Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F82754742
reaxc_hydrogen_bonds_omp.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Fri, Sep 13, 06:18
Size
9 KB
Mime Type
text/x-c
Expires
Sun, Sep 15, 06:18 (2 d)
Engine
blob
Format
Raw Data
Handle
20743507
Attached To
rLAMMPS lammps
reaxc_hydrogen_bonds_omp.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_reaxc_omp.h"
#include <omp.h>
#include "reaxc_hydrogen_bonds_omp.h"
#include "reaxc_bond_orders_omp.h"
#include "reaxc_list.h"
#include "reaxc_valence_angles.h" // To access Calculate_Theta()
#include "reaxc_valence_angles_omp.h" // To access Calculate_dCos_ThetaOMP()
#include "reaxc_vector.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
void Hydrogen_BondsOMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
{
#ifdef OMP_TIMING
double endTimeBase, startTimeBase;
startTimeBase = MPI_Wtime();
#endif
const int nthreads = control->nthreads;
long totalReductionSize = system->N;
#pragma omp parallel default(shared) //default(none)
{
int i, j, k, pi, pk;
int type_i, type_j, type_k;
int start_j, end_j, hb_start_j, hb_end_j;
int hblist[MAX_BONDS];
int itr, top;
int num_hb_intrs = 0;
ivec rel_jk;
double r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2;
double e_hb, e_hb_thr = 0.0, exp_hb2, exp_hb3, CEhb1, CEhb2, CEhb3;
rvec dcos_theta_di, dcos_theta_dj, dcos_theta_dk;
rvec dvec_jk, force, ext_press;
hbond_parameters *hbp;
bond_order_data *bo_ij;
bond_data *pbond_ij;
far_neighbor_data *nbr_jk;
reax_list *bonds, *hbonds;
bond_data *bond_list;
hbond_data *hbond_list;
// tally variables
double fi_tmp[3], fk_tmp[3], delij[3], delkj[3];
bonds = (*lists) + BONDS;
bond_list = bonds->select.bond_list;
hbonds = (*lists) + HBONDS;
hbond_list = hbonds->select.hbond_list;
int natoms = system->n;
int tid = omp_get_thread_num();
const int idelta = 1 + natoms/nthreads;
int ifrom = tid*idelta;
int ito = ((ifrom + idelta) > natoms) ? natoms : ifrom + idelta;
long reductionOffset = (system->N * tid);
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(system->pair_ptr->eflag_either,
system->pair_ptr->vflag_either,
natoms, system->pair_ptr->eatom,
system->pair_ptr->vatom, thr);
/* loops below discover the Hydrogen bonds between i-j-k triplets.
here j is H atom and there has to be some bond between i and j.
Hydrogen bond is between j and k.
so in this function i->X, j->H, k->Z when we map
variables onto the ones in the handout.*/
// for( j = 0; j < system->n; ++j )
for( j = ifrom; j < ito; ++j ) {
/* j has to be of type H */
if( system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1 ) {
/*set j's variables */
type_j = system->my_atoms[j].type;
start_j = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
hb_start_j = Start_Index( system->my_atoms[j].Hindex, hbonds );
hb_end_j = End_Index( system->my_atoms[j].Hindex, hbonds );
if(type_j < 0) continue;
top = 0;
for( pi = start_j; pi < end_j; ++pi ) {
pbond_ij = &( bond_list[pi] );
i = pbond_ij->nbr;
type_i = system->my_atoms[i].type;
if(type_i < 0) continue;
bo_ij = &(pbond_ij->bo_data);
if( system->reax_param.sbp[type_i].p_hbond == 2 &&
bo_ij->BO >= HB_THRESHOLD )
hblist[top++] = pi;
}
for( pk = hb_start_j; pk < hb_end_j; ++pk ) {
/* set k's varibles */
k = hbond_list[pk].nbr;
type_k = system->my_atoms[k].type;
if(type_k < 0) continue;
nbr_jk = hbond_list[pk].ptr;
r_jk = nbr_jk->d;
rvec_Scale( dvec_jk, hbond_list[pk].scl, nbr_jk->dvec );
for( itr = 0; itr < top; ++itr ) {
pi = hblist[itr];
pbond_ij = &( bonds->select.bond_list[pi] );
