Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/USER-REAXC/reaxc_torsion_angles.cpp
e3d0a322729eefficient_neuronet

Last Change
Raw File

reaxc_torsion_angles.cpp
View Options

/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Copyright (2010) Purdue University
Hasan Metin Aktulga, hmaktulga@lbl.gov
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
Please cite the related publication:
H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
"Parallel Reactive Molecular Dynamics: Numerical Methods and
Algorithmic Techniques", Parallel Computing, in press.
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 "pair_reax_c.h"
#include "reaxc_torsion_angles.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
#define MIN_SINE 1e-10
double Calculate_Omega( rvec dvec_ij, double r_ij,
rvec dvec_jk, double r_jk,
rvec dvec_kl, double r_kl,
rvec dvec_li, double r_li,
three_body_interaction_data *p_ijk,
three_body_interaction_data *p_jkl,
rvec dcos_omega_di, rvec dcos_omega_dj,
rvec dcos_omega_dk, rvec dcos_omega_dl,
output_controls *out_control )
{
double unnorm_cos_omega, unnorm_sin_omega, omega;
double sin_ijk, cos_ijk, sin_jkl, cos_jkl;
double htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe;
double arg, poem, tel;
rvec cross_jk_kl;
sin_ijk = sin( p_ijk->theta );
cos_ijk = cos( p_ijk->theta );
sin_jkl = sin( p_jkl->theta );
cos_jkl = cos( p_jkl->theta );
/* omega */
unnorm_cos_omega = -rvec_Dot(dvec_ij, dvec_jk) * rvec_Dot(dvec_jk, dvec_kl) +
SQR( r_jk ) * rvec_Dot( dvec_ij, dvec_kl );
rvec_Cross( cross_jk_kl, dvec_jk, dvec_kl );
unnorm_sin_omega = -r_jk * rvec_Dot( dvec_ij, cross_jk_kl );
omega = atan2( unnorm_sin_omega, unnorm_cos_omega );
htra = r_ij + cos_ijk * ( r_kl * cos_jkl - r_jk );
htrb = r_jk - r_ij * cos_ijk - r_kl * cos_jkl;
htrc = r_kl + cos_jkl * ( r_ij * cos_ijk - r_jk );
hthd = r_ij * sin_ijk * ( r_jk - r_kl * cos_jkl );
hthe = r_kl * sin_jkl * ( r_jk - r_ij * cos_ijk );
hnra = r_kl * sin_ijk * sin_jkl;
hnrc = r_ij * sin_ijk * sin_jkl;
hnhd = r_ij * r_kl * cos_ijk * sin_jkl;
hnhe = r_ij * r_kl * sin_ijk * cos_jkl;
poem = 2.0 * r_ij * r_kl * sin_ijk * sin_jkl;
if( poem < 1e-20 ) poem = 1e-20;
tel = SQR( r_ij ) + SQR( r_jk ) + SQR( r_kl ) - SQR( r_li ) -
2.0 * ( r_ij * r_jk * cos_ijk - r_ij * r_kl * cos_ijk * cos_jkl +
r_jk * r_kl * cos_jkl );
arg = tel / poem;
if( arg > 1.0 ) arg = 1.0;
if( arg < -1.0 ) arg = -1.0;
if( sin_ijk >= 0 && sin_ijk <= MIN_SINE ) sin_ijk = MIN_SINE;
else if( sin_ijk <= 0 && sin_ijk >= -MIN_SINE ) sin_ijk = -MIN_SINE;
if( sin_jkl >= 0 && sin_jkl <= MIN_SINE ) sin_jkl = MIN_SINE;
else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE ) sin_jkl = -MIN_SINE;
// dcos_omega_di
rvec_ScaledSum( dcos_omega_di, (htra-arg*hnra)/r_ij, dvec_ij, -1., dvec_li );
rvec_ScaledAdd( dcos_omega_di,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_dk );
rvec_Scale( dcos_omega_di, 2.0 / poem, dcos_omega_di );
// dcos_omega_dj
rvec_ScaledSum( dcos_omega_dj,-(htra-arg*hnra)/r_ij, dvec_ij,
-htrb / r_jk, dvec_jk );
