/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
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 "forces.h"
#include "box.h"
#include "bond_orders.h"
#include "single_body_interactions.h"
#include "two_body_interactions.h"
#include "three_body_interactions.h"
#include "four_body_interactions.h"
#include "list.h"
#include "print_utils.h"
#include "system_props.h"
#include "QEq.h"
#include "vector.h"
void Dummy_Interaction( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
list **lists, output_controls *out_control )
{
}
void Init_Bonded_Force_Functions( control_params *control )
{
Interaction_Functions[0] = Calculate_Bond_Orders;
Interaction_Functions[1] = Bond_Energy; //*/Dummy_Interaction;
Interaction_Functions[2] = LonePair_OverUnder_Coordination_Energy;
//*/Dummy_Interaction;
Interaction_Functions[3] = Three_Body_Interactions; //*/Dummy_Interaction;
Interaction_Functions[4] = Four_Body_Interactions; //*/Dummy_Interaction;
if ( control->hb_cut > 0 )
Interaction_Functions[5] = Hydrogen_Bonds; //*/Dummy_Interaction;
else Interaction_Functions[5] = Dummy_Interaction;
Interaction_Functions[6] = Dummy_Interaction; //empty
Interaction_Functions[7] = Dummy_Interaction; //empty
Interaction_Functions[8] = Dummy_Interaction; //empty
Interaction_Functions[9] = Dummy_Interaction; //empty
}
void Compute_Bonded_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
list **lists, output_controls *out_control )
{
int i;
// real t_start, t_end, t_elapsed;
#ifdef TEST_ENERGY
/* Mark beginning of a new timestep in each energy file */
fprintf( out_control->ebond, "step: %d\n%6s%6s%12s%12s%12s\n",
data->step, "atom1", "atom2", "bo", "ebond", "total" );
fprintf( out_control->elp, "step: %d\n%6s%12s%12s%12s\n",
data->step, "atom", "nlp", "elp", "total" );
fprintf( out_control->eov, "step: %d\n%6s%12s%12s\n",
data->step, "atom", "eov", "total" );
fprintf( out_control->eun, "step: %d\n%6s%12s%12s\n",
data->step, "atom", "eun", "total" );
fprintf( out_control->eval, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s%12s\n",
data->step, "atom1", "atom2", "atom3",
"angle", "bo(12)", "bo(23)", "eval", "epen", "total" );
fprintf( out_control->epen, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
data->step, "atom1", "atom2", "atom3",
"angle", "bo(12)", "bo(23)", "epen", "total" );
fprintf( out_control->ecoa, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
data->step, "atom1", "atom2", "atom3",
"angle", "bo(12)", "bo(23)", "ecoa", "total" );
fprintf( out_control->ehb, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
data->step, "atom1", "atom2", "atom3",
"r(23)", "angle", "bo(12)", "ehb", "total" );
fprintf( out_control->etor, "step: %d\n%6s%6s%6s%6s%12s%12s%12s%12s\n",
data->step, "atom1", "atom2", "atom3", "atom4",
"phi", "bo(23)", "etor", "total" );
fprintf( out_control->econ, "step:%d\n%6s%6s%6s%6s%12s%12s%12s%12s%12s%12s\n",
data->step, "atom1", "atom2", "atom3", "atom4",
"phi", "bo(12)", "bo(23)", "bo(34)", "econ", "total" );
#endif
/* Implement all the function calls as function pointers */
for ( i = 0; i < NO_OF_INTERACTIONS; i++ )
{
(Interaction_Functions[i])(system, control, data, workspace,
lists, out_control);
#if defined(DEBUG_FOCUS)
fprintf( stderr, "f%d-", i );
#endif
#ifdef TEST_FORCES
(Print_Interactions[i])(system, control, data, workspace,
lists, out_control);
#endif
}
}
void Compute_NonBonded_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
list** lists, output_controls *out_control )
{
real t_start, t_elapsed;
#ifdef TEST_ENERGY
fprintf( out_control->evdw, "step: %d\n%6s%6s%12s%12s%12s\n",
data->step, "atom1", "atom2", "r12", "evdw", "total" );
fprintf( out_control->ecou, "step: %d\n%6s%6s%12s%12s%12s%12s%12s\n",
data->step, "atom1", "atom2", "r12", "q1", "q2", "ecou", "total" );
#endif
t_start = Get_Time( );
QEq( system, control, data, workspace, lists[FAR_NBRS], out_control );
t_elapsed = Get_Timing_Info( t_start );
data->timing.QEq += t_elapsed;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "qeq - " );
#endif
