Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/USER-REAXC/reaxc_forces.cpp
6dd4480482cfefficient_neuronet

Last Change
Raw File

reaxc_forces.cpp
View Options

/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Copyright (2010) Purdue University
Hasan Metin Aktulga, hmaktulga@lbl.gov
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
Please cite the related publication:
H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
"Parallel Reactive Molecular Dynamics: Numerical Methods and
Algorithmic Techniques", Parallel Computing, in press.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
#include "pair_reax_c.h"
#include "reaxc_forces.h"
#include "reaxc_bond_orders.h"
#include "reaxc_bonds.h"
#include "reaxc_hydrogen_bonds.h"
#include "reaxc_io_tools.h"
#include "reaxc_list.h"
#include "reaxc_lookup.h"
#include "reaxc_multi_body.h"
#include "reaxc_nonbonded.h"
#include "reaxc_tool_box.h"
#include "reaxc_torsion_angles.h"
#include "reaxc_valence_angles.h"
#include "reaxc_vector.h"
interaction_function Interaction_Functions[NUM_INTRS];
void Dummy_Interaction( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
{
}
void Init_Force_Functions( control_params *control )
{
Interaction_Functions[0] = BO;
Interaction_Functions[1] = Bonds; //Dummy_Interaction;
Interaction_Functions[2] = Atom_Energy; //Dummy_Interaction;
Interaction_Functions[3] = Valence_Angles; //Dummy_Interaction;
Interaction_Functions[4] = Torsion_Angles; //Dummy_Interaction;
if( control->hbond_cut > 0 )
Interaction_Functions[5] = Hydrogen_Bonds;
else Interaction_Functions[5] = Dummy_Interaction;
Interaction_Functions[6] = Dummy_Interaction; //empty
Interaction_Functions[7] = Dummy_Interaction; //empty
Interaction_Functions[8] = Dummy_Interaction; //empty
Interaction_Functions[9] = Dummy_Interaction; //empty
}
void Compute_Bonded_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
MPI_Comm comm )
{
int i;
/* Implement all force calls as function pointers */
for( i = 0; i < NUM_INTRS; i++ ) {
(Interaction_Functions[i])( system, control, data, workspace,
lists, out_control );
}
}
void Compute_NonBonded_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
MPI_Comm comm )
{
/* van der Waals and Coulomb interactions */
if( control->tabulate == 0 )
vdW_Coulomb_Energy( system, control, data, workspace,
lists, out_control );
else
Tabulated_vdW_Coulomb_Energy( system, control, data, workspace,
lists, out_control );
}
void Compute_Total_Force( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, mpi_datatypes *mpi_data )
{
int i, pj;
reax_list *bonds = (*lists) + BONDS;
for( i = 0; i < system->N; ++i )
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
if( i < bonds->select.bond_list[pj].nbr ) {
if( control->virial == 0 )
Add_dBond_to_Forces( system, i, pj, workspace, lists );
else
Add_dBond_to_Forces_NPT( i, pj, data, workspace, lists );
}
}
void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
int step, int n, int N, int numH, MPI_Comm comm )
{
int i, comp, Hindex;
reax_list *bonds, *hbonds;
double saferzone = system->saferzone;
/* bond list */
if( N > 0 ) {
bonds = *lists + BONDS;
for( i = 0; i < N; ++i ) {
system->my_atoms[i].num_bonds = MAX(Num_Entries(i,bonds)*2, MIN_BONDS);
if( i < N-1 )
comp = Start_Index(i+1, bonds);
else comp = bonds->num_intrs;
if( End_Index(i, bonds) > comp ) {
fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
step, i, End_Index(i,bonds), comp );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
}
/* hbonds list */
if( numH > 0 ) {
hbonds = *lists + HBONDS;
for( i = 0; i < N; ++i ) {
Hindex = system->my_atoms[i].Hindex;
if( Hindex > -1 ) {
system->my_atoms[i].num_hbonds =
(int)(MAX( Num_Entries(Hindex, hbonds)*saferzone, MIN_HBONDS ));
//if( Num_Entries(i, hbonds) >=
//(Start_Index(i+1,hbonds)-Start_Index(i,hbonds))*0.90/*DANGER_ZONE*/){
// workspace->realloc.hbonds = 1;
if( Hindex < numH-1 )
comp = Start_Index(Hindex+1, hbonds);
else comp = hbonds->num_intrs;
if( End_Index(Hindex, hbonds) > comp ) {
fprintf(stderr,"step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n",
step, Hindex, End_Index(Hindex,hbonds), comp );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
}
}
}
void Init_Forces_noQEq( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
MPI_Comm comm ) {
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int btop_i, btop_j, num_bonds, num_hbonds;
int ihb, jhb, ihb_top, jhb_top;
int local, flag, renbr;
double cutoff;
reax_list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
far_nbrs = *lists + FAR_NBRS;
bonds = *lists + BONDS;
hbonds = *lists + HBONDS;
for( i = 0; i < system->n; ++i )
workspace->bond_mark[i] = 0;
for( i = system->n; i < system->N; ++i ) {
workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
}
num_bonds = 0;
num_hbonds = 0;
btop_i = btop_j = 0;
renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
for( i = 0; i < system->N; ++i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
if (type_i < 0) continue;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
if( i < system->n ) {
local = 1;
