schrodinger.application.matsci.interface module

Utilities for building interfaces using pymatgen.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.interface.SubstrateFilmMillers(substrate, film)

Bases: tuple

film

Alias for field number 1

substrate

Alias for field number 0

class schrodinger.application.matsci.interface.Slab(slab, st)

Bases: tuple

slab

Alias for field number 0

st

Alias for field number 1

class schrodinger.application.matsci.interface.SubstrateFilmTerminations(substrate, film)

Bases: tuple

film

Alias for field number 1

substrate

Alias for field number 0

class schrodinger.application.matsci.interface.SubstrateFilmSlabs(terminations, substrate_slab, film_slab)

Bases: tuple

film_slab

Alias for field number 2

substrate_slab

Alias for field number 1

terminations

Alias for field number 0

class schrodinger.application.matsci.interface.SubstrateFilmInterface(interface, interface_st, substrate_st, film_st)

Bases: tuple

film_st

Alias for field number 3

interface

Alias for field number 0

interface_st

Alias for field number 1

substrate_st

Alias for field number 2

exception schrodinger.application.matsci.interface.InterfaceException

Bases: Exception

schrodinger.application.matsci.interface.get_topo_matches(substrate_st, film_st, substrate_max_miller=1, film_max_miller=1, zslgen_kwargs=None, calculate_kwargs=None)

Return topological matches for the given substrate/film pair where the film can be strained.

Parameters:

  • substrate_st (schrodinger.structure.Structure) – the bulk substrate structure

  • film_st (schrodinger.structure.Structure) – the bulk film structure

  • substrate_max_miller (int) – maximum Miller index to generate for substrate surfaces

  • film_max_miller (int) – maximum Miller index to generate for film surfaces

  • zslgen_kwargs (dict or None) – options for pymatgen.analysis.interfaces.zsl.ZSLGenerator if there are any

  • calculate_kwargs (dict or None) – options for pymatgen.analysis.interfaces.substrate_analyzer.SubstrateAnalyzer.calculate if there are any

Raises:

InterfaceException – if there is an issue

Return type:

dict[SubstrateFilmMillers]= pymatgen.analysis.interfaces.substrate_analyzer.SubstrateMatch

Returns:

keys are SubstrateFilmMillers, values are pymatgen.analysis.interfaces.substrate_analyzer.SubstrateMatch

schrodinger.application.matsci.interface.get_slabs(st, millers, generator_kwargs=None, get_slabs_kwargs=None)

Return slabs for the given structure, Miller indices, and other parameters.

Parameters:

  • st (schrodinger.structure.Structure) – the bulk structure

  • millers (tuple[int]) – triple of Miller indices

  • generator_kwargs (dict or None) – options for pymatgen.core.surface.SlabGenerator if there are any

  • get_slabs_kwargs (dict or None) – options for pymatgen.core.surface.SlabGenerator.get_slabs if there are any

Return type:

dict[str]=list[Slab]

Returns:

keys are termination strings, values are lists of Slab

schrodinger.application.matsci.interface.get_title(bulk, tag, millers, termination)

Return the structure title for the given information.

Parameters:

  • bulk (str) – bulk title read from input

  • tag (str) – one of module constants SUBSTRATE or FILM

  • millers (tuple[int]) – triple of Miller indices

  • termination (str) – the slab termination

Return type:

str

Returns:

the structure title

schrodinger.application.matsci.interface.get_interface_slabs(substrate_st, film_st, all_millers, zslgen_kwargs=None)

Return slabs for the given substrate/film pair and their Miller indices that can be made into interfaces.

Parameters:
Raises:

InterfaceException – if there is an issue

Return type:

dict[SubstrateFilmMillers]=dict[SubstrateFilmTerminations ]=`SubstrateFilmSlabs`

Returns:

outer keys are SubstrateFilmMillers, inner keys are SubstrateFilmTerminations, values are SubstrateFilmSlabs

schrodinger.application.matsci.interface.get_interfaces(substrate_st, film_st, all_terminations, zslgen_kwargs=None, get_interfaces_kwargs=None)

Return interfaces for the given substrate/film pair, their Miller indices, and their terminations.

Parameters:

  • substrate_st (schrodinger.structure.Structure) – the bulk substrate structure

  • film_st (schrodinger.structure.Structure) – the bulk film structure

  • all_terminations (dict[SubstrateFilmMillers ]=list[SubstrateFilmTerminations]) – collection of substrate and film Miller indices and terminations

  • zslgen_kwargs (dict or None) – options for pymatgen.analysis.interfaces.zsl.ZSLGenerator if there are any

  • get_interfaces_kwargs (dict or None) – options for pymatgen.analysis.interfaces.coherent_interfaces.CoherentInterfaceBuilder. get_interfaces if there are any

Raises:

InterfaceException – if there is an issue

Return type:

dict[SubstrateFilmMillers]=dict[SubstrateFilmTerminations ]=list[SubstrateFilmInterface]

Returns:

outer keys are SubstrateFilmMillers, inner keys are SubstrateFilmTerminations, values are lists of SubstrateFilmInterface

schrodinger.application.matsci.interface.isnan(value)

Wraps numpy.isnan to take a value of any type and not traceback.