if ( control->tabulate == 0)
vdW_Coulomb_Energy( system, control, data, workspace, lists, out_control );
else
Tabulated_vdW_Coulomb_Energy( system, control, data, workspace,
lists, out_control );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "nonb forces - " );
#endif
#ifdef TEST_FORCES
Print_vdW_Coulomb_Forces( system, control, data, workspace,
lists, out_control );
#endif
}
/* This version of Compute_Total_Force computes forces from coefficients
accumulated by all interaction functions. Saves enormous time & space! */
void Compute_Total_Force( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
list **lists )
{
int i, pj;
list *bonds = (*lists) + BONDS;
for ( i = 0; i < system->N; ++i )
for ( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
if ( i < bonds->select.bond_list[pj].nbr )
{
if ( control->ensemble == NVE || control->ensemble == NVT || control->ensemble == bNVT)
Add_dBond_to_Forces( i, pj, system, data, workspace, lists );
else
Add_dBond_to_Forces_NPT( i, pj, system, data, workspace, lists );
}
}
void Validate_Lists( static_storage *workspace, list **lists, int step, int n,
int Hmax, int Htop, int num_bonds, int num_hbonds )
{
int i, flag;
list *bonds, *hbonds;
bonds = *lists + BONDS;
hbonds = *lists + HBONDS;
/* far neighbors */
if ( Htop > Hmax * DANGER_ZONE )
{
workspace->realloc.Htop = Htop;
if ( Htop > Hmax )
{
fprintf( stderr,
"step%d - ran out of space on H matrix: Htop=%d, max = %d",
step, Htop, Hmax );
exit( INSUFFICIENT_MEMORY );
}
}
/* bond list */
flag = -1;
workspace->realloc.num_bonds = num_bonds;
for ( i = 0; i < n - 1; ++i )
if ( End_Index(i, bonds) >= Start_Index(i + 1, bonds) - 2 )
{
workspace->realloc.bonds = 1;
if ( End_Index(i, bonds) > Start_Index(i + 1, bonds) )
flag = i;
}
if ( flag > -1 )
{
fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
step, flag, End_Index(flag, bonds), Start_Index(flag + 1, bonds) );
exit( INSUFFICIENT_MEMORY );
}
if ( End_Index(i, bonds) >= bonds->num_intrs - 2 )
{
workspace->realloc.bonds = 1;
if ( End_Index(i, bonds) > bonds->num_intrs )
{
fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d bond_end=%d\n",
step, flag, End_Index(i, bonds), bonds->num_intrs );
exit( INSUFFICIENT_MEMORY );
}
}
/* hbonds list */
if ( workspace->num_H > 0 )
{
flag = -1;
workspace->realloc.num_hbonds = num_hbonds;
for ( i = 0; i < workspace->num_H - 1; ++i )
if ( Num_Entries(i, hbonds) >=
(Start_Index(i + 1, hbonds) - Start_Index(i, hbonds)) * DANGER_ZONE )
{
workspace->realloc.hbonds = 1;
if ( End_Index(i, hbonds) > Start_Index(i + 1, hbonds) )
flag = i;
}
if ( flag > -1 )
{
fprintf( stderr, "step%d-hbondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
step, flag, End_Index(flag, hbonds), Start_Index(flag + 1, hbonds) );
exit( INSUFFICIENT_MEMORY );
}
if ( Num_Entries(i, hbonds) >=
(hbonds->num_intrs - Start_Index(i, hbonds)) * DANGER_ZONE )
{
workspace->realloc.hbonds = 1;
if ( End_Index(i, hbonds) > hbonds->num_intrs )
{
fprintf( stderr, "step%d-hbondchk failed: i=%d end(i)=%d hbondend=%d\n",
step, flag, End_Index(i, hbonds), hbonds->num_intrs );
exit( INSUFFICIENT_MEMORY );
}
}
}
}
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, H_sp_top, btop_i, btop_j, num_bonds, num_hbonds;
int ihb, jhb, ihb_top, jhb_top;
int flag, flag_sp;
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, *H_sp;
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;
H_sp = workspace->H_sp;
Htop = 0;
H_sp_top = 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];
//TODO: add to control file, remove
control->r_sp_cut = 8.0;
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;
H_sp->start[i] = H_sp_top;
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;
flag_sp = 0;
if ((data->step - data->prev_steps) % control->reneighbor == 0)
{
if ( nbr_pj->d <= control->r_cut )
{
flag = 1;
if ( nbr_pj->d <= control->r_sp_cut )
{
flag_sp = 1;
}
}
else
{
flag = 0;
flag_sp = 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))
{
if ( nbr_pj->d <= SQR(control->r_sp_cut))
{
flag_sp = 1;
}
