103 lines
3.5 KiB
C++
103 lines
3.5 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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Contributing authors:
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H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama
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Corresponding author:
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Hasan Metin Aktulga, Michigan State University, hma@cse.msu.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_omp.h"
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#include "reaxff_api.h"
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#include <mpi.h>
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#include <cstdlib>
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namespace ReaxFF {
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static void Init_ListsOMP(reax_system *system, control_params *control,
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reax_list **lists)
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{
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int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
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int *hb_top, *bond_top;
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int mincap = system->mincap;
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double safezone = system->safezone;
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double saferzone = system->saferzone;
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auto error = system->error_ptr;
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bond_top = (int*) calloc(system->total_cap, sizeof(int));
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hb_top = (int*) calloc(system->local_cap, sizeof(int));
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Estimate_Storages(system, control, lists,
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&Htop, hb_top, bond_top, &num_3body);
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if (control->hbond_cut > 0) {
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/* init H indexes */
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total_hbonds = 0;
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for (i = 0; i < system->n; ++i) {
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system->my_atoms[i].num_hbonds = hb_top[i];
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total_hbonds += hb_top[i];
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}
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total_hbonds = (int)(MAX(total_hbonds*saferzone,mincap*system->minhbonds));
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Make_List(system->Hcap, total_hbonds, TYP_HBOND,*lists+HBONDS);
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(*lists+HBONDS)->error_ptr = system->error_ptr;
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}
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total_bonds = 0;
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for (i = 0; i < system->N; ++i) {
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system->my_atoms[i].num_bonds = bond_top[i];
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total_bonds += bond_top[i];
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}
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bond_cap = (int)(MAX(total_bonds*safezone, mincap*MIN_BONDS));
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Make_List(system->total_cap, bond_cap, TYP_BOND,*lists+BONDS);
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(*lists+BONDS)->error_ptr = system->error_ptr;
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int nthreads = control->nthreads;
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reax_list *bonds = (*lists)+BONDS;
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for (i = 0; i < bonds->num_intrs; ++i)
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bonds->select.bond_list[i].bo_data.CdboReduction =
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(double*) smalloc(error, sizeof(double)*nthreads, "CdboReduction");
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/* 3bodies list */
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cap_3body = (int)(MAX(num_3body*safezone, MIN_3BODIES));
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Make_List(bond_cap, cap_3body, TYP_THREE_BODY,*lists+THREE_BODIES);
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(*lists+THREE_BODIES)->error_ptr = system->error_ptr;
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free(hb_top);
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free(bond_top);
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}
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void InitializeOMP(reax_system *system, control_params *control,
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simulation_data *data, storage *workspace,
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reax_list **lists, MPI_Comm world)
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{
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Init_System(system,control);
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Init_Simulation_Data(data);
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Init_Workspace(system,control,workspace);
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Init_ListsOMP(system,control,lists);
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if (control->tabulate)
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Init_Lookup_Tables(system,control,workspace,world);
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}
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}
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