rvec_ScaledAdd( dcos_omega_dj,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_dj );
rvec_ScaledAdd( dcos_omega_dj,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_di );
rvec_Scale( dcos_omega_dj, 2.0 / poem, dcos_omega_dj );
// dcos_omega_dk
rvec_ScaledSum( dcos_omega_dk,-(htrc-arg*hnrc)/r_kl, dvec_kl,
htrb / r_jk, dvec_jk );
rvec_ScaledAdd( dcos_omega_dk,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_di );
rvec_ScaledAdd( dcos_omega_dk,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_dj );
rvec_Scale( dcos_omega_dk, 2.0 / poem, dcos_omega_dk );
// dcos_omega_dl
rvec_ScaledSum( dcos_omega_dl, (htrc-arg*hnrc)/r_kl, dvec_kl, 1., dvec_li );
rvec_ScaledAdd( dcos_omega_dl,-(hthe-arg*hnhe)/sin_jkl, p_jkl->dcos_dk );
rvec_Scale( dcos_omega_dl, 2.0 / poem, dcos_omega_dl );
return omega;
}
void Torsion_Angles( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
{
int i, j, k, l, pi, pj, pk, pl, pij, plk, natoms;
int type_i, type_j, type_k, type_l;
int start_j, end_j;
int start_pj, end_pj, start_pk, end_pk;
int num_frb_intrs = 0;
double Delta_j, Delta_k;
double r_ij, r_jk, r_kl, r_li;
double BOA_ij, BOA_jk, BOA_kl;
double exp_tor2_ij, exp_tor2_jk, exp_tor2_kl;
double exp_tor1, exp_tor3_DjDk, exp_tor4_DjDk, exp_tor34_inv;
double exp_cot2_jk, exp_cot2_ij, exp_cot2_kl;
double fn10, f11_DjDk, dfn11, fn12;
double theta_ijk, theta_jkl;
double sin_ijk, sin_jkl;
double cos_ijk, cos_jkl;
double tan_ijk_i, tan_jkl_i;
double omega, cos_omega, cos2omega, cos3omega;
rvec dcos_omega_di, dcos_omega_dj, dcos_omega_dk, dcos_omega_dl;
double CV, cmn, CEtors1, CEtors2, CEtors3, CEtors4;
double CEtors5, CEtors6, CEtors7, CEtors8, CEtors9;
double Cconj, CEconj1, CEconj2, CEconj3;
double CEconj4, CEconj5, CEconj6;
double e_tor, e_con;
rvec dvec_li;
rvec force, ext_press;
ivec rel_box_jl;
// rtensor total_rtensor, temp_rtensor;
four_body_header *fbh;
four_body_parameters *fbp;
bond_data *pbond_ij, *pbond_jk, *pbond_kl;
bond_order_data *bo_ij, *bo_jk, *bo_kl;
three_body_interaction_data *p_ijk, *p_jkl;
double p_tor2 = system->reax_param.gp.l[23];
double p_tor3 = system->reax_param.gp.l[24];
double p_tor4 = system->reax_param.gp.l[25];
double p_cot2 = system->reax_param.gp.l[27];
reax_list *bonds = (*lists) + BONDS;
reax_list *thb_intrs = (*lists) + THREE_BODIES;
// Virial tallying variables
double delil[3], deljl[3], delkl[3];
double eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3];
natoms = system->n;
for( j = 0; j < natoms; ++j ) {
type_j = system->my_atoms[j].type;
Delta_j = workspace->Delta_boc[j];
start_j = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
for( pk = start_j; pk < end_j; ++pk ) {
pbond_jk = &( bonds->select.bond_list[pk] );
k = pbond_jk->nbr;
bo_jk = &( pbond_jk->bo_data );
BOA_jk = bo_jk->BO - control->thb_cut;
if( system->my_atoms[j].orig_id > system->my_atoms[k].orig_id )
continue;
if( system->my_atoms[j].orig_id == system->my_atoms[k].orig_id ) {
if (system->my_atoms[k].x[2] < system->my_atoms[j].x[2]) continue;
if (system->my_atoms[k].x[2] == system->my_atoms[j].x[2] &&
