schrodinger.application.matsci.nano.surfaces_interfaces_mod module

Classes and functions to enumerate surfaces and interfaces.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.matsci.nano.surfaces_interfaces_mod.get_base_names(ref_xtal_asu, ref_base_name_in=None, ads_xtal_asu=None, ads_base_name_in=None)

Return the reference, adsorption, and final combined base names.

Parameters

• ref_xtal_asu (str) – reference xtal input file

• ref_base_name_in (str or None) – reference base name or None if none has been given

• ads_xtal_asu (str or None) – adsorption xtal input file or None if none has been given

• ads_base_name_in (str or None) – adsorption base name or None if none has been given

Return type

str, str or None, str

Returns

reference, adsorption, and final combined base names, the adsorption base name will be None if no adsorption xtal asu is provided

class schrodinger.application.matsci.nano.surfaces_interfaces_mod.ParserWrapper(scriptname, description)

Bases: object

Manages the argparse module to parse user command line arguments.

__init__(scriptname, description)

Create a ParserWrapper instance and process it.

Parameters

• scriptname (str) – name of this script

• description (str) – description of this script

loadIt()

Load ParserWrapper with options.

parseArgs(args)

Parse the command line arguments.

Parameters

args (tuple) – command line arguments

schrodinger.application.matsci.nano.surfaces_interfaces_mod.get_surface_kwargs(options_file)

Return a dictionary of surface options from the given options file.

Parameters

options_file (str or None) – contains options for the surface build or None if there are none in which case the defaults are used

Return type

dict

Returns

contains options for the surface build

schrodinger.application.matsci.nano.surfaces_interfaces_mod.get_interface_kwargs(options_file)

Return a dictionary of interface options from the given options file.

Parameters

options_file (str or None) – contains options for the interface build or None if there are none in which case the defaults are used

Return type

dict

Returns

contains options for the interface build

schrodinger.application.matsci.nano.surfaces_interfaces_mod.get_hkl_indices(flattened_hkl_indices=None, h_min=0, h_max=0, k_min=0, k_max=0, l_min=0, l_max=0)

Collect and return all hkl Miller index triples sorted by increasing l then k then h.

Parameters

• flattened_hkl_indices (list or None) – flattened hkl indices, for example 100, 110, etc. as [1, 0, 0, 1, 1, 0, …]

• h_min (int) – minimum h index

• h_max (int) – maximum h index

• k_min (int) – minimum k index

• k_max (int) – maximum k index

• l_min (int) – minimum l index

• l_max (int) – maximum l index

Raises

ValueError – if there is an issue

Return type

list

Returns

contains sorted tuples of hkl triples

schrodinger.application.matsci.nano.surfaces_interfaces_mod.write_to_file(file_name, structs)

Write the structures to file with the feature’s WAM type

Parameters

• file_name (str) – The path to the file

• structs (list) – List of structures to write to file

class schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces(xtal_asu, surface_kwargs=None, logger=None)

Bases: object

Manage the enumeration of surfaces.

__init__(xtal_asu, surface_kwargs=None, logger=None)

Create an instance.

Parameters

• xtal_asu (schrodinger.structure.Structure) – the crystalline ASU from which to create surfaces

• surface_kwargs (None or dict) – kwargs for the surface build or None if there are none in which case the defaults will be used

• logger (logging.Logger or None) – output logger or None if there isn’t one

getHKLIndices()

Collect and return all hkl Miller index triples for this surface enumeration and sort them according to increasing l then k then h.

Return type

list

Returns

contains sorted tuples of hkl triples

getSurface(cell, hkl, logger=None)

Build and return a slab.Surface.

Parameters

• cell (schrodinger.structure.Structure) – a cell

• hkl (tuple) – a triple of Miller indices

• logger (logging.Logger or None) – output logger or None if there isn’t one

Return type

slab.Surface

Returns

the surface object

logParams()

Log the parameters.

getXtalCell()

Build and return the crystal cell from which surfaces will be created.

Return type

schrodinger.structure.Structure

Returns

the crystal cell

getSurfaces()

Build and return the slab.Surface objects for all surfaces.

Return type

list of slab.Surface

Returns

contains surface objects

writeSurfaces(file_name)

Write surfaces to a Maestro file with the given file name.

Parameters

file_name (str) – file name of the Maestro file

runIt()

Create the surfaces.

class schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces(ref_surfaces, ads_surfaces, interface_kwargs=None, logger=None)

Bases: object

Manage the enumeration of interfaces.

__init__(ref_surfaces, ads_surfaces, interface_kwargs=None, logger=None)

Create an instance.

Parameters

• ref_surfaces (list of schrodinger.structure.Structure) – reference surface ASUs from which interfaces will be created

• ads_surfaces (list of schrodinger.structure.Structure) – adsorption surface ASUs from which interfaces will be created

• interface_kwargs (None or dict) – kwargs for the interface builds or None if there are none in which case the defaults will be used

• logger (logging.Logger or None) – output logger or None if there isn’t one

logParams()

Log the parameters.

getInterface(ref_surface, ads_surface)

Build and return a interface_mod.Interface.

Parameters

• ref_surface (schrodinger.structure.Structure) – reference surface ASU

• ads_surface (schrodinger.structure.Structure) – adsorption surface ASU

Return type

interface_mod.Interface

Returns

the interface object

getInterfaces()

Build and return the interface_mod.Interface objects for all interfaces.

Return type

list of interface_mod.Interface

Returns

contains interface objects

writeInterfaces(file_name)

Write interfaces to a Maestro file with the given file name.

Parameters

file_name (str) – file name of the Maestro file

runIt()

Create the interfaces.

class schrodinger.application.matsci.nano.surfaces_interfaces_mod.SurfacesInterfaces(ref_xtal_asu, ref_surface_kwargs=None, ads_xtal_asu=None, ads_surface_kwargs=None, interface_kwargs=None, logger=None)

Bases: object

Manage the enumeration of surfaces and interfaces.

__init__(ref_xtal_asu, ref_surface_kwargs=None, ads_xtal_asu=None, ads_surface_kwargs=None, interface_kwargs=None, logger=None)

Create an instance.

Parameters

• ref_xtal_asu (schrodinger.structure.Structure) – the crystalline ASU from which to create reference surfaces

• ref_surface_kwargs (None or dict) – kwargs for the reference surface build or None if there are none in which case the defaults will be used

• ads_xtal_asu (None or schrodinger.structure.Structure) – the crystalline ASU from which to create adsorption surfaces or None if interfaces are not needed

• ads_surface_kwargs (None or dict) – kwargs for the adsorption surface build or None if there are none in which case the defaults will be used

• interface_kwargs (None or dict) – kwargs for the interface build or None if there are none in which case the defaults will be used

• logger (logging.Logger or None) – output logger or None if there isn’t one

checkInput()

Check input.

Raises

ValueError – if any input crystal ASU is missing any lattice parameter structure properties

createSurfaces()

Create the surfaces.

Raises

ValueError – if something goes wrong with either surface build

createInterfaces()

Create the interfaces.

runIt()

Create the surfaces and interfaces.