i = pbond_ij->nbr;
if( system->my_atoms[i].orig_id != system->my_atoms[k].orig_id ) {
bo_ij = &(pbond_ij->bo_data);
type_i = system->my_atoms[i].type;
if(type_i < 0) continue;
hbp = &(system->reax_param.hbp[ type_i ][ type_j ][ type_k ]);
++num_hb_intrs;
Calculate_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
&theta, &cos_theta );
/* the derivative of cos(theta) */
Calculate_dCos_ThetaOMP( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
&dcos_theta_di, &dcos_theta_dj,
&dcos_theta_dk );
/* hydrogen bond energy*/
sin_theta2 = sin( theta/2.0 );
sin_xhz4 = SQR(sin_theta2);
sin_xhz4 *= sin_xhz4;
cos_xhz1 = ( 1.0 - cos_theta );
exp_hb2 = exp( -hbp->p_hb2 * bo_ij->BO );
exp_hb3 = exp( -hbp->p_hb3 * ( hbp->r0_hb / r_jk +
r_jk / hbp->r0_hb - 2.0 ) );
e_hb_thr += e_hb = hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4;
CEhb1 = hbp->p_hb1 * hbp->p_hb2 * exp_hb2 * exp_hb3 * sin_xhz4;
CEhb2 = -hbp->p_hb1/2.0 * (1.0 - exp_hb2) * exp_hb3 * cos_xhz1;
CEhb3 = -hbp->p_hb3 *
(-hbp->r0_hb / SQR(r_jk) + 1.0 / hbp->r0_hb) * e_hb;
/* hydrogen bond forces */
bo_ij->Cdbo += CEhb1; // dbo term
if( control->virial == 0 ) {
// dcos terms
rvec_ScaledAdd(workspace->forceReduction[reductionOffset+i], +CEhb2, dcos_theta_di );
rvec_ScaledAdd(workspace->forceReduction[reductionOffset+j], +CEhb2, dcos_theta_dj );
rvec_ScaledAdd(workspace->forceReduction[reductionOffset+k], +CEhb2, dcos_theta_dk );
// dr terms
rvec_ScaledAdd(workspace->forceReduction[reductionOffset+j], -CEhb3/r_jk, dvec_jk );
rvec_ScaledAdd(workspace->forceReduction[reductionOffset+k], +CEhb3/r_jk, dvec_jk );
}
else {
/* for pressure coupling, terms that are not related to bond order
derivatives are added directly into pressure vector/tensor */
rvec_Scale( force, +CEhb2, dcos_theta_di ); // dcos terms
rvec_Add(workspace->forceReduction[reductionOffset+i], force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
rvec_ScaledAdd( workspace->my_ext_pressReduction[tid],1.0, ext_press );
rvec_ScaledAdd(workspace->forceReduction[reductionOffset+j], +CEhb2, dcos_theta_dj );
ivec_Scale( rel_jk, hbond_list[pk].scl, nbr_jk->rel_box );
rvec_Scale( force, +CEhb2, dcos_theta_dk );
rvec_Add(workspace->forceReduction[reductionOffset+k], force );
rvec_iMultiply( ext_press, rel_jk, force );
rvec_ScaledAdd( workspace->my_ext_pressReduction[tid],1.0, ext_press );
// dr terms
rvec_ScaledAdd(workspace->forceReduction[reductionOffset+j],-CEhb3/r_jk, dvec_jk );
rvec_Scale( force, CEhb3/r_jk, dvec_jk );
rvec_Add(workspace->forceReduction[reductionOffset+k], force );
rvec_iMultiply( ext_press, rel_jk, force );
rvec_ScaledAdd( workspace->my_ext_pressReduction[tid],1.0, ext_press );
}
/* tally into per-atom virials */
if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
rvec_ScaledSum( delij, 1., system->my_atoms[j].x,
-1., system->my_atoms[i].x );
rvec_ScaledSum( delkj, 1., system->my_atoms[j].x,
-1., system->my_atoms[k].x );
rvec_Scale(fi_tmp, CEhb2, dcos_theta_di);
rvec_Scale(fk_tmp, CEhb2, dcos_theta_dk);
rvec_ScaledAdd(fk_tmp, CEhb3/r_jk, dvec_jk);
pair_reax_ptr->ev_tally3_thr_proxy(system->pair_ptr,i,j,k,e_hb,0.0,fi_tmp,fk_tmp,delij,delkj,thr);
}
}
}
}
}
}
#pragma omp critical
{
data->my_en.e_hb += e_hb_thr;
}
pair_reax_ptr->reduce_thr_proxy(system->pair_ptr, system->pair_ptr->eflag_either,
system->pair_ptr->vflag_either, thr);
}
#ifdef OMP_TIMING
endTimeBase = MPI_Wtime();
ompTimingData[COMPUTEHBONDSINDEX] += (endTimeBase-startTimeBase);
#endif
}
Event Timeline
Log In to Comment