480 lines
20 KiB
C++
480 lines
20 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_torsion_angles.h"
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#include "reaxc_bond_orders.h"
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#include "reaxc_list.h"
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#include "reaxc_tool_box.h"
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#include "reaxc_vector.h"
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#define MIN_SINE 1e-10
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double Calculate_Omega( rvec dvec_ij, double r_ij,
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rvec dvec_jk, double r_jk,
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rvec dvec_kl, double r_kl,
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rvec dvec_li, double r_li,
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three_body_interaction_data *p_ijk,
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three_body_interaction_data *p_jkl,
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rvec dcos_omega_di, rvec dcos_omega_dj,
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rvec dcos_omega_dk, rvec dcos_omega_dl,
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output_controls * /*out_control*/ )
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{
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double unnorm_cos_omega, unnorm_sin_omega, omega;
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double sin_ijk, cos_ijk, sin_jkl, cos_jkl;
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double htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe;
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double arg, poem, tel;
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rvec cross_jk_kl;
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sin_ijk = sin( p_ijk->theta );
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cos_ijk = cos( p_ijk->theta );
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sin_jkl = sin( p_jkl->theta );
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cos_jkl = cos( p_jkl->theta );
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/* omega */
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unnorm_cos_omega = -rvec_Dot(dvec_ij, dvec_jk) * rvec_Dot(dvec_jk, dvec_kl) +
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SQR( r_jk ) * rvec_Dot( dvec_ij, dvec_kl );
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rvec_Cross( cross_jk_kl, dvec_jk, dvec_kl );
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unnorm_sin_omega = -r_jk * rvec_Dot( dvec_ij, cross_jk_kl );
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omega = atan2( unnorm_sin_omega, unnorm_cos_omega );
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htra = r_ij + cos_ijk * ( r_kl * cos_jkl - r_jk );
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htrb = r_jk - r_ij * cos_ijk - r_kl * cos_jkl;
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htrc = r_kl + cos_jkl * ( r_ij * cos_ijk - r_jk );
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hthd = r_ij * sin_ijk * ( r_jk - r_kl * cos_jkl );
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hthe = r_kl * sin_jkl * ( r_jk - r_ij * cos_ijk );
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hnra = r_kl * sin_ijk * sin_jkl;
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hnrc = r_ij * sin_ijk * sin_jkl;
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hnhd = r_ij * r_kl * cos_ijk * sin_jkl;
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hnhe = r_ij * r_kl * sin_ijk * cos_jkl;
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poem = 2.0 * r_ij * r_kl * sin_ijk * sin_jkl;
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if (poem < 1e-20) poem = 1e-20;
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tel = SQR( r_ij ) + SQR( r_jk ) + SQR( r_kl ) - SQR( r_li ) -
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2.0 * ( r_ij * r_jk * cos_ijk - r_ij * r_kl * cos_ijk * cos_jkl +
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r_jk * r_kl * cos_jkl );
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arg = tel / poem;
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if (arg > 1.0) arg = 1.0;
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if (arg < -1.0) arg = -1.0;
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if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) sin_ijk = MIN_SINE;
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else if( sin_ijk <= 0 && sin_ijk >= -MIN_SINE ) sin_ijk = -MIN_SINE;
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if (sin_jkl >= 0 && sin_jkl <= MIN_SINE) sin_jkl = MIN_SINE;
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else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE ) sin_jkl = -MIN_SINE;
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// dcos_omega_di
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rvec_ScaledSum( dcos_omega_di, (htra-arg*hnra)/r_ij, dvec_ij, -1., dvec_li );
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rvec_ScaledAdd( dcos_omega_di,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_dk );
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rvec_Scale( dcos_omega_di, 2.0 / poem, dcos_omega_di );
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// dcos_omega_dj
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rvec_ScaledSum( dcos_omega_dj,-(htra-arg*hnra)/r_ij, dvec_ij,
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-htrb / r_jk, dvec_jk );
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rvec_ScaledAdd( dcos_omega_dj,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_dj );
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rvec_ScaledAdd( dcos_omega_dj,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_di );
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rvec_Scale( dcos_omega_dj, 2.0 / poem, dcos_omega_dj );
