version 1.20 | version 1.21 |
---|
| |
cvm::error("Error: atomsColValue, if provided, must be non-zero.\n", INPUT_ERROR); | cvm::error("Error: atomsColValue, if provided, must be non-zero.\n", INPUT_ERROR); |
} | } |
| |
| // NOTE: calls to add_atom() and/or add_atom_id() are in the proxy-implemented function |
cvm::load_atoms(atoms_file_name.c_str(), *this, atoms_col, atoms_col_value); | cvm::load_atoms(atoms_file_name.c_str(), *this, atoms_col, atoms_col_value); |
} | } |
} | } |
| |
| |
parse_error |= parse_fitting_options(group_conf); | parse_error |= parse_fitting_options(group_conf); |
| |
| bool b_print_atom_ids = false; |
| get_keyval(group_conf, "printAtomIDs", b_print_atom_ids, false, colvarparse::parse_silent); |
| |
// TODO move this to colvarparse object | // TODO move this to colvarparse object |
check_keywords(group_conf, key.c_str()); | check_keywords(group_conf, key.c_str()); |
if (cvm::get_error()) { | if (cvm::get_error()) { |
| |
cvm::to_str(total_mass)+", total charge = "+ | cvm::to_str(total_mass)+", total charge = "+ |
cvm::to_str(total_charge)+".\n"); | cvm::to_str(total_charge)+".\n"); |
| |
| if (b_print_atom_ids) { |
| cvm::log("Internal definition of the atom group:\n"); |
| } |
| |
cvm::decrease_depth(); | cvm::decrease_depth(); |
| |
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); | return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); |
| |
} | } |
| |
| |
| std::string const cvm::atom_group::print_atom_ids() const |
| { |
| size_t line_count = 0; |
| std::ostringstream os(""); |
| for (size_t i = 0; i < atoms_ids.size(); i++) { |
| os << " " << std::setw(9) << atoms_ids[i]; |
| if (++line_count == 7) { |
| os << "\n"; |
| line_count = 0; |
| } |
| } |
| return os.str(); |
| } |
| |
| |
int cvm::atom_group::parse_fitting_options(std::string const &group_conf) | int cvm::atom_group::parse_fitting_options(std::string const &group_conf) |
{ | { |
bool b_defined_center = get_keyval(group_conf, "centerReference", b_center, false); | bool b_defined_center = get_keyval(group_conf, "centerReference", b_center, false); |