def setUp(self,verbose=False):
abss = AbsSpectrum()
with energy_units("1/cm"):
f = FrequencyAxis(10000.0,2000, 1.0)
a = self._spectral_shape(f, [1.0, 11000.0, 100.0])
abss.axis = f
abss.data = a
self.abss = abss
self.axis = abss.axis
#make a single-molecule system
time = TimeAxis(0.0,1000,1.0)
self.ta = time
with energy_units("1/cm"):
mol1 = Molecule(elenergies=[0.0, 12000.0])
params = dict(ftype="OverdampedBrownian", reorg=20, cortime=100,
T=300)
mol1.set_dipole(0,1,[0.0, 1.0, 0.0])
cf = CorrelationFunction(time, params)
mol1.set_transition_environment((0,1),cf)
abs_calc = AbsSpectrumCalculator(time, system=mol1)
abs_calc.bootstrap(rwa=12000)
abs1 = abs_calc.calculate()
self.abs1 = abs1
def setUp(self,verbose=False):
abss = AbsSpectrum()
with energy_units("1/cm"):
f = FrequencyAxis(10000.0,2000, 1.0)
a = self._spectral_shape(f, [1.0, 11000.0, 100.0])
abss.axis = f
abss.data = a
self.abss = abss
self.axis = abss.axis
#make a single-molecule system
time = TimeAxis(0.0,1000,1.0)
self.ta = time
with energy_units("1/cm"):
mol1 = Molecule(elenergies=[0.0, 12000.0])
params = dict(ftype="OverdampedBrownian", reorg=20, cortime=100,
T=300)
mol1.set_dipole(0,1,[0.0, 1.0, 0.0])
cf = CorrelationFunction(time, params)
mol1.set_transition_environment((0,1),cf)
abs_calc = AbsSpectrumCalculator(time, system=mol1)
abs_calc.bootstrap(rwa=12000)
abs1 = abs_calc.calculate()
self.abs1 = abs1
def test_abs_spectrum_saveablity(self):
"""Testing if AbsSpectrum is saveble
"""
abs1 = self.abs1
drv = "core"
bcs = False
with h5py.File('tempfile.hdf5', driver=drv, backing_store=bcs) as f:
abs1.save(f, test=True)
abs2 = AbsSpectrum()
abs2.load(f, test=True)
numpy.testing.assert_array_equal(abs1.data, abs2.data)
def test_abs_spectrum_saveablity(self):
"""Testing if AbsSpectrum is saveble
"""
abs1 = self.abs1
#drv = "core"
#bcs = False
with tempfile.TemporaryFile() as f:
#with h5py.File('tempfile.hdf5',
# driver=drv,
# backing_store=bcs) as f:
abs1.save(f) #, test=True)
f.seek(0)
abs2 = AbsSpectrum()
abs2 = abs2.load(f) #, test=True)
numpy.testing.assert_array_equal(abs1.data, abs2.data)
def reset_tester():
abss2 = AbsSpectrum()
abss2.set_axis(copy.deepcopy(self.abss.axis))
abss2.set_data(copy.deepcopy(self.abss.data))
return abss2
def _opt_spectral_shape(self, par):
f = self.axis
a = AbsSpectrum(axis=f,data=self._spectral_shape(f, par))
return a
def reset_tester():
abss2 = AbsSpectrum()
abss2.set_axis(copy.deepcopy(self.abss.axis))
abss2.set_data(copy.deepcopy(self.abss.data))
return abss2