def get_selectivity_control(self, rxn_parameters):
"""
return the list of degree of selectivity control for each rxn
:param rxn_parameters: reaction parameters, see solver-base
"""
kT = self._kB * self.temperature
eps = self._mpfloat(self.perturbation_size)
try:
dSdG = numerical_jacobian(self.get_selectivity, rxn_parameters,
self._matrix, eps)
except ValueError(strerror):
resid = str(strerror).rsplit('=', 1)[1]
resid = resid.replace(')', '')
resid.strip()
self.log('jacobian_fail', resid=resid)
dRdG = np.zeros(
(len(self.gas_names),
len(self.adsorbate_names + self.transition_state_names)))
s0 = self.get_selectivity(rxn_parameters)
dSdG *= -kT
dSdG = dSdG.tolist()
DSC = []
for si, Ji in zip(s0, dSdG):
if si == 0:
DSC.append([0.0] * len(Ji))
else:
DSC.append([float(Jj / si) for Jj in Ji])
return DSC
def get_rate_control(self, rxn_parameters):
"""
return list of degree of rate control for each reaction
Ref: Stegelmann et al., DOI: 10.1021/ja9000097
:param rxn_parameters: reaction parameters, see solver-base
"""
kT = self._kB * self.temperature
eps = self._mpfloat(self.perturbation_size)
try:
diff_idxs = range(
len(self.adsorbate_names + self.transition_state_names))
dRdG = numerical_jacobian(self.get_turnover_frequency,
rxn_parameters,
self._matrix,
eps,
diff_idxs=diff_idxs)
except ValueError(strerror):
resid = str(strerror).rsplit('=', 1)[1]
resid = resid.replace(')', '')
resid.strip()
self.log('jacobian_fail', resid=resid)
dRdG = np.zeros(
(len(self.gas_names),
len(self.adsorbate_names + self.transition_state_names)))
t0 = self.get_turnover_frequency(rxn_parameters)
dRdG *= -kT
dRdG = dRdG.tolist()
DRC = []
for ti, Ji in zip(t0, dRdG):
if ti == 0:
DRC.append([0.0] * len(Ji))
else:
DRC.append([float(Jj / ti) for Jj in Ji])
return DRC
def get_selectivity_control(self,rxn_parameters):
kT = self._kB*self.temperature
eps = self._mpfloat(self.perturbation_size)
try:
dSdG = numerical_jacobian(self.get_selectivity,rxn_parameters,self._matrix,eps)
except ValueError,strerror:
resid = str(strerror).rsplit('=',1)[1]
resid = resid.replace(')','')
resid.strip()
self.log('jacobian_fail',resid=resid)
dRdG = np.zeros((len(self.gas_names),len(self.adsorbate_names+self.transition_state_names)))
def get_selectivity_control(self,rxn_parameters):
kT = self._kB*self.temperature
eps = self._mpfloat(self.perturbation_size)
try:
dSdG = numerical_jacobian(self.get_selectivity,rxn_parameters,self._matrix,eps)
except ValueError,strerror:
resid = str(strerror).rsplit('=',1)[1]
resid = resid.replace(')','')
resid.strip()
self.log('jacobian_fail',resid=resid)
dRdG = np.zeros((len(self.gas_names),len(self.adsorbate_names+self.transition_state_names)))
def get_rate_control(self,rxn_parameters):
"""
return list of degree of rate control for each reaction
Ref: Stegelmann et al., DOI: 10.1021/ja9000097
:param rxn_parameters: reaction parameters, see solver-base
"""
kT = self._kB*self.temperature
eps = self._mpfloat(self.perturbation_size)
try:
diff_idxs = range(len(self.adsorbate_names+self.transition_state_names))
dRdG = numerical_jacobian(self.get_turnover_frequency,rxn_parameters,self._matrix,eps,diff_idxs=diff_idxs)
except ValueError, strerror:
resid = str(strerror).rsplit('=',1)[1]
resid = resid.replace(')','')
resid.strip()
self.log('jacobian_fail',resid=resid)
dRdG = np.zeros((len(self.gas_names),len(self.adsorbate_names+self.transition_state_names)))
def get_rate_control(self, rxn_parameters):
"""
return list of degree of rate control for each reaction
Ref: Stegelmann et al., DOI: 10.1021/ja9000097
:param rxn_parameters: reaction parameters, see solver-base
"""
kT = self._kB * self.temperature
eps = self._mpfloat(self.perturbation_size)
try:
diff_idxs = range(
len(self.adsorbate_names + self.transition_state_names))
dRdG = numerical_jacobian(self.get_turnover_frequency,
rxn_parameters,
self._matrix,
eps,
diff_idxs=diff_idxs)
except ValueError, strerror:
resid = str(strerror).rsplit('=', 1)[1]
resid = resid.replace(')', '')
resid.strip()
self.log('jacobian_fail', resid=resid)
dRdG = np.zeros(
(len(self.gas_names),
len(self.adsorbate_names + self.transition_state_names)))
def J(x):
return numerical_jacobian(f, x, self._matrix)
def J(x):
return numerical_jacobian(f,x,self._matrix)