Package schrodinger :: Package application :: Package matsci :: Package nano :: Module slab :: Class Surface

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Class Surface

object --+
         |
        Surface

Manage the building of a surface model.

Instance Methods

__init__(self, supercell, h_index=1, k_index=1, l_index=0, angstrom=False, bottom=None, slab_thickness=None, vacuum_thickness=None, term_frag='hydrogen', term_bond_length=1.5, allow_fragments=False, logger=None)
Create an instance.

setDefaults(self)
Set some parameters to their default values.

setThicknessVector(self, thickness)
Set the vector that defines the thickness.

updateSlabParameters(self)
Update the parameters defining the slab.

updateOrigin(self)
Update the origin.

orientSurface(self, astructure)
Orient the surface for Maestro view.

float, float

getMinMaxZCoord(self)
Return the minimum and maximum atomic z-coordinates of the surface model.

float

getThickness(self)
Determine the length of the thickness vector.

translateSurface(self)
Translate the surface to z = 0.0 along the z-axis.

unsetSurfaceProperties(self)
Unset surface properties.

setSurfaceLatticeProperties(self)
Set surface lattice properties.

setSurfaceOtherProperties(self)
Set surface other properties.

printParams(self)
Log the parameters.

runIt(self, params_only=False)
Create the surface model.

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

Class Variables

NUMDIGITS = 3
hash(x)

MSGWIDTH = 100

Properties

Inherited from object: __class__

Method Details

init(self, supercell, h_index=1, k_index=1, l_index=0, angstrom=False, bottom=None, slab_thickness=None, vacuum_thickness=None, term_frag=`'hydrogen'`, term_bond_length=1.5, allow_fragments=False, logger=None)
(Constructor)

Create an instance.

Parameters:

supercell (schrodinger.structure.Structure) - the crystalline supercell used to define the surface model
h_index (int) - the Miller h-index of the crystal plane to expose
k_index (int) - the Miller k-index of the crystal plane to expose
l_index (int) - the Miller l-index of the crystal plane to expose
angstrom (bool) - specify that slab and vacuum thickness be in units of angstrom rather than inter-planar spacing
bottom (float or None) - the distance along the plane normal to serve as the bottom of the surface model or None if the default is to be used
slab_thickness (float or None) - thickness of the crystalline slab along the c lattice vector or None if the default is to be used
vacuum_thickness (float or None) - thickness of the vacuum layer along the c or None if the default is to be used
term_frag (str) - the fragment by which to terminate the surface model
term_bond_length (float) - the bond length of the bond connecting the surface with the fragment
allow_fragments (bool) - specify if molecular fragments are allowed at the boundary
logger (logging.Logger) - output logger

Overrides: object.__init__

setThicknessVector(self, thickness)

Set the vector that defines the thickness.

Parameters:

thickness (float) - the desired length of the thickness vector in either fractional or Angstrom coordinates

orientSurface(self, astructure)

Orient the surface for Maestro view.

Parameters:

astructure (schrodinger.structure.Structure) - the structure that you want oriented

getMinMaxZCoord(self)

Return the minimum and maximum atomic z-coordinates of the surface model.

Returns: float, float: the min and max z-coordinates

getThickness(self)

Determine the length of the thickness vector.

Returns: float: the thickness to set

runIt(self, params_only=False)

Create the surface model.

Parameters:

params_only (bool) - specifies to exit after the surface parameters have been determined