def save(self, outputFile):
"""
Save the results of the kinetics job to the file located
at `path` on disk.
"""
reaction = self.reaction
ks = []
k0s = []
k0revs = []
krevs = []
logging.info('Saving kinetics for {0}...'.format(reaction))
order = len(self.reaction.reactants)
factor = 1e6 ** (order-1)
f = open(outputFile, 'a')
if self.usedTST:
# If TST is not used, eg. it was given in 'reaction', then this will throw an error.
f.write('# ======= =========== =========== =========== ===============\n')
f.write('# Temp. k (TST) Tunneling k (TST+T) Units\n')
f.write('# ======= =========== =========== =========== ===============\n')
if self.Tlist is None:
Tlist = numpy.array([300,400,500,600,800,1000,1500,2000])
else:
Tlist =self.Tlist.value_si
for T in Tlist:
tunneling = reaction.transitionState.tunneling
reaction.transitionState.tunneling = None
try:
k0 = reaction.calculateTSTRateCoefficient(T) * factor
except SpeciesError:
k0 = 0
reaction.transitionState.tunneling = tunneling
try:
k = reaction.calculateTSTRateCoefficient(T) * factor
kappa = k / k0
except (SpeciesError,ZeroDivisionError):
k = reaction.getRateCoefficient(T)
kappa = 0
logging.info("The species in reaction {} do not have adequate information for TST, using default kinetics values.".format(reaction))
tunneling = reaction.transitionState.tunneling
ks.append(k)
k0s.append(k0)
f.write('# {0:4g} K {1:11.3e} {2:11g} {3:11.3e} {4}\n'.format(T, k0, kappa, k, self.kunits))
f.write('# ======= =========== =========== =========== ===============\n')
f.write('\n\n')
f.write('# ======= ============ =========== ============ ============= =========\n')
f.write('# Temp. Kc (eq) Units krev (TST) krev (TST+T) Units\n')
f.write('# ======= ============ =========== ============ ============= =========\n')
# Initialize Object for Converting Units
if self.Kequnits != ' ':
keq_unit_converter = quantity.Units(self.Kequnits).getConversionFactorFromSI()
else:
keq_unit_converter = 1
for n,T in enumerate(Tlist):
k = ks[n]
k0 = k0s[n]
Keq = keq_unit_converter * reaction.getEquilibriumConstant(T) # getEquilibriumConstant returns SI units
k0rev = k0/Keq
krev = k/Keq
k0revs.append(k0rev)
krevs.append(krev)
f.write('# {0:4g} K {1:11.3e} {2} {3:11.3e} {4:11.3e} {5}\n'.format(T, Keq, self.Kequnits, k0rev, krev, self.krunits))
f.write('# ======= ============ =========== ============ ============= =========\n')
f.write('\n\n')
kinetics0rev = Arrhenius().fitToData(Tlist, numpy.array(k0revs), kunits=self.krunits)
kineticsrev = Arrhenius().fitToData(Tlist, numpy.array(krevs), kunits=self.krunits)
f.write('# krev (TST) = {0} \n'.format(kinetics0rev))
f.write('# krev (TST+T) = {0} \n\n'.format(kineticsrev))
# Reaction path degeneracy is INCLUDED in the kinetics itself!
string = 'kinetics(label={0!r}, kinetics={1!r})'.format(reaction.label, reaction.kinetics)
f.write('{0}\n\n'.format(prettify(string)))
f.close()
# Also save the result to chem.inp
f = open(os.path.join(os.path.dirname(outputFile), 'chem.inp'), 'a')
reaction = self.reaction
kinetics = reaction.kinetics
string = ''
if reaction.kinetics.comment:
for line in reaction.kinetics.comment.split("\n"):
string += "! {0}\n".format(line)
string += '{0!s:51} {1:9.3e} {2:9.3f} {3:9.3f}\n'.format(
reaction,
kinetics.A.value_si * factor,
kinetics.n.value_si,
kinetics.Ea.value_si / 4184.,
)
f.write('{0}\n'.format(string))
f.close()
# We're saving a YAML file for TSs iff structures of the respective reactant/s and product/s are known
if all ([spc.molecule is not None and len(spc.molecule)
for spc in self.reaction.reactants + self.reaction.products]):
self.arkane_species.update_species_attributes(self.reaction.transitionState)
self.arkane_species.reaction_label = reaction.label
self.arkane_species.reactants = [{'label': spc.label, 'adjacency_list': spc.molecule[0].toAdjacencyList()}
for spc in self.reaction.reactants]
self.arkane_species.products = [{'label': spc.label, 'adjacency_list': spc.molecule[0].toAdjacencyList()}
for spc in self.reaction.products]
self.arkane_species.save_yaml(path=os.path.dirname(outputFile))
def write_output(self, output_directory):
"""
Save the results of the kinetics job to the `output.py` file located
in `output_directory`.
