Python Interface¶

The user Python interface is fairly minimal, with the majority of the code implemented in C++. There are substantial bits of Python code for testing the C++ machinery, but they have been marked as private. The full user Python API is documented in Python API. If you would like to extend the Python API, see developer.

Some common operations using the Python API:

Unique basis set for all atoms¶

Usually, you want to define a unique (the same) basis set for the whole system. This can be done by a function call.

obasis = get_gobasis(coordinates, numbers, 'cc-pvdz')

where mol.coordinates and mol.numbers are numpy arrays (see GOBasis), and cc-pvdz is the cc-pVDZ basis set.

HORTON is distributed with most of the popular basis sets. A list of currently supported built-in basis sets can be found here: Packaged Basis Sets. The basis set for a given molecule is constructed with the function get_gobasis()

Specifying different basis sets for different atoms¶

In some cases, you may want to specify different basis sets for different atoms. For example, you might like to use the 3-21G basis set for the hydrogen atom, the 6-31G basis set for the carbon atom, and STO-3G for all remaining atoms:

obasis = get_gobasis(mol.coordinates, mol.numbers, 'sto-3g',
                     element_map={'H':'3-21g', 'C':'6-31g'})

where mol.coordinates and mol.numbers are read from file (see GOBasis), and sto-3g, 3-21g and 6-31g are the basis set names (see :Packaged Basis Sets).

Alternatively, the same result can be obtained by substituting the H and C symbols with their atomic numbers:

obasis = get_gobasis(mol.coordinates, mol.numbers, 'sto-3g',
                     element_map={1:'3-21g', 6:'6-31g'})

You can also override the default basis for selected atoms based on their index, i.e. position in the list of atoms that specify the molecule:

obasis = get_gobasis(mol.coordinates, mol.numbers, 'sto-3g',
                     index_map={0:'3-21g', 2:'6-31g'})

The above example uses the 3-21g basis for the first atom, the 6-31g basis for the third atom and the sto-3g basis for all other atoms.

Loading custom basis sets from file¶

You can also use other basis sets besides the ones that are shipped with HORTON. It is assumed that the basis is available in NWChem format:

mybasis = GOBasisFamily('myname', filename='mybasis.nwchem'),
obasis = get_gobasis(mol.coordinates, mol.numbers, mybasis)

Anywhere you can specify a built-in basis set with a string, you can also use instance of the GOBasisFamily class (mybasis in the example above), e.g. in the arguments default, element_map and index_map of get_gobasis.

Defining basis sets with Python code¶

In some circumstances, it may be useful to generate the basis set with some Python code. For example, the following code generates an even tempered basis for Lithium (without polarization functions):

data/examples/hamiltonian/even_tempered_li.py¶

import numpy as np

from gbasis import GOBasisContraction, GOBasisAtom, get_gobasis

# specify the even tempered basis set
alpha_low = 5e-3
alpha_high = 5e2
nbasis = 30
lnratio = (np.log(alpha_high) - np.log(alpha_low)) / (nbasis - 1)

# build a list of "contractions". These aren't real contractions as every
# contraction only contains one basis function.
bcs = []
for ibasis in range(nbasis):
    alpha = alpha_low * np.exp(lnratio * ibasis)
    # arguments of GOBasisContraction:
    #     shell_type, list of exponents, list of contraction coefficients
    bcs.append(GOBasisContraction(0, np.array([alpha]), np.array([1.0])))

# Finish setting up the basis set:
ba = GOBasisAtom(bcs)
obasis = get_gobasis(np.array([[0.0, 0.0, 0.0]]), np.array([3]), default=ba)

All basis functions in this example are just single s-type primitives, i.e. no contactions are used. At the end of the example, the basis set is constructed for a single Li atom in the origin.

Note that get_gobasis also accepts instances of GOBasisAtom for the arguments default, element_map and index_map.