def test_reprreadprint(self):
"""Test read and print of BasisSet"""
bs = self.basis_set
test_file_gaussian = 'my_basis_gaussian.gbs.tmp'
with open(test_file_gaussian, 'w') as f:
f.write(bs.print('gaussian94'))
bs1 = BasisSet.read(test_file_gaussian, 'gaussian94')
self.assertEqual('<BasisSet my_basis_gaussian>', repr(bs1))
self.assertEqual(bs, bs1)
test_file_gamess = 'my_basis_gamess.gbs.tmp'
with open(test_file_gamess, 'w') as f:
f.write(bs.print('gamess'))
bs2 = BasisSet.read(test_file_gamess, 'gamess')
self.assertEqual(bs, bs2)
test_file_bagel = 'my_basis_bagel.json.tmp'
with open(test_file_bagel, 'w') as f:
f.write(bs.print('bagel'))
#bs3 = BasisSet.read(test_file_bagel, 'bagel')
#self.assertEqual(bs, bs3)
test_file_cfour = 'my_basis_cfour.GENBAS.tmp'
with open(test_file_cfour, 'w') as f:
f.write(bs.print('cfour'))
bs4 = BasisSet.read(test_file_cfour, 'cfour')
self.assertEqual(bs, bs4)
self.assertRaises(SyntaxError, self.basis_set.print, 'turbomole')
for tmp_file in glob('*.tmp'):
os.remove(tmp_file)
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_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_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_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 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])])
open(tmp_basis_file, 'w').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"""
open(tmp_ecp_file, 'w').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'
open(tmp_options_file, 'w').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'
open(tmp_dat_file, 'w').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_reprreadprint(self):
"""Test read and print of BasisSet"""
bs = self.basis_set
test_file_gaussian = 'my_basis_gaussian.gbs.tmp'
with open(test_file_gaussian, 'w') as f:
f.write(bs.print('gaussian94'))
bs1 = BasisSet.read_file(test_file_gaussian, 'gaussian94')
self.assertEqual('<BasisSet my_basis_gaussian.gbs>', repr(bs1))
self.assertEqual(bs, bs1)
test_file_gamess = 'my_basis_gamess.gbs.tmp'
with open(test_file_gamess, 'w') as f:
f.write(bs.print('gamess'))
bs2 = BasisSet.read_file(test_file_gamess, 'gamess')
self.assertEqual(bs, bs2)
test_file_bagel = 'my_basis_bagel.json.tmp'
with open(test_file_bagel, 'w') as f:
f.write(bs.print('bagel'))
bs3 = BasisSet.read_file(test_file_bagel, 'bagel')
self.assertEqual(bs, bs3)
test_file_cfour = 'my_basis_cfour.GENBAS.tmp'
with open(test_file_cfour, 'w') as f:
f.write(bs.print('cfour'))
bs4 = BasisSet.read_file(test_file_cfour, 'cfour')
self.assertEqual(bs, bs4)
test_file_molpro = 'my_basis_molpro.bas.tmp'
with open(test_file_molpro, 'w') as f:
f.write(bs.print('molpro'))
bs4 = BasisSet.read_file(test_file_molpro, 'molpro')
self.assertEqual(bs, bs4)
self.assertRaises(ValueError, self.basis_set.print, 'turbomole')
for tmp_file in glob('*.tmp'):
os.remove(tmp_file)
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)
class TestBasisSet(unittest.TestCase):
"""Test the BasisSet class"""
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_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_iter(self):
bs_it = iter(self.basis_set)
self.assertEqual(self.h, next(bs_it))
self.assertEqual(self.c, next(bs_it))
def test_check_basis_set(self):
"""Test check_basis_set"""
self.assertRaises(SyntaxError, BasisSet.check_basis_set, ({'H': 1}))
self.assertRaises(SyntaxError, BasisSet.check_basis_set,
(OrderedDict([('H', 1)])))
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_reprreadprint(self):
