/************************ initialize system ************************/ int Reposition_Atoms( reax_system *system, control_params *control, simulation_data *data, mpi_datatypes *mpi_data, char *msg ) { int i; rvec dx; /* reposition atoms */ if( control->reposition_atoms == 0 ) { //fit atoms to periodic box rvec_MakeZero( dx ); } else if( control->reposition_atoms == 1 ) { //put center of mass to center rvec_Scale( dx, 0.5, system->big_box.box_norms ); rvec_ScaledAdd( dx, -1., data->xcm ); } else if( control->reposition_atoms == 2 ) { //put center of mass to origin rvec_Scale( dx, -1., data->xcm ); } else { strcpy( msg, "reposition_atoms: invalid option" ); return FAILURE; } for( i = 0; i < system->n; ++i ) // Inc_on_T3_Gen( system->my_atoms[i].x, dx, &(system->big_box) ); rvec_Add( system->my_atoms[i].x, dx ); return SUCCESS; }
void Compute_Pressure(reax_system* system, control_params *control, simulation_data* data, mpi_datatypes *mpi_data) { int i; reax_atom *p_atom; rvec tmp, tx, int_press; simulation_box *big_box = &(system->big_box); /* Calculate internal pressure */ rvec_MakeZero( int_press ); // 0: both int and ext, 1: ext only, 2: int only if( control->press_mode == 0 || control->press_mode == 2 ) { for( i = 0; i < system->n; ++i ) { p_atom = &( system->my_atoms[i] ); /* transform x into unitbox coordinates */ Transform_to_UnitBox( p_atom->x, big_box, 1, tx ); /* this atom's contribution to internal pressure */ rvec_Multiply( tmp, p_atom->f, tx ); rvec_Add( int_press, tmp ); } } /* sum up internal and external pressure */ MPI_Allreduce( int_press, data->int_press, 3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D ); MPI_Allreduce( data->my_ext_press, data->ext_press, 3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D ); /* kinetic contribution */ data->kin_press = 2.*(E_CONV*data->sys_en.e_kin) / (3.*big_box->V*P_CONV); /* Calculate total pressure in each direction */ data->tot_press[0] = data->kin_press - (( data->int_press[0] + data->ext_press[0] ) / ( big_box->box_norms[1] * big_box->box_norms[2] * P_CONV )); data->tot_press[1] = data->kin_press - (( data->int_press[1] + data->ext_press[1] ) / ( big_box->box_norms[0] * big_box->box_norms[2] * P_CONV )); data->tot_press[2] = data->kin_press - (( data->int_press[2] + data->ext_press[2] ) / ( big_box->box_norms[0] * big_box->box_norms[1] * P_CONV )); data->iso_bar.P = ( data->tot_press[0] + data->tot_press[1] + data->tot_press[2] ) / 3.; }
void rvec_unpacker( void *dummy_in, void *dummy_buf, mpi_out_data *out_buf ) { int i; rvec *in = (rvec*) dummy_in; rvec *buf = (rvec*) dummy_buf; for( i = 0; i < out_buf->cnt; ++i ) { rvec_Add( buf[ out_buf->index[i] ], in[i] ); #if defined(DEBUG) fprintf( stderr, "rvec_unpacker: cnt=%d i =%d index[i]=%d\n", out_buf->cnt, i, out_buf->index[i] ); #endif } }
void vdW_Coulomb_Energy( reax_system *system, control_params *control, simulation_data *data, storage *workspace, reax_list **lists, output_controls *out_control ) { int i, j, pj, natoms; int start_i, end_i, flag; rc_tagint orig_i, orig_j; double p_vdW1, p_vdW1i; double powr_vdW1, powgi_vdW1; double tmp, r_ij, fn13, exp1, exp2; double Tap, dTap, dfn13, CEvd, CEclmb, de_core; double dr3gamij_1, dr3gamij_3; double e_ele, e_vdW, e_core, SMALL = 0.0001; double e_lg, de_lg, r_ij5, r_ij6, re6; rvec temp, ext_press; two_body_parameters *twbp; far_neighbor_data *nbr_pj; reax_list *far_nbrs; // Tallying variables: double pe_vdw, f_tmp, delij[3]; natoms = system->n; far_nbrs = (*lists) + FAR_NBRS; p_vdW1 = system->reax_param.gp.l[28]; p_vdW1i = 1.0 / p_vdW1; e_core = 0; e_vdW = 0; e_lg = de_lg = 0.0; for( i = 0; i < natoms; ++i ) { if (system->my_atoms[i].type < 0) continue; start_i = Start_Index(i, far_nbrs); end_i = End_Index(i, far_nbrs); orig_i = system->my_atoms[i].orig_id; for( pj = start_i; pj < end_i; ++pj ) { nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); j = nbr_pj->nbr; if (system->my_atoms[j].type < 0) continue; orig_j = system->my_atoms[j].orig_id; flag = 0; if(nbr_pj->d <= control->nonb_cut) { if (j < natoms) flag = 1; else if (orig_i < orig_j) flag = 1; else if (orig_i == orig_j) { if (nbr_pj->dvec[2] > SMALL) flag = 1; else if (fabs(nbr_pj->dvec[2]) < SMALL) { if (nbr_pj->dvec[1] > SMALL) flag = 1; else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL) flag = 1; } } } if (flag) { r_ij = nbr_pj->d; twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ] [ system->my_atoms[j].type ]); Tap = workspace->Tap[7] * r_ij + workspace->Tap[6]; Tap = Tap * r_ij + workspace->Tap[5]; Tap = Tap * r_ij + workspace->Tap[4]; Tap = Tap * r_ij + workspace->Tap[3]; Tap = Tap * r_ij + workspace->Tap[2]; Tap = Tap * r_ij + workspace->Tap[1]; Tap = Tap * r_ij + workspace->Tap[0]; dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6]; dTap = dTap * r_ij + 5*workspace->Tap[5]; dTap = dTap * r_ij + 4*workspace->Tap[4]; dTap = dTap * r_ij + 3*workspace->Tap[3]; dTap = dTap * r_ij + 2*workspace->Tap[2]; dTap += workspace->Tap[1]/r_ij; /*vdWaals Calculations*/ if(system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3) { // shielding powr_vdW1 = pow(r_ij, p_vdW1); powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1); fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i ); exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) ); exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) ); e_vdW = twbp->D * (exp1 - 2.0 * exp2); data->my_en.e_vdW += Tap * e_vdW; dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) * pow(r_ij, p_vdW1 - 2.0); CEvd = dTap * e_vdW - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13; } else{ // no shielding exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); e_vdW = twbp->D * (exp1 - 2.0 * exp2); data->my_en.e_vdW += Tap * e_vdW; CEvd = dTap * e_vdW - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij; } if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3) { // innner wall e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore))); data->my_en.e_vdW += Tap * e_core; de_core = -(twbp->acore/twbp->rcore) * e_core; CEvd += dTap * e_core + Tap * de_core / r_ij; // lg correction, only if lgvdw is yes if (control->lgflag) { r_ij5 = pow( r_ij, 5.0 ); r_ij6 = pow( r_ij, 6.0 ); re6 = pow( twbp->lgre, 6.0 ); e_lg = -(twbp->lgcij/( r_ij6 + re6 )); data->my_en.e_vdW += Tap * e_lg; de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ; CEvd += dTap * e_lg + Tap * de_lg / r_ij; } } /*Coulomb Calculations*/ dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma ); dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 ); tmp = Tap / dr3gamij_3; data->my_en.e_ele += e_ele = C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp; CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q * ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3; /* tally into per-atom energy */ if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { pe_vdw = Tap * (e_vdW + e_core + e_lg); rvec_ScaledSum( delij, 1., system->my_atoms[i].x, -1., system->my_atoms[j].x ); f_tmp = -(CEvd + CEclmb); system->pair_ptr->ev_tally(i,j,natoms,1,pe_vdw,e_ele, f_tmp,delij[0],delij[1],delij[2]); } if( control->virial == 0 ) { rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec ); rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec ); } else { /* NPT, iNPT or sNPT */ rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec ); rvec_ScaledAdd( workspace->f[i], -1., temp ); rvec_Add( workspace->f[j], temp ); rvec_iMultiply( ext_press, nbr_pj->rel_box, temp ); rvec_Add( data->my_ext_press, ext_press ); } } } } Compute_Polarization_Energy( system, data ); }
