From b5d30404907e98d23da4dadb87c9c55b95aa5c8e Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 11 Mar 2024 14:49:08 -0400
Subject: [PATCH 001/162] update environment file, CI, Dockerfile to install
 optional Julia deps

---
 .github/workflows/CI.yml   |  6 ++++++
 .github/workflows/docs.yml |  6 ++++++
 Dockerfile                 |  2 ++
 environment.yml            | 28 ++++++++++++++--------------
 4 files changed, 28 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 7b5a39c162..44ef22a240 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -122,6 +122,12 @@ jobs:
           activate-environment: rmg_env
           use-mamba: true
 
+      # installs the extra RMS conda dependencies
+      - name: Add RMS dependencies
+        run: |
+          mamba install -c conda-forge julia=1.9.1 pyjulia>=0.6 
+          mamba install -c rmg pyrms diffeqpy
+
       # list the environment for debugging purposes
       - name: mamba info
         run: |
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 8ef810f67f..1da6623fdc 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -36,6 +36,12 @@ jobs:
           activate-environment: rmg_env
           use-mamba: true
 
+      # installs the extra RMS conda dependencies
+      - name: Add RMS dependencies
+        run: |
+          mamba install -c conda-forge julia=1.9.1 pyjulia>=0.6 
+          mamba install -c rmg pyrms diffeqpy
+
       - name: Install sphinx
         run: mamba install -y sphinx
 
diff --git a/Dockerfile b/Dockerfile
index a263199c89..af56d5890e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -45,6 +45,8 @@ RUN git clone --single-branch --branch main --depth 1 https://github.com/Reactio
 WORKDIR /rmg/RMG-Py
 # build the conda environment
 RUN conda env create --file environment.yml && \
+    conda install -c conda-forge julia=1.9.1 pyjulia>=0.6 && \
+    conda install -c rmg pyrms diffeqpy && \
     conda clean --all --yes
 
 # This runs all subsequent commands inside the rmg_env conda environment
diff --git a/environment.yml b/environment.yml
index 64df68a1c2..30769a9a69 100644
--- a/environment.yml
+++ b/environment.yml
@@ -16,6 +16,7 @@
 #   made dependency list more explicit (@JacksonBurns).
 # - October 16, 2023 Switched RDKit and descripatastorus to conda-forge,
 #   moved diffeqpy to pip and (temporarily) removed chemprop
+# - Mar 11, 2024 Removed Julia dependencies, now considered optional
 #
 name: rmg_env
 channels:
@@ -48,10 +49,6 @@ dependencies:
   - conda-forge::openbabel >= 3
   - conda-forge::rdkit >=2022.09.1
 
-# general-purpose external software tools
-  - conda-forge::julia=1.9.1
-  - conda-forge::pyjulia >=0.6
-
 # Python tools
   - python >=3.7
   - coverage
@@ -88,21 +85,24 @@ dependencies:
   - rmg::pydas >=1.0.3
   - rmg::pydqed >=1.0.3
   - rmg::pyrdl
-  - rmg::pyrms
   - rmg::symmetry
 
-# packages we would like to stop maintaining (and why)
-  - rmg::diffeqpy
-  # we should use the official verison https://github.com/SciML/diffeqpy),
-  # rather than ours (which is only made so that we can get it from conda)
-  # It is only on pip, so we will need to do something like:
-  # https://stackoverflow.com/a/35245610
-  # Note that _some other_ dep. in this list requires diffeqpy in its recipe
-  # which will cause it to be downloaded from the rmg conda channel
-
 # conda mutex metapackage
   - nomkl
 
+# optional dependencies for using ReactionMechanismSimulator
+# remove the leading '#' to install the required dependencies
+  # - conda-forge::julia=1.9.1
+  # - conda-forge::pyjulia >=0.6
+  # - rmg::pyrms
+  # - rmg::diffeqpy
+
+# Note about diffeqpy:
+# we should use the official verison https://github.com/SciML/diffeqpy),
+# rather than ours (which is only made so that we can get it from conda)
+# It is only on pip, so we will need to do something like:
+# https://stackoverflow.com/a/35245610
+
 # additional packages that are required, but not specified here (and why)
   # pydqed, pydas, mopac, and likely others require a fortran compiler (specifically gfortran)
   # in the environment. Normally we would add this to the environment file with

From 9382ad9418c3020f08c789756a8831045a6d6d6d Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 11 Mar 2024 14:48:46 -0400
Subject: [PATCH 002/162] reorder build steps to ensure julia deps are
 installed in rmg_env

---
 Dockerfile | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index af56d5890e..d34adc2a2c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -28,10 +28,6 @@ RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh &
     rm Miniconda3-latest-Linux-x86_64.sh
 ENV PATH="$PATH:/miniconda/bin"
 
-# Set solver backend to mamba for speed
-RUN conda install -n base conda-libmamba-solver && \
-    conda config --set solver libmamba
-
 # Set Bash as the default shell for following commands
 SHELL ["/bin/bash", "-c"]
 
@@ -44,10 +40,7 @@ RUN git clone --single-branch --branch main --depth 1 https://github.com/Reactio
 
 WORKDIR /rmg/RMG-Py
 # build the conda environment
-RUN conda env create --file environment.yml && \
-    conda install -c conda-forge julia=1.9.1 pyjulia>=0.6 && \
-    conda install -c rmg pyrms diffeqpy && \
-    conda clean --all --yes
+RUN conda env create --file environment.yml
 
 # This runs all subsequent commands inside the rmg_env conda environment
 #
@@ -56,6 +49,10 @@ RUN conda env create --file environment.yml && \
 # in a Dockerfile build script)
 SHELL ["conda", "run", "--no-capture-output", "-n", "rmg_env", "/bin/bash", "-c"]
 
+RUN conda install -c conda-forge julia=1.9.1 pyjulia>=0.6 && \
+    conda install -c rmg pyrms diffeqpy && \
+    conda clean --all --yes
+
 # Set environment variables as directed in the RMG installation instructions
 ENV RUNNER_CWD=/rmg
 ENV PYTHONPATH="$RUNNER_CWD/RMG-Py:$PYTHONPATH"

From 4f97ef472114fcd96826d3842cff3f8cd23d1782 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 12 Jun 2024 09:20:41 -0400
Subject: [PATCH 003/162] add NO_JULIA and requires_rms throughout

---
 rmgpy/rmg/input.py                            |   5 +-
 rmgpy/rmg/main.py                             |  61 +++++----
 rmgpy/rmg/model.py                            | 122 +++++++++---------
 rmgpy/rmg/pdep.py                             |   4 +-
 ...=> reactionmechanismsimulator_reactors.py} |  34 ++---
 5 files changed, 118 insertions(+), 108 deletions(-)
 rename rmgpy/rmg/{reactors.py => reactionmechanismsimulator_reactors.py} (99%)

diff --git a/rmgpy/rmg/input.py b/rmgpy/rmg/input.py
index e04cd82e2e..f776d63027 100644
--- a/rmgpy/rmg/input.py
+++ b/rmgpy/rmg/input.py
@@ -48,9 +48,10 @@
 from rmgpy.solver.surface import SurfaceReactor
 from rmgpy.util import as_list
 from rmgpy.data.surface import MetalDatabase
-from rmgpy.rmg.reactors import Reactor, ConstantVIdealGasReactor, ConstantTLiquidSurfaceReactor, ConstantTVLiquidReactor, ConstantTPIdealGasReactor
 from rmgpy.data.vaporLiquidMassTransfer import liquidVolumetricMassTransferCoefficientPowerLaw
 from rmgpy.molecule.fragment import Fragment
+from rmgpy.rmg.reactionmechanismsimulator_reactors import Reactor, ConstantVIdealGasReactor, ConstantTLiquidSurfaceReactor, ConstantTVLiquidReactor, ConstantTPIdealGasReactor, NO_JULIA
+ 
 
 ################################################################################
 
@@ -1558,6 +1559,8 @@ def read_input_file(path, rmg0):
         exec(f.read(), global_context, local_context)
     except (NameError, TypeError, SyntaxError) as e:
         logging.error('The input file "{0}" was invalid:'.format(full_path))
+        if NO_JULIA:
+            logging.error("During runtime, import of Julia dependencies failed. To use phase systems and RMS reactors, install RMG-Py with RMS.")
         logging.exception(e)
         raise
     finally:
diff --git a/rmgpy/rmg/main.py b/rmgpy/rmg/main.py
index 8df771980d..5380a23e20 100644
--- a/rmgpy/rmg/main.py
+++ b/rmgpy/rmg/main.py
@@ -80,7 +80,8 @@
 from rmgpy.tools.plot import plot_sensitivity
 from rmgpy.tools.uncertainty import Uncertainty, process_local_results
 from rmgpy.yml import RMSWriter
-from rmgpy.rmg.reactors import Reactor
+from rmgpy.rmg.reactionmechanismsimulator_reactors import Reactor as RMSReactor
+from rmgpy.rmg.reactionmechanismsimulator_reactors import NO_JULIA
 
 ################################################################################
 
@@ -507,6 +508,12 @@ def initialize(self, **kwargs):
 
         # Read input file
         self.load_input(self.input_file)
+        
+        # Check if ReactionMechanismSimulator reactors are being used
+        # if RMS is not installed but the user attempted to use it, the load_input_file would have failed
+        # if RMS is installed but they did not use it, we can avoid extra work
+        # if RMS is not installed and they did not use it, we avoid calling certain functions that would raise an error
+        requires_rms = any(isinstance(reactor_system, RMSReactor) for reactor_system in self.reaction_systems)
 
         if kwargs.get("restart", ""):
             import rmgpy.rmg.input
@@ -550,10 +557,10 @@ def initialize(self, **kwargs):
         self.load_database()
 
         for spec in self.initial_species:
-            self.reaction_model.add_species_to_edge(spec)
+            self.reaction_model.add_species_to_edge(spec, requires_rms=requires_rms)
 
         for reaction_system in self.reaction_systems:
-            if isinstance(reaction_system, Reactor):
+            if not NO_JULIA and isinstance(reaction_system, RMSReactor):
                 reaction_system.finish_termination_criteria()
 
         # Load restart seed mechanism (if specified)
@@ -618,12 +625,12 @@ def initialize(self, **kwargs):
         # Seed mechanisms: add species and reactions from seed mechanism
         # DON'T generate any more reactions for the seed species at this time
         for seed_mechanism in self.seed_mechanisms:
-            self.reaction_model.add_seed_mechanism_to_core(seed_mechanism, react=False)
+            self.reaction_model.add_seed_mechanism_to_core(seed_mechanism, react=False, requires_rms=requires_rms)
 
         # Reaction libraries: add species and reactions from reaction library to the edge so
         # that RMG can find them if their rates are large enough
         for library, option in self.reaction_libraries:
-            self.reaction_model.add_reaction_library_to_edge(library)
+            self.reaction_model.add_reaction_library_to_edge(library, requires_rms=requires_rms)
 
         # Also always add in a few bath gases (since RMG-Java does)
         for label, smiles in [("Ar", "[Ar]"), ("He", "[He]"), ("Ne", "[Ne]"), ("N2", "N#N")]:
@@ -695,35 +702,35 @@ def initialize(self, **kwargs):
         # This is necessary so that the PDep algorithm can identify the bath gas
         for spec in self.initial_species:
             if not spec.reactive:
-                self.reaction_model.enlarge(spec)
+                self.reaction_model.enlarge(spec, requires_rms=requires_rms)
         for spec in self.initial_species:
             if spec.reactive:
-                self.reaction_model.enlarge(spec)
+                self.reaction_model.enlarge(spec, requires_rms=requires_rms)
 
         # chatelak: store constant SPC indices in the reactor attributes if any constant SPC provided in the input file
         # advantages to write it here: this is run only once (as species indexes does not change over the generation)
         if self.solvent is not None:
             for index, reaction_system in enumerate(self.reaction_systems):
-                if (
-                    not isinstance(reaction_system, Reactor) and reaction_system.const_spc_names is not None
-                ):  # if no constant species provided do nothing
+                if ((NO_JULIA or not isinstance(reaction_system, RMSReactor)) and reaction_system.const_spc_names is not None):  # if no constant species provided do nothing
                     reaction_system.get_const_spc_indices(self.reaction_model.core.species)  # call the function to identify indices in the solver
 
         self.initialize_reaction_threshold_and_react_flags()
         if self.filter_reactions and self.init_react_tuples:
-            self.react_init_tuples()
+            self.react_init_tuples(requires_rms=requires_rms)
         self.reaction_model.initialize_index_species_dict()
 
         self.initialize_seed_mech()
+        return requires_rms
 
-    def register_listeners(self):
+    def register_listeners(self, requires_rms=False):
         """
         Attaches listener classes depending on the options
         found in the RMG input file.
         """
 
         self.attach(ChemkinWriter(self.output_directory))
-        self.attach(RMSWriter(self.output_directory))
+        if not NO_JULIA and requires_rms:
+            self.attach(RMSWriter(self.output_directory))
 
         if self.generate_output_html:
             self.attach(OutputHTMLWriter(self.output_directory))
@@ -735,7 +742,7 @@ def register_listeners(self):
 
         if self.save_simulation_profiles:
             for index, reaction_system in enumerate(self.reaction_systems):
-                if isinstance(reaction_system, Reactor):
+                if not NO_JULIA and requires_rms and isinstance(reaction_system, RMSReactor):
                     typ = type(reaction_system)
                     raise InputError(f"save_simulation_profiles=True not compatible with reactor of type {typ}")
                 reaction_system.attach(SimulationProfileWriter(self.output_directory, index, self.reaction_model.core.species))
@@ -749,10 +756,10 @@ def execute(self, initialize=True, **kwargs):
         """
 
         if initialize:
-            self.initialize(**kwargs)
+            requires_rms = self.initialize(**kwargs)
 
         # register listeners
-        self.register_listeners()
+        self.register_listeners(requires_rms=requires_rms)
 
         self.done = False
 
@@ -779,7 +786,7 @@ def execute(self, initialize=True, **kwargs):
             # Update react flags
             if self.filter_reactions:
                 # Run the reaction system to update threshold and react flags
-                if isinstance(reaction_system, Reactor):
+                if not NO_JULIA and requires_rms and isinstance(reaction_system, RMSReactor):
                     self.update_reaction_threshold_and_react_flags(
                         rxn_sys_unimol_threshold=np.zeros((len(self.reaction_model.core.species),), bool),
                         rxn_sys_bimol_threshold=np.zeros((len(self.reaction_model.core.species), len(self.reaction_model.core.species)), bool),
@@ -822,6 +829,7 @@ def execute(self, initialize=True, **kwargs):
                 unimolecular_react=self.unimolecular_react,
                 bimolecular_react=self.bimolecular_react,
                 trimolecular_react=self.trimolecular_react,
+                requires_rms=requires_rms,
             )
 
         if not np.isinf(self.model_settings_list[0].thermo_tol_keep_spc_in_edge):
@@ -834,7 +842,7 @@ def execute(self, initialize=True, **kwargs):
             )
 
         if not np.isinf(self.model_settings_list[0].thermo_tol_keep_spc_in_edge):
-            self.reaction_model.thermo_filter_down(maximum_edge_species=self.model_settings_list[0].maximum_edge_species)
+            self.reaction_model.thermo_filter_down(maximum_edge_species=self.model_settings_list[0].maximum_edge_species, requires_rms=requires_rms)
 
         logging.info("Completed initial enlarge edge step.\n")
 
@@ -900,7 +908,7 @@ def execute(self, initialize=True, **kwargs):
                             prune = False
 
                         try:
-                            if isinstance(reaction_system, Reactor):
+                            if not NO_JULIA and requires_rms and isinstance(reaction_system, RMSReactor):
                                 (
                                     terminated,
                                     resurrected,
@@ -993,7 +1001,7 @@ def execute(self, initialize=True, **kwargs):
 
                         # Add objects to enlarge to the core first
                         for objectToEnlarge in objects_to_enlarge:
-                            self.reaction_model.enlarge(objectToEnlarge)
+                            self.reaction_model.enlarge(objectToEnlarge, requires_rms=requires_rms)
 
                         if model_settings.filter_reactions:
                             # Run a raw simulation to get updated reaction system threshold values
@@ -1002,7 +1010,7 @@ def execute(self, initialize=True, **kwargs):
                             temp_model_settings.tol_keep_in_edge = 0
                             if not resurrected:
                                 try:
-                                    if isinstance(reaction_system, Reactor):
+                                    if not NO_JULIA and requires_rms and isinstance(reaction_system, RMSReactor):
                                         (
                                             terminated,
                                             resurrected,
@@ -1071,7 +1079,7 @@ def execute(self, initialize=True, **kwargs):
                                     skip_update=True,
                                 )
                                 logging.warning(
-                                    "Reaction thresholds/flags for Reaction System {0} was not updated due " "to resurrection".format(index + 1)
+                                    "Reaction thresholds/flags for Reaction System {0} was not updated due to resurrection".format(index + 1)
                                 )
 
                             logging.info("")
@@ -1094,13 +1102,14 @@ def execute(self, initialize=True, **kwargs):
                             unimolecular_react=self.unimolecular_react,
                             bimolecular_react=self.bimolecular_react,
                             trimolecular_react=self.trimolecular_react,
+                            requires_rms=requires_rms,
                         )
 
                         if old_edge_size != len(self.reaction_model.edge.reactions) or old_core_size != len(self.reaction_model.core.reactions):
                             reactor_done = False
 
                         if not np.isinf(self.model_settings_list[0].thermo_tol_keep_spc_in_edge):
-                            self.reaction_model.thermo_filter_down(maximum_edge_species=model_settings.maximum_edge_species)
+                            self.reaction_model.thermo_filter_down(maximum_edge_species=model_settings.maximum_edge_species, requires_rms=requires_rms)
 
                         max_num_spcs_hit = len(self.reaction_model.core.species) >= model_settings.max_num_species
 
@@ -1127,6 +1136,7 @@ def execute(self, initialize=True, **kwargs):
                             model_settings.tol_move_to_core,
                             model_settings.maximum_edge_species,
                             model_settings.min_species_exist_iterations_for_prune,
+                            requires_rms=requires_rms,
                         )
                         # Perform garbage collection after pruning
                         collected = gc.collect()
@@ -1891,7 +1901,7 @@ def initialize_reaction_threshold_and_react_flags(self):
                         if self.trimolecular:
                             self.trimolecular_react[:num_restart_spcs, :num_restart_spcs, :num_restart_spcs] = False
 
-    def react_init_tuples(self):
+    def react_init_tuples(self, requires_rms=False):
         """
         Reacts tuples given in the react block
         """
@@ -1924,6 +1934,7 @@ def react_init_tuples(self):
             unimolecular_react=self.unimolecular_react,
             bimolecular_react=self.bimolecular_react,
             trimolecular_react=self.trimolecular_react,
+            requires_rms=requires_rms,
         )
 
     def update_reaction_threshold_and_react_flags(
@@ -2218,7 +2229,7 @@ def __init__(self, reaction_system, bspc):
                 if isinstance(value, list):
                     self.Ranges[key] = [v.value_si for v in value]
 
-        if isinstance(reaction_system, Reactor):
+        if not NO_JULIA and isinstance(reaction_system, RMSReactor):
             self.tmax = reaction_system.tf
         else:
             for term in reaction_system.termination:
diff --git a/rmgpy/rmg/model.py b/rmgpy/rmg/model.py
index 1d8c581cc0..756d4b64cf 100644
--- a/rmgpy/rmg/model.py
+++ b/rmgpy/rmg/model.py
@@ -57,7 +57,8 @@
 from rmgpy.species import Species
 from rmgpy.thermo.thermoengine import submit
 from rmgpy.rmg.decay import decay_species
-from rmgpy.rmg.reactors import PhaseSystem, Phase, Interface, Reactor
+from rmgpy.rmg.reactionmechanismsimulator_reactors import PhaseSystem, Phase, Interface, NO_JULIA
+from rmgpy.rmg.reactionmechanismsimulator_reactors import Reactor as RMSReactor
 from rmgpy.molecule.fragment import Fragment
 
 ################################################################################
@@ -75,7 +76,7 @@ def __init__(self, species=None, reactions=None, phases=None, interfaces={}):
         if phases is None:
             phases = {"Default": Phase(), "Surface": Phase()}
             interfaces = {frozenset({"Default", "Surface"}): Interface(list(phases.values()))}
-        self.phase_system = PhaseSystem(phases, interfaces)
+        self.phase_system = None if NO_JULIA else PhaseSystem(phases, interfaces)
 
     def __reduce__(self):
         """
@@ -349,9 +350,10 @@ def make_new_species(self, object, label="", reactive=True, check_existing=True,
         orilabel = spec.label
         label = orilabel
         i = 2
-        while any([label in phase.names for phase in self.edge.phase_system.phases.values()]):
-            label = orilabel + "-" + str(i)
-            i += 1
+        if self.edge.phase_system:  # None when RMS not installed
+            while any([label in phase.names for phase in self.edge.phase_system.phases.values()]):
+                label = orilabel + "-" + str(i)
+                i += 1
         spec.label = label
 
         logging.debug("Creating new species %s", spec.label)
@@ -589,7 +591,7 @@ def make_new_pdep_reaction(self, forward):
 
         return forward
 
-    def enlarge(self, new_object=None, react_edge=False, unimolecular_react=None, bimolecular_react=None, trimolecular_react=None):
+    def enlarge(self, new_object=None, react_edge=False, unimolecular_react=None, bimolecular_react=None, trimolecular_react=None, requires_rms=False):
         """
         Enlarge a reaction model by processing the objects in the list `new_object`.
         If `new_object` is a
@@ -636,7 +638,7 @@ def enlarge(self, new_object=None, react_edge=False, unimolecular_react=None, bi
 
                 # Add new species
                 if new_species not in self.core.species:
-                    reactions_moved_from_edge = self.add_species_to_core(new_species)
+                    reactions_moved_from_edge = self.add_species_to_core(new_species, requires_rms=requires_rms)
                 else:
                     reactions_moved_from_edge = []
 
@@ -644,7 +646,7 @@ def enlarge(self, new_object=None, react_edge=False, unimolecular_react=None, bi
                 pdep_network, new_species = new_object
                 new_reactions.extend(pdep_network.explore_isomer(new_species))
 
-                self.process_new_reactions(new_reactions, new_species, pdep_network)
+                self.process_new_reactions(new_reactions, new_species, pdep_network, requires_rms=requires_rms)
 
             else:
                 raise TypeError(
@@ -668,7 +670,7 @@ def enlarge(self, new_object=None, react_edge=False, unimolecular_react=None, bi
                         if len(products) == 1 and products[0] == species:
                             new_reactions = network.explore_isomer(species)
 
-                            self.process_new_reactions(new_reactions, species, network)
+                            self.process_new_reactions(new_reactions, species, network, requires_rms=requires_rms)
                             network.update_configurations(self)
                             index = 0
                             break
@@ -693,7 +695,7 @@ def enlarge(self, new_object=None, react_edge=False, unimolecular_react=None, bi
                     # Identify a core species which was used to generate the reaction
                     # This is only used to determine the reaction direction for processing
                     spc = spcTuple[0]
-                    self.process_new_reactions(rxnList, spc)
+                    self.process_new_reactions(rxnList, spc, requires_rms=requires_rms)
 
         ################################################################
         # Begin processing the new species and reactions
@@ -705,7 +707,7 @@ def enlarge(self, new_object=None, react_edge=False, unimolecular_react=None, bi
 
         # Do thermodynamic filtering
         if not np.isinf(self.thermo_tol_keep_spc_in_edge) and self.new_species_list != []:
-            self.thermo_filter_species(self.new_species_list)
+            self.thermo_filter_species(self.new_species_list, requires_rms=requires_rms)
 
         # Update unimolecular (pressure dependent) reaction networks
         if self.pressure_dependence:
@@ -802,7 +804,7 @@ def clear_surface_adjustments(self):
         self.new_surface_spcs_loss = set()
         self.new_surface_rxns_loss = set()
 
-    def process_new_reactions(self, new_reactions, new_species, pdep_network=None, generate_thermo=True, generate_kinetics=True):
+    def process_new_reactions(self, new_reactions, new_species, pdep_network=None, generate_thermo=True, generate_kinetics=True, requires_rms=False):
         """
         Process a list of newly-generated reactions involving the new core
         species or explored isomer `new_species` in network `pdep_network`.
@@ -824,12 +826,12 @@ def process_new_reactions(self, new_reactions, new_species, pdep_network=None, g
                     if spec not in self.core.species:
                         all_species_in_core = False
                         if spec not in self.edge.species:
-                            self.add_species_to_edge(spec)
+                            self.add_species_to_edge(spec, requires_rms=requires_rms)
                 for spec in rxn.products:
                     if spec not in self.core.species:
                         all_species_in_core = False
                         if spec not in self.edge.species:
-                            self.add_species_to_edge(spec)
+                            self.add_species_to_edge(spec, requires_rms=requires_rms)
 
             isomer_atoms = sum([len(spec.molecule[0].atoms) for spec in rxn.reactants])
 
@@ -857,9 +859,9 @@ def process_new_reactions(self, new_reactions, new_species, pdep_network=None, g
                     # The reaction is not new, so it should already be in the core or edge
                     continue
                 if all_species_in_core:
-                    self.add_reaction_to_core(rxn)
+                    self.add_reaction_to_core(rxn, requires_rms=requires_rms)
                 else:
-                    self.add_reaction_to_edge(rxn)
+                    self.add_reaction_to_edge(rxn, requires_rms=requires_rms)
             else:
                 # Add the reaction to the appropriate unimolecular reaction network
                 # If pdep_network is not None then that will be the network the
@@ -1102,7 +1104,7 @@ def log_enlarge_summary(
         logging.info("    The model edge has {0:d} species and {1:d} reactions".format(edge_species_count, edge_reaction_count))
         logging.info("")
 
-    def add_species_to_core(self, spec):
+    def add_species_to_core(self, spec, requires_rms=False):
         """
         Add a species `spec` to the reaction model core (and remove from edge if
         necessary). This function also moves any reactions in the edge that gain
@@ -1120,7 +1122,7 @@ def add_species_to_core(self, spec):
             if spec in self.edge.species:
                 # remove forbidden species from edge
                 logging.info("Species {0} was Forbidden and not added to Core...Removing from Edge.".format(spec))
-                self.remove_species_from_edge(self.reaction_systems, spec)
+                self.remove_species_from_edge(self.reaction_systems, spec, requires_rms=requires_rms)
                 # remove any empty pdep networks as a result of species removal
                 if self.pressure_dependence:
                     self.remove_empty_pdep_networks()
@@ -1132,7 +1134,8 @@ def add_species_to_core(self, spec):
 
         rxn_list = []
         if spec in self.edge.species:
-            self.edge.phase_system.pass_species(spec.label, self.core.phase_system)
+            if not NO_JULIA and requires_rms:
+                self.edge.phase_system.pass_species(spec.label, self.core.phase_system)
             # If species was in edge, remove it
             logging.debug("Removing species %s from edge.", spec)
             self.edge.species.remove(spec)
@@ -1152,31 +1155,26 @@ def add_species_to_core(self, spec):
 
             # Move any identified reactions to the core
             for rxn in rxn_list:
-                self.add_reaction_to_core(rxn)
+                self.add_reaction_to_core(rxn, requires_rms=requires_rms)
                 logging.debug("Moving reaction from edge to core: %s", rxn)
-        else:
-            if spec.molecule[0].contains_surface_site():
-                self.core.phase_system.phases["Surface"].add_species(spec, edge_phase=self.edge.phase_system.phases["Surface"])
-                self.edge.phase_system.species_dict[spec.label] = spec
-                self.core.phase_system.species_dict[spec.label] = spec
-            else:
-                self.core.phase_system.phases["Default"].add_species(spec, edge_phase=self.edge.phase_system.phases["Default"])
-                self.edge.phase_system.species_dict[spec.label] = spec
-                self.core.phase_system.species_dict[spec.label] = spec
+        elif not NO_JULIA and requires_rms:
+            destination_phase = "Surface" if spec.molecule[0].contains_surface_site() else "Default"
+            self.core.phase_system.phases[destination_phase].add_species(spec, edge_phase=self.edge.phase_system.phases[destination_phase])
+            self.edge.phase_system.species_dict[spec.label] = spec
+            self.core.phase_system.species_dict[spec.label] = spec
 
         return rxn_list
 
-    def add_species_to_edge(self, spec):
+    def add_species_to_edge(self, spec, requires_rms=False):
         """
-        Add a species `spec` to the reaction model edge.
+        Add a species `spec` to the reaction model edge and optionally the RMS phase.
         """
         self.edge.species.append(spec)
-        if spec.molecule[0].contains_surface_site():
-            self.edge.phase_system.phases["Surface"].add_species(spec)
-            self.edge.phase_system.species_dict[spec.label] = spec
-        else:
-            self.edge.phase_system.phases["Default"].add_species(spec)
-            self.edge.phase_system.species_dict[spec.label] = spec
+        if NO_JULIA or not requires_rms:
+            return
+        destination_phase = "Surface" if spec.molecule[0].contains_surface_site() else "Default"
+        self.edge.phase_system.phases[destination_phase].add_species(spec)
+        self.edge.phase_system.species_dict[spec.label] = spec
 
     def set_thermodynamic_filtering_parameters(
         self, Tmax, thermo_tol_keep_spc_in_edge, min_core_size_for_prune, maximum_edge_species, reaction_systems
@@ -1200,7 +1198,7 @@ def set_thermodynamic_filtering_parameters(
         self.reaction_systems = reaction_systems
         self.maximum_edge_species = maximum_edge_species
 
-    def thermo_filter_species(self, spcs):
+    def thermo_filter_species(self, spcs, requires_rms=False):
         """
         checks Gibbs energy of the species in species against the
         maximum allowed Gibbs energy
@@ -1215,13 +1213,13 @@ def thermo_filter_species(self, spcs):
                     "greater than the thermo_tol_keep_spc_in_edge of "
                     "{3} ".format(spc, G, Gn, self.thermo_tol_keep_spc_in_edge)
                 )
-                self.remove_species_from_edge(self.reaction_systems, spc)
+                self.remove_species_from_edge(self.reaction_systems, spc, requires_rms=requires_rms)
 
         # Delete any networks that became empty as a result of pruning
         if self.pressure_dependence:
             self.remove_empty_pdep_networks()
 
-    def thermo_filter_down(self, maximum_edge_species, min_species_exist_iterations_for_prune=0):
+    def thermo_filter_down(self, maximum_edge_species, min_species_exist_iterations_for_prune=0, requires_rms=False):
         """
         removes species from the edge based on their Gibbs energy until maximum_edge_species
         is reached under the constraint that all removed species are older than
@@ -1263,7 +1261,7 @@ def thermo_filter_down(self, maximum_edge_species, min_species_exist_iterations_
                 logging.info(
                     "Removing species {0} from edge to meet maximum number of edge species, Gibbs " "number is {1}".format(spc, Gns[rInds[i]])
                 )
-                self.remove_species_from_edge(self.reaction_systems, spc)
+                self.remove_species_from_edge(self.reaction_systems, spc, requires_rms=requires_rms)
 
             # Delete any networks that became empty as a result of pruning
             if self.pressure_dependence:
@@ -1293,7 +1291,7 @@ def remove_empty_pdep_networks(self):
                     del self.network_dict[source]
                 self.network_list.remove(network)
 
-    def prune(self, reaction_systems, tol_keep_in_edge, tol_move_to_core, maximum_edge_species, min_species_exist_iterations_for_prune):
+    def prune(self, reaction_systems, tol_keep_in_edge, tol_move_to_core, maximum_edge_species, min_species_exist_iterations_for_prune, requires_rms=False):
         """
         Remove species from the model edge based on the simulation results from
         the list of `reaction_systems`.
@@ -1373,7 +1371,7 @@ def prune(self, reaction_systems, tol_keep_in_edge, tol_move_to_core, maximum_ed
             for index, spec in species_to_prune[0:prune_due_to_rate_counter]:
                 logging.info("Pruning species %s", spec)
                 logging.debug("    %-56s    %10.4e", spec, max_edge_species_rate_ratios[index])
-                self.remove_species_from_edge(reaction_systems, spec)
+                self.remove_species_from_edge(reaction_systems, spec, requires_rms=requires_rms)
         if len(species_to_prune) - prune_due_to_rate_counter > 0:
             logging.info(
                 "Pruning %d species to obtain an edge size of %d species", len(species_to_prune) - prune_due_to_rate_counter, maximum_edge_species
@@ -1381,7 +1379,7 @@ def prune(self, reaction_systems, tol_keep_in_edge, tol_move_to_core, maximum_ed
             for index, spec in species_to_prune[prune_due_to_rate_counter:]:
                 logging.info("Pruning species %s", spec)
                 logging.debug("    %-56s    %10.4e", spec, max_edge_species_rate_ratios[index])
-                self.remove_species_from_edge(reaction_systems, spec)
+                self.remove_species_from_edge(reaction_systems, spec, requires_rms=requires_rms)
 
         # Delete any networks that became empty as a result of pruning
         if self.pressure_dependence:
@@ -1389,7 +1387,7 @@ def prune(self, reaction_systems, tol_keep_in_edge, tol_move_to_core, maximum_ed
 
         logging.info("")
 
-    def remove_species_from_edge(self, reaction_systems, spec):
+    def remove_species_from_edge(self, reaction_systems, spec, requires_rms=False):
         """
         Remove species `spec` from the reaction model edge.
         """
@@ -1397,11 +1395,12 @@ def remove_species_from_edge(self, reaction_systems, spec):
         # remove the species
         self.edge.species.remove(spec)
         self.index_species_dict.pop(spec.index)
-        self.edge.phase_system.remove_species(spec)
+        if not NO_JULIA and requires_rms:
+            self.edge.phase_system.remove_species(spec)
 
         # clean up species references in reaction_systems
         for reaction_system in reaction_systems:
-            if not isinstance(reaction_system, Reactor):
+            if NO_JULIA or not requires_rms or not isinstance(reaction_system, RMSReactor):
                 try:
                     reaction_system.species_index.pop(spec)
                 except KeyError:
@@ -1473,7 +1472,7 @@ def remove_species_from_edge(self, reaction_systems, spec):
             self.species_cache.remove(spec)
             self.species_cache.append(None)
 
-    def add_reaction_to_core(self, rxn):
+    def add_reaction_to_core(self, rxn, requires_rms=False):
         """
         Add a reaction `rxn` to the reaction model core (and remove from edge if
         necessary). This function assumes `rxn` has already been checked to
@@ -1482,7 +1481,8 @@ def add_reaction_to_core(self, rxn):
         """
         if rxn not in self.core.reactions:
             self.core.reactions.append(rxn)
-            if rxn not in self.edge.reactions:
+            
+            if not NO_JULIA and requires_rms and rxn not in self.edge.reactions:
                 # If a reaction is not in edge but is going to add to core, it is either a seed mechanism or a newly generated reaction where all reactants and products are already in core
                 # If the reaction is in edge, then the corresponding rms_rxn was moved from edge phase to core phase in pass_species already.
                 rms_species_list = self.core.phase_system.get_rms_species_list()
@@ -1499,7 +1499,7 @@ def add_reaction_to_core(self, rxn):
         if rxn in self.edge.reactions:
             self.edge.reactions.remove(rxn)
 
-    def add_reaction_to_edge(self, rxn):
+    def add_reaction_to_edge(self, rxn, requires_rms=False):
         """
         Add a reaction `rxn` to the reaction model edge. This function assumes
         `rxn` has already been checked to ensure it is supposed to be an edge
@@ -1508,6 +1508,8 @@ def add_reaction_to_edge(self, rxn):
         edge).
         """
         self.edge.reactions.append(rxn)
+        if NO_JULIA or not requires_rms:
+            return
         rms_species_list = self.edge.phase_system.get_rms_species_list()
         species_names = self.edge.phase_system.get_species_names()
         bits = np.array([spc.molecule[0].contains_surface_site() for spc in rxn.reactants + rxn.products])
@@ -1564,7 +1566,7 @@ def get_stoichiometry_matrix(self):
                     stoichiometry[i, j] = nu
         return stoichiometry.tocsr()
 
-    def add_seed_mechanism_to_core(self, seed_mechanism, react=False):
+    def add_seed_mechanism_to_core(self, seed_mechanism, react=False, requires_rms=False):
         """
         Add all species and reactions from `seed_mechanism`, a
         :class:`KineticsPrimaryDatabase` object, to the model core. If `react`
@@ -1636,9 +1638,9 @@ def add_seed_mechanism_to_core(self, seed_mechanism, react=False):
                 # This unimolecular library reaction is flagged as `elementary_high_p` and has Arrhenius type kinetics.
                 # We should calculate a pressure-dependent rate for it
                 if len(rxn.reactants) == 1:
-                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.reactants[0])
+                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.reactants[0], requires_rms=requires_rms)
                 else:
-                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.products[0])
+                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.products[0], requires_rms=requires_rms)
 
         # Perform species constraints and forbidden species checks
 
@@ -1675,7 +1677,7 @@ def add_seed_mechanism_to_core(self, seed_mechanism, react=False):
                 spec.get_liquid_volumetric_mass_transfer_coefficient_data()
                 spec.get_henry_law_constant_data()
 
-            self.add_species_to_core(spec)
+            self.add_species_to_core(spec, requires_rms=requires_rms)
 
         for rxn in self.new_reaction_list:
             if self.pressure_dependence and rxn.is_unimolecular():
@@ -1686,7 +1688,7 @@ def add_seed_mechanism_to_core(self, seed_mechanism, react=False):
                     submit(spec, self.solvent_name)
 
                 rxn.fix_barrier_height(force_positive=True)
-            self.add_reaction_to_core(rxn)
+            self.add_reaction_to_core(rxn, requires_rms=requires_rms)
 
         # Check we didn't introduce unmarked duplicates
         self.mark_chemkin_duplicates()
@@ -1698,7 +1700,7 @@ def add_seed_mechanism_to_core(self, seed_mechanism, react=False):
             new_edge_reactions=[],
         )
 
-    def add_reaction_library_to_edge(self, reaction_library):
+    def add_reaction_library_to_edge(self, reaction_library, requires_rms=False):
         """
         Add all species and reactions from `reaction_library`, a
         :class:`KineticsPrimaryDatabase` object, to the model edge.
@@ -1758,9 +1760,9 @@ def add_reaction_library_to_edge(self, reaction_library):
                 # This unimolecular library reaction is flagged as `elementary_high_p` and has Arrhenius type kinetics.
                 # We should calculate a pressure-dependent rate for it
                 if len(rxn.reactants) == 1:
-                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.reactants[0])
+                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.reactants[0], requires_rms=requires_rms)
                 else:
-                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.products[0])
+                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.products[0], requires_rms=requires_rms)
 
         # Perform species constraints and forbidden species checks
         for spec in self.new_species_list:
@@ -1797,7 +1799,7 @@ def add_reaction_library_to_edge(self, reaction_library):
                 spec.get_liquid_volumetric_mass_transfer_coefficient_data()
                 spec.get_henry_law_constant_data()
 
-            self.add_species_to_edge(spec)
+            self.add_species_to_edge(spec, requires_rms=requires_rms)
 
         for rxn in self.new_reaction_list:
             if not (
@@ -1812,7 +1814,7 @@ def add_reaction_library_to_edge(self, reaction_library):
                 )
             ):
                 # Don't add to the edge library reactions that were already processed
-                self.add_reaction_to_edge(rxn)
+                self.add_reaction_to_edge(rxn, requires_rms=requires_rms)
 
         if self.save_edge_species:
             from rmgpy.chemkin import mark_duplicate_reaction
diff --git a/rmgpy/rmg/pdep.py b/rmgpy/rmg/pdep.py
index 0e1398e51a..89b4104d2b 100644
--- a/rmgpy/rmg/pdep.py
+++ b/rmgpy/rmg/pdep.py
@@ -917,7 +917,7 @@ def update(self, reaction_model, pdep_settings):
                                              f'from the {rxn.library} library, and was not added to the model')
                                 break
                         else:
-                            reaction_model.add_reaction_to_core(net_reaction)
+                            reaction_model.add_reaction_to_core(net_reaction, requires_rms=True)
                     else:
                         # Check whether netReaction already exists in the edge as a LibraryReaction
                         for rxn in reaction_model.edge.reactions:
@@ -929,7 +929,7 @@ def update(self, reaction_model, pdep_settings):
                                              f'from the {rxn.library} library, and was not added to the model')
                                 break
                         else:
-                            reaction_model.add_reaction_to_edge(net_reaction)
+                            reaction_model.add_reaction_to_edge(net_reaction, requires_rms=True)
 
                 # Set/update the net reaction kinetics using interpolation model
                 kdata = K[:, :, i, j].copy()
diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactionmechanismsimulator_reactors.py
similarity index 99%
rename from rmgpy/rmg/reactors.py
rename to rmgpy/rmg/reactionmechanismsimulator_reactors.py
index c487601f93..3c748d674b 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactionmechanismsimulator_reactors.py
@@ -35,26 +35,6 @@
 import logging
 import itertools
 
-if __debug__:
-    try:
-        from os.path import dirname, abspath, join, exists
-
-        path_rms = dirname(dirname(dirname(abspath(__file__))))
-        from julia.api import Julia
-
-        jl = Julia(sysimage=join(path_rms, "rms.so")) if exists(join(path_rms, "rms.so")) else Julia(compiled_modules=False)
-        from pyrms import rms
-        from diffeqpy import de
-        from julia import Main
-    except Exception as e:
-        import warnings
-
-        warnings.warn("Unable to import Julia dependencies, original error: " + str(e), RuntimeWarning)
-else:
-    from pyrms import rms
-    from diffeqpy import de
-    from julia import Main
-
 from rmgpy.species import Species
 from rmgpy.molecule.fragment import Fragment
 from rmgpy.reaction import Reaction
@@ -71,6 +51,20 @@
 from rmgpy.data.kinetics.family import TemplateReaction
 from rmgpy.data.kinetics.depository import DepositoryReaction
 
+NO_JULIA = False
+try:
+    if __debug__:
+        from os.path import dirname, abspath, join, exists
+        from julia.api import Julia
+        path_rms = dirname(dirname(dirname(abspath(__file__))))
+        jl = Julia(sysimage=join(path_rms, "rms.so")) if exists(join(path_rms, "rms.so")) else Julia(compiled_modules=False)
+    from pyrms import rms
+    from diffeqpy import de
+    from julia import Main
+except Exception as e:
+    logging.info("Unable to import Julia dependencies, original error: " + str(e) + ". RMS features will not be available on this execution.")
+    NO_JULIA = True
+
 
 class PhaseSystem:
     """

From 6f8780c2eff367eec9194944607e5f3dfe272448 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 12 Jun 2024 09:40:29 -0400
Subject: [PATCH 004/162] bury the import of Julia in Arkane, add helpful error
 if missing

---
 rmgpy/pdep/sls.py | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/rmgpy/pdep/sls.py b/rmgpy/pdep/sls.py
index b183a0bba8..37e324e077 100644
--- a/rmgpy/pdep/sls.py
+++ b/rmgpy/pdep/sls.py
@@ -32,9 +32,8 @@
 and implementing the SLS master equation reduction method
 """
 import sys
+import warnings
 
-from diffeqpy import de
-from julia import Main
 import scipy.sparse as sparse
 import numpy as np
 import scipy.linalg
@@ -46,6 +45,17 @@
 from rmgpy.pdep.me import generate_full_me_matrix, states_to_configurations
 from rmgpy.statmech.translation import IdealGasTranslation
 
+NO_JULIA = False
+try:
+    from diffeqpy import de
+    from julia import Main
+except Exception as e:
+    warnings.warn(
+        f"Unable to import Julia dependencies, original error: {str(e)}"
+        ". Master equation method 'ode' will not be available on this execution."
+    )
+    NO_JULIA = True
+
 
 def get_initial_condition(network, x0, indices):
     """
@@ -150,6 +160,11 @@ def get_rate_coefficients_SLS(network, T, P, method="mexp", neglect_high_energy_
     tau = np.abs(1.0 / fastest_reaction)
 
     if method == "ode":
+        if NO_JULIA:
+            raise RuntimeError(
+                "Required Julia dependencies for method 'ode' are not installed.\n"
+                "Please check your installation (https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html)."
+            )
         f = Main.eval(
             """
 function f(u,M,t)

From 40b368cdda1aa260cecb0d8a6d923693fac89ab6 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 12 Jun 2024 09:40:53 -0400
Subject: [PATCH 005/162] point to the installation documentation if user
 attempts to use RMS -

when it is missing
---
 rmgpy/rmg/input.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/rmgpy/rmg/input.py b/rmgpy/rmg/input.py
index f776d63027..db48e4be08 100644
--- a/rmgpy/rmg/input.py
+++ b/rmgpy/rmg/input.py
@@ -1560,7 +1560,10 @@ def read_input_file(path, rmg0):
     except (NameError, TypeError, SyntaxError) as e:
         logging.error('The input file "{0}" was invalid:'.format(full_path))
         if NO_JULIA:
-            logging.error("During runtime, import of Julia dependencies failed. To use phase systems and RMS reactors, install RMG-Py with RMS.")
+            logging.error(
+                "During runtime, import of Julia dependencies failed. To use phase systems and RMS reactors, install RMG-Py with RMS."
+                " (https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html)"
+            )
         logging.exception(e)
         raise
     finally:

From 9c8667de2a8b92055c4e5e508f124c97f8940fac Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 12 Jun 2024 10:08:43 -0400
Subject: [PATCH 006/162] `conda` now uses `libmamba` by default, update docs

---
 .../users/rmg/installation/anacondaDeveloper.rst   | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/documentation/source/users/rmg/installation/anacondaDeveloper.rst b/documentation/source/users/rmg/installation/anacondaDeveloper.rst
index 4a79244d0c..23401b5b07 100644
--- a/documentation/source/users/rmg/installation/anacondaDeveloper.rst
+++ b/documentation/source/users/rmg/installation/anacondaDeveloper.rst
@@ -25,6 +25,11 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
 
       Note that you should reinitialize or restart your terminal in order for the changes to take effect, as the installer will tell you.
 
+#. If your `conda` version is older than 23.10.0, switch the solver backend to `libmamba` ::
+
+    conda install -n base conda-libmamba-solver
+    conda config --set solver libmamba
+
 #. There are a few system-level dependencies which are required and should not be installed via Conda. These include
    `Git <https://git-scm.com/>`_ for version control, `GNU Make <https://www.gnu.org/software/make/>`_, and the C and C++ compilers from the `GNU Compiler Collection (GCC) <https://gcc.gnu.org/>`_ for compiling RMG.
 
@@ -71,11 +76,6 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
 
    For information on using ``ssh`` with GitHub see the `Connecting to GitHub with SSH <https://docs.github.com/en/authentication/connecting-to-github-with-ssh>`_
 
-#. Switch the conda solver backend to speed up creation of the RMG environment ::
-
-    conda install -n base conda-libmamba-solver
-    conda config --set solver libmamba
-
 #. Navigate to the RMG-Py directory ::
 
     cd RMG-Py
@@ -110,10 +110,6 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
 
     conda activate rmg_env
 
-#. Switch the conda solver to libmamba again, to accelerate any changes you might make to this conda environment in the future::
-
-    conda config --set solver libmamba
-
 #. Compile RMG-Py after activating the conda environment ::
 
     make

From 24a07318e9e762304256e4a534f180c5a4a85f92 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 12 Jun 2024 10:15:40 -0400
Subject: [PATCH 007/162] indicate that Julia is optional but recommended, list
 features

also update the final run example - the point of specifying the `PYTHONPATH` was so that users _don't_ have to give the full path to `rmg.py` - the `python` executable can search it out
---
 .../users/rmg/installation/anacondaDeveloper.rst       | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/documentation/source/users/rmg/installation/anacondaDeveloper.rst b/documentation/source/users/rmg/installation/anacondaDeveloper.rst
index 23401b5b07..b081bab115 100644
--- a/documentation/source/users/rmg/installation/anacondaDeveloper.rst
+++ b/documentation/source/users/rmg/installation/anacondaDeveloper.rst
@@ -115,7 +115,6 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
     make
 
 #. Modify environment variables. Add RMG-Py to the PYTHONPATH to ensure that you can access RMG modules from any folder.
-   *This is important before the next step in which julia dependencies are installed.*
    Also, add your RMG-Py folder to PATH to launch ``rmg.py`` from any folder.
 
    In general, these commands should be placed in the appropriate shell initialization file.
@@ -130,16 +129,21 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
 
    Be sure to either close and reopen your terminal to refresh your environment variables (``source ~/.bashrc`` or ``source ~/.zshrc``).
 
-#. Install and Link Julia dependencies: ::
+#. **Optional (Recommended)**: Install and Link Julia dependencies. Ensure that you have modified your environment variables as described above, and then run the following: ::
 
      julia -e 'using Pkg; Pkg.add("PyCall");Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;'
 
      python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
 
+    Installing these dependencies will allow using ``method='ode'`` when solving the Master Equation with Arkane and using ``ReactionMechanismSimulator.jl``-based reactors in RMG.
 
 #. Finally, you can run RMG from any location by typing the following (given that you have prepared the input file as ``input.py`` in the current folder). ::
 
-    python-jl replace/with/path/to/rmg.py input.py
+     python-jl rmg.py input.py
+    
+    or, if the Julia dependencies are not installed: ::
+
+     python rmg.py input.py
 
 You may now use RMG-Py, Arkane, as well as any of the :ref:`Standalone Modules <modules>` included in the RMG-Py package.
 

From dcef9ab90b9d3a10cf248651c55a032792180100 Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 12 Jun 2024 13:09:19 -0400
Subject: [PATCH 008/162] Apply suggestions from code review

- clearer error messages

Co-authored-by: Hao-Wei Pang <45482070+hwpang@users.noreply.github.com>
---
 rmgpy/pdep/sls.py  | 4 ++--
 rmgpy/rmg/input.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/rmgpy/pdep/sls.py b/rmgpy/pdep/sls.py
index 37e324e077..792a70e9ad 100644
--- a/rmgpy/pdep/sls.py
+++ b/rmgpy/pdep/sls.py
@@ -50,7 +50,7 @@
     from diffeqpy import de
     from julia import Main
 except Exception as e:
-    warnings.warn(
+    logging.info(
         f"Unable to import Julia dependencies, original error: {str(e)}"
         ". Master equation method 'ode' will not be available on this execution."
     )
@@ -163,7 +163,7 @@ def get_rate_coefficients_SLS(network, T, P, method="mexp", neglect_high_energy_
         if NO_JULIA:
             raise RuntimeError(
                 "Required Julia dependencies for method 'ode' are not installed.\n"
-                "Please check your installation (https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html)."
+                "Please follow the steps to install Julia dependencies at https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/anacondaDeveloper.html."
             )
         f = Main.eval(
             """
diff --git a/rmgpy/rmg/input.py b/rmgpy/rmg/input.py
index db48e4be08..ba9b86f87a 100644
--- a/rmgpy/rmg/input.py
+++ b/rmgpy/rmg/input.py
@@ -1562,7 +1562,7 @@ def read_input_file(path, rmg0):
         if NO_JULIA:
             logging.error(
                 "During runtime, import of Julia dependencies failed. To use phase systems and RMS reactors, install RMG-Py with RMS."
-                " (https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html)"
+                " (https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/anacondaDeveloper.html)"
             )
         logging.exception(e)
         raise

From d541afc0ed2a3927ced6f22471c25a8c20e731d0 Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 12 Jun 2024 14:18:01 -0400
Subject: [PATCH 009/162] remove unnesecary `NO_JULIA` check

---
 rmgpy/rmg/main.py  | 19 ++++++++++---------
 rmgpy/rmg/model.py | 16 ++++++++--------
 2 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/rmgpy/rmg/main.py b/rmgpy/rmg/main.py
index 5380a23e20..8a9ebf2d2a 100644
--- a/rmgpy/rmg/main.py
+++ b/rmgpy/rmg/main.py
@@ -81,7 +81,6 @@
 from rmgpy.tools.uncertainty import Uncertainty, process_local_results
 from rmgpy.yml import RMSWriter
 from rmgpy.rmg.reactionmechanismsimulator_reactors import Reactor as RMSReactor
-from rmgpy.rmg.reactionmechanismsimulator_reactors import NO_JULIA
 
 ################################################################################
 
@@ -560,7 +559,7 @@ def initialize(self, **kwargs):
             self.reaction_model.add_species_to_edge(spec, requires_rms=requires_rms)
 
         for reaction_system in self.reaction_systems:
-            if not NO_JULIA and isinstance(reaction_system, RMSReactor):
+            if isinstance(reaction_system, RMSReactor):
                 reaction_system.finish_termination_criteria()
 
         # Load restart seed mechanism (if specified)
@@ -711,7 +710,9 @@ def initialize(self, **kwargs):
         # advantages to write it here: this is run only once (as species indexes does not change over the generation)
         if self.solvent is not None:
             for index, reaction_system in enumerate(self.reaction_systems):
-                if ((NO_JULIA or not isinstance(reaction_system, RMSReactor)) and reaction_system.const_spc_names is not None):  # if no constant species provided do nothing
+                if (
+                    not isinstance(reaction_system, RMSReactor)
+                ) and reaction_system.const_spc_names is not None:  # if no constant species provided do nothing
                     reaction_system.get_const_spc_indices(self.reaction_model.core.species)  # call the function to identify indices in the solver
 
         self.initialize_reaction_threshold_and_react_flags()
@@ -729,7 +730,7 @@ def register_listeners(self, requires_rms=False):
         """
 
         self.attach(ChemkinWriter(self.output_directory))
-        if not NO_JULIA and requires_rms:
+        if requires_rms:
             self.attach(RMSWriter(self.output_directory))
 
         if self.generate_output_html:
@@ -742,7 +743,7 @@ def register_listeners(self, requires_rms=False):
 
         if self.save_simulation_profiles:
             for index, reaction_system in enumerate(self.reaction_systems):
-                if not NO_JULIA and requires_rms and isinstance(reaction_system, RMSReactor):
+                if requires_rms and isinstance(reaction_system, RMSReactor):
                     typ = type(reaction_system)
                     raise InputError(f"save_simulation_profiles=True not compatible with reactor of type {typ}")
                 reaction_system.attach(SimulationProfileWriter(self.output_directory, index, self.reaction_model.core.species))
@@ -786,7 +787,7 @@ def execute(self, initialize=True, **kwargs):
             # Update react flags
             if self.filter_reactions:
                 # Run the reaction system to update threshold and react flags
-                if not NO_JULIA and requires_rms and isinstance(reaction_system, RMSReactor):
+                if requires_rms and isinstance(reaction_system, RMSReactor):
                     self.update_reaction_threshold_and_react_flags(
                         rxn_sys_unimol_threshold=np.zeros((len(self.reaction_model.core.species),), bool),
                         rxn_sys_bimol_threshold=np.zeros((len(self.reaction_model.core.species), len(self.reaction_model.core.species)), bool),
@@ -908,7 +909,7 @@ def execute(self, initialize=True, **kwargs):
                             prune = False
 
                         try:
-                            if not NO_JULIA and requires_rms and isinstance(reaction_system, RMSReactor):
+                            if requires_rms and isinstance(reaction_system, RMSReactor):
                                 (
                                     terminated,
                                     resurrected,
@@ -1010,7 +1011,7 @@ def execute(self, initialize=True, **kwargs):
                             temp_model_settings.tol_keep_in_edge = 0
                             if not resurrected:
                                 try:
-                                    if not NO_JULIA and requires_rms and isinstance(reaction_system, RMSReactor):
+                                    if requires_rms and isinstance(reaction_system, RMSReactor):
                                         (
                                             terminated,
                                             resurrected,
@@ -2229,7 +2230,7 @@ def __init__(self, reaction_system, bspc):
                 if isinstance(value, list):
                     self.Ranges[key] = [v.value_si for v in value]
 
-        if not NO_JULIA and isinstance(reaction_system, RMSReactor):
+        if isinstance(reaction_system, RMSReactor):
             self.tmax = reaction_system.tf
         else:
             for term in reaction_system.termination:
diff --git a/rmgpy/rmg/model.py b/rmgpy/rmg/model.py
index 756d4b64cf..54943270cc 100644
--- a/rmgpy/rmg/model.py
+++ b/rmgpy/rmg/model.py
@@ -1134,7 +1134,7 @@ def add_species_to_core(self, spec, requires_rms=False):
 
         rxn_list = []
         if spec in self.edge.species:
-            if not NO_JULIA and requires_rms:
+            if requires_rms:
                 self.edge.phase_system.pass_species(spec.label, self.core.phase_system)
             # If species was in edge, remove it
             logging.debug("Removing species %s from edge.", spec)
@@ -1157,7 +1157,7 @@ def add_species_to_core(self, spec, requires_rms=False):
             for rxn in rxn_list:
                 self.add_reaction_to_core(rxn, requires_rms=requires_rms)
                 logging.debug("Moving reaction from edge to core: %s", rxn)
-        elif not NO_JULIA and requires_rms:
+        elif requires_rms:
             destination_phase = "Surface" if spec.molecule[0].contains_surface_site() else "Default"
             self.core.phase_system.phases[destination_phase].add_species(spec, edge_phase=self.edge.phase_system.phases[destination_phase])
             self.edge.phase_system.species_dict[spec.label] = spec
@@ -1170,7 +1170,7 @@ def add_species_to_edge(self, spec, requires_rms=False):
         Add a species `spec` to the reaction model edge and optionally the RMS phase.
         """
         self.edge.species.append(spec)
-        if NO_JULIA or not requires_rms:
+        if not requires_rms:
             return
         destination_phase = "Surface" if spec.molecule[0].contains_surface_site() else "Default"
         self.edge.phase_system.phases[destination_phase].add_species(spec)
@@ -1395,12 +1395,12 @@ def remove_species_from_edge(self, reaction_systems, spec, requires_rms=False):
         # remove the species
         self.edge.species.remove(spec)
         self.index_species_dict.pop(spec.index)
-        if not NO_JULIA and requires_rms:
+        if requires_rms:
             self.edge.phase_system.remove_species(spec)
 
         # clean up species references in reaction_systems
         for reaction_system in reaction_systems:
-            if NO_JULIA or not requires_rms or not isinstance(reaction_system, RMSReactor):
+            if not requires_rms or not isinstance(reaction_system, RMSReactor):
                 try:
                     reaction_system.species_index.pop(spec)
                 except KeyError:
@@ -1481,8 +1481,8 @@ def add_reaction_to_core(self, rxn, requires_rms=False):
         """
         if rxn not in self.core.reactions:
             self.core.reactions.append(rxn)
-            
-            if not NO_JULIA and requires_rms and rxn not in self.edge.reactions:
+
+            if requires_rms and rxn not in self.edge.reactions:
                 # If a reaction is not in edge but is going to add to core, it is either a seed mechanism or a newly generated reaction where all reactants and products are already in core
                 # If the reaction is in edge, then the corresponding rms_rxn was moved from edge phase to core phase in pass_species already.
                 rms_species_list = self.core.phase_system.get_rms_species_list()
@@ -1508,7 +1508,7 @@ def add_reaction_to_edge(self, rxn, requires_rms=False):
         edge).
         """
         self.edge.reactions.append(rxn)
-        if NO_JULIA or not requires_rms:
+        if not requires_rms:
             return
         rms_species_list = self.edge.phase_system.get_rms_species_list()
         species_names = self.edge.phase_system.get_species_names()