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->j[Htop] = j;
H->val[Htop] = self_coef * Tap * EV_to_KCALpMOL / dr3gamij_3;
++Htop;
/* H_sp matrix entry */
if ( flag_sp )
{
H_sp->j[H_sp_top] = j;
H_sp->val[H_sp_top] = self_coef * Tap * EV_to_KCALpMOL / dr3gamij_3;
++H_sp_top;
}
/* 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->j[Htop] = i;
H->val[Htop] = system->reaxprm.sbp[type_i].eta;
++Htop;
H_sp->j[H_sp_top] = i;
H_sp->val[H_sp_top] = system->reaxprm.sbp[type_i].eta;
++H_sp_top;
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 ) );
}
// printf("Htop = %d\n", Htop);
// printf("H_sp_top = %d\n", H_sp_top);
// mark the end of j list
H->start[i] = Htop;
H_sp->start[i] = H_sp_top;
/* 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 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->j[Htop] = j;
H->val[Htop] = 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 );
//fprintf (stderr, " %f - %f - %f \n", nbr_pj->dvec[0], nbr_pj->dvec[1], nbr_pj->dvec[2]);
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->j[Htop] = i;
H->val[Htop] = 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 Estimate_Storage_Sizes( reax_system *system, control_params *control,
list **lists, int *Htop, int *hb_top,
int *bond_top, int *num_3body )
{
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int ihb, jhb;
real r_ij, r2;
real C12, C34, C56;
real BO, BO_s, BO_pi, BO_pi2;
real p_boc1, p_boc2;
list *far_nbrs;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
far_nbrs = *lists + FAR_NBRS;
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);
sbp_i = &(system->reaxprm.sbp[type_i]);
ihb = sbp_i->p_hbond;
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]);
type_j = atom_j->type;
sbp_j = &(system->reaxprm.sbp[type_j]);
twbp = &(system->reaxprm.tbp[type_i][type_j]);
if ( nbr_pj->d <= control->r_cut )
{
++(*Htop);
/* hydrogen bond lists */
if ( control->hb_cut > 0.1 && (ihb == 1 || ihb == 2) &&
nbr_pj->d <= control->hb_cut )
{
jhb = sbp_j->p_hbond;
if ( ihb == 1 && jhb == 2 )
++hb_top[i];
else if ( ihb == 2 && jhb == 1 )
++hb_top[j];
}
/* uncorrected bond orders */
if ( nbr_pj->d <= control->nbr_cut )
{
r_ij = nbr_pj->d;
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 )
{
++bond_top[i];
++bond_top[j];
}
}
}
}
}
*Htop += system->N;
*Htop *= SAFE_ZONE;
for ( i = 0; i < system->N; ++i )
{
hb_top[i] = MAX( hb_top[i] * SAFE_HBONDS, MIN_HBONDS );
*num_3body += SQR(bond_top[i]);
bond_top[i] = MAX( bond_top[i] * 2, MIN_BONDS );
}
*num_3body *= SAFE_ZONE;
}
void Compute_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
list** lists, output_controls *out_control )
{
real t_start, t_elapsed;
t_start = Get_Time( );
if ( !control->tabulate )
Init_Forces( system, control, data, workspace, lists, out_control );
else Init_Forces_Tab( system, control, data, workspace, lists, out_control );
t_elapsed = Get_Timing_Info( t_start );
data->timing.init_forces += t_elapsed;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "init_forces - ");
#endif
t_start = Get_Time( );
Compute_Bonded_Forces( system, control, data, workspace, lists, out_control );
t_elapsed = Get_Timing_Info( t_start );
data->timing.bonded += t_elapsed;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "bonded_forces - ");
#endif
t_start = Get_Time( );
Compute_NonBonded_Forces( system, control, data, workspace,
lists, out_control );
t_elapsed = Get_Timing_Info( t_start );
data->timing.nonb += t_elapsed;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "nonbondeds - ");
#endif
Compute_Total_Force( system, control, data, workspace, lists );
//Print_Total_Force( system, control, data, workspace, lists, out_control );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "totalforces - ");
//Print_Total_Force( system, control, data, workspace, lists, out_control );
#endif
#ifdef TEST_FORCES
Print_Total_Force( system, control, data, workspace, lists, out_control );
Compare_Total_Forces( system, control, data, workspace, lists, out_control );
#endif
#if defined(DEBUG_FOCUS)
fprintf( stderr, "forces - ");
#endif
}