void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control, simulation_data *data, storage *workspace, reax_list **lists, output_controls *out_control ) { int i, j, pj, r, natoms; int type_i, type_j, tmin, tmax; int start_i, end_i, flag; rc_tagint orig_i, orig_j; double r_ij, base, dif; double e_vdW, e_ele; double CEvd, CEclmb, SMALL = 0.0001; double f_tmp, delij[3]; rvec temp, ext_press; far_neighbor_data *nbr_pj; reax_list *far_nbrs; LR_lookup_table *t; natoms = system->n; far_nbrs = (*lists) + FAR_NBRS; e_ele = e_vdW = 0; for( i = 0; i < natoms; ++i ) { type_i = system->my_atoms[i].type; if (type_i < 0) continue; start_i = Start_Index(i,far_nbrs); end_i = End_Index(i,far_nbrs); orig_i = system->my_atoms[i].orig_id; for( pj = start_i; pj < end_i; ++pj ) { nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); j = nbr_pj->nbr; type_j = system->my_atoms[j].type; if (type_j < 0) continue; orig_j = system->my_atoms[j].orig_id; flag = 0; if(nbr_pj->d <= control->nonb_cut) { if (j < natoms) flag = 1; else if (orig_i < orig_j) flag = 1; else if (orig_i == orig_j) { if (nbr_pj->dvec[2] > SMALL) flag = 1; else if (fabs(nbr_pj->dvec[2]) < SMALL) { if (nbr_pj->dvec[1] > SMALL) flag = 1; else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL) flag = 1; } } } if (flag) { r_ij = nbr_pj->d; tmin = MIN( type_i, type_j ); tmax = MAX( type_i, type_j ); t = &( LR[tmin][tmax] ); /* Cubic Spline Interpolation */ r = (int)(r_ij * t->inv_dx); if( r == 0 ) ++r; base = (double)(r+1) * t->dx; dif = r_ij - base; e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif + t->vdW[r].a; e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif + t->ele[r].a; e_ele *= system->my_atoms[i].q * system->my_atoms[j].q; data->my_en.e_vdW += e_vdW; data->my_en.e_ele += e_ele; CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif + t->CEvd[r].a; CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif + t->CEclmb[r].a; CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q; /* tally into per-atom energy */ if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { rvec_ScaledSum( delij, 1., system->my_atoms[i].x, -1., system->my_atoms[j].x ); f_tmp = -(CEvd + CEclmb); system->pair_ptr->ev_tally(i,j,natoms,1,e_vdW,e_ele, f_tmp,delij[0],delij[1],delij[2]); } if( control->virial == 0 ) { rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec ); rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec ); } else { // NPT, iNPT or sNPT rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec ); rvec_ScaledAdd( workspace->f[i], -1., temp ); rvec_Add( workspace->f[j], temp ); rvec_iMultiply( ext_press, nbr_pj->rel_box, temp ); rvec_Add( data->my_ext_press, ext_press ); } } } } Compute_Polarization_Energy( system, data ); }
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; real r_ij, r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2; real 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; // rtensor temp_rtensor, total_rtensor; 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 real 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; /* 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 ) /* 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 ); top = 0; for( pi = start_j; pi < end_j; ++pi ) { pbond_ij = &( bond_list[pi] ); i = pbond_ij->nbr; bo_ij = &(pbond_ij->bo_data); type_i = system->my_atoms[i].type; if( system->reax_param.sbp[type_i].p_hbond == 2 && bo_ij->BO >= HB_THRESHOLD ) hblist[top++] = pi; } // fprintf( stderr, "j: %d, top: %d, hb_start_j: %d, hb_end_j:%d\n", // j, top, hb_start_j, hb_end_j ); 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; 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; r_ij = pbond_ij->d; 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_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; /*fprintf( stdout, "%6d%6d%6d%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f\n", system->my_atoms[i].orig_id, system->my_atoms[j].orig_id, system->my_atoms[k].orig_id, r_jk, theta, hbp->p_hb1, exp_hb2, hbp->p_hb3, hbp->r0_hb, exp_hb3, sin_xhz4, 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 { /* 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->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[i].x, -1., system->my_atoms[j].x ); rvec_ScaledSum( delkj, 1., system->my_atoms[k].x, -1., system->my_atoms[j].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); } #ifdef TEST_ENERGY /* fprintf( out_control->ehb, "%24.15e%24.15e%24.15e\n%24.15e%24.15e%24.15e\n%24.15e%24.15e%24.15e\n", dcos_theta_di[0], dcos_theta_di[1], dcos_theta_di[2], dcos_theta_dj[0], dcos_theta_dj[1], dcos_theta_dj[2], dcos_theta_dk[0], dcos_theta_dk[1], dcos_theta_dk[2]); fprintf( out_control->ehb, "%24.15e%24.15e%24.15e\n", CEhb1, CEhb2, CEhb3 ); */ fprintf( out_control->ehb, //"%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, r_jk, theta, bo_ij->BO, e_hb, data->my_en.e_hb ); #endif #ifdef TEST_FORCES Add_dBO( system, lists, j, pi, +CEhb1, workspace->f_hb ); //dbo term // dcos terms rvec_ScaledAdd( workspace->f_hb[i], +CEhb2, dcos_theta_di ); rvec_ScaledAdd( workspace->f_hb[j], +CEhb2, dcos_theta_dj ); rvec_ScaledAdd( workspace->f_hb[k], +CEhb2, dcos_theta_dk ); // dr terms rvec_ScaledAdd( workspace->f_hb[j], -CEhb3/r_jk, dvec_jk ); rvec_ScaledAdd( workspace->f_hb[k], +CEhb3/r_jk, dvec_jk ); #endif } } } } #if defined(DEBUG) fprintf( stderr, "Number of hydrogen bonds: %d\n", num_hb_intrs ); fprintf( stderr, "Hydrogen Bond Energy: %g\n", data->my_en.e_hb ); fprintf( stderr, "hydbonds: ext_press (%24.15e %24.15e %24.15e)\n", data->ext_press[0], data->ext_press[1], data->ext_press[2] ); #endif }
void Init_Forces(reax_system *system, control_params *control, simulation_data *data, static_storage *workspace, list **lists, output_controls *out_control) { int i, j, pj; int start_i, end_i; int type_i, type_j; int Htop, btop_i, btop_j, num_bonds, num_hbonds; int ihb, jhb, ihb_top, jhb_top; int flag; real r_ij, r2, self_coef; real dr3gamij_1, dr3gamij_3, Tap; //real val, dif, base; real C12, C34, C56; real Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2; real BO, BO_s, BO_pi, BO_pi2; real p_boc1, p_boc2; sparse_matrix *H; list *far_nbrs, *bonds, *hbonds; single_body_parameters *sbp_i, *sbp_j; two_body_parameters *twbp; far_neighbor_data *nbr_pj; //LR_lookup_table *t; reax_atom *atom_i, *atom_j; bond_data *ibond, *jbond; bond_order_data *bo_ij, *bo_ji; far_nbrs = *lists + FAR_NBRS; bonds = *lists + BONDS; hbonds = *lists + HBONDS; H = workspace->H; Htop = 0; num_bonds = 0; num_hbonds = 0; btop_i = btop_j = 0; p_boc1 = system->reaxprm.gp.l[0]; p_boc2 = system->reaxprm.gp.l[1]; for (i = 0; i < system->N; ++i) { atom_i = &(system->atoms[i]); type_i = atom_i->type; start_i = Start_Index(i, far_nbrs); end_i = End_Index(i, far_nbrs); H->start[i] = Htop; btop_i = End_Index(i, bonds); sbp_i = &(system->reaxprm.sbp[type_i]); ihb = ihb_top = -1; if (control->hb_cut > 0 && (ihb = sbp_i->p_hbond) == 1) ihb_top = End_Index(workspace->hbond_index[i], hbonds); for (pj = start_i; pj < end_i; ++pj) { nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); j = nbr_pj->nbr; atom_j = &(system->atoms[j]); flag = 0; if ((data->step - data->prev_steps) % control->reneighbor == 0) { if (nbr_pj->d <= control->r_cut) flag = 1; else flag = 0; } else if ((nbr_pj->d = Sq_Distance_on_T3(atom_i->x, atom_j->x, &(system->box), nbr_pj->dvec)) <= SQR(control->r_cut)) { nbr_pj->d = sqrt(nbr_pj->d); flag = 1; } if (flag) { type_j = system->atoms[j].type; r_ij = nbr_pj->d; sbp_j = &(system->reaxprm.sbp[type_j]); twbp = &(system->reaxprm.tbp[type_i][type_j]); self_coef = (i == j) ? 