pyiron.quickff.quickff module

class pyiron.quickff.quickff.QuickFF(project, job_name)

Bases: pyiron.atomistics.job.atomistic.AtomisticGenericJob

collect_output()

Collect the output files of the external executable and store the information in the HDF5 file. This method has to be implemented in the individual hamiltonians.

detect_ffatypes(ffatypes=None, ffatype_rules=None, ffatype_level=None)

Define atom types by explicitely giving them through the ffatypes keyword, defining atype rules using the ATSELECT language implemented in Yaff (see the Yaff documentation at http://molmod.github.io/yaff/ug_atselect.html) or by specifying the ffatype_level employing the built-in routine in QuickFF.

from_hdf(hdf=None, group_name=None)

Recreates instance from the hdf5 file :param hdf: Path to the hdf5 file :type hdf: str :param group_name: Name of the group which contains the object :type group_name: str

get_structure(iteration_step=- 1, wrap_atoms=True)

Overwrite the get_structure routine from AtomisticGenericJob because we want to avoid defining a unit cell when one does not exist

get_yaff_ff(rcut=28.345892008818783, alpha_scale=3.2, gcut_scale=1.5, smooth_ei=True)

get_yaff_system()

log()

read_abinitio(fn)

set_ei(fn)

set_vdw(fn)

to_hdf(hdf=None, group_name=None)

Store the GenericJob in an HDF5 file

Parameters

• hdf (ProjectHDFio) – HDF5 group object - optional

• group_name (str) – HDF5 subgroup name - optional

write_input()

Write the input files for the external executable. This method has to be implemented in the individual hamiltonians.

class pyiron.quickff.quickff.QuickFFInput(input_file_name=None)

Bases: pyiron.base.generic.parameters.GenericParameters

load_default()

Loading the default settings for the input file.

pyiron.quickff.quickff.collect_output(fn_pars, fn_sys)

pyiron.quickff.quickff.write_chk(input_dict, working_directory='.')

pyiron.quickff.quickff.write_config(input_dict, working_directory='.')

pyiron.quickff.quickff.write_pars(pars, fn, working_directory='.')