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// dcos_omega_dk
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rvec_ScaledSum( dcos_omega_dk,-(htrc-arg*hnrc)/r_kl, dvec_kl,
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htrb / r_jk, dvec_jk );
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rvec_ScaledAdd( dcos_omega_dk,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_di );
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rvec_ScaledAdd( dcos_omega_dk,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_dj );
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rvec_Scale( dcos_omega_dk, 2.0 / poem, dcos_omega_dk );
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// dcos_omega_dl
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rvec_ScaledSum( dcos_omega_dl, (htrc-arg*hnrc)/r_kl, dvec_kl, 1., dvec_li );
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rvec_ScaledAdd( dcos_omega_dl,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_dk );
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rvec_Scale( dcos_omega_dl, 2.0 / poem, dcos_omega_dl );
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return omega;
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}
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void Torsion_Angles( 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, l, pi, pj, pk, pl, pij, plk, natoms;
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int type_i, type_j, type_k, type_l;
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int start_j, end_j;
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int start_pj, end_pj, start_pk, end_pk;
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int num_frb_intrs = 0;
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double Delta_j, Delta_k;
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double r_ij, r_jk, r_kl, r_li;
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double BOA_ij, BOA_jk, BOA_kl;
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double exp_tor2_ij, exp_tor2_jk, exp_tor2_kl;
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double exp_tor1, exp_tor3_DjDk, exp_tor4_DjDk, exp_tor34_inv;
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double exp_cot2_jk, exp_cot2_ij, exp_cot2_kl;
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double fn10, f11_DjDk, dfn11, fn12;
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double theta_ijk, theta_jkl;
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double sin_ijk, sin_jkl;
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double cos_ijk, cos_jkl;
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double tan_ijk_i, tan_jkl_i;
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double omega, cos_omega, cos2omega, cos3omega;
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rvec dcos_omega_di, dcos_omega_dj, dcos_omega_dk, dcos_omega_dl;
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double CV, cmn, CEtors1, CEtors2, CEtors3, CEtors4;
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double CEtors5, CEtors6, CEtors7, CEtors8, CEtors9;
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double Cconj, CEconj1, CEconj2, CEconj3;
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double CEconj4, CEconj5, CEconj6;
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double e_tor, e_con;
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rvec dvec_li;
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rvec force, ext_press;
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ivec rel_box_jl;
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// rtensor total_rtensor, temp_rtensor;
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four_body_header *fbh;
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four_body_parameters *fbp;
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bond_data *pbond_ij, *pbond_jk, *pbond_kl;
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bond_order_data *bo_ij, *bo_jk, *bo_kl;
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three_body_interaction_data *p_ijk, *p_jkl;
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double p_tor2 = system->reax_param.gp.l[23];
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double p_tor3 = system->reax_param.gp.l[24];
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double p_tor4 = system->reax_param.gp.l[25];
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double p_cot2 = system->reax_param.gp.l[27];
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reax_list *bonds = (*lists) + BONDS;
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reax_list *thb_intrs = (*lists) + THREE_BODIES;
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// Virial tallying variables
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double delil[3], deljl[3], delkl[3];
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double eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3];
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natoms = system->n;
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for( j = 0; j < natoms; ++j ) {
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type_j = system->my_atoms[j].type;
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Delta_j = workspace->Delta_boc[j];
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start_j = Start_Index(j, bonds);
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end_j = End_Index(j, bonds);
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for( pk = start_j; pk < end_j; ++pk ) {
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pbond_jk = &( bonds->select.bond_list[pk] );
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k = pbond_jk->nbr;
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bo_jk = &( pbond_jk->bo_data );
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BOA_jk = bo_jk->BO - control->thb_cut;