0.5 : 1.0; /* H matrix entry */ Tap = control->Tap7 * r_ij + control->Tap6; Tap = Tap * r_ij + control->Tap5; Tap = Tap * r_ij + control->Tap4; Tap = Tap * r_ij + control->Tap3; Tap = Tap * r_ij + control->Tap2; Tap = Tap * r_ij + control->Tap1; Tap = Tap * r_ij + control->Tap0; dr3gamij_1 = (r_ij * r_ij * r_ij + twbp->gamma); dr3gamij_3 = POW(dr3gamij_1, 0.33333333333333); H->entries[Htop].j = j; H->entries[Htop].val = self_coef * Tap * EV_to_KCALpMOL / dr3gamij_3; ++Htop; /* hydrogen bond lists */ if (control->hb_cut > 0 && (ihb == 1 || ihb == 2) && nbr_pj->d <= control->hb_cut) { // fprintf( stderr, "%d %d\n", atom1, atom2 ); jhb = sbp_j->p_hbond; if (ihb == 1 && jhb == 2) { hbonds->select.hbond_list[ihb_top].nbr = j; hbonds->select.hbond_list[ihb_top].scl = 1; hbonds->select.hbond_list[ihb_top].ptr = nbr_pj; ++ihb_top; ++num_hbonds; } else if (ihb == 2 && jhb == 1) { jhb_top = End_Index(workspace->hbond_index[j], hbonds); hbonds->select.hbond_list[jhb_top].nbr = i; hbonds->select.hbond_list[jhb_top].scl = -1; hbonds->select.hbond_list[jhb_top].ptr = nbr_pj; Set_End_Index(workspace->hbond_index[j], jhb_top + 1, hbonds); ++num_hbonds; } } /* uncorrected bond orders */ if (far_nbrs->select.far_nbr_list[pj].d <= control->nbr_cut) { r2 = SQR(r_ij); if (sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) { C12 = twbp->p_bo1 * POW(r_ij / twbp->r_s, twbp->p_bo2); BO_s = (1.0 + control->bo_cut) * EXP(C12); } else BO_s = C12 = 0.0; if (sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) { C34 = twbp->p_bo3 * POW(r_ij / twbp->r_p, twbp->p_bo4); BO_pi = EXP(C34); } else BO_pi = C34 = 0.0; if (sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) { C56 = twbp->p_bo5 * POW(r_ij / twbp->r_pp, twbp->p_bo6); BO_pi2 = EXP(C56); } else BO_pi2 = C56 = 0.0; /* Initially BO values are the uncorrected ones, page 1 */ BO = BO_s + BO_pi + BO_pi2; if (BO >= control->bo_cut) { num_bonds += 2; /****** bonds i-j and j-i ******/ ibond = &(bonds->select.bond_list[btop_i]); btop_j = End_Index(j, bonds); jbond = &(bonds->select.bond_list[btop_j]); ibond->nbr = j; jbond->nbr = i; ibond->d = r_ij; jbond->d = r_ij; rvec_Copy(ibond->dvec, nbr_pj->dvec); rvec_Scale(jbond->dvec, -1, nbr_pj->dvec); ivec_Copy(ibond->rel_box, nbr_pj->rel_box); ivec_Scale(jbond->rel_box, -1, nbr_pj->rel_box); ibond->dbond_index = btop_i; jbond->dbond_index = btop_i; ibond->sym_index = btop_j; jbond->sym_index = btop_i; ++btop_i; Set_End_Index(j, btop_j + 1, bonds); bo_ij = &(ibond->bo_data); bo_ji = &(jbond->bo_data); bo_ji->BO = bo_ij->BO = BO; bo_ji->BO_s = bo_ij->BO_s = BO_s; bo_ji->BO_pi = bo_ij->BO_pi = BO_pi; bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2; /* Bond Order page2-3, derivative of total bond order prime */ Cln_BOp_s = twbp->p_bo2 * C12 / r2; Cln_BOp_pi = twbp->p_bo4 * C34 / r2; Cln_BOp_pi2 = twbp->p_bo6 * C56 / r2; /* Only dln_BOp_xx wrt. dr_i is stored here, note that dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */ rvec_Scale(bo_ij->dln_BOp_s, -bo_ij->BO_s * Cln_BOp_s, ibond->dvec); rvec_Scale(bo_ij->dln_BOp_pi, -bo_ij->BO_pi * Cln_BOp_pi, ibond->dvec); rvec_Scale(bo_ij->dln_BOp_pi2, -bo_ij->BO_pi2 * Cln_BOp_pi2, ibond->dvec); rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s); rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi); rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2); /* Only dBOp wrt. dr_i is stored here, note that dBOp/dr_i = -dBOp/dr_j and all others are 0 */ rvec_Scale(bo_ij->dBOp, -(bo_ij->BO_s * Cln_BOp_s + bo_ij->BO_pi * Cln_BOp_pi + bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec); rvec_Scale(bo_ji->dBOp, -1., bo_ij->dBOp); rvec_Add(workspace->dDeltap_self[i], bo_ij->dBOp); rvec_Add(workspace->dDeltap_self[j], bo_ji->dBOp); bo_ij->BO_s -= control->bo_cut; bo_ij->BO -= control->bo_cut; bo_ji->BO_s -= control->bo_cut; bo_ji->BO -= control->bo_cut; workspace->total_bond_order[i] += bo_ij->BO; //currently total_BOp workspace->total_bond_order[j] += bo_ji->BO; //currently total_BOp bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0; bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0; /*fprintf( stderr, "%d %d %g %g %g\n", i+1, j+1, bo_ij->BO, bo_ij->BO_pi, bo_ij->BO_pi2 );*/ /*fprintf( stderr, "Cln_BOp_s: %f, pbo2: %f, C12:%f\n", Cln_BOp_s, twbp->p_bo2, C12 ); fprintf( stderr, "Cln_BOp_pi: %f, pbo4: %f, C34:%f\n", Cln_BOp_pi, twbp->p_bo4, C34 ); fprintf( stderr, "Cln_BOp_pi2: %f, pbo6: %f, C56:%f\n", Cln_BOp_pi2, twbp->p_bo6, C56 );*/ /*fprintf(stderr, "pbo1: %f, pbo2:%f\n", twbp->p_bo1, twbp->p_bo2); fprintf(stderr, "pbo3: %f, pbo4:%f\n", twbp->p_bo3, twbp->p_bo4); fprintf(stderr, "pbo5: %f, pbo6:%f\n", twbp->p_bo5, twbp->p_bo6); fprintf( stderr, "r_s: %f, r_p: %f, r_pp: %f\n", twbp->r_s, twbp->r_p, twbp->r_pp ); fprintf( stderr, "C12: %g, C34:%g, C56:%g\n", C12, C34, C56 );*/ /*fprintf( stderr, "\tfactors: %g %g %g\n", -(bo_ij->BO_s * Cln_BOp_s + bo_ij->BO_pi * Cln_BOp_pi + bo_ij->BO_pi2 * Cln_BOp_pp), -bo_ij->BO_pi * Cln_BOp_pi, -bo_ij->BO_pi2 * Cln_BOp_pi2 );*/ /*fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n", bo_ij->dBOp[0], bo_ij->dBOp[1], bo_ij->dBOp[2] ); fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n", bo_ij->dln_BOp_pi[0], bo_ij->dln_BOp_pi[1], bo_ij->dln_BOp_pi[2] ); fprintf( stderr, "dBOpi2:\t[%g, %g, %g]\n\n", bo_ij->dln_BOp_pi2[0], bo_ij->dln_BOp_pi2[1], bo_ij->dln_BOp_pi2[2] );*/ Set_End_Index(j, btop_j + 1, bonds); } } } } H->entries[Htop].j = i; H->entries[Htop].val = system->reaxprm.sbp[type_i].eta; ++Htop; Set_End_Index(i, btop_i, bonds); if (ihb == 1) Set_End_Index(workspace->hbond_index[i], ihb_top, hbonds); //fprintf( stderr, "%d bonds start: %d, end: %d\n", // i, Start_Index( i, bonds ), End_Index( i, bonds ) ); } // mark the end of j list H->start[i] = Htop; /* validate lists - decide if reallocation is required! */ Validate_Lists(workspace, lists, data->step, system->N, H->m, Htop, num_bonds, num_hbonds); #if defined(DEBUG_FOCUS) fprintf( stderr, "step%d: Htop = %d, num_bonds = %d, num_hbonds = %d\n", data->step, Htop, num_bonds, num_hbonds ); #endif }
void Compute_Bond_Boost_Force_All_Couple(reax_system *system, control_params *control, simulation_data *data, static_storage *workspace, list **lists, output_controls *out_control) { int i, j, pj; int type_i, type_j; int adatom, adatom2; // label the boost atom int nbond, nrad; // Nb int start_i, end_i; real e, emax, r, re, r_max; // eta, eta_max, r, r_e real bo; real A, dA, V; // A(\eta^max), and \Delta A(\eta^max) real *rv, *rv_max; real q, P1, vmax; // q, P1 in equation 13 real S1, S2, f1, f2, C1, C2; real T; real bf, bfactor; // boost force scale rvec df; // boost force reax_atom *atom1, *atom2; bond_order_data *bo_ij; two_body_parameters *twbp; list *bonds; nrad = Find_Radicals(system, control, data, workspace, lists, out_control); //nrad = 0; //printf("-------------------------step %d -----------------\n", data->step); bonds = (*lists) + BONDS; // bond boost parameters q = control->bboost_q; // should read this from control file P1 = control->bboost_P1; vmax = control->bboost_Vmax; // initiate parameters e = 0; adatom = 0; adatom2 = 0; bo = 0.0; re = 0.001; A = 0.0; dA = 0.0; r_max = 0.0; bfactor = 1.0; T = control->T_final; V = 0.0; // bost energy nbond = 0; emax = 0.0; // first get the max bond order for( i=0; i < system->N; ++i ) { start_i = Start_Index(i, bonds); end_i = End_Index(i, bonds); for( pj = start_i; pj < end_i; ++pj ){ if( i < bonds->select.bond_list[pj].nbr ) { j = bonds->select.bond_list[pj].nbr; type_i = system->atoms[i].type; type_j = system->atoms[j].type; twbp = &( system->reaxprm.tbp[type_i][type_j] ); vmax = control->bboost_Vmax; vmax = twbp->v_max; bo_ij = &( bonds->select.bond_list[pj].bo_data ); re = twbp->r_e; // get r_e from ffield.ext r = bonds->select.bond_list[pj].d; e = (r - re)/re; // eta bo = bo_ij->BO; if (bo > q && vmax > 0) { nbond += 1; if ( fabs(emax) < fabs(e) ) { emax = e; adatom = i; adatom2 = j; /* for debug printf("i = %d, j = %d, re = %.2f, r = %.2f ", i, j, re, r); printf("x1 = %.2f, y1 = %.2f, z1 = %.2f, ", \ system->atoms[i].x[0], system->atoms[i].x[1], system->atoms[i].x[2]); printf("x2 = %.2f, y2 = %.2f, z2 = %.2f\n", \ system->atoms[j].x[0], system->atoms[j].x[1], system->atoms[j].x[2]); printf( " %4s %4s\n", \ system->reaxprm.sbp[ system->atoms[i].type ].name, system->reaxprm.sbp[ system->atoms[j].type ].name); */ rv_max = bonds->select.bond_list[pj].dvec; r_max = bonds->select.bond_list[pj].d;; } } } } } int