Adapt Processor to the new Arkane output

arc/mainTest.py

@@ -238,7 +238,8 @@ def test_restart(self):
 
  self.assertTrue(os.path.isfile(os.path.join(project_directory, 'output', 'thermo_parity_plots.pdf')))
 
- with open(os.path.join(project_directory, 'output', 'Species', 'H2O2', 'species_dictionary.txt'), 'r') as f:
+ with open(os.path.join(project_directory, 'output', 'Species', 'H2O2', 'arkane', 'species_dictionary.txt'),
+ 'r') as f:
  lines = f.readlines()
  adj_list = ''
  for line in lines:

arc/plotter.py

@@ -203,13 +203,17 @@ def plot_rotor_scan(angle, v_list, path=None, pivots=None, comment=''):
 
 def log_thermo(label, path):
  """
- Logging thermodata from an Arkane output file
+ Logging thermodata from an Arkane output file.
+
+ Args:
+ label (str, unicode): The species label.
+ path (str, unicode): The path to the folder containing the relevant Arkane output file.
  """
  logger.info('\n\n')
  logger.debug('Thermodata for species {0}'.format(label))
  thermo_block = ''
  log = False
- with open(path, 'r') as f:
+ with open(os.path.join(path, 'output.py'), 'r') as f:
  line = f.readline()
  while line != '':
  if 'Thermodynamics for' in line:
@@ -226,13 +230,17 @@ def log_thermo(label, path):
 
 def log_kinetics(label, path):
  """
- Logging kinetics from an Arkane output file
+ Logging kinetics from an Arkane output file.
+
+ Args:
+ label (str, unicode): The species label.
+ path (str, unicode): The path to the folder containing the relevant Arkane output file.
  """
  logger.info('\n\n')
  logger.debug('Kinetics for species {0}'.format(label))
  kinetics_block = ''
  log = False
- with open(path, 'r') as f:
+ with open(os.path.join(path, 'output.py'), 'r') as f:
  line = f.readline()
  while line != '':
  if 'kinetics(' in line:

arc/processor.py

@@ -88,21 +88,23 @@ def __init__(self, project, project_directory, species_dict, rxn_list, output, u
 
  def _generate_arkane_species_file(self, species):
  """
- A helper function for generating the Arkane species file
- Assigns the input file path to species.arkane_file and returns a desired path for the output file
+ A helper function for generating the Arkane species file.
+ Assigns the input file path to species.arkane_file.
+
+ Args:
+ species (ARCSpecies): The species to process.
+
+ Returns:
+ str, unicode: The Arkane output path.
  """
  folder_name = 'rxns' if species.is_ts else 'Species'
- output_dir = os.path.join(self.project_directory, 'output', folder_name, species.label)
- if not os.path.isdir(output_dir):
- os.makedirs(output_dir)
- output_file_path = [os.path.join(output_dir, species.label + '_arkane_output.py'),
- os.path.join(output_dir, species.label + '_arkane_output_no_BAC.py')]
- if os.path.isfile(os.path.join(output_dir, 'species_dictionary.txt')):
- os.remove(os.path.join(output_dir, 'species_dictionary.txt'))
+ output_path = os.path.join(self.project_directory, 'output', folder_name, species.label, 'arkane')
+ if not os.path.isdir(output_path):
+ os.makedirs(output_path)
 
  if species.yml_path is not None:
  species.arkane_file = species.yml_path
- return output_file_path
+ return output_path
 
  species.determine_symmetry()
  try:
@@ -174,7 +176,7 @@ def _generate_arkane_species_file(self, species):
  with open(input_file_path, 'wb') as f:
  f.write(input_file)
  species.arkane_file = input_file_path
- return output_file_path
+ return output_path
 
  def process(self):
  """Process ARC outputs and generate thermo and kinetics"""
@@ -185,7 +187,7 @@ def process(self):
  unconverged_species = list()
  for species in self.species_dict.values():
  if not species.is_ts and 'ALL converged' in self.output[species.label]['status']:
- output_file_path = self._generate_arkane_species_file(species)
+ output_path = self._generate_arkane_species_file(species)
  unique_arkane_species_label = False
  while not unique_arkane_species_label:
  try:
@@ -199,27 +201,27 @@ def process(self):
  if species.mol_list:
  arkane_spc.molecule = species.mol_list
  species.rmg_species.molecule = species.mol_list # add resonance structures for thermo determination
- statmech_success = self._run_statmech(arkane_spc, species.arkane_file, output_file_path[0],
+ statmech_success = self._run_statmech(arkane_spc, species.arkane_file, output_path,
  use_bac=self.use_bac)
  if not statmech_success:
  continue
 