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if (system->my_atoms[j].orig_id > system->my_atoms[k].orig_id)
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continue;
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if (system->my_atoms[j].orig_id == system->my_atoms[k].orig_id) {
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if (system->my_atoms[k].x[2] < system->my_atoms[j].x[2]) continue;
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if (system->my_atoms[k].x[2] == system->my_atoms[j].x[2] &&
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system->my_atoms[k].x[1] < system->my_atoms[j].x[1]) continue;
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if (system->my_atoms[k].x[2] == system->my_atoms[j].x[2] &&
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system->my_atoms[k].x[1] == system->my_atoms[j].x[1] &&
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system->my_atoms[k].x[0] < system->my_atoms[j].x[0]) continue;
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}
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if (bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs)) {
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pj = pbond_jk->sym_index; // pj points to j on k's list
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if (Num_Entries(pj, thb_intrs)) {
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type_k = system->my_atoms[k].type;
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Delta_k = workspace->Delta_boc[k];
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r_jk = pbond_jk->d;
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start_pk = Start_Index(pk, thb_intrs );
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end_pk = End_Index(pk, thb_intrs );
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start_pj = Start_Index(pj, thb_intrs );
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end_pj = End_Index(pj, thb_intrs );
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exp_tor2_jk = exp( -p_tor2 * BOA_jk );
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exp_cot2_jk = exp( -p_cot2 * SQR(BOA_jk - 1.5) );
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exp_tor3_DjDk = exp( -p_tor3 * (Delta_j + Delta_k) );
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exp_tor4_DjDk = exp( p_tor4 * (Delta_j + Delta_k) );
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exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk);
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f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv;
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for( pi = start_pk; pi < end_pk; ++pi ) {
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p_ijk = &( thb_intrs->select.three_body_list[pi] );
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pij = p_ijk->pthb; // pij is pointer to i on j's bond_list
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pbond_ij = &( bonds->select.bond_list[pij] );
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bo_ij = &( pbond_ij->bo_data );
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if (bo_ij->BO > control->thb_cut/*0*/) {
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i = p_ijk->thb;
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type_i = system->my_atoms[i].type;
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r_ij = pbond_ij->d;
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BOA_ij = bo_ij->BO - control->thb_cut;
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theta_ijk = p_ijk->theta;
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sin_ijk = sin( theta_ijk );
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cos_ijk = cos( theta_ijk );
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//tan_ijk_i = 1. / tan( theta_ijk );
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if (sin_ijk >= 0 && sin_ijk <= MIN_SINE)
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tan_ijk_i = cos_ijk / MIN_SINE;
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else if( sin_ijk <= 0 && sin_ijk >= -MIN_SINE )
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tan_ijk_i = cos_ijk / -MIN_SINE;
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else tan_ijk_i = cos_ijk / sin_ijk;
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exp_tor2_ij = exp( -p_tor2 * BOA_ij );
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exp_cot2_ij = exp( -p_cot2 * SQR(BOA_ij -1.5) );
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for( pl = start_pj; pl < end_pj; ++pl ) {
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p_jkl = &( thb_intrs->select.three_body_list[pl] );
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l = p_jkl->thb;
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plk = p_jkl->pthb; //pointer to l on k's bond_list!
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pbond_kl = &( bonds->select.bond_list[plk] );
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bo_kl = &( pbond_kl->bo_data );
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type_l = system->my_atoms[l].type;
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fbh = &(system->reax_param.fbp[type_i][type_j]
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[type_k][type_l]);
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fbp = &(system->reax_param.fbp[type_i][type_j]
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[type_k][type_l].prm[0]);
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if( i != l && fbh->cnt &&
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bo_kl->BO > control->thb_cut/*0*/ &&
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bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/ ){
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++num_frb_intrs;
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r_kl = pbond_kl->d;
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BOA_kl = bo_kl->BO - control->thb_cut;
