def setUp(self):
"""Set up for every test"""
self.g = Gamessifier()
self.formaldehyde_xyz = Molecule([['O', [0, 1.394, 0]],
['C', [0, 0, 0]],
['H', [0.994, -0.492, 0]],
['H', [-0.994, -0.492, 0]]])
def setUp(self):
"""Set up for every test"""
self.g = Gamessifier()
self.formaldehyde_xyz = Molecule([['O', 0, 1.394, 0], ['C', 0, 0, 0], ['H', 0.994, -0.492, 0], ['H', -0.994, -0.492, 0]])
class TestGamessifier(unittest.TestCase):
"""Tests the Molecule class"""
def setUp(self):
"""Set up for every test"""
self.g = Gamessifier()
self.formaldehyde_xyz = Molecule([['O', [0, 1.394, 0]],
['C', [0, 0, 0]],
['H', [0.994, -0.492, 0]],
['H', [-0.994, -0.492, 0]]])
def test_read_mol(self):
"""Test reading a molecule from a file"""
tmp_geom_file = 'geom.xyz.tmp'
self.formaldehyde_xyz.write(tmp_geom_file)
self.g.read_mol(tmp_geom_file)
self.assertEqual(str(self.g.mol), str(self.formaldehyde_xyz))
os.remove(tmp_geom_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])])
with open(tmp_basis_file, 'w') as f:
f.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_ecp(self):
"""Testing reading an ecp file"""
tmp_ecp_file = 'ecp.dat.tmp'
ecp = """\
H-ECP NONE
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)
self.g.read_ecp(tmp_ecp_file)
os.remove(tmp_ecp_file)
def test_read_options(self):
"""Testing read options"""
self.g.read_options({})
self.assertEqual({}, self.g.options_dict)
self.assertEqual('', self.g.write_options_str())
options_dir = OrderedDict(
[['CONTRL', OrderedDict([['SCFTYP', 'RHF']])],
['SCF', OrderedDict([['DIRSCF', '.TRUE.']])]])
options_str = ' $CONTRL\n SCFTYP=RHF\n $END\n\n $SCF\n DIRSCF=.TRUE.\n $END\n\n'
self.g.read_options(options_dir)
self.assertEqual(options_str, self.g.write_options_str())
tmp_options_file = 'options.dat.tmp'
with open(tmp_options_file, 'w') as f:
f.write(options_str)
self.g.read_options(tmp_options_file)
def test_read_other_data(self):
"""Testing read_other_data"""
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_data(tmp_dat_file)
self.assertEqual(vec, self.g.vec)
self.assertEqual(hess, self.g.hess)
os.remove(tmp_dat_file)
def test_update_options(self):
"""Test update_options"""
self.g.vec = ' $VEC\n123132\n $END'
self.g.options_dict = {'GUESS': {'GUESS': 'HUCKEL'}}
self.g.update_options()
self.assertEqual('MOREAD', self.g.options_dict['GUESS']['GUESS'])
self.g.vec = ' '
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)
class TestGamessifier(unittest.TestCase):
"""Tests the Molecule class"""
def setUp(self):
"""Set up for every test"""
self.g = Gamessifier()
self.formaldehyde_xyz = Molecule([['O', 0, 1.394, 0], ['C', 0, 0, 0], ['H', 0.994, -0.492, 0], ['H', -0.994, -0.492, 0]])
def test_read_mol(self):
"""Test reading a molecule from a file"""
tmp_geom_file = 'geom.xyz.tmp'
self.formaldehyde_xyz.write(tmp_geom_file)
self.g.read_mol(tmp_geom_file)
self.assertEqual(str(self.g.mol), str(self.formaldehyde_xyz))
os.remove(tmp_geom_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_read_ecp(self):
"""Testing reading an ecp file"""
tmp_ecp_file = 'ecp.dat.tmp'
ecp = """\
H-ECP NONE
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)
self.g.read_ecp(tmp_ecp_file)
os.remove(tmp_ecp_file)
def test_read_options(self):
"""Testing read options"""
self.g.read_options({})
self.assertEqual({}, self.g.options_dict)
self.assertEqual('', self.g.write_options_str())
options_dir = OrderedDict([
['CONTRL', OrderedDict([['SCFTYP', 'RHF']])],
['SCF', OrderedDict([['DIRSCF', '.TRUE.']])]
])
options_str = ' $CONTRL\n SCFTYP=RHF\n $END\n\n $SCF\n DIRSCF=.TRUE.\n $END\n\n'
self.g.read_options(options_dir)
self.assertEqual(options_str, self.g.write_options_str())
tmp_options_file = 'options.dat.tmp'
open(tmp_options_file, 'w').write(options_str)
self.g.read_options(tmp_options_file)
def test_read_other_data(self):
"""Testing read_other_data"""
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_data(tmp_dat_file)
self.assertEqual(vec, self.g.vec)
self.assertEqual(hess, self.g.hess)
os.remove(tmp_dat_file)
def test_update_options(self):
"""Test update_options"""
self.g.vec = ' $VEC\n123132\n $END'
self.g.options_dict = {'GUESS': {'GUESS': 'HUCKEL'}}
self.g.update_options()
self.assertEqual('MOREAD', self.g.options_dict['GUESS']['GUESS'])
self.g.vec = ' '
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)