ntmp; if (fabs(emax) < q && nbond > 0 && nrad <= control->bboost_nrad) { data->boost ++ ; // calculate A, and dA S1 = emax/q; S2 = S1 * S1; C1 = 1 - (emax/q)*(emax/q); C2 = 1 - P1*P1*S2; A = C1 * C1 / C2; ntmp = 0; for( i=0; i < system->N; ++i ) { start_i = Start_Index(i, bonds); end_i = End_Index(i, bonds); for( pj = start_i; pj < end_i; ++pj ) { if( i < bonds->select.bond_list[pj].nbr ) { j = bonds->select.bond_list[pj].nbr; type_i = system->atoms[i].type; type_j = system->atoms[j].type; twbp = &( system->reaxprm.tbp[type_i][type_j] ); vmax = control->bboost_Vmax; vmax = twbp->v_max; bo_ij = &( bonds->select.bond_list[pj].bo_data ); r = bonds->select.bond_list[pj].d; re = twbp->r_e; // get r_e from ffield.ext rv = bonds->select.bond_list[pj].dvec; bo = bo_ij->BO; if (bo > q && vmax > 0) { e = (r - re)/re; // eta C1 = 1 - e*e/(q*q); V += vmax / nbond * C1; bf = 2*A*vmax*e/(nbond*q*q*re); if (fabs(e - emax) < 0.00001) { C2 = 1 - e*e*P1*P1/(q*q); f1 = 2/(q*q*re); f2 = f1/2*P1*P1; dA = 2*e*C1/C2*(f1 - f2*C1/C2); } rvec_Scale(df, bf, rv); atom1 = &( system->atoms[i] ); atom2 = &( system->atoms[j] ); rvec_Add(system->atoms[i].f, df); rvec_ScaledAdd(system->atoms[j].f, -1, df); ntmp++; } } } } // add the contribution of evalope function A bf = dA * V; rvec_Scale(df, bf, rv_max); atom1 = &( system->atoms[adatom]); rvec_Add(system->atoms[adatom].f, df); rvec_ScaledAdd(system->atoms[adatom2].f, -1, df); } else { data->boost = 0; } bfactor = exp(4184 * A * V/(T * 8.314)); //bfactor = V; fprintf( out_control->bboost, "%-10d%6d%6d%6d%3d%8.4f%8.4f %44.4f", \ data->step, nbond, adatom, adatom2, nrad, r_max, emax, bfactor ); fprintf( out_control->bboost, " %4s %4s\n", \ system->reaxprm.sbp[ system->atoms[adatom].type ].name, system->reaxprm.sbp[ system->atoms[adatom2].type ].name); fflush( out_control->bboost); }
void Compute_Bond_Boost_Force(reax_system *system, control_params *control, simulation_data *data, static_storage *workspace, list **lists, output_controls *out_control) { int i, j, pj; int type_i, type_j; int adatom, adatom2; // label the boost atom int nbond, nrad; // Nb int start_i, end_i; real e, emax, r, re, r_max; // eta, eta_max, r, r_e real bo; real A, dA, V; // A(\eta^max), and \Delta A(\eta^max) real *rv, *rv_max; real q, P1, vmax; // q, P1 in equation 13 real S1, S2, f1, f2, C1, C2; real bf; // boost force scale rvec df; // boost force reax_atom *atom1, *atom2; bond_order_data *bo_ij; two_body_parameters *twbp; list *bonds; nrad = Find_Radicals(system, control, data, workspace, lists, out_control); //printf("-------------------------step %d -----------------\n", data->step); bonds = (*lists) + BONDS; // bond boost parameters q = control->bboost_q; // should read this from control file P1 = control->bboost_P1; vmax = control->bboost_Vmax; // initiate parameters e = 0; adatom = 0; adatom2 = 0; nbond = 0; emax = 0.0; bo = 0.0; re = 0.001; A = 0.0; dA = 0.0; r_max = 0.0; // first get the max bond order for( i=0; i < system->N; ++i ) { re = 0.001; start_i = Start_Index(i, bonds); end_i = End_Index(i, bonds); for( pj = start_i; pj < end_i; ++pj ){ if( i < bonds->select.bond_list[pj].nbr ) { j = bonds->select.bond_list[pj].nbr; type_i = system->atoms[i].type; type_j = system->atoms[j].type; twbp = &( system->reaxprm.tbp[type_i][type_j] ); bo_ij = &( bonds->select.bond_list[pj].bo_data ); re = twbp->r_e; // get r_e from ffield.ext r = bonds->select.bond_list[pj].d; e = (r - re)/re; // eta //printf("r = %f, re = %f, e = %f\n", r, re, e); bo = bo_ij->BO; if ( (fabs (emax) < fabs(e)) & (bo > q)) { emax = e; adatom = i; adatom2 = j; } } } } /* printf("atom1 = %s ", system->reaxprm.sbp[ system->atoms[adatom].type ].name); printf("atom2 = %s ", system->reaxprm.sbp[ system->atoms[adatom2].type ].name); printf("bo = %f\n", bo); */ V = 0.0; // boost energy if (fabs(emax) < q && nrad == 0) { i = adatom; vmax = control->bboost_Vmax; // calculate A, and dA S1 = emax/q; S2 = S1 * S1; C1 = 1 - (emax/q)*(emax/q); C2 = 1 - P1*P1*S2; A = C1 * C1 / C2; /* printf("S1 = %f, S2 = %f ", S1, S2); printf("C1 = %f, C2 = %f ", C1, C2); printf("A = %f, emax = %f\n", A, emax); */ start_i = Start_Index(i, bonds); end_i = End_Index(i, bonds); for( pj = start_i; pj < end_i; ++pj ) { if( i < bonds->select.bond_list[pj].nbr ) { bo_ij = &( bonds->select.bond_list[pj].bo_data ); bo = bo_ij->BO; if (bo > 0.3) nbond += 1; } } for( pj = start_i; pj < end_i; ++pj ) { if( i < bonds->select.bond_list[pj].nbr ) { bo_ij = &( bonds->select.bond_list[pj].bo_data ); bo = bo_ij->BO; if (bo > 0.3) { j = bonds->select.bond_list[pj].nbr; r = bonds->select.bond_list[pj].d; rv = bonds->select.bond_list[pj].dvec; type_i = system->atoms[i].type; type_j = system->atoms[j].type; twbp = &( system->reaxprm.tbp[type_i][type_j] ); vmax = twbp->v_max; re = twbp->r_e; // get r_e from ffield.ext e = (r - re)/re; // eta C1 = 1 - e*e/(q*q); V += vmax / nbond * C1; bf = 2*A*vmax*e/(nbond*q*re); /* printf("e = %.3f, emax = %.3f, C1 = %.3f, re = %.3f, V = %.3f, A = %.3f bf = %.3f, vmax = %.3f, \n",\ e, emax, C1, re, V, A, bf, vmax); */ if (fabs(e - emax) < 0.00001) { C2 = 1 - e*e*P1*P1/(q*q); f1 = 2/(q*re); f2 = f1/2*P1*P1; dA = 2*e*C1/C2*(f1 - f2*C1/C2); rv_max = bonds->select.bond_list[pj].dvec; r_max = bonds->select.bond_list[pj].d;; } rvec_Scale(df, bf, rv); //rvec_Scale(df, 1/r, df); // assign the boost force atom1 = &( system->atoms[i] ); atom2 = &( system->atoms[j] ); /* printf("ofx = %8.3f ofy = %8.3f ofz = %8.3f \n", system->atoms[i].f[0],\ system->atoms[i].f[1], system->atoms[i].f[2]); */ rvec_Add(system->atoms[i].f, df); //printf(" fx = %8.3f fy = %8.3f fz = %8.3f \n", df[0], df[1], df[2]); /* rvec_Scale(df, -1, df); rvec_Add(system->atoms[j].f, df); */ } } } // add the contribution of evalope function A bf = dA * V; rvec_Scale(df, bf, rv_max); //rvec_Scale(df, 1/r_max, df); //printf("Max bf = %8.3f\n", bf); /* printf("Mfx = %8.3f Mfy = %8.3f Mfz = %8.3f dA = %8.3f V = %8.3f emax = %8.3f \n",\ df[0], df[1], df[2], dA, V, emax); */ atom1 = &( system->atoms[i] ); rvec_Add(system->atoms[i].f, df); } fprintf( out_control->bboost, "%-10d%6d%6d%10.4f%10.4f%10.4f", \ data->step, adatom + 1, adatom2 + 1, bo, emax, A*V ); fprintf( out_control->bboost, " %4s %4s\n", \ system->reaxprm.sbp[ system->atoms[adatom].type ].name, system->reaxprm.sbp[ system->atoms[adatom2].type ].name); fflush( out_control->bboost); }
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; real r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2; real 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 real 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 ]); ++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); } } } } } }
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; double temp, temp_bo_jt, pBOjt7; double p_val1, p_val2, p_val3, p_val4, p_val5; double p_val6, p_val7, p_val8, p_val9, p_val10; double p_pen1, p_pen2, p_pen3, p_pen4; double p_coa1, p_coa2, p_coa3, p_coa4; double trm8, expval6, expval7, expval2theta, expval12theta, exp3ij, exp3jk; double exp_pen2ij, exp_pen2jk, exp_pen3, exp_pen4, trm_pen34, exp_coa2; double dSBO1, dSBO2, SBO, SBO2, CSBO2, SBOp, prod_SBO, vlpadj; double CEval1, CEval2, CEval3, CEval4, CEval5, CEval6, CEval7, CEval8; double CEpen1, CEpen2, CEpen3; double e_ang, e_coa, e_pen; double CEcoa1, CEcoa2, CEcoa3, CEcoa4, CEcoa5; double Cf7ij, Cf7jk, Cf8j, Cf9j; double f7_ij, f7_jk, f8_Dj, f9_Dj; double Ctheta_0, theta_0, theta_00, theta, cos_theta, sin_theta; double BOA_ij, BOA_jk; rvec force, ext_press; // Tallying variables double eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3]; double delij[3], delkj[3]; 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 ) { // Ray: the first one with system->N type_j = system->my_atoms[j].type; if (type_j < 0) continue; 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 ); } 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; type_i = system->my_atoms[i].type; for( pk = start_j; pk < pi; ++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; } } 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 > control->thb_cut) && (bo_jk->BO > control->thb_cut) && (bo_ij->BO * bo_jk->BO > control->thb_cutsq) ) { thbh = &( system->reax_param.thbp[ type_i ][ type_j ][ type_k ] ); for( cnt = 0; cnt < thbh->cnt; ++cnt ) { 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; 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 { 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 ); } /* tally into per-atom virials */ if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { /* Acquire vectors */ rvec_ScaledSum( delij, 1., system->my_atoms[i].x, -1., system->my_atoms[j].x ); rvec_ScaledSum( delkj, 1., system->my_atoms[k].x, -1., system->my_atoms[j].x ); rvec_Scale( fi_tmp, -CEval8, p_ijk->dcos_di ); rvec_Scale( fj_tmp, -CEval8, p_ijk->dcos_dj ); rvec_Scale( fk_tmp, -CEval8, p_ijk->dcos_dk ); eng_tmp = e_ang + e_pen + e_coa; if( system->pair_ptr->evflag) system->pair_ptr->ev_tally(j,j,system->N,1,eng_tmp,0.0,0.0,0.0,0.0,0.0); if( system->pair_ptr->vflag_atom) system->pair_ptr->v_tally3(i,j,k,fi_tmp,fk_tmp,delij,delkj); } } } } } } 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 ); } } }
void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data, storage *workspace, reax_list **lists ) { reax_list *bonds = (*lists) + BONDS; bond_data *nbr_j, *nbr_k; bond_order_data *bo_ij, *bo_ji; dbond_coefficients coef; rvec temp, ext_press; ivec rel_box; int pk, k, j; /* Initializations */ nbr_j = &(bonds->select.bond_list[pj]); j = nbr_j->nbr; bo_ij = &(nbr_j->bo_data); bo_ji = &(bonds->select.bond_list[ nbr_j->sym_index ].bo_data); coef.C1dbo = bo_ij->C1dbo * (bo_ij->Cdbo + bo_ji->Cdbo); coef.C2dbo = bo_ij->C2dbo * (bo_ij->Cdbo + bo_ji->Cdbo); coef.C3dbo = bo_ij->C3dbo * (bo_ij->Cdbo + bo_ji->Cdbo); coef.C1dbopi = bo_ij->C1dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); coef.C2dbopi = bo_ij->C2dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); coef.C3dbopi = bo_ij->C3dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); coef.C4dbopi = bo_ij->C4dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); coef.C1dbopi2 = bo_ij->C1dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); coef.C2dbopi2 = bo_ij->C2dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); coef.C3dbopi2 = bo_ij->C3dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); coef.C4dbopi2 = bo_ij->C4dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); coef.C1dDelta = bo_ij->C1dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); for( pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk ) { nbr_k = &(bonds->select.bond_list[pk]); k = nbr_k->nbr; rvec_Scale(temp, -coef.C2dbo, nbr_k->bo_data.dBOp); /*2nd, dBO*/ rvec_ScaledAdd(temp, -coef.C2dDelta, nbr_k->bo_data.dBOp);/*dDelta*/ rvec_ScaledAdd(temp, -coef.C3dbopi, nbr_k->bo_data.dBOp); /*3rd, dBOpi*/ rvec_ScaledAdd(temp, -coef.C3dbopi2, nbr_k->bo_data.dBOp);/*3rd, dBOpi2*/ /* force */ rvec_Add( workspace->f[k], temp ); /* pressure */ rvec_iMultiply( ext_press, nbr_k->rel_box, temp ); rvec_Add( data->my_ext_press, ext_press ); } /* then atom i itself */ rvec_Scale( temp, coef.C1dbo, bo_ij->dBOp ); /*1st,dBO*/ rvec_ScaledAdd( temp, coef.C2dbo, workspace->dDeltap_self[i] ); /*2nd,dBO*/ rvec_ScaledAdd( temp, coef.C1dDelta, bo_ij->dBOp ); /*1st,dBO*/ rvec_ScaledAdd( temp, coef.C2dDelta, workspace->dDeltap_self[i] );/*2nd,dBO*/ rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/ rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/ rvec_ScaledAdd( temp, coef.C3dbopi, workspace->dDeltap_self[i]);/*3rd,dBOpi*/ rvec_ScaledAdd( temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); /*1st,dBO_pi2*/ rvec_ScaledAdd( temp, coef.C2dbopi2, bo_ij->dBOp ); /*2nd,dBO_pi2*/ rvec_ScaledAdd( temp, coef.C3dbopi2, workspace->dDeltap_self[i] );/*3rd*/ /* force */ rvec_Add( workspace->f[i], temp ); for( pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk ) { nbr_k = &(bonds->select.bond_list[pk]); k = nbr_k->nbr; rvec_Scale( temp, -coef.C3dbo, nbr_k->bo_data.dBOp ); /*3rd,dBO*/ rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp);/*dDelta*/ rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp); /*4th,dBOpi*/ rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp);/*4th,dBOpi2*/ /* force */ rvec_Add( workspace->f[k], temp ); /* pressure */ if( k != i ) { ivec_Sum( rel_box, nbr_k->rel_box, nbr_j->rel_box ); //rel_box(k, i) rvec_iMultiply( ext_press, rel_box, temp ); rvec_Add( data->my_ext_press, ext_press ); } } /* then atom j itself */ rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp ); /*1st, dBO*/ rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] ); /*2nd, dBO*/ rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp ); /*1st, dBO*/ rvec_ScaledAdd( temp, coef.C3dDelta, workspace->dDeltap_self[j]);/*2nd, dBO*/ rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/ rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/ rvec_ScaledAdd( temp, coef.C4dbopi, workspace->dDeltap_self[j]);/*3rd,dBOpi*/ rvec_ScaledAdd( temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); /*1st,dBOpi2*/ rvec_ScaledAdd( temp, -coef.C2dbopi2, bo_ij->dBOp ); /*2nd,dBOpi2*/ rvec_ScaledAdd( temp,coef.C4dbopi2,workspace->dDeltap_self[j]);/*3rd,dBOpi2*/ /* force */ rvec_Add( workspace->f[j], temp ); /* pressure */ rvec_iMultiply( ext_press, nbr_j->rel_box, temp ); rvec_Add( data->my_ext_press, ext_press ); }
int BOp( storage *workspace, reax_list *bonds, double bo_cut, int i, int btop_i, far_neighbor_data *nbr_pj, single_body_parameters *sbp_i, single_body_parameters *sbp_j, two_body_parameters *twbp ) { int j, btop_j; double r2, C12, C34, C56; double Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2; double BO, BO_s, BO_pi, BO_pi2; bond_data *ibond, *jbond; bond_order_data *bo_ij, *bo_ji; j = nbr_pj->nbr; r2 = SQR(nbr_pj->d); if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0 ) { C12 = twbp->p_bo1 * pow( nbr_pj->d / twbp->r_s, twbp->p_bo2 ); BO_s = (1.0 + bo_cut) * exp( C12 ); } else BO_s = C12 = 0.0; if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0 ) { C34 = twbp->p_bo3 * pow( nbr_pj->d / twbp->r_p, twbp->p_bo4 ); BO_pi = exp( C34 ); } else BO_pi = C34 = 0.0; if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0 ) { C56 = twbp->p_bo5 * pow( nbr_pj->d / twbp->r_pp, twbp->p_bo6 ); BO_pi2= exp( C56 ); } else BO_pi2 = C56 = 0.0; /* Initially BO values are the uncorrected ones, page 1 */ BO = BO_s + BO_pi + BO_pi2; if( BO >= bo_cut ) { /****** bonds i-j and j-i ******/ ibond = &( bonds->select.bond_list[btop_i] ); btop_j = End_Index( j, bonds ); jbond = &(bonds->select.bond_list[btop_j]); ibond->nbr = j; jbond->nbr = i; ibond->d = nbr_pj->d; jbond->d = nbr_pj->d; rvec_Copy( ibond->dvec, nbr_pj->dvec ); rvec_Scale( jbond->dvec, -1, nbr_pj->dvec ); ivec_Copy( ibond->rel_box, nbr_pj->rel_box ); ivec_Scale( jbond->rel_box, -1, nbr_pj->rel_box ); ibond->dbond_index = btop_i; jbond->dbond_index = btop_i; ibond->sym_index = btop_j; jbond->sym_index = btop_i; Set_End_Index( j, btop_j+1, bonds ); bo_ij = &( ibond->bo_data ); bo_ji = &( jbond->bo_data ); bo_ji->BO = bo_ij->BO = BO; bo_ji->BO_s = bo_ij->BO_s = BO_s; bo_ji->BO_pi = bo_ij->BO_pi = BO_pi; bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2; /* Bond Order page2-3, derivative of total bond order prime */ Cln_BOp_s = twbp->p_bo2 * C12 / r2; Cln_BOp_pi = twbp->p_bo4 * C34 / r2; Cln_BOp_pi2 = twbp->p_bo6 * C56 / r2; /* Only dln_BOp_xx wrt. dr_i is stored here, note that dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */ rvec_Scale(bo_ij->dln_BOp_s,-bo_ij->BO_s*Cln_BOp_s,ibond->dvec); rvec_Scale(bo_ij->dln_BOp_pi,-bo_ij->BO_pi*Cln_BOp_pi,ibond->dvec); rvec_Scale(bo_ij->dln_BOp_pi2, -bo_ij->BO_pi2*Cln_BOp_pi2,ibond->dvec); rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s); rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi ); rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2 ); rvec_Scale( bo_ij->dBOp, -(bo_ij->BO_s * Cln_BOp_s + bo_ij->BO_pi * Cln_BOp_pi + bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec ); rvec_Scale( bo_ji->dBOp, -1., bo_ij->dBOp ); rvec_Add( workspace->dDeltap_self[i], bo_ij->dBOp ); rvec_Add( workspace->dDeltap_self[j], bo_ji->dBOp ); bo_ij->BO_s -= bo_cut; bo_ij->BO -= bo_cut; bo_ji->BO_s -= bo_cut; bo_ji->BO -= bo_cut; workspace->total_bond_order[i] += bo_ij->BO; //currently total_BOp workspace->total_bond_order[j] += bo_ji->BO; //currently total_BOp bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0; bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0; return 1; } return 0; }