"""Test read and print of BasisSet"""
bs = self.basis_set
test_file_gaussian = 'my_basis_gaussian.gbs.tmp'
with open(test_file_gaussian, 'w') as f:
f.write(bs.print('gaussian94'))
bs1 = BasisSet.read(test_file_gaussian, 'gaussian94')
self.assertEqual('<BasisSet my_basis_gaussian>', repr(bs1))
self.assertEqual(bs, bs1)
test_file_gamess = 'my_basis_gamess.gbs.tmp'
with open(test_file_gamess, 'w') as f:
f.write(bs.print('gamess'))
bs2 = BasisSet.read(test_file_gamess, 'gamess')
self.assertEqual(bs, bs2)
test_file_bagel = 'my_basis_bagel.json.tmp'
with open(test_file_bagel, 'w') as f:
f.write(bs.print('bagel'))
bs3 = BasisSet.read(test_file_bagel, 'bagel')
self.assertEqual(bs, bs3)
test_file_cfour = 'my_basis_cfour.GENBAS.tmp'
with open(test_file_cfour, 'w') as f:
f.write(bs.print('cfour'))
bs4 = BasisSet.read(test_file_cfour, 'cfour')
self.assertEqual(bs, bs4)
test_file_molpro = 'def2-svp.molpro'
bs5 = BasisSet.read(test_file_molpro, 'molpro')
self.assertEqual(len(bs5['O']), 6)
self.assertRaises(SyntaxError, self.basis_set.print, 'turbomole')
for tmp_file in glob('*.tmp'):
os.remove(tmp_file)
def test_values(self):
"""Test values"""
vals = [[
np.array([[1.0, 0.5], [2.0, 0.5]]),
np.array([[0.01, 0.3], [0.2, 0.4], [1.0, 0.3]])
],
[
np.array([[0.1, 0.6], [0.4, 0.4]]),
np.array([[0.1, 0.2], [0.4, 0.3], [3.0, 0.5]])
]]
self.assertEqual(vals[0][0][0][1], self.basis_set.values()[0][0][0][1])
self.assertEqual(vals[0][1][1][0], self.basis_set.values()[0][1][1][0])
class TestBasisSet(unittest.TestCase):
"""Test the BasisSet class"""
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_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_iter(self):
bs_it = iter(self.basis_set)
self.assertEqual(self.h, next(bs_it))
self.assertEqual(self.c, next(bs_it))
def test_check_basis_set(self):
"""Test check_basis_set"""
self.assertRaises(SyntaxError, BasisSet.check_basis_set, ({'H': 1}))
self.assertRaises(SyntaxError, BasisSet.check_basis_set, (OrderedDict([('H', 1)])))
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_reprreadprint(self):
"""Test read and print of BasisSet"""
bs = self.basis_set
test_file_gaussian = 'my_basis_gaussian.gbs.tmp'
with open(test_file_gaussian, 'w') as f:
f.write(bs.print('gaussian94'))
bs1 = BasisSet.read(test_file_gaussian, 'gaussian94')
self.assertEqual('<BasisSet my_basis_gaussian>', repr(bs1))
self.assertEqual(bs, bs1)
test_file_gamess = 'my_basis_gamess.gbs.tmp'
with open(test_file_gamess, 'w') as f:
f.write(bs.print('gamess'))
bs2 = BasisSet.read(test_file_gamess, 'gamess')
self.assertEqual(bs, bs2)
test_file_bagel = 'my_basis_bagel.json.tmp'
with open(test_file_bagel, 'w') as f:
f.write(bs.print('bagel'))
#bs3 = BasisSet.read(test_file_bagel, 'bagel')
#self.assertEqual(bs, bs3)
test_file_cfour = 'my_basis_cfour.GENBAS.tmp'
with open(test_file_cfour, 'w') as f:
f.write(bs.print('cfour'))
bs4 = BasisSet.read(test_file_cfour, 'cfour')
self.assertEqual(bs, bs4)
self.assertRaises(SyntaxError, self.basis_set.print, 'turbomole')
for tmp_file in glob('*.tmp'):
os.remove(tmp_file)
def test_values(self):
"""Test values"""
vals = [[np.array([[1.0, 0.5], [2.0, 0.5]]),
np.array([[0.01, 0.3], [0.2, 0.4], [1.0, 0.3]])],
[np.array([[0.1, 0.6], [0.4, 0.4]]),
np.array([[0.1, 0.2], [0.4, 0.3], [3.0, 0.5]])]]
self.assertEqual(vals[0][0][0][1], self.basis_set.values()[0][0][0][1])
self.assertEqual(vals[0][1][1][0], self.basis_set.values()[0][1][1][0])
