def test_count(self):
"""Test electron count for logfiles without pseudopotentials."""
data, logfile = getdatafile(QChem, "basicQChem4.2", "water_mp4sdq.out")
self.assertEqual(Electrons(data).count(), 10)
self.assertEqual(Electrons(data).count(core=True), 10)
data, logfile = getdatafile(Gaussian, "basicGaussian09", "water_cis.log")
self.assertEqual(Electrons(data).count(), 10)
self.assertEqual(Electrons(data).count(core=True), 10)
def main(log=True):
data1, logfile1 = getdatafile(Gaussian, "CDA", "BH3CO-sp.log")
data2, logfile2 = getdatafile(Gaussian, "CDA", "BH3.log")
data3, logfile3 = getdatafile(Gaussian, "CDA", "CO.log")
fa = CDA(data1)
if not log:
fa.logger.setLevel(logging.ERROR)
fa.calculate([data2, data3])
return fa
def test_mbo_sp(self):
"""Testing Mayer bond orders for restricted single point."""
data, logfile = getdatafile(Gaussian, "basicGaussian09", ["dvb_sp.out"])
mbo = MBO(data)
mbo.logger.setLevel(logging.ERROR)
mbo.calculate()
e_mbo = numpy.loadtxt(os.path.dirname(os.path.realpath(__file__)) + "/dvb_sp.mbo")
self.assertTrue(numpy.all(mbo.fragresults[0] >= e_mbo - 0.25))
self.assertTrue(numpy.all(mbo.fragresults[0] <= e_mbo + 0.25))
def test_mbo_sp(self):
"""Testing Mayer bond orders for restricted single point."""
data, logfile = getdatafile(Gaussian, "basicGaussian09", ["dvb_sp.out"])
mbo = MBO(data)
mbo.logger.setLevel(logging.ERROR)
mbo.calculate()
e_mbo = numpy.loadtxt(os.path.dirname(os.path.realpath(__file__)) + "/dvb_sp.mbo")
self.assertTrue(numpy.all(mbo.fragresults[0] >= e_mbo - 0.25))
self.assertTrue(numpy.all(mbo.fragresults[0] <= e_mbo + 0.25))
def test_mbo_un_sp(self):
"""Testing Mayer bond orders for unrestricted single point."""
data, logfile = getdatafile(Gaussian, "basicGaussian09", "dvb_un_sp.log")
mbo = MBO(data)
mbo.logger.setLevel(logging.ERROR)
mbo.calculate()
e_mbo = numpy.loadtxt(os.path.dirname(os.path.realpath(__file__)) + "/dvb_un_sp.mbo")
bond_orders = mbo.fragresults[0] + mbo.fragresults[1]
self.assertTrue(numpy.all(bond_orders >= e_mbo - 0.30))
self.assertTrue(numpy.all(bond_orders <= e_mbo + 0.30))
def test_nre(self):
"""Testing nuclear repulsion energy for one logfile where it is printed."""
data, logfile = getdatafile(QChem, "basicQChem4.2", "water_mp4sdq.out")
nuclear = Nuclear(data)
nuclear.logger.setLevel(logging.ERROR)
with open(logfile.filename) as f:
output = f.read()
line = re.search('Nuclear Repulsion Energy = .* hartrees', output).group()
nre = float(line.split()[4])
nre = utils.convertor(nre, 'Angstrom', 'bohr')
self.assertAlmostEqual(nuclear.repulsion_energy(), nre, places=7)
def test_nre(self):
"""Testing nuclear repulsion energy for one logfile where it is printed."""
data, logfile = getdatafile(QChem, "basicQChem4.2", "water_mp4sdq.out")
nuclear = Nuclear(data)
nuclear.logger.setLevel(logging.ERROR)
with open(logfile.filename) as f:
output = f.read()
line = re.search('Nuclear Repulsion Energy = .* hartrees',
output).group()
nre = float(line.split()[4])
nre = utils.convertor(nre, 'Angstrom', 'bohr')
self.assertAlmostEqual(nuclear.repulsion_energy(), nre, places=7)
def test_mbo_un_sp(self):
"""Testing Mayer bond orders for unrestricted single point."""
data, logfile = getdatafile(Gaussian, "basicGaussian09",
"dvb_un_sp.log")
mbo = MBO(data)
mbo.logger.setLevel(logging.ERROR)
mbo.calculate()
e_mbo = numpy.loadtxt(
os.path.dirname(os.path.realpath(__file__)) + "/dvb_un_sp.mbo")
bond_orders = mbo.fragresults[0] + mbo.fragresults[1]
self.assertTrue(numpy.all(bond_orders >= e_mbo - 0.30))
self.assertTrue(numpy.all(bond_orders <= e_mbo + 0.30))
def setUp(self):
self.data, self.logfile = getdatafile(Gaussian, "basicGaussian03",
["dvb_un_sp.out"])
self.analysis = CSPA(self.data)
self.analysis.logger.setLevel(0)
self.analysis.calculate()
def setUp(self):
self.data, self.logfile = getdatafile(Gaussian, "basicGaussian03", "dvb_un_sp.out")
self.analysis = CSPA(self.data)
self.analysis.logger.setLevel(0)
self.analysis.calculate()
def test_count_pseudopotential(self):
"""Test electron count for logfiles with pseudopotentials."""
data, logfile = getdatafile(Gaussian, "basicGaussian09", "Mo4OCl4-sp.log")
self.assertEqual(Electrons(data).count(), 120)
self.assertEqual(Electrons(data).count(core=True), 188)
def setUp(self):
self.data, self.logfile = getdatafile(Psi, "basicPsi4.0", ["dvb_sp_rohf.out"])
def setUp(self):
self.data, self.logfile = getdatafile(Gaussian, "basicGaussian09", ["dvb_un_sp.log"])
