1)
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atom->Hindex = system->numH++;
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else atom->Hindex = -1;
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}
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}
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void Reset_Simulation_Data(simulation_data* data)
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{
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memset(&data->my_en,0,sizeof(energy_data));
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}
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void Reset_Workspace(reax_system *system, storage *workspace)
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{
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memset(workspace->total_bond_order, 0, system->total_cap * sizeof(double));
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memset(workspace->dDeltap_self, 0, system->total_cap * sizeof(rvec));
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memset(workspace->CdDelta, 0, system->total_cap * sizeof(double));
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memset(workspace->f, 0, system->total_cap * sizeof(rvec));
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}
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static void Reset_Neighbor_Lists(reax_system *system, control_params *control,
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storage *workspace, reax_list **lists)
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{
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int i, total_bonds, Hindex, total_hbonds;
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reax_list *bonds, *hbonds;
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/* bonds list */
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if (system->N > 0) {
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bonds = (*lists) + BONDS;
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total_bonds = 0;
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/* reset start-end indexes */
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for (i = 0; i < system->N; ++i) {
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Set_Start_Index(i, total_bonds, bonds);
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Set_End_Index(i, total_bonds, bonds);
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total_bonds += system->my_atoms[i].num_bonds;
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}
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/* is reallocation needed? */
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if (total_bonds >= bonds->num_intrs * DANGER_ZONE) {
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workspace->realloc.bonds = 1;
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if (total_bonds >= bonds->num_intrs)
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control->error_ptr->one(FLERR,fmt::format("Not enough space for bonds! "
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"total={} allocated={}\n",
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total_bonds, bonds->num_intrs));
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}
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}
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if (control->hbond_cut > 0 && system->numH > 0) {
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hbonds = (*lists) + HBONDS;
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total_hbonds = 0;
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/* reset start-end indexes */
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for (i = 0; i < system->n; ++i) {
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Hindex = system->my_atoms[i].Hindex;
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if (Hindex > -1) {
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Set_Start_Index(Hindex, total_hbonds, hbonds);
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Set_End_Index(Hindex, total_hbonds, hbonds);
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total_hbonds += system->my_atoms[i].num_hbonds;
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}
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}
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/* is reallocation needed? */
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if (total_hbonds >= hbonds->num_intrs * 0.90/*DANGER_ZONE*/) {
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workspace->realloc.hbonds = 1;
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if (total_hbonds >= hbonds->num_intrs)
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control->error_ptr->one(FLERR,fmt::format("Not enough space for hbonds! "
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"total={} allocated={}\n",
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total_hbonds, hbonds->num_intrs));
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}
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}
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}
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void Reset(reax_system *system, control_params *control,
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simulation_data *data, storage *workspace, reax_list **lists)
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{
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Reset_Atoms(system, control);
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Reset_Simulation_Data(data);
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Reset_Workspace(system, workspace);
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Reset_Neighbor_Lists(system, control, workspace, lists);
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}
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}
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