system->my_atoms[k].x[1] < system->my_atoms[j].x[1]) continue;
if (system->my_atoms[k].x[2] == system->my_atoms[j].x[2] &&
system->my_atoms[k].x[1] == system->my_atoms[j].x[1] &&
system->my_atoms[k].x[0] < system->my_atoms[j].x[0]) continue;
}
if( bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs) ) {
pj = pbond_jk->sym_index; // pj points to j on k's list
if( Num_Entries(pj, thb_intrs) ) {
type_k = system->my_atoms[k].type;
Delta_k = workspace->Delta_boc[k];
r_jk = pbond_jk->d;
start_pk = Start_Index(pk, thb_intrs );
end_pk = End_Index(pk, thb_intrs );
start_pj = Start_Index(pj, thb_intrs );
end_pj = End_Index(pj, thb_intrs );
exp_tor2_jk = exp( -p_tor2 * BOA_jk );
exp_cot2_jk = exp( -p_cot2 * SQR(BOA_jk - 1.5) );
exp_tor3_DjDk = exp( -p_tor3 * (Delta_j + Delta_k) );
exp_tor4_DjDk = exp( p_tor4 * (Delta_j + Delta_k) );
exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk);
f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv;
for( pi = start_pk; pi < end_pk; ++pi ) {
p_ijk = &( thb_intrs->select.three_body_list[pi] );
pij = p_ijk->pthb; // pij is pointer to i on j's bond_list
pbond_ij = &( bonds->select.bond_list[pij] );
bo_ij = &( pbond_ij->bo_data );
if( bo_ij->BO > control->thb_cut/*0*/ ) {
i = p_ijk->thb;
type_i = system->my_atoms[i].type;
r_ij = pbond_ij->d;
BOA_ij = bo_ij->BO - control->thb_cut;
theta_ijk = p_ijk->theta;
sin_ijk = sin( theta_ijk );
cos_ijk = cos( theta_ijk );
//tan_ijk_i = 1. / tan( theta_ijk );
if( sin_ijk >= 0 && sin_ijk <= MIN_SINE )
tan_ijk_i = cos_ijk / MIN_SINE;
else if( sin_ijk <= 0 && sin_ijk >= -MIN_SINE )
tan_ijk_i = cos_ijk / -MIN_SINE;
else tan_ijk_i = cos_ijk / sin_ijk;
exp_tor2_ij = exp( -p_tor2 * BOA_ij );
exp_cot2_ij = exp( -p_cot2 * SQR(BOA_ij -1.5) );
for( pl = start_pj; pl < end_pj; ++pl ) {
p_jkl = &( thb_intrs->select.three_body_list[pl] );
l = p_jkl->thb;
plk = p_jkl->pthb; //pointer to l on k's bond_list!
pbond_kl = &( bonds->select.bond_list[plk] );
bo_kl = &( pbond_kl->bo_data );
type_l = system->my_atoms[l].type;
fbh = &(system->reax_param.fbp[type_i][type_j]
[type_k][type_l]);
fbp = &(system->reax_param.fbp[type_i][type_j]
[type_k][type_l].prm[0]);
if( i != l && fbh->cnt &&
bo_kl->BO > control->thb_cut/*0*/ &&
bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/ ){
++num_frb_intrs;
r_kl = pbond_kl->d;
BOA_kl = bo_kl->BO - control->thb_cut;
theta_jkl = p_jkl->theta;
sin_jkl = sin( theta_jkl );
cos_jkl = cos( theta_jkl );
//tan_jkl_i = 1. / tan( theta_jkl );
if( sin_jkl >= 0 && sin_jkl <= MIN_SINE )
tan_jkl_i = cos_jkl / MIN_SINE;
else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE )
tan_jkl_i = cos_jkl / -MIN_SINE;
else tan_jkl_i = cos_jkl /sin_jkl;
rvec_ScaledSum( dvec_li, 1., system->my_atoms[i].x,
-1., system->my_atoms[l].x );
r_li = rvec_Norm( dvec_li );
/* omega and its derivative */
omega = Calculate_Omega( pbond_ij->dvec, r_ij,
pbond_jk->dvec, r_jk,
pbond_kl->dvec, r_kl,
dvec_li, r_li,
p_ijk, p_jkl,
dcos_omega_di, dcos_omega_dj,
dcos_omega_dk, dcos_omega_dl,
out_control );