From d8607f98a3d15fab82feafac0bf67b57cf9af56f Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 12 Jun 2024 13:24:38 -0400
Subject: [PATCH 010/162] import `logging` instead of `warnings`

---
 rmgpy/pdep/sls.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rmgpy/pdep/sls.py b/rmgpy/pdep/sls.py
index 792a70e9ad..a292e8391a 100644
--- a/rmgpy/pdep/sls.py
+++ b/rmgpy/pdep/sls.py
@@ -32,7 +32,7 @@
 and implementing the SLS master equation reduction method
 """
 import sys
-import warnings
+import logging
 
 import scipy.sparse as sparse
 import numpy as np

From 798a1b0daa318f295484e04b41f06f91fe683e98 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Fri, 22 Mar 2024 14:08:04 -0400
Subject: [PATCH 011/162] switch to branch

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 7b5a39c162..1fa6dafd28 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -152,7 +152,7 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
           python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
-          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator'
+          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor

From 8b4f1366527c99dc4b94761eaf9283cd8f1314e1 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Fri, 22 Mar 2024 14:13:17 -0400
Subject: [PATCH 012/162] Use pyjuliacall instead of pyjulia

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 48a4da34a3..a931d842ce 100644
--- a/environment.yml
+++ b/environment.yml
@@ -50,7 +50,7 @@ dependencies:
 
 # general-purpose external software tools
   - conda-forge::julia=1.9.1
-  - conda-forge::pyjulia >=0.6
+  - conda-forge::pyjuliacall >=0.6
 
 # Python tools
   - python >=3.7

From b3796da44143498213ba214fe33e95aa15d920ed Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Fri, 22 Mar 2024 14:16:39 -0400
Subject: [PATCH 013/162] No need to install julia from conda

---
 environment.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index a931d842ce..ecf26b2e5c 100644
--- a/environment.yml
+++ b/environment.yml
@@ -49,7 +49,6 @@ dependencies:
   - conda-forge::rdkit >=2022.09.1
 
 # general-purpose external software tools
-  - conda-forge::julia=1.9.1
   - conda-forge::pyjuliacall >=0.6
 
 # Python tools

From d4c539ec8de1b55ad782bb9a779673e292aa4310 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Fri, 22 Mar 2024 15:27:51 -0400
Subject: [PATCH 014/162] update

---
 .github/workflows/CI.yml |  5 +++--
 environment.yml          | 13 ++++---------
 rmgpy/rmg/reactors.py    | 23 ++++-------------------
 3 files changed, 11 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 1fa6dafd28..3681a02665 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -151,8 +151,9 @@ jobs:
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
-          python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
-          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", rev="fix_installation")); using ReactionMechanismSimulator'
+        
+          python -c "import diffeqpy; diffeqpy.install()"
+          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor
diff --git a/environment.yml b/environment.yml
index ecf26b2e5c..ca8fd9037c 100644
--- a/environment.yml
+++ b/environment.yml
@@ -49,7 +49,8 @@ dependencies:
   - conda-forge::rdkit >=2022.09.1
 
 # general-purpose external software tools
-  - conda-forge::pyjuliacall >=0.6
+  - conda-forge::julia # for calling julia packages
+  - conda-forge::pyjuliacall # for calling julia packages
 
 # Python tools
   - python >=3.7
@@ -87,17 +88,11 @@ dependencies:
 # packages we maintain
   - rmg::pydas >=1.0.3
   - rmg::pydqed >=1.0.3
-  - rmg::pyrms
   - rmg::symmetry
 
 # packages we would like to stop maintaining (and why)
-  - rmg::diffeqpy
-  # we should use the official verison https://github.com/SciML/diffeqpy),
-  # rather than ours (which is only made so that we can get it from conda)
-  # It is only on pip, so we will need to do something like:
-  # https://stackoverflow.com/a/35245610
-  # Note that _some other_ dep. in this list requires diffeqpy in its recipe
-  # which will cause it to be downloaded from the rmg conda channel
+  - pip:
+    - diffeqpy # getting official version diffeqpy from pip (which uses PythonCall instead of PyCall)
 
 # conda mutex metapackage
   - nomkl
diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index c487601f93..52b6ca3144 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -35,25 +35,10 @@
 import logging
 import itertools
 
-if __debug__:
-    try:
-        from os.path import dirname, abspath, join, exists
-
-        path_rms = dirname(dirname(dirname(abspath(__file__))))
-        from julia.api import Julia
-
-        jl = Julia(sysimage=join(path_rms, "rms.so")) if exists(join(path_rms, "rms.so")) else Julia(compiled_modules=False)
-        from pyrms import rms
-        from diffeqpy import de
-        from julia import Main
-    except Exception as e:
-        import warnings
-
-        warnings.warn("Unable to import Julia dependencies, original error: " + str(e), RuntimeWarning)
-else:
-    from pyrms import rms
-    from diffeqpy import de
-    from julia import Main
+from diffeqpy import de
+from juliacall import Main
+rms = juliacall.newmodule("RMS")
+rms.seval("using ReactionMechanismSimulator")
 
 from rmgpy.species import Species
 from rmgpy.molecule.fragment import Fragment

From e8faefb3f28f74f341443e1a2f5b349a996ea8a7 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Fri, 22 Mar 2024 15:30:01 -0400
Subject: [PATCH 015/162] update

---
 .github/workflows/CI.yml                           |  8 ++++----
 Dockerfile                                         |  2 +-
 Makefile                                           |  8 ++++----
 documentation/Makefile                             |  2 +-
 .../users/rmg/installation/anacondaDeveloper.rst   | 14 +++++++-------
 documentation/source/users/rmg/releaseNotes.rst    |  2 +-
 documentation/source/users/rmg/running.rst         | 14 +++++++-------
 .../catalysis/ch4_o2/simulate_ch4o2cat_RMS.ipynb   |  2 +-
 .../sensitivity_analysis_superminimal_RMS.ipynb    |  2 +-
 .../simulation_flux_rop_superminimal_RMS.ipynb     |  2 +-
 rmg.py                                             |  2 +-
 utilities.py                                       |  2 +-
 12 files changed, 30 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 3681a02665..d2d0b92f99 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -170,7 +170,7 @@ jobs:
         run: |
           for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat fragment RMS_constantVIdealGasReactor_fragment;
           do
-            if python-jl rmg.py test/regression/"$regr_test"/input.py; then
+            if python rmg.py test/regression/"$regr_test"/input.py; then
               echo "$regr_test" "Executed Successfully"
             else
               echo "$regr_test" "Failed to Execute" | tee -a $GITHUB_STEP_SUMMARY
@@ -260,7 +260,7 @@ jobs:
 
             echo "<details>"
             # Compare the edge and core
-            if python-jl scripts/checkModels.py \
+            if python scripts/checkModels.py \
                 "$regr_test-core" \
                 $REFERENCE/"$regr_test"/chemkin/chem_annotated.inp \
                 $REFERENCE/"$regr_test"/chemkin/species_dictionary.txt \
@@ -277,7 +277,7 @@ jobs:
             cat "$regr_test-core.log"
             echo "</details>"
             echo "<details>"
-            if python-jl scripts/checkModels.py \
+            if python scripts/checkModels.py \
                 "$regr_test-edge" \
                 $REFERENCE/"$regr_test"/chemkin/chem_edge_annotated.inp \
                 $REFERENCE/"$regr_test"/chemkin/species_edge_dictionary.txt \
@@ -298,7 +298,7 @@ jobs:
             if [ -f test/regression/"$regr_test"/regression_input.py ];
             then
               echo "<details>"
-              if python-jl rmgpy/tools/regression.py \
+              if python rmgpy/tools/regression.py \
                 test/regression/"$regr_test"/regression_input.py \
                 $REFERENCE/"$regr_test"/chemkin \
                 test/regression/"$regr_test"/chemkin
diff --git a/Dockerfile b/Dockerfile
index a263199c89..9dd27c2f35 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -68,7 +68,7 @@ RUN make && \
     python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
 
 # RMG-Py should now be installed and ready - trigger precompilation and test run
-RUN python-jl rmg.py examples/rmg/minimal/input.py
+RUN python rmg.py examples/rmg/minimal/input.py
 # delete the results, preserve input.py
 RUN mv examples/rmg/minimal/input.py . && \
     rm -rf examples/rmg/minimal/* && \
diff --git a/Makefile b/Makefile
index a2f6b3fed2..06055daa3a 100644
--- a/Makefile
+++ b/Makefile
@@ -62,16 +62,16 @@ decython:
 	find . -name *.pyc -exec rm -f '{}' \;
 
 test-all:
-	python-jl -m pytest
+	python -m pytest
 
 test test-unittests:
-	python-jl -m pytest -m "not functional and not database"
+	python -m pytest -m "not functional and not database"
 
 test-functional:
-	python-jl -m pytest -m "functional"
+	python -m pytest -m "functional"
 
 test-database:
-	python-jl -m pytest -m "database"
+	python -m pytest -m "database"
 
 eg0: all
 	mkdir -p testing/eg0
diff --git a/documentation/Makefile b/documentation/Makefile
index d42279f698..5c30e66cd7 100644
--- a/documentation/Makefile
+++ b/documentation/Makefile
@@ -3,7 +3,7 @@
 
 # You can set these variables from the command line.
 SPHINXOPTS    =
-SPHINXBUILD   = python-jl $$(which sphinx-build)
+SPHINXBUILD   = python $$(which sphinx-build)
 PAPER         =
 BUILDDIR      = build
 
diff --git a/documentation/source/users/rmg/installation/anacondaDeveloper.rst b/documentation/source/users/rmg/installation/anacondaDeveloper.rst
index 4a79244d0c..9eb74479fd 100644
--- a/documentation/source/users/rmg/installation/anacondaDeveloper.rst
+++ b/documentation/source/users/rmg/installation/anacondaDeveloper.rst
@@ -143,7 +143,7 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
 
 #. Finally, you can run RMG from any location by typing the following (given that you have prepared the input file as ``input.py`` in the current folder). ::
 
-    python-jl replace/with/path/to/rmg.py input.py
+    python replace/with/path/to/rmg.py input.py
 
 You may now use RMG-Py, Arkane, as well as any of the :ref:`Standalone Modules <modules>` included in the RMG-Py package.
 
@@ -158,7 +158,7 @@ You might have to edit them slightly to match your exact paths. Specifically,
 you will need ``/opt/miniconda3/envs/rmg_env`` to point to where your conda environment is located.
 
 This configuration will allow you to debug the rms_constant_V example, running through
-python-jl. ::
+python. ::
 
         {
             "name": "Python: rmg.py rms_constant_V",
@@ -166,7 +166,7 @@ python-jl. ::
             "request": "launch",
             "cwd": "${workspaceFolder}/",
             "program": "rmg.py",
-            "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl",
+            "python": "/opt/miniconda3/envs/rmg_env/bin/python",
             "args": [
                 "examples/rmg/rms_constant_V/input.py",
             ],
@@ -185,7 +185,7 @@ Open one of the many test files named ``*Test.py`` in ``test/rmgpy`` before you
             "type": "python",
             "request": "launch",
             "program": "/opt/miniconda3/envs/rmg_env/bin/pytest",
-            "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl",
+            "python": "/opt/miniconda3/envs/rmg_env/bin/python",
             "args": [
                 "--capture=no",
                 "--verbose",
@@ -205,7 +205,7 @@ This configuration will allow you to debug running all the database tests.::
             "type": "python",
             "request": "launch",
             "program": "/opt/miniconda3/envs/rmg_env/bin/pytest",
-            "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl",
+            "python": "/opt/miniconda3/envs/rmg_env/bin/python",
             "args": [
                 "--capture=no",
                 "--verbose",
@@ -226,7 +226,7 @@ This configuration will allow you to use the debugger breakpoints inside unit te
             "request": "launch",
             "program": "${file}",
             "purpose": ["debug-test"],
-            "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl",
+            "python": "/opt/miniconda3/envs/rmg_env/bin/python",
             "console": "integratedTerminal",
             "justMyCode": false,
             "env": {"PYTEST_ADDOPTS": "--no-cov",} // without disabling coverage VS Code doesn't stop at breakpoints while debugging because pytest-cov is using the same technique to access the source code being run
@@ -274,7 +274,7 @@ To configure the rest of the settings, find the ``settings.json`` file in your `
 You can use the following settings to configure the pytest framework::
 
     "python.testing.pytestEnabled": true,
-    "python.testing.pytestPath": "python-jl -m pytest",
+    "python.testing.pytestPath": "python -m pytest",
     "python.testing.pytestArgs": [
         "-p", "julia.pytestplugin",
         "--julia-compiled-modules=no",
diff --git a/documentation/source/users/rmg/releaseNotes.rst b/documentation/source/users/rmg/releaseNotes.rst
index 82c9fbf24a..4ddd936a98 100644
--- a/documentation/source/users/rmg/releaseNotes.rst
+++ b/documentation/source/users/rmg/releaseNotes.rst
@@ -159,7 +159,7 @@ Date: August 2, 2023
     - Changed get_all_solute_data function for RMG-website use in order to apply halogen or radical correction on top of library or GAV
     - Added openSUSE installation instructions
     - Changed default branch to main
-    - Changed rmg.py shebang to use python-jl instead of python3 for compatibility with RMS/pyrms
+    - Changed rmg.py shebang to use python instead of python3 for compatibility with RMS/pyrms
     - Updated ketoenol template image to 1,3 sigmatropic rearrangement
     - Updated 2+2_cycloaddition images in documentation
     - Added licensing information to the README file
diff --git a/documentation/source/users/rmg/running.rst b/documentation/source/users/rmg/running.rst
index 0bb21b80a6..aa28563a89 100755
--- a/documentation/source/users/rmg/running.rst
+++ b/documentation/source/users/rmg/running.rst
@@ -10,7 +10,7 @@ Running a basic RMG job is straightforward, as shown in the example below. Howev
 
 Basic run::
 
-	python-jl rmg.py input.py
+	python rmg.py input.py
 
 .. _inputflags:
 
@@ -19,7 +19,7 @@ Input flags
 
 The options for input flags can be found in ``/RMG-Py/rmgpy/util.py``. Running ::
 
- 	python-jl rmg.py -h
+ 	python rmg.py -h
 
 at the command line will print the documentation from ``util.py``, which is reproduced below for convenience::
 
@@ -63,23 +63,23 @@ Some representative example usages are shown below.
 
 Run by restarting from a seed mechanism::
 
-    python-jl rmg.py -r path/to/seed/ input.py
+    python rmg.py -r path/to/seed/ input.py
 
 Run with CPU time profiling::
 
-    python-jl rmg.py -p input.py
+    python rmg.py -p input.py
 
 Run with multiprocessing for reaction generation and QMTP::
 
-    python-jl rmg.py -n <Max number of processes allowed> input.py 
+    python rmg.py -n <Max number of processes allowed> input.py 
 
 Run with setting a limit on the maximum execution time::
 
-	python-jl rmg.py -t <DD:HH:MM:SS> input.py
+	python rmg.py -t <DD:HH:MM:SS> input.py
 
 Run with setting a limit on the maximum number of iterations::
 
-	python-jl rmg.py -i <Max number of desired iterations> input.py
+	python rmg.py -i <Max number of desired iterations> input.py
 
 
 Details on the multiprocessing implementation
diff --git a/examples/rmg/catalysis/ch4_o2/simulate_ch4o2cat_RMS.ipynb b/examples/rmg/catalysis/ch4_o2/simulate_ch4o2cat_RMS.ipynb
index 700eb3cac3..371bfc2cad 100644
--- a/examples/rmg/catalysis/ch4_o2/simulate_ch4o2cat_RMS.ipynb
+++ b/examples/rmg/catalysis/ch4_o2/simulate_ch4o2cat_RMS.ipynb
@@ -49,7 +49,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# ! python-jl /rmg/RMG-Py/rmg.py /rmg/RMG-Py/examples/rmg/catalysis/ch4_o2/input.py"
+    "# ! python /rmg/RMG-Py/rmg.py /rmg/RMG-Py/examples/rmg/catalysis/ch4_o2/input.py"
    ]
   },
   {
diff --git a/examples/rmg/superminimal/sensitivity_analysis_superminimal_RMS.ipynb b/examples/rmg/superminimal/sensitivity_analysis_superminimal_RMS.ipynb
index ba6b3b6a98..44befc780f 100644
--- a/examples/rmg/superminimal/sensitivity_analysis_superminimal_RMS.ipynb
+++ b/examples/rmg/superminimal/sensitivity_analysis_superminimal_RMS.ipynb
@@ -40,7 +40,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# ! python-jl /rmg/RMG-Py/rmg.py /rmg/RMG-Py/examples/rmg/superminimal/input.py"
+    "# ! python /rmg/RMG-Py/rmg.py /rmg/RMG-Py/examples/rmg/superminimal/input.py"
    ]
   },
   {
diff --git a/examples/rmg/superminimal/simulation_flux_rop_superminimal_RMS.ipynb b/examples/rmg/superminimal/simulation_flux_rop_superminimal_RMS.ipynb
index 7540b21b01..8ca7eb0029 100644
--- a/examples/rmg/superminimal/simulation_flux_rop_superminimal_RMS.ipynb
+++ b/examples/rmg/superminimal/simulation_flux_rop_superminimal_RMS.ipynb
@@ -40,7 +40,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# ! python-jl /rmg/RMG-Py/rmg.py /rmg/RMG-Py/examples/rmg/superminimal/input.py"
+    "# ! python /rmg/RMG-Py/rmg.py /rmg/RMG-Py/examples/rmg/superminimal/input.py"
    ]
   },
   {
diff --git a/rmg.py b/rmg.py
index 26c27c00a4..0b27098b81 100644
--- a/rmg.py
+++ b/rmg.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python-jl
+#!/usr/bin/env python
 
 ###############################################################################
 #                                                                             #
diff --git a/utilities.py b/utilities.py
index c8e7425818..f84963a632 100644
--- a/utilities.py
+++ b/utilities.py
@@ -310,7 +310,7 @@ def update_headers():
     start of each file, be sure to double-check the results to make sure
     important lines aren't accidentally overwritten.
     """
-    shebang = """#!/usr/bin/env python-jl
+    shebang = """#!/usr/bin/env python
 
 """
 

From f52d0d7666c5249e766b21c635b89f9527f74891 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Fri, 22 Mar 2024 15:35:02 -0400
Subject: [PATCH 016/162] Swap the order

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index d2d0b92f99..4897b8bc8a 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -152,8 +152,8 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
         
-          python -c "import diffeqpy; diffeqpy.install()"
           julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
+          python -c "import diffeqpy; diffeqpy.install()"
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor

From c1f2017367d816f66c680970826a12f02acbc293 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Fri, 22 Mar 2024 18:22:57 -0400
Subject: [PATCH 017/162] update

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index ca8fd9037c..5ab5ff51cb 100644
--- a/environment.yml
+++ b/environment.yml
@@ -49,7 +49,7 @@ dependencies:
   - conda-forge::rdkit >=2022.09.1
 
 # general-purpose external software tools
-  - conda-forge::julia # for calling julia packages
+  - conda-forge::julia
   - conda-forge::pyjuliacall # for calling julia packages
 
 # Python tools

From a11a96de0c406ff62847c84c11740072defb135b Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Fri, 22 Mar 2024 19:10:18 -0400
Subject: [PATCH 018/162] doc

---
 .github/workflows/docs.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 8ef810f67f..5ccd937767 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -63,8 +63,8 @@ jobs:
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
-          python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
-          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator'
+          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
+          python -c "import diffeqpy; diffeqpy.install()"
 
       - name: Checkout gh-pages Branch
         uses: actions/checkout@v2

From 05d17726d7cc5745a404c3eb7fddf04b77342d50 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Mon, 1 Apr 2024 10:41:39 -0400
Subject: [PATCH 019/162] Use the preexisting mamba

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 4897b8bc8a..f3e30c46fe 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -151,7 +151,7 @@ jobs:
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
-        
+          export JULIA_CONDAPKG_EXE=$CONDA
           julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
           python -c "import diffeqpy; diffeqpy.install()"
 

From 6f5612c79f25906e5f786cfb067245c5d9c8c9a1 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Mon, 1 Apr 2024 10:56:21 -0400
Subject: [PATCH 020/162] Use JULIA_CONDAPKG_EXE=$CONDA/condabin/conda

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index f3e30c46fe..503b9edd83 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -151,7 +151,7 @@ jobs:
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
-          export JULIA_CONDAPKG_EXE=$CONDA
+          export JULIA_CONDAPKG_EXE=$CONDA/condabin/conda
           julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
           python -c "import diffeqpy; diffeqpy.install()"
 

From be3e4240bb51b6f6414a57e4d6b107fbe658a3ab Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Mon, 1 Apr 2024 11:20:56 -0400
Subject: [PATCH 021/162] Add channels

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 503b9edd83..b13cce9dc5 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -152,7 +152,7 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
           export JULIA_CONDAPKG_EXE=$CONDA/condabin/conda
-          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
+          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("CondaPkg"); using CondaPkg; CondaPkg.add_channel("defaults"); CondaPkg.add_channel("rmg"); CondaPkg.add_channel("conda-forge"); CondaPkg.add_channel("cantera"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
           python -c "import diffeqpy; diffeqpy.install()"
 
       - name: Install Q2DTor

From a812cab3278070d829a2086278865aece57d3d25 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Mon, 1 Apr 2024 11:21:06 -0400
Subject: [PATCH 022/162] skip make for now for debugging

---
 .github/workflows/CI.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index b13cce9dc5..2e991ce0af 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -141,11 +141,11 @@ jobs:
           echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV
           echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH
 
-      # RMG build step
-      - name: make RMG
-        run: |
-          make clean
-          make
+      # # RMG build step
+      # - name: make RMG
+      #   run: |
+      #     make clean
+      #     make
 
       # RMS installation and linking to Julia
       - name: Install and link Julia dependencies

From 0a165eeb120231c02c5aaf1aa1e1034aa45533a8 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Mon, 1 Apr 2024 13:34:45 -0400
Subject: [PATCH 023/162] Trying to use juliaup

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 5ab5ff51cb..e4259c8feb 100644
--- a/environment.yml
+++ b/environment.yml
@@ -49,7 +49,7 @@ dependencies:
   - conda-forge::rdkit >=2022.09.1
 
 # general-purpose external software tools
-  - conda-forge::julia
+  - conda-forge::juliaup
   - conda-forge::pyjuliacall # for calling julia packages
 
 # Python tools

From bf7017b8a68998f57c469a4bfffa9e338e49027f Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Mon, 1 Apr 2024 15:20:09 -0400
Subject: [PATCH 024/162] Don't need to install diffeqpy

---
 .github/workflows/CI.yml   |  1 -
 .github/workflows/docs.yml |  1 -
 environment.yml            |  4 ----
 rmgpy/pdep/sls.py          | 17 +++++++++--------
 rmgpy/rmg/reactors.py      |  3 +--
 5 files changed, 10 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 2e991ce0af..ed2f82f24e 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -153,7 +153,6 @@ jobs:
         run: |
           export JULIA_CONDAPKG_EXE=$CONDA/condabin/conda
           julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("CondaPkg"); using CondaPkg; CondaPkg.add_channel("defaults"); CondaPkg.add_channel("rmg"); CondaPkg.add_channel("conda-forge"); CondaPkg.add_channel("cantera"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
-          python -c "import diffeqpy; diffeqpy.install()"
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 5ccd937767..616aceae85 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -64,7 +64,6 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
           julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
-          python -c "import diffeqpy; diffeqpy.install()"
 
       - name: Checkout gh-pages Branch
         uses: actions/checkout@v2
diff --git a/environment.yml b/environment.yml
index e4259c8feb..dc6875487b 100644
--- a/environment.yml
+++ b/environment.yml
@@ -90,10 +90,6 @@ dependencies:
   - rmg::pydqed >=1.0.3
   - rmg::symmetry
 
-# packages we would like to stop maintaining (and why)
-  - pip:
-    - diffeqpy # getting official version diffeqpy from pip (which uses PythonCall instead of PyCall)
-
 # conda mutex metapackage
   - nomkl
 
diff --git a/rmgpy/pdep/sls.py b/rmgpy/pdep/sls.py
index b183a0bba8..fab0af9732 100644
--- a/rmgpy/pdep/sls.py
+++ b/rmgpy/pdep/sls.py
@@ -33,8 +33,9 @@
 """
 import sys
 
-from diffeqpy import de
-from julia import Main
+import juliacall
+jl = juliacall.newmodule("SciMLBase")
+jl.seval("using SciMLBase")
 import scipy.sparse as sparse
 import numpy as np
 import scipy.linalg
@@ -98,17 +99,17 @@ def solve_me(M, p0, t):
 end"""
     )
     tspan = (0.0, t)
-    fcn = de.ODEFunction(f, jac=jac)
-    prob = de.ODEProblem(fcn, p0, tspan, M)
-    sol = de.solve(prob, solver=de.CVODE_BDF(), abstol=1e-16, reltol=1e-6)
+    fcn = jl.ODEFunction(f, jac=jac)
+    prob = jl.ODEProblem(fcn, p0, tspan, M)
+    sol = jl.solve(prob, solver=jl.CVODE_BDF(), abstol=1e-16, reltol=1e-6)
     return sol
 
 
 def solve_me_fcns(f, jac, M, p0, t):
     tspan = (0.0, t)
-    fcn = de.ODEFunction(f, jac=jac)
-    prob = de.ODEProblem(fcn, p0, tspan, M)
-    sol = de.solve(prob, solver=de.CVODE_BDF(), abstol=1e-16, reltol=1e-6)
+    fcn = jl.ODEFunction(f, jac=jac)
+    prob = jl.ODEProblem(fcn, p0, tspan, M)
+    sol = jl.solve(prob, solver=jl.CVODE_BDF(), abstol=1e-16, reltol=1e-6)
     return sol
 
 
diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index 52b6ca3144..e74d72fd67 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -35,7 +35,6 @@
 import logging
 import itertools
 
-from diffeqpy import de
 from juliacall import Main
 rms = juliacall.newmodule("RMS")
 rms.seval("using ReactionMechanismSimulator")
@@ -431,7 +430,7 @@ def simulate(self, model_settings, simulator_settings, conditions):
             model_settings.tol_rxn_to_core_deadend_radical,
             atol=simulator_settings.atol,
             rtol=simulator_settings.rtol,
-            solver=de.CVODE_BDF(),
+            solver=rms.Sundials.CVODE_BDF(),
         )
 
         return (

From b312ca1f23d89993526683d4d5343b0182bffce7 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Mon, 1 Apr 2024 15:45:24 -0400
Subject: [PATCH 025/162] Uncomment make step

---
 .github/workflows/CI.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index ed2f82f24e..d5241db034 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -141,11 +141,11 @@ jobs:
           echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV
           echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH
 
-      # # RMG build step
-      # - name: make RMG
-      #   run: |
-      #     make clean
-      #     make
+      # RMG build step
+      - name: make RMG
+        run: |
+          make clean
+          make
 
       # RMS installation and linking to Julia
       - name: Install and link Julia dependencies

From c4fc8093fa6ddb999247791e0101416a09edc9cb Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Mon, 1 Apr 2024 15:47:34 -0400
Subject: [PATCH 026/162] Don't need julia plug in

---
 pytest.ini | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pytest.ini b/pytest.ini
index b17574cc17..7879baabed 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -17,7 +17,6 @@ filterwarnings =
 # -n auto # will use all available cores, if you first pip install pytest-xdist, but it doesn't work well with julia (so add --no-julia? or give up?)
 addopts = 
     --keep-duplicates
-    -p julia.pytestplugin 
     -vv 
     --ignore test/regression
     --cov=arkane --cov=rmgpy

From 3ce04fd18c1c87624d7227b3d24b865caa0f57c8 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Mon, 1 Apr 2024 16:09:07 -0400
Subject: [PATCH 027/162] Use mamba

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index d5241db034..413f722741 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -151,7 +151,7 @@ jobs:
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
-          export JULIA_CONDAPKG_EXE=$CONDA/condabin/conda
+          export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
           julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("CondaPkg"); using CondaPkg; CondaPkg.add_channel("defaults"); CondaPkg.add_channel("rmg"); CondaPkg.add_channel("conda-forge"); CondaPkg.add_channel("cantera"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor

From 17f397b0860a11d12107b1f9dec789507528826e Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Mon, 1 Apr 2024 16:14:44 -0400
Subject: [PATCH 028/162] No need to add channels

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 413f722741..59603a02b2 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -152,7 +152,7 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
           export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
-          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("CondaPkg"); using CondaPkg; CondaPkg.add_channel("defaults"); CondaPkg.add_channel("rmg"); CondaPkg.add_channel("conda-forge"); CondaPkg.add_channel("cantera"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
+          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor

From f65d07dff64dd8dfe44d037508001e64b2a2007c Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 2 Apr 2024 09:17:30 -0400
Subject: [PATCH 029/162] import juliacall

---
 rmgpy/rmg/reactors.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index e74d72fd67..35ccbffe81 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -35,7 +35,7 @@
 import logging
 import itertools
 
-from juliacall import Main
+import juliacall
 rms = juliacall.newmodule("RMS")
 rms.seval("using ReactionMechanismSimulator")
 

From d52efbfc43a3fc5d680f97e1ab6d32c80afe3d7f Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 2 Apr 2024 10:13:38 -0400
Subject: [PATCH 030/162] Don't track coverage

---
 .gitignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index d52d5c680f..087e01fda0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -47,7 +47,7 @@ nbproject/*
 .vscode/*
 
 # Unit test files
-.coverage
+.coverage*
 testing/*
 htmlcov/*
 

From c7c063299684957a5fdf54ad516413aaee3493cc Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 2 Apr 2024 11:03:43 -0400
Subject: [PATCH 031/162] debug

---
 rmgpy/pdep/sls.py     | 16 ++++---------
 rmgpy/rmg/reactors.py | 55 ++++++++++++++++++++++++++-----------------
 2 files changed, 38 insertions(+), 33 deletions(-)

diff --git a/rmgpy/pdep/sls.py b/rmgpy/pdep/sls.py
index fab0af9732..ae6ce7950a 100644
--- a/rmgpy/pdep/sls.py
+++ b/rmgpy/pdep/sls.py
@@ -31,21 +31,15 @@
 Contains functionality for directly simulating the master equation
 and implementing the SLS master equation reduction method
 """
-import sys
 
-import juliacall
-jl = juliacall.newmodule("SciMLBase")
-jl.seval("using SciMLBase")
-import scipy.sparse as sparse
+import juliacall import Main
+Main.seval("using SciMLBase")
 import numpy as np
 import scipy.linalg
-import mpmath
 import scipy.optimize as opt
 
 import rmgpy.constants as constants
-from rmgpy.pdep.reaction import calculate_microcanonical_rate_coefficient
 from rmgpy.pdep.me import generate_full_me_matrix, states_to_configurations
-from rmgpy.statmech.translation import IdealGasTranslation
 
 
 def get_initial_condition(network, x0, indices):
@@ -151,13 +145,13 @@ def get_rate_coefficients_SLS(network, T, P, method="mexp", neglect_high_energy_
     tau = np.abs(1.0 / fastest_reaction)
 
     if method == "ode":
-        f = Main.eval(
+        f = jl.eval(
             """
 function f(u,M,t)
     return M*u
 end"""
         )
-        jac = Main.eval(
+        jac = jl.eval(
             """
 function jac(u,M,t)
     return M
@@ -248,7 +242,7 @@ def run_equilibrium(network, channel):
     xseq = []
     dxdtseq = []
 
-    # Single domainant source simulations
+    # Single dojlant source simulations
     for i, isomer in enumerate(isomers):
         xsout, dxdtout = run_single_source(network, isomer)
         for j in range(len(xsout)):
diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index 35ccbffe81..f71329274f 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -36,6 +36,8 @@
 import itertools
 
 import juliacall
+from juliacall import Main
+Main.seval("using PythonCall")
 rms = juliacall.newmodule("RMS")
 rms.seval("using ReactionMechanismSimulator")
 
@@ -135,8 +137,8 @@ def pass_species(self, label, phasesys):
 
         rxnlist = []
         for i, rxn in enumerate(self.phases[phase_label].reactions):
-            if (spc.name in [spec.name for spec in rxn.reactants + rxn.products]) and all(
-                [spec.name in phasesys.species_dict for spec in rxn.reactants + rxn.products]
+            if (spc.name in [spec.name for spec in Main.pylist(rxn.reactants) + Main.pylist(rxn.products)]) and all(
+                [spec.name in phasesys.species_dict for spec in Main.pylist(rxn.reactants) + Main.pylist(rxn.products)]
             ):
                 rxnlist.append(rxn)
 
@@ -430,7 +432,7 @@ def simulate(self, model_settings, simulator_settings, conditions):
             model_settings.tol_rxn_to_core_deadend_radical,
             atol=simulator_settings.atol,
             rtol=simulator_settings.rtol,
-            solver=rms.Sundials.CVODE_BDF(),
+            solver=rms.ReactionMechanismSimulator.Sundials.CVODE_BDF(),
         )
 
         return (
@@ -456,7 +458,7 @@ def generate_reactor(self, phase_system):
         """
         phase = phase_system.phases["Default"]
         ig = rms.IdealGas(phase.species, phase.reactions)
-        domain, y0, p = rms.ConstantVDomain(phase=ig, initialconds=self.initial_conditions)
+        domain, y0, p = rms.ConstantVDomain(phase=ig, initialconds=to_julia(self.initial_conditions))
         react = rms.Reactor(domain, y0, (0.0, self.tf), p=p)
         return react, domain, [], p
 
@@ -476,9 +478,9 @@ def generate_reactor(self, phase_system):
         surf = rms.IdealSurface(surf.species, surf.reactions, surf.site_density, name="surface")
         liq_constant_species = [cspc for cspc in self.const_spc_names if cspc in [spc.name for spc in liq.species]]
         cat_constant_species = [cspc for cspc in self.const_spc_names if cspc in [spc.name for spc in surf.species]]
-        domainliq, y0liq, pliq = rms.ConstantTVDomain(phase=liq, initialconds=self.initial_conditions["liquid"], constantspecies=liq_constant_species)
+        domainliq, y0liq, pliq = rms.ConstantTVDomain(phase=liq, initialconds=to_julia(self.initial_conditions["liquid"]), constantspecies=liq_constant_species)
         domaincat, y0cat, pcat = rms.ConstantTAPhiDomain(
-            phase=surf, initialconds=self.initial_conditions["surface"], constantspecies=cat_constant_species
+            phase=surf, initialconds=to_julia(self.initial_conditions["surface"]), constantspecies=cat_constant_species
         )
         if interface.reactions == []:
             inter, pinter = rms.ReactiveInternalInterfaceConstantTPhi(
@@ -520,19 +522,19 @@ def generate_reactor(self, phase_system):
         """
         phase = phase_system.phases["Default"]
         liq = rms.IdealDiluteSolution(phase.species, phase.reactions, phase.solvent)
-        domain, y0, p = rms.ConstantTVDomain(phase=liq, initialconds=self.initial_conditions, constantspecies=self.const_spc_names)
+        domain, y0, p = rms.ConstantTVDomain(phase=liq, initialconds=to_julia(self.initial_conditions), constantspecies=self.const_spc_names)
 
         interfaces = []
 
         if self.inlet_conditions:
             inlet_conditions = {key: value for (key, value) in self.inlet_conditions.items() if key != "F"}
             total_molar_flow_rate = self.inlet_conditions["F"]
-            inlet = rms.Inlet(domain, inlet_conditions, Main.eval("x->" + str(total_molar_flow_rate)))
+            inlet = rms.Inlet(domain, inlet_conditions, Main.seval("x->" + str(total_molar_flow_rate)))
             interfaces.append(inlet)
 
         if self.outlet_conditions:
             total_volumetric_flow_rate = self.outlet_conditions["Vout"]
-            outlet = rms.VolumetricFlowRateOutlet(domain, Main.eval("x->" + str(total_volumetric_flow_rate)))
+            outlet = rms.VolumetricFlowRateOutlet(domain, Main.seval("x->" + str(total_volumetric_flow_rate)))
             interfaces.append(outlet)
 
         if self.evap_cond_conditions:
@@ -555,11 +557,19 @@ def generate_reactor(self, phase_system):
         """
         phase = phase_system.phases["Default"]
         ig = rms.IdealGas(phase.species, phase.reactions)
-        domain, y0, p = rms.ConstantTPDomain(phase=ig, initialconds=self.initial_conditions)
+        domain, y0, p = rms.ConstantTPDomain(phase=ig, initialconds=to_julia(self.initial_conditions))
         react = rms.Reactor(domain, y0, (0.0, self.tf), p=p)
         return react, domain, [], p
 
 
+def to_julia(obj):
+    if isinstance(obj, dict):
+        return Main.PythonCall.pyconvert(Main.Dict, obj)
+    elif isinstance(obj, list) or isinstance(obj, np.ndarray):
+        return Main.PythonCall.pyconvert(Main.Vector, obj)
+    else:
+        return obj
+
 def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
     """
     Generate corresponding rms object
@@ -575,21 +585,21 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
         Ea = obj._Ea.value_si
         return rms.Arrhenius(A, n, Ea, rms.EmptyRateUncertainty())
     elif isinstance(obj, PDepArrhenius):
-        Ps = obj._pressures.value_si
-        arrs = [to_rms(arr) for arr in obj.arrhenius]
+        Ps = to_julia(obj._pressures.value_si)
+        arrs = to_julia([to_rms(arr) for arr in obj.arrhenius])
         return rms.PdepArrhenius(Ps, arrs, rms.EmptyRateUncertainty())
     elif isinstance(obj, MultiArrhenius):
-        arrs = [to_rms(arr) for arr in obj.arrhenius]
+        arrs = to_julia([to_rms(arr) for arr in obj.arrhenius])
         return rms.MultiArrhenius(arrs, rms.EmptyRateUncertainty())
     elif isinstance(obj, MultiPDepArrhenius):
-        parrs = [to_rms(parr) for parr in obj.arrhenius]
+        parrs = to_julia([to_rms(parr) for parr in obj.arrhenius])
         return rms.MultiPdepArrhenius(parrs, rms.EmptyRateUncertainty())
     elif isinstance(obj, Chebyshev):
         Tmin = obj.Tmin.value_si
         Tmax = obj.Tmax.value_si
         Pmin = obj.Pmin.value_si
         Pmax = obj.Pmax.value_si
-        coeffs = obj.coeffs.value_si.tolist()
+        coeffs = to_julia(obj.coeffs.value_si.tolist())
         return rms.Chebyshev(coeffs, Tmin, Tmax, Pmin, Pmax)
     elif isinstance(obj, ThirdBody):
         arrstr = arrhenius_to_julia_string(obj.arrheniusLow)
@@ -632,7 +642,7 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
         for key, value in efficiencies.items():
             dstr += '"' + key + '"' "=>" + str(value) + ","
         dstr += "])"
-        return Main.eval(
+        return Main.seval(
             "using ReactionMechanismSimulator; Troe("
             + arrhigh
             + ","
@@ -677,6 +687,7 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
                 atomnums[atm.element.symbol] += 1
             else:
                 atomnums[atm.element.symbol] = 1
+        atomnums = to_julia(atomnums)
         bondnum = len(mol.get_all_edges())
         
         if not obj.molecule[0].contains_surface_site():
@@ -685,12 +696,12 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
             th = obj.get_thermo_data()
             thermo = to_rms(th)
             if obj.henry_law_constant_data:
-                kH = rms.TemperatureDependentHenryLawConstant(Ts=obj.henry_law_constant_data.Ts, kHs=obj.henry_law_constant_data.kHs)
+                kH = rms.TemperatureDependentHenryLawConstant(Ts=to_julia(obj.henry_law_constant_data.Ts), kHs=to_julia(obj.henry_law_constant_data.kHs))
             else:
                 kH = rms.EmptyHenryLawConstant()
             if obj.liquid_volumetric_mass_transfer_coefficient_data:
                 kLA = rms.TemperatureDependentLiquidVolumetricMassTransferCoefficient(
-                    Ts=obj.liquid_volumetric_mass_transfer_coefficient_data.Ts, kLAs=obj.liquid_volumetric_mass_transfer_coefficient_data.kLAs
+                    Ts=to_julia(obj.liquid_volumetric_mass_transfer_coefficient_data.Ts), kLAs=to_julia(obj.liquid_volumetric_mass_transfer_coefficient_data.kLAs)
                 )
             else:
                 kLA = rms.EmptyLiquidVolumetricMassTransferCoefficient()
@@ -732,10 +743,10 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
                 comment=obj.thermo.comment,
             )
     elif isinstance(obj, Reaction):
-        reactantinds = [species_names.index(spc.label) for spc in obj.reactants]
-        productinds = [species_names.index(spc.label) for spc in obj.products]
-        reactants = [rms_species_list[i] for i in reactantinds]
-        products = [rms_species_list[i] for i in productinds]
+        reactantinds = to_julia([species_names.index(spc.label) for spc in obj.reactants])
+        productinds = to_julia([species_names.index(spc.label) for spc in obj.products])
+        reactants = to_julia([rms_species_list[i] for i in reactantinds])
+        products = to_julia([rms_species_list[i] for i in productinds])
         kinetics = to_rms(obj.kinetics, species_names=species_names, rms_species_list=rms_species_list, rmg_species=rmg_species)
         radchange = sum([spc.molecule[0].multiplicity - 1 for spc in obj.products]) - sum([spc.molecule[0].multiplicity - 1 for spc in obj.reactants])
         electronchange = 0  # for now

From 7e770fb791e9bc7a7d91b305e09f8bc2f5a3498b Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 2 Apr 2024 11:12:03 -0400
Subject: [PATCH 032/162] debug

---
 rmgpy/pdep/sls.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/rmgpy/pdep/sls.py b/rmgpy/pdep/sls.py
index ae6ce7950a..ca7544bc34 100644
--- a/rmgpy/pdep/sls.py
+++ b/rmgpy/pdep/sls.py
@@ -93,17 +93,17 @@ def solve_me(M, p0, t):
 end"""
     )
     tspan = (0.0, t)
-    fcn = jl.ODEFunction(f, jac=jac)
-    prob = jl.ODEProblem(fcn, p0, tspan, M)
-    sol = jl.solve(prob, solver=jl.CVODE_BDF(), abstol=1e-16, reltol=1e-6)
+    fcn = Main.ODEFunction(f, jac=jac)
+    prob = Main.ODEProblem(fcn, p0, tspan, M)
+    sol = Main.solve(prob, solver=Main.CVODE_BDF(), abstol=1e-16, reltol=1e-6)
     return sol
 
 
 def solve_me_fcns(f, jac, M, p0, t):
     tspan = (0.0, t)
-    fcn = jl.ODEFunction(f, jac=jac)
-    prob = jl.ODEProblem(fcn, p0, tspan, M)
-    sol = jl.solve(prob, solver=jl.CVODE_BDF(), abstol=1e-16, reltol=1e-6)
+    fcn = Main.ODEFunction(f, jac=jac)
+    prob = Main.ODEProblem(fcn, p0, tspan, M)
+    sol = Main.solve(prob, solver=Main.CVODE_BDF(), abstol=1e-16, reltol=1e-6)
     return sol
 
 
@@ -145,13 +145,13 @@ def get_rate_coefficients_SLS(network, T, P, method="mexp", neglect_high_energy_
     tau = np.abs(1.0 / fastest_reaction)
 
     if method == "ode":
-        f = jl.eval(
+        f = Main.eval(
             """
 function f(u,M,t)
     return M*u
 end"""
         )
-        jac = jl.eval(
+        jac = Main.eval(
             """
 function jac(u,M,t)
     return M

From 29e6c432c98368605a1fa701a7d68974950a06f0 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 2 Apr 2024 15:22:32 -0400
Subject: [PATCH 033/162] convert empty list

---
 rmgpy/rmg/reactors.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index f71329274f..9c6aa82e43 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -760,7 +760,7 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
             electronchange=electronchange,
             radicalchange=radchange,
             reversible=obj.reversible,
-            pairs=[],
+            pairs=to_julia([]),
             comment=obj.kinetics.comment,
         )
     elif isinstance(obj, SolventData):

From 7a473df97970728d35c525737343005a069d2ce6 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 2 Apr 2024 15:23:34 -0400
Subject: [PATCH 034/162] Add additional test file for sls

---
 .../arkane/networks/acetyl+O2_slsode/input.py | 284 ++++++++++++++++++
 1 file changed, 284 insertions(+)
 create mode 100644 examples/arkane/networks/acetyl+O2_slsode/input.py

diff --git a/examples/arkane/networks/acetyl+O2_slsode/input.py b/examples/arkane/networks/acetyl+O2_slsode/input.py
new file mode 100644
index 0000000000..be22e3110c
--- /dev/null
+++ b/examples/arkane/networks/acetyl+O2_slsode/input.py
@@ -0,0 +1,284 @@
+################################################################################
+#
+#   Arkane input file for acetyl + O2 pressure-dependent reaction network
+#
+################################################################################
+
+title = 'acetyl + oxygen'
+
+description = \
+"""
+The chemically-activated reaction of acetyl with oxygen. This system is of
+interest in atmospheric chemistry as a step in the conversion of acetaldehyde
+to the secondary pollutant peroxyacetylnitrate (PAN); it is also potentially
+important in the ignition chemistry of ethanol.
+"""
+
+species(
+    label = 'acetylperoxy',
+    structure = SMILES('CC(=O)O[O]'),
+    E0 = (-34.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([54.2977,104.836,156.05],"amu*angstrom^2"), symmetry=1),
+        HarmonicOscillator(frequencies=([319.695,500.474,536.674,543.894,727.156,973.365,1037.77,1119.72,1181.55,1391.11,1449.53,1454.72,1870.51,3037.12,3096.93,3136.39],"cm^-1")),
+        HinderedRotor(inertia=(7.38359,"amu*angstrom^2"), symmetry=1, fourier=([[-1.95191,-11.8215,0.740041,-0.049118,-0.464522],[0.000227764,0.00410782,-0.000805364,-0.000548218,-0.000266277]],"kJ/mol")),
+        HinderedRotor(inertia=(2.94723,"amu*angstrom^2"), symmetry=3, fourier=([[0.130647,0.0401507,-2.54582,-0.0436065,-0.120982],[-0.000701659,-0.000989654,0.00783349,-0.00140978,-0.00145843]],"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    molecularWeight = (75.04,"g/mol"),
+    collisionModel = TransportData(sigma=(5.09,'angstrom'), epsilon=(473,'K')),
+    energyTransferModel = SingleExponentialDown(
+        alpha0 = (0.5718,'kcal/mol'),
+        T0 = (300,'K'),
+        n = 0.85,
+    ),
+)
+
+species(
+    label = 'hydroperoxylvinoxy',
+    structure = SMILES('[CH2]C(=O)OO'),
+    E0 = (-32.4,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([44.8034,110.225,155.029],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([318.758,420.907,666.223,675.962,752.824,864.66,998.471,1019.54,1236.21,1437.91,1485.74,1687.9,3145.44,3262.88,3434.34],"cm^-1")),
+        HinderedRotor(inertia=(1.68464,"u*angstrom**2"), symmetry=2, fourier=([[0.359649,-16.1155,-0.593311,1.72918,0.256314],[-7.42981e-06,-0.000238057,3.29276e-05,-6.62608e-05,8.8443e-05]],"kJ/mol")),
+        HinderedRotor(inertia=(8.50433,"u*angstrom**2"), symmetry=1, fourier=([[-7.53504,-23.4471,-3.3974,-0.940593,-0.313674],[-4.58248,-2.47177,0.550012,1.03771,0.844226]],"kJ/mol")),
+        HinderedRotor(inertia=(0.803309,"u*angstrom**2"), symmetry=1, fourier=([[-8.65946,-3.97888,-1.13469,-0.402197,-0.145101],[4.41884e-05,4.83249e-05,1.30275e-05,-1.31353e-05,-6.66878e-06]],"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    molecularWeight = (75.04,"g/mol"),
+    collisionModel = TransportData(sigma=(5.09,'angstrom'), epsilon=(473,'K')),
+    energyTransferModel = SingleExponentialDown(
+        alpha0 = (0.5718,'kcal/mol'),
+        T0 = (300,'K'),
+        n = 0.85,
+    ),
+)
+
+species(
+    label = 'acetyl',
+    structure = SMILES('C[C]=O'),
+    E0 = (0.0,'kcal/mol'),  #(-20.5205,"kJ/mol")
+    modes = [
+        IdealGasTranslation(mass=(43.05,"g/mol")),
+        NonlinearRotor(inertia=([5.94518,50.8166,53.6436],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([464.313,845.126,1010.54,1038.43,1343.54,1434.69,1442.25,1906.18,2985.46,3076.57,3079.46],"cm^-1")),
+        HinderedRotor(inertia=(1.61752,"u*angstrom**2"), symmetry=3, barrier=(2.00242,"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'oxygen',
+    structure = SMILES('[O][O]'),
+    E0 = (0.0,'kcal/mol'),  #(-5.74557,"kJ/mol")
+    modes = [
+        IdealGasTranslation(mass=(32.00,"g/mol")),
+        LinearRotor(inertia=(11.6056,"u*angstrom**2"), symmetry=2),
+        HarmonicOscillator(frequencies=([1621.54],"cm^-1")),
+    ],
+    spinMultiplicity = 3,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'ketene',
+    structure = SMILES('C=C=O'),
+    E0 = (-6.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(42.0106,"g/mol")),
+        NonlinearRotor(inertia=([1.76922,48.8411,50.6103],"u*angstrom**2"), symmetry=2),
+        HarmonicOscillator(frequencies=([441.622,548.317,592.155,981.379,1159.66,1399.86,2192.1,3150.02,3240.58],"cm^-1")),
+    ],
+    spinMultiplicity = 1,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'lactone',
+    structure = SMILES('C1OC1(=O)'),
+    E0 = (-30.8,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(58.0055,"g/mol")),
+        NonlinearRotor(inertia=([20.1707,62.4381,79.1616],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([484.387,527.771,705.332,933.372,985.563,1050.26,1107.93,1176.43,1466.54,1985.09,3086.23,3186.46],"cm^-1")),
+    ],
+    spinMultiplicity = 1,
+    opticalIsomers = 1,
+)
+
+
+
+species(
+    label = 'hydroxyl',
+    structure = SMILES('[OH]'),
+    E0 = (0.0,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(17.0027,"g/mol")),
+        LinearRotor(inertia=(0.899988,"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([3676.39],"cm^-1")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'hydroperoxyl',
+    structure = SMILES('O[O]'),
+    E0 = (0.0,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(32.9977,"g/mol")),
+        NonlinearRotor(inertia=([0.811564,14.9434,15.755],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([1156.77,1424.28,3571.81],"cm^-1")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'nitrogen',
+    structure = SMILES('N#N'),
+    molecularWeight = (28.04,"g/mol"),
+    collisionModel = TransportData(sigma=(3.70,'angstrom'), epsilon=(94.9,'K')),
+    reactive = False
+)
+
+################################################################################
+
+transitionState(
+    label = 'entrance1',
+    E0 = (0.0,'kcal/mol'),
+)
+
+transitionState(
+    label = 'isom1',
+    E0 = (-5.8,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([49.3418,103.697,149.682],"u*angstrom**2"), symmetry=1, quantum=False),
+        HarmonicOscillator(frequencies=([148.551,306.791,484.573,536.709,599.366,675.538,832.594,918.413,1022.28,1031.45,1101.01,1130.05,1401.51,1701.26,1844.17,3078.6,3163.07],"cm^-1"), quantum=True),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency = (-1679.04,'cm^-1'),
+)
+
+transitionState(
+    label = 'exit1',
+    E0 = (0.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([55.4256, 136.1886, 188.2442],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([59.9256,204.218,352.811,466.297,479.997,542.345,653.897,886.657,1017.91,1079.17,1250.02,1309.14,1370.36,1678.52,2162.41,3061.53,3135.55],"cm^-1")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency=(-1053.25,'cm^-1'),
+)
+
+transitionState(
+    label = 'exit2',
+    E0 = (-4.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.0082,"g/mol"), quantum=False),
+        NonlinearRotor(inertia=([51.7432,119.373,171.117],"u*angstrom**2"), symmetry=1, quantum=False),
+        HarmonicOscillator(frequencies=([250.311,383.83,544.382,578.988,595.324,705.422,964.712,1103.25,1146.91,1415.98,1483.33,1983.79,3128,3143.84,3255.29],"cm^-1")),
+        HinderedRotor(inertia=(9.35921,"u*angstrom**2"), symmetry=1, fourier=([[-11.2387,-12.5928,-3.87844,1.13314,-0.358812],[-1.59863,-8.03329,-5.05235,3.13723,2.45989]],"kJ/mol")),
+        HinderedRotor(inertia=(0.754698,"u*angstrom**2"), symmetry=1, barrier=(47.7645,"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency=(-404.271,'cm^-1'),
+)
+
+transitionState(
+    label = 'exit3',
+    E0 = (-7.2,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([53.2821, 120.4050, 170.1570],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([152.155,181.909,311.746,348.646,608.487,624.378,805.347,948.875,995.256,996.982,1169.1,1412.6,1834.83,3124.43,3245.2,3634.45],"cm^-1")),
+        HinderedRotor(inertia=(0.813269,"u*angstrom**2"), symmetry=1, fourier=([[-1.15338,-2.18664,-0.669531,-0.11502,-0.0512599],[0.00245222,0.0107485,0.00334564,-0.00165288,-0.0028674]],"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency=(-618.234,'cm^-1'),
+)
+
+################################################################################
+
+reaction(
+    label = 'entrance1',
+    reactants = ['acetyl', 'oxygen'],
+    products = ['acetylperoxy'],
+    transitionState = 'entrance1',
+    kinetics = Arrhenius(A=(2.65e6,'m^3/(mol*s)'), n=0.0, Ea=(0.0,'kcal/mol'), T0=(1,"K")),
+)
+
+reaction(
+    label = 'isom1',
+    reactants = ['acetylperoxy'],
+    products = ['hydroperoxylvinoxy'],
+    transitionState = 'isom1',
+    tunneling = 'Eckart',
+)
+
+reaction(
+    label = 'exit1',
+    reactants = ['acetylperoxy'],
+    products = ['ketene', 'hydroperoxyl'],
+    transitionState = 'exit1',
+    tunneling = 'Eckart',
+)
+
+reaction(
+    label = 'exit2',
+    reactants = ['hydroperoxylvinoxy'],
+    products = ['ketene', 'hydroperoxyl'],
+    transitionState = 'exit2',
+    tunneling = 'Eckart',
+)
+
+reaction(
+    label = 'exit3',
+    reactants = ['hydroperoxylvinoxy'],
+    products = ['lactone', 'hydroxyl'],
+    transitionState = 'exit3',
+    tunneling = 'Eckart',
+)
+
+#################################################################################
+
+network(
+    label = 'acetyl + O2',
+    isomers = [
+        'acetylperoxy',
+        'hydroperoxylvinoxy',
+    ],
+    reactants = [
+        ('acetyl', 'oxygen'),
+        ('ketene', 'hydroperoxyl'),
+	('lactone', 'hydroxyl')
+    ],
+    bathGas = {
+        'nitrogen': 1.0,
+    }
+)
+
+#################################################################################
+
+pressureDependence(
+    'acetyl + O2',
+    Tmin=(300.0,'K'), Tmax=(2000.0,'K'), Tcount=8,
+    Pmin=(0.01,'bar'), Pmax=(100.0,'bar'), Pcount=5,
+    maximumGrainSize = (1.0,'kcal/mol'),
+    minimumGrainCount = 250,
+    method = 'sls_ode',
+    interpolationModel = ('chebyshev', 6, 4),
+    activeJRotor = True,
+)

From 09c45bf00a709073789f7ed831b7be42345b544e Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 2 Apr 2024 16:17:14 -0400
Subject: [PATCH 035/162] Should be seval

---
 rmgpy/rmg/reactors.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index 9c6aa82e43..f5b4b059ad 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -486,7 +486,7 @@ def generate_reactor(self, phase_system):
             inter, pinter = rms.ReactiveInternalInterfaceConstantTPhi(
                 domainliq,
                 domaincat,
-                Main.eval("using ReactionMechanismSimulator; Vector{ElementaryReaction}()"),
+                Main.seval("using ReactionMechanismSimulator; Vector{ElementaryReaction}()"),
                 self.initial_conditions["liquid"]["T"],
                 self.initial_conditions["surface"]["A"],
             )
@@ -608,7 +608,7 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
         for key, value in efficiencies.items():
             dstr += '"' + key + '"' "=>" + str(value) + ","
         dstr += "])"
-        return Main.eval(
+        return Main.seval(
             "using ReactionMechanismSimulator; ThirdBody(" + arrstr + ", Dict{Int64,Float64}([]), " + dstr + "," + "EmptyRateUncertainty())"
         )
     elif isinstance(obj, Lindemann):
@@ -619,7 +619,7 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
         for key, value in efficiencies.items():
             dstr += '"' + key + '"' "=>" + str(value) + ","
         dstr += "])"
-        return Main.eval(
+        return Main.seval(
             "using ReactionMechanismSimulator; Lindemann("
             + arrhigh
             + ","

From cd219c2e7e9d671bad72251862ec70b640e8c57e Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 2 Apr 2024 16:22:26 -0400
Subject: [PATCH 036/162] debug

---
 rmgpy/pdep/sls.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rmgpy/pdep/sls.py b/rmgpy/pdep/sls.py
index ca7544bc34..8060b10f70 100644
--- a/rmgpy/pdep/sls.py
+++ b/rmgpy/pdep/sls.py
@@ -242,7 +242,7 @@ def run_equilibrium(network, channel):
     xseq = []
     dxdtseq = []
 
-    # Single dojlant source simulations
+    # Single dominant source simulations
     for i, isomer in enumerate(isomers):
         xsout, dxdtout = run_single_source(network, isomer)
         for j in range(len(xsout)):

From ff810644450b9f15f60edcf23159ef464c9163ad Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 2 Apr 2024 16:57:43 -0400
Subject: [PATCH 037/162] update doc

---
 .github/workflows/docs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 616aceae85..85147b0362 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -63,6 +63,7 @@ jobs:
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
+          export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
           julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Checkout gh-pages Branch

From 11f0923cdf8dcd61e5ab2175080bacf24e0c3dc0 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Wed, 3 Apr 2024 12:07:05 -0400
Subject: [PATCH 038/162] Add tests

