3.5.5. horton.grid.molgrid – Molecular integration grids¶
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class
horton.grid.molgrid.BeckeMolGrid(*args, **kwargs)¶ Bases:
horton.grid.base.IntGridArguments:
- centers
- An array (N, 3) with centers for the atom-centered grids.
- numbers
- An array (N,) with atomic numbers.
Optional arguments:
- pseudo_numbers
- An array (N,) with effective core charges. When not given, this
defaults to
numbers. - agspec
- A specifications of the atomic grid. This can either be an instance of the AtomicGridSpec object, or the first argument of its constructor.
- k
- The order of the switching function in Becke’s weighting scheme.
- random_rotate
- Flag to control random rotation of spherical grids.
- mode
Select one of the following options regarding atomic subgrids:
'discard'(the default) means that all information about subgrids gets discarded.'keep'means that a list of subgrids is kept, including the integration weights of the local grids.'only'means that only the subgrids are constructed and that the computation of the molecular integration weights (based on the Becke partitioning) is skipped.
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__init__(*args, **kwargs)¶ Arguments:
- centers
- An array (N, 3) with centers for the atom-centered grids.
- numbers
- An array (N,) with atomic numbers.
Optional arguments:
- pseudo_numbers
- An array (N,) with effective core charges. When not given, this
defaults to
numbers. - agspec
- A specifications of the atomic grid. This can either be an instance of the AtomicGridSpec object, or the first argument of its constructor.
- k
- The order of the switching function in Becke’s weighting scheme.
- random_rotate
- Flag to control random rotation of spherical grids.
- mode
Select one of the following options regarding atomic subgrids:
'discard'(the default) means that all information about subgrids gets discarded.'keep'means that a list of subgrids is kept, including the integration weights of the local grids.'only'means that only the subgrids are constructed and that the computation of the molecular integration weights (based on the Becke partitioning) is skipped.
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eval_decomposition(*args, **kwargs)¶ Evaluate a spherical decomposition
Arguments:
- cubic_splines
- A list cubic splines, where each item is a radial function that is associated with a corresponding real spherical harmonic.
- center
- The center of the spherically symmetric function
- output
- The output array
Optional arguments:
- cell
- A unit cell when periodic boundary conditions are used.
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eval_spline(*args, **kwargs)¶ Evaluate a spherically symmetric function
Arguments:
- cubic_spline
- A cubic spline with the radial dependence
- center
- The center of the spherically symmetric function
- output
- The output array
Optional arguments:
- cell
- A unit cell when periodic boundary conditions are used.
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classmethod
from_hdf5(grp)¶
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integrate(*args, **kwargs)¶ Integrate the product of all arguments
Arguments:
- data1, data2, …
- All arguments must be arrays with the same size as the number of grid points. The arrays contain the functions, evaluated at the grid points, that must be multiplied and integrated.
Optional arguments:
- center=None
- When given, multipole moments are computed with respect to this center instead of a plain integral.
- lmax=0
- The maximum angular momentum to consider when computing multipole moments
- mtype=1
- The type of multipole moments: 1=“cartesian“, 2=“pure“, 3=“radial“, 4=“surface“.
- segments=None
- This argument can be used to divide the grid in segments. When given, it must be an array with the number of grid points in each consecutive segment. The integration is then carried out over each segment separately and an array of results is returned. The sum over all elements gives back the total integral.
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to_hdf5(grp)¶
-
zeros()¶
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agspec¶ The specifications of the atomic grids.
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becke_weights¶ The becke weights of the grid points
-
centers¶ The positions of the nuclei
-
k¶ The order of the Becke switching function.
-
mode¶ The MO of this molecular grid
-
numbers¶ The element numbers
-
points¶ The grid points.
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pseudo_numbers¶ The effective core charges
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random_rotate¶ The random rotation flag.
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shape¶ The shape of the grid.
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size¶ The size of the grid.
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subgrids¶ A list of grid objects used to construct this grid.
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weights¶ The grid weights.