added input arg for disabling rms yaml write

Author: ChrisBNEU

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=False, 
+            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

@@ -685,8 +685,10 @@ 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))
 
@@ -1116,6 +1118,24 @@ 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('')