def setUp(self):
bfs = BasisFunction('S', [1, 2], [0.5, 0.5])
bfp = BasisFunction('P', [0.01, 0.2, 1], [0.3, 0.4, 0.3])
self.h = Basis('H', [bfs, bfp], 'simple')
bfs = BasisFunction('S', [0.1, 0.4], [0.6, 0.4])
bfp = BasisFunction('P', [0.1, 0.4, 3], [0.2, 0.3, 0.5])
self.c = Basis('C', [bfs, bfp], 'simple')
atoms = OrderedDict([('H', self.h), ('C', self.c)])
self.basis_set = BasisSet(atoms)
def test_write_input(self):
"""Test writing an input to a basis file"""
tmp_basis_file = 'basis.gbs.tmp'
basis_set = BasisSet()
basis_set['H'] = Basis('H', [BasisFunction('S', [1], [1])])
basis_set['O'] = Basis(
'O', [BasisFunction('S', [1], [1]),
BasisFunction('S', [2], [1])])
basis_set['C'] = Basis('C', [
BasisFunction('S', [1], [1]),
BasisFunction('SP', [1, 2], [[0.4, 0.6], [0.1, 0.9]])
])
with open(tmp_basis_file, 'w') as f:
f.write(basis_set.print('gamess'))
tmp_geom_file = 'geom.xyz.tmp'
self.formaldehyde_xyz.write(tmp_geom_file)
tmp_ecp_file = 'ecp.dat.tmp'
ecp = """\
C-ECP GEN 10 2
3 ----- d-ul potential -----
-10.0000000 1 357.3914469
-60.2990287 2 64.6477389
-10.4217834 2 16.0960833
O-ECP NONE"""
with open(tmp_ecp_file, 'w') as f:
f.write(ecp)
tmp_options_file = 'options.dat.tmp'
options_str = ' $CONTRL\n SCFTYP=RHF\n $END\n\n $SCF\n DIRSCF=.TRUE.\n $END\n\n'
with open(tmp_options_file, 'w') as f:
f.write(options_str)
tmp_dat_file = 'dat.tmp'
vec = ' $VEC\n12 23 31\n33241 32523 11.0\n $END'
hess = ' $HESS\n32 43 987\n453 443 11.0\n $END'
data = 'Hey\n' + vec + ' \n random other text\n' + hess + '\n more text\n122\n'
with open(tmp_dat_file, 'w') as f:
f.write(data)
self.g.read(tmp_geom_file, tmp_basis_file, tmp_ecp_file,
tmp_options_file, tmp_dat_file)
tmp_input_file = 'input.inp.tmp'
self.g.write_input(tmp_input_file)
os.remove(tmp_geom_file)
os.remove(tmp_basis_file)
os.remove(tmp_ecp_file)
os.remove(tmp_options_file)
os.remove(tmp_input_file)
os.remove(tmp_dat_file)
def test_change_basis_set(self):
"""Test change_basis_set"""
atoms = OrderedDict([('C', Basis('C',
[BasisFunction('S', [1], [1])]))])
self.basis_set.change_basis_set(atoms)
bad_bs = OrderedDict([('H', 1)])
self.assertRaises(SyntaxError, self.basis_set.change_basis_set,
(bad_bs, ))
def test_getsetdeleq(self):
"""Test __getitem__, __setitem__, __delitem__, and __eq__"""
bfs = BasisFunction('S', [0.2, 0.4], [0.3, 0.7])
b = Basis('B', [bfs])
self.basis_set['B'] = b
self.assertEqual(self.c, self.basis_set['C'])
self.assertEqual(b, self.basis_set['B'])
del self.basis_set['B']
self.assertRaises(KeyError, self.basis_set.__getitem__, 'B')
bfs = BasisFunction('S', [1, 2], [0.5, 0.5])
bfp = BasisFunction('P', [0.01, 0.2, 1], [0.3, 0.4, 0.3])
h = Basis('H', [bfs, bfp])
bfs = BasisFunction('S', [0.1, 0.4], [0.6, 0.4])
bfp = BasisFunction('P', [0.1, 0.4, 3],
[[0.2, 0.3, 0.5], [0.1, 0.3, 0.6]])
c = Basis('C', [bfs, bfp])
atoms = OrderedDict([('H', h), ('C', c)])
atoms = OrderedDict([('H', h)])
basis_set2 = BasisSet(atoms)
self.assertEqual(basis_set2, self.basis_set)
def test_read_basis_set(self):
"""Test reading a basis from a file"""
tmp_basis_file = 'basis.gbs.tmp1'
