LAMMPS#
LAMMPS Input File Generation: atomaton.write_lammps_files#
- atomaton.write_lammps_files.get_lammps_box_parameters(cell_lengths, cell_angles, degrees=True)#
- atomaton.write_lammps_files.get_masses()#
- atomaton.write_lammps_files.write_angle_coeff_section(angle_type_params)#
- atomaton.write_lammps_files.write_angle_section(angle_ids, angle_types, angles, angle_coeffs)#
- atomaton.write_lammps_files.write_atom_section(atom_indicies, molecule_indicies, symbols, positions, charges, pair_coeffs)#
Currently only supports atom type, Full.
- atomaton.write_lammps_files.write_bond_coeff_section(bond_type_params)#
- atomaton.write_lammps_files.write_bond_section(bond_ids, bond_types, bonds, bond_coeffs)#
- atomaton.write_lammps_files.write_box_info(header, cell_lengths, cell_angles)#
- atomaton.write_lammps_files.write_header(cell_lengths, cell_angles, atoms, atom_types, bonds, bond_types, angles, angle_types, dihedrals, dihedral_types, impropers, improper_types)#
- atomaton.write_lammps_files.write_header_comments(header)#
- atomaton.write_lammps_files.write_lammps_data_file(filename, atoms, ff_atom_types, atom_type_params, mol_ids, cell_lengths, cell_angles, all_bonds, all_bond_types, bond_type_params, all_angles, all_angle_types, angle_type_params, all_dihedrals, all_dihedral_types, all_impropers, all_improper_types, degrees=True)#
Generate a LAMMPS data file from various structure information.
- Args:
filename (str): path, including file name, of the file to generate atoms (Atoms): ff_atom_types (list[str, str]): _description_ atom_type_params (_type_): _description_ mol_ids (_type_): _description_ cell_lengths (_type_): _description_ cell_angles (_type_): _description_ all_bonds (_type_): _description_ all_bond_types (_type_): _description_ bond_type_params (_type_): _description_ all_angles (_type_): _description_ all_angle_types (_type_): _description_ angle_type_params (_type_): _description_ all_dihedrals (_type_): _description_ all_dihedral_types (_type_): _description_ all_impropers (_type_): _description_ all_improper_types (_type_): _description_ degrees (bool, optional): _description_. Defaults to True.
- atomaton.write_lammps_files.write_lammps_data_file_alt(filename, cell_lengths, cell_angles)#
- atomaton.write_lammps_files.write_mass_section(atom_types)#
- atomaton.write_lammps_files.write_multibody_terms_header(header, atoms, atom_types, bonds, bond_types, angles, angle_types, dihedrals, dihedral_types, impropers, improper_types)#
- atomaton.write_lammps_files.write_pair_coeff_section(atom_type_params)#
Writes lammps data file section for the individual pair parameters for lennard-jones bonding.
- Args:
atom_type_params (dict[str, list[float…]]): lennard-jones sigma and epsilon for the individual atom type
- Returns:
list[str]: pair coeff lines