void calc_dipole_rrms(system_t *system) {
int i, p;
double carry;
atom_t **aa = system->atom_array;
/* get the dipole RRMS */
for (i = 0; i < system->natoms; i++) {
/* mean square difference */
aa[i]->dipole_rrms = 0;
for (p = 0; p < 3; p++) {
carry = aa[i]->new_mu[p] - aa[i]->old_mu[p];
aa[i]->dipole_rrms += carry * carry;
}
/* normalize */
aa[i]->dipole_rrms /= dddotprod(aa[i]->new_mu, aa[i]->new_mu);
aa[i]->dipole_rrms = sqrt(aa[i]->dipole_rrms);
if (!isfinite(aa[i]->dipole_rrms)) aa[i]->dipole_rrms = 0;
}
#ifdef DEBUG
/*
double totalrms = 0;
for ( i=0; i< system->natoms; i++ ) {
totalrms += aa[i]->dipole_rrms;
}
fprintf(stderr,"TOTAL DIPOLE RRMS %lf\n", totalrms);
*/
#endif
return;
}
void contract_dipoles(system_t *system, int *ranked_array) {
int i, j, ii, jj, p, index;
atom_t **aa = system->atom_array;
for (i = 0; i < system->natoms; i++) {
index = ranked_array[i]; //do them in the order of the ranked index
ii = index * 3;
if (aa[index]->polarizability == 0) { //if not polar
//aa[index]->ef_induced[p] is already 0
aa[index]->new_mu[0] = aa[index]->new_mu[1] = aa[index]->new_mu[2] = 0; //might be redundant?
aa[index]->mu[0] = aa[index]->mu[1] = aa[index]->mu[2] = 0; //might be redundant?
continue;
}
for (j = 0; j < system->natoms; j++) {
jj = j * 3;
if (index != j)
for (p = 0; p < 3; p++)
aa[index]->ef_induced[p] -= dddotprod((system->A_matrix[ii + p] + jj), aa[j]->mu);
} /* end j */
/* dipole is the sum of the static and induced parts */
for (p = 0; p < 3; p++) {
aa[index]->new_mu[p] = aa[index]->polarizability * (aa[index]->ef_static[p] + aa[index]->ef_static_self[p] + aa[index]->ef_induced[p]);
/* Gauss-Seidel */
if (system->polar_gs || system->polar_gs_ranked)
aa[index]->mu[p] = aa[index]->new_mu[p];
}
} /* end matrix multiply */
return;
}
void printboxdim ( pbc_t * pbc ) {
char buffer[MAXLINE];
sprintf(buffer,"INPUT: unit cell volume = %.3f A^3 (cutoff = %.3f A)\n", pbc->volume, pbc->cutoff);
output(buffer);
sprintf(buffer,"INPUT: Basis vectors { a = %8.3lf \tb = %8.3lf \tc = %8.3lf }\n",
sqrt(dddotprod(pbc->basis[0], pbc->basis[0])),
sqrt(dddotprod(pbc->basis[1], pbc->basis[1])),
sqrt(dddotprod(pbc->basis[2], pbc->basis[2])));
output(buffer);
sprintf(buffer,"INPUT: Basis angles { α = %8.3lf \tβ = %8.3lf \tγ = %8.3lf }\n",
180.0/M_PI*acos( dddotprod(pbc->basis[1],pbc->basis[2]) / sqrt( dddotprod(pbc->basis[1], pbc->basis[1]) * dddotprod(pbc->basis[2], pbc->basis[2]) ) ),
180.0/M_PI*acos( dddotprod(pbc->basis[2],pbc->basis[0]) / sqrt( dddotprod(pbc->basis[2], pbc->basis[2]) * dddotprod(pbc->basis[0], pbc->basis[0]) ) ),
180.0/M_PI*acos( dddotprod(pbc->basis[0],pbc->basis[1]) / sqrt( dddotprod(pbc->basis[0], pbc->basis[0]) * dddotprod(pbc->basis[1], pbc->basis[1]) ) ));
output(buffer);
return;
}
void palmo_contraction(system_t *system, int *ranked_array) {
int i, j, ii, jj, index, p;
int N = system->natoms;
atom_t **aa = system->atom_array;
/* calculate change in induced field due to this iteration */
for (i = 0; i < N; i++) {
index = ranked_array[i];
ii = index * 3;
for (p = 0; p < 3; p++)
aa[index]->ef_induced_change[p] = -aa[index]->ef_induced[p];
for (j = 0; j < N; j++) {
jj = j * 3;
if (index != j)
for (p = 0; p < 3; p++)