Parameters:

value (any) – the value to check

Return type:

bool

Returns:

True if the value is not a number

schrodinger.application.matsci.interface.get_millers_tuple_from_str(millers_str)

Return a Millers tuple from a Millers string.

Parameters:

millers_str (str) – the Millers string

Raises:

InterfaceException – if there is an issue

Return type:

tuple(int)

Returns:

the Millers tuple

schrodinger.application.matsci.interface.get_millers_and_terminations(row_idx, row_dict, include_terminations=True)

Return a validated tuple of (substrate millers, film millers) or (substrate millers, film millers, substrate termination, film termination) from the given dictionary of row data.

Parameters:

  • row_idx (int) – the row index, 1-based

  • row_dict (dict[str]=any) – contains row data, keys are columns, values are data of any type

  • include_terminations (bool) – True if including terminations

Raises:

InterfaceException – if there is an issue

Return type:

tuple(tuple, tuple) or tuple(tuple, tuple, str, str)

Returns:

validated tuple of (substrate millers, film millers) or (substrate millers, film millers, substrate termination, film termination)

class schrodinger.application.matsci.interface.TopologicalMatches(substrate_st, film_st, basename, substrate_max_miller=1, film_max_miller=1, zslgen_kwargs=None, calculate_kwargs=None, generate_slabs=False, logger=None)

Bases: object

__init__(substrate_st, film_st, basename, substrate_max_miller=1, film_max_miller=1, zslgen_kwargs=None, calculate_kwargs=None, generate_slabs=False, logger=None)
Parameters:

  • substrate_st (schrodinger.structure.Structure) – the bulk substrate structure

  • film_st (schrodinger.structure.Structure) – the bulk film structure

  • basename (str) – the base name to use for output file naming

  • substrate_max_miller (int) – maximum Miller index to generate for substrate surfaces

  • film_max_miller (int) – maximum Miller index to generate for film surfaces

  • zslgen_kwargs (dict or None) – options for pymatgen.analysis.interfaces.zsl.ZSLGenerator if there are any

  • calculate_kwargs (dict or None) – options for pymatgen.analysis.interfaces.substrate_analyzer.SubstrateAnalyzer.calculate if there are any

  • generate_slabs (bool) – for each topological match generate substrate and film slab models with terminations that are commensurate for interface building

  • logger (logging.Logger) – the logger

generateSlabs(millers, match)

Generate slabs.

Parameters:

  • millers (SubstrateFilmMillers) – substrate and film Miller indices

  • match (pymatgen.analysis.interfaces.substrate_analyzer.SubstrateMatch) – the match object

setMatchDataFrame()

Set the match data frame.

writeOutputFiles()

Write the output files.

run()

Run it.

static getTopologicalMatchesDF(csv_fn, generate_slabs=False)

Return the topological matches dataframe.

Parameters:

  • csv_fn (str) – the topological matches output csv file name

  • generate_slabs (bool) – True if the topological matches was run with the generate slabs option

Raises:

InterfaceException – if there is an issue

Return type:

pandas.DataFrame

Returns:

the topological matches dataframe

class schrodinger.application.matsci.interface.BuildInterfaces(substrate_st, film_st, basename, get_interfaces_kwargs, zslgen_kwargs=None, logger=None)

Bases: object

__init__(substrate_st, film_st, basename, get_interfaces_kwargs, zslgen_kwargs=None, logger=None)
Parameters:

  • substrate_st (schrodinger.structure.Structure) – the bulk substrate structure

  • film_st (schrodinger.structure.Structure) – the bulk film structure

  • basename (str) – the base name to use for output file naming

  • get_interfaces_kwargs (dict[SubstrateFilmMillers]=dict[ SubstrateFilmTerminations]=list[dict]) – outer keys are SubstrateFilmMillers, inner keys are SubstrateFilmTerminations, values are lists of options for pymatgen.analysis.interfaces.coherent_interfaces.CoherentInterfaceBuilder. get_interfaces

  • zslgen_kwargs (dict or None) – options for pymatgen.analysis.interfaces.zsl.ZSLGenerator if there are any

  • logger (logging.Logger) – the logger

static getGetInterfacesKwargs(csv_fn)

Return parameters for building interfaces.

Parameters:

csv_fn (str) – file name for the csv file containing parameters for building interfaces

Raises:

InterfaceException – if there is an issue

Return type:

dict[SubstrateFilmMillers]=dict[SubstrateFilmTerminations]=list[dict]

Returns:

outer keys are SubstrateFilmMillers, inner keys are SubstrateFilmTerminations, values are lists of options for pymatgen.analysis.interfaces.coherent_interfaces.CoherentInterfaceBuilder. get_interfaces

setInterfaceDataFrame()

Set the interface data frame.

writeOutputFiles()

Write the output files.

run()

Run it.