cos_omega = cos( omega );
cos2omega = cos( 2. * omega );
cos3omega = cos( 3. * omega );
/* end omega calculations */
/* torsion energy */
exp_tor1 = exp( fbp->p_tor1 *
SQR(2.0 - bo_jk->BO_pi - f11_DjDk) );
exp_tor2_kl = exp( -p_tor2 * BOA_kl );
exp_cot2_kl = exp( -p_cot2 * SQR(BOA_kl - 1.5) );
fn10 = (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) *
(1.0 - exp_tor2_kl);
CV = 0.5 * ( fbp->V1 * (1.0 + cos_omega) +
fbp->V2 * exp_tor1 * (1.0 - cos2omega) +
fbp->V3 * (1.0 + cos3omega) );
data->my_en.e_tor += e_tor = fn10 * sin_ijk * sin_jkl * CV;
dfn11 = (-p_tor3 * exp_tor3_DjDk +
(p_tor3 * exp_tor3_DjDk - p_tor4 * exp_tor4_DjDk) *
(2.0 + exp_tor3_DjDk) * exp_tor34_inv) *
exp_tor34_inv;
CEtors1 = sin_ijk * sin_jkl * CV;
CEtors2 = -fn10 * 2.0 * fbp->p_tor1 * fbp->V2 * exp_tor1 *
(2.0 - bo_jk->BO_pi - f11_DjDk) * (1.0 - SQR(cos_omega)) *
sin_ijk * sin_jkl;
CEtors3 = CEtors2 * dfn11;
CEtors4 = CEtors1 * p_tor2 * exp_tor2_ij *
(1.0 - exp_tor2_jk) * (1.0 - exp_tor2_kl);
CEtors5 = CEtors1 * p_tor2 *
(1.0 - exp_tor2_ij) * exp_tor2_jk * (1.0 - exp_tor2_kl);
CEtors6 = CEtors1 * p_tor2 *
(1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) * exp_tor2_kl;
cmn = -fn10 * CV;
CEtors7 = cmn * sin_jkl * tan_ijk_i;
CEtors8 = cmn * sin_ijk * tan_jkl_i;
CEtors9 = fn10 * sin_ijk * sin_jkl *
(0.5 * fbp->V1 - 2.0 * fbp->V2 * exp_tor1 * cos_omega +
1.5 * fbp->V3 * (cos2omega + 2.0 * SQR(cos_omega)));
/* end of torsion energy */
/* 4-body conjugation energy */
fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl;
data->my_en.e_con += e_con =
fbp->p_cot1 * fn12 *
(1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);
Cconj = -2.0 * fn12 * fbp->p_cot1 * p_cot2 *
(1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);
CEconj1 = Cconj * (BOA_ij - 1.5e0);
CEconj2 = Cconj * (BOA_jk - 1.5e0);
CEconj3 = Cconj * (BOA_kl - 1.5e0);
CEconj4 = -fbp->p_cot1 * fn12 *
(SQR(cos_omega) - 1.0) * sin_jkl * tan_ijk_i;
CEconj5 = -fbp->p_cot1 * fn12 *
(SQR(cos_omega) - 1.0) * sin_ijk * tan_jkl_i;
CEconj6 = 2.0 * fbp->p_cot1 * fn12 *
cos_omega * sin_ijk * sin_jkl;
/* end 4-body conjugation energy */
/* forces */
bo_jk->Cdbopi += CEtors2;
workspace->CdDelta[j] += CEtors3;
workspace->CdDelta[k] += CEtors3;
bo_ij->Cdbo += (CEtors4 + CEconj1);
bo_jk->Cdbo += (CEtors5 + CEconj2);
bo_kl->Cdbo += (CEtors6 + CEconj3);
if( control->virial == 0 ) {
/* dcos_theta_ijk */
rvec_ScaledAdd( workspace->f[i],
CEtors7 + CEconj4, p_ijk->dcos_dk );
rvec_ScaledAdd( workspace->f[j],
CEtors7 + CEconj4, p_ijk->dcos_dj );
rvec_ScaledAdd( workspace->f[k],
CEtors7 + CEconj4, p_ijk->dcos_di );
/* dcos_theta_jkl */
rvec_ScaledAdd( workspace->f[j],
CEtors8 + CEconj5, p_jkl->dcos_di );
rvec_ScaledAdd( workspace->f[k],
CEtors8 + CEconj5, p_jkl->dcos_dj );
rvec_ScaledAdd( workspace->f[l],
CEtors8 + CEconj5, p_jkl->dcos_dk );
/* dcos_omega */
rvec_ScaledAdd( workspace->f[i],
CEtors9 + CEconj6, dcos_omega_di );
rvec_ScaledAdd( workspace->f[j],
CEtors9 + CEconj6, dcos_omega_dj );
rvec_ScaledAdd( workspace->f[k],
CEtors9 + CEconj6, dcos_omega_dk );
