chemtools.wrappers.grid.MolecularGrid¶
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class
chemtools.wrappers.grid.MolecularGrid(coordinates, numbers, pseudo_numbers, specification='medium', k=3, rotate=False)[source]¶ Becke-Lebedev molecular grid for numerical integrations.
Initialize class.
Parameters: - coordinates (np.ndarray, shape=(M, 3)) – Cartesian coordinates of M atoms in the molecule.
- numbers (np.ndarray, shape=(M,)) – Atomic number of M atoms in the molecule.
- pseudo_numbers (np.ndarray, shape=(M,)) – Pseudo-number of M atoms in the molecule.
- specification (str, optional) – Specification of grid. Either choose from [‘coarse’, ‘medium’, ‘fine’, ‘veryfine’, ‘ultrafine’, ‘insane’] or provide a string of ‘rname:rmin:rmax:nrad:nang’ format. Here ‘rname’ denotes the type of radial grid and can be chosen from [‘linear’, ‘exp’, ‘power’], ‘rmin’ and ‘rmax’ specify the first and last radial grid points in angstrom, ‘nrad’ specify the number of radial grid points, and ‘nang’ specify the number of angular Lebedev-Laikov grid. The ‘nang’ can be chosen from (6, 14, 26, 38, 50, 74, 86, 110, 146, 170, 194, 230, 266, 302, 350, 434, 590, 770, 974, 1202, 1454, 1730, 2030, 2354, 2702, 3074, 3470, 3890, 4334, 4802, 5294, 5810).
- k (int, optional) – The order of the switching function in Becke’s weighting scheme.
- rotate (bool, optional) – Whether to randomly rotate spherical grids.
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classmethod
from_molecule(molecule, specification='medium', k=3, rotate=False)[source]¶ Initialize the class given an instance of Molecule.
Parameters: - molecule (instance of Molecule) – Instance of Molecule class.
- specification (str, optional) – Specification of grid. Either choose from [‘coarse’, ‘medium’, ‘fine’, ‘veryfine’, ‘ultrafine’, ‘insane’] or provide a string of ‘rname:rmin:rmax:nrad:nang’ format. Here ‘rname’ denotes the type of radial grid and can be chosen from [‘linear’, ‘exp’, ‘power’], ‘rmin’ and ‘rmax’ specify the first and last radial grid points in angstrom, ‘nrad’ specify the number of radial grid points, and ‘nang’ specify the number of angular Lebedev-Laikov grid. The ‘nang’ can be chosen from (6, 14, 26, 38, 50, 74, 86, 110, 146, 170, 194, 230, 266, 302, 350, 434, 590, 770, 974, 1202, 1454, 1730, 2030, 2354, 2702, 3074, 3470, 3890, 4334, 4802, 5294, 5810).
- k (int, optional) – The order of the switching function in Becke’s weighting scheme.
- rotate (bool, optional) – Whether to randomly rotate spherical grids.
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classmethod
from_file(fname, specification='medium', k=3, rotate=False)[source]¶ Initialize the class given an instance of Molecule.
Parameters: - fname (str) – Path to molecule’s files.
- specification (str, optional) – Specification of grid. Either choose from [‘coarse’, ‘medium’, ‘fine’, ‘veryfine’, ‘ultrafine’, ‘insane’] or provide a string of ‘rname:rmin:rmax:nrad:nang’ format. Here ‘rname’ denotes the type of radial grid and can be chosen from [‘linear’, ‘exp’, ‘power’], ‘rmin’ and ‘rmax’ specify the first and last radial grid points in angstrom, ‘nrad’ specify the number of radial grid points, and ‘nang’ specify the number of angular Lebedev-Laikov grid. The ‘nang’ can be chosen from (6, 14, 26, 38, 50, 74, 86, 110, 146, 170, 194, 230, 266, 302, 350, 434, 590, 770, 974, 1202, 1454, 1730, 2030, 2354, 2702, 3074, 3470, 3890, 4334, 4802, 5294, 5810).
- k (int, optional) – The order of the switching function in Becke’s weighting scheme.
- rotate (bool, optional) – Whether to randomly rotate spherical grids.
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coordinates¶ Cartesian coordinates of atomic centers.
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numbers¶ Atomic number of atomic centers.
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pseudo_numbers¶ Pseudo atomic number of atomic centers.
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npoints¶ Number of grid points.
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points¶ Cartesian coordinates of grid points.
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weights¶ Integration weight of grid points.