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reaxc_hydrogen_bonds.cpp
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Wed, Jun 5, 01:47

reaxc_hydrogen_bonds.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.h"
#include "reaxc_hydrogen_bonds.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
#include "reaxc_valence_angles.h"
#include "reaxc_vector.h"
void Hydrogen_Bonds( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
{
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, 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;
for( j = 0; j < system->n; ++j )
if( system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1 ) {
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 ]);
if (hbp->r0_hb <= 0.0) continue;
++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_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
&dcos_theta_di, &dcos_theta_dj,
&dcos_theta_dk );
/* hyrogen 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 ) );
data->my_en.e_hb += 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->f[i], +CEhb2, dcos_theta_di );
rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj );
rvec_ScaledAdd( workspace->f[k], +CEhb2, dcos_theta_dk );
// dr terms
rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk );
rvec_ScaledAdd( workspace->f[k], +CEhb3/r_jk, dvec_jk );
}
else {
rvec_Scale( force, +CEhb2, dcos_theta_di ); // dcos terms
rvec_Add( workspace->f[i], force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
rvec_ScaledAdd( workspace->f[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->f[k], force );
rvec_iMultiply( ext_press, rel_jk, force );
rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
// dr terms
rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk );
rvec_Scale( force, CEhb3/r_jk, dvec_jk );
rvec_Add( workspace->f[k], force );
rvec_iMultiply( ext_press, rel_jk, force );
rvec_ScaledAdd( data->my_ext_press, 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);
system->pair_ptr->ev_tally3(i,j,k,e_hb,0.0,fi_tmp,fk_tmp,delij,delkj);
}
}
}
}
}
}

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