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theta_jkl = p_jkl->theta;
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sin_jkl = sin( theta_jkl );
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cos_jkl = cos( theta_jkl );
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//tan_jkl_i = 1. / tan( theta_jkl );
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if (sin_jkl >= 0 && sin_jkl <= MIN_SINE)
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tan_jkl_i = cos_jkl / MIN_SINE;
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else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE )
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tan_jkl_i = cos_jkl / -MIN_SINE;
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else tan_jkl_i = cos_jkl /sin_jkl;
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rvec_ScaledSum( dvec_li, 1., system->my_atoms[i].x,
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-1., system->my_atoms[l].x );
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r_li = rvec_Norm( dvec_li );
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/* omega and its derivative */
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omega = Calculate_Omega( pbond_ij->dvec, r_ij,
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pbond_jk->dvec, r_jk,
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pbond_kl->dvec, r_kl,
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dvec_li, r_li,
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p_ijk, p_jkl,
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dcos_omega_di, dcos_omega_dj,
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dcos_omega_dk, dcos_omega_dl,
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out_control );
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cos_omega = cos( omega );
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cos2omega = cos( 2. * omega );
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cos3omega = cos( 3. * omega );
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/* end omega calculations */
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/* torsion energy */
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exp_tor1 = exp( fbp->p_tor1 *
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SQR(2.0 - bo_jk->BO_pi - f11_DjDk) );
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exp_tor2_kl = exp( -p_tor2 * BOA_kl );
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exp_cot2_kl = exp( -p_cot2 * SQR(BOA_kl - 1.5) );
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fn10 = (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) *
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(1.0 - exp_tor2_kl);
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CV = 0.5 * ( fbp->V1 * (1.0 + cos_omega) +
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fbp->V2 * exp_tor1 * (1.0 - cos2omega) +
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fbp->V3 * (1.0 + cos3omega) );
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data->my_en.e_tor += e_tor = fn10 * sin_ijk * sin_jkl * CV;
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dfn11 = (-p_tor3 * exp_tor3_DjDk +
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(p_tor3 * exp_tor3_DjDk - p_tor4 * exp_tor4_DjDk) *
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(2.0 + exp_tor3_DjDk) * exp_tor34_inv) *
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exp_tor34_inv;
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CEtors1 = sin_ijk * sin_jkl * CV;
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CEtors2 = -fn10 * 2.0 * fbp->p_tor1 * fbp->V2 * exp_tor1 *
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(2.0 - bo_jk->BO_pi - f11_DjDk) * (1.0 - SQR(cos_omega)) *
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sin_ijk * sin_jkl;
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CEtors3 = CEtors2 * dfn11;
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CEtors4 = CEtors1 * p_tor2 * exp_tor2_ij *
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(1.0 - exp_tor2_jk) * (1.0 - exp_tor2_kl);
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CEtors5 = CEtors1 * p_tor2 *
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(1.0 - exp_tor2_ij) * exp_tor2_jk * (1.0 - exp_tor2_kl);
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CEtors6 = CEtors1 * p_tor2 *
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(1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) * exp_tor2_kl;
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cmn = -fn10 * CV;
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CEtors7 = cmn * sin_jkl * tan_ijk_i;
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CEtors8 = cmn * sin_ijk * tan_jkl_i;
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CEtors9 = fn10 * sin_ijk * sin_jkl *
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(0.5 * fbp->V1 - 2.0 * fbp->V2 * exp_tor1 * cos_omega +
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1.5 * fbp->V3 * (cos2omega + 2.0 * SQR(cos_omega)));
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/* end of torsion energy */
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/* 4-body conjugation energy */
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fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl;
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data->my_en.e_con += e_con =
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fbp->p_cot1 * fn12 *
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(1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);
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Cconj = -2.0 * fn12 * fbp->p_cot1 * p_cot2 *
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(1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);
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CEconj1 = Cconj * (BOA_ij - 1.5e0);
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CEconj2 = Cconj * (BOA_jk - 1.5e0);