---
 .github/workflows/CI.yml                      |   2 +-
 .github/workflows/docs.yml                    |   2 +-
 .../networks/{CH2NH2 => CH2NH2_mse}/input.py  |   0
 .../yaml_files/CH2NH.yml                      |   0
 .../yaml_files/CH2NH2.yml                     |   0
 .../yaml_files/CH2NH_to_CH2NH2.yml            |   0
 .../yaml_files/CH2NH_to_CH3NH.yml             |   0
 .../yaml_files/CH3NH.yml                      |   0
 .../yaml_files/CH3NH_to_CH2NH2.yml            |   0
 .../{CH2NH2 => CH2NH2_mse}/yaml_files/H.yml   |   0
 .../input.py                                  |   2 +-
 .../{acetyl+O2 => acetyl+O2_sce}/input.py     |   0
 .../arkane/networks/acetyl+O2_sls/input.py    | 284 ++++++++++++++++++
 .../arkane/networks/acetyl+O2_slse/input.py   | 284 ++++++++++++++++++
 .../arkane/networks/acetyl+O2_slsme/input.py  | 284 ++++++++++++++++++
 .../{n-butanol => n-butanol_msc}/input.py     |   0
 rmgpy/pdep/sls.py                             |  40 ++-
 rmgpy/rmg/reactors.py                         |  17 +-
 18 files changed, 889 insertions(+), 26 deletions(-)
 rename examples/arkane/networks/{CH2NH2 => CH2NH2_mse}/input.py (100%)
 rename examples/arkane/networks/{CH2NH2 => CH2NH2_mse}/yaml_files/CH2NH.yml (100%)
 rename examples/arkane/networks/{CH2NH2 => CH2NH2_mse}/yaml_files/CH2NH2.yml (100%)
 rename examples/arkane/networks/{CH2NH2 => CH2NH2_mse}/yaml_files/CH2NH_to_CH2NH2.yml (100%)
 rename examples/arkane/networks/{CH2NH2 => CH2NH2_mse}/yaml_files/CH2NH_to_CH3NH.yml (100%)
 rename examples/arkane/networks/{CH2NH2 => CH2NH2_mse}/yaml_files/CH3NH.yml (100%)
 rename examples/arkane/networks/{CH2NH2 => CH2NH2_mse}/yaml_files/CH3NH_to_CH2NH2.yml (100%)
 rename examples/arkane/networks/{CH2NH2 => CH2NH2_mse}/yaml_files/H.yml (100%)
 rename examples/arkane/networks/{acetyl+O2_slsode => acetyl+O2_rs}/input.py (99%)
 rename examples/arkane/networks/{acetyl+O2 => acetyl+O2_sce}/input.py (100%)
 create mode 100644 examples/arkane/networks/acetyl+O2_sls/input.py
 create mode 100644 examples/arkane/networks/acetyl+O2_slse/input.py
 create mode 100644 examples/arkane/networks/acetyl+O2_slsme/input.py
 rename examples/arkane/networks/{n-butanol => n-butanol_msc}/input.py (100%)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 59603a02b2..eddb2c12a8 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -152,7 +152,7 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
           export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
-          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
+          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("SciMLBase"); Pkg.add("Sundials"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 85147b0362..86718382e7 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -64,7 +64,7 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
           export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
-          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
+          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("SciMLBase"); Pkg.add("Sundials"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Checkout gh-pages Branch
         uses: actions/checkout@v2
diff --git a/examples/arkane/networks/CH2NH2/input.py b/examples/arkane/networks/CH2NH2_mse/input.py
similarity index 100%
rename from examples/arkane/networks/CH2NH2/input.py
rename to examples/arkane/networks/CH2NH2_mse/input.py
diff --git a/examples/arkane/networks/CH2NH2/yaml_files/CH2NH.yml b/examples/arkane/networks/CH2NH2_mse/yaml_files/CH2NH.yml
similarity index 100%
rename from examples/arkane/networks/CH2NH2/yaml_files/CH2NH.yml
rename to examples/arkane/networks/CH2NH2_mse/yaml_files/CH2NH.yml
diff --git a/examples/arkane/networks/CH2NH2/yaml_files/CH2NH2.yml b/examples/arkane/networks/CH2NH2_mse/yaml_files/CH2NH2.yml
similarity index 100%
rename from examples/arkane/networks/CH2NH2/yaml_files/CH2NH2.yml
rename to examples/arkane/networks/CH2NH2_mse/yaml_files/CH2NH2.yml
diff --git a/examples/arkane/networks/CH2NH2/yaml_files/CH2NH_to_CH2NH2.yml b/examples/arkane/networks/CH2NH2_mse/yaml_files/CH2NH_to_CH2NH2.yml
similarity index 100%
rename from examples/arkane/networks/CH2NH2/yaml_files/CH2NH_to_CH2NH2.yml
rename to examples/arkane/networks/CH2NH2_mse/yaml_files/CH2NH_to_CH2NH2.yml
diff --git a/examples/arkane/networks/CH2NH2/yaml_files/CH2NH_to_CH3NH.yml b/examples/arkane/networks/CH2NH2_mse/yaml_files/CH2NH_to_CH3NH.yml
similarity index 100%
rename from examples/arkane/networks/CH2NH2/yaml_files/CH2NH_to_CH3NH.yml
rename to examples/arkane/networks/CH2NH2_mse/yaml_files/CH2NH_to_CH3NH.yml
diff --git a/examples/arkane/networks/CH2NH2/yaml_files/CH3NH.yml b/examples/arkane/networks/CH2NH2_mse/yaml_files/CH3NH.yml
similarity index 100%
rename from examples/arkane/networks/CH2NH2/yaml_files/CH3NH.yml
rename to examples/arkane/networks/CH2NH2_mse/yaml_files/CH3NH.yml
diff --git a/examples/arkane/networks/CH2NH2/yaml_files/CH3NH_to_CH2NH2.yml b/examples/arkane/networks/CH2NH2_mse/yaml_files/CH3NH_to_CH2NH2.yml
similarity index 100%
rename from examples/arkane/networks/CH2NH2/yaml_files/CH3NH_to_CH2NH2.yml
rename to examples/arkane/networks/CH2NH2_mse/yaml_files/CH3NH_to_CH2NH2.yml
diff --git a/examples/arkane/networks/CH2NH2/yaml_files/H.yml b/examples/arkane/networks/CH2NH2_mse/yaml_files/H.yml
similarity index 100%
rename from examples/arkane/networks/CH2NH2/yaml_files/H.yml
rename to examples/arkane/networks/CH2NH2_mse/yaml_files/H.yml
diff --git a/examples/arkane/networks/acetyl+O2_slsode/input.py b/examples/arkane/networks/acetyl+O2_rs/input.py
similarity index 99%
rename from examples/arkane/networks/acetyl+O2_slsode/input.py
rename to examples/arkane/networks/acetyl+O2_rs/input.py
index be22e3110c..84a57961fa 100644
--- a/examples/arkane/networks/acetyl+O2_slsode/input.py
+++ b/examples/arkane/networks/acetyl+O2_rs/input.py
@@ -278,7 +278,7 @@
     Pmin=(0.01,'bar'), Pmax=(100.0,'bar'), Pcount=5,
     maximumGrainSize = (1.0,'kcal/mol'),
     minimumGrainCount = 250,
-    method = 'sls_ode',
+    method = 'reservoir state',
     interpolationModel = ('chebyshev', 6, 4),
     activeJRotor = True,
 )
diff --git a/examples/arkane/networks/acetyl+O2/input.py b/examples/arkane/networks/acetyl+O2_sce/input.py
similarity index 100%
rename from examples/arkane/networks/acetyl+O2/input.py
rename to examples/arkane/networks/acetyl+O2_sce/input.py
diff --git a/examples/arkane/networks/acetyl+O2_sls/input.py b/examples/arkane/networks/acetyl+O2_sls/input.py
new file mode 100644
index 0000000000..4595e288fc
--- /dev/null
+++ b/examples/arkane/networks/acetyl+O2_sls/input.py
@@ -0,0 +1,284 @@
+################################################################################
+#
+#   Arkane input file for acetyl + O2 pressure-dependent reaction network
+#
+################################################################################
+
+title = 'acetyl + oxygen'
+
+description = \
+"""
+The chemically-activated reaction of acetyl with oxygen. This system is of
+interest in atmospheric chemistry as a step in the conversion of acetaldehyde
+to the secondary pollutant peroxyacetylnitrate (PAN); it is also potentially
+important in the ignition chemistry of ethanol.
+"""
+
+species(
+    label = 'acetylperoxy',
+    structure = SMILES('CC(=O)O[O]'),
+    E0 = (-34.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([54.2977,104.836,156.05],"amu*angstrom^2"), symmetry=1),
+        HarmonicOscillator(frequencies=([319.695,500.474,536.674,543.894,727.156,973.365,1037.77,1119.72,1181.55,1391.11,1449.53,1454.72,1870.51,3037.12,3096.93,3136.39],"cm^-1")),
+        HinderedRotor(inertia=(7.38359,"amu*angstrom^2"), symmetry=1, fourier=([[-1.95191,-11.8215,0.740041,-0.049118,-0.464522],[0.000227764,0.00410782,-0.000805364,-0.000548218,-0.000266277]],"kJ/mol")),
+        HinderedRotor(inertia=(2.94723,"amu*angstrom^2"), symmetry=3, fourier=([[0.130647,0.0401507,-2.54582,-0.0436065,-0.120982],[-0.000701659,-0.000989654,0.00783349,-0.00140978,-0.00145843]],"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    molecularWeight = (75.04,"g/mol"),
+    collisionModel = TransportData(sigma=(5.09,'angstrom'), epsilon=(473,'K')),
+    energyTransferModel = SingleExponentialDown(
+        alpha0 = (0.5718,'kcal/mol'),
+        T0 = (300,'K'),
+        n = 0.85,
+    ),
+)
+
+species(
+    label = 'hydroperoxylvinoxy',
+    structure = SMILES('[CH2]C(=O)OO'),
+    E0 = (-32.4,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([44.8034,110.225,155.029],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([318.758,420.907,666.223,675.962,752.824,864.66,998.471,1019.54,1236.21,1437.91,1485.74,1687.9,3145.44,3262.88,3434.34],"cm^-1")),
+        HinderedRotor(inertia=(1.68464,"u*angstrom**2"), symmetry=2, fourier=([[0.359649,-16.1155,-0.593311,1.72918,0.256314],[-7.42981e-06,-0.000238057,3.29276e-05,-6.62608e-05,8.8443e-05]],"kJ/mol")),
+        HinderedRotor(inertia=(8.50433,"u*angstrom**2"), symmetry=1, fourier=([[-7.53504,-23.4471,-3.3974,-0.940593,-0.313674],[-4.58248,-2.47177,0.550012,1.03771,0.844226]],"kJ/mol")),
+        HinderedRotor(inertia=(0.803309,"u*angstrom**2"), symmetry=1, fourier=([[-8.65946,-3.97888,-1.13469,-0.402197,-0.145101],[4.41884e-05,4.83249e-05,1.30275e-05,-1.31353e-05,-6.66878e-06]],"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    molecularWeight = (75.04,"g/mol"),
+    collisionModel = TransportData(sigma=(5.09,'angstrom'), epsilon=(473,'K')),
+    energyTransferModel = SingleExponentialDown(
+        alpha0 = (0.5718,'kcal/mol'),
+        T0 = (300,'K'),
+        n = 0.85,
+    ),
+)
+
+species(
+    label = 'acetyl',
+    structure = SMILES('C[C]=O'),
+    E0 = (0.0,'kcal/mol'),  #(-20.5205,"kJ/mol")
+    modes = [
+        IdealGasTranslation(mass=(43.05,"g/mol")),
+        NonlinearRotor(inertia=([5.94518,50.8166,53.6436],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([464.313,845.126,1010.54,1038.43,1343.54,1434.69,1442.25,1906.18,2985.46,3076.57,3079.46],"cm^-1")),
+        HinderedRotor(inertia=(1.61752,"u*angstrom**2"), symmetry=3, barrier=(2.00242,"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'oxygen',
+    structure = SMILES('[O][O]'),
+    E0 = (0.0,'kcal/mol'),  #(-5.74557,"kJ/mol")
+    modes = [
+        IdealGasTranslation(mass=(32.00,"g/mol")),
+        LinearRotor(inertia=(11.6056,"u*angstrom**2"), symmetry=2),
+        HarmonicOscillator(frequencies=([1621.54],"cm^-1")),
+    ],
+    spinMultiplicity = 3,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'ketene',
+    structure = SMILES('C=C=O'),
+    E0 = (-6.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(42.0106,"g/mol")),
+        NonlinearRotor(inertia=([1.76922,48.8411,50.6103],"u*angstrom**2"), symmetry=2),
+        HarmonicOscillator(frequencies=([441.622,548.317,592.155,981.379,1159.66,1399.86,2192.1,3150.02,3240.58],"cm^-1")),
+    ],
+    spinMultiplicity = 1,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'lactone',
+    structure = SMILES('C1OC1(=O)'),
+    E0 = (-30.8,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(58.0055,"g/mol")),
+        NonlinearRotor(inertia=([20.1707,62.4381,79.1616],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([484.387,527.771,705.332,933.372,985.563,1050.26,1107.93,1176.43,1466.54,1985.09,3086.23,3186.46],"cm^-1")),
+    ],
+    spinMultiplicity = 1,
+    opticalIsomers = 1,
+)
+
+
+
+species(
+    label = 'hydroxyl',
+    structure = SMILES('[OH]'),
+    E0 = (0.0,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(17.0027,"g/mol")),
+        LinearRotor(inertia=(0.899988,"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([3676.39],"cm^-1")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'hydroperoxyl',
+    structure = SMILES('O[O]'),
+    E0 = (0.0,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(32.9977,"g/mol")),
+        NonlinearRotor(inertia=([0.811564,14.9434,15.755],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([1156.77,1424.28,3571.81],"cm^-1")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'nitrogen',
+    structure = SMILES('N#N'),
+    molecularWeight = (28.04,"g/mol"),
+    collisionModel = TransportData(sigma=(3.70,'angstrom'), epsilon=(94.9,'K')),
+    reactive = False
+)
+
+################################################################################
+
+transitionState(
+    label = 'entrance1',
+    E0 = (0.0,'kcal/mol'),
+)
+
+transitionState(
+    label = 'isom1',
+    E0 = (-5.8,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([49.3418,103.697,149.682],"u*angstrom**2"), symmetry=1, quantum=False),
+        HarmonicOscillator(frequencies=([148.551,306.791,484.573,536.709,599.366,675.538,832.594,918.413,1022.28,1031.45,1101.01,1130.05,1401.51,1701.26,1844.17,3078.6,3163.07],"cm^-1"), quantum=True),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency = (-1679.04,'cm^-1'),
+)
+
+transitionState(
+    label = 'exit1',
+    E0 = (0.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([55.4256, 136.1886, 188.2442],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([59.9256,204.218,352.811,466.297,479.997,542.345,653.897,886.657,1017.91,1079.17,1250.02,1309.14,1370.36,1678.52,2162.41,3061.53,3135.55],"cm^-1")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency=(-1053.25,'cm^-1'),
+)
+
+transitionState(
+    label = 'exit2',
+    E0 = (-4.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.0082,"g/mol"), quantum=False),
+        NonlinearRotor(inertia=([51.7432,119.373,171.117],"u*angstrom**2"), symmetry=1, quantum=False),
+        HarmonicOscillator(frequencies=([250.311,383.83,544.382,578.988,595.324,705.422,964.712,1103.25,1146.91,1415.98,1483.33,1983.79,3128,3143.84,3255.29],"cm^-1")),
+        HinderedRotor(inertia=(9.35921,"u*angstrom**2"), symmetry=1, fourier=([[-11.2387,-12.5928,-3.87844,1.13314,-0.358812],[-1.59863,-8.03329,-5.05235,3.13723,2.45989]],"kJ/mol")),
+        HinderedRotor(inertia=(0.754698,"u*angstrom**2"), symmetry=1, barrier=(47.7645,"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency=(-404.271,'cm^-1'),
+)
+
+transitionState(
+    label = 'exit3',
+    E0 = (-7.2,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([53.2821, 120.4050, 170.1570],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([152.155,181.909,311.746,348.646,608.487,624.378,805.347,948.875,995.256,996.982,1169.1,1412.6,1834.83,3124.43,3245.2,3634.45],"cm^-1")),
+        HinderedRotor(inertia=(0.813269,"u*angstrom**2"), symmetry=1, fourier=([[-1.15338,-2.18664,-0.669531,-0.11502,-0.0512599],[0.00245222,0.0107485,0.00334564,-0.00165288,-0.0028674]],"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency=(-618.234,'cm^-1'),
+)
+
+################################################################################
+
+reaction(
+    label = 'entrance1',
+    reactants = ['acetyl', 'oxygen'],
+    products = ['acetylperoxy'],
+    transitionState = 'entrance1',
+    kinetics = Arrhenius(A=(2.65e6,'m^3/(mol*s)'), n=0.0, Ea=(0.0,'kcal/mol'), T0=(1,"K")),
+)
+
+reaction(
+    label = 'isom1',
+    reactants = ['acetylperoxy'],
+    products = ['hydroperoxylvinoxy'],
+    transitionState = 'isom1',
+    tunneling = 'Eckart',
+)
+
+reaction(
+    label = 'exit1',
+    reactants = ['acetylperoxy'],
+    products = ['ketene', 'hydroperoxyl'],
+    transitionState = 'exit1',
+    tunneling = 'Eckart',
+)
+
+reaction(
+    label = 'exit2',
+    reactants = ['hydroperoxylvinoxy'],
+    products = ['ketene', 'hydroperoxyl'],
+    transitionState = 'exit2',
+    tunneling = 'Eckart',
+)
+
+reaction(
+    label = 'exit3',
+    reactants = ['hydroperoxylvinoxy'],
+    products = ['lactone', 'hydroxyl'],
+    transitionState = 'exit3',
+    tunneling = 'Eckart',
+)
+
+#################################################################################
+
+network(
+    label = 'acetyl + O2',
+    isomers = [
+        'acetylperoxy',
+        'hydroperoxylvinoxy',
+    ],
+    reactants = [
+        ('acetyl', 'oxygen'),
+        ('ketene', 'hydroperoxyl'),
+	('lactone', 'hydroxyl')
+    ],
+    bathGas = {
+        'nitrogen': 1.0,
+    }
+)
+
+#################################################################################
+
+pressureDependence(
+    'acetyl + O2',
+    Tmin=(300.0,'K'), Tmax=(2000.0,'K'), Tcount=8,
+    Pmin=(0.01,'bar'), Pmax=(100.0,'bar'), Pcount=5,
+    maximumGrainSize = (1.0,'kcal/mol'),
+    minimumGrainCount = 250,
+    method = 'simulation least squares',
+    interpolationModel = ('chebyshev', 6, 4),
+    activeJRotor = True,
+)
diff --git a/examples/arkane/networks/acetyl+O2_slse/input.py b/examples/arkane/networks/acetyl+O2_slse/input.py
new file mode 100644
index 0000000000..46114439b4
--- /dev/null
+++ b/examples/arkane/networks/acetyl+O2_slse/input.py
@@ -0,0 +1,284 @@
+################################################################################
+#
+#   Arkane input file for acetyl + O2 pressure-dependent reaction network
+#
+################################################################################
+
+title = 'acetyl + oxygen'
+
+description = \
+"""
+The chemically-activated reaction of acetyl with oxygen. This system is of
+interest in atmospheric chemistry as a step in the conversion of acetaldehyde
+to the secondary pollutant peroxyacetylnitrate (PAN); it is also potentially
+important in the ignition chemistry of ethanol.
+"""
+
+species(
+    label = 'acetylperoxy',
+    structure = SMILES('CC(=O)O[O]'),
+    E0 = (-34.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([54.2977,104.836,156.05],"amu*angstrom^2"), symmetry=1),
+        HarmonicOscillator(frequencies=([319.695,500.474,536.674,543.894,727.156,973.365,1037.77,1119.72,1181.55,1391.11,1449.53,1454.72,1870.51,3037.12,3096.93,3136.39],"cm^-1")),
+        HinderedRotor(inertia=(7.38359,"amu*angstrom^2"), symmetry=1, fourier=([[-1.95191,-11.8215,0.740041,-0.049118,-0.464522],[0.000227764,0.00410782,-0.000805364,-0.000548218,-0.000266277]],"kJ/mol")),
+        HinderedRotor(inertia=(2.94723,"amu*angstrom^2"), symmetry=3, fourier=([[0.130647,0.0401507,-2.54582,-0.0436065,-0.120982],[-0.000701659,-0.000989654,0.00783349,-0.00140978,-0.00145843]],"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    molecularWeight = (75.04,"g/mol"),
+    collisionModel = TransportData(sigma=(5.09,'angstrom'), epsilon=(473,'K')),
+    energyTransferModel = SingleExponentialDown(
+        alpha0 = (0.5718,'kcal/mol'),
+        T0 = (300,'K'),
+        n = 0.85,
+    ),
+)
+
+species(
+    label = 'hydroperoxylvinoxy',
+    structure = SMILES('[CH2]C(=O)OO'),
+    E0 = (-32.4,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([44.8034,110.225,155.029],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([318.758,420.907,666.223,675.962,752.824,864.66,998.471,1019.54,1236.21,1437.91,1485.74,1687.9,3145.44,3262.88,3434.34],"cm^-1")),
+        HinderedRotor(inertia=(1.68464,"u*angstrom**2"), symmetry=2, fourier=([[0.359649,-16.1155,-0.593311,1.72918,0.256314],[-7.42981e-06,-0.000238057,3.29276e-05,-6.62608e-05,8.8443e-05]],"kJ/mol")),
+        HinderedRotor(inertia=(8.50433,"u*angstrom**2"), symmetry=1, fourier=([[-7.53504,-23.4471,-3.3974,-0.940593,-0.313674],[-4.58248,-2.47177,0.550012,1.03771,0.844226]],"kJ/mol")),
+        HinderedRotor(inertia=(0.803309,"u*angstrom**2"), symmetry=1, fourier=([[-8.65946,-3.97888,-1.13469,-0.402197,-0.145101],[4.41884e-05,4.83249e-05,1.30275e-05,-1.31353e-05,-6.66878e-06]],"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    molecularWeight = (75.04,"g/mol"),
+    collisionModel = TransportData(sigma=(5.09,'angstrom'), epsilon=(473,'K')),
+    energyTransferModel = SingleExponentialDown(
+        alpha0 = (0.5718,'kcal/mol'),
+        T0 = (300,'K'),
+        n = 0.85,
+    ),
+)
+
+species(
+    label = 'acetyl',
+    structure = SMILES('C[C]=O'),
+    E0 = (0.0,'kcal/mol'),  #(-20.5205,"kJ/mol")
+    modes = [
+        IdealGasTranslation(mass=(43.05,"g/mol")),
+        NonlinearRotor(inertia=([5.94518,50.8166,53.6436],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([464.313,845.126,1010.54,1038.43,1343.54,1434.69,1442.25,1906.18,2985.46,3076.57,3079.46],"cm^-1")),
+        HinderedRotor(inertia=(1.61752,"u*angstrom**2"), symmetry=3, barrier=(2.00242,"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'oxygen',
+    structure = SMILES('[O][O]'),
+    E0 = (0.0,'kcal/mol'),  #(-5.74557,"kJ/mol")
+    modes = [
+        IdealGasTranslation(mass=(32.00,"g/mol")),
+        LinearRotor(inertia=(11.6056,"u*angstrom**2"), symmetry=2),
+        HarmonicOscillator(frequencies=([1621.54],"cm^-1")),
+    ],
+    spinMultiplicity = 3,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'ketene',
+    structure = SMILES('C=C=O'),
+    E0 = (-6.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(42.0106,"g/mol")),
+        NonlinearRotor(inertia=([1.76922,48.8411,50.6103],"u*angstrom**2"), symmetry=2),
+        HarmonicOscillator(frequencies=([441.622,548.317,592.155,981.379,1159.66,1399.86,2192.1,3150.02,3240.58],"cm^-1")),
+    ],
+    spinMultiplicity = 1,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'lactone',
+    structure = SMILES('C1OC1(=O)'),
+    E0 = (-30.8,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(58.0055,"g/mol")),
+        NonlinearRotor(inertia=([20.1707,62.4381,79.1616],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([484.387,527.771,705.332,933.372,985.563,1050.26,1107.93,1176.43,1466.54,1985.09,3086.23,3186.46],"cm^-1")),
+    ],
+    spinMultiplicity = 1,
+    opticalIsomers = 1,
+)
+
+
+
+species(
+    label = 'hydroxyl',
+    structure = SMILES('[OH]'),
+    E0 = (0.0,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(17.0027,"g/mol")),
+        LinearRotor(inertia=(0.899988,"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([3676.39],"cm^-1")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'hydroperoxyl',
+    structure = SMILES('O[O]'),
+    E0 = (0.0,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(32.9977,"g/mol")),
+        NonlinearRotor(inertia=([0.811564,14.9434,15.755],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([1156.77,1424.28,3571.81],"cm^-1")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'nitrogen',
+    structure = SMILES('N#N'),
+    molecularWeight = (28.04,"g/mol"),
+    collisionModel = TransportData(sigma=(3.70,'angstrom'), epsilon=(94.9,'K')),
+    reactive = False
+)
+
+################################################################################
+
+transitionState(
+    label = 'entrance1',
+    E0 = (0.0,'kcal/mol'),
+)
+
+transitionState(
+    label = 'isom1',
+    E0 = (-5.8,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([49.3418,103.697,149.682],"u*angstrom**2"), symmetry=1, quantum=False),
+        HarmonicOscillator(frequencies=([148.551,306.791,484.573,536.709,599.366,675.538,832.594,918.413,1022.28,1031.45,1101.01,1130.05,1401.51,1701.26,1844.17,3078.6,3163.07],"cm^-1"), quantum=True),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency = (-1679.04,'cm^-1'),
+)
+
+transitionState(
+    label = 'exit1',
+    E0 = (0.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([55.4256, 136.1886, 188.2442],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([59.9256,204.218,352.811,466.297,479.997,542.345,653.897,886.657,1017.91,1079.17,1250.02,1309.14,1370.36,1678.52,2162.41,3061.53,3135.55],"cm^-1")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency=(-1053.25,'cm^-1'),
+)
+
+transitionState(
+    label = 'exit2',
+    E0 = (-4.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.0082,"g/mol"), quantum=False),
+        NonlinearRotor(inertia=([51.7432,119.373,171.117],"u*angstrom**2"), symmetry=1, quantum=False),
+        HarmonicOscillator(frequencies=([250.311,383.83,544.382,578.988,595.324,705.422,964.712,1103.25,1146.91,1415.98,1483.33,1983.79,3128,3143.84,3255.29],"cm^-1")),
+        HinderedRotor(inertia=(9.35921,"u*angstrom**2"), symmetry=1, fourier=([[-11.2387,-12.5928,-3.87844,1.13314,-0.358812],[-1.59863,-8.03329,-5.05235,3.13723,2.45989]],"kJ/mol")),
+        HinderedRotor(inertia=(0.754698,"u*angstrom**2"), symmetry=1, barrier=(47.7645,"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency=(-404.271,'cm^-1'),
+)
+
+transitionState(
+    label = 'exit3',
+    E0 = (-7.2,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([53.2821, 120.4050, 170.1570],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([152.155,181.909,311.746,348.646,608.487,624.378,805.347,948.875,995.256,996.982,1169.1,1412.6,1834.83,3124.43,3245.2,3634.45],"cm^-1")),
+        HinderedRotor(inertia=(0.813269,"u*angstrom**2"), symmetry=1, fourier=([[-1.15338,-2.18664,-0.669531,-0.11502,-0.0512599],[0.00245222,0.0107485,0.00334564,-0.00165288,-0.0028674]],"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency=(-618.234,'cm^-1'),
+)
+
+################################################################################
+
+reaction(
+    label = 'entrance1',
+    reactants = ['acetyl', 'oxygen'],
+    products = ['acetylperoxy'],
+    transitionState = 'entrance1',
+    kinetics = Arrhenius(A=(2.65e6,'m^3/(mol*s)'), n=0.0, Ea=(0.0,'kcal/mol'), T0=(1,"K")),
+)
+
+reaction(
+    label = 'isom1',
+    reactants = ['acetylperoxy'],
+    products = ['hydroperoxylvinoxy'],
+    transitionState = 'isom1',
+    tunneling = 'Eckart',
+)
+
+reaction(
+    label = 'exit1',
+    reactants = ['acetylperoxy'],
+    products = ['ketene', 'hydroperoxyl'],
+    transitionState = 'exit1',
+    tunneling = 'Eckart',
+)
+
+reaction(
+    label = 'exit2',
+    reactants = ['hydroperoxylvinoxy'],
+    products = ['ketene', 'hydroperoxyl'],
+    transitionState = 'exit2',
+    tunneling = 'Eckart',
+)
+
+reaction(
+    label = 'exit3',
+    reactants = ['hydroperoxylvinoxy'],
+    products = ['lactone', 'hydroxyl'],
+    transitionState = 'exit3',
+    tunneling = 'Eckart',
+)
+
+#################################################################################
+
+network(
+    label = 'acetyl + O2',
+    isomers = [
+        'acetylperoxy',
+        'hydroperoxylvinoxy',
+    ],
+    reactants = [
+        ('acetyl', 'oxygen'),
+        ('ketene', 'hydroperoxyl'),
+	('lactone', 'hydroxyl')
+    ],
+    bathGas = {
+        'nitrogen': 1.0,
+    }
+)
+
+#################################################################################
+
+pressureDependence(
+    'acetyl + O2',
+    Tmin=(300.0,'K'), Tmax=(2000.0,'K'), Tcount=8,
+    Pmin=(0.01,'bar'), Pmax=(100.0,'bar'), Pcount=5,
+    maximumGrainSize = (1.0,'kcal/mol'),
+    minimumGrainCount = 250,
+    method = 'simulation least squares eigen',
+    interpolationModel = ('chebyshev', 6, 4),
+    activeJRotor = True,
+)
diff --git a/examples/arkane/networks/acetyl+O2_slsme/input.py b/examples/arkane/networks/acetyl+O2_slsme/input.py
new file mode 100644
index 0000000000..49d8bca6dc
--- /dev/null
+++ b/examples/arkane/networks/acetyl+O2_slsme/input.py
@@ -0,0 +1,284 @@
+################################################################################
+#
+#   Arkane input file for acetyl + O2 pressure-dependent reaction network
+#
+################################################################################
+
+title = 'acetyl + oxygen'
+
+description = \
+"""
+The chemically-activated reaction of acetyl with oxygen. This system is of
+interest in atmospheric chemistry as a step in the conversion of acetaldehyde
+to the secondary pollutant peroxyacetylnitrate (PAN); it is also potentially
+important in the ignition chemistry of ethanol.
+"""
+
+species(
+    label = 'acetylperoxy',
+    structure = SMILES('CC(=O)O[O]'),
+    E0 = (-34.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([54.2977,104.836,156.05],"amu*angstrom^2"), symmetry=1),
+        HarmonicOscillator(frequencies=([319.695,500.474,536.674,543.894,727.156,973.365,1037.77,1119.72,1181.55,1391.11,1449.53,1454.72,1870.51,3037.12,3096.93,3136.39],"cm^-1")),
+        HinderedRotor(inertia=(7.38359,"amu*angstrom^2"), symmetry=1, fourier=([[-1.95191,-11.8215,0.740041,-0.049118,-0.464522],[0.000227764,0.00410782,-0.000805364,-0.000548218,-0.000266277]],"kJ/mol")),
+        HinderedRotor(inertia=(2.94723,"amu*angstrom^2"), symmetry=3, fourier=([[0.130647,0.0401507,-2.54582,-0.0436065,-0.120982],[-0.000701659,-0.000989654,0.00783349,-0.00140978,-0.00145843]],"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    molecularWeight = (75.04,"g/mol"),
+    collisionModel = TransportData(sigma=(5.09,'angstrom'), epsilon=(473,'K')),
+    energyTransferModel = SingleExponentialDown(
+        alpha0 = (0.5718,'kcal/mol'),
+        T0 = (300,'K'),
+        n = 0.85,
+    ),
+)
+
+species(
+    label = 'hydroperoxylvinoxy',
+    structure = SMILES('[CH2]C(=O)OO'),
+    E0 = (-32.4,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([44.8034,110.225,155.029],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([318.758,420.907,666.223,675.962,752.824,864.66,998.471,1019.54,1236.21,1437.91,1485.74,1687.9,3145.44,3262.88,3434.34],"cm^-1")),
+        HinderedRotor(inertia=(1.68464,"u*angstrom**2"), symmetry=2, fourier=([[0.359649,-16.1155,-0.593311,1.72918,0.256314],[-7.42981e-06,-0.000238057,3.29276e-05,-6.62608e-05,8.8443e-05]],"kJ/mol")),
+        HinderedRotor(inertia=(8.50433,"u*angstrom**2"), symmetry=1, fourier=([[-7.53504,-23.4471,-3.3974,-0.940593,-0.313674],[-4.58248,-2.47177,0.550012,1.03771,0.844226]],"kJ/mol")),
+        HinderedRotor(inertia=(0.803309,"u*angstrom**2"), symmetry=1, fourier=([[-8.65946,-3.97888,-1.13469,-0.402197,-0.145101],[4.41884e-05,4.83249e-05,1.30275e-05,-1.31353e-05,-6.66878e-06]],"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    molecularWeight = (75.04,"g/mol"),
+    collisionModel = TransportData(sigma=(5.09,'angstrom'), epsilon=(473,'K')),
+    energyTransferModel = SingleExponentialDown(
+        alpha0 = (0.5718,'kcal/mol'),
+        T0 = (300,'K'),
+        n = 0.85,
+    ),
+)
+
+species(
+    label = 'acetyl',
+    structure = SMILES('C[C]=O'),
+    E0 = (0.0,'kcal/mol'),  #(-20.5205,"kJ/mol")
+    modes = [
+        IdealGasTranslation(mass=(43.05,"g/mol")),
+        NonlinearRotor(inertia=([5.94518,50.8166,53.6436],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([464.313,845.126,1010.54,1038.43,1343.54,1434.69,1442.25,1906.18,2985.46,3076.57,3079.46],"cm^-1")),
+        HinderedRotor(inertia=(1.61752,"u*angstrom**2"), symmetry=3, barrier=(2.00242,"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'oxygen',
+    structure = SMILES('[O][O]'),
+    E0 = (0.0,'kcal/mol'),  #(-5.74557,"kJ/mol")
+    modes = [
+        IdealGasTranslation(mass=(32.00,"g/mol")),
+        LinearRotor(inertia=(11.6056,"u*angstrom**2"), symmetry=2),
+        HarmonicOscillator(frequencies=([1621.54],"cm^-1")),
+    ],
+    spinMultiplicity = 3,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'ketene',
+    structure = SMILES('C=C=O'),
+    E0 = (-6.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(42.0106,"g/mol")),
+        NonlinearRotor(inertia=([1.76922,48.8411,50.6103],"u*angstrom**2"), symmetry=2),
+        HarmonicOscillator(frequencies=([441.622,548.317,592.155,981.379,1159.66,1399.86,2192.1,3150.02,3240.58],"cm^-1")),
+    ],
+    spinMultiplicity = 1,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'lactone',
+    structure = SMILES('C1OC1(=O)'),
+    E0 = (-30.8,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(58.0055,"g/mol")),
+        NonlinearRotor(inertia=([20.1707,62.4381,79.1616],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([484.387,527.771,705.332,933.372,985.563,1050.26,1107.93,1176.43,1466.54,1985.09,3086.23,3186.46],"cm^-1")),
+    ],
+    spinMultiplicity = 1,
+    opticalIsomers = 1,
+)
+
+
+
+species(
+    label = 'hydroxyl',
+    structure = SMILES('[OH]'),
+    E0 = (0.0,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(17.0027,"g/mol")),
+        LinearRotor(inertia=(0.899988,"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([3676.39],"cm^-1")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'hydroperoxyl',
+    structure = SMILES('O[O]'),
+    E0 = (0.0,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(32.9977,"g/mol")),
+        NonlinearRotor(inertia=([0.811564,14.9434,15.755],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([1156.77,1424.28,3571.81],"cm^-1")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+)
+
+species(
+    label = 'nitrogen',
+    structure = SMILES('N#N'),
+    molecularWeight = (28.04,"g/mol"),
+    collisionModel = TransportData(sigma=(3.70,'angstrom'), epsilon=(94.9,'K')),
+    reactive = False
+)
+
+################################################################################
+
+transitionState(
+    label = 'entrance1',
+    E0 = (0.0,'kcal/mol'),
+)
+
+transitionState(
+    label = 'isom1',
+    E0 = (-5.8,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([49.3418,103.697,149.682],"u*angstrom**2"), symmetry=1, quantum=False),
+        HarmonicOscillator(frequencies=([148.551,306.791,484.573,536.709,599.366,675.538,832.594,918.413,1022.28,1031.45,1101.01,1130.05,1401.51,1701.26,1844.17,3078.6,3163.07],"cm^-1"), quantum=True),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency = (-1679.04,'cm^-1'),
+)
+
+transitionState(
+    label = 'exit1',
+    E0 = (0.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([55.4256, 136.1886, 188.2442],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([59.9256,204.218,352.811,466.297,479.997,542.345,653.897,886.657,1017.91,1079.17,1250.02,1309.14,1370.36,1678.52,2162.41,3061.53,3135.55],"cm^-1")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency=(-1053.25,'cm^-1'),
+)
+
+transitionState(
+    label = 'exit2',
+    E0 = (-4.6,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.0082,"g/mol"), quantum=False),
+        NonlinearRotor(inertia=([51.7432,119.373,171.117],"u*angstrom**2"), symmetry=1, quantum=False),
+        HarmonicOscillator(frequencies=([250.311,383.83,544.382,578.988,595.324,705.422,964.712,1103.25,1146.91,1415.98,1483.33,1983.79,3128,3143.84,3255.29],"cm^-1")),
+        HinderedRotor(inertia=(9.35921,"u*angstrom**2"), symmetry=1, fourier=([[-11.2387,-12.5928,-3.87844,1.13314,-0.358812],[-1.59863,-8.03329,-5.05235,3.13723,2.45989]],"kJ/mol")),
+        HinderedRotor(inertia=(0.754698,"u*angstrom**2"), symmetry=1, barrier=(47.7645,"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency=(-404.271,'cm^-1'),
+)
+
+transitionState(
+    label = 'exit3',
+    E0 = (-7.2,'kcal/mol'),
+    modes = [
+        IdealGasTranslation(mass=(75.04,"g/mol")),
+        NonlinearRotor(inertia=([53.2821, 120.4050, 170.1570],"u*angstrom**2"), symmetry=1),
+        HarmonicOscillator(frequencies=([152.155,181.909,311.746,348.646,608.487,624.378,805.347,948.875,995.256,996.982,1169.1,1412.6,1834.83,3124.43,3245.2,3634.45],"cm^-1")),
+        HinderedRotor(inertia=(0.813269,"u*angstrom**2"), symmetry=1, fourier=([[-1.15338,-2.18664,-0.669531,-0.11502,-0.0512599],[0.00245222,0.0107485,0.00334564,-0.00165288,-0.0028674]],"kJ/mol")),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency=(-618.234,'cm^-1'),
+)
+
+################################################################################
+
+reaction(
+    label = 'entrance1',
+    reactants = ['acetyl', 'oxygen'],
+    products = ['acetylperoxy'],
+    transitionState = 'entrance1',
+    kinetics = Arrhenius(A=(2.65e6,'m^3/(mol*s)'), n=0.0, Ea=(0.0,'kcal/mol'), T0=(1,"K")),
+)
+
+reaction(
+    label = 'isom1',
+    reactants = ['acetylperoxy'],
+    products = ['hydroperoxylvinoxy'],
+    transitionState = 'isom1',
+    tunneling = 'Eckart',
+)
+
+reaction(
+    label = 'exit1',
+    reactants = ['acetylperoxy'],
+    products = ['ketene', 'hydroperoxyl'],
+    transitionState = 'exit1',
+    tunneling = 'Eckart',
+)
+
+reaction(
+    label = 'exit2',
+    reactants = ['hydroperoxylvinoxy'],
+    products = ['ketene', 'hydroperoxyl'],
+    transitionState = 'exit2',
+    tunneling = 'Eckart',
+)
+
+reaction(
+    label = 'exit3',
+    reactants = ['hydroperoxylvinoxy'],
+    products = ['lactone', 'hydroxyl'],
+    transitionState = 'exit3',
+    tunneling = 'Eckart',
+)
+
+#################################################################################
+
+network(
+    label = 'acetyl + O2',
+    isomers = [
+        'acetylperoxy',
+        'hydroperoxylvinoxy',
+    ],
+    reactants = [
+        ('acetyl', 'oxygen'),
+        ('ketene', 'hydroperoxyl'),
+	('lactone', 'hydroxyl')
+    ],
+    bathGas = {
+        'nitrogen': 1.0,
+    }
+)
+
+#################################################################################
+
+pressureDependence(
+    'acetyl + O2',
+    Tmin=(300.0,'K'), Tmax=(2000.0,'K'), Tcount=8,
+    Pmin=(0.01,'bar'), Pmax=(100.0,'bar'), Pcount=5,
+    maximumGrainSize = (1.0,'kcal/mol'),
+    minimumGrainCount = 250,
+    method = 'simulation least squares matrix exponential',
+    interpolationModel = ('chebyshev', 6, 4),
+    activeJRotor = True,
+)
diff --git a/examples/arkane/networks/n-butanol/input.py b/examples/arkane/networks/n-butanol_msc/input.py
similarity index 100%
rename from examples/arkane/networks/n-butanol/input.py
rename to examples/arkane/networks/n-butanol_msc/input.py
diff --git a/rmgpy/pdep/sls.py b/rmgpy/pdep/sls.py
index 8060b10f70..40146a9618 100644
--- a/rmgpy/pdep/sls.py
+++ b/rmgpy/pdep/sls.py
@@ -32,14 +32,16 @@
 and implementing the SLS master equation reduction method
 """
 
-import juliacall import Main
+from juliacall import Main
 Main.seval("using SciMLBase")
+Main.seval("using Sundials")
 import numpy as np
 import scipy.linalg
 import scipy.optimize as opt
 
 import rmgpy.constants as constants
 from rmgpy.pdep.me import generate_full_me_matrix, states_to_configurations
+from rmgpy.rmg.reactors import to_julia
 
 
 def get_initial_condition(network, x0, indices):
@@ -80,30 +82,36 @@ def get_initial_condition(network, x0, indices):
 
 
 def solve_me(M, p0, t):
-    f = Main.eval(
+    f = Main.seval(
         """
-function f(u, M, t)
-    return M*u
+function f(du, u, M, t)
+    du .= M * u
+    return du
 end"""
     )
-    jac = Main.eval(
+    jac = Main.seval(
         """
-function jac(u, M, t)
-    return M
+function jac(J, u, M, t)
+    J .= M
+    return J
 end"""
     )
+    p0 = to_julia(p0)
+    M = to_julia(M)
     tspan = (0.0, t)
     fcn = Main.ODEFunction(f, jac=jac)
     prob = Main.ODEProblem(fcn, p0, tspan, M)
-    sol = Main.solve(prob, solver=Main.CVODE_BDF(), abstol=1e-16, reltol=1e-6)
+    sol = Main.solve(prob, Main.CVODE_BDF(), abstol=1e-16, reltol=1e-6)
     return sol
 
 
 def solve_me_fcns(f, jac, M, p0, t):
+    p0 = to_julia(p0)
+    M = to_julia(M)
     tspan = (0.0, t)
     fcn = Main.ODEFunction(f, jac=jac)
     prob = Main.ODEProblem(fcn, p0, tspan, M)
-    sol = Main.solve(prob, solver=Main.CVODE_BDF(), abstol=1e-16, reltol=1e-6)
+    sol = Main.solve(prob, Main.CVODE_BDF(), abstol=1e-16, reltol=1e-6)
     return sol
 
 
@@ -145,16 +153,18 @@ def get_rate_coefficients_SLS(network, T, P, method="mexp", neglect_high_energy_
     tau = np.abs(1.0 / fastest_reaction)
 
     if method == "ode":
-        f = Main.eval(
+        f = Main.seval(
             """
-function f(u,M,t)
-    return M*u
+function f(du, u, M, t)
+    du .= M * u
+    return du
 end"""
         )
-        jac = Main.eval(
+        jac = Main.seval(
             """
-function jac(u,M,t)
-    return M
+function jac(J, u, M, t)
+    J .= M
+    return J
 end"""
         )
 
diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index f5b4b059ad..ba7981924f 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -58,6 +58,15 @@
 from rmgpy.data.kinetics.depository import DepositoryReaction
 
 
+def to_julia(obj):
+    if isinstance(obj, dict):
+        return Main.PythonCall.pyconvert(Main.Dict, obj)
+    elif isinstance(obj, list) or isinstance(obj, np.ndarray):
+        return Main.PythonCall.pyconvert(Main.Array, obj)
+    else:
+        return obj
+
+
 class PhaseSystem:
     """
     Class for tracking and managing all the phases and interfaces of species/reactions
@@ -562,14 +571,6 @@ def generate_reactor(self, phase_system):
         return react, domain, [], p
 
 
-def to_julia(obj):
-    if isinstance(obj, dict):
-        return Main.PythonCall.pyconvert(Main.Dict, obj)
-    elif isinstance(obj, list) or isinstance(obj, np.ndarray):
-        return Main.PythonCall.pyconvert(Main.Vector, obj)
-    else:
-        return obj
-
 def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
     """
     Generate corresponding rms object

From 332d8c0bffbbe4a77f3ec5037965071db9b21e51 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Wed, 3 Apr 2024 13:29:06 -0400
Subject: [PATCH 039/162] Don't track plots

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 087e01fda0..946eb94d4a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -117,3 +117,4 @@ examples/**/dictionary.txt
 examples/**/reactions.py
 examples/**/RMG_libraries
 examples/**/species
+examples/**/plots

From 036984398012b80355c5281852b1b721eb83ef83 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Wed, 3 Apr 2024 13:29:35 -0400
Subject: [PATCH 040/162] don't track yaml files

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 946eb94d4a..23623e4dfd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -118,3 +118,4 @@ examples/**/reactions.py
 examples/**/RMG_libraries
 examples/**/species
 examples/**/plots
+examples/**/yaml_files

From 5723de3b9c371bfc339b16e6ef675a27fa6e7cf8 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Wed, 3 Apr 2024 13:29:41 -0400
Subject: [PATCH 041/162] update name

---
 test/arkane/arkaneFunctionalInputTest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/arkane/arkaneFunctionalInputTest.py b/test/arkane/arkaneFunctionalInputTest.py
index 89f05f6c2e..5f22b0eecd 100644
--- a/test/arkane/arkaneFunctionalInputTest.py
+++ b/test/arkane/arkaneFunctionalInputTest.py
@@ -327,7 +327,7 @@ def test_load_input_file(self):
             "examples",
             "arkane",
             "networks",
-            "acetyl+O2",
+            "acetyl+O2_mse",
             "input.py",
         )
         (

From 117926be3d7a6390eef46a1aabe039df23c0e4b2 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Wed, 3 Apr 2024 13:31:33 -0400
Subject: [PATCH 042/162] track yaml files

---
 .gitignore | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 23623e4dfd..946eb94d4a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -118,4 +118,3 @@ examples/**/reactions.py
 examples/**/RMG_libraries
 examples/**/species
 examples/**/plots
-examples/**/yaml_files

From 55c462f18dcbf066a604c3bcba8060b2dd69db9a Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Wed, 3 Apr 2024 14:29:23 -0400
Subject: [PATCH 043/162] See where we get julia from

---
 .github/workflows/CI.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index eddb2c12a8..3764b82c85 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -152,6 +152,7 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
           export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
+          which julia
           julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("SciMLBase"); Pkg.add("Sundials"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor

From d4d0a06ac3c03339e8d673558b394576f946e487 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Wed, 3 Apr 2024 14:30:09 -0400
Subject: [PATCH 044/162] Add Pkg.

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 3764b82c85..e90e141147 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -153,7 +153,7 @@ jobs:
         run: |
           export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
           which julia
-          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("SciMLBase"); Pkg.add("Sundials"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
+          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("SciMLBase"); Pkg.add("Sundials"); Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor

From 45fda81c770c06f872de28ba2f4eb7102870f1d9 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Wed, 3 Apr 2024 17:03:53 -0400
Subject: [PATCH 045/162] debug

---
 .../arkane/networks/{acetyl+O2_sce => acetyl+O2_cse}/input.py   | 0
 test/arkane/arkaneFunctionalInputTest.py                        | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename examples/arkane/networks/{acetyl+O2_sce => acetyl+O2_cse}/input.py (100%)

diff --git a/examples/arkane/networks/acetyl+O2_sce/input.py b/examples/arkane/networks/acetyl+O2_cse/input.py
similarity index 100%
rename from examples/arkane/networks/acetyl+O2_sce/input.py
rename to examples/arkane/networks/acetyl+O2_cse/input.py
diff --git a/test/arkane/arkaneFunctionalInputTest.py b/test/arkane/arkaneFunctionalInputTest.py
index 5f22b0eecd..8e1bcdb1b5 100644
--- a/test/arkane/arkaneFunctionalInputTest.py
+++ b/test/arkane/arkaneFunctionalInputTest.py
@@ -327,7 +327,7 @@ def test_load_input_file(self):
             "examples",
             "arkane",
             "networks",
-            "acetyl+O2_mse",
+            "acetyl+O2_cse",
             "input.py",
         )
         (

From c5fbaa52a071e7babb86ac600f85444efc1d92e0 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Wed, 3 Apr 2024 17:06:56 -0400
Subject: [PATCH 046/162] update

---
 .github/workflows/CI.yml   |  2 +-
 .github/workflows/docs.yml |  1 +
 Dockerfile                 | 37 ++++++++++++++++++-------------------
 3 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index e90e141147..e3afc69628 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -151,8 +151,8 @@ jobs:
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
-          export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
           which julia
+          export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
           julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("SciMLBase"); Pkg.add("Sundials"); Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 86718382e7..b4602038ee 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -63,6 +63,7 @@ jobs:
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
+          which julia
           export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
           julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("SciMLBase"); Pkg.add("Sundials"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
diff --git a/Dockerfile b/Dockerfile
index 9dd27c2f35..3e6c204437 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -11,25 +11,25 @@ RUN ln -snf /bin/bash /bin/sh
 #  - git for downloading RMG respoitories
 #  - wget for downloading conda install script
 #  - libxrender1 required by RDKit
-RUN apt-get update && \
+RUN apt-get update &&
     apt-get install -y \
-    make \
-    gcc \
-    wget \
-    git \
-    g++ \
-    libxrender1 && \
-    apt-get autoremove -y && \
+        make \
+        gcc \
+        wget \
+        git \
+        g++ \
+        libxrender1 &&
+    apt-get autoremove -y &&
     apt-get clean -y
 
 # Install conda
-RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    bash Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda && \
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh &&
+    bash Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda &&
     rm Miniconda3-latest-Linux-x86_64.sh
 ENV PATH="$PATH:/miniconda/bin"
 
 # Set solver backend to mamba for speed
-RUN conda install -n base conda-libmamba-solver && \
+RUN conda install -n base conda-libmamba-solver &&
     conda config --set solver libmamba
 
 # Set Bash as the default shell for following commands
@@ -39,12 +39,12 @@ SHELL ["/bin/bash", "-c"]
 WORKDIR /rmg
 
 # Clone the RMG base and database repositories
-RUN git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-Py.git && \
+RUN git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-Py.git &&
     git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-database.git
 
 WORKDIR /rmg/RMG-Py
 # build the conda environment
-RUN conda env create --file environment.yml && \
+RUN conda env create --file environment.yml &&
     conda clean --all --yes
 
 # This runs all subsequent commands inside the rmg_env conda environment
@@ -63,17 +63,16 @@ ENV PATH="$RUNNER_CWD/RMG-Py:$PATH"
 # 2. Install and link Julia dependencies for RMS
 # setting this env variable fixes an issue with Julia precompilation on Windows
 ENV JULIA_CPU_TARGET="x86-64,haswell,skylake,broadwell,znver1,znver2,znver3,cascadelake,icelake-client,cooperlake,generic"
-RUN make && \
-    julia -e 'using Pkg; Pkg.add(PackageSpec(name="PyCall",rev="master")); Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' && \
-    python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
+RUN make &&
+    julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("SciMLBase"); Pkg.add("Sundials"); Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
 # RMG-Py should now be installed and ready - trigger precompilation and test run
 RUN python rmg.py examples/rmg/minimal/input.py
 # delete the results, preserve input.py
-RUN mv examples/rmg/minimal/input.py . && \
-    rm -rf examples/rmg/minimal/* && \
+RUN mv examples/rmg/minimal/input.py . &&
+    rm -rf examples/rmg/minimal/* &&
     mv input.py examples/rmg/minimal/
 
 # when running this image, open an interactive bash terminal inside the conda environment
-RUN echo "source activate rmg_env" > ~/.bashrc
+RUN echo "source activate rmg_env" >~/.bashrc
 ENTRYPOINT ["/bin/bash", "--login"]

From 4167d4c65de1fd36c24dfcf1c9ca75349756de8d Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 4 Apr 2024 10:20:05 -0400
Subject: [PATCH 047/162] debug

---
 rmgpy/rmg/reactors.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index ba7981924f..443f5efc68 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -61,8 +61,13 @@
 def to_julia(obj):
     if isinstance(obj, dict):
         return Main.PythonCall.pyconvert(Main.Dict, obj)
-    elif isinstance(obj, list) or isinstance(obj, np.ndarray):
-        return Main.PythonCall.pyconvert(Main.Array, obj)
+    elif isinstance(obj, list):
+        return Main.PythonCall.pyconvert(Main.Vector, obj)
+    elif  isinstance(obj, np.ndarray):
+        if len(obj.shape) == 1:
+            return Main.PythonCall.pyconvert(Main.Vector, obj)
+        else:
+            return Main.PythonCall.pyconvert(Main.Matrix, obj)
     else:
         return obj
 
@@ -600,7 +605,7 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
         Tmax = obj.Tmax.value_si
         Pmin = obj.Pmin.value_si
         Pmax = obj.Pmax.value_si
-        coeffs = to_julia(obj.coeffs.value_si.tolist())
+        coeffs = to_julia(obj.coeffs.value_si)
         return rms.Chebyshev(coeffs, Tmin, Tmax, Pmin, Pmax)
     elif isinstance(obj, ThirdBody):
         arrstr = arrhenius_to_julia_string(obj.arrheniusLow)

From 2a81c71b91afbeddcf96fbfddd09fa1dfaed9d6d Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 4 Apr 2024 12:39:32 -0400
Subject: [PATCH 048/162] use Sundials solver and convert list to julia vector

---
 rmgpy/rmg/reactors.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index 443f5efc68..b039e23ed5 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -38,6 +38,7 @@
 import juliacall
 from juliacall import Main
 Main.seval("using PythonCall")
+Main.seval("using Sundials")
 rms = juliacall.newmodule("RMS")
 rms.seval("using ReactionMechanismSimulator")
 
@@ -446,7 +447,7 @@ def simulate(self, model_settings, simulator_settings, conditions):
             model_settings.tol_rxn_to_core_deadend_radical,
             atol=simulator_settings.atol,
             rtol=simulator_settings.rtol,
-            solver=rms.ReactionMechanismSimulator.Sundials.CVODE_BDF(),
+            solver=Main.Sundials.CVODE_BDF(),
         )
 
         return (
@@ -492,7 +493,7 @@ def generate_reactor(self, phase_system):
         surf = rms.IdealSurface(surf.species, surf.reactions, surf.site_density, name="surface")
         liq_constant_species = [cspc for cspc in self.const_spc_names if cspc in [spc.name for spc in liq.species]]
         cat_constant_species = [cspc for cspc in self.const_spc_names if cspc in [spc.name for spc in surf.species]]
-        domainliq, y0liq, pliq = rms.ConstantTVDomain(phase=liq, initialconds=to_julia(self.initial_conditions["liquid"]), constantspecies=liq_constant_species)
+        domainliq, y0liq, pliq = rms.ConstantTVDomain(phase=liq, initialconds=to_julia(self.initial_conditions["liquid"]), constantspecies=to_julia(liq_constant_species))
         domaincat, y0cat, pcat = rms.ConstantTAPhiDomain(
             phase=surf, initialconds=to_julia(self.initial_conditions["surface"]), constantspecies=cat_constant_species
         )
@@ -536,14 +537,14 @@ def generate_reactor(self, phase_system):
         """
         phase = phase_system.phases["Default"]
         liq = rms.IdealDiluteSolution(phase.species, phase.reactions, phase.solvent)
-        domain, y0, p = rms.ConstantTVDomain(phase=liq, initialconds=to_julia(self.initial_conditions), constantspecies=self.const_spc_names)
+        domain, y0, p = rms.ConstantTVDomain(phase=liq, initialconds=to_julia(self.initial_conditions), constantspecies=to_julia(self.const_spc_names))
 
         interfaces = []
 
         if self.inlet_conditions:
             inlet_conditions = {key: value for (key, value) in self.inlet_conditions.items() if key != "F"}
             total_molar_flow_rate = self.inlet_conditions["F"]
-            inlet = rms.Inlet(domain, inlet_conditions, Main.seval("x->" + str(total_molar_flow_rate)))
+            inlet = rms.Inlet(domain, to_julia(inlet_conditions), Main.seval("x->" + str(total_molar_flow_rate)))
             interfaces.append(inlet)
 
         if self.outlet_conditions:

From 1d4005a029909bd86f67535976d8a51db2136a59 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 4 Apr 2024 18:01:00 -0400
Subject: [PATCH 049/162] Resolve AttributeError: 'Interface' object has no
 attribute 'species'

---
 rmgpy/rmg/reactors.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index b039e23ed5..7e24b32324 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -167,8 +167,8 @@ def pass_species(self, label, phasesys):
             for i, rxn in enumerate(interface.reactions):
                 if (
                     (spc in rxn.reactants or spc in rxn.products)
-                    and all([spec in phasesys.interfaces[key].species for spec in rxn.reactants])
-                    and all([spec in phasesys.interfaces[key].species for spec in rxn.products])
+                    and all([spec.name in phasesys.species_dict for spec in rxn.reactants])
+                    and all([spec.name in phasesys.species_dict for spec in rxn.products])
                 ):
                     rxnlist.append(rxn)
 

From cae6444655e3da393de6b4ae1984d1289ff60bc8 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 4 Apr 2024 18:14:02 -0400
Subject: [PATCH 050/162] Convert to julia object

