185 lines
7.1 KiB
C++
185 lines
7.1 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_hydrogen_bonds.h"
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#include "reaxc_bond_orders.h"
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#include "reaxc_list.h"
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#include "reaxc_valence_angles.h"
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#include "reaxc_vector.h"
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void Hydrogen_Bonds( 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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int i, j, k, pi, pk;
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int type_i, type_j, type_k;
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int start_j, end_j, hb_start_j, hb_end_j;
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int hblist[MAX_BONDS];
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int itr, top;
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int num_hb_intrs = 0;
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ivec rel_jk;
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double r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2;
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double e_hb, exp_hb2, exp_hb3, CEhb1, CEhb2, CEhb3;
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rvec dcos_theta_di, dcos_theta_dj, dcos_theta_dk;
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rvec dvec_jk, force, ext_press;
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hbond_parameters *hbp;
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bond_order_data *bo_ij;
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bond_data *pbond_ij;
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far_neighbor_data *nbr_jk;
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reax_list *bonds, *hbonds;
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bond_data *bond_list;
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hbond_data *hbond_list;
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// tally variables
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double fi_tmp[3], fk_tmp[3], delij[3], delkj[3];
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bonds = (*lists) + BONDS;
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bond_list = bonds->select.bond_list;
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hbonds = (*lists) + HBONDS;
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hbond_list = hbonds->select.hbond_list;
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for( j = 0; j < system->n; ++j )
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if( system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1 ) {
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type_j = system->my_atoms[j].type;
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start_j = Start_Index(j, bonds);
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end_j = End_Index(j, bonds);
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hb_start_j = Start_Index( system->my_atoms[j].Hindex, hbonds );
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hb_end_j = End_Index( system->my_atoms[j].Hindex, hbonds );
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if (type_j < 0) continue;
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top = 0;
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for( pi = start_j; pi < end_j; ++pi ) {
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pbond_ij = &( bond_list[pi] );
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i = pbond_ij->nbr;
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type_i = system->my_atoms[i].type;
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if (type_i < 0) continue;
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bo_ij = &(pbond_ij->bo_data);
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if( system->reax_param.sbp[type_i].p_hbond == 2 &&
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bo_ij->BO >= HB_THRESHOLD )
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hblist[top++] = pi;
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}
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for( pk = hb_start_j; pk < hb_end_j; ++pk ) {
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/* set k's varibles */
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k = hbond_list[pk].nbr;
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type_k = system->my_atoms[k].type;
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if (type_k < 0) continue;
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nbr_jk = hbond_list[pk].ptr;
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r_jk = nbr_jk->d;
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rvec_Scale( dvec_jk, hbond_list[pk].scl, nbr_jk->dvec );
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for( itr = 0; itr < top; ++itr ) {
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pi = hblist[itr];
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pbond_ij = &( bonds->select.bond_list[pi] );
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i = pbond_ij->nbr;
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if( system->my_atoms[i].orig_id != system->my_atoms[k].orig_id ) {
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bo_ij = &(pbond_ij->bo_data);
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type_i = system->my_atoms[i].type;
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if (type_i < 0) continue;
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hbp = &(system->reax_param.hbp[ type_i ][ type_j ][ type_k ]);
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if (hbp->r0_hb <= 0.0) continue;
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++num_hb_intrs;
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Calculate_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
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&theta, &cos_theta );
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/* the derivative of cos(theta) */
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Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
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&dcos_theta_di, &dcos_theta_dj,
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&dcos_theta_dk );
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/* hyrogen bond energy*/
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sin_theta2 = sin( theta/2.0 );
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sin_xhz4 = SQR(sin_theta2);
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sin_xhz4 *= sin_xhz4;
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cos_xhz1 = ( 1.0 - cos_theta );
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exp_hb2 = exp( -hbp->p_hb2 * bo_ij->BO );
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exp_hb3 = exp( -hbp->p_hb3 * ( hbp->r0_hb / r_jk +
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r_jk / hbp->r0_hb - 2.0 ) );
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data->my_en.e_hb += e_hb =
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hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4;
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CEhb1 = hbp->p_hb1 * hbp->p_hb2 * exp_hb2 * exp_hb3 * sin_xhz4;
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CEhb2 = -hbp->p_hb1/2.0 * (1.0 - exp_hb2) * exp_hb3 * cos_xhz1;
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CEhb3 = -hbp->p_hb3 *
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(-hbp->r0_hb / SQR(r_jk) + 1.0 / hbp->r0_hb) * e_hb;
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/* hydrogen bond forces */
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bo_ij->Cdbo += CEhb1; // dbo term
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if( control->virial == 0 ) {
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// dcos terms
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rvec_ScaledAdd( workspace->f[i], +CEhb2, dcos_theta_di );
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rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj );
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rvec_ScaledAdd( workspace->f[k], +CEhb2, dcos_theta_dk );
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// dr terms
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rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk );
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rvec_ScaledAdd( workspace->f[k], +CEhb3/r_jk, dvec_jk );
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}
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else {
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rvec_Scale( force, +CEhb2, dcos_theta_di ); // dcos terms
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rvec_Add( workspace->f[i], force );
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rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
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rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
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rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj );
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ivec_Scale( rel_jk, hbond_list[pk].scl, nbr_jk->rel_box );
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rvec_Scale( force, +CEhb2, dcos_theta_dk );
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rvec_Add( workspace->f[k], force );
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rvec_iMultiply( ext_press, rel_jk, force );
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rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
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// dr terms
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rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk );
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rvec_Scale( force, CEhb3/r_jk, dvec_jk );
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rvec_Add( workspace->f[k], force );
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rvec_iMultiply( ext_press, rel_jk, force );
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rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
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}
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/* tally into per-atom virials */
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if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
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rvec_ScaledSum( delij, 1., system->my_atoms[j].x,
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-1., system->my_atoms[i].x );
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rvec_ScaledSum( delkj, 1., system->my_atoms[j].x,
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-1., system->my_atoms[k].x );
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rvec_Scale(fi_tmp, CEhb2, dcos_theta_di);
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rvec_Scale(fk_tmp, CEhb2, dcos_theta_dk);
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rvec_ScaledAdd(fk_tmp, CEhb3/r_jk, dvec_jk);
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system->pair_ptr->ev_tally3(i,j,k,e_hb,0.0,fi_tmp,fk_tmp,delij,delkj);
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}
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}
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}
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}
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}
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}
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