//output dimer configurations to pqr for verification
void output_pqrs(system_t *system, int nCurves, curveData_t *curve) {
int i;
char filename[500];
for (i = 0; i < nCurves; i++) {
// Apply rotation associated with i-th curve and separate COM by 5 Angstroms
surface_dimer_geometry(system, 5.0, curve[i].alpha1, curve[i].beta1, curve[i].gamma1,
curve[i].alpha2, curve[i].beta2, curve[i].gamma2, 0);
sprintf(filename,
"%s.pqr", curve[i].id);
write_molecules_wrapper(system, filename);
// Restore the molecule to its initial orientation
surface_dimer_geometry(system, 0.0, curve[i].alpha1, curve[i].beta1, curve[i].gamma1,
curve[i].alpha2, curve[i].beta2, curve[i].gamma2, 1);
}
return;
}
//apply trial parameters
void get_curves(system_t *system, int nCurves, curveData_t *curve, double r_min, double r_max, double r_inc) {
int i;
for (i = 0; i < nCurves; i++) {
// Apply rotation associated with i-th curve
surface_dimer_geometry(system, r_min, curve[i].alpha1, curve[i].beta1, curve[i].gamma1,
curve[i].alpha2, curve[i].beta2, curve[i].gamma2, 0);
// Perform the calculation
surface_curve(system, r_min, r_max, r_inc, curve[i].output);
// Restore the molecule to its initial orientation
surface_dimer_geometry(system, r_min, curve[i].alpha1, curve[i].beta1, curve[i].gamma1,
curve[i].alpha2, curve[i].beta2, curve[i].gamma2, 1);
}
// Reset to origin
surface_dimer_geometry(system, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0);
return;
}
void surface_curve(system_t *system, double r_min, double r_max, double r_inc, double *curve) {
int i;
double r;
for (r = r_min, i = 0; r <= r_max; r += r_inc, i++) {
surface_dimer_geometry(system, r, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0);
curve[i] = surface_energy(system, ENERGY_TOTAL);
}
return;
}
/* calculate the isotropic potential energy surface of a molecule */
int surface(system_t *system) {
int ao, bo, go, am, bm, gm, surf_print; /* for surf_output */
int avg_counter;
double avg_factor;
double r, pe_es, pe_rd, pe_polar, pe_vdw, pe_total;
double pe_total_avg, pe_es_avg, pe_rd_avg, pe_polar_avg, pe_vdw_avg;
double alpha_origin, beta_origin, gamma_origin;
double alpha_move, beta_move, gamma_move;
/* open surface trajectory file */
if(system->surf_output) {
if(open_surf_traj_file(system) < 0)
error("Surface: could not open surface trajectory file\n");
}
/* output the potential energy curve */
if(system->surf_preserve) { /* preserve the orientation and only calculate based on displacement */
//apply rotation if given in input file
if ( system->surf_preserve_rotation_on != NULL ) {
surface_dimer_geometry(system, 0.0,
system->surf_preserve_rotation_on->alpha1,
system->surf_preserve_rotation_on->beta1,
system->surf_preserve_rotation_on->gamma1,
system->surf_preserve_rotation_on->alpha2,
system->surf_preserve_rotation_on->beta2,
system->surf_preserve_rotation_on->gamma2, 0);
printf("SURFACE: Setting preserve angles (radians) for molecule 1: %lf %lf %lf\n",
system->surf_preserve_rotation_on->alpha1,
system->surf_preserve_rotation_on->beta1,
system->surf_preserve_rotation_on->gamma1);
printf("SURFACE: Setting preserve angles (radians) for molecule 2: %lf %lf %lf\n",
system->surf_preserve_rotation_on->alpha2,
system->surf_preserve_rotation_on->beta2,
system->surf_preserve_rotation_on->gamma2);
