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lammps/src/USER-OMP/reaxc_forces_omp.cpp
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reaxc_forces_omp.cpp
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/*----------------------------------------------------------------------
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_reaxc_omp.h"
#include "thr_data.h"
#include "reaxc_forces_omp.h"
#include "reaxc_bond_orders_omp.h"
#include "reaxc_bonds_omp.h"
#include "reaxc_hydrogen_bonds_omp.h"
#include "reaxc_io_tools.h"
#include "reaxc_list.h"
#include "reaxc_lookup.h"
#include "reaxc_multi_body_omp.h"
#include "reaxc_nonbonded_omp.h"
#include "reaxc_tool_box.h"
#include "reaxc_torsion_angles_omp.h"
#include "reaxc_valence_angles_omp.h"
#include "reaxc_vector.h"
#if defined(_OPENMP)
#include <omp.h>
#endif
using namespace LAMMPS_NS;
// Functions defined in reaxc_forces.cpp
extern interaction_function Interaction_Functions[];
extern double Compute_H(double, double, double*);
extern double Compute_tabH(double, int, int);
extern void Dummy_Interaction(reax_system*, control_params*, simulation_data*, storage*, reax_list**, output_controls*);
/* ---------------------------------------------------------------------- */
void Init_Force_FunctionsOMP( control_params *control )
{
Interaction_Functions[0] = BOOMP;
Interaction_Functions[1] = BondsOMP; //Dummy_Interaction;
Interaction_Functions[2] = Atom_EnergyOMP; //Dummy_Interaction;
Interaction_Functions[3] = Valence_AnglesOMP; //Dummy_Interaction;
Interaction_Functions[4] = Torsion_AnglesOMP; //Dummy_Interaction;
if( control->hbond_cut > 0 )
Interaction_Functions[5] = Hydrogen_BondsOMP;
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
}
/* ---------------------------------------------------------------------- */
// Only difference with MPI-only version is inclusion of OMP_TIMING statements
void Compute_Bonded_ForcesOMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
MPI_Comm comm )
{
int i;
#ifdef OMP_TIMING
double startTimeBase, endTimeBase;
startTimeBase = MPI_Wtime();
#endif
/* Implement all force calls as function pointers */
for( i = 0; i < NUM_INTRS; i++ ) {
(Interaction_Functions[i])( system, control, data, workspace,
lists, out_control );
}
#ifdef OMP_TIMING
endTimeBase = MPI_Wtime();
ompTimingData[COMPUTEBFINDEX] += (endTimeBase-startTimeBase);
#endif
}
// Only difference with MPI-only version is inclusion of OMP_TIMING statements
void Compute_NonBonded_ForcesOMP( 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 */
#ifdef OMP_TIMING
double endTimeBase, startTimeBase;
startTimeBase = MPI_Wtime();
#endif
if( control->tabulate == 0 )
vdW_Coulomb_Energy_OMP( system, control, data, workspace,
lists, out_control );
else
Tabulated_vdW_Coulomb_Energy_OMP( system, control, data, workspace,
lists, out_control );
#ifdef OMP_TIMING
endTimeBase = MPI_Wtime();
ompTimingData[COMPUTENBFINDEX] += (endTimeBase-startTimeBase);
#endif
}
/* ---------------------------------------------------------------------- */
/* this version of Compute_Total_Force computes forces from
coefficients accumulated by all interaction functions.
