/* this function (a) undoes what make_move() did and (b) determines the next move sequence by calling checkpoint() */
void restore(system_t *system) {
// restore the remaining observables
memcpy(system->observables, system->checkpoint->observables, sizeof(observables_t));
/* restore state by undoing the steps of make_move() */
switch (system->checkpoint->movetype) {
case MOVETYPE_INSERT:
/* take altered out of the list */
if (!system->checkpoint->head) { /* handle the case where we inserted at the head of the list */
system->molecules = system->molecules->next;
} else {
system->checkpoint->head->next = system->checkpoint->tail;
}
unupdate_pairs_insert(system);
free_molecule(system, system->checkpoint->molecule_altered);
system->checkpoint->molecule_altered = NULL; /* Insurance against memory errors */
//reset atom and molecule id's
enumerate_particles(system);
break;
case MOVETYPE_REMOVE:
/* put backup back into the list */
if (!system->checkpoint->head) {
system->molecules = system->checkpoint->molecule_backup;
} else {
system->checkpoint->head->next = system->checkpoint->molecule_backup;
}
system->checkpoint->molecule_backup->next = system->checkpoint->tail;
unupdate_pairs_remove(system);
system->checkpoint->molecule_backup = NULL;
//reset atom and molecule id's
enumerate_particles(system);
break;
case MOVETYPE_VOLUME:
revert_volume_change(system);
break;
default:
/* link the backup into the working list again */
if (!system->checkpoint->head)
system->molecules = system->checkpoint->molecule_backup;
else
system->checkpoint->head->next = system->checkpoint->molecule_backup;
system->checkpoint->molecule_backup->next = system->checkpoint->tail;
free_molecule(system, system->checkpoint->molecule_altered);
system->checkpoint->molecule_altered = NULL; /* Insurance against memory errors */
system->checkpoint->molecule_backup = NULL;
}
/* renormalize charges */
if (system->spectre) spectre_charge_renormalize(system);
/* establish the previous checkpoint again */
checkpoint(system);
return;
}
/* free all of our data structures */
void cleanup(system_t *system) {
int i,j;
#ifdef QM_ROTATION
if(system->quantum_rotation) free_rotational(system);
#endif /* QM_ROTATION */
if(system->polarization && !system->cuda) free_matrices(system);
if(system->polar_wolf_alpha_lookup)
if ( system->polar_wolf_alpha_table )
free(system->polar_wolf_alpha_table);
//need to rebuild atom and pair arrays so we can free everything
system->natoms = countNatoms(system);
rebuild_arrays(system);
free_all_pairs(system);
free_all_molecules(system, system->molecules);
//free our arrays
free(system->molecule_array);
free(system->atom_array);
free(system->pqr_input);
free(system->pqr_output);
free(system->energy_output);
free(system->energy_output_csv);
free(system->virial_output);
if(system->surf_output) free(system->surf_output);
if(system->traj_output) free(system->traj_output);
if(system->traj_input) free(system->traj_input);
if(system->dipole_output) free(system->dipole_output);
if(system->field_output) free(system->field_output);
if(system->frozen_output) free(system->frozen_output);
if(system->surf_preserve_rotation_on) free(system->surf_preserve_rotation_on);
if(system->cavity_bias) free_cavity_grid(system);
if ( system->vdw_eiso_info ) free_vdw_eiso(system->vdw_eiso_info);
// free multi sorbate related stuff
if ( system->fugacities )
free(system->fugacities);
if(system->insert_input) free(system->insert_input);
//insert.pdb arrays and shit
if(system->insertion_molecules_array) free(system->insertion_molecules_array);
if(system->insertion_molecules) free_all_molecules(system, system->insertion_molecules);
// free sorbate info array
free(system->sorbateInfo);
/* free statistics */
