diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp index 8ffd103a9..95b0ab4f6 100644 --- a/src/USER-REAXC/reaxc_valence_angles.cpp +++ b/src/USER-REAXC/reaxc_valence_angles.cpp @@ -1,535 +1,537 @@ /*---------------------------------------------------------------------- PuReMD - Purdue ReaxFF Molecular Dynamics Program Copyright (2010) Purdue University Hasan Metin Aktulga, haktulga@cs.purdue.edu Joseph Fogarty, jcfogart@mail.usf.edu Sagar Pandit, pandit@usf.edu Ananth Y Grama, ayg@cs.purdue.edu 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 "reaxc_types.h" #if defined(PURE_REAX) #include "valence_angles.h" #include "bond_orders.h" #include "list.h" #include "vector.h" #elif defined(LAMMPS_REAX) #include "reaxc_valence_angles.h" #include "reaxc_bond_orders.h" #include "reaxc_list.h" #include "reaxc_vector.h" #endif /* calculates the theta angle between i-j-k */ void Calculate_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk, real *theta, real *cos_theta ) { (*cos_theta) = Dot( dvec_ji, dvec_jk, 3 ) / ( d_ji * d_jk ); if( *cos_theta > 1. ) *cos_theta = 1.0; if( *cos_theta < -1. ) *cos_theta = -1.0; (*theta) = acos( *cos_theta ); } /* calculates the derivative of the cosine of the angle between i-j-k */ void Calculate_dCos_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk, rvec* dcos_theta_di, rvec* dcos_theta_dj, rvec* dcos_theta_dk ) { int t; real sqr_d_ji = SQR(d_ji); real sqr_d_jk = SQR(d_jk); real inv_dists = 1.0 / (d_ji * d_jk); real inv_dists3 = pow( inv_dists, 3 ); real dot_dvecs = Dot( dvec_ji, dvec_jk, 3 ); real Cdot_inv3 = dot_dvecs * inv_dists3; for( t = 0; t < 3; ++t ) { (*dcos_theta_di)[t] = dvec_jk[t] * inv_dists - Cdot_inv3 * sqr_d_jk * dvec_ji[t]; (*dcos_theta_dj)[t] = -(dvec_jk[t] + dvec_ji[t]) * inv_dists + Cdot_inv3 * ( sqr_d_jk * dvec_ji[t] + sqr_d_ji * dvec_jk[t] ); (*dcos_theta_dk)[t] = dvec_ji[t] * inv_dists - Cdot_inv3 * sqr_d_ji * dvec_jk[t]; } } /* this is a 3-body interaction in which the main role is played by j which sits in the middle of the other two. */ void Valence_Angles( reax_system *system, control_params *control, simulation_data *data, storage *workspace, reax_list **lists, output_controls *out_control ) { int i, j, pi, k, pk, t; int type_i, type_j, type_k; int start_j, end_j, start_pk, end_pk; int cnt, num_thb_intrs; real temp, temp_bo_jt, pBOjt7; real p_val1, p_val2, p_val3, p_val4, p_val5; real p_val6, p_val7, p_val8, p_val9, p_val10; real p_pen1, p_pen2, p_pen3, p_pen4; real p_coa1, p_coa2, p_coa3, p_coa4; real trm8, expval6, expval7, expval2theta, expval12theta, exp3ij, exp3jk; real exp_pen2ij, exp_pen2jk, exp_pen3, exp_pen4, trm_pen34, exp_coa2; real dSBO1, dSBO2, SBO, SBO2, CSBO2, SBOp, prod_SBO, vlpadj; real CEval1, CEval2, CEval3, CEval4, CEval5, CEval6, CEval7, CEval8; real CEpen1, CEpen2, CEpen3; real e_ang, e_coa, e_pen; real CEcoa1, CEcoa2, CEcoa3, CEcoa4, CEcoa5; real Cf7ij, Cf7jk, Cf8j, Cf9j; real f7_ij, f7_jk, f8_Dj, f9_Dj; real Ctheta_0, theta_0, theta_00, theta, cos_theta, sin_theta; real r_ij, r_jk; real BOA_ij, BOA_jk; rvec force, ext_press; // rtensor temp_rtensor, total_rtensor; three_body_header *thbh; three_body_parameters *thbp; three_body_interaction_data *p_ijk, *p_kji; bond_data *pbond_ij, *pbond_jk, *pbond_jt; bond_order_data *bo_ij, *bo_jk, *bo_jt; reax_list *bonds = (*lists) + BONDS; reax_list *thb_intrs = (*lists) + THREE_BODIES; /* global parameters used in these calculations */ p_val6 = system->reax_param.gp.l[14]; p_val8 = system->reax_param.gp.l[33]; p_val9 = system->reax_param.gp.l[16]; p_val10 = system->reax_param.gp.l[17]; num_thb_intrs = 0; for( j = 0; j < system->N; ++j ) { // fprintf( out_control->eval, "j: %d\n", j ); type_j = system->my_atoms[j].type; start_j = Start_Index(j, bonds); end_j = End_Index(j, bonds); p_val3 = system->reax_param.sbp[ type_j ].p_val3; p_val5 = system->reax_param.sbp[ type_j ].p_val5; SBOp = 0, prod_SBO = 1; for( t = start_j; t < end_j; ++t ) { bo_jt = &(bonds->select.bond_list[t].bo_data); SBOp += (bo_jt->BO_pi + bo_jt->BO_pi2); temp = SQR( bo_jt->BO ); temp *= temp; temp *= temp; prod_SBO *= exp( -temp ); } /* modifications to match Adri's code - 09/01/09 */ if( workspace->vlpex[j] >= 0 ){ vlpadj = 0; dSBO2 = prod_SBO - 1; } else{ vlpadj = workspace->nlp[j]; dSBO2 = (prod_SBO - 1) * (1 - p_val8 * workspace->dDelta_lp[j]); } SBO = SBOp + (1 - prod_SBO) * (-workspace->Delta_boc[j] - p_val8 * vlpadj); dSBO1 = -8 * prod_SBO * ( workspace->Delta_boc[j] + p_val8 * vlpadj ); if( SBO <= 0 ) SBO2 = 0, CSBO2 = 0; else if( SBO > 0 && SBO <= 1 ) { SBO2 = pow( SBO, p_val9 ); CSBO2 = p_val9 * pow( SBO, p_val9 - 1 ); } else if( SBO > 1 && SBO < 2 ) { SBO2 = 2 - pow( 2-SBO, p_val9 ); CSBO2 = p_val9 * pow( 2 - SBO, p_val9 - 1 ); } else SBO2 = 2, CSBO2 = 0; expval6 = exp( p_val6 * workspace->Delta_boc[j] ); for( pi = start_j; pi < end_j; ++pi ) { Set_Start_Index( pi, num_thb_intrs, thb_intrs ); pbond_ij = &(bonds->select.bond_list[pi]); bo_ij = &(pbond_ij->bo_data); BOA_ij = bo_ij->BO - control->thb_cut; if( BOA_ij/*bo_ij->BO*/ > 0.0 && ( j < system->n || pbond_ij->nbr < system->n ) ) { i = pbond_ij->nbr; r_ij = pbond_ij->d; type_i = system->my_atoms[i].type; // fprintf( out_control->eval, "i: %d\n", i ); /* first copy 3-body intrs from previously computed ones where i>k. in the second for-loop below, we compute only new 3-body intrs where i < k */ for( pk = start_j; pk < pi; ++pk ) { // fprintf( out_control->eval, "pk: %d\n", pk ); start_pk = Start_Index( pk, thb_intrs ); end_pk = End_Index( pk, thb_intrs ); for( t = start_pk; t < end_pk; ++t ) if( thb_intrs->select.three_body_list[t].thb == i ) { p_ijk = &(thb_intrs->select.three_body_list[num_thb_intrs] ); p_kji = &(thb_intrs->select.three_body_list[t]); p_ijk->thb = bonds->select.bond_list[pk].nbr; p_ijk->pthb = pk; p_ijk->theta = p_kji->theta; rvec_Copy( p_ijk->dcos_di, p_kji->dcos_dk ); rvec_Copy( p_ijk->dcos_dj, p_kji->dcos_dj ); rvec_Copy( p_ijk->dcos_dk, p_kji->dcos_di ); ++num_thb_intrs; break; } } /* and this is the second for loop mentioned above */ for( pk = pi+1; pk < end_j; ++pk ) { pbond_jk = &(bonds->select.bond_list[pk]); bo_jk = &(pbond_jk->bo_data); BOA_jk = bo_jk->BO - control->thb_cut; k = pbond_jk->nbr; type_k = system->my_atoms[k].type; p_ijk = &( thb_intrs->select.three_body_list[num_thb_intrs] ); Calculate_Theta( pbond_ij->dvec, pbond_ij->d, pbond_jk->dvec, pbond_jk->d, &theta, &cos_theta ); Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d, pbond_jk->dvec, pbond_jk->d, &(p_ijk->dcos_di), &(p_ijk->dcos_dj), &(p_ijk->dcos_dk) ); p_ijk->thb = k; p_ijk->pthb = pk; p_ijk->theta = theta; sin_theta = sin( theta ); if( sin_theta < 1.0e-5 ) sin_theta = 1.0e-5; ++num_thb_intrs; if( (j < system->n) && (BOA_jk > 0.0) && - (bo_ij->BO * bo_jk->BO > SQR(control->thb_cut)/*0*/) ) { + (bo_ij->BO > control->thb_cut) && + (bo_jk->BO > control->thb_cut) && + (bo_ij->BO * bo_jk->BO > 0.001) ) { r_jk = pbond_jk->d; thbh = &( system->reax_param.thbp[ type_i ][ type_j ][ type_k ] ); /* if( system->my_atoms[i].orig_id < system->my_atoms[k].orig_id ) fprintf( fval, "%6d %6d %6d %7.3f %7.3f %7.3f\n", system->my_atoms[i].orig_id, system->my_atoms[j].orig_id, system->my_atoms[k].orig_id, bo_ij->BO, bo_jk->BO, p_ijk->theta ); else fprintf( fval, "%6d %6d %6d %7.3f %7.3f %7.3f\n", system->my_atoms[k].orig_id, system->my_atoms[j].orig_id, system->my_atoms[i].orig_id, bo_jk->BO, bo_ij->BO, p_ijk->theta ); */ for( cnt = 0; cnt < thbh->cnt; ++cnt ) { // fprintf( out_control->eval, "%6d%6d%6d -- exists in thbp\n", // i+1, j+1, k+1 ); if( fabs(thbh->prm[cnt].p_val1) > 0.001 ) { thbp = &( thbh->prm[cnt] ); /* ANGLE ENERGY */ p_val1 = thbp->p_val1; p_val2 = thbp->p_val2; p_val4 = thbp->p_val4; p_val7 = thbp->p_val7; theta_00 = thbp->theta_00; exp3ij = exp( -p_val3 * pow( BOA_ij, p_val4 ) ); f7_ij = 1.0 - exp3ij; Cf7ij = p_val3 * p_val4 * pow( BOA_ij, p_val4 - 1.0 ) * exp3ij; exp3jk = exp( -p_val3 * pow( BOA_jk, p_val4 ) ); f7_jk = 1.0 - exp3jk; Cf7jk = p_val3 * p_val4 * pow( BOA_jk, p_val4 - 1.0 ) * exp3jk; expval7 = exp( -p_val7 * workspace->Delta_boc[j] ); trm8 = 1.0 + expval6 + expval7; f8_Dj = p_val5 - ( (p_val5 - 1.0) * (2.0 + expval6) / trm8 ); Cf8j = ( (1.0 - p_val5) / SQR(trm8) ) * ( p_val6 * expval6 * trm8 - (2.0 + expval6) * ( p_val6*expval6 - p_val7*expval7 ) ); theta_0 = 180.0 - theta_00 * (1.0 - exp(-p_val10 * (2.0 - SBO2))); theta_0 = DEG2RAD( theta_0 ); expval2theta = exp( -p_val2 * SQR(theta_0 - theta) ); if( p_val1 >= 0 ) expval12theta = p_val1 * (1.0 - expval2theta); else // To avoid linear Me-H-Me angles (6/6/06) expval12theta = p_val1 * -expval2theta; CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta; CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta; CEval3 = Cf8j * f7_ij * f7_jk * expval12theta; CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj * expval2theta * (theta_0 - theta); Ctheta_0 = p_val10 * DEG2RAD(theta_00) * exp( -p_val10 * (2.0 - SBO2) ); CEval5 = -CEval4 * Ctheta_0 * CSBO2; CEval6 = CEval5 * dSBO1; CEval7 = CEval5 * dSBO2; CEval8 = -CEval4 / sin_theta; data->my_en.e_ang += e_ang = f7_ij * f7_jk * f8_Dj * expval12theta; /* END ANGLE ENERGY*/ /* PENALTY ENERGY */ p_pen1 = thbp->p_pen1; p_pen2 = system->reax_param.gp.l[19]; p_pen3 = system->reax_param.gp.l[20]; p_pen4 = system->reax_param.gp.l[21]; exp_pen2ij = exp( -p_pen2 * SQR( BOA_ij - 2.0 ) ); exp_pen2jk = exp( -p_pen2 * SQR( BOA_jk - 2.0 ) ); exp_pen3 = exp( -p_pen3 * workspace->Delta[j] ); exp_pen4 = exp( p_pen4 * workspace->Delta[j] ); trm_pen34 = 1.0 + exp_pen3 + exp_pen4; f9_Dj = ( 2.0 + exp_pen3 ) / trm_pen34; Cf9j = ( -p_pen3 * exp_pen3 * trm_pen34 - (2.0 + exp_pen3) * ( -p_pen3 * exp_pen3 + p_pen4 * exp_pen4 ) ) / SQR( trm_pen34 ); data->my_en.e_pen += e_pen = p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk; CEpen1 = e_pen * Cf9j / f9_Dj; temp = -2.0 * p_pen2 * e_pen; CEpen2 = temp * (BOA_ij - 2.0); CEpen3 = temp * (BOA_jk - 2.0); /* END PENALTY ENERGY */ /* COALITION ENERGY */ p_coa1 = thbp->p_coa1; p_coa2 = system->reax_param.gp.l[2]; p_coa3 = system->reax_param.gp.l[38]; p_coa4 = system->reax_param.gp.l[30]; exp_coa2 = exp( p_coa2 * workspace->Delta_val[j] ); data->my_en.e_coa += e_coa = p_coa1 / (1. + exp_coa2) * exp( -p_coa3 * SQR(workspace->total_bond_order[i]-BOA_ij) ) * exp( -p_coa3 * SQR(workspace->total_bond_order[k]-BOA_jk) ) * exp( -p_coa4 * SQR(BOA_ij - 1.5) ) * exp( -p_coa4 * SQR(BOA_jk - 1.5) ); CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa; CEcoa2 = -2 * p_coa4 * (BOA_jk - 1.5) * e_coa; CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1 + exp_coa2); CEcoa4 = -2 * p_coa3 * (workspace->total_bond_order[i]-BOA_ij) * e_coa; CEcoa5 = -2 * p_coa3 * (workspace->total_bond_order[k]-BOA_jk) * e_coa; /* END COALITION ENERGY */ /* FORCES */ bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4)); bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5)); workspace->CdDelta[j] += ((CEval3 + CEval7) + CEpen1 + CEcoa3); workspace->CdDelta[i] += CEcoa4; workspace->CdDelta[k] += CEcoa5; for( t = start_j; t < end_j; ++t ) { pbond_jt = &( bonds->select.bond_list[t] ); bo_jt = &(pbond_jt->bo_data); temp_bo_jt = bo_jt->BO; temp = CUBE( temp_bo_jt ); pBOjt7 = temp * temp * temp_bo_jt; // fprintf( out_control->eval, "%6d%12.8f\n", // workspace->reverse_map[bonds->select.bond_list[t].nbr], // (CEval6 * pBOjt7) ); bo_jt->Cdbo += (CEval6 * pBOjt7); bo_jt->Cdbopi += CEval5; bo_jt->Cdbopi2 += CEval5; } if( control->virial == 0 ) { rvec_ScaledAdd( workspace->f[i], CEval8, p_ijk->dcos_di ); rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj ); rvec_ScaledAdd( workspace->f[k], CEval8, p_ijk->dcos_dk ); } else { /* terms not related to bond order derivatives are added directly into forces and pressure vector/tensor */ rvec_Scale( force, CEval8, p_ijk->dcos_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], CEval8, p_ijk->dcos_dj ); rvec_Scale( force, CEval8, p_ijk->dcos_dk ); rvec_Add( workspace->f[k], force ); rvec_iMultiply( ext_press, pbond_jk->rel_box, force ); rvec_Add( data->my_ext_press, ext_press ); } #ifdef TEST_ENERGY /*fprintf( out_control->eval, "%12.8f%12.8f%12.8f%12.8f\n", p_val3, p_val4, BOA_ij, BOA_jk ); fprintf(out_control->eval, "%13.8f%13.8f%13.8f%13.8f%13.8f\n", workspace->Delta_e[j], workspace->vlpex[j], dSBO1, dSBO2, vlpadj ); fprintf( out_control->eval, "%12.8f%12.8f%12.8f%12.8f\n", f7_ij, f7_jk, f8_Dj, expval12theta ); fprintf( out_control->eval, "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n", CEval1, CEval2, CEval3, CEval4, CEval5, CEval6, CEval7, CEval8 ); fprintf( out_control->eval, "%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n", p_ijk->dcos_di[0]/sin_theta, p_ijk->dcos_di[1]/sin_theta, p_ijk->dcos_di[2]/sin_theta, p_ijk->dcos_dj[0]/sin_theta, p_ijk->dcos_dj[1]/sin_theta, p_ijk->dcos_dj[2]/sin_theta, p_ijk->dcos_dk[0]/sin_theta, p_ijk->dcos_dk[1]/sin_theta, p_ijk->dcos_dk[2]/sin_theta); fprintf( out_control->eval, "%6d%6d%6d%15.8f%15.8f\n", system->my_atoms[i].orig_id, system->my_atoms[j].orig_id, system->my_atoms[k].orig_id, RAD2DEG(theta), e_ang );*/ fprintf( out_control->eval, //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n", "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f%12.4f\n", system->my_atoms[i].orig_id, system->my_atoms[j].orig_id, system->my_atoms[k].orig_id, RAD2DEG(theta), theta_0, BOA_ij, BOA_jk, e_ang, data->my_en.e_ang ); fprintf( out_control->epen, //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n", "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n", system->my_atoms[i].orig_id, system->my_atoms[j].orig_id, system->my_atoms[k].orig_id, RAD2DEG(theta), BOA_ij, BOA_jk, e_pen, data->my_en.e_pen ); fprintf( out_control->ecoa, //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n", "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n", system->my_atoms[i].orig_id, system->my_atoms[j].orig_id, system->my_atoms[k].orig_id, RAD2DEG(theta), BOA_ij, BOA_jk, e_coa, data->my_en.e_coa ); #endif #ifdef TEST_FORCES /* angle forces */ Add_dBO( system, lists, j, pi, CEval1, workspace->f_ang ); Add_dBO( system, lists, j, pk, CEval2, workspace->f_ang ); Add_dDelta( system, lists, j, CEval3 + CEval7, workspace->f_ang ); for( t = start_j; t < end_j; ++t ) { pbond_jt = &( bonds->select.bond_list[t] ); bo_jt = &(pbond_jt->bo_data); temp_bo_jt = bo_jt->BO; temp = CUBE( temp_bo_jt ); pBOjt7 = temp * temp * temp_bo_jt; Add_dBO( system, lists, j, t, pBOjt7 * CEval6, workspace->f_ang ); Add_dBOpinpi2( system, lists, j, t, CEval5, CEval5, workspace->f_ang, workspace->f_ang ); } rvec_ScaledAdd( workspace->f_ang[i], CEval8, p_ijk->dcos_di ); rvec_ScaledAdd( workspace->f_ang[j], CEval8, p_ijk->dcos_dj ); rvec_ScaledAdd( workspace->f_ang[k], CEval8, p_ijk->dcos_dk ); /* end angle forces */ /* penalty forces */ Add_dDelta( system, lists, j, CEpen1, workspace->f_pen ); Add_dBO( system, lists, j, pi, CEpen2, workspace->f_pen ); Add_dBO( system, lists, j, pk, CEpen3, workspace->f_pen ); /* end penalty forces */ /* coalition forces */ Add_dBO( system, lists, j, pi, CEcoa1 - CEcoa4, workspace->f_coa ); Add_dBO( system, lists, j, pk, CEcoa2 - CEcoa5, workspace->f_coa ); Add_dDelta( system, lists, j, CEcoa3, workspace->f_coa ); Add_dDelta( system, lists, i, CEcoa4, workspace->f_coa ); Add_dDelta( system, lists, k, CEcoa5, workspace->f_coa ); /* end coalition forces */ #endif } } } } } Set_End_Index(pi, num_thb_intrs, thb_intrs ); } } if( num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE ) { workspace->realloc.num_3body = num_thb_intrs; if( num_thb_intrs > thb_intrs->num_intrs ) { fprintf( stderr, "step%d-ran out of space on angle_list: top=%d, max=%d", data->step, num_thb_intrs, thb_intrs->num_intrs ); MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY ); } } //fprintf( stderr,"%d: Number of angle interactions: %d\n", // data->step, num_thb_intrs ); #if defined(DEBUG) fprintf( stderr, "Number of angle interactions: %d\n", num_thb_intrs ); fprintf( stderr, "Angle Energy: %g\t Penalty Energy: %g\t Coalition Energy: %g\t\n", data->my_en.e_ang, data->my_en.e_pen, data->my_en.e_coa ); fprintf( stderr, "3body: ext_press (%12.6f %12.6f %12.6f)\n", data->ext_press[0], data->ext_press[1], data->ext_press[2] ); #endif }