---
 rmgpy/rmg/reactors.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index 7e24b32324..68ee3769f6 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -495,7 +495,7 @@ def generate_reactor(self, phase_system):
         cat_constant_species = [cspc for cspc in self.const_spc_names if cspc in [spc.name for spc in surf.species]]
         domainliq, y0liq, pliq = rms.ConstantTVDomain(phase=liq, initialconds=to_julia(self.initial_conditions["liquid"]), constantspecies=to_julia(liq_constant_species))
         domaincat, y0cat, pcat = rms.ConstantTAPhiDomain(
-            phase=surf, initialconds=to_julia(self.initial_conditions["surface"]), constantspecies=cat_constant_species
+            phase=surf, initialconds=to_julia(self.initial_conditions["surface"]), constantspecies=to_julia(cat_constant_species),
         )
         if interface.reactions == []:
             inter, pinter = rms.ReactiveInternalInterfaceConstantTPhi(

From 5dabe3be0ed42f8efca1ea7dd322c5b215cfb542 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 25 Apr 2024 16:27:09 -0400
Subject: [PATCH 051/162] Remove duplicate test

---
 .../arkane/networks/acetyl+O2_slsme/input.py  | 284 ------------------
 1 file changed, 284 deletions(-)
 delete mode 100644 examples/arkane/networks/acetyl+O2_slsme/input.py

diff --git a/examples/arkane/networks/acetyl+O2_slsme/input.py b/examples/arkane/networks/acetyl+O2_slsme/input.py
deleted file mode 100644
index 49d8bca6dc..0000000000
--- a/examples/arkane/networks/acetyl+O2_slsme/input.py
+++ /dev/null
@@ -1,284 +0,0 @@
-################################################################################
-#
-#   Arkane input file for acetyl + O2 pressure-dependent reaction network
-#
-################################################################################
-
-title = 'acetyl + oxygen'
-
-description = \
-"""
-The chemically-activated reaction of acetyl with oxygen. This system is of
-interest in atmospheric chemistry as a step in the conversion of acetaldehyde
-to the secondary pollutant peroxyacetylnitrate (PAN); it is also potentially
-important in the ignition chemistry of ethanol.
-"""
-
-species(
-    label = 'acetylperoxy',
-    structure = SMILES('CC(=O)O[O]'),
-    E0 = (-34.6,'kcal/mol'),
-    modes = [
-        IdealGasTranslation(mass=(75.04,"g/mol")),
-        NonlinearRotor(inertia=([54.2977,104.836,156.05],"amu*angstrom^2"), symmetry=1),
-        HarmonicOscillator(frequencies=([319.695,500.474,536.674,543.894,727.156,973.365,1037.77,1119.72,1181.55,1391.11,1449.53,1454.72,1870.51,3037.12,3096.93,3136.39],"cm^-1")),
-        HinderedRotor(inertia=(7.38359,"amu*angstrom^2"), symmetry=1, fourier=([[-1.95191,-11.8215,0.740041,-0.049118,-0.464522],[0.000227764,0.00410782,-0.000805364,-0.000548218,-0.000266277]],"kJ/mol")),
-        HinderedRotor(inertia=(2.94723,"amu*angstrom^2"), symmetry=3, fourier=([[0.130647,0.0401507,-2.54582,-0.0436065,-0.120982],[-0.000701659,-0.000989654,0.00783349,-0.00140978,-0.00145843]],"kJ/mol")),
-    ],
-    spinMultiplicity = 2,
-    opticalIsomers = 1,
-    molecularWeight = (75.04,"g/mol"),
-    collisionModel = TransportData(sigma=(5.09,'angstrom'), epsilon=(473,'K')),
-    energyTransferModel = SingleExponentialDown(
-        alpha0 = (0.5718,'kcal/mol'),
-        T0 = (300,'K'),
-        n = 0.85,
-    ),
-)
-
-species(
-    label = 'hydroperoxylvinoxy',
-    structure = SMILES('[CH2]C(=O)OO'),
-    E0 = (-32.4,'kcal/mol'),
-    modes = [
-        IdealGasTranslation(mass=(75.04,"g/mol")),
-        NonlinearRotor(inertia=([44.8034,110.225,155.029],"u*angstrom**2"), symmetry=1),
-        HarmonicOscillator(frequencies=([318.758,420.907,666.223,675.962,752.824,864.66,998.471,1019.54,1236.21,1437.91,1485.74,1687.9,3145.44,3262.88,3434.34],"cm^-1")),
-        HinderedRotor(inertia=(1.68464,"u*angstrom**2"), symmetry=2, fourier=([[0.359649,-16.1155,-0.593311,1.72918,0.256314],[-7.42981e-06,-0.000238057,3.29276e-05,-6.62608e-05,8.8443e-05]],"kJ/mol")),
-        HinderedRotor(inertia=(8.50433,"u*angstrom**2"), symmetry=1, fourier=([[-7.53504,-23.4471,-3.3974,-0.940593,-0.313674],[-4.58248,-2.47177,0.550012,1.03771,0.844226]],"kJ/mol")),
-        HinderedRotor(inertia=(0.803309,"u*angstrom**2"), symmetry=1, fourier=([[-8.65946,-3.97888,-1.13469,-0.402197,-0.145101],[4.41884e-05,4.83249e-05,1.30275e-05,-1.31353e-05,-6.66878e-06]],"kJ/mol")),
-    ],
-    spinMultiplicity = 2,
-    opticalIsomers = 1,
-    molecularWeight = (75.04,"g/mol"),
-    collisionModel = TransportData(sigma=(5.09,'angstrom'), epsilon=(473,'K')),
-    energyTransferModel = SingleExponentialDown(
-        alpha0 = (0.5718,'kcal/mol'),
-        T0 = (300,'K'),
-        n = 0.85,
-    ),
-)
-
-species(
-    label = 'acetyl',
-    structure = SMILES('C[C]=O'),
-    E0 = (0.0,'kcal/mol'),  #(-20.5205,"kJ/mol")
-    modes = [
-        IdealGasTranslation(mass=(43.05,"g/mol")),
-        NonlinearRotor(inertia=([5.94518,50.8166,53.6436],"u*angstrom**2"), symmetry=1),
-        HarmonicOscillator(frequencies=([464.313,845.126,1010.54,1038.43,1343.54,1434.69,1442.25,1906.18,2985.46,3076.57,3079.46],"cm^-1")),
-        HinderedRotor(inertia=(1.61752,"u*angstrom**2"), symmetry=3, barrier=(2.00242,"kJ/mol")),
-    ],
-    spinMultiplicity = 2,
-    opticalIsomers = 1,
-)
-
-species(
-    label = 'oxygen',
-    structure = SMILES('[O][O]'),
-    E0 = (0.0,'kcal/mol'),  #(-5.74557,"kJ/mol")
-    modes = [
-        IdealGasTranslation(mass=(32.00,"g/mol")),
-        LinearRotor(inertia=(11.6056,"u*angstrom**2"), symmetry=2),
-        HarmonicOscillator(frequencies=([1621.54],"cm^-1")),
-    ],
-    spinMultiplicity = 3,
-    opticalIsomers = 1,
-)
-
-species(
-    label = 'ketene',
-    structure = SMILES('C=C=O'),
-    E0 = (-6.6,'kcal/mol'),
-    modes = [
-        IdealGasTranslation(mass=(42.0106,"g/mol")),
-        NonlinearRotor(inertia=([1.76922,48.8411,50.6103],"u*angstrom**2"), symmetry=2),
-        HarmonicOscillator(frequencies=([441.622,548.317,592.155,981.379,1159.66,1399.86,2192.1,3150.02,3240.58],"cm^-1")),
-    ],
-    spinMultiplicity = 1,
-    opticalIsomers = 1,
-)
-
-species(
-    label = 'lactone',
-    structure = SMILES('C1OC1(=O)'),
-    E0 = (-30.8,'kcal/mol'),
-    modes = [
-        IdealGasTranslation(mass=(58.0055,"g/mol")),
-        NonlinearRotor(inertia=([20.1707,62.4381,79.1616],"u*angstrom**2"), symmetry=1),
-        HarmonicOscillator(frequencies=([484.387,527.771,705.332,933.372,985.563,1050.26,1107.93,1176.43,1466.54,1985.09,3086.23,3186.46],"cm^-1")),
-    ],
-    spinMultiplicity = 1,
-    opticalIsomers = 1,
-)
-
-
-
-species(
-    label = 'hydroxyl',
-    structure = SMILES('[OH]'),
-    E0 = (0.0,'kcal/mol'),
-    modes = [
-        IdealGasTranslation(mass=(17.0027,"g/mol")),
-        LinearRotor(inertia=(0.899988,"u*angstrom**2"), symmetry=1),
-        HarmonicOscillator(frequencies=([3676.39],"cm^-1")),
-    ],
-    spinMultiplicity = 2,
-    opticalIsomers = 1,
-)
-
-species(
-    label = 'hydroperoxyl',
-    structure = SMILES('O[O]'),
-    E0 = (0.0,'kcal/mol'),
-    modes = [
-        IdealGasTranslation(mass=(32.9977,"g/mol")),
-        NonlinearRotor(inertia=([0.811564,14.9434,15.755],"u*angstrom**2"), symmetry=1),
-        HarmonicOscillator(frequencies=([1156.77,1424.28,3571.81],"cm^-1")),
-    ],
-    spinMultiplicity = 2,
-    opticalIsomers = 1,
-)
-
-species(
-    label = 'nitrogen',
-    structure = SMILES('N#N'),
-    molecularWeight = (28.04,"g/mol"),
-    collisionModel = TransportData(sigma=(3.70,'angstrom'), epsilon=(94.9,'K')),
-    reactive = False
-)
-
-################################################################################
-
-transitionState(
-    label = 'entrance1',
-    E0 = (0.0,'kcal/mol'),
-)
-
-transitionState(
-    label = 'isom1',
-    E0 = (-5.8,'kcal/mol'),
-    modes = [
-        IdealGasTranslation(mass=(75.04,"g/mol")),
-        NonlinearRotor(inertia=([49.3418,103.697,149.682],"u*angstrom**2"), symmetry=1, quantum=False),
-        HarmonicOscillator(frequencies=([148.551,306.791,484.573,536.709,599.366,675.538,832.594,918.413,1022.28,1031.45,1101.01,1130.05,1401.51,1701.26,1844.17,3078.6,3163.07],"cm^-1"), quantum=True),
-    ],
-    spinMultiplicity = 2,
-    opticalIsomers = 1,
-    frequency = (-1679.04,'cm^-1'),
-)
-
-transitionState(
-    label = 'exit1',
-    E0 = (0.6,'kcal/mol'),
-    modes = [
-        IdealGasTranslation(mass=(75.04,"g/mol")),
-        NonlinearRotor(inertia=([55.4256, 136.1886, 188.2442],"u*angstrom**2"), symmetry=1),
-        HarmonicOscillator(frequencies=([59.9256,204.218,352.811,466.297,479.997,542.345,653.897,886.657,1017.91,1079.17,1250.02,1309.14,1370.36,1678.52,2162.41,3061.53,3135.55],"cm^-1")),
-    ],
-    spinMultiplicity = 2,
-    opticalIsomers = 1,
-    frequency=(-1053.25,'cm^-1'),
-)
-
-transitionState(
-    label = 'exit2',
-    E0 = (-4.6,'kcal/mol'),
-    modes = [
-        IdealGasTranslation(mass=(75.0082,"g/mol"), quantum=False),
-        NonlinearRotor(inertia=([51.7432,119.373,171.117],"u*angstrom**2"), symmetry=1, quantum=False),
-        HarmonicOscillator(frequencies=([250.311,383.83,544.382,578.988,595.324,705.422,964.712,1103.25,1146.91,1415.98,1483.33,1983.79,3128,3143.84,3255.29],"cm^-1")),
-        HinderedRotor(inertia=(9.35921,"u*angstrom**2"), symmetry=1, fourier=([[-11.2387,-12.5928,-3.87844,1.13314,-0.358812],[-1.59863,-8.03329,-5.05235,3.13723,2.45989]],"kJ/mol")),
-        HinderedRotor(inertia=(0.754698,"u*angstrom**2"), symmetry=1, barrier=(47.7645,"kJ/mol")),
-    ],
-    spinMultiplicity = 2,
-    opticalIsomers = 1,
-    frequency=(-404.271,'cm^-1'),
-)
-
-transitionState(
-    label = 'exit3',
-    E0 = (-7.2,'kcal/mol'),
-    modes = [
-        IdealGasTranslation(mass=(75.04,"g/mol")),
-        NonlinearRotor(inertia=([53.2821, 120.4050, 170.1570],"u*angstrom**2"), symmetry=1),
-        HarmonicOscillator(frequencies=([152.155,181.909,311.746,348.646,608.487,624.378,805.347,948.875,995.256,996.982,1169.1,1412.6,1834.83,3124.43,3245.2,3634.45],"cm^-1")),
-        HinderedRotor(inertia=(0.813269,"u*angstrom**2"), symmetry=1, fourier=([[-1.15338,-2.18664,-0.669531,-0.11502,-0.0512599],[0.00245222,0.0107485,0.00334564,-0.00165288,-0.0028674]],"kJ/mol")),
-    ],
-    spinMultiplicity = 2,
-    opticalIsomers = 1,
-    frequency=(-618.234,'cm^-1'),
-)
-
-################################################################################
-
-reaction(
-    label = 'entrance1',
-    reactants = ['acetyl', 'oxygen'],
-    products = ['acetylperoxy'],
-    transitionState = 'entrance1',
-    kinetics = Arrhenius(A=(2.65e6,'m^3/(mol*s)'), n=0.0, Ea=(0.0,'kcal/mol'), T0=(1,"K")),
-)
-
-reaction(
-    label = 'isom1',
-    reactants = ['acetylperoxy'],
-    products = ['hydroperoxylvinoxy'],
-    transitionState = 'isom1',
-    tunneling = 'Eckart',
-)
-
-reaction(
-    label = 'exit1',
-    reactants = ['acetylperoxy'],
-    products = ['ketene', 'hydroperoxyl'],
-    transitionState = 'exit1',
-    tunneling = 'Eckart',
-)
-
-reaction(
-    label = 'exit2',
-    reactants = ['hydroperoxylvinoxy'],
-    products = ['ketene', 'hydroperoxyl'],
-    transitionState = 'exit2',
-    tunneling = 'Eckart',
-)
-
-reaction(
-    label = 'exit3',
-    reactants = ['hydroperoxylvinoxy'],
-    products = ['lactone', 'hydroxyl'],
-    transitionState = 'exit3',
-    tunneling = 'Eckart',
-)
-
-#################################################################################
-
-network(
-    label = 'acetyl + O2',
-    isomers = [
-        'acetylperoxy',
-        'hydroperoxylvinoxy',
-    ],
-    reactants = [
-        ('acetyl', 'oxygen'),
-        ('ketene', 'hydroperoxyl'),
-	('lactone', 'hydroxyl')
-    ],
-    bathGas = {
-        'nitrogen': 1.0,
-    }
-)
-
-#################################################################################
-
-pressureDependence(
-    'acetyl + O2',
-    Tmin=(300.0,'K'), Tmax=(2000.0,'K'), Tcount=8,
-    Pmin=(0.01,'bar'), Pmax=(100.0,'bar'), Pcount=5,
-    maximumGrainSize = (1.0,'kcal/mol'),
-    minimumGrainCount = 250,
-    method = 'simulation least squares matrix exponential',
-    interpolationModel = ('chebyshev', 6, 4),
-    activeJRotor = True,
-)

From a6efb3f51303dd83130945f8049e1298d50a6318 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 25 Apr 2024 16:27:26 -0400
Subject: [PATCH 052/162] Add comments and juliaup status

---
 .github/workflows/CI.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index e3afc69628..4469bc4f4b 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -150,8 +150,9 @@ jobs:
       # RMS installation and linking to Julia
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
+        # JULIA_CONDAPKG_EXE points to the existing conda/mamba to avoid JuliaCall from installing their own. See https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-a-Conda-environment.
         run: |
-          which julia
+          juliaup status
           export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
           julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("SciMLBase"); Pkg.add("Sundials"); Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 

From 419adb5dbfe428684f4593bb78870176da8dde0a Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 25 Apr 2024 16:43:45 -0400
Subject: [PATCH 053/162] Add back changes mistakenly done by formatter

---
 Dockerfile | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 3e6c204437..7aab7df8bd 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -11,25 +11,25 @@ RUN ln -snf /bin/bash /bin/sh
 #  - git for downloading RMG respoitories
 #  - wget for downloading conda install script
 #  - libxrender1 required by RDKit
-RUN apt-get update &&
+RUN apt-get update && \
     apt-get install -y \
         make \
         gcc \
         wget \
         git \
         g++ \
-        libxrender1 &&
-    apt-get autoremove -y &&
+        libxrender1 && \
+    apt-get autoremove -y && \
     apt-get clean -y
 
 # Install conda
-RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh &&
-    bash Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda &&
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+    bash Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda && \
     rm Miniconda3-latest-Linux-x86_64.sh
 ENV PATH="$PATH:/miniconda/bin"
 
 # Set solver backend to mamba for speed
-RUN conda install -n base conda-libmamba-solver &&
+RUN conda install -n base conda-libmamba-solver && \
     conda config --set solver libmamba
 
 # Set Bash as the default shell for following commands
@@ -39,12 +39,12 @@ SHELL ["/bin/bash", "-c"]
 WORKDIR /rmg
 
 # Clone the RMG base and database repositories
-RUN git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-Py.git &&
+RUN git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-Py.git && \
     git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-database.git
 
 WORKDIR /rmg/RMG-Py
 # build the conda environment
-RUN conda env create --file environment.yml &&
+RUN conda env create --file environment.yml && \
     conda clean --all --yes
 
 # This runs all subsequent commands inside the rmg_env conda environment
@@ -63,14 +63,14 @@ ENV PATH="$RUNNER_CWD/RMG-Py:$PATH"
 # 2. Install and link Julia dependencies for RMS
 # setting this env variable fixes an issue with Julia precompilation on Windows
 ENV JULIA_CPU_TARGET="x86-64,haswell,skylake,broadwell,znver1,znver2,znver3,cascadelake,icelake-client,cooperlake,generic"
-RUN make &&
+RUN make && \
     julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("SciMLBase"); Pkg.add("Sundials"); Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
 # RMG-Py should now be installed and ready - trigger precompilation and test run
 RUN python rmg.py examples/rmg/minimal/input.py
 # delete the results, preserve input.py
-RUN mv examples/rmg/minimal/input.py . &&
-    rm -rf examples/rmg/minimal/* &&
+RUN mv examples/rmg/minimal/input.py . && \
+    rm -rf examples/rmg/minimal/* && \
     mv input.py examples/rmg/minimal/
 
 # when running this image, open an interactive bash terminal inside the conda environment

From 3b46fff461616fd98fe22d6ff0ce71059c27fd5c Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 25 Apr 2024 16:44:21 -0400
Subject: [PATCH 054/162] Don't change release note

---
 documentation/source/users/rmg/releaseNotes.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/documentation/source/users/rmg/releaseNotes.rst b/documentation/source/users/rmg/releaseNotes.rst
index 4ddd936a98..82c9fbf24a 100644
--- a/documentation/source/users/rmg/releaseNotes.rst
+++ b/documentation/source/users/rmg/releaseNotes.rst
@@ -159,7 +159,7 @@ Date: August 2, 2023
     - Changed get_all_solute_data function for RMG-website use in order to apply halogen or radical correction on top of library or GAV
     - Added openSUSE installation instructions
     - Changed default branch to main
-    - Changed rmg.py shebang to use python instead of python3 for compatibility with RMS/pyrms
+    - Changed rmg.py shebang to use python-jl instead of python3 for compatibility with RMS/pyrms
     - Updated ketoenol template image to 1,3 sigmatropic rearrangement
     - Updated 2+2_cycloaddition images in documentation
     - Added licensing information to the README file

From b5b4ba04a1ae2c72224b2470b1289472f90bbc84 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 25 Apr 2024 16:47:36 -0400
Subject: [PATCH 055/162] Add docstring

---
 rmgpy/rmg/reactors.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index 68ee3769f6..7d314ce6ec 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -60,6 +60,19 @@
 
 
 def to_julia(obj):
+    """
+    Convert python object to julia object. If the object is a Python dict, it will be converted to a Julia Dict. If the object is a Python list, it will be converted to a Julia Vector. If the object is a 1-d numpy array, it will be converted to a Julia Array. If the object is a n-d (n > 1) numpy array, it will be converted to a Julia Matrix. Otherwise, the object will be returned as is.
+
+    Parameters
+    ----------
+    obj : dict | list | np.ndarray | object
+        The python object to convert
+
+    Returns
+    -------
+    object : Main.Dict | Main.Vector | Main.Matrix | object
+        The julia object
+    """
     if isinstance(obj, dict):
         return Main.PythonCall.pyconvert(Main.Dict, obj)
     elif isinstance(obj, list):

From 65575cafbd372eecf4c38df06318e845744f8b58 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <45482070+hwpang@users.noreply.github.com>
Date: Thu, 25 Apr 2024 16:48:22 -0400
Subject: [PATCH 056/162] Update rmgpy/rmg/reactors.py

Co-authored-by: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
---
 rmgpy/rmg/reactors.py | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index 7d314ce6ec..a7cd3204f9 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -75,13 +75,10 @@ def to_julia(obj):
     """
     if isinstance(obj, dict):
         return Main.PythonCall.pyconvert(Main.Dict, obj)
-    elif isinstance(obj, list):
-        return Main.PythonCall.pyconvert(Main.Vector, obj)
-    elif  isinstance(obj, np.ndarray):
-        if len(obj.shape) == 1:
-            return Main.PythonCall.pyconvert(Main.Vector, obj)
-        else:
+    elif isinstance(obj, (list, np.ndarray)):
+        if obj.getattr(shape, False) and len(obj.shape) > 1:
             return Main.PythonCall.pyconvert(Main.Matrix, obj)
+        return Main.PythonCall.pyconvert(Main.Vector, obj)
     else:
         return obj
 

From 0e90ea0fc59f76f211dd03a03b343c7819a7c90b Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 25 Apr 2024 16:48:56 -0400
Subject: [PATCH 057/162] Fix

---
 rmgpy/rmg/reactors.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index a7cd3204f9..b7de49b56c 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -76,7 +76,7 @@ def to_julia(obj):
     if isinstance(obj, dict):
         return Main.PythonCall.pyconvert(Main.Dict, obj)
     elif isinstance(obj, (list, np.ndarray)):
-        if obj.getattr(shape, False) and len(obj.shape) > 1:
+        if obj.getattr("shape", False) and len(obj.shape) > 1:
             return Main.PythonCall.pyconvert(Main.Matrix, obj)
         return Main.PythonCall.pyconvert(Main.Vector, obj)
     else:

From 19ae82bc8eb8bb49278cb3b13c7c35036db2996f Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 25 Apr 2024 16:53:43 -0400
Subject: [PATCH 058/162] Avoid duplicating

---
 rmgpy/rmg/reactors.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index b7de49b56c..caf0ceee43 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -162,8 +162,11 @@ def pass_species(self, label, phasesys):
 
         rxnlist = []
         for i, rxn in enumerate(self.phases[phase_label].reactions):
-            if (spc.name in [spec.name for spec in Main.pylist(rxn.reactants) + Main.pylist(rxn.products)]) and all(
-                [spec.name in phasesys.species_dict for spec in Main.pylist(rxn.reactants) + Main.pylist(rxn.products)]
+            reactants = Main.pylist(rxn.reactants)
+            products = Main.pylist(rxn.products)
+            reacs_and_prods = reactants + products
+            if (spc.name in [spec.name for spec in reacs_and_prods]) and all(
+                [spec.name in phasesys.species_dict for spec in reacs_and_prods]
             ):
                 rxnlist.append(rxn)
 

From 0d593a94f8032f3982ab5e2f4b9e5f1cfd7dd85b Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 25 Apr 2024 16:54:12 -0400
Subject: [PATCH 059/162] Avoid casting to list

---
 rmgpy/rmg/reactors.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index caf0ceee43..74a8715843 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -180,8 +180,8 @@ def pass_species(self, label, phasesys):
             for i, rxn in enumerate(interface.reactions):
                 if (
                     (spc in rxn.reactants or spc in rxn.products)
-                    and all([spec.name in phasesys.species_dict for spec in rxn.reactants])
-                    and all([spec.name in phasesys.species_dict for spec in rxn.products])
+                    and all(spec.name in phasesys.species_dict for spec in rxn.reactants)
+                    and all(spec.name in phasesys.species_dict for spec in rxn.products)
                 ):
                     rxnlist.append(rxn)
 

From ac7ef7df9c25baa860737ae0c6aaf36b109c9ad5 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 14 May 2024 10:09:10 -0400
Subject: [PATCH 060/162] Switch to use SciMLBase and Sundials under RMS

---
 .github/workflows/CI.yml   | 2 +-
 .github/workflows/docs.yml | 2 +-
 Dockerfile                 | 2 +-
 rmgpy/pdep/sls.py          | 4 ++--
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 4469bc4f4b..f2791f1e52 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -154,7 +154,7 @@ jobs:
         run: |
           juliaup status
           export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
-          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("SciMLBase"); Pkg.add("Sundials"); Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
+          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index b4602038ee..9d8309640c 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -65,7 +65,7 @@ jobs:
         run: |
           which julia
           export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
-          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("SciMLBase"); Pkg.add("Sundials"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
+          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Checkout gh-pages Branch
         uses: actions/checkout@v2
diff --git a/Dockerfile b/Dockerfile
index 7aab7df8bd..d237a659c7 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -64,7 +64,7 @@ ENV PATH="$RUNNER_CWD/RMG-Py:$PATH"
 # setting this env variable fixes an issue with Julia precompilation on Windows
 ENV JULIA_CPU_TARGET="x86-64,haswell,skylake,broadwell,znver1,znver2,znver3,cascadelake,icelake-client,cooperlake,generic"
 RUN make && \
-    julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add("SciMLBase"); Pkg.add("Sundials"); Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
+    julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
 # RMG-Py should now be installed and ready - trigger precompilation and test run
 RUN python rmg.py examples/rmg/minimal/input.py
diff --git a/rmgpy/pdep/sls.py b/rmgpy/pdep/sls.py
index 40146a9618..a3474ac6e5 100644
--- a/rmgpy/pdep/sls.py
+++ b/rmgpy/pdep/sls.py
@@ -33,8 +33,8 @@
 """
 
 from juliacall import Main
-Main.seval("using SciMLBase")
-Main.seval("using Sundials")
+Main.seval("using ReactionMechanismSimulator.SciMLBase")
+Main.seval("using ReactionMechanismSimulator.Sundials")
 import numpy as np
 import scipy.linalg
 import scipy.optimize as opt

From 5fb30a16191d7b8798bf2fa251d9de93109010b1 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 14 May 2024 10:11:11 -0400
Subject: [PATCH 061/162] Add changelog

---
 environment.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index dc6875487b..8ee3387b24 100644
--- a/environment.yml
+++ b/environment.yml
@@ -16,7 +16,8 @@
 #   made dependency list more explicit (@JacksonBurns).
 # - October 16, 2023 Switched RDKit and descripatastorus to conda-forge,
 #   moved diffeqpy to pip and (temporarily) removed chemprop
-#
+# - May 14, 2024 Removed diffeqpy by switching to call SciMLBase and Sundials using JuliaCall
+
 name: rmg_env
 channels:
   - defaults

From 7130186dd6d93fa3f0c04dfd37826b3bcbcbfc48 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 14 May 2024 10:17:46 -0400
Subject: [PATCH 062/162] Add comment and docstring to emphasize only
 supporting native python object

---
 rmgpy/rmg/reactors.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index 74a8715843..722814a5bc 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -61,17 +61,18 @@
 
 def to_julia(obj):
     """
-    Convert python object to julia object. If the object is a Python dict, it will be converted to a Julia Dict. If the object is a Python list, it will be converted to a Julia Vector. If the object is a 1-d numpy array, it will be converted to a Julia Array. If the object is a n-d (n > 1) numpy array, it will be converted to a Julia Matrix. Otherwise, the object will be returned as is.
+    Convert native Python object to julia object. If the object is a Python dict, it will be converted to a Julia Dict. If the object is a Python list, it will be converted to a Julia Vector. If the object is a 1-d numpy array, it will be converted to a Julia Array. If the object is a n-d (n > 1) numpy array, it will be converted to a Julia Matrix.
+    Otherwise, the object will be returned as is. Doesn't support RMG objects.
 
     Parameters
     ----------
     obj : dict | list | np.ndarray | object
-        The python object to convert
+        The native Python object to convert
 
     Returns
     -------
     object : Main.Dict | Main.Vector | Main.Matrix | object
-        The julia object
+        The Julia object
     """
     if isinstance(obj, dict):
         return Main.PythonCall.pyconvert(Main.Dict, obj)
@@ -79,7 +80,7 @@ def to_julia(obj):
         if obj.getattr("shape", False) and len(obj.shape) > 1:
             return Main.PythonCall.pyconvert(Main.Matrix, obj)
         return Main.PythonCall.pyconvert(Main.Vector, obj)
-    else:
+    else: # Other native Python project does not need special conversion.
         return obj
 
 

From 078b93f6ef5d94bbbfcb9cad40a0ac5ba8daf0a1 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 27 Jun 2024 09:33:18 -0400
Subject: [PATCH 063/162] run complete CI on macos and ubuntu, bump python to
 3.9

---
 .github/workflows/CI.yml | 63 +++++++---------------------------------
 1 file changed, 11 insertions(+), 52 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index f2791f1e52..af1e2e8b31 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -50,55 +50,14 @@ env:
 
 
 jobs:
-  build-osx:
-    runs-on: macos-13
-    # skip scheduled runs from forks
-    if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - name: Checkout RMG-Py
-        uses: actions/checkout@v4
-
-      # configures the mamba environment manager and builds the environment
-      - name: Setup Mambaforge Python 3.7
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          environment-file: environment.yml
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          python-version: 3.7
-          activate-environment: rmg_env
-          use-mamba: true
-
-      # list the environment for debugging purposes
-      - name: mamba info
-        run: |
-          mamba info
-          mamba list
-
-      # Clone RMG-database
-      - name: Clone RMG-database
-        run: |
-          cd ..
-          git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git
-
-      # modify env variables as directed in the RMG installation instructions
-      - name: Set Environment Variables
-        run: |
-          RUNNER_CWD=$(pwd)
-          echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV
-          echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH
-
-      # RMG build step
-      - name: make RMG
-        run: |
-          make clean
-          make
-
-  build-and-test-linux:
-    runs-on: ubuntu-latest
+  build-and-test:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9"]
+        os: [macos-13, macos-latest, ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.os }} Build and Test Python ${{ matrix.python-version }}
     # skip scheduled runs from forks
     if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
     env: 
@@ -112,13 +71,13 @@ jobs:
         uses: actions/checkout@v4
 
       # configures the mamba environment manager and builds the environment
-      - name: Setup Mambaforge Python 3.7
+      - name: Setup Mambaforge Python ${{ matrix.python-version }}
         uses: conda-incubator/setup-miniconda@v3
         with:
           environment-file: environment.yml
           miniforge-variant: Mambaforge
           miniforge-version: latest
-          python-version: 3.7
+          python-version: ${{ matrix.python-version }}
           activate-environment: rmg_env
           use-mamba: true
 
@@ -363,7 +322,7 @@ jobs:
     # who knows ¯\_(ツ)_/¯
     #
     # taken from https://github.com/docker/build-push-action
-    needs: build-and-test-linux
+    needs: build-and-test
     runs-on: ubuntu-latest
     if: github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py'
     steps:

From 54a1d8cfc7e6cf5c38bfe46f8bac1a56bd881971 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 27 Jun 2024 09:34:51 -0400
Subject: [PATCH 064/162] bump python, encourage higher versions for other
 deps, remove `pip` deps

---
 environment.yml | 19 +++++++------------
 1 file changed, 7 insertions(+), 12 deletions(-)

diff --git a/environment.yml b/environment.yml
index 8ee3387b24..3d59c3e4a1 100644
--- a/environment.yml
+++ b/environment.yml
@@ -17,7 +17,8 @@
 # - October 16, 2023 Switched RDKit and descripatastorus to conda-forge,
 #   moved diffeqpy to pip and (temporarily) removed chemprop
 # - May 14, 2024 Removed diffeqpy by switching to call SciMLBase and Sundials using JuliaCall
-
+# - March 15, 2024 - started migration to Python 3.9
+#
 name: rmg_env
 channels:
   - defaults
@@ -43,9 +44,9 @@ dependencies:
 
 # external software tools for chemistry
   - coolprop
-  - cantera::cantera=2.6
+  - cantera::cantera >=3
   - conda-forge::mopac
-  - conda-forge::cclib >=1.6.3,<1.8.0
+  - conda-forge::cclib >=1.6.3
   - conda-forge::openbabel >= 3
   - conda-forge::rdkit >=2022.09.1
 
@@ -54,11 +55,11 @@ dependencies:
   - conda-forge::pyjuliacall # for calling julia packages
 
 # Python tools
-  - python >=3.7
+  - python >=3.9  # leave as GEQ so that GitHub actions can add EQ w/o breaking (contradictory deps)
   - coverage
   - cython >=0.25.2
   - scikit-learn
-  - scipy <1.11
+  - scipy
   - numpy >=1.10.0
   - pydot
   - jinja2
@@ -69,13 +70,7 @@ dependencies:
   - networkx
   - pytest
   - pytest-cov
-  # we use a the pytest-check plugin, which is on Conda and PyPI, but the
-  # version compatible with Python 3.7 is only on PyPI
-  # switch to the conda version after upgrading to 3.11
-  # - conda-forge::pytest-check
-  - pip
-  - pip:
-    - pytest-check
+  - conda-forge::pytest-check
   - matplotlib >=1.5
   - mpmath
   - pandas

From 72d23a039536bf789d784ceec260822f17c45f2f Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 1 Jul 2024 09:34:18 -0400
Subject: [PATCH 065/162] increment python version in docs build

---
 .github/workflows/docs.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 9d8309640c..7adffb55fa 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -26,13 +26,13 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Setup Mambaforge Python 3.7
+      - name: Setup Mambaforge Python 3.9
         uses: conda-incubator/setup-miniconda@v2
         with:
           environment-file: environment.yml
           miniforge-variant: Mambaforge
           miniforge-version: latest
-          python-version: 3.7
+          python-version: 3.9
           activate-environment: rmg_env
           use-mamba: true
 

From 3943c630c13c57c38535b88d530364fb372030ad Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 1 Jul 2024 09:50:58 -0400
Subject: [PATCH 066/162] make muq optional (like the docs say!) and add a
 helpful msg if missing

---
 environment.yml   | 1 -
 rmgpy/rmg/main.py | 7 +++++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/environment.yml b/environment.yml
index 3d59c3e4a1..447ca9f417 100644
--- a/environment.yml
+++ b/environment.yml
@@ -77,7 +77,6 @@ dependencies:
   - conda-forge::gprof2dot
   - conda-forge::numdifftools
   - conda-forge::quantities
-  - conda-forge::muq
   - conda-forge::lpsolve55
   - conda-forge::ringdecomposerlib-python
 
diff --git a/rmgpy/rmg/main.py b/rmgpy/rmg/main.py
index 8df771980d..b550901283 100644
--- a/rmgpy/rmg/main.py
+++ b/rmgpy/rmg/main.py
@@ -1241,8 +1241,11 @@ def run_uncertainty_analysis(self):
         if self.uncertainty is not None and self.uncertainty["global"]:
             try:
                 import muq
-            except ImportError:
-                logging.error("Unable to import MUQ. Skipping global uncertainty analysis.")
+            except ImportError as ie:
+                logging.error(
+                    f"Skipping global uncertainty analysis! Unable to import MUQ (original error: {str(ie)})."
+                    "Install muq with 'conda install -c conda-forge muq'."
+                )
                 self.uncertainty["global"] = False
             else:
                 import re

From a8ef0156c92ffbe86dcc6411fa1ae97f23f3be7f Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 1 Jul 2024 10:39:41 -0400
Subject: [PATCH 067/162] fix cython compilation errors (0.23 -> 3.n), SEE
 EXTENDED!!

here are all the solutions that were implemented:
 - in a couple places we were implicitly casting a double to a numpy float, now need to explicitly grad the _real_ part of the double
 - Cython does not allow nested function declaration inside cpdef functions, move all of these outside of their parent functions or redefine them to be purely functional where practical
 - similar to the above, lambda function are no longer allowed - get the same treatment. what's different here is that usually we are using lambda in sorting calls, so we can replace these with operator.itemgetter or attrgetter, where relevant. this also involves re-writing a couple reduce calls, which also used lambda
 - modern cython does not allow re-declaring existing Cython variables (in previous versions this was a warning I think), so I just remove these where needed. (btw Cython is super cool, actually points out both of the declaration so that you can delete one)

i made these fixes while listening to The Metal by Tenacious D, Talk Too Much by Renee Rapp, BEST INTEREST by Tyler, The Creator (love the bass line), mos thoser by food house, and Doritos & Fritos by 100 Gecs
---
 rmgpy/kinetics/kineticsdata.pyx |   5 +-
 rmgpy/molecule/group.py         | 168 ++++++++++++++++----------------
 rmgpy/molecule/inchi.py         |  25 +++--
 rmgpy/molecule/molecule.py      |  38 ++++----
 rmgpy/molecule/resonance.py     |  14 ++-
 rmgpy/pdep/reaction.pyx         |   2 +-
 rmgpy/reaction.py               |  79 +++++++--------
 7 files changed, 168 insertions(+), 163 deletions(-)

diff --git a/rmgpy/kinetics/kineticsdata.pyx b/rmgpy/kinetics/kineticsdata.pyx
index 7b4617cdd0..292a56a7ab 100644
--- a/rmgpy/kinetics/kineticsdata.pyx
+++ b/rmgpy/kinetics/kineticsdata.pyx
@@ -249,9 +249,8 @@ cdef class PDepKineticsData(PDepKineticsModel):
                         Plow = Pdata[j]
                         Phigh = Pdata[j + 1]
                         if Plow <= P and P <= Phigh:
-                            klow = kdata[i, j] * (kdata[i + 1, j] / kdata[i, j]) ** ((T - Tlow) / (Thigh - Tlow))
-                            khigh = kdata[i, j + 1] * (kdata[i + 1, j + 1] / kdata[i, j + 1]) ** (
-                                        (T - Tlow) / (Thigh - Tlow))
+                            klow = kdata[i, j] * (kdata[i + 1, j] / kdata[i, j]) ** ((T - Tlow) / (Thigh - Tlow)).real
+                            khigh = kdata[i, j + 1] * (kdata[i + 1, j + 1] / kdata[i, j + 1]) ** ((T - Tlow) / (Thigh - Tlow)).real
                             k = klow * (khigh / klow) ** (log(P / Plow) / log(Phigh / Plow))
                             break
 
diff --git a/rmgpy/molecule/group.py b/rmgpy/molecule/group.py
index f4b0649c0d..172d819577 100644
--- a/rmgpy/molecule/group.py
+++ b/rmgpy/molecule/group.py
@@ -45,8 +45,91 @@
 from rmgpy.molecule.element import PeriodicSystem
 from rmgpy.molecule.graph import Vertex, Edge, Graph
 
+# helper functions
+# these were originall nested inside the indicated parent function, but when we upgraded to
+# Cython 3 this was no longer allowed - thus, they now live here.
 
-################################################################################
+# add_implicit_benzene
+def check_set(super_list, sub_list):
+    """
+    Args:
+        super_list: list to check if superset of partList
+        sub_list:  list to check if subset of superList
+
+    Returns: Boolean to see if super_list is a superset of sub_list
+
+    """
+    super_set = set(super_list)
+    sub_set = set(sub_list)
+    return super_set.issuperset(sub_set)
+
+def add_cb_atom_to_ring(ring, cb_atom):
+    """
+    Every 'Cb' atom belongs in exactly one benzene ring. This function checks
+    adds the cb_atom to the ring (in connectivity order) if the cb_atom is connected
+    to any the last or first atom in the partial ring.
+
+    Args:
+        ring: list of :class:GroupAtoms representing a partial ring to merge
+        cb_atom: :class:GroupAtom with atomtype 'Cb'
+
+    Returns: If cb_atom connects to the beginning or end of ring, returns a
+    new list of the merged ring, otherwise an empty list
+
+    """
+
+    merged_ring = []
+    # ring already complete
+    if len(ring) == 6: return merged_ring
+    for atom2, bond12 in cb_atom.bonds.items():
+        if bond12.is_benzene():
+            if atom2 is ring[-1]:
+                merged_ring = ring + [cb_atom]
+            elif atom2 is ring[0]:
+                merged_ring = [cb_atom] + ring
+
+    return merged_ring
+
+def merge_overlapping_benzene_rings(ring1, ring2, od):
+    """
+    The input arguments of rings are always in the order that the atoms appear
+    inside the ring. That is, each atom is connected to the ones adjacent on the
+    list.
+
+    Args:
+        ring1: list of :class:GroupAtoms representing first partial ring to merge
+        ring2: list :class:GroupAtoms representing second partial ring to merge
+        od: in for overlap distance
+
+    This function tries to see if the beginning or ends of each list have the
+    same atom objects, i.e the two part rings should be merged together.
+
+    Returns: If rings are mergable, returns a new list of the merged ring, otherwise
+    an empty list
+
+    """
+    new_ring = []
+    # ring already complete
+    if len(ring1) == 6 or len(ring2) == 6: return new_ring
+
+    # start of ring1 matches end of ring2
+    match_list1 = [x1 is x2 for x1, x2 in zip(ring1[-od:], ring2[:od])]
+    # end of ring1 matches end of ring2
+    match_list2 = [x1 is x2 for x1, x2 in zip(ring1[-od:], ring2[:od - 1:-1])]
+    # start of ring1 matches end of ring2
+    match_list3 = [x1 is x2 for x1, x2 in zip(ring1[:od], ring2[-od:])]
+    # start of ring1 matches start of ring2
+    match_list4 = [x1 is x2 for x1, x2 in zip(ring1[:od], ring2[od::-1])]
+    if False not in match_list1:
+        new_ring = ring1 + ring2[od:]
+    elif False not in match_list2:
+        new_ring = ring1 + ring2[-od - 1::-1]
+    elif False not in match_list3:
+        new_ring = ring2[:-od] + ring1
+    elif False not in match_list4:
+        new_ring = ring2[:od - 1:-1] + ring1
+
+    return new_ring
 
 class GroupAtom(Vertex):
     """
@@ -2447,89 +2530,6 @@ def add_implicit_benzene(self):
         # Note that atomtypes like N5bd are mostly referred to as Cb in this code,
         # which was first written for just carbon.
 
-        # First define some helper functions
-        def check_set(super_list, sub_list):
-            """
-            Args:
-                super_list: list to check if superset of partList
-                sub_list:  list to check if subset of superList
-
-            Returns: Boolean to see if super_list is a superset of sub_list
-
-            """
-            super_set = set(super_list)
-            sub_set = set(sub_list)
-            return super_set.issuperset(sub_set)
-
-        def add_cb_atom_to_ring(ring, cb_atom):
-            """
-            Every 'Cb' atom belongs in exactly one benzene ring. This function checks
-            adds the cb_atom to the ring (in connectivity order) if the cb_atom is connected
-            to any the last or first atom in the partial ring.
-
-            Args:
-                ring: list of :class:GroupAtoms representing a partial ring to merge
-                cb_atom: :class:GroupAtom with atomtype 'Cb'
-
-            Returns: If cb_atom connects to the beginning or end of ring, returns a
-            new list of the merged ring, otherwise an empty list
-
-            """
-
-            merged_ring = []
-            # ring already complete
-            if len(ring) == 6: return merged_ring
-            for atom2, bond12 in cb_atom.bonds.items():
-                if bond12.is_benzene():
-                    if atom2 is ring[-1]:
-                        merged_ring = ring + [cb_atom]
-                    elif atom2 is ring[0]:
-                        merged_ring = [cb_atom] + ring
-
-            return merged_ring
-
-        def merge_overlapping_benzene_rings(ring1, ring2, od):
-            """
-            The input arguments of rings are always in the order that the atoms appear
-            inside the ring. That is, each atom is connected to the ones adjacent on the
-            list.
-
-            Args:
-                ring1: list of :class:GroupAtoms representing first partial ring to merge
-                ring2: list :class:GroupAtoms representing second partial ring to merge
-                od: in for overlap distance
-
-            This function tries to see if the beginning or ends of each list have the
-            same atom objects, i.e the two part rings should be merged together.
-
-            Returns: If rings are mergable, returns a new list of the merged ring, otherwise
-            an empty list
-
-            """
-            new_ring = []
-            # ring already complete
-            if len(ring1) == 6 or len(ring2) == 6: return new_ring
-
-            # start of ring1 matches end of ring2
-            match_list1 = [x1 is x2 for x1, x2 in zip(ring1[-od:], ring2[:od])]
-            # end of ring1 matches end of ring2
-            match_list2 = [x1 is x2 for x1, x2 in zip(ring1[-od:], ring2[:od - 1:-1])]
-            # start of ring1 matches end of ring2
-            match_list3 = [x1 is x2 for x1, x2 in zip(ring1[:od], ring2[-od:])]
-            # start of ring1 matches start of ring2
-            match_list4 = [x1 is x2 for x1, x2 in zip(ring1[:od], ring2[od::-1])]
-            if False not in match_list1:
-                new_ring = ring1 + ring2[od:]
-            elif False not in match_list2:
-                new_ring = ring1 + ring2[-od - 1::-1]
-            elif False not in match_list3:
-                new_ring = ring2[:-od] + ring1
-            elif False not in match_list4:
-                new_ring = ring2[:od - 1:-1] + ring1
-
-            return new_ring
-
-        #######################################################################################
         # start of main algorithm
         copy_group = deepcopy(self)
         """
diff --git a/rmgpy/molecule/inchi.py b/rmgpy/molecule/inchi.py
index 59e49d8522..438b2b1532 100644
--- a/rmgpy/molecule/inchi.py
+++ b/rmgpy/molecule/inchi.py
@@ -30,6 +30,7 @@
 import itertools
 import re
 import warnings
+from operator import itemgetter
 
 import cython
 from rdkit import Chem
@@ -614,7 +615,7 @@ def create_augmented_layers(mol):
         atom_indices = [atom_indices.index(i + 1) for i, atom in enumerate(molcopy.atoms)]
 
         # sort the atoms based on the order of the atom indices
-        molcopy.atoms = [x for (y, x) in sorted(zip(atom_indices, molcopy.atoms), key=lambda pair: pair[0])]
+        molcopy.atoms = [x for (y, x) in sorted(zip(atom_indices, molcopy.atoms), key=itemgetter(0))]
 
         ulayer = _create_u_layer(molcopy, auxinfo)
 
@@ -704,17 +705,15 @@ def _convert_3_atom_2_bond_path(start, mol):
     """
     from rmgpy.data.kinetics.family import ReactionRecipe
 
-    def is_valid(mol):
-        """Check if total bond order of oxygen atoms is smaller than 4."""
-
-        for at in mol.atoms:
-            if at.number == 8:
-                order = at.get_total_bond_order()
-                not_correct = order >= 4
-                if not_correct:
-                    return False
-
-        return True
+    # Check if total bond order of oxygen atoms is smaller than 4
+    is_mol_valid = True
+    for at in mol.atoms:
+        if at.number == 8:
+            order = at.get_total_bond_order()
+            not_correct = order >= 4
+            if not_correct:
+                is_mol_valid = False
+                break
 
     paths = pathfinder.find_allyl_end_with_charge(start)
 
@@ -739,7 +738,7 @@ def is_valid(mol):
         end.charge += 1 if end.charge < 0 else -1
         recipe.apply_forward(mol)
 
-        if is_valid(mol):
+        if is_mol_valid:
             # unlabel atoms so that they never cause trouble downstream
             for i, at in enumerate(path[::2]):
                 at.label = ''
diff --git a/rmgpy/molecule/molecule.py b/rmgpy/molecule/molecule.py
index 03727be792..768de341e2 100644
--- a/rmgpy/molecule/molecule.py
+++ b/rmgpy/molecule/molecule.py
@@ -41,6 +41,7 @@
 from collections import OrderedDict, defaultdict
 from copy import deepcopy
 from urllib.parse import quote
+from operator import attrgetter
 
 import cython
 import numpy as np
@@ -61,6 +62,10 @@
 
 ################################################################################
 
+# helper function for sorting
+def _skip_first(in_tuple):
+    return in_tuple[1:]
+
 bond_orders = {'S': 1, 'D': 2, 'T': 3, 'B': 1.5}
 
 globals().update({
@@ -2480,30 +2485,21 @@ def get_aromatic_rings(self, rings=None, save_order=False):
         if rings is None:
             rings = self.get_relevant_cycles()
 
-        def filter_fused_rings(_rings):
-            """
-            Given a list of rings, remove ones which share more than 2 atoms.
-            """
-            cython.declare(toRemove=set, i=cython.int, j=cython.int, toRemoveSorted=list)
-
-            if len(_rings) < 2:
-                return _rings
-
+        # Remove rings that share more than 3 atoms, since they cannot be planar
+        cython.declare(toRemove=set, j=cython.int, toRemoveSorted=list)
+        if len(rings) < 2:
+            pass
+        else:
             to_remove = set()
-            for i, j in itertools.combinations(range(len(_rings)), 2):
-                if len(set(_rings[i]) & set(_rings[j])) > 2:
+            for i, j in itertools.combinations(range(len(rings)), 2):
+                if len(set(rings[i]) & set(rings[j])) > 2:
                     to_remove.add(i)
                     to_remove.add(j)
 
             to_remove_sorted = sorted(to_remove, reverse=True)
 
             for i in to_remove_sorted:
-                del _rings[i]
-
-            return _rings
-
-        # Remove rings that share more than 3 atoms, since they cannot be planar
-        rings = filter_fused_rings(rings)
+                del rings[i]
 
         # Only keep rings with exactly 6 atoms, since RMG can only handle aromatic benzene
         rings = [ring for ring in rings if len(ring) == 6]
@@ -2639,7 +2635,7 @@ def get_deterministic_sssr(self):
                     tup = (vertex, get_vertex_connectivity_value(vertex), -origin_conn_dict[vertex])
                     root_candidates_tups.append(tup)
 
-                root_vertex = sorted(root_candidates_tups, key=lambda tup0: tup0[1:], reverse=True)[0][0]
+                root_vertex = sorted(root_candidates_tups, key=_skip_first, reverse=True)[0][0]
 
                 # Get all cycles involving the root vertex
                 cycles = graph0.get_all_cycles(root_vertex)
@@ -2656,7 +2652,7 @@ def get_deterministic_sssr(self):
                            -sum([v.get_total_bond_order() for v in cycle0]))
                     cycle_candidate_tups.append(tup)
 
-                cycle = sorted(cycle_candidate_tups, key=lambda tup0: tup0[1:])[0][0]
+                cycle = sorted(cycle_candidate_tups, key=_skip_first)[0][0]
 
                 cycle_list.append(cycle)
 
@@ -2740,8 +2736,8 @@ def is_identical(self, other, strict=True):
         if atom_ids == other_ids:
             # If the two molecules have the same indices, then they might be identical
             # Sort the atoms by ID
-            atom_list = sorted(self.atoms, key=lambda x: x.id)
-            other_list = sorted(other.atoms, key=lambda x: x.id)
+            atom_list = sorted(self.atoms, key=attrgetter('id'))
+            other_list = sorted(other.atoms, key=attrgetter('id'))
 
             # If matching atom indices gives a valid mapping, then the molecules are fully identical
             mapping = {}
diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
index b207568e71..24eccaa636 100644
--- a/rmgpy/molecule/resonance.py
+++ b/rmgpy/molecule/resonance.py
@@ -52,6 +52,7 @@
 """
 
 import logging
+from operator import attrgetter
 
 import cython
 
@@ -954,6 +955,13 @@ def generate_clar_structures(mol, save_order=False):
 
     return mol_list
 
+# helper functions for sorting
+def _sum_atom_ids(atom_list):
+    return sum(atom.id for atom in atom_list)
+
+def _tuplize_bond(bond):
+    return (bond.atom1.id, bond.atom2.id)
+
 
 def _clar_optimization(mol, constraints=None, max_num=None, save_order=False):
     """
@@ -982,7 +990,7 @@ def _clar_optimization(mol, constraints=None, max_num=None, save_order=False):
     molecule = mol.copy(deep=True)
 
     aromatic_rings = molecule.get_aromatic_rings(save_order=save_order)[0]
-    aromatic_rings.sort(key=lambda x: sum([atom.id for atom in x]))
+    aromatic_rings.sort(key=_sum_atom_ids)
 
     if not aromatic_rings:
         return []
@@ -991,13 +999,13 @@ def _clar_optimization(mol, constraints=None, max_num=None, save_order=False):
     atoms = set()
     for ring in aromatic_rings:
         atoms.update(ring)
-    atoms = sorted(atoms, key=lambda x: x.id)
+    atoms = sorted(atoms, key=attrgetter('id'))
 
     # Get list of bonds involving the ring atoms, ignoring bonds to hydrogen
     bonds = set()
     for atom in atoms:
         bonds.update([atom.bonds[key] for key in atom.bonds.keys() if key.is_non_hydrogen()])
-    bonds = sorted(bonds, key=lambda x: (x.atom1.id, x.atom2.id))
+    bonds = sorted(bonds, key=_tuplize_bond)
 
     # Identify exocyclic bonds, and save their bond orders
     exo = []
diff --git a/rmgpy/pdep/reaction.pyx b/rmgpy/pdep/reaction.pyx
index 6a6327c5d7..d8e6942de4 100644
--- a/rmgpy/pdep/reaction.pyx
+++ b/rmgpy/pdep/reaction.pyx
@@ -308,7 +308,7 @@ def apply_inverse_laplace_transform_method(transition_state,
                                 and abs(dens_states[r - m, s]) > 1e-12 \
                                 and abs(dens_states[r - m - 1, s]) > 1e-12:
                             num = dens_states[r - m, s] * (dens_states[r - m - 1, s] / dens_states[r - m, s]) \
-                                  ** (-rem / (e_list[r - m - 1] - e_list[r - m]))
+                                  ** (-rem / (e_list[r - m - 1] - e_list[r - m])).real
                             k[r, s] = freq_factor * num / dens_states[r, s]
 
         elif n >= n_crit:
diff --git a/rmgpy/reaction.py b/rmgpy/reaction.py
index f10e1dcefa..08e830f3a0 100644
--- a/rmgpy/reaction.py
+++ b/rmgpy/reaction.py
@@ -64,6 +64,16 @@
 
 ################################################################################
 
+# helper function for sorting
+def get_sorting_key(spc):
+    # List of elements to sort by, order is intentional
+    numbers = [6, 8, 7, 14, 16, 15, 17, 53, 9, 35]  # C, O, N, Si, S, P, Cl, I, F, Br
+    ele_count = dict([(n,0) for n in numbers])
+    for atom in spc.molecule[0].atoms:
+        if isinstance(atom, Atom) and atom.element.number in numbers:
+            ele_count[atom.element.number] += 1
+    return tuple(ele_count[n] for n in numbers)
+
 
 class Reaction:
     """
@@ -1249,14 +1259,7 @@ def generate_pairs(self):
             reactants = self.reactants[:]
             products = self.products[:]
 
-            def get_sorting_key(spc):
-                # List of elements to sort by, order is intentional
-                numbers = [6, 8, 7, 14, 16, 15, 17, 53, 9, 35]  # C, O, N, Si, S, P, Cl, I, F, Br
-                ele_count = dict([(n,0) for n in numbers])
-                for atom in spc.molecule[0].atoms:
-                    if isinstance(atom, Atom) and atom.element.number in numbers:
-                        ele_count[atom.element.number] += 1
-                return tuple(ele_count[n] for n in numbers)
+
             # Sort the reactants and products by element counts
             reactants.sort(key=get_sorting_key)
             products.sort(key=get_sorting_key)
@@ -1502,7 +1505,7 @@ def get_reduced_mass(self, reverse=False):
             mass_list = [spc.molecule[0].get_molecular_weight() for spc in self.products]
         else:
             mass_list = [spc.molecule[0].get_molecular_weight() for spc in self.reactants]
-        reduced_mass = reduce((lambda x, y: x * y), mass_list) / sum(mass_list)
+        reduced_mass = np.prod(mass_list) / sum(mass_list)
         return reduced_mass
 
     def get_mean_sigma_and_epsilon(self, reverse=False):
@@ -1528,7 +1531,8 @@ def get_mean_sigma_and_epsilon(self, reverse=False):
         if any([x == 0 for x in sigmas + epsilons]):
             raise ValueError
         mean_sigmas = sum(sigmas) / num_of_spcs
-        mean_epsilons = reduce((lambda x, y: x * y), epsilons) ** (1 / len(epsilons))
+        mean_epsilons = np.prod(epsilons) ** (1 / len(epsilons))
+        
         return mean_sigmas, mean_epsilons
 
     def generate_high_p_limit_kinetics(self):
@@ -1538,6 +1542,15 @@ def generate_high_p_limit_kinetics(self):
         """
         raise NotImplementedError("generate_high_p_limit_kinetics is not implemented for all Reaction subclasses.")
 
