interface_builder_driver.py Command Help

Command: $SCHRODINGER/run interface_builder_gui_dir/interface_builder_driver.py

usage: $SCHRODINGER/run interface_builder_gui_dir/interface_builder_driver.py
       [-h] -substrate_file SUBSTRATE_FILE -film_file FILM_FILE
       [-topological_matches]
       [-substrate_max_miller_idx SUBSTRATE_MAX_MILLER_IDX]
       [-film_max_miller_idx FILM_MAX_MILLER_IDX]
       [-calculate_kwargs_file CALCULATE_KWARGS_FILE] [-generate_terminations]
       [-interfaces_file INTERFACES_FILE] [-allow_duplicates]
       [-no_slab_extraction] [-no_reduce_to_primitive]
       [-zslgen_kwargs_file ZSLGEN_KWARGS_FILE] [-HOST <hostname>] [-SAVE]
       [-JOBNAME JOBNAME]

Driver for building interfaces. Copyright Schrodinger, LLC. All rights
reserved.

options:
  -h, -help             Show this help message and exit.
  -substrate_file SUBSTRATE_FILE
                        Input file for the substrate structure. (default:
                        None)
  -film_file FILM_FILE  Input file for the film structure. (default: None)
  -zslgen_kwargs_file ZSLGEN_KWARGS_FILE
                        Use this option to specify a json file of custom
                        keyword arguments for https://pymatgen.org/pymatgen.an
                        alysis.interfaces.html#pymatgen.analysis.interfaces.zs
                        l.ZSLGenerator. (default: None)

Topological matches:
  -topological_matches  For a given substrate and film run Zur and McGill (J.
                        Appl. Phys. 55 (2) 378 1984) topological matching to
                        find suitable Miller index pairs for film growth. For
                        more information visit https://pymatgen.org/pymatgen.a
                        nalysis.interfaces.html#pymatgen.analysis.interfaces.s
                        ubstrate_analyzer.SubstrateAnalyzer. (default: False)
  -substrate_max_miller_idx SUBSTRATE_MAX_MILLER_IDX
                        Maximum Miller index for the substrate. (default: 1)
  -film_max_miller_idx FILM_MAX_MILLER_IDX
                        Maximum Miller index for the film. (default: 1)
  -calculate_kwargs_file CALCULATE_KWARGS_FILE
                        Use this option to specify a json file of custom
                        keyword arguments for https://pymatgen.org/pymatgen.an
                        alysis.interfaces.html#pymatgen.analysis.interfaces.su
                        bstrate_analyzer.SubstrateAnalyzer.calculate.
                        (default: None)
  -generate_terminations
                        For each topological match generate substrate and film
                        terminations that are commensurate for interface
                        building. (default: False)

Interfaces:
  -interfaces_file INTERFACES_FILE
                        File name for the csv file containing parameters for
                        building interfaces. The following columns are
                        required: "substrate_miller_idxs", "film_miller_idxs",
                        "substrate_termination", and "film_termination". The
                        following columns have default values and so are
                        optional: "in_unit_planes", "substrate_thickness",
                        "film_thickness", "vacuum_over_film/Ang.", and
                        "gap/Ang.". The output csv file obtained when running
                        with the flags "-topological_matches" and
                        "-generate_terminations" defines some of these columns
                        with the proper formatting, for example Miller indices
                        should be formatted like "(1, -1, 0)" strings and
                        in_unit_planes should be True or False booleans. If
                        True then the thicknesses are taken in unitless plane
                        units otherwise they are taken in Ang. The missing
                        columns can be added to that file and it used as input
                        here. This file is required if not running with flag
                        -topological_matches. (default: None)
  -allow_duplicates     By default only unique interfaces are returned. Use
                        this option to instead return all built interfaces
                        (including duplicates). (default: False)
  -no_slab_extraction   By default the individual substrate and film slab
                        models are extracted from each built interface model
                        and returned alongside the interface models. Use this
                        flag to instead only return the interface models.
                        (default: False)
  -no_reduce_to_primitive
                        By default interface, and if relevant slab, cells are
                        reduced to their primitive form. Use this flag to skip
                        this reduction and instead potentially return
                        conventional cells. (default: False)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)
  -SAVE                 Return zip archive of job directory at job completion.
                        (default: False)
  -JOBNAME JOBNAME      Provide an explicit name for the job. (default: None)