Allow disabling of RMS yaml writer for speedup

documentation/source/users/rmg/input.rst

@@ -956,6 +956,7 @@ Miscellaneous options::
         saveSeedToDatabase=True,
         units='si',
         generateOutputHTML=True,
+        generateRMSEachIter=True,
         generatePlots=False,
         saveSimulationProfiles=True,
         verboseComments=False,
@@ -976,6 +977,8 @@ The ``units`` field is set to ``si``.  Currently there are no other unit options
 Setting ``generateOutputHTML`` to ``True`` will let RMG know that you want to save 2-D images (png files in the local ``species`` folder) of all species in the generated core model.  It will save a visualized
 HTML file for your model containing all the species and reactions.  Turning this feature off by setting it to ``False`` may save memory if running large jobs.
 
+Setting ``generateRMSEachIter`` to ``True`` will have rmg generate an output yaml file containing the core mechanism for the current iteration, with the number of core species appended to the name of the file (e.g. for 28 core species, the file will be named ``chem28.rms``). If it is ``False`` then only one file will be generated at the end of the run. A value of ``False`` may result in a faster run, as this feature can take up a lot of cpu time. 
+
 Setting ``generatePlots`` to ``True`` will generate a number of plots describing the statistics of the RMG job, including the reaction model core and edge size and memory use versus  execution time. These will be placed in the output directory in the plot/ folder.
 
 Setting ``saveSimulationProfiles`` to ``True`` will make RMG save csv files of the simulation in .csv files in the ``solver/`` folder.  The filename will be ``simulation_1_26.csv`` where the first number corresponds to the reaciton system, and the second number corresponds to the total number of species at the point of the simulation.  Therefore, the highest second number will indicate the latest simulation that RMG has complete while enlarging the core model.  The information inside the csv file will provide the time, reactor volume in m^3, as well as mole fractions of the individual species.

rmgpy/rmg/input.py

@@ -1337,8 +1337,8 @@ def pressure_dependence(
 
 def options(name='Seed', generateSeedEachIteration=True, saveSeedToDatabase=False, units='si', saveRestartPeriod=None,
             generateOutputHTML=False, generatePlots=False, saveSimulationProfiles=False, verboseComments=False,
-            saveEdgeSpecies=False, keepIrreversible=False, trimolecularProductReversible=True, wallTime='00:00:00:00',
-            saveSeedModulus=-1):
+            saveEdgeSpecies=False, keepIrreversible=False, trimolecularProductReversible=True, generateRMSEachIter=True, 
+            wallTime='00:00:00:00', saveSeedModulus=-1):
     if saveRestartPeriod:
         logging.warning("`saveRestartPeriod` flag was set in the input file, but this feature has been removed. Please "
                         "remove this line from the input file. This will throw an error after RMG-Py 3.1. For "
@@ -1352,6 +1352,7 @@ def options(name='Seed', generateSeedEachIteration=True, saveSeedToDatabase=Fals
     if generateOutputHTML:
         logging.warning('Generate Output HTML option was turned on. Note that this will slow down model generation.')
     rmg.generate_output_html = generateOutputHTML
+    rmg.generate_rms_each_iter = generateRMSEachIter
     rmg.generate_plots = generatePlots
     rmg.save_simulation_profiles = saveSimulationProfiles
     rmg.verbose_comments = verboseComments
@@ -1800,6 +1801,7 @@ def save_input_file(path, rmg):
     f.write('options(\n')
     f.write('    units = "{0}",\n'.format(rmg.units))
     f.write('    generateOutputHTML = {0},\n'.format(rmg.generate_output_html))
+    f.write('    generateRMSEachIter = {0},\n'.format(rmg.generate_rms_each_iter))
     f.write('    generatePlots = {0},\n'.format(rmg.generate_plots))
     f.write('    saveSimulationProfiles = {0},\n'.format(rmg.save_simulation_profiles))
     f.write('    saveEdgeSpecies = {0},\n'.format(rmg.save_edge_species))

rmgpy/rmg/main.py

@@ -723,8 +723,10 @@ def register_listeners(self):
         """
 
         self.attach(ChemkinWriter(self.output_directory))
-        self.attach(RMSWriter(self.output_directory))
 
+        if self.generate_rms_each_iter:
+            self.attach(RMSWriter(self.output_directory))
+
         if self.generate_output_html:
             self.attach(OutputHTMLWriter(self.output_directory))
 
@@ -1187,6 +1189,24 @@ def execute(self, initialize=True, **kwargs):
         except Exception:
             logging.exception("Could not generate Cantera files for some reason.")
 
