/// For AMBER topologies, the segment id is automatically set to
/// "MAIN" (the segment id assigned by NAMD's AMBER topology parser),
/// and is therefore optional when an AMBER topology is used
int colvarproxy_namd::init_atom(cvm::residue_id const &residue,
std::string const &atom_name,
std::string const &segment_id)
{
int const aid = check_atom_id(residue, atom_name, segment_id);
for (size_t i = 0; i < atoms_ids.size(); i++) {
if (atoms_ids[i] == aid) {
// this atom id was already recorded
atoms_ncopies[i] += 1;
return i;
}
}
if (cvm::debug())
log("Adding atom \""+
atom_name+"\" in residue "+
cvm::to_str(residue)+
" (index "+cvm::to_str(aid)+
") for collective variables calculation.\n");
int const index = add_atom_slot(aid);
modifyRequestedAtoms().add(aid);
update_atom_properties(index);
return index;
}
int colvarproxy_namd::init_atom(int atom_number)
{
// save time by checking first whether this atom has been requested before
// (this is more common than a non-valid atom number)
int aid = (atom_number-1);
for (size_t i = 0; i < atoms_ids.size(); i++) {
if (atoms_ids[i] == aid) {
// this atom id was already recorded
atoms_ncopies[i] += 1;
return i;
}
}
aid = check_atom_id(atom_number);
if (aid < 0) {
return INPUT_ERROR;
}
int const index = add_atom_slot(aid);
modifyRequestedAtoms().add(aid);
update_atom_properties(index);
return index;
}
int colvarproxy_namd::reset()
{
int error_code = COLVARS_OK;
// Unrequest all atoms and group from NAMD
modifyRequestedAtoms().clear();
modifyRequestedGroups().clear();
atoms_map.clear();
// Clear internal Proxy records
error_code |= colvarproxy::reset();
return error_code;
}
int GlobalMasterFreeEnergy::requestAtom(int atomid)
{
if ( atomid < 0 || atomid >= molecule->numAtoms ) return -1; // failure
modifyRequestedAtoms().add(atomid);
return 0; // success
}
