jarvis.io.lammps package

Submodules

jarvis.io.lammps.inputs module

Module for writing LAMMPS input files.

class jarvis.io.lammps.inputs.LammpsData(lammps_box=[], species=[], charges=[], cart_coords=[], element_order=[])

Bases: object

Construct Lammps data file.

atoms_to_lammps(atoms, origin=(0, 0, 0))

Convert Atoms object to Lammps data.

classmethod from_dict(d={})

Construct from a dictionary.

lammps_to_atoms()

Convert Lammps data to Atoms object.

read_data(filename='lammps.data', element_order=[], potential_file='pot.mod', verbose=True)

Read Lammps data file.

to_dict()

Convert the infor to a dictionary.

write_file(filename='lammps.data')

Write Lammps data input file.

class jarvis.io.lammps.inputs.LammpsInput(LammpsDataObj=None, pbc=['p', 'p', 'p'])

Bases: object

Construct LAMMPS input.

classmethod from_dict(d={})

Costruct class from a dictionary.

to_dict()

Convert to a dictionary.

write_lammps_in(lammps_in='init.mod', lammps_in1='potential.mod', lammps_in2='in.main', lammps_trj=None, lammps_data=None, parameters={})

Write lammps input file.

From ase with custom modifications LAMMPS input is devided into three parts

Args:

lammps_in: generally”init.mod”, with unit and conversion factor information

lammps_in1: generally “potential.mod”, with force-field/potential style and element type information

lammps_in2: generally “in.elastic”, a generic main input file to be fed in LAMMPS usin lmp_*<…,parameters[‘exec’]

parameters: input parameters

jarvis.io.lammps.outputs module

Function to analze LAMMPS output.

jarvis.io.lammps.outputs.analyze_log(log='log.lammps')

Analyzes log.lammps file.

Please note, the output format heavily depends on the input file A generic input is taken here. Args:

log: path to log.lammps file

Returns:

en: energy/atom press: pressure toten: total energy cij: elastic constants

jarvis.io.lammps.outputs.get_chem_pot(all_json_data={})

Get minumum energy for each elemental specie.

jarvis.io.lammps.outputs.parse_folder(path='bulk@mp-1487_fold/bulk@mp-1487')

Parse individual LAMMPS run.

jarvis.io.lammps.outputs.parse_full_ff_folder(path='Mishin-Ni-Al-2009.eam.alloy_nist')

Parse complete FF calculation folder.

jarvis.io.lammps.outputs.parse_log(log='log.lammps')

Analyzes log.lammps file.

Please note, the output format heavily depends on the input file A generic input is taken here. Args:

log: path to log.lammps file

Returns:

en: energy/atom

press: pressure

toten: total energy

cij: elastic constants

jarvis.io.lammps.outputs.parse_material_calculation_folder(path='bulk@mp-1487_fold', jid='x')

Parse individual LAMMPS material run.

with optimization, vacancy, phonon, surface etc.

jarvis.io.lammps.outputs.parse_potential_mod(mod='potential.mod')

Parse potentials.mod input file.

jarvis.io.lammps.outputs.read_data(data=None, ff=None, element_order=[])

Read LAMMPS data file.

Args:

data: data file path

ff: potential.mod/potential information file path

Returns:

Atoms object

jarvis.io.lammps.outputs.read_dump(data=None)

Read LAMMPS dump file.

Module contents

Modules for reading and writing LAMMPS files.