basis_set = BasisSet()
basis_set['B'] = Basis('B',
[BasisFunction('S', [0.2, 0.4], [0.3, 0.7])])
open(tmp_basis_file, 'w').write(basis_set.print('gamess'))
self.g.read_basis_set(tmp_basis_file)
self.assertEqual(basis_set, self.g.basis_set)
os.remove(tmp_basis_file)
def test_lengetsetdeleq(self):
"""Test __len__, __getitem__ and __setitem__, __delitem__, __eq__"""
self.assertEqual(3, len(self.basis))
bf = BasisFunction('F', [4, 9], [0.1, 0.9])
self.basis[0] = bf
self.assertEqual(bf, self.basis[0])
self.assertRaises(SyntaxError, self.basis.__setitem__, 0, 1)
del self.basis[2]
self.assertRaises(IndexError, self.basis.__getitem__, 2)
basis = Basis('C', [self.bfsp])
basis2 = Basis('C', [self.bfsp])
self.assertEqual(basis, basis2)
def test_decontracted(self):
"""Tests decontraction of basis function"""
bf1 = BasisFunction('S', [1], [1])
bf2 = BasisFunction('S', [2], [1])
decon1 = list(self.bfs.decontracted())
self.assertEqual(decon1[0], bf1)
self.assertEqual(decon1[1], bf2)
bfs1 = BasisFunction('S', [0.1], [1])
bfs2 = BasisFunction('S', [0.4], [1])
bfs3 = BasisFunction('S', [3], [1])
bfp1 = BasisFunction('P', [0.1], [1])
bfp2 = BasisFunction('P', [0.4], [1])
bfp3 = BasisFunction('P', [3], [1])
decon2 = list(self.bfsp.decontracted())
self.assertEqual(decon2[0], bfs1)
self.assertEqual(decon2[1], bfs2)
self.assertEqual(decon2[2], bfs3)
self.assertEqual(decon2[3], bfp1)
self.assertEqual(decon2[4], bfp2)
self.assertEqual(decon2[5], bfp3)
def test_check_coeffs(self):
"""Test check_exps"""
BasisFunction.check_coeffs(np.arange(5))
BasisFunction.check_coeffs(np.arange(9).reshape((3, 3)))
self.assertRaises(ValueError, BasisFunction.check_exps,
np.arange(8).reshape((2, 2, 2)))
def test_check_exps(self):
"""Test check_exps"""
BasisFunction.check_exps([1, 2])
self.assertRaises(ValueError, BasisFunction.check_exps, [1, 2, -3])
def setUp(self):
self.bfs = BasisFunction('S', [1, 2], [0.5, 0.5])
self.bfp = BasisFunction('P', [0.01, 0.2, 1], [0.3, 0.4, 0.3])
self.bfd = BasisFunction('D', [1, 2], [[0.3, 0.7], [0.4, 0.6]])
self.bfsp = BasisFunction('SP', [0.1, 0.4, 3],
[[0.2, 0.3, 0.5], [0.1, 0.3, 0.6]])
class TestBasisFunction(unittest.TestCase):
"""Tests a BasisFunction"""
def setUp(self):
self.bfs = BasisFunction('S', [1, 2], [0.5, 0.5])
self.bfp = BasisFunction('P', [0.01, 0.2, 1], [0.3, 0.4, 0.3])
self.bfd = BasisFunction('D', [1, 2], [[0.3, 0.7], [0.4, 0.6]])
self.bfsp = BasisFunction('SP', [0.1, 0.4, 3],
[[0.2, 0.3, 0.5], [0.1, 0.3, 0.6]])
def test_len(self):
"""Test __len__"""
self.assertEqual(2, len(self.bfs))
self.assertEqual(3, len(self.bfp))
self.assertEqual(2, len(self.bfd))
self.assertEqual(3, len(self.bfsp))
def test_getseteq(self):
"""Test __getitem__ and __setitem__"""
# Convert np.array to list to prevent error in case.py as the truth value of an array is ambiguous
self.assertEqual([1.0, 0.5], list(self.bfs[0]))
# Convert to a list of lists
self.assertEqual([[0.01, 0.3], [1.0, 0.3]],
list(map(list, self.bfp[::2])))
self.bfs[0] = [1, 2]
self.assertEqual([1.0, 2], list(self.bfs[0]))
self.assertRaises(ValueError, self.bfs.__setitem__, 1, [1, 2, 4])
