Package schrodinger :: Package application :: Package matsci :: Package nano :: Module interface_mod :: Class Interface

Class Interface

object --+
         |
        Interface

Manage the building of an interface model.

Instance Methods

[hide private]

__init__(self, ref_layer, ads_layer, bot_layer='reference', strain_a=0.5, strain_b=0.5, strain_gamma=5.0, separation=0.0, max_extents=10, translate_a=0.0, translate_b=0.0, base_name=None, logger=None)
Create an instance.

setBaseName(self)
Set a base name.

setLatticeProperties(self)
Set lattice parameter attributes for both the reference and adsorption layers.

setHKL(self)
Set hkl for both the reference and adsorption layers.

tuple, float

getExtentsAndStrainedLength(self, index, strain)
For the lattice vector specified with the given index return (1) the reference and adsorption layer extents necessary to bring the extended lengths to within the specified amount of strain and (2) the strained adsorption layer length.

float

getStrainedAngle(self)
Return the strained adsorption layer angle.

setStrainedAdsorptionLatticeProperties(self, strained_a, strained_b, strained_gamma)
Set the strained lattice parameter attributes for the adsorption layer.

setInterfaceLatticeProperties(self)
Set the lattice parameter attributes for the interface model.

logParams(self)
Log the parameters.

numpy.array

getOrigin(self, lattice_params)
Return the origin in units of Angstrom for the given lattice parameters.

translateTopLayer(self, ref_layer, ads_layer)
Translate the top layer.

schrodinger.structure.Structure

getInterface(self, ref_layer, ads_layer)
Build the interface model from the two finalized layers and return it.

setInterfaceProperties(self)
Set some interface properties.

list

getUpdatedCParams(self, in_params)
Return the set of lattice parameters with an updated c parameter.

schrodinger.structure.Structure

buildLayer(self, cell, in_params, extents)
Build a layer by extending the input slab cell, also eliminate any PBC bonds along the c lattice vector.

schrodinger.structure.Structure, schrodinger.structure.Structure

buildLayers(self, ref_extents, ads_extents)
Build the reference and adsorption layers by extending the input slab cells, also eliminate any PBC bonds along the c lattice vector.

schrodinger.structure.Structure

getStrainedAdsorptionLayer(self, ads_layer)
Return the strained adsorption layer.

runIt(self)
Create the interface model.

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

Class Variables

[hide private]

MSGWIDTH = 100

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, ref_layer, ads_layer, bot_layer=`'reference'`, strain_a=0.5, strain_b=0.5, strain_gamma=5.0, separation=0.0, max_extents=10, translate_a=0.0, translate_b=0.0, base_name=None, logger=None)
(Constructor)

Create an instance.

Parameters:

ref_layer (schrodinger.structure.Structure) - the reference layer used to define the interface model
ads_layer (schrodinger.structure.Structure) - the adsorption layer used to define the interface model
bot_layer (str) - specifies which layer, reference or adsorption, is the bottom layer of the interface model
strain_a (float) - the amount of strain allowed along the a lattice vector of the adsorption layer in units of Angstrom
strain_b (float) - the amount of strain allowed along the b lattice vector of the adsorption layer in units of Angstrom
strain_gamma (float) - the amount of strain allowed along the gamma angle of the adsorption layer in units of degrees
separation (float) - the separation between the reference and adsorption layers in units of Angstrom
max_extents (int) - the maximum allowable extent
translate_a (float) - the amount by which to translate the top layer, relative to the bottom layer, along the a lattice vector
translate_b (float) - the amount by which to translate the top layer, relative to the bottom layer, along the b lattice vector
base_name (str) - a base name used to name output
logger (logging.Logger) - output logger

Overrides: object.__init__

getExtentsAndStrainedLength(self, index, strain)

For the lattice vector specified with the given index return (1) the reference and adsorption layer extents necessary to bring the extended lengths to within the specified amount of strain and (2) the strained adsorption layer length.

