schrodinger.application.matsci.nano.slab module

Classes and functions to create surface models.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.nano.slab.ParserWrapper(scriptname, description)

Bases: object

Manages the argparse module to parse user command line arguments.

__init__(scriptname, description)

Create a ParserWrapper instance and process it.

Parameters

  • scriptname (str) – name of this script

  • description (str) – description of this script

loadIt()

Load ParserWrapper with all options.

loadHKLOptions()

Load ParserWrapper with hkl options.

loadOptions()

Load ParserWrapper with options.

loadEnumeration()

Load ParserWrapper with enumeration options.

loadRequired()

Load ParserWrapper with required options.

loadCommon()

Load ParserWrapper with common options.

parseArgs(args)

Parse the command line arguments.

Parameters

args (tuple) – command line arguments

class schrodinger.application.matsci.nano.slab.Surface(cell, h_index=1, k_index=1, l_index=0, normal_c=False, bottom=0.0, slab_thickness=1.0, vacuum_thickness=2.0, terminal_fragment='none', overlap_threshold=0.1, do_bonding=None, do_bond_orders=True, surface_st=None, logger=None)

Bases: object

Manage the building of a surface model.

NUMDIGITS = 3
MSGWIDTH = 100
__init__(cell, h_index=1, k_index=1, l_index=0, normal_c=False, bottom=0.0, slab_thickness=1.0, vacuum_thickness=2.0, terminal_fragment='none', overlap_threshold=0.1, do_bonding=None, do_bond_orders=True, surface_st=None, logger=None)

Create an instance.

Parameters

  • cell (schrodinger.structure.Structure) – the crystalline cell 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

  • bottom (float or None) – the distance along the plane normal in fractional coordinates to serve as the bottom of the surface model

  • slab_thickness (float or None) – thickness of the crystalline slab along the plane normal in fractional coordinates

  • vacuum_thickness (float or None) – thickness of the vacuum layer along the plane normal in fractional coordinates

  • terminal_fragment (str) – the fragment by which to terminate the surface

  • overlap_threshold (float) – (Ang) distance used to define overlapping atoms

  • do_bonding (bool or None) – whether to do the bonding, i.e. connecting atoms, see do_bond_orders kwarg for assigning bond orders, if None it is determined from the other input

  • do_bond_orders (bool) – whether to do the bond orders, used only if bonding is enabled

  • surface_st (structure.Structure) – If passed, atom coordinates and PBC will be used after the surface is built, but before any other manipulations (generate normal for example).

  • logger (logging.Logger) – output logger

getLatticeProperties(cell)

Get the lattice properties.

Raise

ValueError if missing PDB PBC

buildSlab()

Build the slab.

pruneIt()

Prune the slab cell.

Raise

ValueError if the slab model has zero atoms

Return type

dict

Returns

contains bonding pairs that need termination, keys are outside atom indices, values are inside atom indices

doTermination(terminal_pairs_dict)

Do the termination.

Parameters

terminal_pairs_dict (dict) – contains bonding pairs that need termination, keys are outside atom indices, values are inside atom indices

addVacuum()

Add vacuum.

setSurfaceProperties()

Set surface properties.

printParams()

Log the parameters.

runIt()

Create the surface model.

schrodinger.application.matsci.nano.slab.get_hkl(astructure)

Return an hkl Miller index triple for the given structure. If any of the structure properties are missing then by convention return (0, 0, 1).

Parameters

astructure (schrodinger.structure.Structure) – the structure for which you want the Miller indices

Return type

tuple

Returns

hkl Miller index triple

schrodinger.application.matsci.nano.slab.set_hkl(astructure, hkl)

Set hkl Miller indices to a given structure.

Parameters
schrodinger.application.matsci.nano.slab.maestro_rotate_cell(astructure, origin, a_vec, b_vec, c_vec)

Rotate the cell for proper Maestro view.

Parameters

  • astructure (schrodinger.structure.Structure) – the structure that you want rotated

  • origin (numpy.array) – the origin

  • a_vec (numpy.array) – the a lattice vector

  • b_vec (numpy.array) – the b lattice vector

  • c_vec (numpy.array) – the c lattice vector

Return type

schrodinger.structure.Structure and four numpy.array

Returns

rotated structure and vectors