self.bfd[0] = [1, 0.2, 0.3]
self.assertEqual([1.0, 0.2, 0.3], list(self.bfd[0]))
self.bfsp[0] = [1, 2, 4]
self.assertEqual([1, 2, 4], list(self.bfsp[0]))
self.assertRaises(ValueError, self.bfsp.__setitem__, 1, [1, 2])
self.assertEqual(self.bfs, self.bfs)
def test_check_exps(self):
"""Test check_exps"""
BasisFunction.check_exps([1, 2])
self.assertRaises(ValueError, BasisFunction.check_exps, [1, 2, -3])
def test_check_coeffs(self):
"""Test check_exps"""
BasisFunction.check_coeffs(np.arange(5))
BasisFunction.check_coeffs(np.arange(9).reshape((3, 3)))
self.assertRaises(ValueError, BasisFunction.check_exps,
np.arange(8).reshape((2, 2, 2)))
def test_exps_coeffs(self):
"""Test exps and coeffs"""
self.assertEqual([1, 2], list(self.bfs.exps))
self.assertEqual([0.3, 0.4, 0.3], list(self.bfp.coeffs))
cs = np.array([[0.3, 0.4], [0.7, 0.6]])
aaa_equal(cs, self.bfd.coeffs)
def test_reprprint(self):
"""Test print"""
s_gamess = '''S 2
1 1.0000000 0.5000000
2 2.0000000 0.5000000
'''
p_gaussian94 = '''P 3
0.0100000 0.3000000
0.2000000 0.4000000
1.0000000 0.3000000
'''
sp_gaussian94 = '''SP 3
0.1000000 0.2000000 0.1000000
0.4000000 0.3000000 0.3000000
3.0000000 0.5000000 0.6000000
'''
self.assertEqual('<BasisFunction S 2>', repr(self.bfs))
self.assertEqual('<BasisFunction P 3>', repr(self.bfp))
self.assertEqual('<BasisFunction SP 3x2>', repr(self.bfsp))
self.assertEqual(s_gamess, self.bfs.print('gamess'))
self.assertEqual(p_gaussian94, self.bfp.print())
self.assertEqual(sp_gaussian94, self.bfsp.print())
def test_decontracted(self):
"""Tests decontraction of basis function"""
bf1 = BasisFunction('S', [1], [1])
bf2 = BasisFunction('S', [2], [1])
decon1 = list(self.bfs.decontracted())
self.assertEqual(decon1[0], bf1)
self.assertEqual(decon1[1], bf2)
bfs1 = BasisFunction('S', [0.1], [1])
bfs2 = BasisFunction('S', [0.4], [1])
bfs3 = BasisFunction('S', [3], [1])
bfp1 = BasisFunction('P', [0.1], [1])
bfp2 = BasisFunction('P', [0.4], [1])
bfp3 = BasisFunction('P', [3], [1])
decon2 = list(self.bfsp.decontracted())
self.assertEqual(decon2[0], bfs1)
self.assertEqual(decon2[1], bfs2)
self.assertEqual(decon2[2], bfs3)
self.assertEqual(decon2[3], bfp1)
self.assertEqual(decon2[4], bfp2)
self.assertEqual(decon2[5], bfp3)
def setUp(self):
self.bfs = BasisFunction('S', [1, 2], [0.5, 0.5])
self.bfp = BasisFunction('P', [0.01, 0.2, 1], [0.3, 0.4, 0.3])
self.bfsp = BasisFunction('SP', [0.1, 0.4, 3],
[[0.2, 0.3, 0.5], [0.1, 0.3, 0.6]])
self.basis = Basis('C', [self.bfs, self.bfp, self.bfsp])
def test_check_exps(self):
"""Test check_exps"""
BasisFunction.check_exps([1, 2])
self.assertRaises(ValueError, BasisFunction.check_exps, [1, 2, -3])
def setUp(self):
self.bfs = BasisFunction('S', [1, 2], [0.5, 0.5])
self.bfp = BasisFunction('P', [0.01, 0.2, 1], [0.3, 0.4, 0.3])
self.bfd = BasisFunction('D', [1, 2], [0.3, 0.7], [0.4, 0.6])
self.bfsp = BasisFunction('SP', [0.1, 0.4, 3], [0.2, 0.3, 0.5], [0.1, 0.3, 0.6])
class TestBasisFunction(unittest.TestCase):
"""Tests a BasisFunction"""
def setUp(self):
self.bfs = BasisFunction('S', [1, 2], [0.5, 0.5])
