Package schrodinger :: Package application :: Package matsci :: Package nano :: Module surfaces_interfaces_mod :: Class Surfaces

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Class Surfaces

object --+
         |
        Surfaces

Manage the enumeration of surfaces.

Instance Methods

[hide private]

__init__(self, xtal_asu, surface_kwargs=None, logger=None)
Create an instance.

list

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

slab.Surface

getSurface(self, cell, hkl, params_only=False, origin=None, logger=None)
Build and return a slab.Surface.

list

getXtalExtents(self)
Return crystal extents that are large enough to ensure proper creation of surface models for all requested surfaces.

logParams(self)
Log the parameters.

schrodinger.structure.Structure

getXtalSuperCell(self)
Build and return the crystal super cell from which surfaces will be created.

list of slab.Surface

getSurfaces(self)
Build and return the slab.Surface objects for all surfaces.

writeSurfaces(self, file_name)
Write surfaces to a Maestro file with the given file name.

runIt(self)
Create the surfaces.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, xtal_asu, surface_kwargs=None, logger=None)
(Constructor)

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

Overrides: object.__init__

getHKLIndices(self)

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

Returns: list

contains sorted tuples of hkl triples

Raises:

ValueError - if there are zero valid hkl triples

getSurface(self, cell, hkl, params_only=False, origin=None, logger=None)

Build and return a slab.Surface.

Parameters:

cell (schrodinger.structure.Structure) - a cell
hkl (tuple) - a triple of Miller indices
params_only (bool) - specifies that only surface parameters are needed, i.e. the surface build exits early
origin (numpy.array or None) - specify the origin or use None to use the default origin
logger (logging.Logger or None) - output logger or None if there isn't one

Returns: slab.Surface

the surface object

getXtalExtents(self)

Return crystal extents that are large enough to ensure proper creation of surface models for all requested surfaces.

Returns: list: integer crystal extents

getXtalSuperCell(self)

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

Returns: schrodinger.structure.Structure: the crystal super cell

getSurfaces(self)

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

Returns: list of slab.Surface: contains surface objects

writeSurfaces(self, file_name)

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

Parameters:

file_name (str) - file name of the Maestro file

Class Surfaces

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

getHKLIndices(self)

getSurface(self, cell, hkl, params_only=False, origin=None, logger=None)

getXtalExtents(self)

getXtalSuperCell(self)

getSurfaces(self)

writeSurfaces(self, file_name)

init(self, xtal_asu, surface_kwargs=None, logger=None)
(Constructor)