void Add_dBond_to_Forces( reax_system *system, int i, int pj, storage *workspace, reax_list **lists ) { reax_list *bonds = (*lists) + BONDS; bond_data *nbr_j, *nbr_k; bond_order_data *bo_ij, *bo_ji; dbond_coefficients coef; int pk, k, j; /* Virial Tallying variables */ rvec fi_tmp, fj_tmp, fk_tmp, delij, delji, delki, delkj, temp; /* Initializations */ nbr_j = &(bonds->select.bond_list[pj]); j = nbr_j->nbr; bo_ij = &(nbr_j->bo_data); bo_ji = &(bonds->select.bond_list[ nbr_j->sym_index ].bo_data); coef.C1dbo = bo_ij->C1dbo * (bo_ij->Cdbo + bo_ji->Cdbo); coef.C2dbo = bo_ij->C2dbo * (bo_ij->Cdbo + bo_ji->Cdbo); coef.C3dbo = bo_ij->C3dbo * (bo_ij->Cdbo + bo_ji->Cdbo); coef.C1dbopi = bo_ij->C1dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); coef.C2dbopi = bo_ij->C2dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); coef.C3dbopi = bo_ij->C3dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); coef.C4dbopi = bo_ij->C4dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi); coef.C1dbopi2 = bo_ij->C1dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); coef.C2dbopi2 = bo_ij->C2dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); coef.C3dbopi2 = bo_ij->C3dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); coef.C4dbopi2 = bo_ij->C4dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2); coef.C1dDelta = bo_ij->C1dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]); // forces on i rvec_Scale( temp, coef.C1dbo, bo_ij->dBOp ); rvec_ScaledAdd( temp, coef.C2dbo, workspace->dDeltap_self[i] ); rvec_ScaledAdd( temp, coef.C1dDelta, bo_ij->dBOp ); rvec_ScaledAdd( temp, coef.C2dDelta, workspace->dDeltap_self[i] ); rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi ); rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp ); rvec_ScaledAdd( temp, coef.C3dbopi, workspace->dDeltap_self[i]); rvec_ScaledAdd( temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); rvec_ScaledAdd( temp, coef.C2dbopi2, bo_ij->dBOp ); rvec_ScaledAdd( temp, coef.C3dbopi2, workspace->dDeltap_self[i] ); rvec_Add( workspace->f[i], temp ); if( system->pair_ptr->vflag_atom) { rvec_Scale(fi_tmp, -1.0, temp); rvec_ScaledSum( delij, 1., system->my_atoms[i].x,-1., system->my_atoms[j].x ); system->pair_ptr->v_tally(i,fi_tmp,delij); } // forces on j rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp ); rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] ); rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp ); rvec_ScaledAdd( temp, coef.C3dDelta, workspace->dDeltap_self[j]); rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi ); rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp ); rvec_ScaledAdd( temp, coef.C4dbopi, workspace->dDeltap_self[j]); rvec_ScaledAdd( temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); rvec_ScaledAdd( temp, -coef.C2dbopi2, bo_ij->dBOp ); rvec_ScaledAdd( temp, coef.C4dbopi2, workspace->dDeltap_self[j]); rvec_Add( workspace->f[j], temp ); if( system->pair_ptr->vflag_atom) { rvec_Scale(fj_tmp, -1.0, temp); rvec_ScaledSum( delji, 1., system->my_atoms[j].x,-1., system->my_atoms[i].x ); system->pair_ptr->v_tally(j,fj_tmp,delji); } // forces on k: i neighbor for( pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk ) { nbr_k = &(bonds->select.bond_list[pk]); k = nbr_k->nbr; rvec_Scale( temp, -coef.C2dbo, nbr_k->bo_data.dBOp); rvec_ScaledAdd( temp, -coef.C2dDelta, nbr_k->bo_data.dBOp); rvec_ScaledAdd( temp, -coef.C3dbopi, nbr_k->bo_data.dBOp); rvec_ScaledAdd( temp, -coef.C3dbopi2, nbr_k->bo_data.dBOp); rvec_Add( workspace->f[k], temp ); if( system->pair_ptr->vflag_atom ) { rvec_Scale(fk_tmp, -1.0, temp); rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); system->pair_ptr->v_tally(k,fk_tmp,delki); rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x); system->pair_ptr->v_tally(k,fk_tmp,delkj); } } // forces on k: j neighbor for( pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk ) { nbr_k = &(bonds->select.bond_list[pk]); k = nbr_k->nbr; rvec_Scale( temp, -coef.C3dbo, nbr_k->bo_data.dBOp ); rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp); rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp); rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp); rvec_Add( workspace->f[k], temp ); if( system->pair_ptr->vflag_atom ) { rvec_Scale(fk_tmp, -1.0, temp); rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); system->pair_ptr->v_tally(k,fk_tmp,delki); rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x); system->pair_ptr->v_tally(k,fk_tmp,delkj); } } }
void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control, simulation_data *data, storage *workspace, reax_list **lists, output_controls *out_control ) { int i, j, pj, r, natoms, steps, update_freq, update_energies; int type_i, type_j, tmin, tmax; int start_i, end_i, orig_i, orig_j; real r_ij, base, dif; real e_vdW, e_ele; real CEvd, CEclmb; rvec temp, ext_press; far_neighbor_data *nbr_pj; reax_list *far_nbrs; LR_lookup_table *t; natoms = system->n; far_nbrs = (*lists) + FAR_NBRS; steps = data->step - data->prev_steps; update_freq = out_control->energy_update_freq; update_energies = update_freq > 0 && steps % update_freq == 0; e_ele = e_vdW = 0; for( i = 0; i < natoms; ++i ) { type_i = system->my_atoms[i].type; start_i = Start_Index(i,far_nbrs); end_i = End_Index(i,far_nbrs); orig_i = system->my_atoms[i].orig_id; for( pj = start_i; pj < end_i; ++pj ) { nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); j = nbr_pj->nbr; orig_j = system->my_atoms[j].orig_id; if( nbr_pj->d <= control->nonb_cut && (j < natoms || orig_i < orig_j) ) { j = nbr_pj->nbr; type_j = system->my_atoms[j].type; r_ij = nbr_pj->d; tmin = MIN( type_i, type_j ); tmax = MAX( type_i, type_j ); t = &( LR[tmin][tmax] ); //t = &( LR[type_i][type_j] ); /* Cubic Spline Interpolation */ r = (int)(r_ij * t->inv_dx); if( r == 0 ) ++r; base = (real)(r+1) * t->dx; dif = r_ij - base; //fprintf(stderr, "r: %f, i: %d, base: %f, dif: %f\n", r, i, base, dif); if( update_energies ) { e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif + t->vdW[r].a; e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif + t->ele[r].a; e_ele *= system->my_atoms[i].q * system->my_atoms[j].q; data->my_en.e_vdW += e_vdW; data->my_en.e_ele += e_ele; } CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif + t->CEvd[r].a; CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif + t->CEclmb[r].a; CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q; if( control->virial == 0 ) { rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec ); rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec ); } else { // NPT, iNPT or sNPT /* for pressure coupling, terms not related to bond order derivatives are added directly into pressure vector/tensor */ rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec ); rvec_ScaledAdd( workspace->f[i], -1., temp ); rvec_Add( workspace->f[j], temp ); rvec_iMultiply( ext_press, nbr_pj->rel_box, temp ); rvec_Add( data->my_ext_press, ext_press ); } #ifdef TEST_ENERGY //fprintf( out_control->evdw, "%6d%6d%24.15e%24.15e%24.15e\n", fprintf( out_control->evdw, "%6d%6d%12.4f%12.4f%12.4f\n", system->my_atoms[i].orig_id, system->my_atoms[j].orig_id, r_ij, e_vdW, data->my_en.e_vdW ); //fprintf(out_control->ecou,"%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n", fprintf( out_control->ecou, "%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, r_ij, system->my_atoms[i].q, system->my_atoms[j].q, e_ele, data->my_en.e_ele ); #endif #ifdef TEST_FORCES rvec_ScaledAdd( workspace->f_vdw[i], -CEvd, nbr_pj->dvec ); rvec_ScaledAdd( workspace->f_vdw[j], +CEvd, nbr_pj->dvec ); rvec_ScaledAdd( workspace->f_ele[i], -CEclmb, nbr_pj->dvec ); rvec_ScaledAdd( workspace->f_ele[j], +CEclmb, nbr_pj->dvec ); #endif } } } Compute_Polarization_Energy( system, data ); }