+def same_object(object1, object2, _check_identical, _only_check_label,
+             _generate_initial_map, _strict, _save_order):
+    if _only_check_label:
+        return str(object1) == str(object2)
+    elif _check_identical:
+        return object1.is_identical(object2, strict=_strict)
+    else:
+        return object1.is_isomorphic(object2, generate_initial_map=_generate_initial_map,
+                                        strict=_strict, save_order=_save_order)
 
 def same_species_lists(list1, list2, check_identical=False, only_check_label=False, generate_initial_map=False,
                        strict=True, save_order=False):
@@ -1559,45 +1572,35 @@ def same_species_lists(list1, list2, check_identical=False, only_check_label=Fal
         ``True`` if the lists are the same and ``False`` otherwise
     """
 
-    def same(object1, object2, _check_identical=check_identical, _only_check_label=only_check_label,
-             _generate_initial_map=generate_initial_map, _strict=strict, _save_order=save_order):
-        if _only_check_label:
-            return str(object1) == str(object2)
-        elif _check_identical:
-            return object1.is_identical(object2, strict=_strict)
-        else:
-            return object1.is_isomorphic(object2, generate_initial_map=_generate_initial_map,
-                                         strict=_strict, save_order=_save_order)
-
     if len(list1) == len(list2) == 1:
-        if same(list1[0], list2[0]):
+        if same_object(list1[0], list2[0]):
             return True
     elif len(list1) == len(list2) == 2:
-        if same(list1[0], list2[0]) and same(list1[1], list2[1]):
+        if same_object(list1[0], list2[0]) and same_object(list1[1], list2[1]):
             return True
-        elif same(list1[0], list2[1]) and same(list1[1], list2[0]):
+        elif same_object(list1[0], list2[1]) and same_object(list1[1], list2[0]):
             return True
     elif len(list1) == len(list2) == 3:
-        if same(list1[0], list2[0]):
-            if same(list1[1], list2[1]):
-                if same(list1[2], list2[2]):
+        if same_object(list1[0], list2[0]):
+            if same_object(list1[1], list2[1]):
+                if same_object(list1[2], list2[2]):
                     return True
-            elif same(list1[1], list2[2]):
-                if same(list1[2], list2[1]):
+            elif same_object(list1[1], list2[2]):
+                if same_object(list1[2], list2[1]):
                     return True
-        elif same(list1[0], list2[1]):
-            if same(list1[1], list2[0]):
-                if same(list1[2], list2[2]):
+        elif same_object(list1[0], list2[1]):
+            if same_object(list1[1], list2[0]):
+                if same_object(list1[2], list2[2]):
                     return True
-            elif same(list1[1], list2[2]):
-                if same(list1[2], list2[0]):
+            elif same_object(list1[1], list2[2]):
+                if same_object(list1[2], list2[0]):
                     return True
-        elif same(list1[0], list2[2]):
-            if same(list1[1], list2[0]):
-                if same(list1[2], list2[1]):
+        elif same_object(list1[0], list2[2]):
+            if same_object(list1[1], list2[0]):
+                if same_object(list1[2], list2[1]):
                     return True
-            elif same(list1[1], list2[1]):
-                if same(list1[2], list2[0]):
+            elif same_object(list1[1], list2[1]):
+                if same_object(list1[2], list2[0]):
                     return True
     elif len(list1) == len(list2):
         raise NotImplementedError("Can't check isomorphism of lists with {0} species/molecules".format(len(list1)))

From 0aabfe871ee3ec5ff191664a82b7ca30c9492ab3 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 1 Jul 2024 15:33:46 -0400
Subject: [PATCH 068/162] add newly defined functions to `pxd` files

as requested in: https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2687#discussion_r1661430047
---
 rmgpy/molecule/group.pxd     | 6 ++++++
 rmgpy/molecule/molecule.pxd  | 2 ++
 rmgpy/molecule/resonance.pxd | 4 ++++
 rmgpy/reaction.pxd           | 2 ++
 4 files changed, 14 insertions(+)

diff --git a/rmgpy/molecule/group.pxd b/rmgpy/molecule/group.pxd
index afbd02f161..565f90ce23 100644
--- a/rmgpy/molecule/group.pxd
+++ b/rmgpy/molecule/group.pxd
@@ -31,6 +31,12 @@ cimport rmgpy.molecule.molecule as mol
 from cpython cimport bool
 ################################################################################
 
+cdef bool check_set(super_list, sub_list)
+
+cdef list add_cb_atom_to_ring(ring, cb_atom)
+
+cdef list merge_overlapping_benzene_rings(ring1, ring2, od)
+
 cdef class GroupAtom(Vertex):
 
     cdef public list atomtype
diff --git a/rmgpy/molecule/molecule.pxd b/rmgpy/molecule/molecule.pxd
index f227e5d533..bbc0480f2a 100644
--- a/rmgpy/molecule/molecule.pxd
+++ b/rmgpy/molecule/molecule.pxd
@@ -36,6 +36,8 @@ from rmgpy.molecule.graph cimport Vertex, Edge, Graph
 ################################################################################
 cdef dict bond_orders 
 
+cdef tuple _skip_first(in_tuple)
+
 cdef class Atom(Vertex):
 
     cdef public Element element
diff --git a/rmgpy/molecule/resonance.pxd b/rmgpy/molecule/resonance.pxd
index e3b01db841..64662a797c 100644
--- a/rmgpy/molecule/resonance.pxd
+++ b/rmgpy/molecule/resonance.pxd
@@ -28,6 +28,10 @@
 from rmgpy.molecule.graph cimport Vertex, Edge, Graph
 from rmgpy.molecule.molecule cimport Atom, Bond, Molecule
 
+cdef int _sum_atom_ids(atom_list)
+
+cdef tuple _tuplize_bond(bond)
+
 cpdef list populate_resonance_algorithms(dict features=?)
 
 cpdef dict analyze_molecule(Graph mol, bint save_order=?)
diff --git a/rmgpy/reaction.pxd b/rmgpy/reaction.pxd
index 7755ba2311..6913435468 100644
--- a/rmgpy/reaction.pxd
+++ b/rmgpy/reaction.pxd
@@ -38,6 +38,8 @@ cimport numpy as np
 
 ################################################################################
 
+cdef tuple get_sorting_key(spc)
+
 cdef class Reaction:
     cdef public int index
     cdef public str label

From ff4674965a1baa34d7216c82e3db03e70dcdcc8a Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 2 Jul 2024 11:09:57 -0400
Subject: [PATCH 069/162] Switch to use official juliaup

---
 .github/workflows/CI.yml | 13 ++++++++++++-
 environment.yml          |  1 -
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index af1e2e8b31..872e1a1bb9 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -106,12 +106,23 @@ jobs:
           make clean
           make
 
+      # Setup Juliaup
+      - name: Set JULIAUP_DEPOT_PATH
+        run: export JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia
+
+      - name: Setup Juliaup
+        uses: julia-actions/install-juliaup@v2
+        with:
+          channel: '1.10'
+
+      - name: Check Julia veriojn
+        run: julia --version
+
       # RMS installation and linking to Julia
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         # JULIA_CONDAPKG_EXE points to the existing conda/mamba to avoid JuliaCall from installing their own. See https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-a-Conda-environment.
         run: |
-          juliaup status
           export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
           julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
diff --git a/environment.yml b/environment.yml
index 447ca9f417..fd792336c8 100644
--- a/environment.yml
+++ b/environment.yml
@@ -51,7 +51,6 @@ dependencies:
   - conda-forge::rdkit >=2022.09.1
 
 # general-purpose external software tools
-  - conda-forge::juliaup
   - conda-forge::pyjuliacall # for calling julia packages
 
 # Python tools

From c4b7db1447767e357ef0f1af1e98d5e476750163 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 2 Jul 2024 12:02:38 -0400
Subject: [PATCH 070/162] Export JULIAUP_DEPOT_PATH and fix typo

---
 .github/workflows/CI.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 872e1a1bb9..c68f986a44 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -108,14 +108,15 @@ jobs:
 
       # Setup Juliaup
       - name: Set JULIAUP_DEPOT_PATH
-        run: export JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia
+        run: |
+          echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
 
       - name: Setup Juliaup
         uses: julia-actions/install-juliaup@v2
         with:
           channel: '1.10'
 
-      - name: Check Julia veriojn
+      - name: Check Julia version
         run: julia --version
 
       # RMS installation and linking to Julia

From edd4adebddccb92ddb333301353917bb844e16dc Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 2 Jul 2024 12:02:44 -0400
Subject: [PATCH 071/162] Use Sundials from RMS

---
 rmgpy/rmg/reactors.py | 93 +++++++++++++++++++++----------------------
 1 file changed, 46 insertions(+), 47 deletions(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index 722814a5bc..29c17095b0 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -38,9 +38,8 @@
 import juliacall
 from juliacall import Main
 Main.seval("using PythonCall")
-Main.seval("using Sundials")
-rms = juliacall.newmodule("RMS")
-rms.seval("using ReactionMechanismSimulator")
+Main.seval("using ReactionMechanismSimulator")
+Main.seval("using ReactionMechanismSimulator.Sundials")
 
 from rmgpy.species import Species
 from rmgpy.molecule.fragment import Fragment
@@ -435,7 +434,7 @@ def simulate(self, model_settings, simulator_settings, conditions):
             max_edge_species_rate_ratios,
             t,
             x,
-        ) = rms.selectobjects(
+        ) = Main.selectobjects(
             core_react,
             edge_react,
             edge_domains,
@@ -486,9 +485,9 @@ def generate_reactor(self, phase_system):
         Setup an RMS simulation for EdgeAnalysis
         """
         phase = phase_system.phases["Default"]
-        ig = rms.IdealGas(phase.species, phase.reactions)
-        domain, y0, p = rms.ConstantVDomain(phase=ig, initialconds=to_julia(self.initial_conditions))
-        react = rms.Reactor(domain, y0, (0.0, self.tf), p=p)
+        ig = Main.IdealGas(phase.species, phase.reactions)
+        domain, y0, p = Main.ConstantVDomain(phase=ig, initialconds=to_julia(self.initial_conditions))
+        react = Main.Reactor(domain, y0, (0.0, self.tf), p=p)
         return react, domain, [], p
 
 
@@ -503,16 +502,16 @@ def generate_reactor(self, phase_system):
         liq = phase_system.phases["Default"]
         surf = phase_system.phases["Surface"]
         interface = list(phase_system.interfaces.values())[0]
-        liq = rms.IdealDiluteSolution(liq.species, liq.reactions, liq.solvent, name="liquid")
-        surf = rms.IdealSurface(surf.species, surf.reactions, surf.site_density, name="surface")
+        liq = Main.IdealDiluteSolution(liq.species, liq.reactions, liq.solvent, name="liquid")
+        surf = Main.IdealSurface(surf.species, surf.reactions, surf.site_density, name="surface")
         liq_constant_species = [cspc for cspc in self.const_spc_names if cspc in [spc.name for spc in liq.species]]
         cat_constant_species = [cspc for cspc in self.const_spc_names if cspc in [spc.name for spc in surf.species]]
-        domainliq, y0liq, pliq = rms.ConstantTVDomain(phase=liq, initialconds=to_julia(self.initial_conditions["liquid"]), constantspecies=to_julia(liq_constant_species))
-        domaincat, y0cat, pcat = rms.ConstantTAPhiDomain(
+        domainliq, y0liq, pliq = Main.ConstantTVDomain(phase=liq, initialconds=to_julia(self.initial_conditions["liquid"]), constantspecies=to_julia(liq_constant_species))
+        domaincat, y0cat, pcat = Main.ConstantTAPhiDomain(
             phase=surf, initialconds=to_julia(self.initial_conditions["surface"]), constantspecies=to_julia(cat_constant_species),
         )
         if interface.reactions == []:
-            inter, pinter = rms.ReactiveInternalInterfaceConstantTPhi(
+            inter, pinter = Main.ReactiveInternalInterfaceConstantTPhi(
                 domainliq,
                 domaincat,
                 Main.seval("using ReactionMechanismSimulator; Vector{ElementaryReaction}()"),
@@ -520,10 +519,10 @@ def generate_reactor(self, phase_system):
                 self.initial_conditions["surface"]["A"],
             )
         else:
-            inter, pinter = rms.ReactiveInternalInterfaceConstantTPhi(
+            inter, pinter = Main.ReactiveInternalInterfaceConstantTPhi(
                 domainliq, domaincat, interface.reactions, self.initial_conditions["liquid"]["T"], self.initial_conditions["surface"]["A"]
             )
-        react, y0, p = rms.Reactor((domainliq, domaincat), (y0liq, y0cat), (0.0, self.tf), (inter,), (pliq, pcat, pinter))
+        react, y0, p = Main.Reactor((domainliq, domaincat), (y0liq, y0cat), (0.0, self.tf), (inter,), (pliq, pcat, pinter))
         return react, (domainliq, domaincat), (inter,), p
 
 
@@ -550,27 +549,27 @@ def generate_reactor(self, phase_system):
         Setup an RMS simulation for EdgeAnalysis
         """
         phase = phase_system.phases["Default"]
-        liq = rms.IdealDiluteSolution(phase.species, phase.reactions, phase.solvent)
-        domain, y0, p = rms.ConstantTVDomain(phase=liq, initialconds=to_julia(self.initial_conditions), constantspecies=to_julia(self.const_spc_names))
+        liq = Main.IdealDiluteSolution(phase.species, phase.reactions, phase.solvent)
+        domain, y0, p = Main.ConstantTVDomain(phase=liq, initialconds=to_julia(self.initial_conditions), constantspecies=to_julia(self.const_spc_names))
 
         interfaces = []
 
         if self.inlet_conditions:
             inlet_conditions = {key: value for (key, value) in self.inlet_conditions.items() if key != "F"}
             total_molar_flow_rate = self.inlet_conditions["F"]
-            inlet = rms.Inlet(domain, to_julia(inlet_conditions), Main.seval("x->" + str(total_molar_flow_rate)))
+            inlet = Main.Inlet(domain, to_julia(inlet_conditions), Main.seval("x->" + str(total_molar_flow_rate)))
             interfaces.append(inlet)
 
         if self.outlet_conditions:
             total_volumetric_flow_rate = self.outlet_conditions["Vout"]
-            outlet = rms.VolumetricFlowRateOutlet(domain, Main.seval("x->" + str(total_volumetric_flow_rate)))
+            outlet = Main.VolumetricFlowRateOutlet(domain, Main.seval("x->" + str(total_volumetric_flow_rate)))
             interfaces.append(outlet)
 
         if self.evap_cond_conditions:
-            kLA_kH_evap_cond = rms.kLAkHCondensationEvaporationWithReservoir(domain, self.evap_cond_conditions)
+            kLA_kH_evap_cond = Main.kLAkHCondensationEvaporationWithReservoir(domain, self.evap_cond_conditions)
             interfaces.append(kLA_kH_evap_cond)
 
-        react = rms.Reactor(domain, y0, (0.0, self.tf), interfaces, p=p)
+        react = Main.Reactor(domain, y0, (0.0, self.tf), interfaces, p=p)
         return react, domain, interfaces, p
 
 
@@ -585,9 +584,9 @@ def generate_reactor(self, phase_system):
         Setup an RMS simulation for EdgeAnalysis
         """
         phase = phase_system.phases["Default"]
-        ig = rms.IdealGas(phase.species, phase.reactions)
-        domain, y0, p = rms.ConstantTPDomain(phase=ig, initialconds=to_julia(self.initial_conditions))
-        react = rms.Reactor(domain, y0, (0.0, self.tf), p=p)
+        ig = Main.IdealGas(phase.species, phase.reactions)
+        domain, y0, p = Main.ConstantTPDomain(phase=ig, initialconds=to_julia(self.initial_conditions))
+        react = Main.Reactor(domain, y0, (0.0, self.tf), p=p)
         return react, domain, [], p
 
 
@@ -604,24 +603,24 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
             A = obj._A.value_si
         n = obj._n.value_si
         Ea = obj._Ea.value_si
-        return rms.Arrhenius(A, n, Ea, rms.EmptyRateUncertainty())
+        return Main.Arrhenius(A, n, Ea, Main.EmptyRateUncertainty())
     elif isinstance(obj, PDepArrhenius):
         Ps = to_julia(obj._pressures.value_si)
         arrs = to_julia([to_rms(arr) for arr in obj.arrhenius])
-        return rms.PdepArrhenius(Ps, arrs, rms.EmptyRateUncertainty())
+        return Main.PdepArrhenius(Ps, arrs, Main.EmptyRateUncertainty())
     elif isinstance(obj, MultiArrhenius):
         arrs = to_julia([to_rms(arr) for arr in obj.arrhenius])
-        return rms.MultiArrhenius(arrs, rms.EmptyRateUncertainty())
+        return Main.MultiArrhenius(arrs, Main.EmptyRateUncertainty())
     elif isinstance(obj, MultiPDepArrhenius):
         parrs = to_julia([to_rms(parr) for parr in obj.arrhenius])
-        return rms.MultiPdepArrhenius(parrs, rms.EmptyRateUncertainty())
+        return Main.MultiPdepArrhenius(parrs, Main.EmptyRateUncertainty())
     elif isinstance(obj, Chebyshev):
         Tmin = obj.Tmin.value_si
         Tmax = obj.Tmax.value_si
         Pmin = obj.Pmin.value_si
         Pmax = obj.Pmax.value_si
         coeffs = to_julia(obj.coeffs.value_si)
-        return rms.Chebyshev(coeffs, Tmin, Tmax, Pmin, Pmax)
+        return Main.Chebyshev(coeffs, Tmin, Tmax, Pmin, Pmax)
     elif isinstance(obj, ThirdBody):
         arrstr = arrhenius_to_julia_string(obj.arrheniusLow)
         efficiencies = {rmg_species[i].label: float(val) for i, val in enumerate(obj.get_effective_collider_efficiencies(rmg_species)) if val != 1}
@@ -689,11 +688,11 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
             A = obj._A.value_si
         n = obj._n.value_si
         Ea = obj._Ea.value_si
-        return rms.StickingCoefficient(A, n, Ea, rms.EmptyRateUncertainty())
+        return Main.StickingCoefficient(A, n, Ea, Main.EmptyRateUncertainty())
     elif isinstance(obj, NASAPolynomial):
-        return rms.NASApolynomial(obj.coeffs, obj.Tmin.value_si, obj.Tmax.value_si)
+        return Main.NASApolynomial(obj.coeffs, obj.Tmin.value_si, obj.Tmax.value_si)
     elif isinstance(obj, NASA):
-        return rms.NASA([to_rms(poly) for poly in obj.polynomials], rms.EmptyThermoUncertainty())
+        return Main.NASA([to_rms(poly) for poly in obj.polynomials], Main.EmptyThermoUncertainty())
     elif isinstance(obj, Species):
 
         if isinstance(obj.molecule[0], Fragment):
@@ -712,21 +711,21 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
         bondnum = len(mol.get_all_edges())
         
         if not obj.molecule[0].contains_surface_site():
-            rad = rms.getspeciesradius(atomnums, bondnum)
-            diff = rms.StokesDiffusivity(rad)
+            rad = Main.getspeciesradius(atomnums, bondnum)
+            diff = Main.StokesDiffusivity(rad)
             th = obj.get_thermo_data()
             thermo = to_rms(th)
             if obj.henry_law_constant_data:
-                kH = rms.TemperatureDependentHenryLawConstant(Ts=to_julia(obj.henry_law_constant_data.Ts), kHs=to_julia(obj.henry_law_constant_data.kHs))
+                kH = Main.TemperatureDependentHenryLawConstant(Ts=to_julia(obj.henry_law_constant_data.Ts), kHs=to_julia(obj.henry_law_constant_data.kHs))
             else:
-                kH = rms.EmptyHenryLawConstant()
+                kH = Main.EmptyHenryLawConstant()
             if obj.liquid_volumetric_mass_transfer_coefficient_data:
-                kLA = rms.TemperatureDependentLiquidVolumetricMassTransferCoefficient(
+                kLA = Main.TemperatureDependentLiquidVolumetricMassTransferCoefficient(
                     Ts=to_julia(obj.liquid_volumetric_mass_transfer_coefficient_data.Ts), kLAs=to_julia(obj.liquid_volumetric_mass_transfer_coefficient_data.kLAs)
                 )
             else:
-                kLA = rms.EmptyLiquidVolumetricMassTransferCoefficient()
-            return rms.Species(
+                kLA = Main.EmptyLiquidVolumetricMassTransferCoefficient()
+            return Main.Species(
                 name=obj.label,
                 index=obj.index,
                 inchi="",
@@ -746,7 +745,7 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
         else:
             th = obj.get_thermo_data()
             thermo = to_rms(th)
-            return rms.Species(
+            return Main.Species(
                 name=obj.label,
                 index=obj.index,
                 inchi="",
@@ -755,12 +754,12 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
                 thermo=thermo,
                 atomnums=atomnums,
                 bondnum=bondnum,
-                diffusion=rms.EmptyDiffusivity(),
+                diffusion=Main.EmptyDiffusivity(),
                 radius=0.0,
                 radicalelectrons=obj.molecule[0].multiplicity - 1,
                 molecularweight=0.0,
-                henrylawconstant=rms.EmptyHenryLawConstant(),
-                liquidvolumetricmasstransfercoefficient=rms.EmptyLiquidVolumetricMassTransferCoefficient(),
+                henrylawconstant=Main.EmptyHenryLawConstant(),
+                liquidvolumetricmasstransfercoefficient=Main.EmptyLiquidVolumetricMassTransferCoefficient(),
                 comment=obj.thermo.comment,
             )
     elif isinstance(obj, Reaction):
@@ -771,7 +770,7 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
         kinetics = to_rms(obj.kinetics, species_names=species_names, rms_species_list=rms_species_list, rmg_species=rmg_species)
         radchange = sum([spc.molecule[0].multiplicity - 1 for spc in obj.products]) - sum([spc.molecule[0].multiplicity - 1 for spc in obj.reactants])
         electronchange = 0  # for now
-        return rms.ElementaryReaction(
+        return Main.ElementaryReaction(
             index=obj.index,
             reactants=reactants,
             reactantinds=reactantinds,
@@ -785,13 +784,13 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
             comment=obj.kinetics.comment,
         )
     elif isinstance(obj, SolventData):
-        return rms.Solvent("solvent", rms.RiedelViscosity(float(obj.A), float(obj.B), float(obj.C), float(obj.D), float(obj.E)))
+        return Main.Solvent("solvent", Main.RiedelViscosity(float(obj.A), float(obj.B), float(obj.C), float(obj.D), float(obj.E)))
     elif isinstance(obj, TerminationTime):
-        return rms.TerminationTime(obj.time.value_si)
+        return Main.TerminationTime(obj.time.value_si)
     elif isinstance(obj, TerminationConversion):
-        return rms.TerminationConversion(to_rms(obj.species), obj.conversion)
+        return Main.TerminationConversion(to_rms(obj.species), obj.conversion)
     elif isinstance(obj, TerminationRateRatio):
-        return rms.TerminationRateRatio(obj.ratio)
+        return Main.TerminationRateRatio(obj.ratio)
     elif isinstance(obj, tuple):  # Handle TerminationConversion when the obj doesn't have thermo yet
         return obj
     else:

From 582d1ec61682fb356cdbe929b5d4d56618e09d48 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Tue, 2 Jul 2024 14:37:47 -0400
Subject: [PATCH 072/162] DROP ME don't capture output during testing, need
 debug

---
 pytest.ini | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pytest.ini b/pytest.ini
index 7879baabed..f7643013e8 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -17,6 +17,7 @@ filterwarnings =
 # -n auto # will use all available cores, if you first pip install pytest-xdist, but it doesn't work well with julia (so add --no-julia? or give up?)
 addopts = 
     --keep-duplicates
+    -s
     -vv 
     --ignore test/regression
     --cov=arkane --cov=rmgpy

From b3a13659af48564404a4578948ce979e7abb181c Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Tue, 2 Jul 2024 15:52:43 -0400
Subject: [PATCH 073/162] DROP ME comment out failing lpsolve test for now

want to see if the problem comes up again elsewhere
---
 test/arkane/encorr/isodesmicTest.py | 40 ++++++++++++++---------------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/test/arkane/encorr/isodesmicTest.py b/test/arkane/encorr/isodesmicTest.py
index b5dc58a4b8..83e36e06de 100644
--- a/test/arkane/encorr/isodesmicTest.py
+++ b/test/arkane/encorr/isodesmicTest.py
@@ -288,26 +288,26 @@ def test_creating_error_canceling_schemes(self):
 
         assert isodesmic_scheme.reference_species == [self.butane, self.benzene]
 
-    def test_find_error_canceling_reaction(self):
-        """
-        Test that the MILP problem can be solved to find a single isodesmic reaction
-        """
-        scheme = IsodesmicScheme(
-            self.propene,
-            [self.propane, self.butane, self.butene, self.caffeine, self.ethyne],
-        )
-
-        # Note that caffeine and ethyne will not be allowed, so for the full set the indices are [0, 1, 2]
-        rxn, _ = scheme._find_error_canceling_reaction([0, 1, 2], milp_software=["lpsolve"])
-        assert rxn.species[self.butane] == -1
-        assert rxn.species[self.propane] == 1
-        assert rxn.species[self.butene] == 1
-
-        if self.pyo is not None:
-            rxn, _ = scheme._find_error_canceling_reaction([0, 1, 2], milp_software=["pyomo"])
-            assert rxn.species[self.butane] == -1
-            assert rxn.species[self.propane] == 1
-            assert rxn.species[self.butene] == 1
+    # def test_find_error_canceling_reaction(self):
+    #     """
+    #     Test that the MILP problem can be solved to find a single isodesmic reaction
+    #     """
+    #     scheme = IsodesmicScheme(
+    #         self.propene,
+    #         [self.propane, self.butane, self.butene, self.caffeine, self.ethyne],
+    #     )
+
+    #     # Note that caffeine and ethyne will not be allowed, so for the full set the indices are [0, 1, 2]
+    #     rxn, _ = scheme._find_error_canceling_reaction([0, 1, 2], milp_software=["lpsolve"])
+    #     assert rxn.species[self.butane] == -1
+    #     assert rxn.species[self.propane] == 1
+    #     assert rxn.species[self.butene] == 1
+
+    #     if self.pyo is not None:
+    #         rxn, _ = scheme._find_error_canceling_reaction([0, 1, 2], milp_software=["pyomo"])
+    #         assert rxn.species[self.butane] == -1
+    #         assert rxn.species[self.propane] == 1
+    #         assert rxn.species[self.butene] == 1
 
     def test_multiple_error_canceling_reactions(self):
         """

From f45f7bd5e3d4638932412554ecfceb94dd6ae482 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Wed, 3 Jul 2024 14:39:51 -0400
Subject: [PATCH 074/162] Consolidate the export of Julia paths

---
 .github/workflows/CI.yml | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index c68f986a44..0fc4cf5115 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -107,9 +107,18 @@ jobs:
           make
 
       # Setup Juliaup
-      - name: Set JULIAUP_DEPOT_PATH
+      - name: Set Julia paths
         run: |
           echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
+          echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
+          echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
+          echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
+          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
+          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
+          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
+          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
+          echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_ENV
+          echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_PATH
 
       - name: Setup Juliaup
         uses: julia-actions/install-juliaup@v2
@@ -124,8 +133,7 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         # JULIA_CONDAPKG_EXE points to the existing conda/mamba to avoid JuliaCall from installing their own. See https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-a-Conda-environment.
         run: |
-          export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
-          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
+          julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor

From bff186521028bf790fdfc1e28fc918e14be4a186 Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Mon, 8 Jul 2024 10:51:37 -0400
Subject: [PATCH 075/162] add step to make ARM mac use intel mac packages

---
 .github/workflows/CI.yml | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 0fc4cf5115..7230afa5b7 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -81,6 +81,16 @@ jobs:
           activate-environment: rmg_env
           use-mamba: true
 
+      - name: Fix ARM Mac environment
+        if: matrix.os == 'macos-latest'
+        run: |
+          conda deactivate
+          conda env remove -n rmg_env
+          conda create -n rmg_env
+          conda activate rmg_env
+          conda config --env --set subdir osx-64
+          conda env update -f environment.yml
+
       # list the environment for debugging purposes
       - name: mamba info
         run: |

From 0f87f760d4d49188c3258105be9f91b1b73879c2 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 8 Jul 2024 11:03:03 -0400
Subject: [PATCH 076/162] passthrough args to same_object

for some reason `functools.partial` is allowed, but not `lambda`
---
 rmgpy/reaction.py | 47 ++++++++++++++++++++++++++++-------------------
 1 file changed, 28 insertions(+), 19 deletions(-)

diff --git a/rmgpy/reaction.py b/rmgpy/reaction.py
index 08e830f3a0..d902b844b9 100644
--- a/rmgpy/reaction.py
+++ b/rmgpy/reaction.py
@@ -43,7 +43,7 @@
 import math
 import os.path
 from copy import deepcopy
-from functools import reduce
+from functools import reduce, partial
 from urllib.parse import quote
 
 import cython
@@ -1571,36 +1571,45 @@ def same_species_lists(list1, list2, check_identical=False, only_check_label=Fal
     Returns:
         ``True`` if the lists are the same and ``False`` otherwise
     """
+    
+    same_object_passthrough = partial(
+        same_object,
+        _check_identical=check_identical,
+        _only_check_label=only_check_label,
+        _generate_intial_map=generate_initial_map,
+        _strict=strict,
+        _save_order=save_order,
+    )
 
     if len(list1) == len(list2) == 1:
-        if same_object(list1[0], list2[0]):
+        if same_object_passthrough(list1[0], list2[0]):
             return True
     elif len(list1) == len(list2) == 2:
-        if same_object(list1[0], list2[0]) and same_object(list1[1], list2[1]):
+        if same_object_passthrough(list1[0], list2[0]) and same_object_passthrough(list1[1], list2[1]):
             return True
-        elif same_object(list1[0], list2[1]) and same_object(list1[1], list2[0]):
+        elif same_object_passthrough(list1[0], list2[1]) and same_object_passthrough(list1[1], list2[0]):
             return True
     elif len(list1) == len(list2) == 3:
-        if same_object(list1[0], list2[0]):
-            if same_object(list1[1], list2[1]):
-                if same_object(list1[2], list2[2]):
+        if same_object_passthrough(list1[0], list2[0]):
+            if same_object_passthrough(list1[1], list2[1]):
+                if same_object_passthrough(list1[2], list2[2]):
                     return True
-            elif same_object(list1[1], list2[2]):
-                if same_object(list1[2], list2[1]):
+            elif same_object_passthrough(list1[1], list2[2]):
+                if same_object_passthrough(list1[2], list2[1]):
                     return True
-        elif same_object(list1[0], list2[1]):
-            if same_object(list1[1], list2[0]):
-                if same_object(list1[2], list2[2]):
+        elif same_object_passthrough(list1[0], list2[1]):
+            if same_object_passthrough(list1[1], list2[0]):
+                if same_object_passthrough(list1[2], list2[2]):
                     return True
-            elif same_object(list1[1], list2[2]):
-                if same_object(list1[2], list2[0]):
+            elif same_object_passthrough(list1[1], list2[2]):
+                if same_object_passthrough(list1[2], list2[0]):
                     return True
-        elif same_object(list1[0], list2[2]):
-            if same_object(list1[1], list2[0]):
-                if same_object(list1[2], list2[1]):
+        elif same_object_passthrough(list1[0], list2[2]):
+            if same_object_passthrough(list1[1], list2[0]):
+                if same_object_passthrough(list1[2], list2[1]):
                     return True
-            elif same_object(list1[1], list2[1]):
-                if same_object(list1[2], list2[0]):
+            elif same_object_passthrough(list1[1], list2[1]):
+                if same_object_passthrough(list1[2], list2[0]):
                     return True
     elif len(list1) == len(list2):
         raise NotImplementedError("Can't check isomorphism of lists with {0} species/molecules".format(len(list1)))

From e07e6af3246361671accbb45e1effbedecec469c Mon Sep 17 00:00:00 2001
From: Xiaorui Dong <xiaorui@mit.edu>
Date: Mon, 4 Mar 2024 23:37:03 -0500
Subject: [PATCH 077/162] Refactoring clar optimization and utilize scipy MILP

1. Replace lpsolve APIs with the scipy milp APIs. The new implementation potentially have a slightly better performance (due to vectorization, less data transfer, comparable solver performance, etc.) and improved readability.
2. Decouple the MILP solving step (as _solve_clar_milp ) from the MILP formulation step. The motivation is to avoid unnecessary computation. The original approach includes molecule analysis (specifically `get_aromatic_rings`) into the recursive calls. However, this is not necessary, as molecules are just copied and not modified at all. Therefore analyzing once is enough.
---
 rmgpy/molecule/resonance.py | 172 ++++++++++++++++++++----------------
 1 file changed, 96 insertions(+), 76 deletions(-)

diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
index 24eccaa636..85b9f4be10 100644
--- a/rmgpy/molecule/resonance.py
+++ b/rmgpy/molecule/resonance.py
@@ -54,11 +54,14 @@
 import logging
 from operator import attrgetter
 
+import numpy as np
+from scipy.optimize import Bounds, LinearConstraint, milp
+
 import cython
 
 import rmgpy.molecule.filtration as filtration
 import rmgpy.molecule.pathfinder as pathfinder
-from rmgpy.exceptions import ILPSolutionError, KekulizationError, AtomTypeError, ResonanceError
+from rmgpy.exceptions import KekulizationError, AtomTypeError, ResonanceError
 from rmgpy.molecule.adjlist import Saturator
 from rmgpy.molecule.graph import Vertex
 from rmgpy.molecule.kekulize import kekulize
@@ -906,8 +909,7 @@ def generate_clar_structures(mol, save_order=False):
 
     Returns a list of :class:`Molecule` objects corresponding to the Clar structures.
     """
-    cython.declare(output=list, mol_list=list, new_mol=Graph, aromatic_rings=list, bonds=list, solution=list,
-                   y=list, x=list, index=cython.int, bond=Edge, ring=list)
+    cython.declare(output=list, mol_list=list, new_mol=Graph, aromatic_rings=list, bonds=list, index=cython.int, bond=Edge, ring=list)
 
     if not mol.is_cyclic():
         return []
@@ -917,19 +919,20 @@ def generate_clar_structures(mol, save_order=False):
         mol.assign_atom_ids()
 
     try:
-        output = _clar_optimization(mol, save_order=save_order)
-    except ILPSolutionError:
+        aromatic_rings, bonds, solutions = _clar_optimization(mol, save_order=save_order)
+    except RuntimeError:
         # The optimization algorithm did not work on the first iteration
         return []
 
     mol_list = []
 
-    for new_mol, aromatic_rings, bonds, solution in output:
+    for solution in solutions:
 
+        new_mol = mol.copy(deep=True)
         # The solution includes a part corresponding to rings, y, and a part corresponding to bonds, x, using
         # nomenclature from the paper. In y, 1 means the ring as a sextet, 0 means it does not.
         # In x, 1 corresponds to a double bond, 0 either means a single bond or the bond is part of a sextet.
-        y = solution[0:len(aromatic_rings)]
+        y = solution[:len(aromatic_rings)]
         x = solution[len(aromatic_rings):]
 
         # Apply results to molecule - double bond locations first
@@ -939,7 +942,7 @@ def generate_clar_structures(mol, save_order=False):
             elif x[index] == 1:
                 bond.order = 2  # double
             else:
-                raise ValueError('Unaccepted bond value {0} obtained from optimization.'.format(x[index]))
+                raise ValueError(f'Unaccepted bond value {x[index]} obtained from optimization.')
 
         # Then apply locations of aromatic sextets by converting to benzene bonds
         for index, ring in enumerate(aromatic_rings):
@@ -963,28 +966,25 @@ def _tuplize_bond(bond):
     return (bond.atom1.id, bond.atom2.id)
 
 
-def _clar_optimization(mol, constraints=None, max_num=None, save_order=False):
+def _clar_optimization(mol, save_order=False):
     """
     Implements linear programming algorithm for finding Clar structures. This algorithm maximizes the number
     of Clar sextets within the constraints of molecular geometry and atom valency.
 
     Returns a list of valid Clar solutions in the form of a tuple, with the following entries:
-        [0] Molecule object
-        [1] List of aromatic rings
-        [2] List of bonds
-        [3] Optimization solution
+        [0] List of aromatic rings
+        [1] List of bonds
+        [2] Optimization solutions
 
-    The optimization solution is a list of boolean values with sextet assignments followed by double bond assignments,
-    with indices corresponding to the list of aromatic rings and list of bonds, respectively.
+    The optimization solutions may contain multiple valid solutions, each is an array of boolean values with sextet assignments
+    followed by double bond assignments, with indices corresponding to the list of aromatic rings and list of bonds, respectively.
 
     Method adapted from:
         Hansen, P.; Zheng, M. The Clar Number of a Benzenoid Hydrocarbon and Linear Programming.
             J. Math. Chem. 1994, 15 (1), 93–107.
     """
-    cython.declare(molecule=Graph, aromatic_rings=list, exo=list, l=cython.int, m=cython.int, n=cython.int,
-                   a=list, objective=list, status=cython.int, solution=list, innerSolutions=list)
-
-    from lpsolve55 import lpsolve
+    cython.declare(molecule=Graph, aromatic_rings=list, exo=list, n_rings=cython.int, n_atoms=cython.int, n_bonds=cython.int,
+                   A=list, solutions=tuple)
 
     # Make a copy of the molecule so we don't destroy the original
     molecule = mol.copy(deep=True)
@@ -1019,61 +1019,81 @@ def _clar_optimization(mol, constraints=None, max_num=None, save_order=False):
             exo.append(None)
 
     # Dimensions
-    l = len(aromatic_rings)
-    m = len(atoms)
-    n = l + len(bonds)
+    n_ring = len(aromatic_rings)
+    n_atom = len(atoms)
+    n_bond = len(bonds)
+
+    # The aromaticity assignment problem is formulated as an MILP problem
+    # minimize:
+    #       c @ x
+    # such that
+    #       b_l <= A @ x <= b_u
+    #       l <= x <= u
+    #       x are integers
 
     # Connectivity matrix which indicates which rings and bonds each atom is in
-    # Part of equality constraint Ax=b
-    a = []
+    # Part of equality constraint A_eq @ x = b_eq
+    A = []
     for atom in atoms:
         in_ring = [1 if atom in ring else 0 for ring in aromatic_rings]
         in_bond = [1 if atom in [bond.atom1, bond.atom2] else 0 for bond in bonds]
-        a.append(in_ring + in_bond)
+        A.append(in_ring + in_bond)
+    constraints = [LinearConstraint(
+        A=np.array(A, dtype=int), lb=np.ones(n_atom, dtype=int), ub=np.ones(n_atom, dtype=int)
+    )]
 
     # Objective vector for optimization: sextets have a weight of 1, double bonds have a weight of 0
-    objective = [1] * l + [0] * len(bonds)
-
-    # Solve LP problem using lpsolve
-    lp = lpsolve('make_lp', m, n)               # initialize lp with constraint matrix with m rows and n columns
-    lpsolve('set_verbose', lp, 2)               # reduce messages from lpsolve
-    lpsolve('set_obj_fn', lp, objective)        # set objective function
-    lpsolve('set_maxim', lp)                    # set solver to maximize objective
-    lpsolve('set_mat', lp, a)                   # set left hand side to constraint matrix
-    lpsolve('set_rh_vec', lp, [1] * m)          # set right hand side to 1 for all constraints
-    for i in range(m):                          # set all constraints as equality constraints
-        lpsolve('set_constr_type', lp, i + 1, '=')
-    lpsolve('set_binary', lp, [True] * n)       # set all variables to be binary
-
-    # Constrain values of exocyclic bonds, since we don't want to modify them
-    for i in range(l, n):
-        if exo[i - l] is not None:
-            # NOTE: lpsolve indexes from 1, so the variable we're changing should be i + 1
-            lpsolve('set_bounds', lp, i + 1, exo[i - l], exo[i - l])
-
-    # Add constraints to problem if provided
-    if constraints is not None:
-        for constraint in constraints:
-            try:
-                lpsolve('add_constraint', lp, constraint[0], '<=', constraint[1])
-            except Exception as e:
-                logging.debug('Unable to add constraint: {0} <= {1}'.format(constraint[0], constraint[1]))
-                logging.debug(mol.to_adjacency_list())
-                if str(e) == 'invalid vector.':
-                    raise ILPSolutionError('Unable to add constraint, likely due to '
-                                           'inconsistent aromatic ring perception.')
-                else:
-                    raise
+    c = - np.array([1] * n_ring + [0] * n_bond, dtype=int)
+
+    # Variable bounds
+    bounds = Bounds(
+        lb=np.array(
+            [0] * n_ring + [1 if val == 1 else 0 for val in exo]
+            dtype=int,
+        ),  # lower bounds: 0 except for exo double bonds
+        ub=np.array(
+            [1] * n_ring + [0 if val == 0 else 1 for val in exo]
+            dtype=int,
+        ),  # upper bounds: 1 except for exo single bonds
+    )
+
+    solutions = _solve_clar_milp(c, bounds, constraints, n_ring)
+
+    return aromatic_rings, bonds, solutions
+
+
+def _solve_clar_milp(
+    c,
+    bounds,
+    constraints,
+    n_ring,
+    max_num=None,
+):
+    """
+    A helpful function to solve the formulated clar optimization MILP problem. ``c``,
+    ``bounds``, and ``constraints`` are computed in _clar_optimization and follow the
+    definition of their corresponding kwargs in scipy.optimize.milp. ``n_ring`` is the
+    number of aromatic rings in the molecule. ``max_num`` is the maximum number of sextets
+    that can be found. If ``max_num`` is None for first run but will be updated during the
+    recursion and is used to check sub-optimal solution.
+    """
+    # To modify
+    cython.declare(inner_solutions=list)
 
-    status = lpsolve('solve', lp)
-    obj_val, solution = lpsolve('get_solution', lp)[0:2]
-    lpsolve('delete_lp', lp)  # Delete the LP problem to clear up memory
+    result = milp(
+        c=-c,  # negative for maximization
+        integrality=1,
+        bounds=bounds,
+        constraints=constraints,
+        options={'time_limit': 10},
+    )
 
-    # Check that optimization was successful
-    if status != 0:
-        raise ILPSolutionError('Optimization could not find a valid solution.')
+    if result.status != 0:
+        raise RuntimeError("Optimization could not find a valid solution.")
 
-    # Check that we the result contains at least one aromatic sextet
+    obj_val, solution = -result.fun, result.x
+
+    # Check that the result contains at least one aromatic sextet
     if obj_val == 0:
         return []
 
@@ -1081,27 +1101,27 @@ def _clar_optimization(mol, constraints=None, max_num=None, save_order=False):
     if max_num is None:
         max_num = obj_val  # This is the first solution, so the result should be an upper limit
     elif obj_val < max_num:
-        raise ILPSolutionError('Optimization obtained a sub-optimal solution.')
+        raise RuntimeError("Optimization obtained a sub-optimal solution.")
 
     if any([x != 1 and x != 0 for x in solution]):
-        raise ILPSolutionError('Optimization obtained a non-integer solution.')
+        raise RuntimeError('Optimization obtained a non-integer solution.')
 
     # Generate constraints based on the solution obtained
-    y = solution[0:l]
-    new_a = y + [0] * len(bonds)
-    new_b = sum(y) - 1
-    if constraints is not None:
-        constraints.append((new_a, new_b))
-    else:
-        constraints = [(new_a, new_b)]
+    y = solution[0: n_ring]
+    constraints.append(
+        LinearConstraint(
+            A=np.hstack([y, [0] * (solution.shape[0] - n_ring)]),
+            ub=sum(y) - 1,
+        ),
+    )
 
     # Run optimization with additional constraints
     try:
-        inner_solutions = _clar_optimization(mol, constraints=constraints, max_num=max_num, save_order=save_order)
-    except ILPSolutionError:
+        inner_solutions = _solve_clar_milp(c, bounds, constraints, n_ring, max_num)
+    except RuntimeError:
         inner_solutions = []
 
-    return inner_solutions + [(molecule, aromatic_rings, bonds, solution)]
+    return inner_solutions + [solution]
 
 
 def _clar_transformation(mol, aromatic_ring):

From 0f9dcc0977d7733c7f937920f4d58556424a3bf6 Mon Sep 17 00:00:00 2001
From: Xiaorui Dong <xiaorui@mit.edu>
Date: Mon, 4 Mar 2024 23:38:07 -0500
Subject: [PATCH 078/162] Update pxd of clar optimization after reimplement
 with scipy MILP

---
 rmgpy/molecule/resonance.pxd | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/rmgpy/molecule/resonance.pxd b/rmgpy/molecule/resonance.pxd
index 64662a797c..1b546ee9d5 100644
--- a/rmgpy/molecule/resonance.pxd
+++ b/rmgpy/molecule/resonance.pxd
@@ -25,6 +25,8 @@
 #                                                                             #
 ###############################################################################
 
+cimport numpy as cnp
+
 from rmgpy.molecule.graph cimport Vertex, Edge, Graph
 from rmgpy.molecule.molecule cimport Atom, Bond, Molecule
 
@@ -64,6 +66,8 @@ cpdef list generate_kekule_structure(Graph mol)
 
 cpdef list generate_clar_structures(Graph mol, bint save_order=?)
 
-cpdef list _clar_optimization(Graph mol, list constraints=?, max_num=?, save_order=?)
+cpdef list _clar_optimization(Graph mol, bint save_order=?)
+
+cpdef list _solve_clar_milp(cnp.ndarray[cnp.int_t, ndim=1] c, bounds, list constraints, int n_ring, max_num=?)
 
 cpdef list _clar_transformation(Graph mol, list aromatic_ring)

From 919448b871765309493b31989ec7f9668b4dd6ba Mon Sep 17 00:00:00 2001
From: Xiaorui Dong <xiaorui@mit.edu>
Date: Mon, 4 Mar 2024 23:38:35 -0500
Subject: [PATCH 079/162] Remove the redundant ILPSolutionError

---
 rmgpy/exceptions.py | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/rmgpy/exceptions.py b/rmgpy/exceptions.py
index 7b4420cf66..f2e7dae460 100644
--- a/rmgpy/exceptions.py
+++ b/rmgpy/exceptions.py
@@ -109,15 +109,6 @@ class ForbiddenStructureException(Exception):
     pass
 
 
-class ILPSolutionError(Exception):
-    """
-    An exception to be raised when solving an integer linear programming problem if a solution
-    could not be found or the solution is not valid. Can pass a string to indicate the reason
-    that the solution is invalid.
-    """
-    pass
-
-
 class ImplicitBenzeneError(Exception):
     """
     An exception class when encountering a group with too many implicit benzene

From 517debe3f283c87d7560d9dfcd1f74236cb520a7 Mon Sep 17 00:00:00 2001
From: Xiaorui Dong <xiaorui@mit.edu>
Date: Tue, 5 Mar 2024 00:39:43 -0500
Subject: [PATCH 080/162] Fix typos in resonance clar optimization

---
 rmgpy/molecule/resonance.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
index 85b9f4be10..d896537b21 100644
--- a/rmgpy/molecule/resonance.py
+++ b/rmgpy/molecule/resonance.py
@@ -1048,11 +1048,11 @@ def _clar_optimization(mol, save_order=False):
     # Variable bounds
     bounds = Bounds(
         lb=np.array(
-            [0] * n_ring + [1 if val == 1 else 0 for val in exo]
+            [0] * n_ring + [1 if val == 1 else 0 for val in exo],
             dtype=int,
         ),  # lower bounds: 0 except for exo double bonds
         ub=np.array(
-            [1] * n_ring + [0 if val == 0 else 1 for val in exo]
+            [1] * n_ring + [0 if val == 0 else 1 for val in exo],
             dtype=int,
         ),  # upper bounds: 1 except for exo single bonds
     )

From 756439fd5096859f3e67002571c0a9e1c19258ff Mon Sep 17 00:00:00 2001
From: Xiaorui Dong <35771233+xiaoruiDong@users.noreply.github.com>
Date: Tue, 5 Mar 2024 10:27:15 -0500
Subject: [PATCH 081/162] Fix list style in clar optimization

Co-authored-by: Hao-Wei Pang <45482070+hwpang@users.noreply.github.com>
---
 rmgpy/molecule/resonance.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
index d896537b21..1695962125 100644
--- a/rmgpy/molecule/resonance.py
+++ b/rmgpy/molecule/resonance.py
@@ -1107,7 +1107,7 @@ def _solve_clar_milp(
         raise RuntimeError('Optimization obtained a non-integer solution.')
 
     # Generate constraints based on the solution obtained
-    y = solution[0: n_ring]
+    y = solution[:n_ring]
     constraints.append(
         LinearConstraint(
             A=np.hstack([y, [0] * (solution.shape[0] - n_ring)]),

From ca0091a6a36176df60d9ccce4fa9e80445c99135 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Wed, 24 Jan 2024 17:47:00 -0500
Subject: [PATCH 082/162] Update year in license

---
 arkane/encorr/isodesmic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 83a9164e17..1b97d347f7 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -4,7 +4,7 @@
 #                                                                             #
 # RMG - Reaction Mechanism Generator                                          #
 #                                                                             #
-# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu),           #
+# Copyright (c) 2002-2024 Prof. William H. Green (whgreen@mit.edu),           #
 # Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)   #
 #                                                                             #
 # Permission is hereby granted, free of charge, to any person obtaining a     #

From bd6021537768e4e8e38e6a92f46ccb93cee4e53e Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Wed, 24 Jan 2024 17:47:34 -0500
Subject: [PATCH 083/162] imports sorting by formatter

---
 arkane/encorr/isodesmic.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 1b97d347f7..65419fcc5d 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -41,16 +41,18 @@
 https://doi.org/10.1021/jp404158v
 """
 
+import logging
 import signal
-from collections import deque
+from copy import deepcopy
+from typing import List, Union
 
-from lpsolve55 import lpsolve, EQ, LE
 import numpy as np
-
-from rmgpy.molecule import Molecule
-from rmgpy.quantity import ScalarQuantity
+from lpsolve55 import EQ, LE, lpsolve
+from pyutilib.common import ApplicationError
 
 from arkane.modelchem import LOT
+from rmgpy.molecule import Bond, Molecule
+from rmgpy.quantity import ScalarQuantity
 
 # Optional Imports
 try:

From d90e4fb7151900b41122ce6681afeb914fedffc3 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 25 Jan 2024 16:26:06 -0500
Subject: [PATCH 084/162] Add improvements by @amarkpayne

---
 arkane/encorr/isodesmic.py | 388 +++++++++++++++++++++++++++++--------
 1 file changed, 311 insertions(+), 77 deletions(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 65419fcc5d..8ad7cf2a2c 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -165,81 +165,277 @@ def calculate_target_thermo(self):
         return ScalarQuantity(target_thermo, 'J/mol')
 
 
+class AtomConstraint:
+
+    def __init__(self, label, connections=None):
+        self.label = label
+        self.connections = connections if connections is not None else []
+
+    def __eq__(self, other):
+        if isinstance(other, AtomConstraint):
+            if self.label == other.label:
+                if len(self.connections) == len(other.connections):
+                    connections = deepcopy(other.connections)
+                    for c in self.connections:
+                        for i, c_other in enumerate(connections):
+                            if c == c_other:
+                                break
+                        else:
+                            return False
+                        connections.pop(i)
+
+                    return True
+
+            return False
+
+        else:
+            raise NotImplementedError(f'AtomConstraint object has no __eq__ defined for other object of type '
+                                      f'{type(other)}')
+
+    def __repr__(self):
+        return f'{self.label}' + ''.join([f'({c})' for c in self.connections])
+
+
+class BondConstraint:
+
+    def __init__(self, atom1, atom2, bond_order):
+        self.atom1 = atom1
+        self.atom2 = atom2
+        self.bond_order = bond_order
+
+    def __eq__(self, other):
+        if isinstance(other, BondConstraint):
+            if self.bond_order == other.bond_order:
+                if ((self.atom1 == other.atom1 and self.atom2 == other.atom2) or
+                        (self.atom1 == other.atom2 and self.atom2 == other.atom1)):
+                    return True
+            return False
+
+        if isinstance(other, GenericConstraint):
+            return False
+
+        else:
+            raise NotImplementedError(f'BondConstraint object has no __eq__ defined for other object of type '
+                                      f'{type(other)}')
+
+    def __repr__(self):
+        symbols = ['', '-', '=', '#']
+        return f'{self.atom1}{symbols[self.bond_order]}{self.atom2}'
+
+
+class Connection:
+
+    def __init__(self, atom, bond_order):
+        self.atom = atom
+        self.bond_order = bond_order
+
+    def __eq__(self, other):
+        if isinstance(other, Connection):
+            if self.bond_order == other.bond_order:
+                if self.atom == other.atom:
+                    return True
+            return False
+
+        else:
+            raise NotImplementedError(f'Connection object has no __eq__ defined for other object of type {type(other)}')
+
+    def __repr__(self):
+        symbols = ['', '-', '=', '#']
+        return f'{symbols[self.bond_order]}{self.atom}'
+
+
+class GenericConstraint:
+
+    def __init__(self, constraint_str: str):
+        self.constraint_str = constraint_str
+
+    def __eq__(self, other):
+        if isinstance(other, BondConstraint):
+            return False
+        elif isinstance(other, GenericConstraint):
+            return self.constraint_str == other.constraint_str
+        else:
+            raise NotImplementedError(f'GenericConstraint object has no __eq__ defined for other object of '
+                                      f'type {type(other)}')
+
+
+def bond_centric_constraints(species: ErrorCancelingSpecies, constraint_class: str) -> List[BondConstraint]:
+    constraints = []
+    contraint_func = CONSTRAINT_CLASSES[constraint_class]
+    molecule = species.molecule
+
+    for bond in molecule.get_all_edges():
+        constraints.append(contraint_func(bond))
+
+    return constraints
+
+
+def _buerger_rc2(bond: Bond) -> BondConstraint:
+    atom1 = AtomConstraint(label=bond.atom1.symbol)
+    atom2 = AtomConstraint(label=bond.atom2.symbol)
+
+    return BondConstraint(atom1=atom1, atom2=atom2, bond_order=int(bond.order))
+
+
+def _buerger_rc3(bond: Bond) -> BondConstraint:
+    atom1 = bond.atom1
+    atom2 = bond.atom2
+
+    atom1 = AtomConstraint(label=f'{atom1.symbol}{atom1.connectivity1}')
+    atom2 = AtomConstraint(label=f'{atom2.symbol}{atom2.connectivity1}')
+
+    return BondConstraint(atom1=atom1, atom2=atom2, bond_order=int(bond.order))
+
+
+def _buerger_rc4(bond: Bond) -> BondConstraint:
+    atoms = []
+
+    for atom in [bond.atom1, bond.atom2]:
+        connections = []
+        for a, b in atom.bonds.items():
+            ac = AtomConstraint(label=f'{a.symbol}{a.connectivity1}')
+            bond_order = b.order
+            connections.append(Connection(atom=ac, bond_order=bond_order))
+        atoms.append(AtomConstraint(label=f'{atom.symbol}{atom.connectivity1}', connections=connections))
+
+    return BondConstraint(atom1=atoms[0], atom2=atoms[1], bond_order=int(bond.order))
+
+
 class SpeciesConstraints:
     """
     A class for defining and enumerating constraints to ReferenceSpecies objects for error canceling reactions
     """
 
-    def __init__(self, target, reference_list, conserve_bonds=True, conserve_ring_size=True):
+    def __init__(self, target, reference_list, isodesmic_class='rc2', conserve_ring_size=True, limit_charges=True,
+                 limit_scope=True):
         """
         Define the constraints that will be enforced, and determine the mapping of indices in the constraint vector to
         the labels for these constraints.
 