rvec_ScaledAdd( workspace->f[l],
CEtors9 + CEconj6, dcos_omega_dl );
}
else {
ivec_Sum(rel_box_jl, pbond_jk->rel_box, pbond_kl->rel_box);
/* dcos_theta_ijk */
rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_dk );
rvec_Add( workspace->f[i], force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
rvec_Add( data->my_ext_press, ext_press );
rvec_ScaledAdd( workspace->f[j],
CEtors7 + CEconj4, p_ijk->dcos_dj );
rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_di );
rvec_Add( workspace->f[k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
rvec_Add( data->my_ext_press, ext_press );
/* dcos_theta_jkl */
rvec_ScaledAdd( workspace->f[j],
CEtors8 + CEconj5, p_jkl->dcos_di );
rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dj );
rvec_Add( workspace->f[k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
rvec_Add( data->my_ext_press, ext_press );
rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dk );
rvec_Add( workspace->f[l], force );
rvec_iMultiply( ext_press, rel_box_jl, force );
rvec_Add( data->my_ext_press, ext_press );
/* dcos_omega */
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_di );
rvec_Add( workspace->f[i], force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
rvec_Add( data->my_ext_press, ext_press );
rvec_ScaledAdd( workspace->f[j],
CEtors9 + CEconj6, dcos_omega_dj );
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dk );
rvec_Add( workspace->f[k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
rvec_Add( data->my_ext_press, ext_press );
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dl );
rvec_Add( workspace->f[l], force );
rvec_iMultiply( ext_press, rel_box_jl, force );
rvec_Add( data->my_ext_press, ext_press );
}
/* tally into per-atom virials */
if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
// acquire vectors
rvec_ScaledSum( delil, 1., system->my_atoms[l].x,
-1., system->my_atoms[i].x );
rvec_ScaledSum( deljl, 1., system->my_atoms[l].x,
-1., system->my_atoms[j].x );
rvec_ScaledSum( delkl, 1., system->my_atoms[l].x,
-1., system->my_atoms[k].x );
// dcos_theta_ijk
rvec_Scale( fi_tmp, CEtors7 + CEconj4, p_ijk->dcos_dk );
rvec_Scale( fj_tmp, CEtors7 + CEconj4, p_ijk->dcos_dj );
rvec_Scale( fk_tmp, CEtors7 + CEconj4, p_ijk->dcos_di );
// dcos_theta_jkl
rvec_ScaledAdd( fj_tmp, CEtors8 + CEconj5, p_jkl->dcos_di );
rvec_ScaledAdd( fk_tmp, CEtors8 + CEconj5, p_jkl->dcos_dj );
// dcos_omega
rvec_ScaledAdd( fi_tmp, CEtors9 + CEconj6, dcos_omega_di );
rvec_ScaledAdd( fj_tmp, CEtors9 + CEconj6, dcos_omega_dj );
rvec_ScaledAdd( fk_tmp, CEtors9 + CEconj6, dcos_omega_dk );
// tally
eng_tmp = e_tor + e_con;
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(j,k,natoms,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
if( system->pair_ptr->vflag_atom)
system->pair_ptr->v_tally4(i,j,k,l,fi_tmp,fj_tmp,fk_tmp,delil,deljl,delkl);
}
} // pl check ends
} // pl loop ends
} // pi check ends
} // pi loop ends
} // k-j neighbor check ends
} // j-k neighbor check ends
} // pk loop ends
} // j loop
}
c4science · Help