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', do_bonding=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', do_bonding=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
  • do_bonding (bool or None) – whether to do the bonding, i.e. both connecting atoms and assigning bond orders, if None it is determined from the other input
  • 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:
  • astructure (schrodinger.structure.Structure) – the structure for which you want the Miller indices
  • hkl (list) – hkl Miller indices
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