Saves enormous time & space! */
void Compute_Total_ForceOMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, mpi_datatypes *mpi_data )
{
#ifdef OMP_TIMING
double startTimeBase,endTimeBase;
startTimeBase = MPI_Wtime();
#endif
int natoms = system->N;
int nthreads = control->nthreads;
long totalReductionSize = system->N * nthreads;
reax_list *bonds = (*lists) + BONDS;
#if defined(_OPENMP)
#pragma omp parallel default(shared) //default(none)
#endif
{
int i, j, k, pj, pk, start_j, end_j;
#if defined(_OPENMP)
int tid = omp_get_thread_num();
#else
int tid = 0;
#endif
bond_order_data *bo_jk;
class PairReaxCOMP *pair_reax_ptr;
pair_reax_ptr = static_cast<class PairReaxCOMP*>(system->pair_ptr);
class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid);
pair_reax_ptr->ev_setup_thr_proxy(0, 1, natoms, system->pair_ptr->eatom,
system->pair_ptr->vatom, thr);
#if defined(_OPENMP)
#pragma omp for schedule(guided)
#endif
for (i = 0; i < system->N; ++i) {
for (j = 0; j < nthreads; ++j)
workspace->CdDelta[i] += workspace->CdDeltaReduction[system->N*j+i];
}
#if defined(_OPENMP)
#pragma omp for schedule(dynamic,50)
#endif
for (j = 0; j < system->N; ++j) {
start_j = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
for (pk = start_j; pk < end_j; ++pk) {
bo_jk = &( bonds->select.bond_list[pk].bo_data );
for (k = 0; k < nthreads; ++k)
bo_jk->Cdbo += bo_jk->CdboReduction[k];
}
}
// #pragma omp for schedule(guided) //(dynamic,50)
// 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_ForcesOMP( system, i, pj, workspace, lists );
// else
// Add_dBond_to_Forces_NPTOMP(system, i, pj, data, workspace, lists );
// }
if(control->virial == 0) {
#if defined(_OPENMP)
#pragma omp for schedule(dynamic,50)
#endif
for (i = 0; i < system->N; ++i) {
const int startj = Start_Index(i, bonds);
const int endj = End_Index(i, bonds);
for (pj = startj; pj < endj; ++pj)
if (i < bonds->select.bond_list[pj].nbr)
Add_dBond_to_ForcesOMP( system, i, pj, workspace, lists );
}
} else {
#if defined(_OPENMP)
#pragma omp for schedule(dynamic,50)
#endif
for (i = 0; i < system->N; ++i) {
const int startj = Start_Index(i, bonds);
const int endj = End_Index(i, bonds);
for (pj = startj; pj < endj; ++pj)
if (i < bonds->select.bond_list[pj].nbr)
Add_dBond_to_Forces_NPTOMP(system, i, pj, data, workspace, lists );
}
} // if(virial == 0)
pair_reax_ptr->reduce_thr_proxy(system->pair_ptr, 0, 1, thr);
#if defined(_OPENMP)
#pragma omp for schedule(guided)
#endif
for (i = 0; i < system->N; ++i) {
for (j = 0; j < nthreads; ++j)
rvec_Add( workspace->f[i], workspace->forceReduction[system->N*j+i] );
}
#if defined(_OPENMP)
#pragma omp for schedule(guided)
#endif
for (i = 0; i < totalReductionSize; i++) {
workspace->forceReduction[i][0] = 0;
workspace->forceReduction[i][1] = 0;
workspace->forceReduction[i][2] = 0;
workspace->CdDeltaReduction[i] = 0;
}
} // parallel region
if (control->virial)
for (int i=0; i < nthreads; ++i) {
rvec_Add(data->my_ext_press, workspace->my_ext_pressReduction[i]);
workspace->my_ext_pressReduction[i][0] = 0;
workspace->my_ext_pressReduction[i][1] = 0;
workspace->my_ext_pressReduction[i][2] = 0;
}
#ifdef OMP_TIMING
endTimeBase = MPI_Wtime();
ompTimingData[COMPUTETFINDEX] += (endTimeBase-startTimeBase);
#endif
}
/* ---------------------------------------------------------------------- */
void Validate_ListsOMP( 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;
reallocate_data *realloc = &(workspace->realloc);
double saferzone = system->saferzone;
#if defined(_OPENMP)
#pragma omp parallel default(shared) private(i, comp, Hindex)
#endif
{
/* bond list */
if( N > 0 ) {
bonds = *lists + BONDS;
#if defined(_OPENMP)
#pragma omp for schedule(guided)
#endif
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;
#if defined(_OPENMP)
#pragma omp for schedule(guided)
#endif
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( 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 );
}
}