+        # if we're not writing rms files each iteration, only write one at the end.
+        if not self.generate_rms_each_iter:
+            from rmgpy.yml import write_yml
+
+            # make rms dir
+            dirname = os.path.join(self.output_directory, "rms")
+            if os.path.exists(dirname):
+                # The directory already exists, so delete it (and all its content!)
+                shutil.rmtree(dirname)
+            os.mkdir(dirname)
+
+            # save final rms file
+            solvent_data = None
+            if self.solvent:
+                solvent_data = self.database.solvation.get_solvent_data(self.solvent)
+            write_yml(self.reaction_model.core.species, self.reaction_model.core.reactions, solvent=self.solvent, solvent_data=solvent_data,
+                    path=os.path.join(dirname, 'chem.rms'))
+
         self.check_model()
         # Write output file
         logging.info("")

rmgpy/yml.py

@@ -99,7 +99,7 @@ def get_mech_dict(spcs, rxns, solvent='solvent', solvent_data=None):
 
 
 def get_radicals(spc):
-    if spc.molecule[0].to_smiles() == "[O][O]":  # treat oxygen as stable to improve radical analysis
+    if spc.molecule[0].smiles == "[O][O]":  # treat oxygen as stable to improve radical analysis
         return 0
     else:
         return spc.molecule[0].multiplicity-1
@@ -112,7 +112,7 @@ def obj_to_dict(obj, spcs, names=None, label="solvent"):
         result_dict["type"] = "Species"
         if obj.contains_surface_site():
             result_dict["adjlist"] = obj.molecule[0].to_adjacency_list()
-        result_dict["smiles"] = obj.molecule[0].to_smiles()
+        result_dict["smiles"] = obj.molecule[0].smiles
         result_dict["thermo"] = obj_to_dict(obj.thermo, spcs)
         result_dict["radicalelectrons"] = get_radicals(obj)
         if obj.liquid_volumetric_mass_transfer_coefficient_data:

test/regression/RMS_CSTR_liquid_oxidation/input.py

@@ -62,5 +62,6 @@
 )
 
 options(
+    generateRMSEachIter=False,
     saveEdgeSpecies=True,
 )

test/regression/RMS_constantVIdealGasReactor_superminimal/input.py

@@ -47,4 +47,5 @@
 options(
     units='si',
     saveEdgeSpecies=True,
+    generateRMSEachIter=False,
 )

test/regression/RMS_liquidSurface_ch4o2cat/input.py

@@ -85,4 +85,5 @@
 options(
     units="si",
     saveEdgeSpecies=True,
+    generateRMSEachIter=False,
 )

test/regression/aromatics/input.py

@@ -57,5 +57,6 @@
     saveSimulationProfiles = False,
     saveEdgeSpecies = True,
     verboseComments = False,
+    generateRMSEachIter=False,
 )
 

test/regression/liquid_oxidation/input.py

@@ -63,4 +63,5 @@
 
 options(
     saveEdgeSpecies=True,
+    generateRMSEachIter=False,
 )

test/regression/nitrogen/input.py

@@ -57,6 +57,7 @@
 options(
     units='si',
     saveEdgeSpecies=True,
+    generateRMSEachIter=False,
 )
 
 generatedSpeciesConstraints(

test/regression/oxidation/input.py

@@ -74,6 +74,7 @@
     generatePlots=False,
     saveEdgeSpecies=True,
     saveSimulationProfiles=False,
+    generateRMSEachIter=False,
 )
 
 generatedSpeciesConstraints(

test/regression/sulfur/input.py

@@ -64,6 +64,7 @@
 
 options(
     generateOutputHTML=False,
+    generateRMSEachIter=False,
     generatePlots=False,
     saveEdgeSpecies=True,
     saveSimulationProfiles=False,

test/regression/superminimal/input.py

@@ -56,6 +56,7 @@
     units='si',
     saveRestartPeriod=None,
     generateOutputHTML=True,
+    generateRMSEachIter=False,
     generatePlots=True,
     saveEdgeSpecies=True,
     saveSimulationProfiles=True,

test/rmgpy/rmg/mainTest.py

@@ -87,6 +87,12 @@ def test_rmg_execute(self):
         assert isinstance(self.rmg.database, RMGDatabase)
         assert self.rmg.done
 
+    def test_disable_rms_yaml_writer(self):
+        """
+        generateRMSEachIter = False in input should set the corresponding property in RMG instance
+        """
+        self.assertFalse(self.rmg.generate_rms_each_iter)
+
     def test_rmg_increases_reactions(self):
         """Test that RMG.execute increases reactions and species."""
         assert len(self.rmg.reaction_model.core.reactions) > 0

test/rmgpy/test_data/mainTest/input.py

@@ -73,6 +73,7 @@
     name='testSeed',
     units='si',
     generateSeedEachIteration=True,
+    generateRMSEachIter=False,
     saveSeedToDatabase=True,
     generateOutputHTML=False,
     generatePlots=False,