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Sat, Nov 16, 21:08

reaxc_nonbonded.cpp
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/*----------------------------------------------------------------------
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_types.h"
#include "reaxc_nonbonded.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
#include "reaxc_vector.h"
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 Compute_Polarization_Energy( reax_system *system, simulation_data *data )
{
int i, type_i;
double q, en_tmp;
data->my_en.e_pol = 0.0;
for( i = 0; i < system->n; i++ ) {
type_i = system->my_atoms[i].type;
if (type_i < 0) continue;
q = system->my_atoms[i].q;
en_tmp = KCALpMOL_to_EV * (system->reax_param.sbp[type_i].chi * q +
(system->reax_param.sbp[type_i].eta / 2.) * SQR(q));
data->my_en.e_pol += en_tmp;
/* tally into per-atom energy */
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,i,system->n,1,0.0,en_tmp,0.0,0.0,0.0,0.0);
}
}
void LR_vdW_Coulomb( reax_system *system, storage *workspace,
control_params *control, int i, int j, double r_ij, LR_data *lr )
{
double p_vdW1 = system->reax_param.gp.l[28];
double p_vdW1i = 1.0 / p_vdW1;
double powr_vdW1, powgi_vdW1;
double tmp, fn13, exp1, exp2;
double Tap, dTap, dfn13;
double dr3gamij_1, dr3gamij_3;
double e_core, de_core;
double e_lg, de_lg, r_ij5, r_ij6, re6;
two_body_parameters *twbp;
twbp = &(system->reax_param.tbp[i][j]);
e_core = 0;
de_core = 0;
e_lg = de_lg = 0.0;
/* calculate taper and its derivative */
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) );
lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2);
dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i-1.0) * pow(r_ij, p_vdW1-2.0);
lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) -
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) );
lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2);
lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) -
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)));
lr->e_vdW += Tap * e_core;
de_core = -(twbp->acore/twbp->rcore) * e_core;
lr->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 ));
lr->e_vdW += Tap * e_lg;
de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ;
lr->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;
lr->H = EV_to_KCALpMOL * tmp;
lr->e_ele = C_ele * tmp;
lr->CEclmb = C_ele * ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
}

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