intermol.lammps.lammps_parser module

class intermol.lammps.lammps_parser.LammpsParser(in_file, system=None, unit_set='real')

Bases: object

A class containing methods to read and write LAMMPS files.

SCALE_FROM = 0.5

SCALE_INTO = 2.0

canonical_angle(kwds, angle, direction)

Convert from the canonical form of this interaction.

canonical_bond(kwds, bond, direction='into')

Convert to/from the canonical form of this interaction.

canonical_dihedral(params, dihedral, direction='into')

Convert from the canonical form of this interaction.

create_kwds_from_entries(entries, force_class, offset=0)

get_force_atoms(force, forceclass)

Return the atoms involved in a force.

get_force_bondingtypes(force, forceclass)

Return the atoms involved in a force.

get_parameter_kwds_from_force(force)

get_parameter_list_from_force(force)

lammps_angle_types = {'charmm': <class 'intermol.forces.urey_bradley_angle_type.UreyBradleyAngleType'>, 'cosine': <class 'intermol.forces.cosine_angle_type.CosineAngleType'>, 'harmonic': <class 'intermol.forces.harmonic_angle_type.HarmonicAngleType'>}

lammps_angles = {'charmm': <class 'intermol.forces.urey_bradley_angle_type.UreyBradleyAngle'>, 'cosine': <class 'intermol.forces.cosine_angle_type.CosineAngle'>, 'harmonic': <class 'intermol.forces.harmonic_angle_type.HarmonicAngle'>}

lammps_bond_types = {'nonlinear': <class 'intermol.forces.nonlinear_bond_type.NonlinearBondType'>, 'quartic': <class 'intermol.forces.quartic_breakable_bond_type.QuarticBreakableBondType'>, 'morse': <class 'intermol.forces.morse_bond_type.MorseBondType'>, 'harmonic': <class 'intermol.forces.harmonic_bond_type.HarmonicBondType'>, 'fene/expand': <class 'intermol.forces.fene_expandable_bond_type.FeneExpandableBondType'>, 'class2': <class 'intermol.forces.quartic_bond_type.QuarticBondType'>}

lammps_bonds = {'nonlinear': <class 'intermol.forces.nonlinear_bond_type.NonlinearBond'>, 'quartic': <class 'intermol.forces.quartic_breakable_bond_type.QuarticBreakableBond'>, 'morse': <class 'intermol.forces.morse_bond_type.MorseBond'>, 'harmonic': <class 'intermol.forces.harmonic_bond_type.HarmonicBond'>, 'fene/expand': <class 'intermol.forces.fene_expandable_bond_type.FeneExpandableBond'>, 'class2': <class 'intermol.forces.quartic_bond_type.QuarticBond'>}

lammps_dihedral_types = {'charmm': <class 'intermol.forces.proper_periodic_dihedral_type.ProperPeriodicDihedralType'>, 'multi/harmonic': <class 'intermol.forces.rb_dihedral_type.RbDihedralType'>, 'opls': <class 'intermol.forces.fourier_dihedral_type.FourierDihedralType'>}

lammps_dihedrals = {'charmm': <class 'intermol.forces.proper_periodic_dihedral_type.ProperPeriodicDihedral'>, 'multi/harmonic': <class 'intermol.forces.rb_dihedral_type.RbDihedral'>, 'opls': <class 'intermol.forces.fourier_dihedral_type.FourierDihedral'>}

lammps_improper_types = {'cvff': <class 'intermol.forces.trig_dihedral_type.TrigDihedralType'>, 'harmonic': <class 'intermol.forces.improper_harmonic_dihedral_type.ImproperHarmonicDihedralType'>}

lammps_impropers = {'cvff': <class 'intermol.forces.trig_dihedral_type.TrigDihedral'>, 'harmonic': <class 'intermol.forces.improper_harmonic_dihedral_type.ImproperHarmonicDihedral'>}

lookup_lammps_angles = {<class 'intermol.forces.urey_bradley_angle_type.UreyBradleyAngle'>: 'charmm', <class 'intermol.forces.harmonic_angle_type.HarmonicAngle'>: 'harmonic', <class 'intermol.forces.cosine_angle_type.CosineAngle'>: 'cosine'}