void Init_Forces_Tab(reax_system *system, control_params *control, simulation_data *data, static_storage *workspace, list **lists, output_controls *out_control) { int i, j, pj; int start_i, end_i; int type_i, type_j; int Htop, btop_i, btop_j, num_bonds, num_hbonds; int tmin, tmax, r; int ihb, jhb, ihb_top, jhb_top; int flag; real r_ij, r2, self_coef; real val, dif, base; real C12, C34, C56; real Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2; real BO, BO_s, BO_pi, BO_pi2; real p_boc1, p_boc2; sparse_matrix *H; list *far_nbrs, *bonds, *hbonds; single_body_parameters *sbp_i, *sbp_j; two_body_parameters *twbp; far_neighbor_data *nbr_pj; LR_lookup_table *t; reax_atom *atom_i, *atom_j; bond_data *ibond, *jbond; bond_order_data *bo_ij, *bo_ji; far_nbrs = *lists + FAR_NBRS; bonds = *lists + BONDS; hbonds = *lists + HBONDS; H = workspace->H; Htop = 0; num_bonds = 0; num_hbonds = 0; btop_i = btop_j = 0; p_boc1 = system->reaxprm.gp.l[0]; p_boc2 = system->reaxprm.gp.l[1]; for (i = 0; i < system->N; ++i) { atom_i = &(system->atoms[i]); type_i = atom_i->type; start_i = Start_Index(i, far_nbrs); end_i = End_Index(i, far_nbrs); H->start[i] = Htop; btop_i = End_Index(i, bonds); sbp_i = &(system->reaxprm.sbp[type_i]); ihb = ihb_top = -1; if (control->hb_cut > 0 && (ihb = sbp_i->p_hbond) == 1) ihb_top = End_Index(workspace->hbond_index[i], hbonds); for (pj = start_i; pj < end_i; ++pj) { nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); j = nbr_pj->nbr; atom_j = &(system->atoms[j]); flag = 0; if ((data->step - data->prev_steps) % control->reneighbor == 0) { if (nbr_pj->d <= control->r_cut) flag = 1; else flag = 0; } else if ((nbr_pj->d = Sq_Distance_on_T3(atom_i->x, atom_j->x, &(system->box), nbr_pj->dvec)) <= SQR(control->r_cut)) { nbr_pj->d = sqrt(nbr_pj->d); flag = 1; } if (flag) { type_j = system->atoms[j].type; r_ij = nbr_pj->d; sbp_j = &(system->reaxprm.sbp[type_j]); twbp = &(system->reaxprm.tbp[type_i][type_j]); self_coef = (i == j) ? 0.5 : 1.0; tmin = MIN( type_i, type_j ); tmax = MAX( type_i, type_j ); t = &(LR[tmin][tmax]); /* cubic spline interpolation */ r = (int) (r_ij * t->inv_dx); if (r == 0) ++r; base = (real) (r + 1) * t->dx; dif = r_ij - base; val = ((t->ele[r].d * dif + t->ele[r].c) * dif + t->ele[r].b) * dif + t->ele[r].a; val *= EV_to_KCALpMOL / C_ele; H->entries[Htop].j = j; H->entries[Htop].val = self_coef * val; ++Htop; /* hydrogen bond lists */ if (control->hb_cut > 0 && (ihb == 1 || ihb == 2) && nbr_pj->d <= control->hb_cut) { // fprintf( stderr, "%d %d\n", atom1, atom2 ); jhb = sbp_j->p_hbond; if (ihb == 1 && jhb == 2) { hbonds->select.hbond_list[ihb_top].nbr = j; hbonds->select.hbond_list[ihb_top].scl = 1; hbonds->select.hbond_list[ihb_top].ptr = nbr_pj; ++ihb_top; ++num_hbonds; } else if (ihb == 2 && jhb == 1) { jhb_top = End_Index(workspace->hbond_index[j], hbonds); hbonds->select.hbond_list[jhb_top].nbr = i; hbonds->select.hbond_list[jhb_top].scl = -1; hbonds->select.hbond_list[jhb_top].ptr = nbr_pj; Set_End_Index(workspace->hbond_index[j], jhb_top + 1, hbonds); ++num_hbonds; } } /* uncorrected bond orders */ if (far_nbrs->select.far_nbr_list[pj].d <= control->nbr_cut) { r2 = SQR(r_ij); if (sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) { C12 = twbp->p_bo1 * POW(r_ij / twbp->r_s, twbp->p_bo2); BO_s = (1.0 + control->bo_cut) * EXP(C12); } else BO_s = C12 = 0.0; if (sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) { C34 = twbp->p_bo3 * POW(r_ij / twbp->r_p, twbp->p_bo4); BO_pi = EXP(C34); } else BO_pi = C34 = 0.0; if (sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) { C56 = twbp->p_bo5 * POW(r_ij / twbp->r_pp, twbp->p_bo6); BO_pi2 = EXP(C56); } else BO_pi2 = C56 = 0.0; /* Initially BO values are the uncorrected ones, page 1 */ BO = BO_s + BO_pi + BO_pi2; if (BO >= control->bo_cut) { num_bonds += 2; /****** bonds i-j and j-i ******/ ibond = &(bonds->select.bond_list[btop_i]); btop_j = End_Index(j, bonds); jbond = &(bonds->select.bond_list[btop_j]); ibond->nbr = j; jbond->nbr = i; ibond->d = r_ij; jbond->d = r_ij; rvec_Copy(ibond->dvec, nbr_pj->dvec); rvec_Scale(jbond->dvec, -1, nbr_pj->dvec); ivec_Copy(ibond->rel_box, nbr_pj->rel_box); ivec_Scale(jbond->rel_box, -1, nbr_pj->rel_box); ibond->dbond_index = btop_i; jbond->dbond_index = btop_i; ibond->sym_index = btop_j; jbond->sym_index = btop_i; ++btop_i; Set_End_Index(j, btop_j + 1, bonds); bo_ij = &(ibond->bo_data); bo_ji = &(jbond->bo_data); bo_ji->BO = bo_ij->BO = BO; bo_ji->BO_s = bo_ij->BO_s = BO_s; bo_ji->BO_pi = bo_ij->BO_pi = BO_pi; bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2; /* Bond Order page2-3, derivative of total bond order prime */ Cln_BOp_s = twbp->p_bo2 * C12 / r2; Cln_BOp_pi = twbp->p_bo4 * C34 / r2; Cln_BOp_pi2 = twbp->p_bo6 * C56 / r2; /* Only dln_BOp_xx wrt. dr_i is stored here, note that dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */ rvec_Scale(bo_ij->dln_BOp_s, -bo_ij->BO_s * Cln_BOp_s, ibond->dvec); rvec_Scale(bo_ij->dln_BOp_pi, -bo_ij->BO_pi * Cln_BOp_pi, ibond->dvec); rvec_Scale(bo_ij->dln_BOp_pi2, -bo_ij->BO_pi2 * Cln_BOp_pi2, ibond->dvec); rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s); rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi); rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2); /* Only dBOp wrt. dr_i is stored here, note that dBOp/dr_i = -dBOp/dr_j and all others are 0 */ rvec_Scale(bo_ij->dBOp, -(bo_ij->BO_s * Cln_BOp_s + bo_ij->BO_pi * Cln_BOp_pi + bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec); rvec_Scale(bo_ji->dBOp, -1., bo_ij->dBOp); rvec_Add(workspace->dDeltap_self[i], bo_ij->dBOp); rvec_Add(workspace->dDeltap_self[j], bo_ji->dBOp); bo_ij->BO_s -= control->bo_cut; bo_ij->BO -= control->bo_cut; bo_ji->BO_s -= control->bo_cut; bo_ji->BO -= control->bo_cut; workspace->total_bond_order[i] += bo_ij->BO; //currently total_BOp workspace->total_bond_order[j] += bo_ji->BO; //currently total_BOp bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0; bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0; Set_End_Index(j, btop_j + 1, bonds); } } } } H->entries[Htop].j = i; H->entries[Htop].val = system->reaxprm.sbp[type_i].eta; ++Htop; Set_End_Index(i, btop_i, bonds); if (ihb == 1) Set_End_Index(workspace->hbond_index[i], ihb_top, hbonds); } // mark the end of j list H->start[i] = Htop; /* validate lists - decide if reallocation is required! */ Validate_Lists(workspace, lists, data->step, system->N, H->m, Htop, num_bonds, num_hbonds); #if defined(DEBUG_FOCUS) fprintf( stderr, "step%d: Htop = %d, num_bonds = %d, num_hbonds = %d\n", data->step, Htop, num_bonds, num_hbonds ); //Print_Bonds( system, bonds, "sbonds.out" ); //Print_Bond_List2( system, bonds, "sbonds.out" ); //Print_Sparse_Matrix2( H, "H.out" ); #endif }