self.bfp = BasisFunction('P', [0.01, 0.2, 1], [0.3, 0.4, 0.3])
self.bfd = BasisFunction('D', [1, 2], [0.3, 0.7], [0.4, 0.6])
self.bfsp = BasisFunction('SP', [0.1, 0.4, 3], [0.2, 0.3, 0.5], [0.1, 0.3, 0.6])
def test_len(self):
"""Test __len__"""
self.assertEqual(2, len(self.bfs))
self.assertEqual(3, len(self.bfp))
self.assertEqual(2, len(self.bfd))
self.assertEqual(3, len(self.bfsp))
def test_getseteq(self):
"""Test __getitem__ and __setitem__"""
# Convert np.array to list to prevent error in case.py as the truth value of an array is ambiguous
self.assertEqual([1.0, 0.5], list(self.bfs[0]))
# Convert to a list of lists
self.assertEqual([[0.01, 0.3], [1.0, 0.3]], list(map(list, self.bfp[::2])))
self.bfs[0] = [1, 2]
self.assertEqual([1.0, 2], list(self.bfs[0]))
self.assertRaises(ValueError, self.bfs.__setitem__, 1, [1, 2, 4])
self.bfd[0] = [1, 0.2, 0.3]
self.assertEqual([1.0, 0.2, 0.3], list(self.bfd[0]))
self.bfsp[0] = [1, 2, 4]
self.assertEqual([1, 2, 4], list(self.bfsp[0]))
self.assertRaises(ValueError, self.bfsp.__setitem__, 1, [1, 2])
self.assertEqual(self.bfs, self.bfs)
def test_check_exps(self):
"""Test check_exps"""
BasisFunction.check_exps([1, 2])
self.assertRaises(ValueError, BasisFunction.check_exps, [1, 2, -3])
def test_exps_coeffs_coeffs2(self):
"""Test exps, coeffs, and coeffs2"""
self.assertEqual([1, 2], list(self.bfs.exps))
self.assertEqual([0.3, 0.4, 0.3], list(self.bfp.coeffs))
self.assertEqual([0.4, 0.6], list(self.bfd.coeffs2))
def test_reprprint(self):
"""Test print"""
s_gamess = '''S 2
1 1.0000000 0.5000000
2 2.0000000 0.5000000
'''
p_gaussian94 = '''P 3
0.0100000 0.3000000
0.2000000 0.4000000
1.0000000 0.3000000
'''
sp_gaussian94 = '''SP 3
0.1000000 0.2000000 0.1000000
0.4000000 0.3000000 0.3000000
3.0000000 0.5000000 0.6000000
'''
self.assertEqual('<BasisFunction S 2>', repr(self.bfs))
self.assertEqual('<BasisFunction P 3>', repr(self.bfp))
self.assertEqual('<BasisFunction SP 3x2>', repr(self.bfsp))
self.assertEqual(s_gamess, self.bfs.print('gamess'))
self.assertEqual(p_gaussian94, self.bfp.print())
#print(self.bfsp.print())
self.assertEqual(sp_gaussian94, self.bfsp.print())
def test_decontracted(self):
"""Tests decontraction of basis function"""
bf1 = BasisFunction('S', [1], [1])
bf2 = BasisFunction('S', [2], [1])
decon1 = list(self.bfs.decontracted())
self.assertEqual(decon1[0], bf1)
self.assertEqual(decon1[1], bf2)
bfs1 = BasisFunction('S', [0.1], [1])
bfs2 = BasisFunction('S', [0.4], [1])
bfs3 = BasisFunction('S', [3 ], [1])
bfp1 = BasisFunction('P', [0.1], [1])
bfp2 = BasisFunction('P', [0.4], [1])
bfp3 = BasisFunction('P', [3 ], [1])
decon2 = list(self.bfsp.decontracted())
self.assertEqual(decon2[0], bfs1)
self.assertEqual(decon2[1], bfs2)
self.assertEqual(decon2[2], bfs3)
self.assertEqual(decon2[3], bfp1)
self.assertEqual(decon2[4], bfp2)
self.assertEqual(decon2[5], bfp3)
def test_check_coeffs(self):
"""Test check_exps"""
BasisFunction.check_coeffs(np.arange(5))
BasisFunction.check_coeffs(np.arange(9).reshape((3, 3)))
self.assertRaises(ValueError, BasisFunction.check_exps, np.arange(8).reshape((2, 2, 2)))