def setUp(self):
"""Initializes unit tests."""
# Tools of Gaussian type orbitals
from BioNanoLEGO.GaussBasis.Tools import get_basis_data
# Sets the minimum number of correct digits
self.MIN_DIGITS = 8
# Test of hydrogen with cc-pcvdz basis set
self.basis_data = get_basis_data('cc-pcvdz',int(1))
self.atom_idx = int(1)
self.atom_coords = [0.0]*3
self.ref_spher_coefs = [[[0.34068906546973732,0.57789076418581309, \
0.65773997994295252,0.26141493616307782], \
[0.00000000000000000,0.00000000000000000, \
0.00000000000000000,0.52153672708181154]], \
[[1.9584045348700287]]]
return
def __init__(self,molecule,basis_set=DEFAULT_BASIS,atom_basis=[]):
"""Initializes the real solid-harmonic Gaussians.
molecule: The molecule class defined in Molecule.py.
basis_set: A string like '6-31G**' gives the basis set for all atoms,
except for those specified by keyword atom_basis. Default is 6-31G**.
atom_basis: A list like [['6-31G**',xrange(4)], ['cc-pVDZ',[1,4,5]], ['STO-6G',6]]
specifying individual basis set for each atom. The indices of atoms
start from 0, and ends at the number of atoms minus 1. Note here,
the atom with index 1 is given two basis set '6-31G**' and 'cc-pVDZ',
which is useful for auxiliary basis sets. Default is [].
"""
# Shell of real solid-harmonic Gaussians
from BioNanoLEGO.GaussBasis.Shell import SpherShell
num_atoms = len(molecule)
# Generates the list of basis sets of atoms in the molecule
list_basis = [[]]*num_atoms
for each_basis,atom_group in atom_basis:
# List of atoms, such as ['6-31G**',xrange(4)], or ['cc-pVDZ',[1,4,5]]
try:
for atom_idx in atom_group:
if 0 <= atom_idx < num_atoms:
# Appends auxiliary basis set
if list_basis[atom_idx]:
list_basis[atom_idx].append(each_basis)
else:
list_basis[atom_idx] = [each_basis]
else:
raise IndexError("Atom index %d out of range!" %atom_idx)
# single atom, such as ['STO-3G',6]
except:
if 0 <= atom_group < num_atoms:
# Appends auxiliary basis set
if list_basis[atom_group]:
list_basis[atom_group].append(each_basis)
else:
list_basis[atom_group] = [each_basis]
else:
raise IndexError("Atom index %d out of range!" %atom_idx)
# Shell list
self.shells = []
self.num_shells = int(0)
self.num_basis_functions = int(-1)
# Start index of the basis functions in each shell, in the list of [-1,i1,i2,...,i_nshell]
self.idx_shell = [int(-1)]
# Index of list of atomic basis sets
atom_idx = int(0)
# Generates the basis set(s) for each atom
for atom in molecule.atoms: #FIXME: I really do not want to touch the attribute of molecule!
atom_id = atom.getAtomID()
atom_coords = atom.getCoords()
# Gets the list of basis set(s) for this atom
if list_basis[atom_idx]:
list_atom_basis = list_basis[atom_idx]
else:
list_atom_basis = [basis_set]
# Loops over all the basis set(s) for this atom
for each_basis in list_atom_basis:
basis_data = get_basis_data(each_basis,atom.getAtomicNumber())
# Shell by shell
for ang_number,expnts,coefs_shell in basis_data:
shell_data = SpherShell(atom_id,atom_coords,ang_number,expnts,coefs_shell)
self.shells.append(shell_data)
self.num_shells += 1
self.num_basis_functions += shell_data.getNumContrs()*(2*shell_data.ang_number+1)
self.idx_shell.append(self.num_basis_functions)
atom_idx += 1
# Since we first set the number of basis functions as -1
self.num_basis_functions += 1
