uint32_t atom_index_by_id(const char *id)
{
atom_def_t *atom;
uint32_t index;
if ((atom = find_atom_by_id(id)) != NULL)
index = atom->index;
else
index = ATOM_INVALID_INDEX;
return index;
}
uint32_t atom_create(const char *id, const char *name)
{
atom_def_t *atom;
uint32_t index = ATOM_INVALID_INDEX;
if (id && name) {
if ((atom = find_atom_by_id(id)) == NULL) {
if ((atom = create_atom(id, name)) != NULL)
index = atom->index;
}
else {
if (!strcmp(name, atom->name))
index = atom->index;
else {
OHM_ERROR("videoep: incosistent multiple definition of "
"atom '%s' ('%s' vs. '%s')", id, name, atom->name);
}
}
}
return index;
}
int surface_dimer_parameters(system_t *system, param_g *params) {
int i = 0; // generic counter
molecule_t *molecule_ptr;
atom_t *atom_ptr;
param_t *param_ptr;
// Default bond partner for atoms without explicit site neighbor
atom_t *origin = calloc( sizeof(atom_t), 1 ); // calloc sets pos[] fields all to 0
memnullcheck( origin, sizeof(atom_t), __LINE__-1, __FILE__);
system->polar_damp = params->alpha;
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) {
for (param_ptr = params->type_params; param_ptr; param_ptr = param_ptr->next) {
if( !strcasecmp( param_ptr->atomtype, atom_ptr->atomtype )) {
atom_ptr->charge = param_ptr->charge;
atom_ptr->epsilon = param_ptr->epsilon;
atom_ptr->sigma = param_ptr->sigma;
atom_ptr->omega = param_ptr->omega;
atom_ptr->polarizability = param_ptr->pol;
atom_ptr->c6 = param_ptr->c6;
atom_ptr->c8 = param_ptr->c8;
atom_ptr->c10 = param_ptr->c10;
double perturbation_vector[3];
// Find the the atom that defines the bond axis and store for easy reference
atom_t *snPtr = 0;
if( atom_ptr->site_neighbor_id == 0 )
snPtr = origin;
else {
snPtr = find_atom_by_id( system, atom_ptr->site_neighbor_id );
if( !snPtr ) {
snPtr = origin;
printf( "\n*** WARNING ***\n" );
printf( "Bonding partner for atom %d not found ", atom_ptr->bond_id );
printf( "--> %d, possibly invalid. Using origin.\n\n", atom_ptr->site_neighbor_id );
}
}
// Generate the vector along which the dr perturbations will occur
for (i = 0; i < 3; i++)
perturbation_vector[i] = atom_ptr->pos[i] - snPtr->pos[i];
// Determine how much the bond vector should be scaled to increase the length by dr.
double scale = find_scale_factor(perturbation_vector[0], perturbation_vector[1], perturbation_vector[2], param_ptr->dr);
// Scale the perturbation vector
for (i = 0; i < 3; i++)
perturbation_vector[i] *= scale;
// Add the vector back to the bond partner coordinates to get the new position.
for (i = 0; i < 3; i++)
atom_ptr->pos[i] = snPtr->pos[i] + perturbation_vector[i];
}
} // for param_ptr
} // for atom_ptr
} // for molecule_ptr
free(origin);
return (0);
}