free(system->nodestats);
free(system->avg_nodestats);
free(system->observables);
free(system->avg_observables);
free(system->checkpoint->observables);
if ( system->checkpoint->molecule_backup != NULL )
free_molecule(system, system->checkpoint->molecule_backup);
free(system->checkpoint);
/*free histogram stuff*/
for ( i=0; i<system->grids->histogram->x_dim; i++ ) {
for ( j=0; j<system->grids->histogram->y_dim; j++ ) {
free(system->grids->histogram->grid[i][j]);
}
free(system->grids->histogram->grid[i]);
}
if ( !rank ) {
for ( i=0; i<system->grids->histogram->x_dim; i++ ) {
for ( j=0; j<system->grids->histogram->y_dim; j++ ) {
free(system->grids->avg_histogram->grid[i][j]);
}
free(system->grids->avg_histogram->grid[i]);
}
free(system->grids->avg_histogram->grid);
}
free(system->grids->histogram->grid);
free(system->grids->avg_histogram);
free(system->grids->histogram);
free(system->grids);
free(system->histogram_output);
/* free fit input lists*/
if ( system->fit_input_list.data.count > 0 ) {
fileNode_t *node = &(system->fit_input_list);
fileNode_t *nextnode;
//the first one is statically declared
//the others are malloc'd in input.c
if ( node->next ) node=node->next;
while ( node->next ) {
nextnode=node->next;
free(node->data.filename);
free(node);
node=nextnode;
}
free(node->data.filename);
free(node);
}
free(system->pqr_restart);
free(system->pbc);
free(system->job_name); // (CRC)
kill_rng();
free(system);
}
/* apply what was already determined in checkpointing */
void make_move(system_t *system) {
int i, j, k, p, q;
cavity_t *cavities_array;
int cavities_array_counter, random_index;
double com[3], rand[3];
molecule_t *molecule_ptr;
atom_t *atom_ptr;
pair_t *pair_ptr;
/* update the cavity grid prior to making a move */
if (system->cavity_bias) {
cavity_update_grid(system);
system->checkpoint->biased_move = 0;
}
switch (system->checkpoint->movetype) {
case MOVETYPE_INSERT: /* insert a molecule at a random pos and orientation */
/* umbrella sampling */
if (system->cavity_bias && system->cavities_open) {
/* doing a biased move - this flag lets mc.c know about it */
system->checkpoint->biased_move = 1;
/* make an array of possible insertion points */
cavities_array = calloc(system->cavities_open, sizeof(cavity_t));
memnullcheck(cavities_array, system->cavities_open * sizeof(cavity_t), __LINE__ - 1, __FILE__);
for (i = 0, cavities_array_counter = 0; i < system->cavity_grid_size; i++) {
for (j = 0; j < system->cavity_grid_size; j++) {
for (k = 0; k < system->cavity_grid_size; k++) {
if (!system->cavity_grid[i][j][k].occupancy) {
for (p = 0; p < 3; p++)
cavities_array[cavities_array_counter].pos[p] = system->cavity_grid[i][j][k].pos[p];
++cavities_array_counter;
}
} /* end k */
} /* end j */
} /* end i */
/* insert randomly at one of the free cavity points */
random_index = (system->cavities_open - 1) - (int)rint(((double)(system->cavities_open - 1)) * get_rand(system));
for (p = 0; p < 3; p++)
com[p] = cavities_array[random_index].pos[p];
/* free the insertion array */
free(cavities_array);
} // end umbrella
else {
/* insert the molecule to a random location within the unit cell */
for (p = 0; p < 3; p++)
rand[p] = 0.5 - get_rand(system);
for (p = 0; p < 3; p++)
for (q = 0, com[p] = 0; q < 3; q++)
com[p] += system->pbc->basis[q][p] * rand[q];
}
/* process the inserted molecule */
for (atom_ptr = system->checkpoint->molecule_backup->atoms; atom_ptr; atom_ptr = atom_ptr->next) {
/* move the molecule back to the origin and then assign it to com */
for (p = 0; p < 3; p++)
atom_ptr->pos[p] += com[p] - system->checkpoint->molecule_backup->com[p];
}
/* update the molecular com */
for (p = 0; p < 3; p++)
system->checkpoint->molecule_backup->com[p] = com[p];
