def main(log=True):
data1, logfile1 = getfile(Gaussian, "CDA", "BH3CO-sp.log")
data2, logfile2 = getfile(Gaussian, "CDA", "BH3.log")
data3, logfile3 = getfile(Gaussian, "CDA", "CO.log")
fa = CDA(data1)
if not log:
fa.logger.setLevel(logging.ERROR)
fa.calculate([data2, data3])
return fa
def main(log=True):
data1, logfile1 = getfile(Gaussian, "CDA", "BH3CO-sp.log")
data2, logfile2 = getfile(Gaussian, "CDA", "BH3.log")
data3, logfile3 = getfile(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 = getfile(Gaussian, "basicGaussian09", "dvb_sp.out")
mbo = MBO(data)
mbo.logger.setLevel(logging.ERROR)
mbo.calculate()
e_mbo = numpy.loadtxt("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 = getfile(Gaussian, "basicGaussian09", "dvb_un_sp.log")
mbo = MBO(data)
mbo.logger.setLevel(logging.ERROR)
mbo.calculate()
e_mbo = numpy.loadtxt("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 = getfile(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 = getfile(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 setUp(self):
self.data, self.logfile = getfile(Gaussian, "basicGaussian03", "dvb_sp.out")
self.analysis = CSPA(self.data)
self.analysis.logger.setLevel(0)
self.analysis.calculate()
def setUp(self):
self.data, self.logfile = getfile(Gaussian, "basicGaussian03",
"dvb_sp.out")
self.analysis = CSPA(self.data)
self.analysis.logger.setLevel(0)
self.analysis.calculate()