schrodinger.application.matsci.nano.interface_mod module¶
Classes and functions to create interface models.
Copyright Schrodinger, LLC. All rights reserved.
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schrodinger.application.matsci.nano.interface_mod.
get_formulas_basename
(unit_cell_1, unit_cell_2)¶ Return a formatted basename containing the two unit cell formulas for the given two unit cells.
Parameters: - unit_cell_1 (
schrodinger.structure.Structure
) – the first unit cell - unit_cell_2 (
schrodinger.structure.Structure
) – the second unit cell
Return type: str
Returns: the formatted basename containing the two unit cell formulas
- unit_cell_1 (
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schrodinger.application.matsci.nano.interface_mod.
lcm_approx
(smaller, larger, tolerance=0.0, max_mult=10, threshold=1e-10)¶ From the two given numbers return two least common multiples (LCMs) that are within the specified tolerance of each other. If the numbers are integers and the tolerance is zero then this function is equivalent to the traditional LCM and the two returned LCMs will be identical integers. Raise a ValueError if either integer multiplier is larger than the given maximum.
Parameters: - smaller (float) – the smaller number
- larger (float) – the larger number
- tolerance (float) – a parameter controlling the extent to which two floats may be considered equivalent
- max_mult (int) – the maximum allowable multiplier, supported to avoid potentially very long loops given that the inputs are floats compared using a specified tolerance
- threshold (float) – a parameter controlling numerical precision
Raises: ValueError – if either integer multipler is larger than the given maximum
Return type: tuple, tuple
Returns: the first tuple contains the two LCMs, the second contains the two integer multipliers, i.e. those integers which when multiplied by the inputs produce the LCMs
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schrodinger.application.matsci.nano.interface_mod.
list_to_string
(alist, accuracy=3, separator=', ')¶ Return a formatted string containing the floats in the given list rounded to the given accuracy and separated by the given separator.
Parameters: - alist (list) – list of floats
- accuracy (int) – used to round the floats
- separator (str) – used to separate the rounded floats
Return type: str
Returns: the formatted string
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schrodinger.application.matsci.nano.interface_mod.
del_atom_props
(astructure, keys=['s_matsci_f1f2f3', 'r_matsci_f1', 'r_matsci_f2', 'r_matsci_f3'])¶ Delete the given atom properties from the given structure.
Parameters: - astructure (
schrodinger.structure.Structure
) – the structure from which to delete atom properties - keys (list) – keys of atom properties to be deleted
- astructure (
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class
schrodinger.application.matsci.nano.interface_mod.
ParserWrapper
(scriptname, description)¶ Bases:
object
Manages the argparse module to parse user command line arguments.
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loadIt
()¶ Load ParserWrapper with all options.
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loadRequired
()¶ Load ParserWrapper with required options.
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loadOptions
()¶ Load ParserWrapper with options.
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loadCommon
()¶ Load ParserWrapper with common options.
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parseArgs
(args)¶ Parse the command line arguments.
Parameters: args (tuple) – command line arguments
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class
schrodinger.application.matsci.nano.interface_mod.
Interface
(ref_layer, ads_layer, bot_layer='reference', strain_a=0.5, strain_b=0.5, strain_alpha=5.0, strain_beta=5.0, strain_gamma=5.0, separation=0.0, max_extents=10, translate_a=0.0, translate_b=0.0, base_name=None, logger=None)¶ Bases:
object
Manage the building of an interface model.
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MSGWIDTH
= 100¶
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setIsInfinite
()¶ Set the is_infinite attributes.
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setBaseName
()¶ Set a base name.
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setLatticeProperties
()¶ Set lattice parameter attributes for both the reference and adsorption layers.
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setHKL
()¶ Set hkl for both the reference and adsorption layers.
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getExtentsAndStrainedLength
(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
Raises: ValueError – if either extent is larger than the allowable maximum
Return type: tuple, float
Returns: the tuple contains the reference and adsorption layer integer extents, the float is the strained adsorption layer length in units of Angstrom
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getStrainedAngle
(index, strain)¶ Return the strained adsorption layer angle.
Parameters: - index (int) – the angle index
- strain (float) – the allowable amount of strain in degrees
Raises: ValueError – if the reference and adsorption layer angles are not within the specified amount of strain
Return type: float
Returns: strained adsorption layer angle in units of degree
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setStrainedAdsorptionLatticeProperties
(strained_a, strained_b, strained_alpha, strained_beta, 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_alpha (float) – the strained lattice alpha parameter in units of degree
- strained_beta (float) – the strained lattice beta parameter in units of degree
- strained_gamma (float) – the strained lattice gamma parameter in units of degree
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setInterfaceLatticeProperties
()¶ Set the lattice parameter attributes for the interface model.
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logParams
()¶ Log the parameters.
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getOrigin
(lattice_params)¶ Return the origin in units of Angstrom for the given lattice parameters.
Parameters: lattice_params (list) – the six lattice parameters Return type: numpy.array Returns: the origin in units of Angstrom
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translateTopLayer
(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
- ref_layer (
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getInterface
(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
Return type: Returns: the interface model
- ref_layer (
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setInterfaceProperties
()¶ Set some interface properties.
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getUpdatedCParams
(in_params)¶ Return the set of lattice parameters with an updated c parameter.
Parameters: in_params (list) – the six lattice parameters Return type: list Returns: the six lattice parameters with c updated
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buildLayer
(cell, in_params, extents, is_infinite)¶ 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
- is_infinite (bool) – whether the slab cell is infinite
Return type: Returns: extended layer
- cell (
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buildLayers
(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
Return type: schrodinger.structure.Structure
,schrodinger.structure.Structure
Returns: extended reference and adsorption layers
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getStrainedAdsorptionLayer
(ads_layer)¶ Return the strained adsorption layer.
Parameters: ads_layer ( schrodinger.structure.Structure
) – the extended unstrained adsorption layerReturn type: schrodinger.structure.Structure
Returns: the strained adsorption layer
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runIt
()¶ Create the interface model.
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