460 lines
14 KiB
C++
460 lines
14 KiB
C++
/*----------------------------------------------------------------------
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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, in press.
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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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<http://www.gnu.org/licenses/>.
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----------------------------------------------------------------------*/
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#include "pair_reaxc.h"
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#include "reaxc_forces.h"
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#include "reaxc_bond_orders.h"
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#include "reaxc_bonds.h"
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#include "reaxc_hydrogen_bonds.h"
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#include "reaxc_io_tools.h"
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#include "reaxc_list.h"
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#include "reaxc_lookup.h"
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#include "reaxc_multi_body.h"
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#include "reaxc_nonbonded.h"
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#include "reaxc_tool_box.h"
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#include "reaxc_torsion_angles.h"
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#include "reaxc_valence_angles.h"
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#include "reaxc_vector.h"
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interaction_function Interaction_Functions[NUM_INTRS];
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void Dummy_Interaction( reax_system *system, control_params *control,
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simulation_data *data, storage *workspace,
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reax_list **lists, output_controls *out_control )
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{
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}
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void Init_Force_Functions( control_params *control )
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{
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Interaction_Functions[0] = BO;
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Interaction_Functions[1] = Bonds; //Dummy_Interaction;
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Interaction_Functions[2] = Atom_Energy; //Dummy_Interaction;
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Interaction_Functions[3] = Valence_Angles; //Dummy_Interaction;
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Interaction_Functions[4] = Torsion_Angles; //Dummy_Interaction;
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if( control->hbond_cut > 0 )
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Interaction_Functions[5] = Hydrogen_Bonds;
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else Interaction_Functions[5] = Dummy_Interaction;
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Interaction_Functions[6] = Dummy_Interaction; //empty
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Interaction_Functions[7] = Dummy_Interaction; //empty
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Interaction_Functions[8] = Dummy_Interaction; //empty
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Interaction_Functions[9] = Dummy_Interaction; //empty
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}
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void Compute_Bonded_Forces( reax_system *system, control_params *control,
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simulation_data *data, storage *workspace,
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reax_list **lists, output_controls *out_control,
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MPI_Comm comm )
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{
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int i;
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/* Implement all force calls as function pointers */
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for( i = 0; i < NUM_INTRS; i++ ) {
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(Interaction_Functions[i])( system, control, data, workspace,
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lists, out_control );
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}
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}
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void Compute_NonBonded_Forces( reax_system *system, control_params *control,
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simulation_data *data, storage *workspace,
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reax_list **lists, output_controls *out_control,
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MPI_Comm comm )
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{
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/* van der Waals and Coulomb interactions */
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if( control->tabulate == 0 )
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vdW_Coulomb_Energy( system, control, data, workspace,
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lists, out_control );
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else
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Tabulated_vdW_Coulomb_Energy( system, control, data, workspace,
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lists, out_control );
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}
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void Compute_Total_Force( reax_system *system, control_params *control,
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simulation_data *data, storage *workspace,
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reax_list **lists, mpi_datatypes *mpi_data )
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{
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int i, pj;
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reax_list *bonds = (*lists) + BONDS;
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for( i = 0; i < system->N; ++i )
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for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
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if( i < bonds->select.bond_list[pj].nbr ) {
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if( control->virial == 0 )
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Add_dBond_to_Forces( system, i, pj, workspace, lists );
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else
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Add_dBond_to_Forces_NPT( i, pj, data, workspace, lists );
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}
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}
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void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
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int step, int n, int N, int numH, MPI_Comm comm )
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{
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int i, comp, Hindex;
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reax_list *bonds, *hbonds;
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double saferzone = system->saferzone;
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/* bond list */
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if( N > 0 ) {
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bonds = *lists + BONDS;
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for( i = 0; i < N; ++i ) {
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system->my_atoms[i].num_bonds = MAX(Num_Entries(i,bonds)*2, MIN_BONDS);
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if( i < N-1 )
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comp = Start_Index(i+1, bonds);
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else comp = bonds->num_intrs;
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if( End_Index(i, bonds) > comp ) {
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fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
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step, i, End_Index(i,bonds), comp );
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MPI_Abort( comm, INSUFFICIENT_MEMORY );
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}
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}
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}
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/* hbonds list */
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if( numH > 0 ) {
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hbonds = *lists + HBONDS;
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for( i = 0; i < N; ++i ) {
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Hindex = system->my_atoms[i].Hindex;
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if( Hindex > -1 ) {
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system->my_atoms[i].num_hbonds =
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(int)(MAX( Num_Entries(Hindex, hbonds)*saferzone, MIN_HBONDS ));
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//if( Num_Entries(i, hbonds) >=
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//(Start_Index(i+1,hbonds)-Start_Index(i,hbonds))*0.90/*DANGER_ZONE*/){
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// workspace->realloc.hbonds = 1;
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if( Hindex < numH-1 )
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comp = Start_Index(Hindex+1, hbonds);
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else comp = hbonds->num_intrs;
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if( End_Index(Hindex, hbonds) > comp ) {
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fprintf(stderr,"step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n",