/* give it a random orientation */
rotate(system, system->checkpoint->molecule_backup, system->pbc, 1.0);
// insert into the list
if (system->num_insertion_molecules) {
// If inserting a molecule from an insertion list, we will always insert at the end
system->checkpoint->head->next = system->checkpoint->molecule_backup;
system->checkpoint->molecule_backup->next = NULL;
} else {
if (!system->checkpoint->head) { // if we're at the start of the list:
system->molecules = system->checkpoint->molecule_backup;
} else {
system->checkpoint->head->next = system->checkpoint->molecule_backup;
}
system->checkpoint->molecule_backup->next = system->checkpoint->molecule_altered;
}
/* set new altered and tail to reflect the insertion */
system->checkpoint->molecule_altered = system->checkpoint->molecule_backup;
system->checkpoint->tail = system->checkpoint->molecule_altered->next;
system->checkpoint->molecule_backup = NULL;
if (system->num_insertion_molecules) { //multi sorbate
// Free all pair memory in the list
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) {
pair_ptr = atom_ptr->pairs;
while (pair_ptr) {
pair_t *temp = pair_ptr;
pair_ptr = pair_ptr->next;
free(temp);
}
}
}
// Generate new pairs lists for all atoms in system
setup_pairs(system);
} // only one sorbate
else
update_pairs_insert(system);
//reset atom and molecule id's
enumerate_particles(system);
break;
case MOVETYPE_REMOVE: /* remove a randomly chosen molecule */
if (system->cavity_bias) {
if (get_rand(system) < pow((1.0 - system->avg_observables->cavity_bias_probability),
((double)system->cavity_grid_size * system->cavity_grid_size * system->cavity_grid_size)))
system->checkpoint->biased_move = 0;
else
system->checkpoint->biased_move = 1;
}
/* remove 'altered' from the list */
if (!system->checkpoint->head) { /* handle the case where we're removing from the start of the list */
system->checkpoint->molecule_altered = system->molecules;
system->molecules = system->molecules->next;
} else {
system->checkpoint->head->next = system->checkpoint->tail;
}
free_molecule(system, system->checkpoint->molecule_altered);
system->checkpoint->molecule_altered = NULL; /* Insurance against memory errors */
update_pairs_remove(system);
//reset atom and molecule id's
enumerate_particles(system);
break;
case MOVETYPE_DISPLACE:
/* change coords of 'altered' */
if (system->rd_anharmonic)
displace_1D(system, system->checkpoint->molecule_altered, system->move_factor);
else if (system->spectre)
spectre_displace(system, system->checkpoint->molecule_altered, system->move_factor,
system->spectre_max_charge, system->spectre_max_target);
else if (system->gwp) {
if (system->checkpoint->molecule_altered->atoms->gwp_spin) {
displace(system, system->checkpoint->molecule_altered, system->pbc, system->gwp_probability, system->rot_factor);
displace_gwp(system, system->checkpoint->molecule_altered, system->gwp_probability);
} else
displace(system, system->checkpoint->molecule_altered, system->pbc, system->move_factor, system->rot_factor);
} else
displace(system, system->checkpoint->molecule_altered, system->pbc, system->move_factor, system->rot_factor);
break;
case MOVETYPE_ADIABATIC:
/* change coords of 'altered' */
displace(system, system->checkpoint->molecule_altered, system->pbc, system->adiabatic_probability, 1.0);
break;
case MOVETYPE_SPINFLIP:
if (get_rand(system) < 0.5)
system->checkpoint->molecule_altered->nuclear_spin = NUCLEAR_SPIN_PARA;
else
system->checkpoint->molecule_altered->nuclear_spin = NUCLEAR_SPIN_ORTHO;
break;
case MOVETYPE_VOLUME:
volume_change(system); // I don't want to contribute to the god damned mess -- kmclaugh
break;
default:
error(
"MC_MOVES: invalid mc move\n");
die(-1);
}
return;
}
