pyiron.quickff.quickff module¶
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class
pyiron.quickff.quickff.
QuickFF
(project, job_name)[source]¶ Bases:
pyiron.atomistics.job.atomistic.AtomisticGenericJob
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collect_output
()[source]¶ 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.
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detect_ffatypes
(ffatypes=None, ffatype_rules=None, ffatype_level=None)[source]¶ 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.
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from_hdf
(hdf=None, group_name=None)[source]¶ 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
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get_structure
(iteration_step=- 1, wrap_atoms=True)[source]¶ Overwrite the get_structure routine from AtomisticGenericJob because we want to avoid defining a unit cell when one does not exist
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