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This commit is contained in:
Stan Gerald Moore
2021-09-08 16:01:45 -06:00
parent 165efcdb07
commit 7c5a9841f7
2 changed files with 105 additions and 105 deletions
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208
src/REAXFF/reaxff_nonbonded.cpp
View File

@ -225,68 +225,68 @@ namespace ReaxFF {
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;
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;
flag = 0;
/* kinetic energy terms */
double xcut = 0.5 * ( system->reax_param.sbp[ system->my_atoms[i].type ].bcut_acks2
+ system->reax_param.sbp[ system->my_atoms[j].type ].bcut_acks2 );
/* kinetic energy terms */
double xcut = 0.5 * ( system->reax_param.sbp[ system->my_atoms[i].type ].bcut_acks2
+ system->reax_param.sbp[ system->my_atoms[j].type ].bcut_acks2 );
if(nbr_pj->d <= xcut) {
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(nbr_pj->d <= xcut) {
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) {
if (flag) {
d = nbr_pj->d / xcut;
bond_softness = system->reax_param.gp.l[34] * pow( d, 3.0 )
* pow( 1.0 - d, 6.0 );
d = nbr_pj->d / xcut;
bond_softness = system->reax_param.gp.l[34] * pow( d, 3.0 )
* pow( 1.0 - d, 6.0 );
if ( bond_softness > 0.0 )
{
/* Coulombic energy contribution */
effpot_diff = workspace->s[system->N + i]
- workspace->s[system->N + j];
e_ele = -0.5 * KCALpMOL_to_EV * bond_softness
* SQR( effpot_diff );
if ( bond_softness > 0.0 )
{
/* Coulombic energy contribution */
effpot_diff = workspace->s[system->N + i]
- workspace->s[system->N + j];
e_ele = -0.5 * KCALpMOL_to_EV * bond_softness
* SQR( effpot_diff );
data->my_en.e_ele += e_ele;
data->my_en.e_ele += e_ele;
/* forces contribution */
d_bond_softness = system->reax_param.gp.l[34]
* 3.0 / xcut * pow( d, 2.0 )
* pow( 1.0 - d, 5.0 ) * (1.0 - 3.0 * d);
d_bond_softness = -0.5 * d_bond_softness
* SQR( effpot_diff );
d_bond_softness = KCALpMOL_to_EV * d_bond_softness
/ nbr_pj->d;
/* forces contribution */
d_bond_softness = system->reax_param.gp.l[34]
* 3.0 / xcut * pow( d, 2.0 )
* pow( 1.0 - d, 5.0 ) * (1.0 - 3.0 * d);
d_bond_softness = -0.5 * d_bond_softness
* SQR( effpot_diff );
d_bond_softness = KCALpMOL_to_EV * d_bond_softness
/ nbr_pj->d;
/* 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 = -d_bond_softness;
system->pair_ptr->ev_tally(i,j,natoms,1,0.0,e_ele,
f_tmp,delij[0],delij[1],delij[2]);
}
/* 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 = -d_bond_softness;
system->pair_ptr->ev_tally(i,j,natoms,1,0.0,e_ele,
f_tmp,delij[0],delij[1],delij[2]);
}
rvec_ScaledAdd( workspace->f[i], -d_bond_softness, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f[j], d_bond_softness, nbr_pj->dvec );
}
}
rvec_ScaledAdd( workspace->f[i], -d_bond_softness, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f[j], d_bond_softness, nbr_pj->dvec );
}
}
}
}
@ -401,68 +401,68 @@ namespace ReaxFF {
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;
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;
flag = 0;
/* kinetic energy terms */
xcut = 0.5 * ( system->reax_param.sbp[ system->my_atoms[i].type ].bcut_acks2
+ system->reax_param.sbp[ system->my_atoms[j].type ].bcut_acks2 );
/* kinetic energy terms */
xcut = 0.5 * ( system->reax_param.sbp[ system->my_atoms[i].type ].bcut_acks2
+ system->reax_param.sbp[ system->my_atoms[j].type ].bcut_acks2 );
if(nbr_pj->d <= xcut) {
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(nbr_pj->d <= xcut) {
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) {
if (flag) {
d = nbr_pj->d / xcut;
bond_softness = system->reax_param.gp.l[34] * pow( d, 3.0 )
* pow( 1.0 - d, 6.0 );
d = nbr_pj->d / xcut;
bond_softness = system->reax_param.gp.l[34] * pow( d, 3.0 )
* pow( 1.0 - d, 6.0 );
if ( bond_softness > 0.0 )
{
/* Coulombic energy contribution */
effpot_diff = workspace->s[system->N + i]
- workspace->s[system->N + j];
e_ele = -0.5 * KCALpMOL_to_EV * bond_softness
* SQR( effpot_diff );
if ( bond_softness > 0.0 )
{
/* Coulombic energy contribution */
effpot_diff = workspace->s[system->N + i]
- workspace->s[system->N + j];
e_ele = -0.5 * KCALpMOL_to_EV * bond_softness
* SQR( effpot_diff );
data->my_en.e_ele += e_ele;
data->my_en.e_ele += e_ele;
/* forces contribution */
d_bond_softness = system->reax_param.gp.l[34]
* 3.0 / xcut * pow( d, 2.0 )
* pow( 1.0 - d, 5.0 ) * (1.0 - 3.0 * d);
d_bond_softness = -0.5 * d_bond_softness
* SQR( effpot_diff );
d_bond_softness = KCALpMOL_to_EV * d_bond_softness
/ nbr_pj->d;
/* forces contribution */
d_bond_softness = system->reax_param.gp.l[34]
* 3.0 / xcut * pow( d, 2.0 )
* pow( 1.0 - d, 5.0 ) * (1.0 - 3.0 * d);
d_bond_softness = -0.5 * d_bond_softness
* SQR( effpot_diff );
d_bond_softness = KCALpMOL_to_EV * d_bond_softness
/ nbr_pj->d;
/* 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 = -d_bond_softness;
system->pair_ptr->ev_tally(i,j,natoms,1,0.0,e_ele,
f_tmp,delij[0],delij[1],delij[2]);
}
/* 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 = -d_bond_softness;
system->pair_ptr->ev_tally(i,j,natoms,1,0.0,e_ele,
f_tmp,delij[0],delij[1],delij[2]);
}
rvec_ScaledAdd( workspace->f[i], -d_bond_softness, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f[j], d_bond_softness, nbr_pj->dvec );
}
}
rvec_ScaledAdd( workspace->f[i], -d_bond_softness, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f[j], d_bond_softness, nbr_pj->dvec );
}
}
}
}

2
src/fix_efield.cpp
View File

@ -503,7 +503,7 @@ double* FixEfield::get_energy()
domain->unmap(x[i],image[i],unwrap);
energy[i] -= fx*unwrap[0] + fy*unwrap[1] + fz*unwrap[2];
if (fabs(fx*(x[i][0]-unwrap[0])) + fabs(fy*(x[i][1]-unwrap[1])) +
if (fabs(fx*(x[i][0]-unwrap[0])) + fabs(fy*(x[i][1]-unwrap[1])) +
fabs(fz*(x[i][2]-unwrap[2])) > 0.0)
warn_flag_local = 1;
}