1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
|
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test logfiles related to basis sets"""
import os
import unittest
from skip import skipForParser
__filedir__ = os.path.realpath(os.path.dirname(__file__))
class GenericBasisTest(unittest.TestCase):
"""Generic basis set unittest"""
# The number of contraction per atom, by atom number.
contractions = { 1: 1, 6: 3 }
# Number of components in each contraction by subshell type,
# so that we can infer nbasis from gbasis. Note how we assume
# the basis set is not is spherical representation.
names = ['S', 'P', 'D', 'F', 'G']
multiple = {'S': 1, 'P': 3, 'D': 6, 'F': 10, 'G': 15}
multiple_spher = {'S': 1, 'P': 3, 'D': 5, 'F': 7, 'G': 9}
spherical = False
# These are the expected exponents and coefficients for the first
# Gaussians in particular shells for hydrogen and carbon atoms.
gbasis_H_1s_func0 = [3.42525, 0.15433]
gbasis_C_2s_func0 = [2.9412, -0.1000]
gbasis_C_2p_func0 = [2.9412, 0.1559]
@skipForParser('Molcas','The parser is still being developed so we skip this test')
@skipForParser('Turbomole','The parser is still being developed so we skip this test')
def testgbasis(self):
"""Is gbasis the right length?"""
self.assertEquals(self.data.natom, len(self.data.gbasis))
@skipForParser('Molcas','The parser is still being developed so we skip this test')
@skipForParser('Turbomole','The parser is still being developed so we skip this test')
def testnames(self):
"""Are the name of basis set functions acceptable?"""
for atom in self.data.gbasis:
for fns in atom:
self.assert_(fns[0] in self.names,
"%s not one of S or P" % fns[0])
@skipForParser('Molcas','The parser is still being developed so we skip this test')
@skipForParser('Turbomole','The parser is still being developed so we skip this test')
def testsizeofbasis(self):
"""Is the basis set the correct size?"""
total = 0
multiple = self.multiple_spher if self.spherical else self.multiple
for atom in self.data.gbasis:
for (ftype, contraction) in atom:
total += multiple[ftype]
self.assertEquals(self.data.nbasis, total)
@skipForParser('Molcas','The parser is still being developed so we skip this test')
@skipForParser('Turbomole','The parser is still being developed so we skip this test')
def testcontractions(self):
"""Are the number of contractions on all atoms correct?"""
for iatom, atom in enumerate(self.data.gbasis):
atomno = self.data.atomnos[iatom]
self.assertEquals(len(atom), self.contractions[atomno])
@skipForParser('Molcas','The parser is still being developed so we skip this test')
@skipForParser('Turbomole','The parser is still being developed so we skip this test')
def testprimitives(self):
"""Are all primitives 2-tuples?"""
for atom in self.data.gbasis:
for ftype, contraction in atom:
for primitive in contraction:
self.assertEquals(len(primitive), 2)
@skipForParser('Molcas','The parser is still being developed so we skip this test')
@skipForParser('Turbomole','The parser is still being developed so we skip this test')
def testcoeffs(self):
"""Are the atomic basis set exponents and coefficients correct?"""
for iatom,atom in enumerate(self.data.gbasis):
if self.data.atomnos[iatom] == 1:
coeffs = atom[0][1]
self.assertAlmostEqual(coeffs[0][0], self.gbasis_H_1s_func0[0], 4)
self.assertAlmostEqual(coeffs[0][1], self.gbasis_H_1s_func0[1], 4)
else:
s_coeffs = atom[1][1]
p_coeffs = atom[2][1]
self.assertAlmostEqual(s_coeffs[0][0], self.gbasis_C_2s_func0[0], 4)
self.assertAlmostEqual(p_coeffs[0][0], self.gbasis_C_2p_func0[0], 4)
self.assertAlmostEqual(s_coeffs[0][1], self.gbasis_C_2s_func0[1], 4)
self.assertAlmostEqual(p_coeffs[0][1], self.gbasis_C_2p_func0[1], 4)
class JaguarBasisTest(GenericBasisTest):
"""Customized basis set unittest"""
# For some reason, Jaguar seems to use slightly different coefficients for
# contractions in the STO-3G basis set. Or perhaps we don't understand something.
gbasis_H_1s_func0 = [3.42525, 0.24050]
gbasis_C_2s_func0 = [2.941249, -0.29565]
gbasis_C_2p_func0 = [2.941249, 0.22135]
class GenericBigBasisTest(GenericBasisTest):
"""Generic big basis set unittest"""
contractions = { 6: 20 }
@unittest.skip('Write up a new test, and/or revise the one inherited.')
def testcoeffs(self):
"""Are the basis set coefficients correct?"""
self.assertEqual(1, 1)
@unittest.skip('# of contractions is 20 for VQZ, but 29 for CVQZ; unify files first.')
def testcontractions(self):
""""""
self.assertEqual(1, 1)
class DALTONBigBasisTest(GenericBigBasisTest):
"""Customized big basis set unittest"""
spherical = True
class GaussianBigBasisTest(GenericBigBasisTest):
"""Customized big basis set unittest"""
spherical = True
class JaguarBigBasisTest(GenericBigBasisTest):
"""Customized big basis set unittest"""
spherical = True
# Jaguar only goes up to F functions.
names = ['S', 'P', 'D', 'F']
class MolcasBigBasisTest(GenericBigBasisTest):
"""Customized big basis set unittest"""
spherical = True
class MolproBigBasisTest(GenericBigBasisTest):
"""Customized big basis set unittest"""
spherical = True
class Psi4BigBasisTest(GenericBigBasisTest):
"""Customized big basis set unittest"""
spherical = True
class QChemBigBasisTest(GenericBigBasisTest):
"""Customized big basis set unittest"""
spherical = True
if __name__=="__main__":
import sys
sys.path.insert(1, os.path.join(__filedir__, ".."))
from test_data import DataSuite
suite = DataSuite(['Basis'])
suite.testall()
|