}
}
} // omp parallel
}
void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
MPI_Comm comm ) {
#ifdef OMP_TIMING
double startTimeBase, endTimeBase;
startTimeBase = MPI_Wtime();
#endif
int i, j, pi, pj;
int start_i, end_i, start_j, end_j;
int type_i, type_j;
int ihb, jhb, ihb_top, jhb_top;
int local, flag;
double r_ij, cutoff;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
bond_data *ibond, *jbond;
reax_list *far_nbrs = *lists + FAR_NBRS;
reax_list *bonds = *lists + BONDS;
reax_list *hbonds = *lists + HBONDS;
int num_bonds = 0;
int num_hbonds = 0;
int btop_i = 0;
int btop_j = 0;
int renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
// We will use CdDeltaReduction as a temporary (double) buffer to accumulate total_bond_order
// This is safe because CdDeltaReduction is currently zeroed and its accumulation doesn't start until BondsOMP()
double * tmp_bond_order = workspace->CdDeltaReduction;
// We do the same with forceReduction as a temporary (rvec) buffer to accumulate dDeltap_self
// This is safe because forceReduction is currently zeroed and its accumulation does start until Hydrogen_BondsOMP()
rvec * tmp_ddelta = workspace->forceReduction;
/* uncorrected bond orders */
cutoff = control->bond_cut;
#if defined(_OPENMP)
#pragma omp parallel default(shared) \
private(i, atom_i, type_i, pi, start_i, end_i, sbp_i, btop_i, ibond, ihb, ihb_top, \
j, atom_j, type_j, pj, start_j, end_j, sbp_j, nbr_pj, jbond, jhb, twbp)
#endif
{
int nthreads = control->nthreads;
#if defined(_OPENMP)
int tid = omp_get_thread_num();
#else
int tid = 0;
#endif
long reductionOffset = system->N * tid;
long totalReductionSize = system->N * nthreads;
#if defined(_OPENMP)
#pragma omp for schedule(dynamic,50) reduction(+ : num_bonds)
#endif
for (i = 0; i < system->N; ++i) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
sbp_i = &(system->reax_param.sbp[type_i]);
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
if (nbr_pj->d <= cutoff) {
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
type_j = atom_j->type;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
// #pragma omp critical
// {
// btop_i = End_Index(i, bonds);
// if( BOp(workspace, bonds, control->bo_cut, i, btop_i, nbr_pj, sbp_i, sbp_j, twbp) ) {
// num_bonds++;
// btop_i++;
// Set_End_Index(i, btop_i, bonds);
// }
// }
// Trying to minimize time spent in critical section by moving initial part of BOp()
// outside of critical section.
// Start top portion of BOp()
int jj = nbr_pj->nbr;
double C12, C34, C56;
double BO, BO_s, BO_pi, BO_pi2;
double bo_cut = control->bo_cut;
if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0 ) {
C12 = twbp->p_bo1 * pow( nbr_pj->d / twbp->r_s, twbp->p_bo2 );
BO_s = (1.0 + 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( nbr_pj->d / 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( nbr_pj->d / 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;
// End top portion of BOp()
if(BO >= bo_cut) {
int btop_j;
// Update indices in critical section
#if defined(_OPENMP)
#pragma omp critical
#endif
{
btop_i = End_Index( i, bonds );
btop_j = End_Index( j, bonds );
Set_End_Index( j, btop_j+1, bonds );
Set_End_Index( i, btop_i+1, bonds );
} // omp critical
// Finish remaining BOp() work
BOp_OMP(workspace, bonds, bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp, btop_j,
C12, C34, C56, BO, BO_s, BO_pi, BO_pi2);
bond_data * ibond = &(bonds->select.bond_list[btop_i]);
bond_order_data * bo_ij = &(ibond->bo_data);
bond_data * jbond = &(bonds->select.bond_list[btop_j]);
bond_order_data * bo_ji = &(jbond->bo_data);
workspace->total_bond_order[i] += bo_ij->BO;
tmp_bond_order[reductionOffset + j] += bo_ji->BO;
rvec_Add(workspace->dDeltap_self[i], bo_ij->dBOp);
rvec_Add(tmp_ddelta[reductionOffset + j], bo_ji->dBOp);
btop_i++;
num_bonds++;
} // if(BO>=bo_cut)
} // if(cutoff)
} // for(pj)
} // for(i)
// Need to wait for all indices and tmp arrays accumulated.