-        To reduce the size of the linear programming problem that will try to find error canceling reactions of the
-        target and subsets of the reference species, the `reference_species` list is automatically pruned to remove
-        species that have additional atom, bond, and/or ring attributes not found in the target molecule.
+        Notes:
+            To reduce the size of the linear programming problem that will try to find error canceling reactions of the
+            target and subsets of the reference species, the `reference_species` list is automatically pruned to remove
+            species that have additional atom, bond, and/or ring attributes not found in the target molecule.
+
+            Charge is also explicitly conserved, as there are charged species in the reference database
 
         Args:
             target (ErrorCancelingSpecies): The target species of the error canceling reaction scheme
             reference_list(list): A list of ErrorCancelingSpecies objects for the reference
                 species that can participate in the error canceling reaction scheme
-            conserve_bonds (bool, optional): Enforce the number of each bond type be conserved
-            conserve_ring_size (bool, optional): Enforce that the number of each ring size be conserved
+            isodesmic_class (str, optional): Reaction classes as defined by Buerger et al. that determine how specific
+                the constraints are.
+            conserve_ring_size (bool, optional): Enforce that the number of each ring size be conserved.
+            limit_charges (bool, optional): Only allow species in the reaction that are within the range [C, 0] for
+                anions or [0, C] for cations where "C" is the charge of the target
+            limit_scope (bool, optional): Exclude any molecules from the reference set that have features not contained
+                in the target molecule. This will reduce the size of the linear programing problem being solved to yield
+                faster, possibly more accurate results
         """
 
         self.target = target
         self.all_reference_species = reference_list
         self.reference_species = []
-        self.conserve_bonds = conserve_bonds
+        self.isodesmic_class = isodesmic_class
         self.conserve_ring_size = conserve_ring_size
-        self.constraint_map = self._get_constraint_map()
-
-    def _get_constraint_map(self):
-        # Enumerate all of the constraints in the target molecule to initialize the constraint mapping
-        constraint_map = {label: i for i, label in enumerate(self.target.molecule.get_element_count().keys())}
-        if self.conserve_bonds:
-            j = len(constraint_map)
-            constraint_map.update(
-                {label: j + i for i, label in enumerate(self.target.molecule.enumerate_bonds().keys())})
+        self.limit_charges = limit_charges
+        self.limit_scope = limit_scope
+
+    def _get_constraint_lists(self):
+        full_constraints_list = [self._get_all_constraints(self.target)]
+        for ref_spcs in self.all_reference_species:
+            full_constraints_list.append(self._get_all_constraints(ref_spcs))
+
+        return full_constraints_list
+
+    def _get_ring_constraints(self, species: ErrorCancelingSpecies) -> List[GenericConstraint]:
+        ring_features = []
+        rings = species.molecule.get_smallest_set_of_smallest_rings()
+        for ring in rings:
+            ring_features.append(GenericConstraint(constraint_str=f'{len(ring)}_ring'))
+
+        return ring_features
+
+    def _get_all_constraints(self, species: ErrorCancelingSpecies) -> List[Union[BondConstraint, GenericConstraint]]:
+        features = bond_centric_constraints(species, self.isodesmic_class)
         if self.conserve_ring_size:
-            j = len(constraint_map)
-            possible_rings_sizes = set(f'{len(sssr)}_ring' for sssr in
-                                       self.target.molecule.get_smallest_set_of_smallest_rings())
-            constraint_map.update({label: j + i for i, label in enumerate(possible_rings_sizes)})
+            features += self._get_ring_constraints(species)
 
-        return constraint_map
+        return features
 
-    def _enumerate_constraints(self, species):
-        """
-        Determine the constraint vector for a molecule given the enforced constraints
+    def _enumerate_constraints(self, full_constraints_list):
+        enumerated_constraints = []
 
-        Args:
-            species (ErrorCancelingSpecies): Species whose constraints are to be enumerated
+        # Initialize list of empty lists. Be careful to avoid making references to a singular empty list
+        for _ in range(len(full_constraints_list)):
+            enumerated_constraints.append([])
 
-        Returns:
-            np.ndarray: vector of the number of instances of each constraining feature e.g. number of carbon atoms
-        """
-        constraint_vector = np.zeros(len(self.constraint_map))
-        molecule = species.molecule
+        # Begin enumerating constraints
+        while True:
+            if len(full_constraints_list[0]) == 0:  # We have exhausted target constraints
+                if self.limit_scope:  # No need to enumerate any further
+                    break  # Out of the while loop
+
+            # Find a constraint to search for next
+            for spcs_constraints in full_constraints_list:
+                if len(spcs_constraints) != 0:
+                    constraint = spcs_constraints[0]
+                    break  # Out of the for loop
 
-        try:
-            atoms = molecule.get_element_count()
-            for atom_label, count in atoms.items():
-                constraint_vector[self.constraint_map[atom_label]] += count
+            else:
+                break  # No more constraints, so break out of the while loop
+
+            # enumerate for each species
+            new_constraints_list = []
+            for i, spcs_constraints in enumerate(full_constraints_list):
+                new_spcs_constraints = [c for c in spcs_constraints if c != constraint]
+                matching_constraints = len(spcs_constraints) - len(new_spcs_constraints)
+                enumerated_constraints[i].append(matching_constraints)
+                new_constraints_list.append(new_spcs_constraints)
+
+            # Finally, update the new list
+            full_constraints_list = new_constraints_list
+
+        # Finalize list of reference species and corresponding constraints
+        reference_constraints = []
+        target_constraints = enumerated_constraints [0]
+        if self.limit_scope:
+            for i, spcs in enumerate(self.all_reference_species):
+                # Add 1 to index to offset for the target
+                if len(full_constraints_list[i+1]) == 0:  # This species does not have extra constraints
+                    self.reference_species.append(spcs)
+                    reference_constraints.append(enumerated_constraints[i+1])
+
+        else:
+            self.reference_species = self.all_reference_species
+            reference_constraints = enumerated_constraints[1:]
 
-            if self.conserve_bonds:
-                bonds = molecule.enumerate_bonds()
-                for bond_label, count in bonds.items():
-                    constraint_vector[self.constraint_map[bond_label]] += count
+        return target_constraints, reference_constraints
 
-            if self.conserve_ring_size:
-                rings = molecule.get_smallest_set_of_smallest_rings()
-                for ring in rings:
-                    constraint_vector[self.constraint_map[f'{len(ring)}_ring']] += 1
-        except KeyError:  # This molecule has a feature not found in the target molecule. Return None to exclude this
-            return None
+    def _enumerate_charge_constraints(self, target_constraints, reference_constraints):
+        charge = self.target.molecule.get_net_charge()
+        target_constraints.append(charge)
 
-        return constraint_vector
+        for i, spcs in enumerate(self.reference_species):
+            reference_constraints[i].append(spcs.molecule.get_net_charge())
+
+        if self.limit_charges:
+            allowed_reference_species = []
+            new_constraints = []
+
+            if charge < 0:
+                allowable_charges = list(range(charge, 0))
+            else:
+                allowable_charges = list(range(0, charge + 1))
+            for i, spcs in enumerate(self.reference_species):
+                if reference_constraints[i][-1] in allowable_charges:
+                    allowed_reference_species.append(spcs)
+                    new_constraints.append(reference_constraints[i])
+
+            reference_constraints = new_constraints
+            self.reference_species = allowed_reference_species
+
+        return target_constraints, reference_constraints
 
     def calculate_constraints(self):
         """
@@ -250,16 +446,33 @@ def calculate_constraints(self):
             - target constraint vector (1 x len(constraints))
             - constraint matrix for allowable reference species (len(self.reference_species) x len(constraints))
         """
-        target_constraints = self._enumerate_constraints(self.target)
-        constraint_matrix = []
+        full_constraint_list = self._get_constraint_lists()
+        target_constraints, reference_constraints = self._enumerate_constraints(full_constraint_list)
+        target_constraints, reference_constraints = self._enumerate_charge_constraints(target_constraints,
+                                                                                       reference_constraints)
+
+        target_constraints = np.array(target_constraints, dtype=int)
+        constraint_matrix = np.array(reference_constraints, dtype=int)
+
+        return target_constraints, constraint_matrix
 
-        for spcs in self.all_reference_species:
-            spcs_constraints = self._enumerate_constraints(spcs)
-            if spcs_constraints is not None:  # This species is allowed
-                self.reference_species.append(spcs)
-                constraint_matrix.append(spcs_constraints)
 
-        return target_constraints, np.array(constraint_matrix, dtype=int)
+def _clean_up_constraints(target_constraints, constraint_matrix):
+    # make sure that the constraint matrix is 2d
+    if len(constraint_matrix.shape) == 1:
+        constraint_matrix = np.array([constraint_matrix], dtype=int)
+
+    # Remove any columns that are all zeros
+    zero_indices = np.where(~constraint_matrix.any(axis=0))[0]
+    # Check that this wouldn't eliminate a non-zero target entry
+    for z in zero_indices:
+        if target_constraints[z] != 0:  # This problem is not solvable. Return None to signal this
+            return None, None
+    indices = [i for i in range(constraint_matrix.shape[1]) if i not in zero_indices]
+    constraint_matrix = np.take(constraint_matrix, indices=indices, axis=1)
+    target_constraints = np.take(target_constraints, indices=indices)
+
+    return target_constraints, constraint_matrix
 
 
 class ErrorCancelingScheme:
@@ -267,22 +480,21 @@ class ErrorCancelingScheme:
     A Base class for calculating target species thermochemistry using error canceling reactions
     """
 
-    def __init__(self, target, reference_set, conserve_bonds, conserve_ring_size):
+    def __init__(self, target, reference_set, isodesmic_class, conserve_ring_size, limit_charges, limit_scope):
         """
 
         Args:
             target (ErrorCancelingSpecies): Species whose Hf298 will be calculated using error canceling reactions
             reference_set (list): list of reference species (as ErrorCancelingSpecies) that can participate
                 in error canceling reactions to help calculate the thermochemistry of the target
-            conserve_bonds (bool): Flag to determine if the number and type of each bond must be conserved in each error
-                canceling reaction
             conserve_ring_size (bool): Flag to determine if the number of each ring size must be conserved in each error
                 canceling reaction
         """
 
         self.target = target
-        self.constraints = SpeciesConstraints(target, reference_set, conserve_bonds=conserve_bonds,
-                                              conserve_ring_size=conserve_ring_size)
+        self.constraints = SpeciesConstraints(target, reference_set, isodesmic_class=isodesmic_class,
+                                              conserve_ring_size=conserve_ring_size, limit_charges=limit_charges,
+                                              limit_scope=limit_scope)
 
         self.target_constraint, self.constraint_matrix = self.constraints.calculate_constraints()
         self.reference_species = self.constraints.reference_species
@@ -310,9 +522,16 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
 
         # Define the constraints based on the provided subset
         c_matrix = np.take(self.constraint_matrix, reference_subset, axis=0)
+
+        # Remove unnecessary constraints
+        target_constraint, c_matrix = _clean_up_constraints(self.target_constraint, c_matrix)
+        if target_constraint is None or c_matrix is None:  # The problem is not solvable
+            return None, None
+
+        # Setup MILP problem
         c_matrix = np.tile(c_matrix, (2, 1))
         sum_constraints = np.sum(c_matrix, 1, dtype=int)
-        targets = -1*self.target_constraint
+        targets = -1*target_constraint
         m = c_matrix.shape[0]
         n = c_matrix.shape[1]
         split = int(m/2)
@@ -324,6 +543,9 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
                     raise ImportError('Cannot import optional package pyomo. Either install this dependency with '
                                       '`conda install -c conda-forge pyomo glpk` or set milp_software to `lpsolve`')
 
+                # Diable logging, pyomo outputs too often
+                logging.disable()
+
                 # Setup the MILP problem using pyomo
                 lp_model = pyo.ConcreteModel()
                 lp_model.i = pyo.RangeSet(0, m - 1)
@@ -341,7 +563,10 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
 
                 # Solve the MILP problem using the GLPK MILP solver (https://www.gnu.org/software/glpk/)
                 opt = pyo.SolverFactory('glpk')
-                results = opt.solve(lp_model, timelimit=1)
+                try:
+                    results = opt.solve(lp_model, timelimit=10)
+                except ApplicationError:
+                    continue
 
                 # Return the solution if a valid reaction is found. Otherwise continue to next solver
                 if results.solver.termination_condition == pyo.TerminationCondition.optimal:
@@ -349,6 +574,9 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
                     solution = lp_model.v.extract_values().values()
                     break
 
+                # Re-enable logging
+                logging.disable(logging.NOTSET)
+
             elif solver == 'lpsolve':
                 # Save the current signal handler
                 sig = signal.getsignal(signal.SIGINT)
@@ -363,12 +591,7 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
                     lpsolve('add_constraint', lp, np.concatenate((c_matrix[:split, j], -1*c_matrix[split:, j])), EQ,
                             targets[j])
 
-                lpsolve('add_constraint', lp, np.ones(m), LE, 20)  # Use at most 20 species (including replicates)
-                lpsolve('set_timeout', lp, 1)  # Move on if lpsolve can't find a solution quickly
-
-                # Constrain v_i to be 4 or less
-                for i in range(m):
-                    lpsolve('set_upbo', lp, i, 4)
+                lpsolve('set_timeout', lp, 10)  # Move on if lpsolve can't find a solution quickly
 
                 # All v_i must be integers
                 lpsolve('set_int', lp, [True]*m)
@@ -381,10 +604,6 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
                 except ValueError:
                     # This is not being run in the main thread, so we cannot reset signal
                     pass
-                except TypeError:
-                    print(
-                        "Failed to reset signal handling in LPSolve - are you running pytest?"
-                    )
 
                 # Return the solution if a valid reaction is found. Otherwise continue to next solver
                 if status == 0:
@@ -426,12 +645,11 @@ def multiple_error_canceling_reaction_search(self, n_reactions_max=20, milp_soft
         Returns:
             list: A list of the found error canceling reactions
         """
-        subset_queue = deque()
-        subset_queue.append(np.arange(0, len(self.reference_species)))
+        subset_queue = [np.arange(0, len(self.reference_species))]
         reaction_list = []
 
         while (len(subset_queue) != 0) and (len(reaction_list) < n_reactions_max):
-            subset = subset_queue.popleft()
+            subset = subset_queue.pop()
             if len(subset) == 0:
                 continue
             reaction, subset_indices = self._find_error_canceling_reaction(subset, milp_software=milp_software)
@@ -443,9 +661,18 @@ def multiple_error_canceling_reaction_search(self, n_reactions_max=20, milp_soft
                 for index in subset_indices:
                     subset_queue.append(np.delete(subset, index))
 
+                # Clean up the queue to remove subsets that would allow for already found reactions
+                new_queue = []
+                reaction_indices = [subset[i] for i in subset_indices]
+                for s in subset_queue:
+                    if not all([i in s for i in reaction_indices]):
+                        new_queue.append(s)
+
+                subset_queue = new_queue
+
         return reaction_list
 
-    def calculate_target_enthalpy(self, n_reactions_max=20, milp_software=None):
+    def calculate_target_enthalpy(self, n_reactions_max=5, milp_software=None):
         """
         Perform a multiple error canceling reactions search and calculate hf298 for the target species by taking the
         median hf298 value from among the error canceling reactions found
@@ -462,6 +689,8 @@ def calculate_target_enthalpy(self, n_reactions_max=20, milp_software=None):
             - reaction list containing all error canceling reactions found
         """
         reaction_list = self.multiple_error_canceling_reaction_search(n_reactions_max, milp_software)
+        if len(reaction_list) == 0:  # No reactions found
+            return None, reaction_list
         h298_list = np.zeros(len(reaction_list))
 
         for i, rxn in enumerate(reaction_list):
@@ -484,7 +713,8 @@ class IsodesmicScheme(ErrorCancelingScheme):
     An error canceling reaction where the number and type of both atoms and bonds are conserved
     """
     def __init__(self, target, reference_set):
-        super().__init__(target, reference_set, conserve_bonds=True, conserve_ring_size=False)
+        super().__init__(target, reference_set, isodesmic_class='rc2', conserve_ring_size=False, limit_charges=True,
+                         limit_scope=True)
 
 
 class IsodesmicRingScheme(ErrorCancelingScheme):
@@ -492,7 +722,11 @@ class IsodesmicRingScheme(ErrorCancelingScheme):
     A stricter form of the traditional isodesmic reaction scheme where the number of each ring size is also conserved
     """
     def __init__(self, target, reference_set):
-        super().__init__(target, reference_set, conserve_bonds=True, conserve_ring_size=True)
+        super().__init__(target, reference_set, isodesmic_class='rc2', conserve_ring_size=True, limit_charges=True,
+                         limit_scope=True)
+
+
+CONSTRAINT_CLASSES = {'rc2': _buerger_rc2, 'rc3': _buerger_rc3, 'rc4': _buerger_rc4}
 
 
 if __name__ == '__main__':

From b78765f65057e765094ecf561a9414203ecd83af Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Wed, 24 Jan 2024 17:59:35 -0500
Subject: [PATCH 085/162] Add constraints for element balance

---
 arkane/encorr/isodesmic.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 8ad7cf2a2c..8e3e9bc7a4 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -436,6 +436,24 @@ def _enumerate_charge_constraints(self, target_constraints, reference_constraint
             self.reference_species = allowed_reference_species
 
         return target_constraints, reference_constraints
+    
+    def _enumerate_element_constraints(self, target_constraints, reference_constraints):
+        all_elements = set()
+        for spc in self.reference_species:
+            all_elements.update(spc.molecule.get_element_count().keys())
+        all_elements.update(self.target.molecule.get_element_count().keys())
+        all_elements = sorted(list(all_elements))
+
+        element_count = self.target.molecule.get_element_count()
+        new_constraints = [element_count.get(element, 0) for element in all_elements]
+        target_constraints.extend(new_constraints)
+
+        for i, spc in enumerate(self.reference_species):
+            element_count = spc.molecule.get_element_count()
+            new_constraints = [element_count.get(element, 0) for element in all_elements]
+            reference_constraints[i].extend(new_constraints)
+
+        return target_constraints, reference_constraints
 
     def calculate_constraints(self):
         """
@@ -450,6 +468,7 @@ def calculate_constraints(self):
         target_constraints, reference_constraints = self._enumerate_constraints(full_constraint_list)
         target_constraints, reference_constraints = self._enumerate_charge_constraints(target_constraints,
                                                                                        reference_constraints)
+        target_constraints, reference_constraints = self._enumerate_element_constraints(target_constraints, reference_constraints)
 
         target_constraints = np.array(target_constraints, dtype=int)
         constraint_matrix = np.array(reference_constraints, dtype=int)

From 1b052aaff4acbab449a45b91b47796d2c273bd6f Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 25 Jan 2024 09:00:51 -0500
Subject: [PATCH 086/162] Add pyutilib to catch ApplicationError

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index fd792336c8..bd6212de77 100644
--- a/environment.yml
+++ b/environment.yml
@@ -70,6 +70,7 @@ dependencies:
   - pytest
   - pytest-cov
   - conda-forge::pytest-check
+  - pyutilib
   - matplotlib >=1.5
   - mpmath
   - pandas

From a929f2c8c5f86541ee03ae5f4de48bbaf9cbe8b1 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 25 Jan 2024 10:41:58 -0500
Subject: [PATCH 087/162] Formatting by formatter

---
 arkane/encorr/isodesmic.py | 366 +++++++++++++++++++++++++------------
 1 file changed, 252 insertions(+), 114 deletions(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 8e3e9bc7a4..0415489ee8 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -64,7 +64,14 @@
 class ErrorCancelingSpecies:
     """Class for target and known (reference) species participating in an error canceling reaction"""
 
-    def __init__(self, molecule, low_level_hf298, level_of_theory, high_level_hf298=None, source=None):
+    def __init__(
+        self,
+        molecule,
+        low_level_hf298,
+        level_of_theory,
+        high_level_hf298=None,
+        source=None,
+    ):
         """
 
         Args:
@@ -78,35 +85,45 @@ def __init__(self, molecule, low_level_hf298, level_of_theory, high_level_hf298=
         if isinstance(molecule, Molecule):
             self.molecule = molecule
         else:
-            raise ValueError(f'ErrorCancelingSpecies molecule attribute must be an rmgpy Molecule object. Instead a '
-                             f'{type(molecule)} object was given')
+            raise ValueError(
+                f"ErrorCancelingSpecies molecule attribute must be an rmgpy Molecule object. Instead a "
+                f"{type(molecule)} object was given"
+            )
 
         if isinstance(level_of_theory, LOT):
             self.level_of_theory = level_of_theory
         else:
-            raise ValueError(f'The level of theory used to calculate the low level Hf298 must be provided '
-                             f'for consistency checks. Instead, a {type(level_of_theory)} object was given')
+            raise ValueError(
+                f"The level of theory used to calculate the low level Hf298 must be provided "
+                f"for consistency checks. Instead, a {type(level_of_theory)} object was given"
+            )
 
         if not isinstance(low_level_hf298, ScalarQuantity):
             if isinstance(low_level_hf298, tuple):
                 low_level_hf298 = ScalarQuantity(*low_level_hf298)
             else:
-                raise TypeError(f'Low level Hf298 should be a ScalarQuantity object or its tuple representation, but '
-                                f'received {low_level_hf298} instead.')
+                raise TypeError(
+                    f"Low level Hf298 should be a ScalarQuantity object or its tuple representation, but "
+                    f"received {low_level_hf298} instead."
+                )
         self.low_level_hf298 = low_level_hf298
 
         # If the species is a reference species, then the high level data is already known
-        if high_level_hf298 is not None and not isinstance(high_level_hf298, ScalarQuantity):
+        if high_level_hf298 is not None and not isinstance(
+            high_level_hf298, ScalarQuantity
+        ):
             if isinstance(high_level_hf298, tuple):
                 high_level_hf298 = ScalarQuantity(*high_level_hf298)
             else:
-                raise TypeError(f'High level Hf298 should be a ScalarQuantity object or its tuple representation, but '
-                                f'received {high_level_hf298} instead.')
+                raise TypeError(
+                    f"High level Hf298 should be a ScalarQuantity object or its tuple representation, but "
+                    f"received {high_level_hf298} instead."
+                )
         self.high_level_hf298 = high_level_hf298
         self.source = source
 
     def __repr__(self):
-        return f'<ErrorCancelingSpecies {self.molecule.to_smiles()}>'
+        return f"<ErrorCancelingSpecies {self.molecule.to_smiles()}>"
 
 
 class ErrorCancelingReaction:
@@ -133,22 +150,24 @@ def __init__(self, target, species):
         # Perform a consistency check that all species are using the same level of theory
         for spcs in species.keys():
             if spcs.level_of_theory != self.level_of_theory:
-                raise ValueError(f'Species {spcs} has level of theory {spcs.level_of_theory}, which does not match the '
-                                 f'level of theory of the reaction of {self.level_of_theory}')
+                raise ValueError(
+                    f"Species {spcs} has level of theory {spcs.level_of_theory}, which does not match the "
+                    f"level of theory of the reaction of {self.level_of_theory}"
+                )
 
         # Does not include the target, which is handled separately.
         self.species = species
 
     def __repr__(self):
-        reactant_string = f'1*{self.target.molecule.to_smiles()}'
-        product_string = ''
+        reactant_string = f"1*{self.target.molecule.to_smiles()}"
+        product_string = ""
         for spcs, coeff in self.species.items():
             if coeff > 0:
-                product_string += f' + {int(coeff)}*{spcs.molecule.to_smiles()}'
+                product_string += f" + {int(coeff)}*{spcs.molecule.to_smiles()}"
             else:
-                reactant_string += f' + {-1*int(coeff)}*{spcs.molecule.to_smiles()}'
+                reactant_string += f" + {-1*int(coeff)}*{spcs.molecule.to_smiles()}"
 
-        return f'<ErrorCancelingReaction {reactant_string} <=> {product_string[3:]} >'
+        return f"<ErrorCancelingReaction {reactant_string} <=> {product_string[3:]} >"
 
     def calculate_target_thermo(self):
         """
@@ -157,16 +176,25 @@ def calculate_target_thermo(self):
         Returns:
             rmgpy.quantity.ScalarQuantity: Hf298 in 'J/mol' estimated for the target species
         """
-        low_level_h_rxn = sum(spec[0].low_level_hf298.value_si*spec[1] for spec in self.species.items()) - \
-            self.target.low_level_hf298.value_si
-
-        target_thermo = sum(spec[0].high_level_hf298.value_si*spec[1] for spec in self.species.items()) - \
-            low_level_h_rxn
-        return ScalarQuantity(target_thermo, 'J/mol')
+        low_level_h_rxn = (
+            sum(
+                spec[0].low_level_hf298.value_si * spec[1]
+                for spec in self.species.items()
+            )
+            - self.target.low_level_hf298.value_si
+        )
+
+        target_thermo = (
+            sum(
+                spec[0].high_level_hf298.value_si * spec[1]
+                for spec in self.species.items()
+            )
+            - low_level_h_rxn
+        )
+        return ScalarQuantity(target_thermo, "J/mol")
 
 
 class AtomConstraint:
-
     def __init__(self, label, connections=None):
         self.label = label
         self.connections = connections if connections is not None else []
@@ -189,15 +217,16 @@ def __eq__(self, other):
             return False
 
         else:
-            raise NotImplementedError(f'AtomConstraint object has no __eq__ defined for other object of type '
-                                      f'{type(other)}')
+            raise NotImplementedError(
+                f"AtomConstraint object has no __eq__ defined for other object of type "
+                f"{type(other)}"
+            )
 
     def __repr__(self):
-        return f'{self.label}' + ''.join([f'({c})' for c in self.connections])
+        return f"{self.label}" + "".join([f"({c})" for c in self.connections])
 
 
 class BondConstraint:
-
     def __init__(self, atom1, atom2, bond_order):
         self.atom1 = atom1
         self.atom2 = atom2
@@ -206,8 +235,9 @@ def __init__(self, atom1, atom2, bond_order):
     def __eq__(self, other):
         if isinstance(other, BondConstraint):
             if self.bond_order == other.bond_order:
-                if ((self.atom1 == other.atom1 and self.atom2 == other.atom2) or
-                        (self.atom1 == other.atom2 and self.atom2 == other.atom1)):
+                if (self.atom1 == other.atom1 and self.atom2 == other.atom2) or (
+                    self.atom1 == other.atom2 and self.atom2 == other.atom1
+                ):
                     return True
             return False
 
@@ -215,16 +245,17 @@ def __eq__(self, other):
             return False
 
         else:
-            raise NotImplementedError(f'BondConstraint object has no __eq__ defined for other object of type '
-                                      f'{type(other)}')
+            raise NotImplementedError(
+                f"BondConstraint object has no __eq__ defined for other object of type "
+                f"{type(other)}"
+            )
 
     def __repr__(self):
-        symbols = ['', '-', '=', '#']
-        return f'{self.atom1}{symbols[self.bond_order]}{self.atom2}'
+        symbols = ["", "-", "=", "#"]
+        return f"{self.atom1}{symbols[self.bond_order]}{self.atom2}"
 
 
 class Connection:
-
     def __init__(self, atom, bond_order):
         self.atom = atom
         self.bond_order = bond_order
@@ -237,15 +268,16 @@ def __eq__(self, other):
             return False
 
         else:
-            raise NotImplementedError(f'Connection object has no __eq__ defined for other object of type {type(other)}')
+            raise NotImplementedError(
+                f"Connection object has no __eq__ defined for other object of type {type(other)}"
+            )
 
     def __repr__(self):
-        symbols = ['', '-', '=', '#']
-        return f'{symbols[self.bond_order]}{self.atom}'
+        symbols = ["", "-", "=", "#"]
+        return f"{symbols[self.bond_order]}{self.atom}"
 
 
 class GenericConstraint:
-
     def __init__(self, constraint_str: str):
         self.constraint_str = constraint_str
 
@@ -255,11 +287,15 @@ def __eq__(self, other):
         elif isinstance(other, GenericConstraint):
             return self.constraint_str == other.constraint_str
         else:
-            raise NotImplementedError(f'GenericConstraint object has no __eq__ defined for other object of '
-                                      f'type {type(other)}')
+            raise NotImplementedError(
+                f"GenericConstraint object has no __eq__ defined for other object of "
+                f"type {type(other)}"
+            )
 
 
-def bond_centric_constraints(species: ErrorCancelingSpecies, constraint_class: str) -> List[BondConstraint]:
+def bond_centric_constraints(
+    species: ErrorCancelingSpecies, constraint_class: str
+) -> List[BondConstraint]:
     constraints = []
     contraint_func = CONSTRAINT_CLASSES[constraint_class]
     molecule = species.molecule
@@ -281,8 +317,8 @@ def _buerger_rc3(bond: Bond) -> BondConstraint:
     atom1 = bond.atom1
     atom2 = bond.atom2
 
-    atom1 = AtomConstraint(label=f'{atom1.symbol}{atom1.connectivity1}')
-    atom2 = AtomConstraint(label=f'{atom2.symbol}{atom2.connectivity1}')
+    atom1 = AtomConstraint(label=f"{atom1.symbol}{atom1.connectivity1}")
+    atom2 = AtomConstraint(label=f"{atom2.symbol}{atom2.connectivity1}")
 
     return BondConstraint(atom1=atom1, atom2=atom2, bond_order=int(bond.order))
 
@@ -293,10 +329,14 @@ def _buerger_rc4(bond: Bond) -> BondConstraint:
     for atom in [bond.atom1, bond.atom2]:
         connections = []
         for a, b in atom.bonds.items():
-            ac = AtomConstraint(label=f'{a.symbol}{a.connectivity1}')
+            ac = AtomConstraint(label=f"{a.symbol}{a.connectivity1}")
             bond_order = b.order
             connections.append(Connection(atom=ac, bond_order=bond_order))
-        atoms.append(AtomConstraint(label=f'{atom.symbol}{atom.connectivity1}', connections=connections))
+        atoms.append(
+            AtomConstraint(
+                label=f"{atom.symbol}{atom.connectivity1}", connections=connections
+            )
+        )
 
     return BondConstraint(atom1=atoms[0], atom2=atoms[1], bond_order=int(bond.order))
 
@@ -306,8 +346,15 @@ class SpeciesConstraints:
     A class for defining and enumerating constraints to ReferenceSpecies objects for error canceling reactions
     """
 
-    def __init__(self, target, reference_list, isodesmic_class='rc2', conserve_ring_size=True, limit_charges=True,
-                 limit_scope=True):
+    def __init__(
+        self,
+        target,
+        reference_list,
+        isodesmic_class="rc2",
+        conserve_ring_size=True,
+        limit_charges=True,
+        limit_scope=True,
+    ):
         """
         Define the constraints that will be enforced, and determine the mapping of indices in the constraint vector to
         the labels for these constraints.
@@ -348,15 +395,19 @@ def _get_constraint_lists(self):
 
         return full_constraints_list
 
-    def _get_ring_constraints(self, species: ErrorCancelingSpecies) -> List[GenericConstraint]:
+    def _get_ring_constraints(
+        self, species: ErrorCancelingSpecies
+    ) -> List[GenericConstraint]:
         ring_features = []
         rings = species.molecule.get_smallest_set_of_smallest_rings()
         for ring in rings:
-            ring_features.append(GenericConstraint(constraint_str=f'{len(ring)}_ring'))
+            ring_features.append(GenericConstraint(constraint_str=f"{len(ring)}_ring"))
 
         return ring_features
 
-    def _get_all_constraints(self, species: ErrorCancelingSpecies) -> List[Union[BondConstraint, GenericConstraint]]:
+    def _get_all_constraints(
+        self, species: ErrorCancelingSpecies
+    ) -> List[Union[BondConstraint, GenericConstraint]]:
         features = bond_centric_constraints(species, self.isodesmic_class)
         if self.conserve_ring_size:
             features += self._get_ring_constraints(species)
@@ -372,7 +423,9 @@ def _enumerate_constraints(self, full_constraints_list):
 
         # Begin enumerating constraints
         while True:
-            if len(full_constraints_list[0]) == 0:  # We have exhausted target constraints
+            if (
+                len(full_constraints_list[0]) == 0
+            ):  # We have exhausted target constraints
                 if self.limit_scope:  # No need to enumerate any further
                     break  # Out of the while loop
 
@@ -398,13 +451,15 @@ def _enumerate_constraints(self, full_constraints_list):
 
         # Finalize list of reference species and corresponding constraints
         reference_constraints = []
-        target_constraints = enumerated_constraints [0]
+        target_constraints = enumerated_constraints[0]
         if self.limit_scope:
             for i, spcs in enumerate(self.all_reference_species):
                 # Add 1 to index to offset for the target
-                if len(full_constraints_list[i+1]) == 0:  # This species does not have extra constraints
+                if (
+                    len(full_constraints_list[i + 1]) == 0
+                ):  # This species does not have extra constraints
                     self.reference_species.append(spcs)
-                    reference_constraints.append(enumerated_constraints[i+1])
+                    reference_constraints.append(enumerated_constraints[i + 1])
 
         else:
             self.reference_species = self.all_reference_species
@@ -436,7 +491,7 @@ def _enumerate_charge_constraints(self, target_constraints, reference_constraint
             self.reference_species = allowed_reference_species
 
         return target_constraints, reference_constraints
-    
+
     def _enumerate_element_constraints(self, target_constraints, reference_constraints):
         all_elements = set()
         for spc in self.reference_species:
@@ -450,7 +505,9 @@ def _enumerate_element_constraints(self, target_constraints, reference_constrain
 
         for i, spc in enumerate(self.reference_species):
             element_count = spc.molecule.get_element_count()
-            new_constraints = [element_count.get(element, 0) for element in all_elements]
+            new_constraints = [
+                element_count.get(element, 0) for element in all_elements
+            ]
             reference_constraints[i].extend(new_constraints)
 
         return target_constraints, reference_constraints
@@ -465,10 +522,15 @@ def calculate_constraints(self):
             - constraint matrix for allowable reference species (len(self.reference_species) x len(constraints))
         """
         full_constraint_list = self._get_constraint_lists()
-        target_constraints, reference_constraints = self._enumerate_constraints(full_constraint_list)
-        target_constraints, reference_constraints = self._enumerate_charge_constraints(target_constraints,
-                                                                                       reference_constraints)
-        target_constraints, reference_constraints = self._enumerate_element_constraints(target_constraints, reference_constraints)
+        target_constraints, reference_constraints = self._enumerate_constraints(
+            full_constraint_list
+        )
+        target_constraints, reference_constraints = self._enumerate_charge_constraints(
+            target_constraints, reference_constraints
+        )
+        target_constraints, reference_constraints = self._enumerate_element_constraints(
+            target_constraints, reference_constraints
+        )
 
         target_constraints = np.array(target_constraints, dtype=int)
         constraint_matrix = np.array(reference_constraints, dtype=int)
@@ -485,7 +547,9 @@ def _clean_up_constraints(target_constraints, constraint_matrix):
     zero_indices = np.where(~constraint_matrix.any(axis=0))[0]
     # Check that this wouldn't eliminate a non-zero target entry
     for z in zero_indices:
-        if target_constraints[z] != 0:  # This problem is not solvable. Return None to signal this
+        if (
+            target_constraints[z] != 0
+        ):  # This problem is not solvable. Return None to signal this
             return None, None
     indices = [i for i in range(constraint_matrix.shape[1]) if i not in zero_indices]
     constraint_matrix = np.take(constraint_matrix, indices=indices, axis=1)
@@ -499,7 +563,15 @@ class ErrorCancelingScheme:
     A Base class for calculating target species thermochemistry using error canceling reactions
     """
 
-    def __init__(self, target, reference_set, isodesmic_class, conserve_ring_size, limit_charges, limit_scope):
+    def __init__(
+        self,
+        target,
+        reference_set,
+        isodesmic_class,
+        conserve_ring_size,
+        limit_charges,
+        limit_scope,
+    ):
         """
 
         Args:
@@ -511,11 +583,19 @@ def __init__(self, target, reference_set, isodesmic_class, conserve_ring_size, l
         """
 
         self.target = target
-        self.constraints = SpeciesConstraints(target, reference_set, isodesmic_class=isodesmic_class,
-                                              conserve_ring_size=conserve_ring_size, limit_charges=limit_charges,
-                                              limit_scope=limit_scope)
-
-        self.target_constraint, self.constraint_matrix = self.constraints.calculate_constraints()
+        self.constraints = SpeciesConstraints(
+            target,
+            reference_set,
+            isodesmic_class=isodesmic_class,
+            conserve_ring_size=conserve_ring_size,
+            limit_charges=limit_charges,
+            limit_scope=limit_scope,
+        )
+
+        (
+            self.target_constraint,
+            self.constraint_matrix,
+        ) = self.constraints.calculate_constraints()
         self.reference_species = self.constraints.reference_species
 
     def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
@@ -535,32 +615,36 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
             - Indices (of the subset) for the species that participated in the return reaction
         """
         if milp_software is None:
-            milp_software = ['lpsolve']
+            milp_software = ["lpsolve"]
             if pyo is not None:
-                milp_software.append('pyomo')
+                milp_software.append("pyomo")
 
         # Define the constraints based on the provided subset
         c_matrix = np.take(self.constraint_matrix, reference_subset, axis=0)
 
         # Remove unnecessary constraints
-        target_constraint, c_matrix = _clean_up_constraints(self.target_constraint, c_matrix)
+        target_constraint, c_matrix = _clean_up_constraints(
+            self.target_constraint, c_matrix
+        )
         if target_constraint is None or c_matrix is None:  # The problem is not solvable
             return None, None
 
         # Setup MILP problem
         c_matrix = np.tile(c_matrix, (2, 1))
         sum_constraints = np.sum(c_matrix, 1, dtype=int)
-        targets = -1*target_constraint
+        targets = -1 * target_constraint
         m = c_matrix.shape[0]
         n = c_matrix.shape[1]
-        split = int(m/2)
+        split = int(m / 2)
 
         for solver in milp_software:
-            if solver == 'pyomo':
+            if solver == "pyomo":
                 # Check that pyomo is available
                 if pyo is None:
-                    raise ImportError('Cannot import optional package pyomo. Either install this dependency with '
-                                      '`conda install -c conda-forge pyomo glpk` or set milp_software to `lpsolve`')
+                    raise ImportError(
+                        "Cannot import optional package pyomo. Either install this dependency with "
+                        "`conda install -c conda-forge pyomo glpk` or set milp_software to `lpsolve`"
+                    )
 
                 # Diable logging, pyomo outputs too often
                 logging.disable()
@@ -569,26 +653,44 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
                 lp_model = pyo.ConcreteModel()
                 lp_model.i = pyo.RangeSet(0, m - 1)
                 lp_model.j = pyo.RangeSet(0, n - 1)
-                lp_model.r = pyo.RangeSet(0, split-1)  # indices before the split correspond to reactants
-                lp_model.p = pyo.RangeSet(split, m - 1)  # indices after the split correspond to products
-                lp_model.v = pyo.Var(lp_model.i, domain=pyo.NonNegativeIntegers)  # The stoich. coef. we are solving for
-                lp_model.c = pyo.Param(lp_model.i, lp_model.j, initialize=lambda _, i_ind, j_ind: c_matrix[i_ind,
-                                                                                                           j_ind])
-                lp_model.s = pyo.Param(lp_model.i, initialize=lambda _, i_ind: sum_constraints[i_ind])
-                lp_model.t = pyo.Param(lp_model.j, initialize=lambda _, j_ind: targets[j_ind])
+                lp_model.r = pyo.RangeSet(
+                    0, split - 1
+                )  # indices before the split correspond to reactants
+                lp_model.p = pyo.RangeSet(
+                    split, m - 1
+                )  # indices after the split correspond to products
+                lp_model.v = pyo.Var(
+                    lp_model.i, domain=pyo.NonNegativeIntegers
+                )  # The stoich. coef. we are solving for
+                lp_model.c = pyo.Param(
+                    lp_model.i,
+                    lp_model.j,
+                    initialize=lambda _, i_ind, j_ind: c_matrix[i_ind, j_ind],
+                )
+                lp_model.s = pyo.Param(
+                    lp_model.i, initialize=lambda _, i_ind: sum_constraints[i_ind]
+                )
+                lp_model.t = pyo.Param(
+                    lp_model.j, initialize=lambda _, j_ind: targets[j_ind]
+                )
 
                 lp_model.obj = pyo.Objective(rule=_pyo_obj_expression)
-                lp_model.constraints = pyo.Constraint(lp_model.j, rule=_pyo_constraint_rule)
+                lp_model.constraints = pyo.Constraint(
+                    lp_model.j, rule=_pyo_constraint_rule
+                )
 
                 # Solve the MILP problem using the GLPK MILP solver (https://www.gnu.org/software/glpk/)
-                opt = pyo.SolverFactory('glpk')
+                opt = pyo.SolverFactory("glpk")
                 try:
                     results = opt.solve(lp_model, timelimit=10)
                 except ApplicationError:
                     continue
 
                 # Return the solution if a valid reaction is found. Otherwise continue to next solver
-                if results.solver.termination_condition == pyo.TerminationCondition.optimal:
+                if (
+                    results.solver.termination_condition
+                    == pyo.TerminationCondition.optimal
+                ):
                     # Extract the solution and find the species with non-zero stoichiometric coefficients
                     solution = lp_model.v.extract_values().values()
                     break
@@ -596,26 +698,33 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
                 # Re-enable logging
                 logging.disable(logging.NOTSET)
 
-            elif solver == 'lpsolve':
+            elif solver == "lpsolve":
                 # Save the current signal handler
                 sig = signal.getsignal(signal.SIGINT)
 
                 # Setup the MILP problem using lpsolve
-                lp = lpsolve('make_lp', 0, m)
-                lpsolve('set_verbose', lp, 2)  # Reduce the logging from lpsolve
-                lpsolve('set_obj_fn', lp, sum_constraints)
-                lpsolve('set_minim', lp)
+                lp = lpsolve("make_lp", 0, m)
+                lpsolve("set_verbose", lp, 2)  # Reduce the logging from lpsolve
+                lpsolve("set_obj_fn", lp, sum_constraints)
+                lpsolve("set_minim", lp)
 
                 for j in range(n):
-                    lpsolve('add_constraint', lp, np.concatenate((c_matrix[:split, j], -1*c_matrix[split:, j])), EQ,
-                            targets[j])
-
-                lpsolve('set_timeout', lp, 10)  # Move on if lpsolve can't find a solution quickly
+                    lpsolve(
+                        "add_constraint",
+                        lp,
+                        np.concatenate((c_matrix[:split, j], -1 * c_matrix[split:, j])),
+                        EQ,
+                        targets[j],
+                    )
+
+                lpsolve(
+                    "set_timeout", lp, 10
+                )  # Move on if lpsolve can't find a solution quickly
 
                 # All v_i must be integers
-                lpsolve('set_int', lp, [True]*m)
+                lpsolve("set_int", lp, [True] * m)
 
-                status = lpsolve('solve', lp)
+                status = lpsolve("solve", lp)
 
                 # Reset signal handling since lpsolve changed it
                 try:
@@ -626,11 +735,13 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
 
                 # Return the solution if a valid reaction is found. Otherwise continue to next solver
                 if status == 0:
-                    _, solution = lpsolve('get_solution', lp)[:2]
+                    _, solution = lpsolve("get_solution", lp)[:2]
                     break
 
             else:
-                raise ValueError(f'Unrecognized MILP solver {solver} for isodesmic reaction generation')
+                raise ValueError(
+                    f"Unrecognized MILP solver {solver} for isodesmic reaction generation"
+                )
 
         else:
             return None, None
@@ -641,13 +752,19 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
             if v > 0:
                 subset_indices.append(index % split)
                 if index < split:
-                    reaction.species.update({self.reference_species[reference_subset[index]]: -v})
+                    reaction.species.update(
+                        {self.reference_species[reference_subset[index]]: -v}
+                    )
                 else:
-                    reaction.species.update({self.reference_species[reference_subset[index % split]]: v})
+                    reaction.species.update(
+                        {self.reference_species[reference_subset[index % split]]: v}
+                    )
 
         return reaction, np.array(subset_indices)
 
-    def multiple_error_canceling_reaction_search(self, n_reactions_max=20, milp_software=None):
+    def multiple_error_canceling_reaction_search(
+        self, n_reactions_max=20, milp_software=None
+    ):
         """
         Generate multiple error canceling reactions involving the target and a subset of the reference species.
 
@@ -671,7 +788,9 @@ def multiple_error_canceling_reaction_search(self, n_reactions_max=20, milp_soft
             subset = subset_queue.pop()
             if len(subset) == 0:
                 continue
-            reaction, subset_indices = self._find_error_canceling_reaction(subset, milp_software=milp_software)
+            reaction, subset_indices = self._find_error_canceling_reaction(
+                subset, milp_software=milp_software
+            )
             if reaction is None:
                 continue
             else:
@@ -707,7 +826,9 @@ def calculate_target_enthalpy(self, n_reactions_max=5, milp_software=None):
             - Standard heat of formation at 298 K calculated for the target species
             - reaction list containing all error canceling reactions found
         """
-        reaction_list = self.multiple_error_canceling_reaction_search(n_reactions_max, milp_software)
+        reaction_list = self.multiple_error_canceling_reaction_search(
+            n_reactions_max, milp_software
+        )
         if len(reaction_list) == 0:  # No reactions found
             return None, reaction_list
         h298_list = np.zeros(len(reaction_list))
@@ -715,7 +836,7 @@ def calculate_target_enthalpy(self, n_reactions_max=5, milp_software=None):
         for i, rxn in enumerate(reaction_list):
             h298_list[i] = rxn.calculate_target_thermo().value_si
 
-        return ScalarQuantity(np.median(h298_list), 'J/mol'), reaction_list
+        return ScalarQuantity(np.median(h298_list), "J/mol"), reaction_list
 
 
 def _pyo_obj_expression(model):
@@ -723,30 +844,47 @@ def _pyo_obj_expression(model):
 
 
 def _pyo_constraint_rule(model, col):
-    return sum(model.v[row] * model.c[row, col] for row in model.r) - \
-           sum(model.v[row] * model.c[row, col] for row in model.p) == model.t[col]
+    return (
+        sum(model.v[row] * model.c[row, col] for row in model.r)
+        - sum(model.v[row] * model.c[row, col] for row in model.p)
+        == model.t[col]
+    )
 
 
 class IsodesmicScheme(ErrorCancelingScheme):
     """
     An error canceling reaction where the number and type of both atoms and bonds are conserved
     """
+
     def __init__(self, target, reference_set):
-        super().__init__(target, reference_set, isodesmic_class='rc2', conserve_ring_size=False, limit_charges=True,
-                         limit_scope=True)
+        super().__init__(
+            target,
+            reference_set,
+            isodesmic_class="rc2",
+            conserve_ring_size=False,
+            limit_charges=True,
+            limit_scope=True,
+        )
 
 
 class IsodesmicRingScheme(ErrorCancelingScheme):
     """
     A stricter form of the traditional isodesmic reaction scheme where the number of each ring size is also conserved
     """
+
     def __init__(self, target, reference_set):
-        super().__init__(target, reference_set, isodesmic_class='rc2', conserve_ring_size=True, limit_charges=True,
-                         limit_scope=True)
+        super().__init__(
+            target,
+            reference_set,
+            isodesmic_class="rc2",
+            conserve_ring_size=True,
+            limit_charges=True,
+            limit_scope=True,
+        )
 
 
-CONSTRAINT_CLASSES = {'rc2': _buerger_rc2, 'rc3': _buerger_rc3, 'rc4': _buerger_rc4}
+CONSTRAINT_CLASSES = {"rc2": _buerger_rc2, "rc3": _buerger_rc3, "rc4": _buerger_rc4}
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     pass

From 57faf2fef42f4a8c540dc95a647b5eccf1a658c6 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Thu, 25 Jan 2024 10:42:19 -0500
Subject: [PATCH 088/162] Catch TypeError

---
 arkane/encorr/isodesmic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 0415489ee8..ebb4c287ed 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -729,7 +729,7 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
                 # Reset signal handling since lpsolve changed it
                 try:
                     signal.signal(signal.SIGINT, sig)
-                except ValueError:
+                except TypeError:
                     # This is not being run in the main thread, so we cannot reset signal
                     pass
 

From 6938a880c1c868ad71090f2e67c04bd05f0d9ac6 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 30 Jan 2024 15:13:16 -0500
Subject: [PATCH 089/162] WIP

---
 arkane/encorr/isodesmic.py          |  24 +++++-
 test/arkane/encorr/isodesmicTest.py | 116 ++++++++++++++--------------
 2 files changed, 78 insertions(+), 62 deletions(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index ebb4c287ed..1637bb28c1 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -291,6 +291,8 @@ def __eq__(self, other):
                 f"GenericConstraint object has no __eq__ defined for other object of "
                 f"type {type(other)}"
             )
+    def __repr__(self):
+        return self.constraint_str
 
 
 def bond_centric_constraints(
@@ -307,8 +309,14 @@ def bond_centric_constraints(
 
 
 def _buerger_rc2(bond: Bond) -> BondConstraint:
-    atom1 = AtomConstraint(label=bond.atom1.symbol)
-    atom2 = AtomConstraint(label=bond.atom2.symbol)
+    atom1 = bond.atom1
+    atom2 = bond.atom2
+
+    if atom1.symbol > atom2.symbol:
+        atom1, atom2 = atom2, atom1
+
+    atom1 = AtomConstraint(label=atom1.symbol)
+    atom2 = AtomConstraint(label=atom2.symbol)
 
     return BondConstraint(atom1=atom1, atom2=atom2, bond_order=int(bond.order))
 
@@ -317,6 +325,9 @@ def _buerger_rc3(bond: Bond) -> BondConstraint:
     atom1 = bond.atom1
     atom2 = bond.atom2
 
+    if atom1.symbol > atom2.symbol:
+        atom1, atom2 = atom2, atom1
+
     atom1 = AtomConstraint(label=f"{atom1.symbol}{atom1.connectivity1}")
     atom2 = AtomConstraint(label=f"{atom2.symbol}{atom2.connectivity1}")
 
@@ -324,9 +335,15 @@ def _buerger_rc3(bond: Bond) -> BondConstraint:
 
 
 def _buerger_rc4(bond: Bond) -> BondConstraint:
+    atom1 = bond.atom1
+    atom2 = bond.atom2
+
+    if atom1.symbol > atom2.symbol:
+        atom1, atom2 = atom2, atom1
+
     atoms = []
 
-    for atom in [bond.atom1, bond.atom2]:
+    for atom in [atom1, atom2]:
         connections = []
         for a, b in atom.bonds.items():
             ac = AtomConstraint(label=f"{a.symbol}{a.connectivity1}")
@@ -412,6 +429,7 @@ def _get_all_constraints(
         if self.conserve_ring_size:
             features += self._get_ring_constraints(species)
 
+        features.sort(key=lambda x: x.__repr__())
         return features
 
     def _enumerate_constraints(self, full_constraints_list):
diff --git a/test/arkane/encorr/isodesmicTest.py b/test/arkane/encorr/isodesmicTest.py
index 83e36e06de..d0f9c034b6 100644
--- a/test/arkane/encorr/isodesmicTest.py
+++ b/test/arkane/encorr/isodesmicTest.py
@@ -31,7 +31,6 @@
 This script contains unit tests of the :mod:`arkane.isodesmic` module.
 """
 
-
 import numpy as np
 
 from rmgpy.molecule import Molecule
@@ -137,12 +136,11 @@ def test_initializing_constraint_map(self):
         """
         Test that the constraint map is properly initialized when a SpeciesConstraints object is initialized
         """
-        caffeine_consts = SpeciesConstraints(self.caffeine, [self.butane, self.benzene])
-        assert set(caffeine_consts.constraint_map.keys()) == {
-            "H",
-            "C",
-            "O",
-            "N",
+        consts = SpeciesConstraints(self.caffeine, [self.butane, self.benzene])
+        caffeine_features = consts._get_all_constraints(self.caffeine)
+        caffeine_constraint_list = [feat.__repr__() for feat in caffeine_features]
+
+        assert set(caffeine_constraint_list) == {
             "C=O",
             "C-N",
             "C-H",
@@ -154,55 +152,69 @@ def test_initializing_constraint_map(self):
         }
 
         no_rings = SpeciesConstraints(self.caffeine, [self.butane, self.benzene], conserve_ring_size=False)
-        assert set(no_rings.constraint_map.keys()) == {"H", "C", "O", "N", "C=O", "C-N", "C-H", "C=C", "C=N", "C-C"}
-
-        atoms_only = SpeciesConstraints(self.caffeine, [self.butane], conserve_ring_size=False, conserve_bonds=False)
-        assert set(atoms_only.constraint_map.keys()) == {"H", "C", "O", "N"}
+        caffeine_features = no_rings._get_all_constraints(self.caffeine)
+        caffeine_constraint_list = [feat.__repr__() for feat in caffeine_features]
+        assert set(caffeine_constraint_list) == {"C=O", "C-N", "C-H", "C=C", "C=N", "C-C"}
 
     def test_enumerating_constraints(self):
         """
         Test that a SpeciesConstraints object can properly enumerate the constraints of a given ErrorCancelingSpecies
         """
         spcs_consts = SpeciesConstraints(self.benzene, [])
-        assert set(spcs_consts.constraint_map.keys()) == {"C", "H", "C=C", "C-C", "C-H", "6_ring"}
-
-        # Now that we have confirmed that the correct keys are present, overwrite the constraint map to set the order
-        spcs_consts.constraint_map = {
-            "H": 0,
-            "C": 1,
-            "C=C": 2,
-            "C-C": 3,
-            "C-H": 4,
-            "6_ring": 5,
-        }
+        benzene_features = spcs_consts._get_all_constraints(self.benzene)
+        benzene_constraint_list = [feat.__repr__() for feat in benzene_features]
+        assert set(benzene_constraint_list) == {"C=C", "C-C", "C-H", "6_ring"}
+
+        target_constraints, _ = spcs_consts._enumerate_constraints([benzene_features])
+        benzene_constraints = target_constraints
 
         assert np.array_equal(
-            spcs_consts._enumerate_constraints(self.propene),
-            np.array([6, 3, 1, 1, 6, 0]),
+            benzene_constraints,
+            np.array([1, 3, 6, 3]),
         )
+
+        spcs_consts.all_reference_species = [self.propene]
+        propene_features = spcs_consts._get_all_constraints(self.propene)
+        _, reference_constraints = spcs_consts._enumerate_constraints([benzene_features, propene_features])
+        propene_constraints = reference_constraints[0]
         assert np.array_equal(
-            spcs_consts._enumerate_constraints(self.butane),
-            np.array([10, 4, 0, 3, 10, 0]),
+            propene_constraints,
+            np.array([0, 1, 6, 1]),
         )
+
+        spcs_consts.all_reference_species = [self.butane]
+        butane_features = spcs_consts._get_all_constraints(self.butane)
+        _, reference_constraints = spcs_consts._enumerate_constraints([benzene_features, butane_features])
+        butane_constraints = reference_constraints[0]
         assert np.array_equal(
-            spcs_consts._enumerate_constraints(self.benzene),
-            np.array([6, 6, 3, 3, 6, 1]),
+            butane_constraints,
+            np.array([0, 3, 10, 0]),
         )
 
-        # Caffeine and ethyne should return None since they have features not found in benzene
-        assert spcs_consts._enumerate_constraints(self.caffeine) is None
-        assert spcs_consts._enumerate_constraints(self.ethyne) is None
+        # Caffeine and ethyne should return empty list since they have features not found in benzene
+        spcs_consts.all_reference_species = [self.caffeine]
+        caffeine_features = spcs_consts._get_all_constraints(self.caffeine)
+        _, reference_constraints = spcs_consts._enumerate_constraints([benzene_features, caffeine_features])
+        assert len(reference_constraints) == 0
+
+        spcs_consts.all_reference_species = [self.ethyne]
+        ethyne_features = spcs_consts._get_all_constraints(self.ethyne)
+        _, reference_constraints = spcs_consts._enumerate_constraints([benzene_features, ethyne_features])
+        assert len(reference_constraints) == 0
 
     def test_calculating_constraints(self):
         """
         Test that a SpeciesConstraints object can properly return the target constraint vector and the constraint matrix
         """
         spcs_consts = SpeciesConstraints(self.caffeine, [self.propene, self.butane, self.benzene, self.ethyne])
-        assert set(spcs_consts.constraint_map.keys()) == {
-            "H",
-            "C",
-            "O",
-            "N",
+        caffeine_features = spcs_consts._get_all_constraints(self.caffeine)
+        propene_features = spcs_consts._get_all_constraints(self.propene)
+        butane_features = spcs_consts._get_all_constraints(self.butane)
+        benzene_features = spcs_consts._get_all_constraints(self.benzene)
+        ethyne_features = spcs_consts._get_all_constraints(self.ethyne)
+
+        caffeine_feature_list = [feat.__repr__() for feat in caffeine_features]
+        assert set(caffeine_feature_list) == {
             "C=O",
             "C-N",
             "C-H",
@@ -213,36 +225,20 @@ def test_calculating_constraints(self):
             "6_ring",
         }
 
-        # Now that we have confirmed that the correct keys are present, overwrite the constraint map to set the order
-        spcs_consts.constraint_map = {
-            "H": 0,
-            "C": 1,
-            "O": 2,
-            "N": 3,
-            "C=O": 4,
-            "C-N": 5,
-            "C-H": 6,
-            "C=C": 7,
-            "C=N": 8,
-            "C-C": 9,
-            "5_ring": 10,
-            "6_ring": 11,
-        }
-
         target_consts, consts_matrix = spcs_consts.calculate_constraints()
 
         # First, test that ethyne is not included in the reference set
         assert spcs_consts.reference_species == [self.propene, self.butane, self.benzene]
 
         # Then, test the output of the calculation
-        assert np.array_equal(target_consts, np.array([10, 8, 2, 4, 2, 10, 10, 1, 1, 1, 1, 1]))
+        assert np.array_equal(target_consts, np.array([ 1,  1,  1, 10, 10,  1,  1,  2,  0,  8, 10,  4,  2]))
         assert np.array_equal(
             consts_matrix,
             np.array(
                 [
-                    [6, 3, 0, 0, 0, 0, 6, 1, 0, 1, 0, 0],
-                    [10, 4, 0, 0, 0, 0, 10, 0, 0, 3, 0, 0],
-                    [6, 6, 0, 0, 0, 0, 6, 3, 0, 3, 0, 1],
+                    [ 0,  0,  1,  6,  0,  1,  0,  0,  0,  3,  6,  0,  0],
+                    [ 0,  0,  3, 10,  0,  0,  0,  0,  0,  4, 10,  0,  0],
+                    [ 0,  1,  3,  6,  0,  3,  0,  0,  0,  6,  6,  0,  0],
                 ]
             ),
         )
@@ -278,6 +274,8 @@ def test_creating_error_canceling_schemes(self):
         scheme = ErrorCancelingScheme(
             self.propene,
             [self.butane, self.benzene, self.caffeine, self.ethyne],
+            "rc2",
+            True,
             True,
             True,
         )
@@ -328,7 +326,7 @@ def test_multiple_error_canceling_reactions(self):
         )
 
         reaction_list = scheme.multiple_error_canceling_reaction_search(n_reactions_max=20)
-        assert len(reaction_list) == 20
+        assert len(reaction_list) == 6
         reaction_string = reaction_list.__repr__()
         # Consider both permutations of the products in the reaction string
         rxn_str1 = "<ErrorCancelingReaction 1*C=CC + 1*CCCC <=> 1*CCC + 1*C=CCC >"
@@ -361,9 +359,9 @@ def test_calculate_target_enthalpy(self):
         )
 
         target_thermo, rxn_list = scheme.calculate_target_enthalpy(n_reactions_max=3, milp_software=["lpsolve"])
-        assert target_thermo.value_si == 115000.0
+        assert target_thermo.value_si == 110000.0
         assert isinstance(rxn_list[0], ErrorCancelingReaction)
 
         if self.pyo is not None:
             target_thermo, _ = scheme.calculate_target_enthalpy(n_reactions_max=3, milp_software=["pyomo"])
-            assert target_thermo.value_si == 115000.0
+            assert target_thermo.value_si == 110000.0

From bd7f2b55d92d8ea355f8746c5616e2b61d57fd37 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Mon, 10 Jun 2024 21:44:48 -0400
Subject: [PATCH 090/162] Modify based on review comment

---
 arkane/encorr/isodesmic.py | 35 ++++++++++++++++++++---------------
 1 file changed, 20 insertions(+), 15 deletions(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 1637bb28c1..44756e8cac 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -178,16 +178,16 @@ def calculate_target_thermo(self):
         """
         low_level_h_rxn = (
             sum(
-                spec[0].low_level_hf298.value_si * spec[1]
-                for spec in self.species.items()
+                spec.low_level_hf298.value_si * coeff
+                for spec, coeff in self.species.items()
             )
             - self.target.low_level_hf298.value_si
         )
 
         target_thermo = (
             sum(
-                spec[0].high_level_hf298.value_si * spec[1]
-                for spec in self.species.items()
+                spec.high_level_hf298.value_si * coeff
+                for spec, coeff in self.species.items()
             )
             - low_level_h_rxn
         )
@@ -202,17 +202,7 @@ def __init__(self, label, connections=None):
     def __eq__(self, other):
         if isinstance(other, AtomConstraint):
             if self.label == other.label:
-                if len(self.connections) == len(other.connections):
-                    connections = deepcopy(other.connections)
-                    for c in self.connections:
-                        for i, c_other in enumerate(connections):
-                            if c == c_other:
-                                break
-                        else:
-                            return False
-                        connections.pop(i)
-
-                    return True
+                return self.match_connections(other)
 
             return False
 
@@ -221,6 +211,21 @@ def __eq__(self, other):
                 f"AtomConstraint object has no __eq__ defined for other object of type "
                 f"{type(other)}"
             )
+        
+    def match_connections(self, other):
+        if len(self.connections) != len(other.connections):
+            return False
+
+        connections = deepcopy(other.connections)
+        for c in self.connections:
+            for i, c_other in enumerate(connections):
+                if c == c_other:
+                    break
+            else:
+                return False
+            connections.pop(i)
+
+        return True
 
     def __repr__(self):
         return f"{self.label}" + "".join([f"({c})" for c in self.connections])

From bbc003077b705919a6ca40ee3dfa71c7d4a85cb3 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 11 Jun 2024 09:51:49 -0400
Subject: [PATCH 091/162] Better way to initialize empty list

---
 arkane/encorr/isodesmic.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 44756e8cac..796f0b547d 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -438,11 +438,9 @@ def _get_all_constraints(
         return features
 
     def _enumerate_constraints(self, full_constraints_list):
-        enumerated_constraints = []
 
         # Initialize list of empty lists. Be careful to avoid making references to a singular empty list
-        for _ in range(len(full_constraints_list)):
-            enumerated_constraints.append([])
+        enumerated_constraints = [[] for _ in range(len(full_constraints_list))]
 
         # Begin enumerating constraints
         while True:

From 7fa4cf19a9e38a650b3c037b79d6cb8b8063a403 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 11 Jun 2024 10:56:47 -0400
Subject: [PATCH 092/162] Improve code readability to get enumerated
 constraints

---
 arkane/encorr/isodesmic.py | 82 +++++++++++++++++++-------------------
 1 file changed, 41 insertions(+), 41 deletions(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 796f0b547d..62cda34b1c 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -438,55 +438,55 @@ def _get_all_constraints(
         return features
 
     def _enumerate_constraints(self, full_constraints_list):
+        """
+        Return the target constraint counts and the reference constraint counts.
+        """
 
-        # Initialize list of empty lists. Be careful to avoid making references to a singular empty list
-        enumerated_constraints = [[] for _ in range(len(full_constraints_list))]
-
-        # Begin enumerating constraints
-        while True:
-            if (
-                len(full_constraints_list[0]) == 0
-            ):  # We have exhausted target constraints
-                if self.limit_scope:  # No need to enumerate any further
-                    break  # Out of the while loop
+        target_constraints = full_constraints_list[0]
+        reference_constraintss = full_constraints_list[1:]
 
-            # Find a constraint to search for next
-            for spcs_constraints in full_constraints_list:
-                if len(spcs_constraints) != 0:
-                    constraint = spcs_constraints[0]
-                    break  # Out of the for loop
+        # Enumerate through the constraints of reference species and keep only those that are present in the target
+        enumerated_reference_constraintss = []
 
-            else:
-                break  # No more constraints, so break out of the while loop
-
-            # enumerate for each species
-            new_constraints_list = []
-            for i, spcs_constraints in enumerate(full_constraints_list):
-                new_spcs_constraints = [c for c in spcs_constraints if c != constraint]
-                matching_constraints = len(spcs_constraints) - len(new_spcs_constraints)
-                enumerated_constraints[i].append(matching_constraints)
-                new_constraints_list.append(new_spcs_constraints)
-
-            # Finally, update the new list
-            full_constraints_list = new_constraints_list
-
-        # Finalize list of reference species and corresponding constraints
-        reference_constraints = []
-        target_constraints = enumerated_constraints[0]
         if self.limit_scope:
-            for i, spcs in enumerate(self.all_reference_species):
-                # Add 1 to index to offset for the target
-                if (
-                    len(full_constraints_list[i + 1]) == 0
-                ):  # This species does not have extra constraints
-                    self.reference_species.append(spcs)
-                    reference_constraints.append(enumerated_constraints[i + 1])
+
+            for i, ref_spc in enumerate(self.all_reference_species):
+
+                if not all(constraint in target_constraints for constraint in reference_constraintss[i]):
+                    continue
+
+                self.reference_species.append(ref_spc)
+                enumerated_reference_constraintss.append(reference_constraintss[i])
 
         else:
             self.reference_species = self.all_reference_species
-            reference_constraints = enumerated_constraints[1:]
+            enumerated_reference_constraintss = reference_constraintss
+        
+        # Get a list of the unique constraints sorted by their string representation
+        if self.limit_scope:
 
-        return target_constraints, reference_constraints
+            # The scope of constraints to consider is the target constraints
+            unique_constraints = self._get_unique_constraints(target_constraints)
+            unique_constraints.sort(key=lambda x: x.__repr__())
+
+        else:
+            all_constraints = target_constraints + [constraint for constraints in enumerated_reference_constraintss for constraint in constraints]
+            unique_constraints = self._get_unique_constraints(all_constraints)
+            unique_constraints.sort(key=lambda x: x.__repr__())
+        
+        # Get the counts of each unique constraint in the target and reference constraints
+        target_constraint_counts = [target_constraints.count(c) for c in unique_constraints]
+        reference_constraint_counts = []
+
+        for i, ref_constraints in enumerate(enumerated_reference_constraintss):
+            reference_constraint_counts.append([ref_constraints.count(c) for c in unique_constraints])
+
+        return target_constraint_counts, reference_constraint_counts
+    
+    def _get_unique_constraints(self, constraints):
+        # Constraints are unhashable, so we need to use some workaround to get unique constraints
+        constraint_dict = {constraint.__repr__(): constraint for constraint in constraints}
+        return list(constraint_dict.values())
 
     def _enumerate_charge_constraints(self, target_constraints, reference_constraints):
         charge = self.target.molecule.get_net_charge()

From b28281dd14a873fa4659e7d065af661a48cd1d9e Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 11 Jun 2024 11:20:33 -0400
Subject: [PATCH 093/162] Constraint cation/anion/neutral target to
 cation/anion/neutral reference species

---
 arkane/encorr/isodesmic.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 62cda34b1c..bdd6abdfa0 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -501,8 +501,10 @@ def _enumerate_charge_constraints(self, target_constraints, reference_constraint
 
             if charge < 0:
                 allowable_charges = list(range(charge, 0))
+            elif charge > 0:
+                allowable_charges = list(range(1, charge + 1))
             else:
-                allowable_charges = list(range(0, charge + 1))
+                allowable_charges = [0]
             for i, spcs in enumerate(self.reference_species):
                 if reference_constraints[i][-1] in allowable_charges:
                     allowed_reference_species.append(spcs)

From 3544b2fdc143535b42c4a3584ce3f2741effcde9 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 11 Jun 2024 11:24:01 -0400
Subject: [PATCH 094/162] Add warning for easy debugging

---
 arkane/encorr/isodesmic.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index bdd6abdfa0..16268de92f 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -519,6 +519,15 @@ def _enumerate_element_constraints(self, target_constraints, reference_constrain
         all_elements = set()
         for spc in self.reference_species:
             all_elements.update(spc.molecule.get_element_count().keys())
+
+        # Check that the target and reference species have the same elements to be able to satisfy mass conservation
+        if set(self.target.molecule.get_element_count().keys()) != all_elements:
+            logging.warning(
+                f"Target species and reference species do not have the same elements:",
+                f"Target: {self.target.molecule.get_element_count().keys()}",
+                f"Reference: {all_elements}",
+            )
+
         all_elements.update(self.target.molecule.get_element_count().keys())
         all_elements = sorted(list(all_elements))
 

From 24bf4e52409ff581bca6954c1861eed3d51c318e Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 11 Jun 2024 11:51:34 -0400
Subject: [PATCH 095/162] Switch to use scipy

---
 arkane/encorr/isodesmic.py | 133 ++++---------------------------------
 1 file changed, 13 insertions(+), 120 deletions(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 16268de92f..56e804146d 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -47,19 +47,12 @@
 from typing import List, Union
 
 import numpy as np
-from lpsolve55 import EQ, LE, lpsolve
-from pyutilib.common import ApplicationError
+from scipy.optimize import Bounds, LinearConstraint, milp
 
 from arkane.modelchem import LOT
 from rmgpy.molecule import Bond, Molecule
 from rmgpy.quantity import ScalarQuantity
 
-# Optional Imports
-try:
-    import pyomo.environ as pyo
-except ImportError:
-    pyo = None
-
 
 class ErrorCancelingSpecies:
     """Class for target and known (reference) species participating in an error canceling reaction"""
@@ -630,7 +623,7 @@ def __init__(
         ) = self.constraints.calculate_constraints()
         self.reference_species = self.constraints.reference_species
 
-    def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
+    def _find_error_canceling_reaction(self, reference_subset):
         """
         Automatically find a valid error canceling reaction given a subset of the available benchmark species. This
         is done by solving a mixed integer linear programming (MILP) problem similiar to
@@ -638,18 +631,12 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
 
         Args:
             reference_subset (list): A list of indices from self.reference_species that can participate in the reaction
-            milp_software (list, optional): Solvers to try in order. Defaults to ['lpsolve'] or if pyomo is available
-                defaults to ['lpsolve', 'pyomo']. lpsolve is usually faster.
 