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CEconj3 = Cconj * (BOA_kl - 1.5e0);
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CEconj4 = -fbp->p_cot1 * fn12 *
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(SQR(cos_omega) - 1.0) * sin_jkl * tan_ijk_i;
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CEconj5 = -fbp->p_cot1 * fn12 *
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(SQR(cos_omega) - 1.0) * sin_ijk * tan_jkl_i;
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CEconj6 = 2.0 * fbp->p_cot1 * fn12 *
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cos_omega * sin_ijk * sin_jkl;
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/* end 4-body conjugation energy */
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/* forces */
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bo_jk->Cdbopi += CEtors2;
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workspace->CdDelta[j] += CEtors3;
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workspace->CdDelta[k] += CEtors3;
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bo_ij->Cdbo += (CEtors4 + CEconj1);
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bo_jk->Cdbo += (CEtors5 + CEconj2);
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bo_kl->Cdbo += (CEtors6 + CEconj3);
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if (control->virial == 0) {
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/* dcos_theta_ijk */
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rvec_ScaledAdd( workspace->f[i],
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CEtors7 + CEconj4, p_ijk->dcos_dk );
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rvec_ScaledAdd( workspace->f[j],
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CEtors7 + CEconj4, p_ijk->dcos_dj );
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rvec_ScaledAdd( workspace->f[k],
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CEtors7 + CEconj4, p_ijk->dcos_di );
|
|
|
|
/* dcos_theta_jkl */
|
|
rvec_ScaledAdd( workspace->f[j],
|
|
CEtors8 + CEconj5, p_jkl->dcos_di );
|
|
rvec_ScaledAdd( workspace->f[k],
|
|
CEtors8 + CEconj5, p_jkl->dcos_dj );
|
|
rvec_ScaledAdd( workspace->f[l],
|
|
CEtors8 + CEconj5, p_jkl->dcos_dk );
|
|
|
|
/* dcos_omega */
|
|
rvec_ScaledAdd( workspace->f[i],
|
|
CEtors9 + CEconj6, dcos_omega_di );
|
|
rvec_ScaledAdd( workspace->f[j],
|
|
CEtors9 + CEconj6, dcos_omega_dj );
|
|
rvec_ScaledAdd( workspace->f[k],
|
|
CEtors9 + CEconj6, dcos_omega_dk );
|
|
rvec_ScaledAdd( workspace->f[l],
|
|
CEtors9 + CEconj6, dcos_omega_dl );
|
|
}
|
|
else {
|
|
ivec_Sum(rel_box_jl, pbond_jk->rel_box, pbond_kl->rel_box);
|
|
|
|
/* dcos_theta_ijk */
|
|
rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_dk );
|
|
rvec_Add( workspace->f[i], force );
|
|
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
|
|
rvec_Add( data->my_ext_press, ext_press );
|
|
|
|
rvec_ScaledAdd( workspace->f[j],
|
|
CEtors7 + CEconj4, p_ijk->dcos_dj );
|
|
|
|
rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_di );
|
|
rvec_Add( workspace->f[k], force );
|
|
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
|
|
rvec_Add( data->my_ext_press, ext_press );
|
|
|
|
|
|
/* dcos_theta_jkl */
|
|
rvec_ScaledAdd( workspace->f[j],
|
|
CEtors8 + CEconj5, p_jkl->dcos_di );
|
|
|
|
rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dj );
|
|
rvec_Add( workspace->f[k], force );
|
|
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
|
|
rvec_Add( data->my_ext_press, ext_press );
|
|
|
|
rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dk );
|
|
rvec_Add( workspace->f[l], force );
|
|
rvec_iMultiply( ext_press, rel_box_jl, force );
|
|
rvec_Add( data->my_ext_press, ext_press );
|
|
|
|
|
|
/* dcos_omega */
|
|
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_di );
|
|
rvec_Add( workspace->f[i], force );
|
|
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
|
|
rvec_Add( data->my_ext_press, ext_press );
|
|
|
|
rvec_ScaledAdd( workspace->f[j],
|
|
CEtors9 + CEconj6, dcos_omega_dj );
|
|
|
|
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dk );
|
|
rvec_Add( workspace->f[k], force );
|
|
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
|
|
rvec_Add( data->my_ext_press, ext_press );
|
|
|
|
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dl );
|
|
rvec_Add( workspace->f[l], force );
|
|
rvec_iMultiply( ext_press, rel_box_jl, force );
|
|
rvec_Add( data->my_ext_press, ext_press );
|
|
}
|
|
|
|
/* tally into per-atom virials */
|
|
if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
|
|
|
|
// acquire vectors
|
|
rvec_ScaledSum( delil, 1., system->my_atoms[l].x,
|
|
-1., system->my_atoms[i].x );
|
|
rvec_ScaledSum( deljl, 1., system->my_atoms[l].x,
|
|
-1., system->my_atoms[j].x );
|
|
rvec_ScaledSum( delkl, 1., system->my_atoms[l].x,
|
|
-1., system->my_atoms[k].x );
|
|
// dcos_theta_ijk
|
|
rvec_Scale( fi_tmp, CEtors7 + CEconj4, p_ijk->dcos_dk );
|
|
rvec_Scale( fj_tmp, CEtors7 + CEconj4, p_ijk->dcos_dj );
|
|
rvec_Scale( fk_tmp, CEtors7 + CEconj4, p_ijk->dcos_di );
|
|
|
|
// dcos_theta_jkl
|
|
rvec_ScaledAdd( fj_tmp, CEtors8 + CEconj5, p_jkl->dcos_di );
|
|
rvec_ScaledAdd( fk_tmp, CEtors8 + CEconj5, p_jkl->dcos_dj );
|
|
|
|
// dcos_omega
|
|
rvec_ScaledAdd( fi_tmp, CEtors9 + CEconj6, dcos_omega_di );
|
|
rvec_ScaledAdd( fj_tmp, CEtors9 + CEconj6, dcos_omega_dj );
|
|
rvec_ScaledAdd( fk_tmp, CEtors9 + CEconj6, dcos_omega_dk );
|
|
|
|
// tally
|
|
eng_tmp = e_tor + e_con;
|
|
if (system->pair_ptr->evflag)
|
|
system->pair_ptr->ev_tally(j,k,natoms,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
|
|
if (system->pair_ptr->vflag_atom)
|
|
system->pair_ptr->v_tally4(i,j,k,l,fi_tmp,fj_tmp,fk_tmp,delil,deljl,delkl);
|
|
}
|
|
} // pl check ends
|
|
} // pl loop ends
|
|
} // pi check ends
|
|
} // pi loop ends
|
|
} // k-j neighbor check ends
|
|
} // j-k neighbor check ends
|
|
} // pk loop ends
|
|
} // j loop
|
|
}
|