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reaxc_valence_angles.cpp
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Wed, Jun 26, 22:01

reaxc_valence_angles.cpp
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/*----------------------------------------------------------------------
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*/) ) {
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_boc[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
}

Event Timeline

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