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_word_list_from_file(afile)

Return a list of words from the given file.

Parameters:afile (str) – file name
Return type:list
Returns:contains words from the given file
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
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.

Raises:ValueError – if there are zero valid hkl triples
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:
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.