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

[frames] | no frames]

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=0.0, slab_thickness=1.0, vacuum_thickness=2.0, term_frag='hydrogen', term_bond_length=1.5, allow_fragments=False, logger=None)
Create an instance.

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

updateSlabParameters(self)
Update the parameters defining the slab.

numpy.array

updateOrigin(self, origin)
Update the origin.

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

float

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

unsetSurfaceProperties(self)
Unset surface properties.

setSurfaceProperties(self)
Set surface properties.

printParams(self)
Log the parameters.

runIt(self)
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

THRESHOLD = 0.0001

Properties

Inherited from object: __class__

Method Details

init(self, supercell, h_index=1, k_index=1, l_index=0, angstrom=False, bottom=0.0, slab_thickness=1.0, vacuum_thickness=2.0, 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) - the distance along the plane normal to serve as the bottom of the surface model
slab_thickness (float) - thickness of the crystalline slab along the c lattice vector
vacuum_thickness (float) - thickness of the vacuum layer along the c
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

updateOrigin(self, origin)

Update the origin.

Parameters:

origin (numpy.array) - the origin

Returns: numpy.array

updated origin

orientSurface(self, astructure)

Orient the surface for Maestro view.

Parameters:

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

translateSurface(self)

Translate the surface to z = 0.0 along the z-axis.

Returns: float: the minimum distance along z to a non-terminating atom, if no termination is performed then this is the amount by which the surface was translated