"""
reaction = self.reaction
ks, k0s, k0_revs, k_revs = [], [], [], []
logging.info('Saving kinetics for {0}...'.format(reaction))
order = len(self.reaction.reactants)
factor = 1e6**(order - 1)
f = open(os.path.join(output_directory, 'output.py'), 'a')
if self.usedTST:
# If TST is not used, eg. it was given in 'reaction', then this will throw an error.
f.write(
'# ======= =========== =========== =========== ===============\n'
)
f.write('# Temp. k (TST) Tunneling k (TST+T) Units\n')
f.write(
'# ======= =========== =========== =========== ===============\n'
)
if self.Tlist is None:
t_list = np.array([300, 400, 500, 600, 800, 1000, 1500, 2000])
else:
t_list = self.Tlist.value_si
for T in t_list:
tunneling = reaction.transition_state.tunneling
reaction.transition_state.tunneling = None
try:
k0 = reaction.calculate_tst_rate_coefficient(T) * factor
except SpeciesError:
k0 = 0
reaction.transition_state.tunneling = tunneling
try:
k = reaction.calculate_tst_rate_coefficient(T) * factor
kappa = k / k0
except (SpeciesError, ZeroDivisionError):
k = reaction.get_rate_coefficient(T)
kappa = 0
logging.info(
"The species in reaction {0} do not have adequate information for TST, "
"using default kinetics values.".format(reaction))
tunneling = reaction.transition_state.tunneling
ks.append(k)
k0s.append(k0)
f.write(
'# {0:4g} K {1:11.3e} {2:11g} {3:11.3e} {4}\n'.format(
T, k0, kappa, k, self.k_units))
f.write(
'# ======= =========== =========== =========== ===============\n'
)
f.write('\n\n')
f.write(
'# ======= ============ =========== ============ ============= =========\n'
)
f.write(
'# Temp. Kc (eq) Units k_rev (TST) k_rev (TST+T) Units\n'
)
f.write(
'# ======= ============ =========== ============ ============= =========\n'
)
# Initialize Object for Converting Units
if self.K_eq_units != ' ':
keq_unit_converter = quantity.Units(
self.K_eq_units).get_conversion_factor_from_si()
else:
keq_unit_converter = 1
for n, T in enumerate(t_list):
k = ks[n]
k0 = k0s[n]
K_eq = keq_unit_converter * reaction.get_equilibrium_constant(
T) # returns SI units
k0_rev = k0 / K_eq
k_rev = k / K_eq
k0_revs.append(k0_rev)
k_revs.append(k_rev)
f.write(
'# {0:4g} K {1:11.3e} {2} {3:11.3e} {4:11.3e} {5}\n'
.format(T, K_eq, self.K_eq_units, k0_rev, k_rev,
self.k_r_units))
f.write(
'# ======= ============ =========== ============ ============= =========\n'
)
f.write('\n\n')
kinetics_0_rev = Arrhenius().fit_to_data(t_list,
np.array(k0_revs),
kunits=self.k_r_units)
kinetics_rev = Arrhenius().fit_to_data(t_list,
np.array(k_revs),
kunits=self.k_r_units)
f.write('# k_rev (TST) = {0} \n'.format(kinetics_0_rev))
f.write('# k_rev (TST+T) = {0} \n\n'.format(kinetics_rev))
# Reaction path degeneracy is INCLUDED in the kinetics itself!
rxn_str = 'kinetics(label={0!r}, kinetics={1!r})'.format(
reaction.label, reaction.kinetics)
f.write('{0}\n\n'.format(prettify(rxn_str)))
f.close()