cutoff = MAX( control->hbond_cut, control->bond_cut );
}
else {
local = 0;
cutoff = control->bond_cut;
}
ihb = -1;
ihb_top = -1;
if( local && control->hbond_cut > 0 ) {
ihb = sbp_i->p_hbond;
if( ihb == 1 )
ihb_top = End_Index( atom_i->Hindex, hbonds );
else ihb_top = -1;
}
/* update i-j distance - check if j is within cutoff */
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
if( renbr ) {
if( nbr_pj->d <= cutoff )
flag = 1;
else flag = 0;
}
else{
nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
if( nbr_pj->d <= SQR(cutoff) ) {
nbr_pj->d = sqrt(nbr_pj->d);
flag = 1;
}
else {
flag = 0;
}
}
if( flag ) {
type_j = atom_j->type;
if (type_j < 0) continue;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( local ) {
/* hydrogen bond lists */
if( control->hbond_cut > 0 && (ihb==1 || ihb==2) &&
nbr_pj->d <= control->hbond_cut ) {
// fprintf( stderr, "%d %d\n", atom1, atom2 );
jhb = sbp_j->p_hbond;
if( ihb == 1 && jhb == 2 ) {
hbonds->select.hbond_list[ihb_top].nbr = j;
hbonds->select.hbond_list[ihb_top].scl = 1;
hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
++ihb_top;
++num_hbonds;
}
else if( j < system->n && ihb == 2 && jhb == 1 ) {
jhb_top = End_Index( atom_j->Hindex, hbonds );
hbonds->select.hbond_list[jhb_top].nbr = i;
hbonds->select.hbond_list[jhb_top].scl = -1;
hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds );
++num_hbonds;
}
}
}
if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
nbr_pj->d <= control->bond_cut &&
BOp( workspace, bonds, control->bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
num_bonds += 2;
++btop_i;
if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
}
}
}
}
Set_End_Index( i, btop_i, bonds );
if( local && ihb == 1 )
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
Validate_Lists( system, workspace, lists, data->step,
system->n, system->N, system->numH, comm );
}
void Estimate_Storages( reax_system *system, control_params *control,
reax_list **lists, int *Htop, int *hb_top,
int *bond_top, int *num_3body, MPI_Comm comm )
{
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int ihb, jhb;
int local;
double cutoff;
double r_ij;
double C12, C34, C56;
double BO, BO_s, BO_pi, BO_pi2;
reax_list *far_nbrs;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
int mincap = system->mincap;
double safezone = system->safezone;
double saferzone = system->saferzone;
far_nbrs = *lists + FAR_NBRS;
*Htop = 0;
memset( hb_top, 0, sizeof(int) * system->local_cap );
memset( bond_top, 0, sizeof(int) * system->total_cap );
*num_3body = 0;
for( i = 0; i < system->N; ++i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
if (type_i < 0) continue;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
sbp_i = &(system->reax_param.sbp[type_i]);
if( i < system->n ) {
local = 1;
cutoff = control->nonb_cut;
++(*Htop);
ihb = sbp_i->p_hbond;
}
else {
local = 0;
cutoff = control->bond_cut;
ihb = -1;
}
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
if(nbr_pj->d <= cutoff) {
type_j = system->my_atoms[j].type;
if (type_j < 0) continue;
r_ij = nbr_pj->d;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( local ) {
if( j < system->n || atom_i->orig_id < atom_j->orig_id ) //tryQEq ||1
++(*Htop);
/* hydrogen bond lists */
if( control->hbond_cut > 0.1 && (ihb==1 || ihb==2) &&
nbr_pj->d <= control->hbond_cut ) {
jhb = sbp_j->p_hbond;
if( ihb == 1 && jhb == 2 )
++hb_top[i];
else if( j < system->n && ihb == 2 && jhb == 1 )
++hb_top[j];
}
}
/* uncorrected bond orders */
if( nbr_pj->d <= control->bond_cut ) {
if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) {
C12 = twbp->p_bo1 * pow( r_ij / twbp->r_s, twbp->p_bo2 );
BO_s = (1.0 + control->bo_cut) * exp( C12 );
}
else BO_s = C12 = 0.0;
if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) {
C34 = twbp->p_bo3 * pow( r_ij / twbp->r_p, twbp->p_bo4 );
BO_pi = exp( C34 );
}
else BO_pi = C34 = 0.0;
if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) {
C56 = twbp->p_bo5 * pow( r_ij / twbp->r_pp, twbp->p_bo6 );
BO_pi2= exp( C56 );
}
else BO_pi2 = C56 = 0.0;
/* Initially BO values are the uncorrected ones, page 1 */
BO = BO_s + BO_pi + BO_pi2;
if( BO >= control->bo_cut ) {
++bond_top[i];
++bond_top[j];
}
}
}
}
}
*Htop = (int)(MAX( *Htop * safezone, mincap * MIN_HENTRIES ));
for( i = 0; i < system->n; ++i )
hb_top[i] = (int)(MAX( hb_top[i] * saferzone, MIN_HBONDS ));
for( i = 0; i < system->N; ++i ) {
*num_3body += SQR(bond_top[i]);
bond_top[i] = MAX( bond_top[i] * 2, MIN_BONDS );
}
}
void Compute_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
mpi_datatypes *mpi_data )
{
MPI_Comm comm = mpi_data->world;
Init_Forces_noQEq( system, control, data, workspace,
lists, out_control, comm );
/********* bonded interactions ************/
Compute_Bonded_Forces( system, control, data, workspace,
lists, out_control, mpi_data->world );
/********* nonbonded interactions ************/
Compute_NonBonded_Forces( system, control, data, workspace,
lists, out_control, mpi_data->world );
/*********** total force ***************/
Compute_Total_Force( system, control, data, workspace, lists, mpi_data );
}
c4science · Help