aa[index]->ef_induced_change[p] -= dddotprod(system->A_matrix[ii + p] + jj, aa[j]->mu);
}
}
return;
}
/* get the induction energy */
double polar(system_t *system) {
molecule_t *molecule_ptr;
atom_t *atom_ptr;
int num_iterations;
double potential;
char linebuf[MAXLINE];
/* take measures to let N fluctuate */
if( (system->ensemble == ENSEMBLE_UVT || system->ensemble == ENSEMBLE_REPLAY) && !system->polar_zodid )
thole_resize_matrices(system);
/* get the A matrix */
if(!system->polar_zodid) {
thole_amatrix(system);
if(system->polarizability_tensor) {
output("POLAR: A matrix:\n");
print_matrix(3*((int)system->checkpoint->thole_N_atom), system->A_matrix);
}
}
/* find the dipoles */
if ( system->polar_ewald_full ) {
//do a full-ewald polarization treatment
ewald_full(system);
} else if(system->polar_iterative) {
//solve the self-consistent problem
thole_field(system); //calc e-field
num_iterations = thole_iterative(system); //calc dipoles
system->nodestats->polarization_iterations = (double)num_iterations; //statistics
system->observables->dipole_rrms = get_dipole_rrms(system);
if ( system->iter_success ) {
switch ( system->ensemble ) {
case ENSEMBLE_UVT:
case ENSEMBLE_NVT:
case ENSEMBLE_NVE:
case ENSEMBLE_NPT:
sprintf(linebuf,"POLAR: polarization iterative solver convergence failure on mc step %d.\n", system->step);
error(linebuf);
break;
case ENSEMBLE_REPLAY:
sprintf(linebuf,"POLAR: polarization iterative solver convergence failure on configuration %d.\n", system->step);
error(linebuf);
break;
case ENSEMBLE_SURF:
case ENSEMBLE_SURF_FIT:
case ENSEMBLE_TE:
default:
sprintf(linebuf,"POLAR: polarization iterative solver failed to reach convergence.\n");
error(linebuf);
}
}
} else {
//do matrix inversion
thole_field(system); //calc e-field
thole_bmatrix(system); //matrix inversion
thole_bmatrix_dipoles(system); //get dipoles
/* output the 3x3 molecular polarizability tensor */
if(system->polarizability_tensor) {
output("POLAR: B matrix:\n");
print_matrix(3*((int)system->checkpoint->thole_N_atom), system->B_matrix);
thole_polarizability_tensor(system);
die(0);
}
}
/* calculate the polarization energy as 1/2 mu*E */
potential = 0;
for(molecule_ptr = system->molecules; molecule_ptr; molecule_ptr = molecule_ptr->next) {
for(atom_ptr = molecule_ptr->atoms; atom_ptr; atom_ptr = atom_ptr->next) {
potential += dddotprod(atom_ptr->mu,atom_ptr->ef_static);
if(system->polar_palmo)
potential += dddotprod(atom_ptr->mu,atom_ptr->ef_induced_change);
}
}
potential *= -0.5;
#ifdef DEBUG
fprintf(stderr,"mu MOLECULE ATOM * DIPOLES * STATIC * INDUCED * pot/atom -0.5*mu*E_s\n");
for(molecule_ptr = system->molecules; molecule_ptr; molecule_ptr = molecule_ptr->next) {
for(atom_ptr = molecule_ptr->atoms; atom_ptr; atom_ptr = atom_ptr->next) {
fprintf(stderr,"mu %4d %4d * %8.5lf %8.5lf %8.5lf * %8.5lf %8.5lf %8.5lf * %8.5lf %8.5lf %8.5lf * %lf %lf\n",
molecule_ptr->id, atom_ptr->id,
atom_ptr->mu[0], atom_ptr->mu[1], atom_ptr->mu[2],
atom_ptr->ef_static[0], atom_ptr->ef_static[1], atom_ptr->ef_static[2],
atom_ptr->ef_induced[0], atom_ptr->ef_induced[1], atom_ptr->ef_induced[2],
potential/system->natoms, -0.5*atom_ptr->mu[0]*atom_ptr->ef_static[0]);
}
}
#endif
return(potential);
}