lookup_lammps_bonds = {<class 'intermol.forces.quartic_breakable_bond_type.QuarticBreakableBond'>: 'quartic', <class 'intermol.forces.quartic_bond_type.QuarticBond'>: 'class2', <class 'intermol.forces.fene_expandable_bond_type.FeneExpandableBond'>: 'fene/expand', <class 'intermol.forces.morse_bond_type.MorseBond'>: 'morse', <class 'intermol.forces.harmonic_bond_type.HarmonicBond'>: 'harmonic', <class 'intermol.forces.harmonic_potential_bond_type.HarmonicPotentialBond'>: 'harmonic', <class 'intermol.forces.nonlinear_bond_type.NonlinearBond'>: 'nonlinear'}

lookup_lammps_dihedrals = {<class 'intermol.forces.proper_periodic_dihedral_type.ProperPeriodicDihedral'>: 'charmm', <class 'intermol.forces.rb_dihedral_type.RbDihedral'>: 'multi/harmonic', <class 'intermol.forces.trig_dihedral_type.TrigDihedral'>: 'Trig', <class 'intermol.forces.fourier_dihedral_type.FourierDihedral'>: 'opls'}

lookup_lammps_impropers = {<class 'intermol.forces.trig_dihedral_type.TrigDihedral'>: 'cvff', <class 'intermol.forces.improper_harmonic_dihedral_type.ImproperHarmonicDihedral'>: 'harmonic'}

parse_angle_coeffs(data_lines)

parse_angle_style(line)

parse_angles(data_lines)

parse_atom_style(line)

Note

Assuming ‘full’ as default for everything else.

parse_atoms(data_lines)

Read atoms from data file.

parse_bond_coeffs(data_lines)

parse_bond_style(line)

parse_bonded_style(line)

parse_bonds(data_lines)

parse_boundary(line)

parse_box(line, dim)

Read box information from data file.

Parameters:

• line (str) – Current line in input file.
• dim (int) – Dimension specified in line.

parse_dihedral_coeffs(data_lines)

parse_dihedral_style(line)

parse_dihedrals(data_lines)

parse_dimension(line)

parse_force(data_lines, force_classes, forceSet, n=0)

Read bonds, angles, dihedrals, impropers from data file.

parse_force_coeffs(data_lines, force_name, force_classes, force_style, lammps_forces, canonical_force)

Read force coefficients from data file.

parse_improper_coeffs(data_lines)

parse_improper_style(line)

parse_impropers(data_lines)

parse_kspace_style(line)

Note

Currently ignored.

parse_masses(data_lines)

Read masses from data file.

parse_pair_coeffs(data_lines)

Read pair coefficients from data file.

parse_pair_modify(line)

parse_pair_style(line)

parse_read_data(line)

parse_special_bonds(line)

parse_units(line)

parse_velocities(data_lines)

read()

Reads a LAMMPS input file and a data file specified within.

Parameters:input_file (str) – Name of LAMMPS input file to read in.

read_data(data_file)

Reads a LAMMPS data file.

Parameters:data_file (str) – name of LAMMPS data file to read in.

read_input()

Reads a LAMMPS input file.

Parameters:input_file (str) – Name of LAMMPS input file to read in.

set_units(unit_set)

Set what unit set to use.

write(unit_set='real')

Writes a LAMMPS data and corresponding input file.

Parameters:

• data_file (str) – Name of LAMMPS data file to write to.
• unit_set (str) – LAMMPS unit set for output file.

write_angles(mol_type, offset)

write_bonds(mol_type, offset)

write_dihedrals(mol_type, offset)

Separate dihedrals from impropers.

write_forces(forces, offset, force_name, lookup_lammps_force, lammps_force_types, canonical_force)

The general force writing function.

Currently supports bonds, angles, dihedrals, impropers.

write_impropers(mol_type, offset)

Separate dihedrals from impropers.

write_virtuals(mol_type, offset)

intermol.lammps.lammps_parser.load_lammps(in_file)

Load a LAMMPS input file into a System.

Parameters:

• in_file –
• include_dir –
• defines –

Returns:

Return type:

system

intermol.lammps.lammps_parser.write_lammps(in_file, system, unit_set='real')

Load a LAMMPS input file into a System.

Parameters:

• in_file –
• include_dir –
• defines –

Returns:

Return type:

system