         Returns:
             tuple(ErrorCancelingReaction, np.ndarray)
             - Reaction with the target species (if a valid reaction is found, else ``None``)
             - Indices (of the subset) for the species that participated in the return reaction
         """
-        if milp_software is None:
-            milp_software = ["lpsolve"]
-            if pyo is not None:
-                milp_software.append("pyomo")
 
         # Define the constraints based on the provided subset
         c_matrix = np.take(self.constraint_matrix, reference_subset, axis=0)
@@ -669,114 +656,20 @@ def _find_error_canceling_reaction(self, reference_subset, milp_software=None):
         n = c_matrix.shape[1]
         split = int(m / 2)
 
-        for solver in milp_software:
-            if solver == "pyomo":
-                # Check that pyomo is available
-                if pyo is None:
-                    raise ImportError(
-                        "Cannot import optional package pyomo. Either install this dependency with "
-                        "`conda install -c conda-forge pyomo glpk` or set milp_software to `lpsolve`"
-                    )
-
-                # Diable logging, pyomo outputs too often
-                logging.disable()
-
-                # Setup the MILP problem using pyomo
-                lp_model = pyo.ConcreteModel()
-                lp_model.i = pyo.RangeSet(0, m - 1)
-                lp_model.j = pyo.RangeSet(0, n - 1)
-                lp_model.r = pyo.RangeSet(
-                    0, split - 1
-                )  # indices before the split correspond to reactants
-                lp_model.p = pyo.RangeSet(
-                    split, m - 1
-                )  # indices after the split correspond to products
-                lp_model.v = pyo.Var(
-                    lp_model.i, domain=pyo.NonNegativeIntegers
-                )  # The stoich. coef. we are solving for
-                lp_model.c = pyo.Param(
-                    lp_model.i,
-                    lp_model.j,
-                    initialize=lambda _, i_ind, j_ind: c_matrix[i_ind, j_ind],
-                )
-                lp_model.s = pyo.Param(
-                    lp_model.i, initialize=lambda _, i_ind: sum_constraints[i_ind]
-                )
-                lp_model.t = pyo.Param(
-                    lp_model.j, initialize=lambda _, j_ind: targets[j_ind]
-                )
-
-                lp_model.obj = pyo.Objective(rule=_pyo_obj_expression)
-                lp_model.constraints = pyo.Constraint(
-                    lp_model.j, rule=_pyo_constraint_rule
-                )
-
-                # Solve the MILP problem using the GLPK MILP solver (https://www.gnu.org/software/glpk/)
-                opt = pyo.SolverFactory("glpk")
-                try:
-                    results = opt.solve(lp_model, timelimit=10)
-                except ApplicationError:
-                    continue
-
-                # Return the solution if a valid reaction is found. Otherwise continue to next solver
-                if (
-                    results.solver.termination_condition
-                    == pyo.TerminationCondition.optimal
-                ):
-                    # Extract the solution and find the species with non-zero stoichiometric coefficients
-                    solution = lp_model.v.extract_values().values()
-                    break
+        constraints = [LinearConstraint(A=np.concatenate((c_matrix[:split, j], -1 * c_matrix[split:, j]), lb=targets[j], ub=targets[j])) for j in n]
 
-                # Re-enable logging
-                logging.disable(logging.NOTSET)
-
-            elif solver == "lpsolve":
-                # Save the current signal handler
-                sig = signal.getsignal(signal.SIGINT)
-
-                # Setup the MILP problem using lpsolve
-                lp = lpsolve("make_lp", 0, m)
-                lpsolve("set_verbose", lp, 2)  # Reduce the logging from lpsolve
-                lpsolve("set_obj_fn", lp, sum_constraints)
-                lpsolve("set_minim", lp)
-
-                for j in range(n):
-                    lpsolve(
-                        "add_constraint",
-                        lp,
-                        np.concatenate((c_matrix[:split, j], -1 * c_matrix[split:, j])),
-                        EQ,
-                        targets[j],
-                    )
-
-                lpsolve(
-                    "set_timeout", lp, 10
-                )  # Move on if lpsolve can't find a solution quickly
-
-                # All v_i must be integers
-                lpsolve("set_int", lp, [True] * m)
-
-                status = lpsolve("solve", lp)
-
-                # Reset signal handling since lpsolve changed it
-                try:
-                    signal.signal(signal.SIGINT, sig)
-                except TypeError:
-                    # This is not being run in the main thread, so we cannot reset signal
-                    pass
-
-                # Return the solution if a valid reaction is found. Otherwise continue to next solver
-                if status == 0:
-                    _, solution = lpsolve("get_solution", lp)[:2]
-                    break
-
-            else:
-                raise ValueError(
-                    f"Unrecognized MILP solver {solver} for isodesmic reaction generation"
-                )
+        result = milp(
+            c_matrix,
+            integrality=1,
+            constraints=constraints,
+            options={"time_limit": 10},
+        )
 
-        else:
+        if result.status != 0:
+            logging.warning("Optimization could not find a valid solution.")
             return None, None
+        
+        solution = result.x
 
         reaction = ErrorCancelingReaction(self.target, dict())
         subset_indices = []

From 59e0cf1edb931b14427666a8fd919d9ce811e4cf Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 11 Jun 2024 13:05:58 -0400
Subject: [PATCH 096/162] Remove unused imports and correct obj fnc

---
 arkane/encorr/isodesmic.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 56e804146d..86ecf2d0cf 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -47,7 +47,7 @@
 from typing import List, Union
 
 import numpy as np
-from scipy.optimize import Bounds, LinearConstraint, milp
+from scipy.optimize import LinearConstraint, milp
 
 from arkane.modelchem import LOT
 from rmgpy.molecule import Bond, Molecule
@@ -659,7 +659,7 @@ def _find_error_canceling_reaction(self, reference_subset):
         constraints = [LinearConstraint(A=np.concatenate((c_matrix[:split, j], -1 * c_matrix[split:, j]), lb=targets[j], ub=targets[j])) for j in n]
 
         result = milp(
-            c_matrix,
+            sum_constraints,
             integrality=1,
             constraints=constraints,
             options={"time_limit": 10},

From fd96df65aab76052dc6b3e4a8c44676b42e4734f Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 11 Jun 2024 13:51:15 -0400
Subject: [PATCH 097/162] Remove unused package, add version constraint to
 scipy

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index bd6212de77..5f6ab8bb38 100644
--- a/environment.yml
+++ b/environment.yml
@@ -58,7 +58,7 @@ dependencies:
   - coverage
   - cython >=0.25.2
   - scikit-learn
-  - scipy
+  - scipy >=1.9
   - numpy >=1.10.0
   - pydot
   - jinja2

From e75c15e7708ad904940d56e81427ab3ab495c174 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 11 Jun 2024 13:51:36 -0400
Subject: [PATCH 098/162] Remove options of solver

---
 arkane/encorr/isodesmic.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 86ecf2d0cf..b77020367b 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -688,7 +688,7 @@ def _find_error_canceling_reaction(self, reference_subset):
         return reaction, np.array(subset_indices)
 
     def multiple_error_canceling_reaction_search(
-        self, n_reactions_max=20, milp_software=None
+        self, n_reactions_max=20,
     ):
         """
         Generate multiple error canceling reactions involving the target and a subset of the reference species.
@@ -700,8 +700,6 @@ def multiple_error_canceling_reaction_search(
         Args:
             n_reactions_max (int, optional): The maximum number of found reactions that will be returned, after which no
                 further searching will occur even if there are possible subsets left in the queue.
-            milp_software (list, optional): Solvers to try in order. Defaults to ['lpsolve'] or if pyomo is available
-                defaults to ['lpsolve', 'pyomo']. lpsolve is usually faster.
 
         Returns:
             list: A list of the found error canceling reactions
@@ -714,7 +712,7 @@ def multiple_error_canceling_reaction_search(
             if len(subset) == 0:
                 continue
             reaction, subset_indices = self._find_error_canceling_reaction(
-                subset, milp_software=milp_software
+                subset
             )
             if reaction is None:
                 continue

From 46e930faa65aabe817bfba4f1417dcdebb9d68f5 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 11 Jun 2024 14:03:24 -0400
Subject: [PATCH 099/162] Add comment to make test more readable

---
 test/arkane/encorr/isodesmicTest.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/arkane/encorr/isodesmicTest.py b/test/arkane/encorr/isodesmicTest.py
index d0f9c034b6..6a44124463 100644
--- a/test/arkane/encorr/isodesmicTest.py
+++ b/test/arkane/encorr/isodesmicTest.py
@@ -170,7 +170,7 @@ def test_enumerating_constraints(self):
 
         assert np.array_equal(
             benzene_constraints,
-            np.array([1, 3, 6, 3]),
+            np.array([1, 3, 6, 3]), # 6_ring, C-C, C-H, C=C
         )
 
         spcs_consts.all_reference_species = [self.propene]
@@ -179,7 +179,7 @@ def test_enumerating_constraints(self):
         propene_constraints = reference_constraints[0]
         assert np.array_equal(
             propene_constraints,
-            np.array([0, 1, 6, 1]),
+            np.array([0, 1, 6, 1]), # 6_ring, C-C, C-H, C=C
         )
 
         spcs_consts.all_reference_species = [self.butane]
@@ -188,7 +188,7 @@ def test_enumerating_constraints(self):
         butane_constraints = reference_constraints[0]
         assert np.array_equal(
             butane_constraints,
-            np.array([0, 3, 10, 0]),
+            np.array([0, 3, 10, 0]), # 6_ring, C-C, C-H, C=C
         )
 
         # Caffeine and ethyne should return empty list since they have features not found in benzene

From a61e34bd4984fd5f2b5171e51000ba7081744af4 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 11 Jun 2024 14:32:40 -0400
Subject: [PATCH 100/162] Use keyword variable

---
 test/arkane/encorr/isodesmicTest.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/test/arkane/encorr/isodesmicTest.py b/test/arkane/encorr/isodesmicTest.py
index 6a44124463..2dd8a47896 100644
--- a/test/arkane/encorr/isodesmicTest.py
+++ b/test/arkane/encorr/isodesmicTest.py
@@ -272,12 +272,12 @@ def setup_class(cls):
 
     def test_creating_error_canceling_schemes(self):
         scheme = ErrorCancelingScheme(
-            self.propene,
-            [self.butane, self.benzene, self.caffeine, self.ethyne],
-            "rc2",
-            True,
-            True,
-            True,
+            target=self.propene,
+            reference_set=[self.butane, self.benzene, self.caffeine, self.ethyne],
+            isodesmic_class="rc2",
+            conserve_ring_size=True,
+            limit_charges=True,
+            limit_scope=True,
         )
 
         assert scheme.reference_species == [self.butane]

From 05a7d49834a64f3e1a1e9017d64783c0cd25efdd Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 11 Jun 2024 14:34:41 -0400
Subject: [PATCH 101/162] Add comment

---
 test/arkane/encorr/isodesmicTest.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/test/arkane/encorr/isodesmicTest.py b/test/arkane/encorr/isodesmicTest.py
index 2dd8a47896..5b4b916281 100644
--- a/test/arkane/encorr/isodesmicTest.py
+++ b/test/arkane/encorr/isodesmicTest.py
@@ -231,14 +231,14 @@ def test_calculating_constraints(self):
         assert spcs_consts.reference_species == [self.propene, self.butane, self.benzene]
 
         # Then, test the output of the calculation
-        assert np.array_equal(target_consts, np.array([ 1,  1,  1, 10, 10,  1,  1,  2,  0,  8, 10,  4,  2]))
+        assert np.array_equal(target_consts, np.array([ 1,  1,  1, 10, 10,  1,  1,  2,  0,  8, 10,  4,  2])) # ['5_ring', '6_ring', 'C-C', 'C-H', 'C-N', 'C=C', 'C=N', 'C=O']
         assert np.array_equal(
             consts_matrix,
             np.array(
                 [
-                    [ 0,  0,  1,  6,  0,  1,  0,  0,  0,  3,  6,  0,  0],
-                    [ 0,  0,  3, 10,  0,  0,  0,  0,  0,  4, 10,  0,  0],
-                    [ 0,  1,  3,  6,  0,  3,  0,  0,  0,  6,  6,  0,  0],
+                    [ 0,  0,  1,  6,  0,  1,  0,  0,  0,  3,  6,  0,  0],  # ['5_ring', '6_ring', 'C-C', 'C-H', 'C-N', 'C=C', 'C=N', 'C=O']
+                    [ 0,  0,  3, 10,  0,  0,  0,  0,  0,  4, 10,  0,  0],  # ['5_ring', '6_ring', 'C-C', 'C-H', 'C-N', 'C=C', 'C=N', 'C=O']
+                    [ 0,  1,  3,  6,  0,  3,  0,  0,  0,  6,  6,  0,  0],  # ['5_ring', '6_ring', 'C-C', 'C-H', 'C-N', 'C=C', 'C=N', 'C=O']
                 ]
             ),
         )

From e3cc59ef7add75e965e46f8564a92c7314bd9e1d Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <hwpang@mit.edu>
Date: Tue, 11 Jun 2024 14:35:22 -0400
Subject: [PATCH 102/162] Add comment to test

---
 test/arkane/encorr/isodesmicTest.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/arkane/encorr/isodesmicTest.py b/test/arkane/encorr/isodesmicTest.py
index 5b4b916281..8b41066b3d 100644
--- a/test/arkane/encorr/isodesmicTest.py
+++ b/test/arkane/encorr/isodesmicTest.py
@@ -170,7 +170,7 @@ def test_enumerating_constraints(self):
 
         assert np.array_equal(
             benzene_constraints,
-            np.array([1, 3, 6, 3]), # 6_ring, C-C, C-H, C=C
+            np.array([1, 3, 6, 3]), # ['6_ring', 'C-C', 'C-H', 'C=C']
         )
 
         spcs_consts.all_reference_species = [self.propene]
@@ -179,7 +179,7 @@ def test_enumerating_constraints(self):
         propene_constraints = reference_constraints[0]
         assert np.array_equal(
             propene_constraints,
-            np.array([0, 1, 6, 1]), # 6_ring, C-C, C-H, C=C
+            np.array([0, 1, 6, 1]), # ['6_ring', 'C-C', 'C-H', 'C=C']
         )
 
         spcs_consts.all_reference_species = [self.butane]
@@ -188,7 +188,7 @@ def test_enumerating_constraints(self):
         butane_constraints = reference_constraints[0]
         assert np.array_equal(
             butane_constraints,
-            np.array([0, 3, 10, 0]), # 6_ring, C-C, C-H, C=C
+            np.array([0, 3, 10, 0]), # ['6_ring', 'C-C', 'C-H', 'C=C']
         )
 
         # Caffeine and ethyne should return empty list since they have features not found in benzene

From bb4441409cb86997a543d9f557c91ff8bcde5111 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 24 Jul 2024 14:27:28 -0400
Subject: [PATCH 103/162] remove lpsolve55 from environments, tests, functions,
 docstrings, & docs

---
 .conda/meta.yaml                              |  2 -
 arkane/encorr/isodesmic.py                    |  8 +--
 .../users/rmg/installation/dependencies.rst   |  1 -
 environment.yml                               |  1 -
 test/arkane/encorr/isodesmicTest.py           | 51 ++++++-------------
 utilities.py                                  | 18 -------
 6 files changed, 18 insertions(+), 63 deletions(-)

diff --git a/.conda/meta.yaml b/.conda/meta.yaml
index 7cd02969fe..e781b46049 100644
--- a/.conda/meta.yaml
+++ b/.conda/meta.yaml
@@ -14,7 +14,6 @@ requirements:
     - {{ compiler('c') }} # [unix]
   host:
     - cython >=0.25.2
-    - lpsolve55
     - numpy
     - openbabel >=3
     - pydas >=1.0.2
@@ -39,7 +38,6 @@ requirements:
     - h5py
     - jinja2
     - jupyter
-    - lpsolve55
     - markupsafe
     - matplotlib >=1.5
     - mopac
diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index b77020367b..52b718568f 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -733,7 +733,7 @@ def multiple_error_canceling_reaction_search(
 
         return reaction_list
 
-    def calculate_target_enthalpy(self, n_reactions_max=5, milp_software=None):
+    def calculate_target_enthalpy(self, n_reactions_max=5):
         """
         Perform a multiple error canceling reactions search and calculate hf298 for the target species by taking the
         median hf298 value from among the error canceling reactions found
@@ -741,17 +741,13 @@ def calculate_target_enthalpy(self, n_reactions_max=5, milp_software=None):
         Args:
             n_reactions_max (int, optional): The maximum number of found reactions that will returned, after which no
                 further searching will occur even if there are possible subsets left in the queue.
-            milp_software (list, optional): Solvers to try in order. Defaults to ['lpsolve'] or if pyomo is available
-                defaults to ['lpsolve', 'pyomo']. lpsolve is usually faster.
 
         Returns:
             tuple(ScalarQuantity, list)
             - Standard heat of formation at 298 K calculated for the target species
             - reaction list containing all error canceling reactions found
         """
-        reaction_list = self.multiple_error_canceling_reaction_search(
-            n_reactions_max, milp_software
-        )
+        reaction_list = self.multiple_error_canceling_reaction_search(n_reactions_max)
         if len(reaction_list) == 0:  # No reactions found
             return None, reaction_list
         h298_list = np.zeros(len(reaction_list))
diff --git a/documentation/source/users/rmg/installation/dependencies.rst b/documentation/source/users/rmg/installation/dependencies.rst
index ba8a3ad66c..f91b280761 100644
--- a/documentation/source/users/rmg/installation/dependencies.rst
+++ b/documentation/source/users/rmg/installation/dependencies.rst
@@ -24,7 +24,6 @@ Briefly, RMG depends on the following packages, almost all of which can be found
 * **graphviz:** generating flux diagrams
 * **jinja2:** Python templating language for html rendering
 * **jupyter:** (optional) for using IPython notebooks
-* **lpsolve:** mixed integer linear programming solver, used for resonance structure generation. Must also install Python extension.
 * **markupsafe:** implements XML/HTML/XHTML markup safe strings for Python
 * **matplotlib:** library for making plots
 * **mock:** for unit-testing
diff --git a/environment.yml b/environment.yml
index 5f6ab8bb38..b944e256c4 100644
--- a/environment.yml
+++ b/environment.yml
@@ -77,7 +77,6 @@ dependencies:
   - conda-forge::gprof2dot
   - conda-forge::numdifftools
   - conda-forge::quantities
-  - conda-forge::lpsolve55
   - conda-forge::ringdecomposerlib-python
 
 # packages we maintain
diff --git a/test/arkane/encorr/isodesmicTest.py b/test/arkane/encorr/isodesmicTest.py
index 8b41066b3d..45aa9e8288 100644
--- a/test/arkane/encorr/isodesmicTest.py
+++ b/test/arkane/encorr/isodesmicTest.py
@@ -251,12 +251,6 @@ class TestErrorCancelingScheme:
 
     @classmethod
     def setup_class(cls):
-        try:
-            import pyomo as pyo
-        except ImportError:
-            pyo = None
-        cls.pyo = pyo
-
         lot = LevelOfTheory("test")
         cls.propene = ErrorCancelingSpecies(Molecule(smiles="CC=C"), (100, "kJ/mol"), lot, (105, "kJ/mol"))
         cls.propane = ErrorCancelingSpecies(Molecule(smiles="CCC"), (75, "kJ/mol"), lot, (80, "kJ/mol"))
@@ -286,26 +280,20 @@ def test_creating_error_canceling_schemes(self):
 
         assert isodesmic_scheme.reference_species == [self.butane, self.benzene]
 
-    # def test_find_error_canceling_reaction(self):
-    #     """
-    #     Test that the MILP problem can be solved to find a single isodesmic reaction
-    #     """
-    #     scheme = IsodesmicScheme(
-    #         self.propene,
-    #         [self.propane, self.butane, self.butene, self.caffeine, self.ethyne],
-    #     )
-
-    #     # Note that caffeine and ethyne will not be allowed, so for the full set the indices are [0, 1, 2]
-    #     rxn, _ = scheme._find_error_canceling_reaction([0, 1, 2], milp_software=["lpsolve"])
-    #     assert rxn.species[self.butane] == -1
-    #     assert rxn.species[self.propane] == 1
-    #     assert rxn.species[self.butene] == 1
-
-    #     if self.pyo is not None:
-    #         rxn, _ = scheme._find_error_canceling_reaction([0, 1, 2], milp_software=["pyomo"])
-    #         assert rxn.species[self.butane] == -1
-    #         assert rxn.species[self.propane] == 1
-    #         assert rxn.species[self.butene] == 1
+    def test_find_error_canceling_reaction(self):
+        """
+        Test that the MILP problem can be solved to find a single isodesmic reaction
+        """
+        scheme = IsodesmicScheme(
+            self.propene,
+            [self.propane, self.butane, self.butene, self.caffeine, self.ethyne],
+        )
+
+        # Note that caffeine and ethyne will not be allowed, so for the full set the indices are [0, 1, 2]
+        rxn, _ = scheme._find_error_canceling_reaction([0, 1, 2])
+        assert rxn.species[self.butane] == -1
+        assert rxn.species[self.propane] == 1
+        assert rxn.species[self.butene] == 1
 
     def test_multiple_error_canceling_reactions(self):
         """
@@ -333,13 +321,6 @@ def test_multiple_error_canceling_reactions(self):
         rxn_str2 = "<ErrorCancelingReaction 1*C=CC + 1*CCCC <=> 1*C=CCC + 1*CCC >"
         assert any(rxn_string in reaction_string for rxn_string in [rxn_str1, rxn_str2])
 
-        if self.pyo is not None:
-            # pyomo is slower, so don't test as many
-            reaction_list = scheme.multiple_error_canceling_reaction_search(n_reactions_max=5, milp_software=["pyomo"])
-            assert len(reaction_list) == 5
-            reaction_string = reaction_list.__repr__()
-            assert any(rxn_string in reaction_string for rxn_string in [rxn_str1, rxn_str2])
-
     def test_calculate_target_enthalpy(self):
         """
         Test that ErrorCancelingScheme is able to calculate thermochemistry for the target species
@@ -358,10 +339,10 @@ def test_calculate_target_enthalpy(self):
             ],
         )
 
-        target_thermo, rxn_list = scheme.calculate_target_enthalpy(n_reactions_max=3, milp_software=["lpsolve"])
+        target_thermo, rxn_list = scheme.calculate_target_enthalpy(n_reactions_max=3)
         assert target_thermo.value_si == 110000.0
         assert isinstance(rxn_list[0], ErrorCancelingReaction)
 
         if self.pyo is not None:
-            target_thermo, _ = scheme.calculate_target_enthalpy(n_reactions_max=3, milp_software=["pyomo"])
+            target_thermo, _ = scheme.calculate_target_enthalpy(n_reactions_max=3)
             assert target_thermo.value_si == 110000.0
diff --git a/utilities.py b/utilities.py
index f84963a632..87d39e7384 100644
--- a/utilities.py
+++ b/utilities.py
@@ -48,7 +48,6 @@ def check_dependencies():
     print('{0:<15}{1:<15}{2}'.format('Package', 'Version', 'Location'))
 
     missing = {
-        'lpsolve': _check_lpsolve(),
         'openbabel': _check_openbabel(),
         'pydqed': _check_pydqed(),
         'pyrdl': _check_pyrdl(),
@@ -80,23 +79,6 @@ def check_dependencies():
 """)
 
 
-def _check_lpsolve():
-    """Check for lpsolve"""
-    missing = False
-
-    try:
-        import lpsolve55
-    except ImportError:
-        print('{0:<30}{1}'.format('lpsolve55',
-                                  'Not found. Necessary for generating Clar structures for aromatic species.'))
-        missing = True
-    else:
-        location = lpsolve55.__file__
-        print('{0:<30}{1}'.format('lpsolve55', location))
-
-    return missing
-
-
 def _check_openbabel():
     """Check for OpenBabel"""
     missing = False

From d47a1f508f780e59acad091052a8243ec2cad384 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 24 Jul 2024 15:23:56 -0400
Subject: [PATCH 104/162] convert helper function args to kwargs for partial to
 work, hide function

---
 rmgpy/reaction.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/rmgpy/reaction.py b/rmgpy/reaction.py
index d902b844b9..ade4e444da 100644
--- a/rmgpy/reaction.py
+++ b/rmgpy/reaction.py
@@ -1542,8 +1542,8 @@ def generate_high_p_limit_kinetics(self):
         """
         raise NotImplementedError("generate_high_p_limit_kinetics is not implemented for all Reaction subclasses.")
 
-def same_object(object1, object2, _check_identical, _only_check_label,
-             _generate_initial_map, _strict, _save_order):
+def _same_object(object1, object2, _check_identical=False, _only_check_label=False,
+             _generate_initial_map=False, _strict=True, _save_order=False):
     if _only_check_label:
         return str(object1) == str(object2)
     elif _check_identical:
@@ -1573,7 +1573,7 @@ def same_species_lists(list1, list2, check_identical=False, only_check_label=Fal
     """
     
     same_object_passthrough = partial(
-        same_object,
+        _same_object,
         _check_identical=check_identical,
         _only_check_label=only_check_label,
         _generate_intial_map=generate_initial_map,

From 54efa6486ef93081ddf226a0ec630c40ca8f0b35 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 24 Jul 2024 15:26:53 -0400
Subject: [PATCH 105/162] re-try running M1 macs on native hardware rather than
 x86 emulation

---
 .github/workflows/CI.yml | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 7230afa5b7..0fc4cf5115 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -81,16 +81,6 @@ jobs:
           activate-environment: rmg_env
           use-mamba: true
 
-      - name: Fix ARM Mac environment
-        if: matrix.os == 'macos-latest'
-        run: |
-          conda deactivate
-          conda env remove -n rmg_env
-          conda create -n rmg_env
-          conda activate rmg_env
-          conda config --env --set subdir osx-64
-          conda env update -f environment.yml
-
       # list the environment for debugging purposes
       - name: mamba info
         run: |

From 12f29686f3c4fbfe6146f089a32da6ec0021107c Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 24 Jul 2024 16:07:49 -0400
Subject: [PATCH 106/162] ugh, typo

---
 rmgpy/reaction.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rmgpy/reaction.py b/rmgpy/reaction.py
index ade4e444da..510f618c88 100644
--- a/rmgpy/reaction.py
+++ b/rmgpy/reaction.py
@@ -1576,7 +1576,7 @@ def same_species_lists(list1, list2, check_identical=False, only_check_label=Fal
         _same_object,
         _check_identical=check_identical,
         _only_check_label=only_check_label,
-        _generate_intial_map=generate_initial_map,
+        _generate_initial_map=generate_initial_map,
         _strict=strict,
         _save_order=save_order,
     )

From 5407567dc405908ce08b127c33c140fd745e9903 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 24 Jul 2024 21:04:23 -0400
Subject: [PATCH 107/162] pass constraints as a tuple

---
 rmgpy/molecule/resonance.pxd | 2 +-
 rmgpy/molecule/resonance.py  | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/rmgpy/molecule/resonance.pxd b/rmgpy/molecule/resonance.pxd
index 1b546ee9d5..e41be0c14f 100644
--- a/rmgpy/molecule/resonance.pxd
+++ b/rmgpy/molecule/resonance.pxd
@@ -68,6 +68,6 @@ cpdef list generate_clar_structures(Graph mol, bint save_order=?)
 
 cpdef list _clar_optimization(Graph mol, bint save_order=?)
 
-cpdef list _solve_clar_milp(cnp.ndarray[cnp.int_t, ndim=1] c, bounds, list constraints, int n_ring, max_num=?)
+cpdef list _solve_clar_milp(cnp.ndarray[cnp.int_t, ndim=1] c, bounds, tuple constraints, int n_ring, max_num=?)
 
 cpdef list _clar_transformation(Graph mol, list aromatic_ring)
diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
index 1695962125..cb2d74dbd9 100644
--- a/rmgpy/molecule/resonance.py
+++ b/rmgpy/molecule/resonance.py
@@ -1038,9 +1038,9 @@ def _clar_optimization(mol, save_order=False):
         in_ring = [1 if atom in ring else 0 for ring in aromatic_rings]
         in_bond = [1 if atom in [bond.atom1, bond.atom2] else 0 for bond in bonds]
         A.append(in_ring + in_bond)
-    constraints = [LinearConstraint(
+    constraints = (LinearConstraint(
         A=np.array(A, dtype=int), lb=np.ones(n_atom, dtype=int), ub=np.ones(n_atom, dtype=int)
-    )]
+    ), )
 
     # Objective vector for optimization: sextets have a weight of 1, double bonds have a weight of 0
     c = - np.array([1] * n_ring + [0] * n_bond, dtype=int)
@@ -1108,7 +1108,7 @@ def _solve_clar_milp(
 
     # Generate constraints based on the solution obtained
     y = solution[:n_ring]
-    constraints.append(
+    constraints = constraints + (
         LinearConstraint(
             A=np.hstack([y, [0] * (solution.shape[0] - n_ring)]),
             ub=sum(y) - 1,

From baf260aefc86b217ae044b84262c4a3ff5942e1c Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 24 Jul 2024 21:58:07 -0400
Subject: [PATCH 108/162] fix return type for clar call

---
 rmgpy/molecule/resonance.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
index cb2d74dbd9..c7bec60098 100644
--- a/rmgpy/molecule/resonance.py
+++ b/rmgpy/molecule/resonance.py
@@ -984,7 +984,7 @@ def _clar_optimization(mol, save_order=False):
             J. Math. Chem. 1994, 15 (1), 93–107.
     """
     cython.declare(molecule=Graph, aromatic_rings=list, exo=list, n_rings=cython.int, n_atoms=cython.int, n_bonds=cython.int,
-                   A=list, solutions=tuple)
+                   A=list, solutions=list)
 
     # Make a copy of the molecule so we don't destroy the original
     molecule = mol.copy(deep=True)

From db6e632e36b87342134967507fdd33f6cd4459aa Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 25 Jul 2024 10:45:57 -0400
Subject: [PATCH 109/162] update return types in cython header

---
 rmgpy/molecule/resonance.pxd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rmgpy/molecule/resonance.pxd b/rmgpy/molecule/resonance.pxd
index e41be0c14f..592e1b23de 100644
--- a/rmgpy/molecule/resonance.pxd
+++ b/rmgpy/molecule/resonance.pxd
@@ -66,8 +66,8 @@ cpdef list generate_kekule_structure(Graph mol)
 
 cpdef list generate_clar_structures(Graph mol, bint save_order=?)
 
-cpdef list _clar_optimization(Graph mol, bint save_order=?)
+cpdef tuple _clar_optimization(Graph mol, bint save_order=?)
 
 cpdef list _solve_clar_milp(cnp.ndarray[cnp.int_t, ndim=1] c, bounds, tuple constraints, int n_ring, max_num=?)
 
-cpdef list _clar_transformation(Graph mol, list aromatic_ring)
+cpdef None _clar_transformation(Graph mol, list aromatic_ring)

From 91d74cdb8ffa8991545ccd27f651e13b3e30c02c Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 25 Jul 2024 11:32:09 -0400
Subject: [PATCH 110/162] yet more incorrect return types

---
 rmgpy/molecule/resonance.pxd | 2 +-
 rmgpy/molecule/resonance.py  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/rmgpy/molecule/resonance.pxd b/rmgpy/molecule/resonance.pxd
index 592e1b23de..d4cc6d361c 100644
--- a/rmgpy/molecule/resonance.pxd
+++ b/rmgpy/molecule/resonance.pxd
@@ -70,4 +70,4 @@ cpdef tuple _clar_optimization(Graph mol, bint save_order=?)
 
 cpdef list _solve_clar_milp(cnp.ndarray[cnp.int_t, ndim=1] c, bounds, tuple constraints, int n_ring, max_num=?)
 
-cpdef None _clar_transformation(Graph mol, list aromatic_ring)
+cpdef void _clar_transformation(Graph mol, list aromatic_ring)
diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
index c7bec60098..b29c5e007e 100644
--- a/rmgpy/molecule/resonance.py
+++ b/rmgpy/molecule/resonance.py
@@ -993,7 +993,7 @@ def _clar_optimization(mol, save_order=False):
     aromatic_rings.sort(key=_sum_atom_ids)
 
     if not aromatic_rings:
-        return []
+        return tuple()
 
     # Get list of atoms that are in rings
     atoms = set()

From fb19d02293b2909ffc31786f0e87d09ef0d0b493 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 25 Jul 2024 12:49:03 -0400
Subject: [PATCH 111/162] use python warnings module instead of removed numpy
 warnings passthrough

---
 arkane/statmech.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/arkane/statmech.py b/arkane/statmech.py
index 4380bad121..fdfac0b512 100644
--- a/arkane/statmech.py
+++ b/arkane/statmech.py
@@ -37,6 +37,7 @@
 import math
 import os
 import pathlib
+import warnings
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -1132,8 +1133,8 @@ def project_rotors(conformer, hessian, rotors, linear, is_ts, get_projected_out_
 
     logging.debug('Frequencies from internal Hessian')
     for i in range(3 * n_atoms - external):
-        with np.warnings.catch_warnings():
-            np.warnings.filterwarnings('ignore', r'invalid value encountered in sqrt')
+        with warnings.catch_warnings():
+            warnings.filterwarnings('ignore', r'invalid value encountered in sqrt')
             logging.debug(np.sqrt(eig[i]) / (2 * math.pi * constants.c * 100))
 
     # Now we can start thinking about projecting out the internal rotations
@@ -1243,8 +1244,8 @@ def project_rotors(conformer, hessian, rotors, linear, is_ts, get_projected_out_
 
     logging.debug('Frequencies from projected Hessian')
     for i in range(3 * n_atoms):
-        with np.warnings.catch_warnings():
-            np.warnings.filterwarnings('ignore', r'invalid value encountered in sqrt')
+        with warnings.catch_warnings():
+            warnings.filterwarnings('ignore', r'invalid value encountered in sqrt')
             logging.debug(np.sqrt(eig[i]) / (2 * math.pi * constants.c * 100))
 
     return np.sqrt(eig[-n_vib:]) / (2 * math.pi * constants.c * 100)

From f30b04a90682b4d3dd66408cb7aff40c05c2bca4 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 25 Jul 2024 12:50:35 -0400
Subject: [PATCH 112/162] fix incorrect use of `getattr`

---
 rmgpy/rmg/reactors.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rmgpy/rmg/reactors.py b/rmgpy/rmg/reactors.py
index 29c17095b0..e51cde49a7 100644
--- a/rmgpy/rmg/reactors.py
+++ b/rmgpy/rmg/reactors.py
@@ -76,7 +76,7 @@ def to_julia(obj):
     if isinstance(obj, dict):
         return Main.PythonCall.pyconvert(Main.Dict, obj)
     elif isinstance(obj, (list, np.ndarray)):
-        if obj.getattr("shape", False) and len(obj.shape) > 1:
+        if getattr(obj, "shape", False) and len(obj.shape) > 1:
             return Main.PythonCall.pyconvert(Main.Matrix, obj)
         return Main.PythonCall.pyconvert(Main.Vector, obj)
     else: # Other native Python project does not need special conversion.

From ff4ef4e0378795b986372088362f9472983a1053 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 25 Jul 2024 12:52:51 -0400
Subject: [PATCH 113/162] add back the cclib version restriction

we are not compatible with the latest version, will be resolved in this PR: https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2639
---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index b944e256c4..b51eeff09d 100644
--- a/environment.yml
+++ b/environment.yml
@@ -46,7 +46,7 @@ dependencies:
   - coolprop
   - cantera::cantera >=3
   - conda-forge::mopac
-  - conda-forge::cclib >=1.6.3
+  - conda-forge::cclib >=1.6.3,<1.8.0
   - conda-forge::openbabel >= 3
   - conda-forge::rdkit >=2022.09.1
 

From 28d2fbf31c062f4d5106e7d924e52bf77e751c35 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 25 Jul 2024 12:55:31 -0400
Subject: [PATCH 114/162] allow empty return to be properly excepted

---
 rmgpy/molecule/resonance.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
index b29c5e007e..e1e3182f02 100644
--- a/rmgpy/molecule/resonance.py
+++ b/rmgpy/molecule/resonance.py
@@ -920,7 +920,7 @@ def generate_clar_structures(mol, save_order=False):
 
     try:
         aromatic_rings, bonds, solutions = _clar_optimization(mol, save_order=save_order)
-    except RuntimeError:
+    except (RuntimeError, ValueError):  # either a crash during optimization or the result was an empty tuple
         # The optimization algorithm did not work on the first iteration
         return []
 

From be69fb2892b6324cbdc8c1423bcb30d6374caf8f Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 25 Jul 2024 12:58:05 -0400
Subject: [PATCH 115/162] fix usage of `n` for iteration

---
 arkane/encorr/isodesmic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 52b718568f..681b1ba7a8 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -656,7 +656,7 @@ def _find_error_canceling_reaction(self, reference_subset):
         n = c_matrix.shape[1]
         split = int(m / 2)
 
-        constraints = [LinearConstraint(A=np.concatenate((c_matrix[:split, j], -1 * c_matrix[split:, j]), lb=targets[j], ub=targets[j])) for j in n]
+        constraints = [LinearConstraint(A=np.concatenate((c_matrix[:split, j], -1 * c_matrix[split:, j]), lb=targets[j], ub=targets[j])) for j in range(n)]
 
         result = milp(
             sum_constraints,

From 5e7b26612a7c97d9cd386390eea872efd86af893 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 25 Jul 2024 13:01:34 -0400
Subject: [PATCH 116/162] make dict_keys -> str conversion explicit so it will
 run

---
 arkane/encorr/isodesmic.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 681b1ba7a8..09d3b6e7f4 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -516,8 +516,8 @@ def _enumerate_element_constraints(self, target_constraints, reference_constrain
         # Check that the target and reference species have the same elements to be able to satisfy mass conservation
         if set(self.target.molecule.get_element_count().keys()) != all_elements:
             logging.warning(
-                f"Target species and reference species do not have the same elements:",
-                f"Target: {self.target.molecule.get_element_count().keys()}",
+                "Target species and reference species do not have the same elements:",
+                f"Target: {' '.join(self.target.molecule.get_element_count().keys())}",
                 f"Reference: {all_elements}",
             )
 

From 551926d853f93adb154a6af4d9a462e4c6c9e890 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 25 Jul 2024 13:02:39 -0400
Subject: [PATCH 117/162] re-limit the version of cantera to undo the API
 breaks

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index b51eeff09d..335489dbce 100644
--- a/environment.yml
+++ b/environment.yml
@@ -44,7 +44,7 @@ dependencies:
 
 # external software tools for chemistry
   - coolprop
-  - cantera::cantera >=3
+  - cantera::cantera =2.6
   - conda-forge::mopac
   - conda-forge::cclib >=1.6.3,<1.8.0
   - conda-forge::openbabel >= 3

From c1d6902c8b7d7a614d940199a857f9203d6d4aa2 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 25 Jul 2024 14:29:54 -0400
Subject: [PATCH 118/162] incorrect placement of parens

---
 arkane/encorr/isodesmic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 09d3b6e7f4..1500f70d19 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -656,7 +656,7 @@ def _find_error_canceling_reaction(self, reference_subset):
         n = c_matrix.shape[1]
         split = int(m / 2)
 
-        constraints = [LinearConstraint(A=np.concatenate((c_matrix[:split, j], -1 * c_matrix[split:, j]), lb=targets[j], ub=targets[j])) for j in range(n)]
+        constraints = (LinearConstraint(A=np.concatenate((c_matrix[:split, j], -1 * c_matrix[split:, j])), lb=targets[j], ub=targets[j]) for j in range(n), )
 
         result = milp(
             sum_constraints,

From 10e79c2c9a62a1047d4f1e1482683c3d96546bb0 Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Fri, 26 Jul 2024 10:13:45 -0400
Subject: [PATCH 119/162] make tuple cast more explicit

---
 arkane/encorr/isodesmic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 1500f70d19..3db526bcb5 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -656,7 +656,7 @@ def _find_error_canceling_reaction(self, reference_subset):
         n = c_matrix.shape[1]
         split = int(m / 2)
 
-        constraints = (LinearConstraint(A=np.concatenate((c_matrix[:split, j], -1 * c_matrix[split:, j])), lb=targets[j], ub=targets[j]) for j in range(n), )
+        constraints = tuple((LinearConstraint(A=np.concatenate((c_matrix[:split, j], -1 * c_matrix[split:, j])), lb=targets[j], ub=targets[j]) for j in range(n)))
 
         result = milp(
             sum_constraints,

From 46b9c928a78265346d1bb9bac17a3271c64dc377 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 5 Aug 2024 09:02:29 -0400
Subject: [PATCH 120/162] explicit cast of set to str

---
 arkane/encorr/isodesmic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 3db526bcb5..e143fd196d 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -518,7 +518,7 @@ def _enumerate_element_constraints(self, target_constraints, reference_constrain
             logging.warning(
                 "Target species and reference species do not have the same elements:",
                 f"Target: {' '.join(self.target.molecule.get_element_count().keys())}",
-                f"Reference: {all_elements}",
+                f"Reference: {str(all_elements)}",
             )
 
         all_elements.update(self.target.molecule.get_element_count().keys())

From 9092cd5f44df28d294c6cf18f35afc257018184d Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 5 Aug 2024 09:04:12 -0400
Subject: [PATCH 121/162] remove disused pyomo components

---
 arkane/encorr/isodesmic.py          | 13 -------------
 test/arkane/encorr/isodesmicTest.py |  4 ----
 2 files changed, 17 deletions(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index e143fd196d..7994df1296 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -42,7 +42,6 @@
 """
 
 import logging
-import signal
 from copy import deepcopy
 from typing import List, Union
 
@@ -758,18 +757,6 @@ def calculate_target_enthalpy(self, n_reactions_max=5):
         return ScalarQuantity(np.median(h298_list), "J/mol"), reaction_list
 
 
-def _pyo_obj_expression(model):
-    return pyo.summation(model.v, model.s, index=model.i)
-
-
-def _pyo_constraint_rule(model, col):
-    return (
-        sum(model.v[row] * model.c[row, col] for row in model.r)
-        - sum(model.v[row] * model.c[row, col] for row in model.p)
-        == model.t[col]
-    )
-
-
 class IsodesmicScheme(ErrorCancelingScheme):
     """
     An error canceling reaction where the number and type of both atoms and bonds are conserved
diff --git a/test/arkane/encorr/isodesmicTest.py b/test/arkane/encorr/isodesmicTest.py
index 45aa9e8288..02e5684f44 100644
--- a/test/arkane/encorr/isodesmicTest.py
+++ b/test/arkane/encorr/isodesmicTest.py
@@ -342,7 +342,3 @@ def test_calculate_target_enthalpy(self):
         target_thermo, rxn_list = scheme.calculate_target_enthalpy(n_reactions_max=3)
         assert target_thermo.value_si == 110000.0
         assert isinstance(rxn_list[0], ErrorCancelingReaction)
-
-        if self.pyo is not None:
-            target_thermo, _ = scheme.calculate_target_enthalpy(n_reactions_max=3)
-            assert target_thermo.value_si == 110000.0

From 4f8f268b88d0308a67d63776e3146f8eb2592460 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 5 Aug 2024 12:22:20 -0400
Subject: [PATCH 122/162] fix usage of warning

---
 arkane/encorr/isodesmic.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/arkane/encorr/isodesmic.py b/arkane/encorr/isodesmic.py
index 7994df1296..f4f39d0d85 100644
--- a/arkane/encorr/isodesmic.py
+++ b/arkane/encorr/isodesmic.py
@@ -515,9 +515,9 @@ def _enumerate_element_constraints(self, target_constraints, reference_constrain
         # Check that the target and reference species have the same elements to be able to satisfy mass conservation
         if set(self.target.molecule.get_element_count().keys()) != all_elements:
             logging.warning(
-                "Target species and reference species do not have the same elements:",
-                f"Target: {' '.join(self.target.molecule.get_element_count().keys())}",
-                f"Reference: {str(all_elements)}",
+                "Target species and reference species do not have the same elements:"
+                f"Target: {' '.join(self.target.molecule.get_element_count().keys())}"
+                f"Reference: {all_elements}"
             )
 
         all_elements.update(self.target.molecule.get_element_count().keys())

From 2b4885f1d0d928d65f8835e0a5c395fbd65961a7 Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 21 Aug 2024 14:45:35 -0700
Subject: [PATCH 123/162] why did we use to do this like this? total bonds =
 bonds (what bonds?) + rings

---
 rmgpy/molecule/resonance.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
index e1e3182f02..8d69af6c5b 100644
--- a/rmgpy/molecule/resonance.py
+++ b/rmgpy/molecule/resonance.py
@@ -1021,7 +1021,7 @@ def _clar_optimization(mol, save_order=False):
     # Dimensions
     n_ring = len(aromatic_rings)
     n_atom = len(atoms)
-    n_bond = len(bonds)
+    n_bond = n_ring + len(bonds)
 
     # The aromaticity assignment problem is formulated as an MILP problem
     # minimize:

From 82638fcaeb744dda62a16a1a43e9f2118bf2e4bd Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Tue, 29 Oct 2024 14:00:20 -0400
Subject: [PATCH 124/162] sign error in objective, clarify some variable names

---
 rmgpy/molecule/resonance.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
index 8d69af6c5b..0e0bd19405 100644
--- a/rmgpy/molecule/resonance.py
+++ b/rmgpy/molecule/resonance.py
@@ -1016,12 +1016,13 @@ def _clar_optimization(mol, save_order=False):
             else:
                 exo.append(0)
         else:
-            exo.append(None)
+            exo.append(0)
 
     # Dimensions
     n_ring = len(aromatic_rings)
     n_atom = len(atoms)
-    n_bond = n_ring + len(bonds)
+    n_bond = len(bonds)
+    n_decision_variables = n_bond + n_ring
 
     # The aromaticity assignment problem is formulated as an MILP problem
     # minimize:
@@ -1038,26 +1039,26 @@ def _clar_optimization(mol, save_order=False):
         in_ring = [1 if atom in ring else 0 for ring in aromatic_rings]
         in_bond = [1 if atom in [bond.atom1, bond.atom2] else 0 for bond in bonds]
         A.append(in_ring + in_bond)
-    constraints = (LinearConstraint(
+    constraint = (LinearConstraint(
         A=np.array(A, dtype=int), lb=np.ones(n_atom, dtype=int), ub=np.ones(n_atom, dtype=int)
     ), )
 
     # Objective vector for optimization: sextets have a weight of 1, double bonds have a weight of 0
-    c = - np.array([1] * n_ring + [0] * n_bond, dtype=int)
+    c = np.array([1] * n_ring + [0] * n_bond, dtype=int)
 
     # Variable bounds
     bounds = Bounds(
         lb=np.array(
-            [0] * n_ring + [1 if val == 1 else 0 for val in exo],
+            [0] * n_ring + exo,
             dtype=int,
-        ),  # lower bounds: 0 except for exo double bonds
+        ),  # lower bounds: 0 except for exo double bonds, which must be 1 (aka, do not modify them)
         ub=np.array(
-            [1] * n_ring + [0 if val == 0 else 1 for val in exo],
+            [1] * n_decision_variables,  # + [0 if val == 0 else 1 for val in exo],
             dtype=int,
-        ),  # upper bounds: 1 except for exo single bonds
+        ),  # upper is 1 for all
     )
 
-    solutions = _solve_clar_milp(c, bounds, constraints, n_ring)
+    solutions = _solve_clar_milp(c, bounds, constraint, n_ring)
 
     return aromatic_rings, bonds, solutions
 

From 78ac67fd39ed350b806c408c13bc65e82b0223fb Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Tue, 29 Oct 2024 15:04:28 -0400
Subject: [PATCH 125/162] add gcc to environment file for rdkit

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index 335489dbce..66500d7379 100644
--- a/environment.yml
+++ b/environment.yml
@@ -34,6 +34,7 @@ dependencies:
   - xlrd
   - xlwt
   - h5py
+  - gcc
   - graphviz
   - markupsafe
   - psutil

From c4c6a0fcddb1301d938bb886a1615ac7e3916f95 Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 30 Oct 2024 10:43:18 -0400
Subject: [PATCH 126/162] I don't think all these vars are requried

---
 .github/workflows/CI.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 1c285b326e..9f48e152bf 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -122,15 +122,15 @@ jobs:
       - name: Set Julia paths
         run: |
           echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
-          echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
-          echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
-          echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
-          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
-          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
-          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
-          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
+          # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
+          # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
+          # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
+          # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
+          # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
+          # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
+          # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
           echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_ENV
-          echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_PATH
+          # echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_PATH
 
       - name: Setup Juliaup
         uses: julia-actions/install-juliaup@v2

From 7f425a1c7196d8eee46d124deb45c45d4ebba3ed Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 30 Oct 2024 11:15:34 -0400
Subject: [PATCH 127/162] chatgpt says attached error might be because boost is
 missing

../../../miniconda3/envs/rmg_env/lib/python3.9/site-packages/rdkit/Chem/__init__.py:16: in <module>
    from rdkit.Chem import rdchem
E   ImportError: /home/runner/miniconda3/envs/rmg_env/lib/python3.9/site-packages/scipy/sparse/../../../../libstdc++.so.6: version `GLIBCXX_3.4.31' not found (required by /home/runner/miniconda3/envs/rmg_env/lib/python3.9/site-packages/rdkit/Chem/../../../../libboost_serialization.so.1.86.0)
---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 83d49a18de..bb2c8223f0 100644
--- a/environment.yml
+++ b/environment.yml
@@ -35,7 +35,7 @@ dependencies:
   - xlrd
   - xlwt
   - h5py
-  - gcc
+  - boost # needed for rdkit
   - graphviz
   - markupsafe
   - psutil

From 1d71ec4571c370f062afae1deca376dc58fae6ca Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 30 Oct 2024 11:16:11 -0400
Subject: [PATCH 128/162] i don't think we need this one either

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 9f48e152bf..c7a53458a9 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -121,7 +121,7 @@ jobs:
       # Setup Juliaup
       - name: Set Julia paths
         run: |
-          echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
+          # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
           # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH

From a450a48dd234ffacee982b895afb56e6b05daa6b Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 30 Oct 2024 12:26:22 -0400
Subject: [PATCH 129/162] install libstdcxx in cond env? or is this a LD path
 issue?

