def execute(self, outputFile, plot, format='pdf', print_summary=True):
"""Execute a PressureDependenceJob"""
for config in self.network.isomers + self.network.reactants + self.network.products:
for spec in config.species:
if spec.conformer.E0 is None:
raise AttributeError('species {0} is missing energy for its conformer'.format(spec.label))
# set transition state Energy if not set previously using same method as RMG pdep
for reaction in self.network.pathReactions:
transitionState = reaction.transitionState
if transitionState.conformer and transitionState.conformer.E0 is None:
transitionState.conformer.E0 = (sum([spec.conformer.E0.value_si for spec in reaction.reactants])
+ reaction.kinetics.Ea.value_si, 'J/mol')
logging.info('Approximated transitions state E0 for reaction {3} from kinetics '
'A={0}, n={1}, Ea={2} J/mol'.format(reaction.kinetics.A.value_si,
reaction.kinetics.n.value_si,
reaction.kinetics.Ea.value_si, reaction.label))
if print_summary:
self.network.printSummary()
if outputFile is not None:
self.draw(os.path.dirname(outputFile), format)
self.initialize()
self.K = self.network.calculateRateCoefficients(self.Tlist.value_si, self.Plist.value_si, self.method)
self.fitInterpolationModels()
if outputFile is not None:
self.save(outputFile)
if plot:
self.plot(os.path.dirname(outputFile))
if self.sensitivity_conditions is not None:
perturbation = 0.1 # kcal/mol
logging.info('\n\nRunning sensitivity analysis...')
for i in xrange(3):
try:
sa(self, os.path.dirname(outputFile), perturbation=perturbation)
except (InvalidMicrocanonicalRateError, ModifiedStrongCollisionError) as exept:
logging.warn("Could not complete the sensitivity analysis with a perturbation of {0}"
" kcal/mol, trying {1} kcal/mol instead.".format(
perturbation, perturbation / 2.0))
perturbation /= 2.0
else:
break
else:
logging.error("Could not complete the sensitivity analysis even with a perturbation of {0}"
" kcal/mol".format(perturbation))
raise exept
logging.info("Completed the sensitivity analysis using a perturbation of {0} kcal/mol".format(
perturbation))
logging.debug('Finished pdep job for reaction {0}.'.format(self.network.label))
logging.debug(repr(self.network))
def execute(self, outputFile, plot, format='pdf', print_summary=True):
for config in self.network.isomers + self.network.reactants + self.network.products:
for spec in config.species:
if spec.conformer.E0 is None:
raise AttributeError('species {0} is missing energy for its conformer'.format(spec.label))
# set transition state Energy if not set previously using same method as RMG pdep
for reaction in self.network.pathReactions:
transitionState = reaction.transitionState
if transitionState.conformer and transitionState.conformer.E0 is None:
transitionState.conformer.E0 = (sum([spec.conformer.E0.value_si for spec in reaction.reactants]) + reaction.kinetics.Ea.value_si,"J/mol")
logging.info('Approximated transitions state E0 for reaction {3} from kinetics '
'A={0}, n={1}, Ea={2} J/mol'.format(reaction.kinetics.A.value_si,reaction.kinetics.n.value_si,reaction.kinetics.Ea.value_si,reaction.label))
if print_summary:
self.network.printSummary()
if outputFile is not None:
self.draw(os.path.dirname(outputFile), format)
self.initialize()
self.K = self.network.calculateRateCoefficients(self.Tlist.value_si, self.Plist.value_si, self.method)
self.fitInterpolationModels()
if outputFile is not None:
self.save(outputFile)
if plot:
self.plot(os.path.dirname(outputFile))
if self.sensitivity_conditions is not None:
perturbation = 0.1 # kcal/mol
logging.info('\n\nRunning sensitivity analysis...')
for i in xrange(3):
try:
sa(self, os.path.dirname(outputFile), perturbation=perturbation)
except (InvalidMicrocanonicalRateError, ModifiedStrongCollisionError) as exept:
logging.warn("Could not complete the sensitivity analysis with a perturbation of {0}"
" kcal/mol, trying {1} kcal/mol instead.".format(
perturbation, perturbation / 2.0))
perturbation /= 2.0
else:
break
else:
logging.error("Could not complete the sensitivity analysis even with a perturbation of {0}"
" kcal/mol".format(perturbation))
raise exept
logging.info("Completed the sensitivity analysis using a perturbation of {0} kcal/mol".format(
perturbation))
logging.debug('Finished pdep job for reaction {0}.'.format(self.network.label))
logging.debug(repr(self.network))
def execute(self, outputFile=None, plot=True):
"""
Execute the kinetics job, saving the results to the given `outputFile` on disk.
"""
if self.Tlist is not None:
self.generateKinetics(self.Tlist.value_si)
else:
self.generateKinetics()
if outputFile is not None:
self.save(outputFile)
if plot:
self.plot(os.path.dirname(outputFile))
self.draw(os.path.dirname(outputFile))
if self.sensitivity_conditions is not None:
logging.info('\n\nRunning sensitivity analysis...')
sa(self, os.path.dirname(outputFile))
logging.debug('Finished kinetics job for reaction {0}.'.format(self.reaction))
logging.debug(repr(self.reaction))
def execute(self, output_directory=None, plot=True):
"""
Execute the kinetics job, saving the results within
the `output_directory`.
If `plot` is True, then plots of the raw and fitted values for the kinetics
will be saved.
"""
self.generateKinetics()
if output_directory is not None:
try:
self.write_output(output_directory)
except Exception as e:
logging.warning(
"Could not write kinetics output file due to error: "
"{0} in reaction {1}".format(e, self.reaction.label))
try:
self.write_chemkin(output_directory)
except Exception as e:
logging.warning(
"Could not write kinetics chemkin output due to error: "
"{0} in reaction {1}".format(e, self.reaction.label))
if plot:
try:
self.plot(output_directory)
except Exception as e:
logging.warning("Could not plot kinetics due to error: "
"{0} in reaction {1}".format(
e, self.reaction.label))
try:
self.draw(output_directory)
except:
logging.warning(
"Could not draw reaction {1} due to error: {0}".format(
e, self.reaction.label))
if self.sensitivity_conditions is not None:
logging.info('\n\nRunning sensitivity analysis...')
sa(self, output_directory)
logging.debug('Finished kinetics job for reaction {0}.'.format(
self.reaction))
logging.debug(repr(self.reaction))