Make drawing all PES diagrams an option in the input file.

You can set generatePESDiagrams=True in the options() block
of an input file if you want to save them all.
This is presumably a runtime penalty, or at least a hard disk space penalty,
and probably shouldn't be a default.
Default is False.

Author: rwest

documentation/source/users/rmg/input.rst

@@ -965,6 +965,7 @@ Miscellaneous options::
         units='si',
         generateOutputHTML=True,
         generatePlots=False,
+		generatePESDiagrams=False,
         saveSimulationProfiles=True,
         verboseComments=False,
         saveEdgeSpecies=True,
@@ -986,6 +987,8 @@ HTML file for your model containing all the species and reactions.  Turning this
 
 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 ``generatePESDiagrams`` to ``True`` will generate potential energy surface diagrams for each pressure dependent network in the model.  These diagrams will be saved in the ``pdep/`` folder in the output directory. Only applicable if pressure dependence is enabled.
+
 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.
 
 Setting ``verboseComments`` to ``True`` will make RMG generate chemkin files with complete verbose commentary for the kinetic and thermo parameters.  This will be helpful in debugging what values are being averaged for the kinetics.  Note that this may produce very large files.

examples/rmg/1,3-hexadiene/input.py

@@ -89,4 +89,5 @@
     units='si',
     generateOutputHTML=False,
     generatePlots=False,
+    generatePESDiagrams=True,
 )

examples/rmg/commented/input.py

@@ -217,6 +217,8 @@
     generateOutputHTML=True,
     # generates plots of the RMG's performance statistics. Not helpful if you just want a model.
     generatePlots=False,
+    # generates potential energy surface diagrams for pressure dependent networks in the model.
+    generatePESDiagrams=False,
     # saves mole fraction of species in 'solver/' to help you create plots
     saveSimulationProfiles=False,
     # gets RMG to output comments on where kinetics were obtained in the chemkin file.

examples/rmg/ethane-oxidation/input.py

@@ -67,4 +67,5 @@
     units='si',
     generateOutputHTML=False,
     generatePlots=False,
+    generatePESDiagrams=True,
 )

rmgpy/rmg/input.py

@@ -1369,7 +1369,7 @@ def pressure_dependence(
 
 
 def options(name='Seed', generateSeedEachIteration=True, saveSeedToDatabase=False, units='si', saveRestartPeriod=None,
-            generateOutputHTML=False, generatePlots=False, saveSimulationProfiles=False, verboseComments=False,
+            generateOutputHTML=False, generatePlots=False, generatePESDiagrams=False, saveSimulationProfiles=False, verboseComments=False,
             saveEdgeSpecies=False, keepIrreversible=False, trimolecularProductReversible=True, wallTime='00:00:00:00',
             saveSeedModulus=-1):
     if saveRestartPeriod:
@@ -1386,6 +1386,9 @@ def options(name='Seed', generateSeedEachIteration=True, saveSeedToDatabase=Fals
         logging.warning('Generate Output HTML option was turned on. Note that this will slow down model generation.')
     rmg.generate_output_html = generateOutputHTML
     rmg.generate_plots = generatePlots
+    rmg.generate_PES_diagrams = generatePESDiagrams
+    if generatePESDiagrams:
+        logging.info('Potential Energy Surface diagrams will be generated in the "pdep" folder.')
     rmg.save_simulation_profiles = saveSimulationProfiles
     rmg.verbose_comments = verboseComments
     if saveEdgeSpecies:
@@ -1835,6 +1838,7 @@ def save_input_file(path, rmg):
     f.write('    units = "{0}",\n'.format(rmg.units))
     f.write('    generateOutputHTML = {0},\n'.format(rmg.generate_output_html))
     f.write('    generatePlots = {0},\n'.format(rmg.generate_plots))
+    f.write('    generatePESDiagrams = {0},\n'.format(rmg.generate_PES_diagrams))
     f.write('    saveSimulationProfiles = {0},\n'.format(rmg.save_simulation_profiles))
     f.write('    saveEdgeSpecies = {0},\n'.format(rmg.save_edge_species))
     f.write('    keepIrreversible = {0},\n'.format(rmg.keep_irreversible))

rmgpy/rmg/main.py

@@ -143,6 +143,7 @@ class RMG(util.Subject):
     `units`                                                    The unit system to use to save output files (currently must be 'si')
     `generate_output_html`                                     ``True`` to draw pictures of the species and reactions, saving a visualized model in an output HTML file.  ``False`` otherwise
     `generate_plots`                                           ``True`` to generate plots of the job execution statistics after each iteration, ``False`` otherwise
+    `generate_PES_diagrams`                                    ``True`` to generate potential energy surface diagrams for pressure dependent networks in the model, ``False`` otherwise
     `verbose_comments`                                         ``True`` to keep the verbose comments for database estimates, ``False`` otherwise
     `save_edge_species`                                        ``True`` to save chemkin and HTML files of the edge species, ``False`` otherwise
     `keep_irreversible`                                        ``True`` to keep ireversibility of library reactions as is ('<=>' or '=>'). ``False`` (default) to force all library reactions to be reversible ('<=>')
@@ -222,6 +223,7 @@ def clear(self):
         self.units = "si"
         self.generate_output_html = None
         self.generate_plots = None
+        self.generate_PES_diagrams = None
         self.save_simulation_profiles = None
         self.verbose_comments = None
         self.save_edge_species = None
@@ -271,6 +273,7 @@ def load_input(self, path=None):
         if self.pressure_dependence:
             self.pressure_dependence.output_file = self.output_directory
             self.reaction_model.pressure_dependence = self.pressure_dependence
+            self.pressure_dependence.generate_PES_diagrams = self.generate_PES_diagrams
         if self.solvent:
             self.reaction_model.solvent_name = self.solvent
 

rmgpy/rmg/pdep.py

@@ -872,6 +872,8 @@ def update(self, reaction_model, pdep_settings, requires_rms=False):
         if output_directory:
             job.save_input_file(
                 os.path.join(output_directory, 'pdep', 'network{0:d}_{1:d}.py'.format(self.index, len(self.isomers))))
+            if pdep_settings.generate_PES_diagrams:
+                job.draw(os.path.join(output_directory, 'pdep'), filename_stem=f'network{self.index:d}_{len(self.isomers):d}', file_format='pdf')
 
         # Calculate the rate coefficients
         self.initialize(Tmin, Tmax, Pmin, Pmax, maximum_grain_size, minimum_grain_count, active_j_rotor, active_k_rotor,