pymatgen.io.lammps.utils module

class LammpsRunner(input_filename='lammps.in', bin='lammps')

Bases: object

LAMMPS wrapper

Parameters:

• input_filename (string) – input file name
• bin (string) – command to run, excluding the input file name

run()

Write the input/data files and run LAMMPS.

class PackmolRunner(mols, param_list, input_file='pack.inp', tolerance=2.0, filetype='xyz', control_params={'maxit': 20, 'nloop': 600}, auto_box=True, output_file='packed.xyz', bin='packmol')

Bases: object

Wrapper for the Packmol software that can be used to pack various types of molecules into a one single unit.

Parameters:

• mols – list of Molecules to pack
• input_file – name of the packmol input file
• tolerance – min distance between the atoms
• filetype – input/output structure file type
• control_params – packmol control parameters dictionary. Basically all parameters other than structure/atoms
• param_list – list of parameters containing dicts for each molecule
• auto_box – put the molecule assembly in a box
• output_file – output file name. The extension will be adjusted according to the filetype

convert_obatoms_to_molecule(atoms, residue_name=None, site_property='ff_map')

Convert list of openbabel atoms to MOlecule.

Parameters:

• atoms ([OBAtom]) – list of OBAtom objects
• residue_name (str) – the key in self.map_residue_to_mol. Usec to restore the site properties in the final packed molecule.
• site_property (str) – the site property to be restored.

Returns:

Molecule object

restore_site_properties(site_property='ff_map', filename=None)

Restore the site properties for the final packed molecule.

Parameters:

• site_property (str) –
• filename (str) – path to the final packed molecule.

Returns:

Molecule

run(copy_to_current_on_exit=False, site_property=None)

Write the input file to the scratch directory, run packmol and return the packed molecule.

Parameters:

• copy_to_current_on_exit (bool) – Whether or not to copy the packmol input/output files from the scratch directory to the current directory.
• site_property (str) – if set then the specified site property for the the final packed molecule will be restored.

Returns:

Molecule object

write_pdb(mol, filename, name=None, num=None)

dump the molecule into pdb file with custom residue name and number.

class Polymer(start_monomer, s_head, s_tail, monomer, head, tail, end_monomer, e_head, e_tail, n_units, link_distance=1.0, linear_chain=False)

Bases: object

Generate polymer chain via Random walk. At each position there are a total of 5 possible moves(excluding the previous direction).

Parameters:

• start_monomer (Molecule) – Starting molecule
• s_head (int) – starting atom index of the start_monomer molecule
• s_tail (int) – tail atom index of the start_monomer
• monomer (Molecule) – The monomer
• head (int) – index of the atom in the monomer that forms the head
• tail (int) – tail atom index. monomers will be connected from tail to head
• end_monomer (Molecule) – Terminal molecule
• e_head (int) – starting atom index of the end_monomer molecule
• e_tail (int) – tail atom index of the end_monomer
• n_units (int) – number of monomer units excluding the start and terminal molecules
• link_distance (float) – distance between consecutive monomers
• linear_chain (bool) – linear or random walk polymer chain