}
for(r = system->surf_min; r <= system->surf_max; r += system->surf_inc) {
/* calculate the energy */
surface_dimer_geometry(system, r, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0);
if(system->surf_decomp) {
pe_es = surface_energy(system, ENERGY_ES);
pe_rd = surface_energy(system, ENERGY_RD);
pe_polar = surface_energy(system, ENERGY_POLAR);
pe_vdw = surface_energy(system, ENERGY_VDW);
printf("%.5f %.5f %.5f %.5f %.5f\n", r, pe_es, pe_rd, pe_polar, pe_vdw);
fflush(stdout);
} else {
pe_total = surface_energy(system, ENERGY_TOTAL);
printf("%.5f %.5f\n", r, pe_total);
fflush(stdout);
}
}
} else { /* default is to do isotropic averaging */
for(r = system->surf_min; r <= system->surf_max; r+= system->surf_inc) {
/* zero the averages for this r value */
avg_counter = 0;
pe_total_avg = 0;
pe_es_avg = 0;
pe_rd_avg = 0;
pe_polar_avg = 0;
pe_vdw_avg = 0;
ao = 0;
bo = 0;
go = 0;
am = 0;
bm = 0;
gm = 0;
surf_print = 0;
/* average over the angles */
for(alpha_origin = 0; alpha_origin <= 2.0*M_PI; alpha_origin += system->surf_ang) {
for(beta_origin = 0; beta_origin <= M_PI; beta_origin += system->surf_ang) {
for(gamma_origin = 0; gamma_origin <= 2.0*M_PI; gamma_origin += system->surf_ang) {
for(alpha_move = 0; alpha_move <= 2.0*M_PI; alpha_move += system->surf_ang) {
for(beta_move = 0; beta_move <= M_PI; beta_move += system->surf_ang) {
for(gamma_move = 0; gamma_move <= 2.0*M_PI; gamma_move += system->surf_ang) {
++gm;
++avg_counter;
avg_factor = ((double)(avg_counter - 1))/((double)(avg_counter));
surface_dimer_geometry(system, r, alpha_origin, beta_origin, gamma_origin, alpha_move, beta_move, gamma_move, 0);
if(system->surf_print_level == 6)
surf_print = 1;
if(system->surf_output && surf_print == 1)
write_surface_traj(system->file_pointers.fp_surf, system);
surf_print = 0; /* turn off printing */
if(system->surf_decomp) {
pe_es = surface_energy(system, ENERGY_ES);
pe_rd = surface_energy(system, ENERGY_RD);
pe_polar = surface_energy(system, ENERGY_POLAR);
pe_vdw = surface_energy(system, ENERGY_VDW);
pe_es_avg = pe_es_avg*avg_factor + (pe_es/((double)avg_counter));
pe_rd_avg = pe_rd_avg*avg_factor + (pe_rd/((double)avg_counter));
pe_polar_avg = pe_polar_avg*avg_factor + (pe_polar/((double)avg_counter));
pe_vdw_avg = pe_vdw_avg*avg_factor + (pe_vdw/((double)avg_counter));
} else {
pe_total = surface_energy(system, ENERGY_TOTAL);
pe_total_avg = pe_total_avg*avg_factor + (pe_total/((double)avg_counter));
}
//unrotate (not the most efficent thing to be doing, but oh well)
surface_dimer_geometry(system, 0.0, alpha_origin, beta_origin, gamma_origin, alpha_move, beta_move, gamma_move, 1);
} /* end gamma_move */
++bm;
if(system->surf_print_level == 5)
surf_print = 1;
} /* end beta_move */
++am;
if(system->surf_print_level == 4)
surf_print = 1;
} /* end alpha_move */
++go;
if(system->surf_print_level == 3)
surf_print = 1;
} /* end gamma_origin */
++bo;
if(system->surf_print_level == 2)
surf_print = 1;
} /* end beta_origin */
++ao;
if (system->surf_print_level == 1)
surf_print = 1;
} /* end alpha_origin */
if(system->surf_decomp) {
printf("%.5f %.5f %.5f %.5f\n", r, pe_es_avg, pe_rd_avg, pe_polar_avg);
fflush(stdout);
} else {
printf("%.5f %.5f\n", r, pe_total_avg);
fflush(stdout);
}
} /* end r */
}
return(0);
}
