| 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); |