Parameters:

index (int) - an index used to specify along which direction to get the extents, i.e. 0 is a, 1 is b, 2 is c
strain (float) - the amount of strain allowed along the given lattice vector of the adsorption layer in units of Angstrom

Returns: tuple, float

the tuple contains the reference and adsorption layer integer extents, the float is the strained adsorption layer length in units of Angstrom

Raises:

ValueError - if either extent is larger than the allowable maximum

getStrainedAngle(self)

Return the strained adsorption layer angle.

Returns: float

strained adsorption layer angle in units of degree

Raises:

ValueError - if the reference and adsorption layer gamma angles are not within the specified amount of strain

setStrainedAdsorptionLatticeProperties(self, strained_a, strained_b, strained_gamma)

Set the strained lattice parameter attributes for the adsorption layer.

Parameters:

strained_a (float) - the strained lattice a parameter in units of Angstrom
strained_b (float) - the strained lattice b parameter in units of Angstrom
strained_gamma (float) - the strained lattice gamma parameter in units of degree

getOrigin(self, lattice_params)

Return the origin in units of Angstrom for the given lattice parameters.

Parameters:

lattice_params (list) - the six lattice parameters

Returns: numpy.array

the origin in units of Angstrom

translateTopLayer(self, ref_layer, ads_layer)

Translate the top layer.

Parameters:

ref_layer (schrodinger.structure.Structure) - the reference layer
ads_layer (schrodinger.structure.Structure) - the adsorption layer

getInterface(self, ref_layer, ads_layer)

Build the interface model from the two finalized layers and return it.

Parameters:

ref_layer (schrodinger.structure.Structure) - the final reference layer
ads_layer (schrodinger.structure.Structure) - the final adsorption layer

Returns: schrodinger.structure.Structure

the interface model

getUpdatedCParams(self, in_params)

Return the set of lattice parameters with an updated c parameter.

Parameters:

in_params (list) - the six lattice parameters

Returns: list

the six lattice parameters with c updated

buildLayer(self, cell, in_params, extents)

Build a layer by extending the input slab cell, also eliminate any PBC bonds along the c lattice vector.

Parameters:

cell (schrodinger.structure.Structure) - slab cell to extend
in_params (list) - the six lattice parameters
extents (list) - extents for layer

Returns: schrodinger.structure.Structure

extended layer

buildLayers(self, ref_extents, ads_extents)

Build the reference and adsorption layers by extending the input slab cells, also eliminate any PBC bonds along the c lattice vector.

Parameters:

ref_extents (list) - extents for reference layer
ads_extents (list) - extents for adsorption layer

Returns: schrodinger.structure.Structure, schrodinger.structure.Structure

extended reference and adsorption layers

getStrainedAdsorptionLayer(self, ads_layer)

Return the strained adsorption layer.

Parameters:

ads_layer (schrodinger.structure.Structure) - the extended unstrained adsorption layer

Returns: schrodinger.structure.Structure

the strained adsorption layer

Class Interface

__init__(self, ref_layer, ads_layer, bot_layer='reference', strain_a=0.5, strain_b=0.5, strain_gamma=5.0, separation=0.0, max_extents=10, translate_a=0.0, translate_b=0.0, base_name=None, logger=None) (Constructor)

getExtentsAndStrainedLength(self, index, strain)

getStrainedAngle(self)

setStrainedAdsorptionLatticeProperties(self, strained_a, strained_b, strained_gamma)

getOrigin(self, lattice_params)

translateTopLayer(self, ref_layer, ads_layer)

getInterface(self, ref_layer, ads_layer)

getUpdatedCParams(self, in_params)

buildLayer(self, cell, in_params, extents)

buildLayers(self, ref_extents, ads_extents)

getStrainedAdsorptionLayer(self, ads_layer)

init(self, ref_layer, ads_layer, bot_layer=`'reference'`, strain_a=0.5, strain_b=0.5, strain_gamma=5.0, separation=0.0, max_extents=10, translate_a=0.0, translate_b=0.0, base_name=None, logger=None)
(Constructor)