void vdW_Coulomb_Energy( reax_system *system, control_params *control, simulation_data *data, storage *workspace, reax_list **lists, output_controls *out_control ) { int i, j, pj, natoms; int start_i, end_i, orig_i, orig_j; real p_vdW1, p_vdW1i; real powr_vdW1, powgi_vdW1; real tmp, r_ij, fn13, exp1, exp2; real Tap, dTap, dfn13, CEvd, CEclmb, de_core; real dr3gamij_1, dr3gamij_3; real e_ele, e_vdW, e_core; rvec temp, ext_press; two_body_parameters *twbp; far_neighbor_data *nbr_pj; reax_list *far_nbrs; // rtensor temp_rtensor, total_rtensor; natoms = system->n; far_nbrs = (*lists) + FAR_NBRS; p_vdW1 = system->reax_param.gp.l[28]; p_vdW1i = 1.0 / p_vdW1; e_core = 0; e_vdW = 0; for( i = 0; i < natoms; ++i ) { start_i = Start_Index(i, far_nbrs); end_i = End_Index(i, far_nbrs); orig_i = system->my_atoms[i].orig_id; //fprintf( stderr, "i:%d, start_i: %d, end_i: %d\n", i, start_i, end_i ); for( pj = start_i; pj < end_i; ++pj ) { nbr_pj = &(far_nbrs->select.far_nbr_list[pj]); j = nbr_pj->nbr; orig_j = system->my_atoms[j].orig_id; if( nbr_pj->d <= control->nonb_cut && (j < natoms || orig_i < orig_j) ) { r_ij = nbr_pj->d; twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ] [ system->my_atoms[j].type ]); /* Calculate Taper and its derivative */ // Tap = nbr_pj->Tap; -- precomputed during compte_H Tap = workspace->Tap[7] * r_ij + workspace->Tap[6]; Tap = Tap * r_ij + workspace->Tap[5]; Tap = Tap * r_ij + workspace->Tap[4]; Tap = Tap * r_ij + workspace->Tap[3]; Tap = Tap * r_ij + workspace->Tap[2]; Tap = Tap * r_ij + workspace->Tap[1]; Tap = Tap * r_ij + workspace->Tap[0]; dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6]; dTap = dTap * r_ij + 5*workspace->Tap[5]; dTap = dTap * r_ij + 4*workspace->Tap[4]; dTap = dTap * r_ij + 3*workspace->Tap[3]; dTap = dTap * r_ij + 2*workspace->Tap[2]; dTap += workspace->Tap[1]/r_ij; /*vdWaals Calculations*/ if(system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3) { // shielding powr_vdW1 = pow(r_ij, p_vdW1); powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1); fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i ); exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) ); exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) ); e_vdW = twbp->D * (exp1 - 2.0 * exp2); data->my_en.e_vdW += Tap * e_vdW; dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) * pow(r_ij, p_vdW1 - 2.0); CEvd = dTap * e_vdW - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13; } else{ // no shielding exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); e_vdW = twbp->D * (exp1 - 2.0 * exp2); data->my_en.e_vdW += Tap * e_vdW; CEvd = dTap * e_vdW - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij; } if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3) { // innner wall e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore))); data->my_en.e_vdW += Tap * e_core; de_core = -(twbp->acore/twbp->rcore) * e_core; CEvd += dTap * e_core + Tap * de_core / r_ij; } /*Coulomb Calculations*/ dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma ); dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 ); tmp = Tap / dr3gamij_3; data->my_en.e_ele += e_ele = C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp; CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q * ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3; // fprintf( fout, "%5d %5d %10.6f %10.6f\n", // MIN( system->my_atoms[i].orig_id, system->my_atoms[j].orig_id ), // MAX( system->my_atoms[i].orig_id, system->my_atoms[j].orig_id ), // CEvd, CEclmb ); if( control->virial == 0 ) { rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec ); rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec ); } else { /* NPT, iNPT or sNPT */ /* for pressure coupling, terms not related to bond order derivatives are added directly into pressure vector/tensor */ rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec ); rvec_ScaledAdd( workspace->f[i], -1., temp ); rvec_Add( workspace->f[j], temp ); rvec_iMultiply( ext_press, nbr_pj->rel_box, temp ); rvec_Add( data->my_ext_press, ext_press ); // fprintf( stderr, "nonbonded(%d,%d): rel_box (%f %f %f) // force(%f %f %f) ext_press (%12.6f %12.6f %12.6f)\n", // i, j, nbr_pj->rel_box[0], nbr_pj->rel_box[1], nbr_pj->rel_box[2], // temp[0], temp[1], temp[2], // data->ext_press[0], data->ext_press[1], data->ext_press[2] ); } #ifdef TEST_ENERGY // fprintf( out_control->evdw, // "%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f\n", // workspace->Tap[7],workspace->Tap[6],workspace->Tap[5], // workspace->Tap[4],workspace->Tap[3],workspace->Tap[2], // workspace->Tap[1], Tap ); //fprintf( out_control->evdw, "%6d%6d%24.15e%24.15e%24.15e\n", fprintf( out_control->evdw, "%6d%6d%12.4f%12.4f%12.4f\n", system->my_atoms[i].orig_id, system->my_atoms[j].orig_id, r_ij, e_vdW, data->my_en.e_vdW ); //fprintf(out_control->ecou,"%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n", fprintf( out_control->ecou, "%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, r_ij, system->my_atoms[i].q, system->my_atoms[j].q, e_ele, data->my_en.e_ele ); #endif #ifdef TEST_FORCES rvec_ScaledAdd( workspace->f_vdw[i], -CEvd, nbr_pj->dvec ); rvec_ScaledAdd( workspace->f_vdw[j], +CEvd, nbr_pj->dvec ); rvec_ScaledAdd( workspace->f_ele[i], -CEclmb, nbr_pj->dvec ); rvec_ScaledAdd( workspace->f_ele[j], +CEclmb, nbr_pj->dvec ); #endif } } } #if defined(DEBUG) fprintf( stderr, "nonbonded: ext_press (%12.6f %12.6f %12.6f)\n", data->ext_press[0], data->ext_press[1], data->ext_press[2] ); MPI_Barrier( MPI_COMM_WORLD ); #endif Compute_Polarization_Energy( system, data ); }
/* IMPORTANT: This function assumes that current kinetic energy * the system is already computed * * IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs * to be added when there are long-range interactions or long-range * corrections to short-range interactions present. * We may want to add that for more accuracy. */ void Compute_Pressure(reax_system* system, control_params *control, simulation_data* data, mpi_datatypes *mpi_data) { int i; reax_atom *p_atom; rvec tmp, tx, int_press; simulation_box *big_box = &(system->big_box); /* Calculate internal pressure */ rvec_MakeZero( int_press ); // 0: both int and ext, 1: ext only, 2: int only if( control->press_mode == 0 || control->press_mode == 2 ) { for( i = 0; i < system->n; ++i ) { p_atom = &( system->my_atoms[i] ); /* transform x into unitbox coordinates */ Transform_to_UnitBox( p_atom->x, big_box, 1, tx ); /* this atom's contribution to internal pressure */ rvec_Multiply( tmp, p_atom->f, tx ); rvec_Add( int_press, tmp ); #if defined(DEBUG) fprintf( stderr, "%8d%8.2f%8.2f%8.2f", i+1, p_atom->x[0], p_atom->x[1], p_atom->x[2] ); fprintf( stderr, "%8.2f%8.2f%8.2f", p_atom->f[0], p_atom->f[1], p_atom->f[2] ); fprintf( stderr, "%8.2f%8.2f%8.2f\n", int_press[0], int_press[1], int_press[2] ); #endif } } /* sum up internal and external pressure */ #if defined(DEBUG) fprintf(stderr,"p%d:p_int(%10.5f %10.5f %10.5f)p_ext(%10.5f %10.5f %10.5f)\n", system->my_rank, int_press[0], int_press[1], int_press[2], data->my_ext_press[0], data->my_ext_press[1], data->my_ext_press[2] ); #endif MPI_Allreduce( int_press, data->int_press, 3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D ); MPI_Allreduce( data->my_ext_press, data->ext_press, 3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D ); #if defined(DEBUG) fprintf( stderr, "p%d: %10.5f %10.5f %10.5f\n", system->my_rank, data->int_press[0], data->int_press[1], data->int_press[2] ); fprintf( stderr, "p%d: %10.5f %10.5f %10.5f\n", system->my_rank, data->ext_press[0], data->ext_press[1], data->ext_press[2] ); #endif /* kinetic contribution */ data->kin_press = 2.*(E_CONV*data->sys_en.e_kin) / (3.*big_box->V*P_CONV); /* Calculate total pressure in each direction */ data->tot_press[0] = data->kin_press - (( data->int_press[0] + data->ext_press[0] ) / ( big_box->box_norms[1] * big_box->box_norms[2] * P_CONV )); data->tot_press[1] = data->kin_press - (( data->int_press[1] + data->ext_press[1] ) / ( big_box->box_norms[0] * big_box->box_norms[2] * P_CONV )); data->tot_press[2] = data->kin_press - (( data->int_press[2] + data->ext_press[2] ) / ( big_box->box_norms[0] * big_box->box_norms[1] * P_CONV )); /* Average pressure for the whole box */ data->iso_bar.P = ( data->tot_press[0] + data->tot_press[1] + data->tot_press[2] ) / 3.; }