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step, Hindex, End_Index(Hindex,hbonds), comp );
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MPI_Abort( comm, INSUFFICIENT_MEMORY );
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}
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}
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}
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}
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}
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void Init_Forces_noQEq( reax_system *system, control_params *control,
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simulation_data *data, storage *workspace,
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reax_list **lists, output_controls *out_control,
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MPI_Comm comm ) {
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int i, j, pj;
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int start_i, end_i;
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int type_i, type_j;
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int btop_i, btop_j, num_bonds, num_hbonds;
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int ihb, jhb, ihb_top, jhb_top;
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int local, flag, renbr;
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double cutoff;
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reax_list *far_nbrs, *bonds, *hbonds;
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single_body_parameters *sbp_i, *sbp_j;
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two_body_parameters *twbp;
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far_neighbor_data *nbr_pj;
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reax_atom *atom_i, *atom_j;
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far_nbrs = *lists + FAR_NBRS;
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bonds = *lists + BONDS;
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hbonds = *lists + HBONDS;
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for( i = 0; i < system->n; ++i )
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workspace->bond_mark[i] = 0;
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for( i = system->n; i < system->N; ++i ) {
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workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
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}
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num_bonds = 0;
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num_hbonds = 0;
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btop_i = btop_j = 0;
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renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
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for( i = 0; i < system->N; ++i ) {
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atom_i = &(system->my_atoms[i]);
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type_i = atom_i->type;
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if (type_i < 0) continue;
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start_i = Start_Index(i, far_nbrs);
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end_i = End_Index(i, far_nbrs);
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btop_i = End_Index( i, bonds );
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sbp_i = &(system->reax_param.sbp[type_i]);
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if( i < system->n ) {
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local = 1;
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cutoff = MAX( control->hbond_cut, control->bond_cut );
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}
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else {
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local = 0;
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cutoff = control->bond_cut;
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}
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ihb = -1;
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ihb_top = -1;
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if( local && control->hbond_cut > 0 ) {
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ihb = sbp_i->p_hbond;
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if( ihb == 1 )
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ihb_top = End_Index( atom_i->Hindex, hbonds );
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else ihb_top = -1;
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}
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/* update i-j distance - check if j is within cutoff */
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for( pj = start_i; pj < end_i; ++pj ) {
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nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
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j = nbr_pj->nbr;
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atom_j = &(system->my_atoms[j]);
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if( renbr ) {
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if( nbr_pj->d <= cutoff )
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flag = 1;
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else flag = 0;
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}
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else{
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nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
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nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
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nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
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nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
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if( nbr_pj->d <= SQR(cutoff) ) {
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nbr_pj->d = sqrt(nbr_pj->d);
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flag = 1;
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}
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else {
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flag = 0;
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}
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}
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if( flag ) {
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type_j = atom_j->type;
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if (type_j < 0) continue;
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sbp_j = &(system->reax_param.sbp[type_j]);
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twbp = &(system->reax_param.tbp[type_i][type_j]);
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if( local ) {
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/* hydrogen bond lists */
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if( control->hbond_cut > 0 && (ihb==1 || ihb==2) &&
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nbr_pj->d <= control->hbond_cut ) {
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// fprintf( stderr, "%d %d\n", atom1, atom2 );
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jhb = sbp_j->p_hbond;
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if( ihb == 1 && jhb == 2 ) {
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hbonds->select.hbond_list[ihb_top].nbr = j;
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hbonds->select.hbond_list[ihb_top].scl = 1;
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hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
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++ihb_top;
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++num_hbonds;
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}
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else if( j < system->n && ihb == 2 && jhb == 1 ) {
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jhb_top = End_Index( atom_j->Hindex, hbonds );
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hbonds->select.hbond_list[jhb_top].nbr = i;
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hbonds->select.hbond_list[jhb_top].scl = -1;
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hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
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Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds );
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++num_hbonds;
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}
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}
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}
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if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
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nbr_pj->d <= control->bond_cut &&
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BOp( workspace, bonds, control->bo_cut,
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i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
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num_bonds += 2;
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++btop_i;
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if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
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workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
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else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
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workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
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}
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}
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}
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}
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Set_End_Index( i, btop_i, bonds );
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if( local && ihb == 1 )
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Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