  if species.generate_thermo:
  thermo_job = ThermoJob(arkane_spc, 'NASA')
- thermo_job.execute(outputFile=output_file_path[0], plot=False)
+ thermo_job.execute(output_directory=output_path, plot=False)
  species.thermo = arkane_spc.getThermoData()
- plotter.log_thermo(species.label, path=output_file_path[0])
+ plotter.log_thermo(species.label, path=output_path)
  species_for_thermo_lib.append(species)
  if self.use_bac and self.sp_level:
  # If BAC was used, save another Arkane YAML file of this species with no BAC, so it can be used
  # for further rate calculations if needed (where the conformer.E0 has no BAC)
- statmech_success = self._run_statmech(arkane_spc, species.arkane_file, output_file_path[1],
+ statmech_success = self._run_statmech(arkane_spc, species.arkane_file, output_path,
  use_bac=False)
- if statmech_success:
- arkane_spc.label += str('_no_BAC')
- arkane_spc.thermo = None # otherwise thermo won't be calculated, although we don't really care
- thermo_job = ThermoJob(arkane_spc, 'NASA')
- thermo_job.execute(outputFile=output_file_path[1], plot=False)
+ # if statmech_success:
+ #  arkane_spc.label += str('_no_BAC')
+ #  arkane_spc.thermo = None # otherwise thermo won't be calculated, although we don't really care
+ #  thermo_job = ThermoJob(arkane_spc, 'NASA')
+ #  thermo_job.execute(output_directory=output_path, plot=False)
  try:
  species.rmg_thermo = self.rmgdb.thermo.getThermoData(species.rmg_species)
  except (ValueError, AttributeError) as e:
@@ -243,7 +245,7 @@ def process(self):
  self.copy_freq_output_for_ts(species.label)
  success = True
  rxn_list_for_kinetics_plots.append(rxn)
- output_file_path = self._generate_arkane_species_file(species)[0]
+ output_path = self._generate_arkane_species_file(species)
  arkane_ts = arkane_transition_state(str(species.label), species.arkane_file)
  arkane_spc_dict[species.label] = arkane_ts
  self._run_statmech(arkane_ts, species.arkane_file, kinetics=True)
@@ -266,7 +268,7 @@ def process(self):
  kinetics_job = KineticsJob(reaction=arkane_rxn, Tmin=self.t_min, Tmax=self.t_max, Tcount=self.t_count)
  logger.info('Calculating rate for reaction {0}'.format(rxn.label))
  try:
- kinetics_job.execute(outputFile=output_file_path, plot=False)
+ kinetics_job.execute(output_directory=output_path, plot=False)
  except (ValueError, OverflowError) as e:
  # ValueError: One or both of the barrier heights of -9.3526 and 62.683 kJ/mol encountered in Eckart
  # method are invalid.
@@ -282,7 +284,7 @@ def process(self):
  success = False
  if success:
  rxn.kinetics = kinetics_job.reaction.kinetics
- plotter.log_kinetics(species.label, path=output_file_path)
+ plotter.log_kinetics(species.label, path=output_path)
  rxn.rmg_reactions = rmgdb.determine_rmg_kinetics(rmgdb=self.rmgdb, reaction=rxn.rmg_reaction,
  dh_rxn298=rxn.dh_rxn298)
 
@@ -317,13 +319,13 @@ def process(self):
  f.write(str(' SMILES: {0}'.format(spc.mol.toSMILES())))
  f.write(str('\n'))
 
- def _run_statmech(self, arkane_spc, arkane_file, output_file_path=None, use_bac=False, kinetics=False, plot=False):
+ def _run_statmech(self, arkane_spc, arkane_file, output_path=None, use_bac=False, kinetics=False, plot=False):
  """A helper function for running an Arkane statmech job
 
  Args:
  arkane_spc (str, unicode): An Arkane species() function representor.
  arkane_file (str, unicode): The path to the Arkane species file (either in .py or YAML form).
- output_file_path (str, unicode): The path to the Arkane output.py file.
+ output_path (str, unicode): The path to the folder containing the Arkane output.py file.
  use_bac (bool): A flag indicating whether or not to use bond additivity corrections (True to use).
  kinetics (bool) A flag indicating whether this specie is part of a kinetics job.
  plot (bool): A flag indicating whether to plot a PDF of the calculated thermo properties (True to plot)
@@ -344,7 +346,7 @@ def _run_statmech(self, arkane_spc, arkane_file, output_file_path=None, use_bac=
  # (defaults to 1 and prints a warning if not found)
  stat_mech_job.frequencyScaleFactor = self.freq_scale_factor or assign_frequency_scale_factor(self.freq_level)
  try:
- stat_mech_job.execute(outputFile=output_file_path, plot=plot)
+ stat_mech_job.execute(output_directory=os.path.join(output_path, 'output.py'), plot=plot)
  except Exception:
  success = False
  return success
@@ -377,13 +379,16 @@ def _clean_output_directory(self):
  elif '_rotor' in file_name: # move to the rotor directory
  shutil.move(src=os.path.join(species_path, file_name),
  dst=os.path.join(species_path, 'rotors', file_name))
- if os.path.exists(os.path.join(species_path, 'species')): # This is where Arkane saves the YAML file
- species_yaml_files = os.listdir(os.path.join(species_path, 'species'))
+
+ # Arkane YAML files:
+ species_yaml_base_path = os.path.join(species_path, 'arkane', 'species')
+ if os.path.exists(species_yaml_base_path): # The Arkane YAML file is here
+ species_yaml_files = os.listdir(species_yaml_base_path)
  if species_yaml_files:
  for yml_file in species_yaml_files:
- shutil.move(src=os.path.join(species_path, 'species', yml_file),
- dst=os.path.join(species_path, yml_file))
- shutil.rmtree(os.path.join(species_path, 'species'))
+ shutil.move(src=os.path.join(species_yaml_base_path, yml_file),
+ dst=os.path.join(species_path, 'arkane', yml_file))
+ shutil.rmtree(species_yaml_base_path)
 
  def copy_freq_output_for_ts(self, label):
  """

arc/scheduler.py

@@ -563,7 +563,7 @@ def schedule_jobs(self):
  # delete the label only if it represents an empty dictionary
  del self.running_jobs[label]
 
- if self.timer:
+ if self.timer and job_list:
  time.sleep(30) # wait 30 sec before bugging the servers again.
  t = time.time() - self.report_time
  if t > 3600: