# Source code for moldesign.orbitals.basis

```
# Copyright 2016 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import numpy as np
from moldesign.utils import Attribute
from . import toplevel, MolecularOrbitals
[docs]class PrimitiveBase(object):
def __init__(self, *args, **kwargs):
raise NotImplementedError()
def __call__(self, position):
raise NotImplementedError()
@property
def norm(self, other):
raise NotImplementedError()
@toplevel
[docs]class BasisSet(MolecularOrbitals):
"""
Stores a basis, typically of atomic orbitals.
This is a special orbital type
"""
overlaps = Attribute('_overlaps')
h1e = Attribute('_h1e')
def __init__(self, mol, orbitals, name=None,
h1e=None, overlaps=None,
angulartype=None,
**kwargs):
self.mol = mol
self.orbitals = orbitals
self.coeffs = np.identity(len(self.orbitals))
self.basis = self
self.orbtype = 'aobasis'
self.angulartype = angulartype
assert self.angulartype in (None, 'spherical', 'cartesian')
self.wfn = None
for iorb, orbital in enumerate(self.orbitals):
orbital.index = iorb
orbital.coeffs = self.coeffs[iorb, :]
orbital.basis = self
self.basisname = name
self.h1e = h1e
self.overlaps = overlaps
for kw, val in kwargs.iteritems():
setattr(self, kw, val)
self.on_atom = {}
for fn in self.orbitals:
self.on_atom.setdefault(fn.atom, []).append(fn)
def __call__(self, coords, coeffs=None):
"""Calculate the value of each basis function at the specified coordinates.
Note:
This is just a pass-through to a specific implementation - PYSCF's eval_ao routine
for now.
Args:
coords (Array[length]): List of coordinates.
coeffs (Vector): List of ao coefficients (optional; if not passed, all basis fn
values are returned)
Returns:
Array[length]: if ``coeffs`` is not passed, an array of basis fn values at each
coordinate. Otherwise, a list of orbital values at each coordinate
"""
from moldesign.interfaces.pyscf_interface import basis_values
return basis_values(self.wfn.mol, self, coords, coeffs=coeffs,
positions=self.wfn.positions)
def __repr__(self):
return '<%s (%s) of %s>' % (self.__class__.__name__, self.basisname, self.mol)
@property
def fock(self):
return self.wfn.fock_ao
@property
def density_matrix(self):
return self.wfn.density_matrix_ao
```