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

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Module slab

Classes and functions to create surface models.

Classes

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ParserWrapper
Manages the argparse module to parse user command line arguments.

CheckInput
Manage checking user input.

Surface
Manage the building of a surface model.

Functions

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list

get_lattice_parameters(astructure)
Return the a, b, c, alpha, beta, and gamma lattice parameters.

tuple

get_hkl(astructure)
Return an hkl Miller index triple for the given structure.

schrodinger.structure.Structure and four numpy.array

maestro_rotate_cell(astructure, origin, a_vec, b_vec, c_vec)
Rotate the cell for proper Maestro view.

Variables

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__doc__ = ...

_version = '$Revision 0.0 $'

XYZ_VECTORS = [array([ 1., 0., 0.]), array([ 0., 1., 0.]),...

OUTFILE_SUFFIX = '-surface'

H_INDEX_DEFAULT = 1

K_INDEX_DEFAULT = 1

L_INDEX_DEFAULT = 0
hash(x)

MIN_IDX_DEFAULT = 0
hash(x)

MAX_IDX_DEFAULT = 1

H_INDEX_MIN_DEFAULT = 0
hash(x)

H_INDEX_MAX_DEFAULT = 1

K_INDEX_MIN_DEFAULT = 0
hash(x)

K_INDEX_MAX_DEFAULT = 1

L_INDEX_MIN_DEFAULT = 0
hash(x)

L_INDEX_MAX_DEFAULT = 1

ANGSTROM_DEFAULT = False
hash(x)

NONE = None
hash(x)

BOTTOM_DEFAULT = 0.0

SLAB_THICKNESS_DEFAULT = 1.0

VACUUM_THICKNESS_DEFAULT = 2.0

NANOPARTICLE_SHAPE = 'parallelepiped'

PARALLELEPIPED_SIDE_FACES = [1, 2, 4, 5]

ALLOW_FRAGMENTS = False
hash(x)

H_INDEX_KEY = 'i_matsci_h_Miller_idx'

K_INDEX_KEY = 'i_matsci_k_Miller_idx'

L_INDEX_KEY = 'i_matsci_l_Miller_idx'

HKL_INDEX_KEYS = ['i_matsci_h_Miller_idx', 'i_matsci_k_Miller_...

C_BUFFER_LEN_ANG = 5.0

__package__ = 'schrodinger.application.matsci.nano'

Function Details

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get_lattice_parameters(astructure)

Return the a, b, c, alpha, beta, and gamma lattice parameters.

Parameters:

astructure (schrodinger.structure.Structure) - the structure for which you want the lattice parameters

Returns: list

the a, b, c, alpha, beta, and gamma lattice parameters

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

Returns: tuple

hkl Miller index triple

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

Returns: schrodinger.structure.Structure and four numpy.array

rotated structure and vectors

Variables Details

[hide private]

doc

Value:

"""
Classes and functions to create surface models.

Copyright Schrodinger, LLC.  All rights reserved."""

XYZ_VECTORS

Value:

[array([ 1.,  0.,  0.]),
 array([ 0.,  1.,  0.]),
 array([ 0.,  0.,  1.])]

HKL_INDEX_KEYS

Value:

['i_matsci_h_Miller_idx',
 'i_matsci_k_Miller_idx',
 'i_matsci_l_Miller_idx']