#if defined(_OPENMP)
#pragma omp barrier
#endif
#if defined(_OPENMP)
#pragma omp for schedule(dynamic,50)
#endif
for(i=0; i<system->N; i++)
for(int t=0; t<nthreads; t++) {
const int indx = t*system->N + i;
workspace->dDeltap_self[i][0] += tmp_ddelta[indx][0];
workspace->dDeltap_self[i][1] += tmp_ddelta[indx][1];
workspace->dDeltap_self[i][2] += tmp_ddelta[indx][2];
workspace->total_bond_order[i] += tmp_bond_order[indx];
}
/* hydrogen bond list */
if (control->hbond_cut > 0) {
cutoff = control->hbond_cut;
#if defined(_OPENMP)
#pragma omp for schedule(dynamic,50) reduction(+ : num_hbonds)
#endif
for (i = 0; i < system->n; ++i) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
sbp_i = &(system->reax_param.sbp[type_i]);
ihb = sbp_i->p_hbond;
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if (ihb == 1 || ihb == 2) {
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
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]);
type_j = atom_j->type;
if(type_j < 0) continue;
sbp_j = &(system->reax_param.sbp[type_j]);
jhb = sbp_j->p_hbond;
if (nbr_pj->d <= control->hbond_cut) {
int iflag = 0;
int jflag = 0;
if(ihb==1 && jhb==2) iflag = 1;
else if(j<system->n && ihb == 2 && jhb == 1) jflag = 1;
if(iflag || jflag) {
if(iflag) {
ihb_top = End_Index(atom_i->Hindex, hbonds);
Set_End_Index(atom_i->Hindex, ihb_top+1, hbonds);
} else if(jflag) {
jhb_top = End_Index(atom_j->Hindex, hbonds);
Set_End_Index(atom_j->Hindex, jhb_top+1, hbonds);
}
if(iflag) {
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;
} else if(jflag) {
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;
}
num_hbonds++;
} // if(iflag || jflag)
}
}
}
} // omp critical
}
} // if(control->hbond > 0)
// Zero buffers for others to use as intended.
#if defined(_OPENMP)
#pragma omp for schedule(guided)
#endif
for(i=0; i<totalReductionSize; i++) {
tmp_ddelta[i][0] = 0.0;
tmp_ddelta[i][1] = 0.0;
tmp_ddelta[i][2] = 0.0;
tmp_bond_order[i] = 0.0;
}
} // omp
workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
Validate_ListsOMP( system, workspace, lists, data->step,
system->n, system->N, system->numH, comm );
#ifdef OMP_TIMING
endTimeBase = MPI_Wtime();
ompTimingData[COMPUTEIFINDEX] += (endTimeBase-startTimeBase);
#endif
}
/* ---------------------------------------------------------------------- */
void Compute_ForcesOMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
mpi_datatypes *mpi_data )
{
int qeq_flag;
MPI_Comm comm = mpi_data->world;
// Init Forces
#if defined(LOG_PERFORMANCE)
double t_start = 0;
if( system->my_rank == MASTER_NODE )
t_start = Get_Time( );
#endif
Init_Forces_noQEq_OMP( system, control, data, workspace,
lists, out_control, comm );
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( comm );
if( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.init_forces) );
#endif
// Bonded Interactions
Compute_Bonded_ForcesOMP( system, control, data, workspace,
lists, out_control, mpi_data->world );
#if defined(LOG_PERFORMANCE)
if( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.bonded) );
#endif
// Nonbonded Interactions
Compute_NonBonded_ForcesOMP( system, control, data, workspace,
lists, out_control, mpi_data->world );
#if defined(LOG_PERFORMANCE)
if( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.nonb) );
#endif
// Total Force
Compute_Total_ForceOMP( system, control, data, workspace, lists, mpi_data );
#if defined(LOG_PERFORMANCE)
if( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.bonded) );
#endif
}
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