Package schrodinger :: Package application :: Package jaguar :: Module basis

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Module basis

Utility functions for dealing with Jaguar basis sets

Classes

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_BasisSet
BasisSet(name, backup, nstar, nplus, is_ecp, is_ps, numd, numf)

BasisSet
A Pythonic wrapper for basis set information.

Functions

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mmjag_function(func)
A decorator that wraps functions with mmjag_initialize and mmjag_terminate.

BasisSet

get_basis(*args, **kwargs)
Get information about the specified basis set

BasisSet

get_basis_by_name(*args, **kwargs)
Get information about the specified basis set

iter

get_bases()
Get information about all basis set

str

default_basis(*args, **kwargs)
Get the default basis set for the specified structure.

tuple

num_functions(*args, **kwargs)
Calculate the number of basis functions that will be used for the given basis set and structure

tuple

num_functions_per_atom(*args, **kwargs)
Calculate the number of basis functions that will be used for the given basis set and specified atom

tuple

num_functions_all_atoms(*args, **kwargs)
Calculate the number of basis functions that will be used for the given basis set and structure

tuple

parse_basis(basis)
Parse the given basis set name and determine that number of *'s and +'s.

Variables

[hide private]

DUMMY_ATOM_TYPES = set([61, 150])

__package__ = 'schrodinger.application.jaguar'

Function Details

[hide private]

get_basis(*args, **kwargs)

Get information about the specified basis set

Parameters:

i (int) - The index of the basis set to get information about

Returns: BasisSet

Information about the specified basis set

Decorators:

@mmjag_function

get_basis_by_name(*args, **kwargs)

Get information about the specified basis set

Parameters:

i (int) - The name of the basis set to get information about

Returns: BasisSet

Information about the specified basis set

Decorators:

@mmjag_function

get_bases()

Get information about all basis set

Returns: iter: An iterator for basis sets, where each basis set is returned as a BasisSet object

default_basis(*args, **kwargs)

Get the default basis set for the specified structure.

Parameters:

struc (schrodinger.structure.Structure or NoneType) - The structure to retrieve the default basis set for. If not given, then the default basis set (6-31G**) will be returned.

Returns: str

The appropriate default basis set

Decorators:

@mmjag_function

num_functions(*args, **kwargs)

Calculate the number of basis functions that will be used for the given basis set and structure

Parameters:

basis_name (str) - The basis set to determine the number of basis functions for
struc (schrodinger.structure.Structure) - The structure to determine the number of basis functions for
func_type (int) - Whether d and f functions are counted as Cartesian or non- Cartesian. Must be one of mm.MMJAG_BASIS_DEFAULT, mm.MMJAG_BASIS_CARTESIAN, or mm.MMJAG_BASIS_NONCARTESIAN.

Returns: tuple

A tuple of

The number of basis functions (int). Will be zero if the basis set does not cover all atoms of the structure.
Are pseudospectral calculations possible (bool)

Decorators:

@mmjag_function

num_functions_per_atom(*args, **kwargs)

Calculate the number of basis functions that will be used for the given basis set and specified atom

Parameters:

basis_name (str) - The basis set
struc (schrodinger.structure.Structure) - The structure containing atom_num
atom_num (int) - The atom index in struc to calculate the number of basis functions for
func_type (int) - Whether d and f functions are counted as Cartesian or non- Cartesian. Must be one of mm.MMJAG_BASIS_DEFAULT, mm.MMJAG_BASIS_CARTESIAN, or mm.MMJAG_BASIS_NONCARTESIAN.

Returns: tuple

A tuple of

The number of basis functions (int). Will be zero if the basis set does not cover the atom.
Are pseudospectral calculations possible (bool)

Decorators:

@mmjag_function

num_functions_all_atoms(*args, **kwargs)

Calculate the number of basis functions that will be used for the given basis set and structure

Parameters:

basis_name (str) - The basis set to determine the number of basis functions for
struc (schrodinger.structure.Structure) - The structure to determine the number of basis functions for
per_atom (dict) - An optional dictionary of {atom index: basis name} for per-atom basis sets.
func_type (int) - Whether d and f functions are counted as Cartesian or non- Cartesian. Must be one of mm.MMJAG_BASIS_DEFAULT, mm.MMJAG_BASIS_CARTESIAN, or mm.MMJAG_BASIS_NONCARTESIAN.

Returns: tuple

A tuple of

The number of basis functions for the entire structure (int). Will be zero if the basis sets do not cover all atoms of the structure.
Are pseudospectral calculations possible (bool)
A list of the number of basis functions per atom (util.OneIndexedList)

Decorators:

@mmjag_function

parse_basis(basis)

Parse the given basis set name and determine that number of *'s and +'s.

Parameters:

basis (str) - The full basis set name

Returns: tuple

A tuple of

The basis set name with the *'s and +'s stripped (str)
The polarization function count (i.e. the number of *'s) (int)
The diffuse function count (i.e. the number of +'s) (int)