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}
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workspace->realloc.num_bonds = num_bonds;
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workspace->realloc.num_hbonds = num_hbonds;
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Validate_Lists( system, workspace, lists, data->step,
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system->n, system->N, system->numH, comm );
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}
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void Estimate_Storages( reax_system *system, control_params *control,
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reax_list **lists, int *Htop, int *hb_top,
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int *bond_top, int *num_3body, MPI_Comm comm )
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{
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int i, j, pj;
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int start_i, end_i;
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int type_i, type_j;
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int ihb, jhb;
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int local;
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double cutoff;
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double r_ij;
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double C12, C34, C56;
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double BO, BO_s, BO_pi, BO_pi2;
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reax_list *far_nbrs;
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single_body_parameters *sbp_i, *sbp_j;
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two_body_parameters *twbp;
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far_neighbor_data *nbr_pj;
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reax_atom *atom_i, *atom_j;
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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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far_nbrs = *lists + FAR_NBRS;
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*Htop = 0;
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memset( hb_top, 0, sizeof(int) * system->local_cap );
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memset( bond_top, 0, sizeof(int) * system->total_cap );
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*num_3body = 0;
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for( i = 0; i < system->N; ++i ) {
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atom_i = &(system->my_atoms[i]);
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type_i = atom_i->type;
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if (type_i < 0) continue;
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start_i = Start_Index(i, far_nbrs);
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end_i = End_Index(i, far_nbrs);
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sbp_i = &(system->reax_param.sbp[type_i]);
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if( i < system->n ) {
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local = 1;
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cutoff = control->nonb_cut;
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++(*Htop);
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ihb = sbp_i->p_hbond;
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}
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else {
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local = 0;
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cutoff = control->bond_cut;
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ihb = -1;
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}
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for( pj = start_i; pj < end_i; ++pj ) {
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nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
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j = nbr_pj->nbr;
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atom_j = &(system->my_atoms[j]);
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if(nbr_pj->d <= cutoff) {
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type_j = system->my_atoms[j].type;
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if (type_j < 0) continue;
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r_ij = nbr_pj->d;
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sbp_j = &(system->reax_param.sbp[type_j]);
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twbp = &(system->reax_param.tbp[type_i][type_j]);
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if( local ) {
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if( j < system->n || atom_i->orig_id < atom_j->orig_id ) //tryQEq ||1
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++(*Htop);
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/* hydrogen bond lists */
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if( control->hbond_cut > 0.1 && (ihb==1 || ihb==2) &&
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nbr_pj->d <= control->hbond_cut ) {
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jhb = sbp_j->p_hbond;
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if( ihb == 1 && jhb == 2 )
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++hb_top[i];
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else if( j < system->n && ihb == 2 && jhb == 1 )
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++hb_top[j];
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}
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}
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/* uncorrected bond orders */
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if( nbr_pj->d <= control->bond_cut ) {
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if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) {
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C12 = twbp->p_bo1 * pow( r_ij / twbp->r_s, twbp->p_bo2 );
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BO_s = (1.0 + control->bo_cut) * exp( C12 );
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}
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else BO_s = C12 = 0.0;
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if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) {
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C34 = twbp->p_bo3 * pow( r_ij / twbp->r_p, twbp->p_bo4 );
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BO_pi = exp( C34 );
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}
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else BO_pi = C34 = 0.0;
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if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) {
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C56 = twbp->p_bo5 * pow( r_ij / twbp->r_pp, twbp->p_bo6 );
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BO_pi2= exp( C56 );
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}
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else BO_pi2 = C56 = 0.0;
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/* Initially BO values are the uncorrected ones, page 1 */
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BO = BO_s + BO_pi + BO_pi2;
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if( BO >= control->bo_cut ) {
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++bond_top[i];
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++bond_top[j];
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}
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}
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}
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}
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}
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*Htop = (int)(MAX( *Htop * safezone, mincap * MIN_HENTRIES ));
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for( i = 0; i < system->n; ++i )
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hb_top[i] = (int)(MAX( hb_top[i] * saferzone, MIN_HBONDS ));
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for( i = 0; i < system->N; ++i ) {
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*num_3body += SQR(bond_top[i]);
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bond_top[i] = MAX( bond_top[i] * 2, MIN_BONDS );
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}
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}
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void Compute_Forces( reax_system *system, control_params *control,
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simulation_data *data, storage *workspace,
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reax_list **lists, output_controls *out_control,
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mpi_datatypes *mpi_data )
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{
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MPI_Comm comm = mpi_data->world;
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Init_Forces_noQEq( system, control, data, workspace,
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lists, out_control, comm );
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/********* bonded interactions ************/
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Compute_Bonded_Forces( system, control, data, workspace,
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lists, out_control, mpi_data->world );
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/********* nonbonded interactions ************/
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Compute_NonBonded_Forces( system, control, data, workspace,
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lists, out_control, mpi_data->world );
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/*********** total force ***************/
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Compute_Total_Force( system, control, data, workspace, lists, mpi_data );
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}
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