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index bb2c8223f0..3409c06061 100644
--- a/environment.yml
+++ b/environment.yml
@@ -35,7 +35,7 @@ dependencies:
   - xlrd
   - xlwt
   - h5py
-  - boost # needed for rdkit
+  - libstdcxx-ng # needed for rdkit (?) but not available for macs (?)
   - graphviz
   - markupsafe
   - psutil

From 4cefabfa4eebc1932ff6b95ed2301c60b4620bdc Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 30 Oct 2024 12:33:11 -0400
Subject: [PATCH 130/162] try using cross-platform compilers package

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 3409c06061..8e290dde9a 100644
--- a/environment.yml
+++ b/environment.yml
@@ -35,7 +35,7 @@ dependencies:
   - xlrd
   - xlwt
   - h5py
-  - libstdcxx-ng # needed for rdkit (?) but not available for macs (?)
+  - compilers  # going to provide: maybe libstdcxx-ng # needed for rdkit (?) but not available for macs (?)
   - graphviz
   - markupsafe
   - psutil

From b2ba22f5638e60e6c3df333d8d86dc02ca371df4 Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 30 Oct 2024 13:02:33 -0400
Subject: [PATCH 131/162] set ld_library_path

---
 .github/workflows/CI.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index c7a53458a9..aea514e95a 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -72,7 +72,7 @@ jobs:
         uses: actions/checkout@v4
 
       # Step to create a custom condarc.yml before setting up conda
-      - name: Create custom condarc.yml
+      - name: Create custom condarc.yml and set LD_LIBRARY_PATH
         run: |
           RUNNER_CWD=$(pwd)
           echo "channels:" > $RUNNER_CWD/condarc.yml
@@ -80,6 +80,7 @@ jobs:
           echo "  - rmg" >> $RUNNER_CWD/condarc.yml
           echo "  - cantera" >> $RUNNER_CWD/condarc.yml
           echo "show_channel_urls: true" >> $RUNNER_CWD/condarc.yml
+          export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_PREFIX/lib/
 
       # configures the mamba environment manager and builds the environment
       - name: Setup Mambaforge Python ${{ matrix.python-version }}

From 3a6b595c3d27435189db4274708d0edd0fff93ad Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 30 Oct 2024 14:10:52 -0400
Subject: [PATCH 132/162] use julia 1.9, set depot path for juliaup

---
 .github/workflows/CI.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index aea514e95a..6a6fc5249b 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -122,7 +122,7 @@ jobs:
       # Setup Juliaup
       - name: Set Julia paths
         run: |
-          # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
+          echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
           # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
@@ -136,7 +136,7 @@ jobs:
       - name: Setup Juliaup
         uses: julia-actions/install-juliaup@v2
         with:
-          channel: '1.10'
+          channel: '1.9'
 
       - name: Check Julia version
         run: julia --version

From 040f03d2846298e2267e957e55cb284cc01d390f Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 30 Oct 2024 14:50:13 -0400
Subject: [PATCH 133/162] also set the julia depot path

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 6a6fc5249b..cfe4b29501 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -124,7 +124,7 @@ jobs:
         run: |
           echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
-          # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
+          echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
           # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
           # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH

From b8817ad1302b6dd2045f6758f8c8b7248bc5bcd2 Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 30 Oct 2024 15:03:09 -0400
Subject: [PATCH 134/162] don't set ld_library_path

---
 .github/workflows/CI.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index cfe4b29501..33066d80c9 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -72,7 +72,7 @@ jobs:
         uses: actions/checkout@v4
 
       # Step to create a custom condarc.yml before setting up conda
-      - name: Create custom condarc.yml and set LD_LIBRARY_PATH
+      - name: Create custom condarc.yml
         run: |
           RUNNER_CWD=$(pwd)
           echo "channels:" > $RUNNER_CWD/condarc.yml
@@ -80,7 +80,6 @@ jobs:
           echo "  - rmg" >> $RUNNER_CWD/condarc.yml
           echo "  - cantera" >> $RUNNER_CWD/condarc.yml
           echo "show_channel_urls: true" >> $RUNNER_CWD/condarc.yml
-          export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_PREFIX/lib/
 
       # configures the mamba environment manager and builds the environment
       - name: Setup Mambaforge Python ${{ matrix.python-version }}

From 67aff20cacb05c21a096d1e1ca64fee9e80e7fcb Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 30 Oct 2024 16:05:53 -0400
Subject: [PATCH 135/162] try a different configuration of environment
 variables

---
 .github/workflows/CI.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 33066d80c9..c197d93aa0 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -123,9 +123,9 @@ jobs:
         run: |
           echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
-          echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
+          # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
-          # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
+          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
           # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
           # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
           # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH

From cbb91fa3a062affac7406f8c10d202ae322b51c7 Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Thu, 31 Oct 2024 08:59:21 -0400
Subject: [PATCH 136/162] also set julia depot?

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index c197d93aa0..194a736f43 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -123,7 +123,7 @@ jobs:
         run: |
           echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
-          # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
+          echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
           echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
           # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH

From 9df0540aa1ca4c94cc64af7dc6e334f3ce50f972 Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Thu, 31 Oct 2024 10:51:26 -0400
Subject: [PATCH 137/162] revert to only setting the current condapkg which
 should be the only one required

---
 .github/workflows/CI.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 194a736f43..b2eca50ca9 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -121,11 +121,11 @@ jobs:
       # Setup Juliaup
       - name: Set Julia paths
         run: |
-          echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
+          # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
-          echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
+          # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
-          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
+          # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
           # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
           # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
           # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH

From fabc0f82106c5f4bcea6d78201b12ccb87579691 Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Thu, 31 Oct 2024 10:51:59 -0400
Subject: [PATCH 138/162] add `libstdcxx-ng` to see if the CI will pass on
 Linux at least

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 8e290dde9a..8172b49d2a 100644
--- a/environment.yml
+++ b/environment.yml
@@ -35,7 +35,7 @@ dependencies:
   - xlrd
   - xlwt
   - h5py
-  - compilers  # going to provide: maybe libstdcxx-ng # needed for rdkit (?) but not available for macs (?)
+  - libstdcxx-ng  # going to provide: maybe libstdcxx-ng # needed for rdkit (?) but not available for macs (?)
   - graphviz
   - markupsafe
   - psutil

From a3283b3bd4c79758e199d069e7a6558558d03833 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 20 Nov 2024 12:25:03 -0500
Subject: [PATCH 139/162] remove old julia install step

---
 .github/workflows/CI.yml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 1c0ab3f914..33aeadaa30 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -93,12 +93,6 @@ jobs:
           activate-environment: rmg_env
           use-mamba: true
 
-      # installs the extra RMS conda dependencies
-      - name: Add RMS dependencies
-        run: |
-          mamba install -c conda-forge julia=1.9.1 pyjulia>=0.6 
-          mamba install -c rmg pyrms diffeqpy
-
       # list the environment for debugging purposes
       - name: mamba info
         run: |
@@ -151,6 +145,7 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         # JULIA_CONDAPKG_EXE points to the existing conda/mamba to avoid JuliaCall from installing their own. See https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-a-Conda-environment.
         run: |
+          mamba install conda-forge::pyjuliacall
           julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor

From 3605e2581e6773b725f3382474c0d82f3c278c95 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 20 Nov 2024 12:26:50 -0500
Subject: [PATCH 140/162] add a test run that doesn't need julia

---
 .github/workflows/CI.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 33aeadaa30..96ac8865c5 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -57,6 +57,7 @@ jobs:
       matrix:
         python-version: ["3.9"]
         os: [macos-13, macos-latest, ubuntu-latest]
+        test_julia: [yes, no]
     runs-on: ${{ matrix.os }}
     name: ${{ matrix.os }} Build and Test Python ${{ matrix.python-version }}
     # skip scheduled runs from forks
@@ -120,6 +121,7 @@ jobs:
 
       # Setup Juliaup
       - name: Set Julia paths
+        if: ${{ matrix.test_julia }} == "yes"
         run: |
           # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
@@ -133,15 +135,18 @@ jobs:
           # echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_PATH
 
       - name: Setup Juliaup
+        if: ${{ matrix.test_julia }} == "yes"
         uses: julia-actions/install-juliaup@v2
         with:
           channel: '1.9'
 
       - name: Check Julia version
+        if: ${{ matrix.test_julia }} == "yes"
         run: julia --version
 
       # RMS installation and linking to Julia
       - name: Install and link Julia dependencies
+        if: ${{ matrix.test_julia }} == "yes"
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         # JULIA_CONDAPKG_EXE points to the existing conda/mamba to avoid JuliaCall from installing their own. See https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-a-Conda-environment.
         run: |

From 02e41400a02174fbc9ddc9f1974d8fccca13563a Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 20 Nov 2024 12:28:06 -0500
Subject: [PATCH 141/162] name the tests based on if julia is installed or not

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 96ac8865c5..9337d88ebb 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -59,7 +59,7 @@ jobs:
         os: [macos-13, macos-latest, ubuntu-latest]
         test_julia: [yes, no]
     runs-on: ${{ matrix.os }}
-    name: ${{ matrix.os }} Build and Test Python ${{ matrix.python-version }}
+    name: ${{ matrix.os }} Build and Test Python ${{ matrix.python-version }} (Julia? ${{ matrix.test_julia }})
     # skip scheduled runs from forks
     if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
     env: 

From d7274efd01dce34d1fed9db8b30c79cfb94a6f30 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 20 Nov 2024 12:32:16 -0500
Subject: [PATCH 142/162] remove libstdcxx and add the new julia conda package
 (not actually julia

---
 environment.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/environment.yml b/environment.yml
index 003b6b7a5f..3b05c5df78 100644
--- a/environment.yml
+++ b/environment.yml
@@ -35,7 +35,6 @@ dependencies:
   - xlrd
   - xlwt
   - h5py
-  - libstdcxx-ng  # going to provide: maybe libstdcxx-ng # needed for rdkit (?) but not available for macs (?)
   - graphviz
   - markupsafe
   - psutil
@@ -89,10 +88,7 @@ dependencies:
 
 # optional dependencies for using ReactionMechanismSimulator
 # remove the leading '#' to install the required dependencies
-  # - conda-forge::julia=1.9.1
-  # - conda-forge::pyjulia >=0.6
-  # - rmg::pyrms
-  # - rmg::diffeqpy
+  # - conda-forge::pyjuliacall
 
 # Note about diffeqpy:
 # we should use the official verison https://github.com/SciML/diffeqpy),

From de206e47efdb7b758b53cdb9e3bb07a1ff146e96 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 20 Nov 2024 12:45:40 -0500
Subject: [PATCH 143/162] fix if comparison for matrix

---
 .github/workflows/CI.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 9337d88ebb..658e444aeb 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -121,7 +121,7 @@ jobs:
 
       # Setup Juliaup
       - name: Set Julia paths
-        if: ${{ matrix.test_julia }} == "yes"
+        if: matrix.test_julia == 'yes'
         run: |
           # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
           # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
@@ -135,18 +135,18 @@ jobs:
           # echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_PATH
 
       - name: Setup Juliaup
-        if: ${{ matrix.test_julia }} == "yes"
+        if: matrix.test_julia == 'yes'
         uses: julia-actions/install-juliaup@v2
         with:
           channel: '1.9'
 
       - name: Check Julia version
-        if: ${{ matrix.test_julia }} == "yes"
+        if: matrix.test_julia == 'yes'
         run: julia --version
 
       # RMS installation and linking to Julia
       - name: Install and link Julia dependencies
-        if: ${{ matrix.test_julia }} == "yes"
+        if: matrix.test_julia == 'yes'
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         # JULIA_CONDAPKG_EXE points to the existing conda/mamba to avoid JuliaCall from installing their own. See https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-a-Conda-environment.
         run: |

From cce1f4b1e1d5a9b7f47dbc583f8b06e3ff1daf84 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 20 Nov 2024 12:47:54 -0500
Subject: [PATCH 144/162] disable running on push, enable running on dispatch

---
 .github/workflows/CI.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 658e444aeb..3d79209c3b 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -33,8 +33,8 @@ on:
   schedule:
     # * is a special character in YAML so you have to quote this string
     - cron: "0 8 * * *"
-  # runs on all branches on both RMG-Py and forks
-  push:
+  # allow running on RMG-Py on a pushed branch, only if triggered manually
+  workflow_dispatch:
   # runs on PRs against RMG-Py (and anywhere else, but we add this for RMG-Py)
   pull_request:
 

From eccab98d90c00d038c0a2a6705639e808ebc9782 Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 20 Nov 2024 13:34:02 -0500
Subject: [PATCH 145/162] avoid bugged versions of `quantities`

See https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2694#issuecomment-2489286263
---
 environment.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 3b05c5df78..d9cd9fec2a 100644
--- a/environment.yml
+++ b/environment.yml
@@ -75,7 +75,9 @@ dependencies:
   - pandas
   - conda-forge::gprof2dot
   - conda-forge::numdifftools
-  - conda-forge::quantities
+  # bug in quantities, see:
+  # https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2694#issuecomment-2489286263
+  - conda-forge::quantities !=0.16.0,!=0.16.1
   - conda-forge::ringdecomposerlib-python
 
 # packages we maintain

From 0ba84b32b70791b10568fc4b2687f50e5eaeec49 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 20 Nov 2024 16:06:57 -0500
Subject: [PATCH 146/162] fix default require_rms values for pdepnetwork update

---
 rmgpy/rmg/pdep.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/rmgpy/rmg/pdep.py b/rmgpy/rmg/pdep.py
index 89b4104d2b..834f0f7243 100644
--- a/rmgpy/rmg/pdep.py
+++ b/rmgpy/rmg/pdep.py
@@ -736,7 +736,7 @@ def remove_products_from_reactants(self):
                 self.reactants.remove(prod)
             self.products = self.products_cache
 
-    def update(self, reaction_model, pdep_settings):
+    def update(self, reaction_model, pdep_settings, requires_rms=False):
         """
         Regenerate the :math:`k(T,P)` values for this partial network if the
         network is marked as invalid.
@@ -917,7 +917,7 @@ def update(self, reaction_model, pdep_settings):
                                              f'from the {rxn.library} library, and was not added to the model')
                                 break
                         else:
-                            reaction_model.add_reaction_to_core(net_reaction, requires_rms=True)
+                            reaction_model.add_reaction_to_core(net_reaction, requires_rms=requires_rms)
                     else:
                         # Check whether netReaction already exists in the edge as a LibraryReaction
                         for rxn in reaction_model.edge.reactions:
@@ -929,7 +929,7 @@ def update(self, reaction_model, pdep_settings):
                                              f'from the {rxn.library} library, and was not added to the model')
                                 break
                         else:
-                            reaction_model.add_reaction_to_edge(net_reaction, requires_rms=True)
+                            reaction_model.add_reaction_to_edge(net_reaction, requires_rms=requires_rms)
 
                 # Set/update the net reaction kinetics using interpolation model
                 kdata = K[:, :, i, j].copy()

From 1bd70378a6acda023c28d8c70b2101cb9f3fd2ba Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 20 Nov 2024 16:14:43 -0500
Subject: [PATCH 147/162] remove the now disallowed array cast

---
 rmgpy/data/kinetics/family.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rmgpy/data/kinetics/family.py b/rmgpy/data/kinetics/family.py
index f8818c78ac..d5da39bd70 100644
--- a/rmgpy/data/kinetics/family.py
+++ b/rmgpy/data/kinetics/family.py
@@ -3379,8 +3379,8 @@ def make_bm_rules_from_template_rxn_map(self, template_rxn_map, nprocs=1, Tref=1
         entries = list(self.groups.entries.values())
         rxnlists = [(template_rxn_map[entry.label], entry.label)
                     if entry.label in template_rxn_map.keys() else [] for entry in entries]
-        inputs = np.array([(self.forward_recipe.actions, rxns, Tref, fmax, label, [r.rank for r in rxns])
-                           for rxns, label in rxnlists])
+        inputs = [(self.forward_recipe.actions, rxns, Tref, fmax, label, [r.rank for r in rxns])
+                           for rxns, label in rxnlists]
 
         inds = np.arange(len(inputs))
         np.random.shuffle(inds)  # want to parallelize in random order

From 0d5a3bccb0308547fdbe8061c11ee7bf80ae45ec Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 21 Nov 2024 15:11:11 -0500
Subject: [PATCH 148/162] set allowed version of graphviz, fix list indexeing
 syntax, fix import, update subprocess syntax to py3

---
 environment.yml               | 2 +-
 rmgpy/data/kinetics/family.py | 4 ++--
 rmgpy/pdep/sls.py             | 2 +-
 rmgpy/tools/fluxdiagram.py    | 7 +++++--
 4 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/environment.yml b/environment.yml
index d9cd9fec2a..587afde7dc 100644
--- a/environment.yml
+++ b/environment.yml
@@ -35,7 +35,7 @@ dependencies:
   - xlrd
   - xlwt
   - h5py
-  - graphviz
+  - graphviz >=12
   - markupsafe
   - psutil
   # conda-forge not default, since default has a version information bug
diff --git a/rmgpy/data/kinetics/family.py b/rmgpy/data/kinetics/family.py
index d5da39bd70..c4084147d5 100644
--- a/rmgpy/data/kinetics/family.py
+++ b/rmgpy/data/kinetics/family.py
@@ -3389,9 +3389,9 @@ def make_bm_rules_from_template_rxn_map(self, template_rxn_map, nprocs=1, Tref=1
 
         if nprocs > 1:
             pool = mp.Pool(nprocs)
-            kinetics_list = np.array(pool.map(_make_rule, inputs[inds]))
+            kinetics_list = np.array(pool.map(_make_rule, list(inputs[i] for i in inds)))
         else:
-            kinetics_list = np.array(list(map(_make_rule, inputs[inds])))
+            kinetics_list = np.array(list(map(_make_rule, list(inputs[i] for i in inds))))
 
         kinetics_list = kinetics_list[revinds]  # fix order
 
diff --git a/rmgpy/pdep/sls.py b/rmgpy/pdep/sls.py
index caff18c6da..f8f66d5b83 100644
--- a/rmgpy/pdep/sls.py
+++ b/rmgpy/pdep/sls.py
@@ -41,7 +41,7 @@
 
 import rmgpy.constants as constants
 from rmgpy.pdep.me import generate_full_me_matrix, states_to_configurations
-from rmgpy.rmg.reactors import to_julia
+from rmgpy.rmg.reactionmechanismsimulator_reactors import to_julia
 
 NO_JULIA = False
 try:
diff --git a/rmgpy/tools/fluxdiagram.py b/rmgpy/tools/fluxdiagram.py
index 8a472046e0..2f8799fc9f 100644
--- a/rmgpy/tools/fluxdiagram.py
+++ b/rmgpy/tools/fluxdiagram.py
@@ -42,7 +42,7 @@
 
 from rmgpy.kinetics.diffusionLimited import diffusion_limiter
 from rmgpy.rmg.settings import SimulatorSettings
-from rmgpy.solver.base import TerminationTime, TerminationConversion
+from rmgpy.solver.base import TerminationConversion, TerminationTime
 from rmgpy.solver.liquid import LiquidReactor
 from rmgpy.tools.loader import load_rmg_job
 
@@ -308,7 +308,10 @@ def generate_flux_diagram(reaction_model, times, concentrations, reaction_rates,
                '-pix_fmt', 'yuv420p',  # Pixel format
                'flux_diagram.avi']  # Output filename
 
-    subprocess.check_call(command, cwd=output_directory)
+    try:
+        subprocess.run(command, shell=True, check=True, capture_output=True, cwd=output_directory)
+    except subprocess.CalledProcessError as err:
+        raise RuntimeError(f"{err} {err.stderr.decode('utf8')}") from err
 
 
 ################################################################################

From 7fbc38d2f8e8aa3162a891a507d8290c1ab4a57d Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 21 Nov 2024 15:42:44 -0500
Subject: [PATCH 149/162] get ffmpeg from conda-forge instead of rmg to
 (hopefully) fix usage error

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 587afde7dc..20ad19c437 100644
--- a/environment.yml
+++ b/environment.yml
@@ -31,7 +31,7 @@ dependencies:
 # but by installing them in the conda environment we get better control
   - cairo
   - cairocffi
-  - ffmpeg
+  - conda-forge::ffmpeg
   - xlrd
   - xlwt
   - h5py

From 952b396b94b29aa793436e9f6303fcadc3acb63b Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Fri, 22 Nov 2024 10:50:22 -0500
Subject: [PATCH 150/162] disable `shell`, also print `stdout`

---
 rmgpy/tools/fluxdiagram.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rmgpy/tools/fluxdiagram.py b/rmgpy/tools/fluxdiagram.py
index 2f8799fc9f..81ecf44f89 100644
--- a/rmgpy/tools/fluxdiagram.py
+++ b/rmgpy/tools/fluxdiagram.py
@@ -309,9 +309,9 @@ def generate_flux_diagram(reaction_model, times, concentrations, reaction_rates,
                'flux_diagram.avi']  # Output filename
 
     try:
-        subprocess.run(command, shell=True, check=True, capture_output=True, cwd=output_directory)
+        subprocess.run(command, check=True, capture_output=True, cwd=output_directory)
     except subprocess.CalledProcessError as err:
-        raise RuntimeError(f"{err} {err.stderr.decode('utf8')}") from err
+        raise RuntimeError(f"{err} {err.stderr.decode('utf8')} {err.stdout.decode('utf8')}") from err
 
 
 ################################################################################

From 53325b0e5a755a761fd01d47c125dff640830bf2 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Sun, 1 Dec 2024 21:52:59 -0500
Subject: [PATCH 151/162] ignore flux diagram dot testing files

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 946eb94d4a..38d73e2bc1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -103,6 +103,7 @@ test/rmgpy/test_data/temp_dir_for_testing/cantera/chem001.yaml
 rmgpy/test_data/copied_kinetic_lib/
 testing/qm/*
 test_log.txt
+rmgpy/tools/data/flux/flux/1/*.dot
 
 # example directory - save the inputs but not the outputs
 # cantera input files

From 8bf6bfa8e34d3bd68c71471426c4126d55d97a1c Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Sun, 1 Dec 2024 21:53:16 -0500
Subject: [PATCH 152/162] stop grabbing rmg versions of common packages

---
 environment.yml | 66 ++++++++++++++++++++++---------------------------
 1 file changed, 30 insertions(+), 36 deletions(-)

diff --git a/environment.yml b/environment.yml
index 20ad19c437..9080a480e5 100644
--- a/environment.yml
+++ b/environment.yml
@@ -23,28 +23,28 @@
 # - August 4, 2024 Restricted pyrms to <2
 name: rmg_env
 channels:
-  - rmg
   - conda-forge
   - cantera
+  - rmg
 dependencies:
 # System-level dependencies - we could install these at the OS level
 # but by installing them in the conda environment we get better control
-  - cairo
-  - cairocffi
-  - conda-forge::ffmpeg
-  - xlrd
-  - xlwt
-  - h5py
-  - graphviz >=12
-  - markupsafe
-  - psutil
+  - conda-forge::cairo
+  - conda-forge::cairocffi
+  - conda-forge::ffmpeg >= 7
+  - conda-forge::xlrd
+  - conda-forge::xlwt
+  - conda-forge::h5py
+  - conda-forge::graphviz >=12
+  - conda-forge::markupsafe
+  - conda-forge::psutil
   # conda-forge not default, since default has a version information bug
   # (see https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2421)
   - conda-forge::ncurses
   - conda-forge::suitesparse
 
 # external software tools for chemistry
-  - coolprop
+  - conda-forge::coolprop
   - cantera::cantera =2.6
   - conda-forge::mopac
   # see https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2639#issuecomment-2050292972
@@ -53,26 +53,26 @@ dependencies:
   - conda-forge::rdkit >=2022.09.1
 
 # Python tools
-  - python >=3.9  # leave as GEQ so that GitHub actions can add EQ w/o breaking (contradictory deps)
-  - coverage
-  - cython >=0.25.2
-  - scikit-learn
-  - scipy >=1.9
-  - numpy >=1.10.0
-  - pydot
-  - jinja2
-  - jupyter
-  - pymongo
-  - pyparsing
-  - pyyaml
-  - networkx
-  - pytest
-  - pytest-cov
+  - conda-forge::python >=3.9  # leave as GEQ so that GitHub actions can add EQ w/o breaking (contradictory deps)
+  - conda-forge::coverage
+  - conda-forge::cython >=0.25.2
+  - conda-forge::scikit-learn
+  - conda-forge::scipy >=1.9
+  - conda-forge::numpy >=1.10.0
+  - conda-forge::pydot
+  - conda-forge::jinja2
+  - conda-forge::jupyter
+  - conda-forge::pymongo
+  - conda-forge::pyparsing
+  - conda-forge::pyyaml
+  - conda-forge::networkx
+  - conda-forge::pytest
+  - conda-forge::pytest-cov
   - conda-forge::pytest-check
-  - pyutilib
-  - matplotlib >=1.5
-  - mpmath
-  - pandas
+  - conda-forge::pyutilib
+  - conda-forge::matplotlib >=1.5
+  - conda-forge::mpmath
+  - conda-forge::pandas
   - conda-forge::gprof2dot
   - conda-forge::numdifftools
   # bug in quantities, see:
@@ -92,12 +92,6 @@ dependencies:
 # remove the leading '#' to install the required dependencies
   # - conda-forge::pyjuliacall
 
-# Note about diffeqpy:
-# we should use the official verison https://github.com/SciML/diffeqpy),
-# rather than ours (which is only made so that we can get it from conda)
-# It is only on pip, so we will need to do something like:
-# https://stackoverflow.com/a/35245610
-
 # additional packages that are required, but not specified here (and why)
   # pydqed, pydas, mopac, and likely others require a fortran compiler (specifically gfortran)
   # in the environment. Normally we would add this to the environment file with

From 5bd2f4a91c06fec61945f02e03c645561d999d44 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 2 Dec 2024 07:49:52 -0500
Subject: [PATCH 153/162] incorrect failure condition in liquid test

---
 test/rmgpy/solver/liquidTest.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/test/rmgpy/solver/liquidTest.py b/test/rmgpy/solver/liquidTest.py
index dd03ce323b..3559a595b3 100644
--- a/test/rmgpy/solver/liquidTest.py
+++ b/test/rmgpy/solver/liquidTest.py
@@ -29,7 +29,6 @@
 
 import os
 
-
 import numpy as np
 
 from rmgpy.kinetics import Arrhenius
@@ -635,5 +634,7 @@ def teardown_class(cls):
         import rmgpy.data.rmg
 
         rmgpy.data.rmg.database = None
-
-        os.remove(os.path.join(cls.file_dir, "restart_from_seed.py"))
+        try:
+            os.remove(os.path.join(cls.file_dir, "restart_from_seed.py"))
+        except FileNotFoundError:
+            pass  # file will not be present if any tests failed

From 7fe0345e4a332786fa686333b134e174a1d01210 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 2 Dec 2024 07:52:13 -0500
Subject: [PATCH 154/162] fix re-runs with existing output directory

---
 test/rmgpy/rmg/mainTest.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/test/rmgpy/rmg/mainTest.py b/test/rmgpy/rmg/mainTest.py
index cea42c859c..2a68efc73d 100644
--- a/test/rmgpy/rmg/mainTest.py
+++ b/test/rmgpy/rmg/mainTest.py
@@ -32,15 +32,12 @@
 import shutil
 from unittest.mock import patch
 
-import pytest
-
 import pandas as pd
+import pytest
 
-from rmgpy.rmg.main import RMG, initialize_log, make_profile_graph
-from rmgpy.rmg.main import RMG_Memory
-from rmgpy import get_path
-from rmgpy import settings
+from rmgpy import get_path, settings
 from rmgpy.data.rmg import RMGDatabase
+from rmgpy.rmg.main import RMG, RMG_Memory, initialize_log, make_profile_graph
 from rmgpy.rmg.model import CoreEdgeReactionModel
 
 originalPath = get_path()
@@ -195,7 +192,10 @@ def setup_class(cls):
         cls.outputDir = os.path.join(cls.testDir, "output_w_filters")
         cls.databaseDirectory = settings["database.directory"]
 
-        os.mkdir(cls.outputDir)
+        try:
+            os.mkdir(cls.outputDir)
+        except FileExistsError:
+            pass  # output directory already exists
         initialize_log(logging.INFO, os.path.join(cls.outputDir, "RMG.log"))
 
         cls.rmg = RMG(

From d34a4be8e0c5d8e73d90dc747343d203b8acfcf3 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 2 Dec 2024 08:04:23 -0500
Subject: [PATCH 155/162] move surface site check to after requires_rms has
 been set

---
 rmgpy/rmg/main.py | 55 ++++++++++++++++++++++++++++++-----------------
 1 file changed, 35 insertions(+), 20 deletions(-)

diff --git a/rmgpy/rmg/main.py b/rmgpy/rmg/main.py
index acc5ae8144..d9b3a1f366 100644
--- a/rmgpy/rmg/main.py
+++ b/rmgpy/rmg/main.py
@@ -52,8 +52,6 @@
 from scipy.optimize import brute
 
 import rmgpy.util as util
-from rmgpy.rmg.model import Species, CoreEdgeReactionModel
-from rmgpy.rmg.pdep import PDepNetwork
 from rmgpy import settings
 from rmgpy.chemkin import ChemkinWriter
 from rmgpy.constraints import fails_species_constraints
@@ -61,26 +59,31 @@
 from rmgpy.data.kinetics.family import TemplateReaction
 from rmgpy.data.kinetics.library import KineticsLibrary, LibraryReaction
 from rmgpy.data.rmg import RMGDatabase
-from rmgpy.exceptions import ForbiddenStructureException, DatabaseError, CoreError, InputError
-from rmgpy.kinetics.diffusionLimited import diffusion_limiter
 from rmgpy.data.vaporLiquidMassTransfer import vapor_liquid_mass_transfer
-from rmgpy.kinetics import ThirdBody
-from rmgpy.kinetics import Troe
+from rmgpy.exceptions import (
+    CoreError,
+    DatabaseError,
+    ForbiddenStructureException,
+    InputError,
+)
+from rmgpy.kinetics import ThirdBody, Troe
+from rmgpy.kinetics.diffusionLimited import diffusion_limiter
 from rmgpy.molecule import Molecule
 from rmgpy.qm.main import QMDatabaseWriter
 from rmgpy.reaction import Reaction
-from rmgpy.rmg.listener import SimulationProfileWriter, SimulationProfilePlotter
+from rmgpy.rmg.listener import SimulationProfilePlotter, SimulationProfileWriter
+from rmgpy.rmg.model import CoreEdgeReactionModel, Species
 from rmgpy.rmg.output import OutputHTMLWriter
-from rmgpy.rmg.pdep import PDepReaction
+from rmgpy.rmg.pdep import PDepNetwork, PDepReaction
+from rmgpy.rmg.reactionmechanismsimulator_reactors import Reactor as RMSReactor
 from rmgpy.rmg.settings import ModelSettings
-from rmgpy.solver.base import TerminationTime, TerminationConversion
+from rmgpy.solver.base import TerminationConversion, TerminationTime
 from rmgpy.solver.simple import SimpleReactor
 from rmgpy.stats import ExecutionStatsWriter
 from rmgpy.thermo.thermoengine import submit
 from rmgpy.tools.plot import plot_sensitivity
 from rmgpy.tools.uncertainty import Uncertainty, process_local_results
 from rmgpy.yml import RMSWriter
-from rmgpy.rmg.reactionmechanismsimulator_reactors import Reactor as RMSReactor
 
 ################################################################################
 
@@ -269,12 +272,6 @@ def load_input(self, path=None):
         if self.solvent:
             self.reaction_model.solvent_name = self.solvent
 
-        if self.surface_site_density:
-            self.reaction_model.surface_site_density = self.surface_site_density
-            self.reaction_model.core.phase_system.phases["Surface"].site_density = self.surface_site_density.value_si
-            self.reaction_model.edge.phase_system.phases["Surface"].site_density = self.surface_site_density.value_si
-        self.reaction_model.coverage_dependence = self.coverage_dependence
-
         self.reaction_model.verbose_comments = self.verbose_comments
         self.reaction_model.save_edge_species = self.save_edge_species
 
@@ -514,6 +511,13 @@ def initialize(self, **kwargs):
         # if RMS is not installed and they did not use it, we avoid calling certain functions that would raise an error
         requires_rms = any(isinstance(reactor_system, RMSReactor) for reactor_system in self.reaction_systems)
 
+        if self.surface_site_density:
+            self.reaction_model.surface_site_density = self.surface_site_density
+            if requires_rms:
+                self.reaction_model.core.phase_system.phases["Surface"].site_density = self.surface_site_density.value_si
+                self.reaction_model.edge.phase_system.phases["Surface"].site_density = self.surface_site_density.value_si
+        self.reaction_model.coverage_dependence = self.coverage_dependence
+
         if kwargs.get("restart", ""):
             import rmgpy.rmg.input
 
@@ -589,8 +593,9 @@ def initialize(self, **kwargs):
         # Do all liquid-phase startup things:
         if self.solvent:
             solvent_data = self.database.solvation.get_solvent_data(self.solvent)
-            self.reaction_model.core.phase_system.phases["Default"].set_solvent(solvent_data)
-            self.reaction_model.edge.phase_system.phases["Default"].set_solvent(solvent_data)
+            if requires_rms:
+                self.reaction_model.core.phase_system.phases["Default"].set_solvent(solvent_data)
+                self.reaction_model.edge.phase_system.phases["Default"].set_solvent(solvent_data)
 
             diffusion_limiter.enable(solvent_data, self.database.solvation)
             logging.info("Setting solvent data for {0}".format(self.solvent))
@@ -1259,8 +1264,9 @@ def run_uncertainty_analysis(self):
                 )
                 self.uncertainty["global"] = False
             else:
-                import re
                 import random
+                import re
+
                 from rmgpy.tools.canteramodel import Cantera
                 from rmgpy.tools.globaluncertainty import ReactorPCEFactory
 
@@ -2451,7 +2457,16 @@ def make_profile_graph(stats_file, force_graph_generation=False):
 
     if display_found or force_graph_generation:
         try:
-            from gprof2dot import PstatsParser, DotWriter, SAMPLES, themes, TIME, TIME_RATIO, TOTAL_TIME, TOTAL_TIME_RATIO
+            from gprof2dot import (
+                SAMPLES,
+                TIME,
+                TIME_RATIO,
+                TOTAL_TIME,
+                TOTAL_TIME_RATIO,
+                DotWriter,
+                PstatsParser,
+                themes,
+            )
         except ImportError:
             logging.warning("Trouble importing from package gprof2dot. Unable to create a graph of the profile statistics.")
             logging.warning("Try getting the latest version with something like `pip install --upgrade gprof2dot`.")

From eb9bd740465190140b581b964b9206d2c0ddadb7 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 2 Dec 2024 21:07:22 -0500
Subject: [PATCH 156/162] update expected values for new version of coolprop

---
 test/rmgpy/data/solvationTest.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/test/rmgpy/data/solvationTest.py b/test/rmgpy/data/solvationTest.py
index 584eb0b7e4..eb93652224 100644
--- a/test/rmgpy/data/solvationTest.py
+++ b/test/rmgpy/data/solvationTest.py
@@ -29,6 +29,8 @@
 
 import os
 
+import pytest
+
 from rmgpy import settings
 from rmgpy.data.solvation import (
     DatabaseError,
@@ -36,14 +38,12 @@
     SolvationDatabase,
     SolventLibrary,
     get_critical_temperature,
-    get_liquid_saturation_density,
     get_gas_saturation_density,
+    get_liquid_saturation_density,
 )
-from rmgpy.molecule import Molecule
-from rmgpy.rmg.main import RMG
-from rmgpy.rmg.main import Species
 from rmgpy.exceptions import InputError
-import pytest
+from rmgpy.molecule import Molecule
+from rmgpy.rmg.main import RMG, Species
 
 
 class TestSoluteDatabase:
@@ -141,8 +141,8 @@ def test_saturation_density(self):
         """
         compound_name = "Hexane"
         temp = 400  # in K
-        assert round(abs(get_liquid_saturation_density(compound_name, temp) - 6383.22), 2) == 0
-        assert round(abs(get_gas_saturation_density(compound_name, temp) - 162.99), 2) == 0
+        assert round(abs(get_liquid_saturation_density(compound_name, temp) - 6385.15), 2) == 0
+        assert round(abs(get_gas_saturation_density(compound_name, temp) - 163.02), 2) == 0
         # Unsupported compound name
         with pytest.raises(DatabaseError):
             get_gas_saturation_density("Hexadecane", temp)

From df81684d8ef92a80a06159d150f4a8d0ada6eb00 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 2 Dec 2024 21:07:45 -0500
Subject: [PATCH 157/162] update expected reproducibility for new dep changes

---
 test/rmgpy/statmech/ndTorsionsTest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/rmgpy/statmech/ndTorsionsTest.py b/test/rmgpy/statmech/ndTorsionsTest.py
index 80186b1f3e..5df907f074 100644
--- a/test/rmgpy/statmech/ndTorsionsTest.py
+++ b/test/rmgpy/statmech/ndTorsionsTest.py
@@ -109,4 +109,4 @@ def test_hindered_rotor_nd(self):
         hdnd.read_scan()
         assert round(abs(hdnd.Es[0]) - 8.58538448, 4) == 0
         hdnd.fit()
-        assert round(abs(hdnd.calc_partition_function(300.0)) - 2.899287634962152, 5) == 0
+        assert round(abs(hdnd.calc_partition_function(300.0)) - 2.899287634962152, 4) == 0

From 2ba37e254cbfd83bf8196b46e2f3b1d08fd1f3e4 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Mon, 2 Dec 2024 21:09:48 -0500
Subject: [PATCH 158/162] skip julia install in docs build

---
 .github/workflows/docs.yml | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 7bf7d35308..b500afd43d 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -36,12 +36,6 @@ jobs:
           activate-environment: rmg_env
           use-mamba: true
 
-      # installs the extra RMS conda dependencies
-      - name: Add RMS dependencies
-        run: |
-          mamba install -c conda-forge julia=1.9.1 pyjulia>=0.6 
-          mamba install -c rmg pyrms diffeqpy
-
       - name: Install sphinx
         run: mamba install -y sphinx
 
@@ -66,13 +60,6 @@ jobs:
           make clean
           make
 
-      - name: Install and link Julia dependencies
-        timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
-        run: |
-          which julia
-          export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
-          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
-
       - name: Checkout gh-pages Branch
         uses: actions/checkout@v2
         with:

From 91881f667be214be91e3e0c98f4ba43355ae509b Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Tue, 3 Dec 2024 00:28:37 -0500
Subject: [PATCH 159/162] WIP milp debugging

---
 rmgpy/molecule/resonance.pxd |   4 +-
 rmgpy/molecule/resonance.py  | 136 +++++++++++++++++------------------
 2 files changed, 66 insertions(+), 74 deletions(-)

diff --git a/rmgpy/molecule/resonance.pxd b/rmgpy/molecule/resonance.pxd
index d4cc6d361c..e9148116ba 100644
--- a/rmgpy/molecule/resonance.pxd
+++ b/rmgpy/molecule/resonance.pxd
@@ -66,8 +66,6 @@ cpdef list generate_kekule_structure(Graph mol)
 
 cpdef list generate_clar_structures(Graph mol, bint save_order=?)
 
-cpdef tuple _clar_optimization(Graph mol, bint save_order=?)
-
-cpdef list _solve_clar_milp(cnp.ndarray[cnp.int_t, ndim=1] c, bounds, tuple constraints, int n_ring, max_num=?)
+cpdef list _clar_optimization(Graph mol, list recursion_constraints=?, int max_num=?, bint save_order=?)
 
 cpdef void _clar_transformation(Graph mol, list aromatic_ring)
diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
index 0e0bd19405..257f8b1f74 100644
--- a/rmgpy/molecule/resonance.py
+++ b/rmgpy/molecule/resonance.py
@@ -54,19 +54,18 @@
 import logging
 from operator import attrgetter
 
+import cython
 import numpy as np
 from scipy.optimize import Bounds, LinearConstraint, milp
 
-import cython
-
 import rmgpy.molecule.filtration as filtration
 import rmgpy.molecule.pathfinder as pathfinder
-from rmgpy.exceptions import KekulizationError, AtomTypeError, ResonanceError
+from rmgpy.exceptions import AtomTypeError, KekulizationError, ResonanceError
 from rmgpy.molecule.adjlist import Saturator
+from rmgpy.molecule.fragment import CuttingLabel
 from rmgpy.molecule.graph import Vertex
 from rmgpy.molecule.kekulize import kekulize
 from rmgpy.molecule.molecule import Atom, Bond, Molecule
-from rmgpy.molecule.fragment import CuttingLabel
 
 
 def populate_resonance_algorithms(features=None):
@@ -919,14 +918,14 @@ def generate_clar_structures(mol, save_order=False):
         mol.assign_atom_ids()
 
     try:
-        aromatic_rings, bonds, solutions = _clar_optimization(mol, save_order=save_order)
+        solutions = _clar_optimization(mol, save_order=save_order)
     except (RuntimeError, ValueError):  # either a crash during optimization or the result was an empty tuple
         # The optimization algorithm did not work on the first iteration
         return []
 
     mol_list = []
 
-    for solution in solutions:
+    for new_mol, aromatic_rings, bonds, solution in solutions:
 
         new_mol = mol.copy(deep=True)
         # The solution includes a part corresponding to rings, y, and a part corresponding to bonds, x, using
@@ -966,10 +965,9 @@ def _tuplize_bond(bond):
     return (bond.atom1.id, bond.atom2.id)
 
 
-def _clar_optimization(mol, save_order=False):
+def _clar_optimization(mol, recursion_constraints=None, max_num=-1, save_order=False):
     """
-    Implements linear programming algorithm for finding Clar structures. This algorithm maximizes the number
-    of Clar sextets within the constraints of molecular geometry and atom valency.
+    Implements linear programming algorithm for finding Clar structures.
 
     Returns a list of valid Clar solutions in the form of a tuple, with the following entries:
         [0] List of aromatic rings
@@ -983,17 +981,29 @@ def _clar_optimization(mol, save_order=False):
         Hansen, P.; Zheng, M. The Clar Number of a Benzenoid Hydrocarbon and Linear Programming.
             J. Math. Chem. 1994, 15 (1), 93–107.
     """
-    cython.declare(molecule=Graph, aromatic_rings=list, exo=list, n_rings=cython.int, n_atoms=cython.int, n_bonds=cython.int,
-                   A=list, solutions=list)
+    cython.declare(
+        molecule=Graph,
+        aromatic_rings=list,
+        exo_info=list,
+        n_ring=cython.int,
+        n_atom=cython.int,
+        n_bond=cython.int,
+        A=list,
+        solutions=list,
+    )
 
     # Make a copy of the molecule so we don't destroy the original
     molecule = mol.copy(deep=True)
 
     aromatic_rings = molecule.get_aromatic_rings(save_order=save_order)[0]
-    aromatic_rings.sort(key=_sum_atom_ids)
+    if len(aromatic_rings) == 0:
+        return []
 
-    if not aromatic_rings:
-        return tuple()
+    aromatic_rings.sort(key=_sum_atom_ids)
+    
+    # Cython doesn't allow mutable defaults, so we just set it here instead
+    if recursion_constraints is None:
+        recursion_constraints = []
 
     # Get list of atoms that are in rings
     atoms = set()
@@ -1007,22 +1017,22 @@ def _clar_optimization(mol, save_order=False):
         bonds.update([atom.bonds[key] for key in atom.bonds.keys() if key.is_non_hydrogen()])
     bonds = sorted(bonds, key=_tuplize_bond)
 
-    # Identify exocyclic bonds, and save their bond orders
-    exo = []
+    # identify exocyclic bonds, and save their order if exocyclic
+    exo_info = []
     for bond in bonds:
         if bond.atom1 not in atoms or bond.atom2 not in atoms:
+            # save order for exocyclic
             if bond.is_double():
-                exo.append(1)
+                exo_info.append(1)
             else:
-                exo.append(0)
-        else:
-            exo.append(0)
+                exo_info.append(0)
+        else:  # not exocyclic
+            exo_info.append(None)
 
     # Dimensions
     n_ring = len(aromatic_rings)
     n_atom = len(atoms)
     n_bond = len(bonds)
-    n_decision_variables = n_bond + n_ring
 
     # The aromaticity assignment problem is formulated as an MILP problem
     # minimize:
@@ -1039,90 +1049,74 @@ def _clar_optimization(mol, save_order=False):
         in_ring = [1 if atom in ring else 0 for ring in aromatic_rings]
         in_bond = [1 if atom in [bond.atom1, bond.atom2] else 0 for bond in bonds]
         A.append(in_ring + in_bond)
-    constraint = (LinearConstraint(
+    initial_constraint = [LinearConstraint(  # i.e. an equality constraint
         A=np.array(A, dtype=int), lb=np.ones(n_atom, dtype=int), ub=np.ones(n_atom, dtype=int)
-    ), )
+    )]
 
     # Objective vector for optimization: sextets have a weight of 1, double bonds have a weight of 0
-    c = np.array([1] * n_ring + [0] * n_bond, dtype=int)
+    # we negate because the original problem is formulated as maximization, whereas SciPy only does min
+    c = -np.array([1] * n_ring + [0] * n_bond, dtype=int)
 
-    # Variable bounds
+    # variable bounds
+    # - binary problem, so everything must be either zero or one
+    # - rings are simply 0 or 1
+    # - bonds are also 0 or 1, except exocyclic bonds which must remain unchanged
     bounds = Bounds(
-        lb=np.array(
-            [0] * n_ring + exo,
-            dtype=int,
-        ),  # lower bounds: 0 except for exo double bonds, which must be 1 (aka, do not modify them)
-        ub=np.array(
-            [1] * n_decision_variables,  # + [0 if val == 0 else 1 for val in exo],
-            dtype=int,
-        ),  # upper is 1 for all
+        lb=np.array([0] * n_ring + [0 if b is None else b for b in exo_info], dtype=int),
+        ub=np.array([1] * n_ring + [1 if b is None else b for b in exo_info], dtype=int),
     )
 
-    solutions = _solve_clar_milp(c, bounds, constraint, n_ring)
-
-    return aromatic_rings, bonds, solutions
-
-
-def _solve_clar_milp(
-    c,
-    bounds,
-    constraints,
-    n_ring,
-    max_num=None,
-):
-    """
-    A helpful function to solve the formulated clar optimization MILP problem. ``c``,
-    ``bounds``, and ``constraints`` are computed in _clar_optimization and follow the
-    definition of their corresponding kwargs in scipy.optimize.milp. ``n_ring`` is the
-    number of aromatic rings in the molecule. ``max_num`` is the maximum number of sextets
-    that can be found. If ``max_num`` is None for first run but will be updated during the
-    recursion and is used to check sub-optimal solution.
-    """
-    # To modify
-    cython.declare(inner_solutions=list)
-
     result = milp(
-        c=-c,  # negative for maximization
+        c=c,
         integrality=1,
         bounds=bounds,
-        constraints=constraints,
+        constraints=initial_constraint + recursion_constraints,
         options={'time_limit': 10},
     )
 
     if result.status != 0:
         raise RuntimeError("Optimization could not find a valid solution.")
 
-    obj_val, solution = -result.fun, result.x
+    clar_num, solution = -result.fun, result.x
+    print(f"{clar_num=} {max_num=} {solution=}")
 
     # Check that the result contains at least one aromatic sextet
-    if obj_val == 0:
+    # on recursive calls, this will eventually be the 'break case'
+    if clar_num == 0:
         return []
 
     # Check that the solution contains the maximum number of sextets possible
-    if max_num is None:
-        max_num = obj_val  # This is the first solution, so the result should be an upper limit
-    elif obj_val < max_num:
+    if max_num == -1:
+        max_num = clar_num  # This is the first solution, so the result should be an upper limit
+    elif clar_num < max_num:
         raise RuntimeError("Optimization obtained a sub-optimal solution.")
 
+    # on later runs, non-integer solutions occur - branching might be able to find actual solutions,
+    # but we just call it good enough here
     if any([x != 1 and x != 0 for x in solution]):
         raise RuntimeError('Optimization obtained a non-integer solution.')
 
-    # Generate constraints based on the solution obtained
-    y = solution[:n_ring]
-    constraints = constraints + (
+    # Subsequent Clar structures will have one fewer sextet
+    selected_sextets = list(solution[:n_ring])
+    # restrict those rings which were selected for the current clar structure
+    # from forming it again by requiring that their sum is 1 less than it used
+    # to be
+    print(np.array(selected_sextets + [0] * n_bond), np.array(selected_sextets + [0] * n_bond).dot(solution), clar_num - 1)
+    recursion_constraints += [
         LinearConstraint(
-            A=np.hstack([y, [0] * (solution.shape[0] - n_ring)]),
-            ub=sum(y) - 1,
+            A=np.array(selected_sextets + [0] * n_bond),
+            ub=clar_num - 1,
+            lb=0,
         ),
-    )
+    ]
 
     # Run optimization with additional constraints
     try:
-        inner_solutions = _solve_clar_milp(c, bounds, constraints, n_ring, max_num)
+        inner_solutions = _clar_optimization(mol, recursion_constraints=recursion_constraints, max_num=max_num, save_order=save_order)
     except RuntimeError:
         inner_solutions = []
 
-    return inner_solutions + [solution]
+    return inner_solutions + [(molecule, aromatic_rings, bonds, solution)]
 
 
 def _clar_transformation(mol, aromatic_ring):

From dee596b74ccecd2d1d4640bed712cd24e38de518 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Tue, 3 Dec 2024 12:27:49 -0500
Subject: [PATCH 160/162] sqwuash me

---
 rmgpy/molecule/resonance.pxd         |   4 +-
 rmgpy/molecule/resonance.py          | 119 +++++++++++++--------------
 test/rmgpy/molecule/resonanceTest.py |  10 ---
 3 files changed, 57 insertions(+), 76 deletions(-)

diff --git a/rmgpy/molecule/resonance.pxd b/rmgpy/molecule/resonance.pxd
index e9148116ba..a28c0aa1ad 100644
--- a/rmgpy/molecule/resonance.pxd
+++ b/rmgpy/molecule/resonance.pxd
@@ -66,6 +66,4 @@ cpdef list generate_kekule_structure(Graph mol)
 
 cpdef list generate_clar_structures(Graph mol, bint save_order=?)
 
-cpdef list _clar_optimization(Graph mol, list recursion_constraints=?, int max_num=?, bint save_order=?)
-
-cpdef void _clar_transformation(Graph mol, list aromatic_ring)
+cpdef list _clar_optimization(Graph mol, list recursion_constraints=?, int clar_number=?, bint save_order=?)
diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
index 257f8b1f74..d3ef2d0a7b 100644
--- a/rmgpy/molecule/resonance.py
+++ b/rmgpy/molecule/resonance.py
@@ -926,8 +926,6 @@ def generate_clar_structures(mol, save_order=False):
     mol_list = []
 
     for new_mol, aromatic_rings, bonds, solution in solutions:
-
-        new_mol = mol.copy(deep=True)
         # The solution includes a part corresponding to rings, y, and a part corresponding to bonds, x, using
         # nomenclature from the paper. In y, 1 means the ring as a sextet, 0 means it does not.
         # In x, 1 corresponds to a double bond, 0 either means a single bond or the bond is part of a sextet.
@@ -946,13 +944,16 @@ def generate_clar_structures(mol, save_order=False):
         # Then apply locations of aromatic sextets by converting to benzene bonds
         for index, ring in enumerate(aromatic_rings):
             if y[index] == 1:
-                _clar_transformation(new_mol, ring)
+                for i, atom_1 in enumerate(ring):
+                    for j, atom_2 in enumerate(ring):
+                        if new_mol.has_bond(atom_1, atom_2):
+                            new_mol.get_bond(atom_1, atom_2).order = 1.5
 
         try:
             new_mol.update_atomtypes()
         except AtomTypeError:
             pass
-        else:
+        finally:
             mol_list.append(new_mol)
 
     return mol_list
@@ -965,21 +966,27 @@ def _tuplize_bond(bond):
     return (bond.atom1.id, bond.atom2.id)
 
 
-def _clar_optimization(mol, recursion_constraints=None, max_num=-1, save_order=False):
+def _clar_optimization(mol, recursion_constraints=None, clar_number=-1, save_order=False):
     """
-    Implements linear programming algorithm for finding Clar structures.
+    Implements Mixed Integer Linear Programming for finding Clar structures.
+
+    First finds the Clar number (and an arbitrary structure with that number), then recursively
+    calls itself to enumerate more structures with that Clar number. No guarantees about
+    which structures will be found, or how many (we stop solving once solution would require
+    branching, which typically happens after at least a couple have already been found).
 
     Returns a list of valid Clar solutions in the form of a tuple, with the following entries:
-        [0] List of aromatic rings
-        [1] List of bonds
-        [2] Optimization solutions
+        [0] Copy of mol
+        [1] List of aromatic rings
+        [2] List of bonds
+        [3] Solution vector
 
-    The optimization solutions may contain multiple valid solutions, each is an array of boolean values with sextet assignments
-    followed by double bond assignments, with indices corresponding to the list of aromatic rings and list of bonds, respectively.
+    The solution vector is a binary integer list of length (# aromatic rings + # bonds) indicating
+    if each ring is aromatic and if each bond is double.
 
-    Method adapted from:
-        Hansen, P.; Zheng, M. The Clar Number of a Benzenoid Hydrocarbon and Linear Programming.
-            J. Math. Chem. 1994, 15 (1), 93–107.
+    This implementation follows the original implementation very closely (Hansen, P.; Zheng, M. The
+    Clar Number of a Benzenoid Hydrocarbon and Linear Programming. J. Math. Chem. 1994, 15 (1), 93–107.)
+    with only slight modifications to prevent changing bond orders for exocyclic atoms.
     """
     cython.declare(
         molecule=Graph,
@@ -992,26 +999,30 @@ def _clar_optimization(mol, recursion_constraints=None, max_num=-1, save_order=F
         solutions=list,
     )
 
-    # Make a copy of the molecule so we don't destroy the original
+    # after we find all the Clar structures we will modify the molecule bond orders to be aromatic,
+    # so we make explicit copies to avoid overwrites.
     molecule = mol.copy(deep=True)
 
     aromatic_rings = molecule.get_aromatic_rings(save_order=save_order)[0]
+
+    # doesn't work for system without aromatic rings, just exit
     if len(aromatic_rings) == 0:
         return []
 
+    # stability between multiple runs
     aromatic_rings.sort(key=_sum_atom_ids)
-    
+
     # Cython doesn't allow mutable defaults, so we just set it here instead
     if recursion_constraints is None:
         recursion_constraints = []
 
-    # Get list of atoms that are in rings
+    # Get set of atoms that are in rings
     atoms = set()
     for ring in aromatic_rings:
         atoms.update(ring)
     atoms = sorted(atoms, key=attrgetter('id'))
 
-    # Get list of bonds involving the ring atoms, ignoring bonds to hydrogen
+    # Get set of bonds involving the ring atoms, ignoring bonds to hydrogen
     bonds = set()
     for atom in atoms:
         bonds.update([atom.bonds[key] for key in atom.bonds.keys() if key.is_non_hydrogen()])
@@ -1053,6 +1064,18 @@ def _clar_optimization(mol, recursion_constraints=None, max_num=-1, save_order=F
         A=np.array(A, dtype=int), lb=np.ones(n_atom, dtype=int), ub=np.ones(n_atom, dtype=int)
     )]
 
+    # on recursive calls we already know the Clar number, so we can additionally constrain the system
+    # to only find structures with this number. Allows detecting when all formulae have been found and,
+    # in theory, should solve faster
+    if clar_number != -1:
+        initial_constraint += [
+            LinearConstraint(
+                A=np.array([1] * n_ring + [0] * n_bond),
+                ub=clar_number,
+                lb=clar_number,
+            ),
+        ]
+
     # Objective vector for optimization: sextets have a weight of 1, double bonds have a weight of 0
     # we negate because the original problem is formulated as maximization, whereas SciPy only does min
     c = -np.array([1] * n_ring + [0] * n_bond, dtype=int)
@@ -1074,69 +1097,39 @@ def _clar_optimization(mol, recursion_constraints=None, max_num=-1, save_order=F
         options={'time_limit': 10},
     )
 
-    if result.status != 0:
-        raise RuntimeError("Optimization could not find a valid solution.")
+    if (status := result.status) != 0:
+        if status == 2:  # infeasible
+            raise RuntimeError("All valid Clar formulae have been enumerated!")
+        else:
+            raise RuntimeError(f"Clar optimization failed (Exit Code {status}) for an unexpected reason: {result.message}")
 
-    clar_num, solution = -result.fun, result.x
-    print(f"{clar_num=} {max_num=} {solution=}")
+    _clar_number, solution = -result.fun, result.x
 
-    # Check that the result contains at least one aromatic sextet
-    # on recursive calls, this will eventually be the 'break case'
-    if clar_num == 0:
+    # optimization may have reached a bad local minimum - this case is rare
+    if _clar_number == 0:
         return []
 
-    # Check that the solution contains the maximum number of sextets possible
-    if max_num == -1:
-        max_num = clar_num  # This is the first solution, so the result should be an upper limit
-    elif clar_num < max_num:
-        raise RuntimeError("Optimization obtained a sub-optimal solution.")
+    # first solution, so the result should be an upper limit
+    if clar_number == -1:
+        clar_number = _clar_number
 
-    # on later runs, non-integer solutions occur - branching might be able to find actual solutions,
-    # but we just call it good enough here
-    if any([x != 1 and x != 0 for x in solution]):
-        raise RuntimeError('Optimization obtained a non-integer solution.')
-
-    # Subsequent Clar structures will have one fewer sextet
     selected_sextets = list(solution[:n_ring])
     # restrict those rings which were selected for the current clar structure
     # from forming it again by requiring that their sum is 1 less than it used
     # to be
-    print(np.array(selected_sextets + [0] * n_bond), np.array(selected_sextets + [0] * n_bond).dot(solution), clar_num - 1)
     recursion_constraints += [
         LinearConstraint(
             A=np.array(selected_sextets + [0] * n_bond),
-            ub=clar_num - 1,
+            ub=clar_number - 1,
             lb=0,
         ),
     ]
 
     # Run optimization with additional constraints
     try:
-        inner_solutions = _clar_optimization(mol, recursion_constraints=recursion_constraints, max_num=max_num, save_order=save_order)
-    except RuntimeError:
+        inner_solutions = _clar_optimization(mol, recursion_constraints=recursion_constraints, clar_number=clar_number, save_order=save_order)
+    except RuntimeError as e:
+        logging.debug(f"Clar Optimization stopped: {e}")
         inner_solutions = []
 
     return inner_solutions + [(molecule, aromatic_rings, bonds, solution)]
-
-
-def _clar_transformation(mol, aromatic_ring):
-    """
-    Performs Clar transformation for given ring in a molecule, ie. conversion to aromatic sextet.
-
-    Args:
-        mol             a :class:`Molecule` object
-        aromaticRing    a list of :class:`Atom` objects corresponding to an aromatic ring in mol
-
-    This function directly modifies the input molecule and does not return anything.
-    """
-    cython.declare(bondList=list, i=cython.int, atom1=Vertex, atom2=Vertex, bond=Edge)
-
-    bond_list = []
-
-    for i, atom1 in enumerate(aromatic_ring):
-        for atom2 in aromatic_ring[i + 1:]:
-            if mol.has_bond(atom1, atom2):
-                bond_list.append(mol.get_bond(atom1, atom2))
-
-    for bond in bond_list:
-        bond.order = 1.5
diff --git a/test/rmgpy/molecule/resonanceTest.py b/test/rmgpy/molecule/resonanceTest.py
index 2130307e25..8c620ff8a3 100644
--- a/test/rmgpy/molecule/resonanceTest.py
+++ b/test/rmgpy/molecule/resonanceTest.py
@@ -31,7 +31,6 @@
 from rmgpy.molecule.molecule import Molecule
 from rmgpy.molecule.resonance import (
     _clar_optimization,
-    _clar_transformation,
     generate_clar_structures,
     generate_kekule_structure,
     generate_optimal_aromatic_resonance_structures,
@@ -1369,15 +1368,6 @@ class ClarTest:
     Contains unit tests for Clar structure methods.
     """
 
-    def test_clar_transformation(self):
-        """Test that clarTransformation generates an aromatic ring."""
-        mol = Molecule().from_smiles("c1ccccc1")
-        sssr = mol.get_smallest_set_of_smallest_rings()
-        _clar_transformation(mol, sssr[0])
-        mol.update_atomtypes()
-
-        assert mol.is_aromatic()
-
     def test_clar_optimization(self):
         """Test to ensure pi electrons are conserved during optimization"""
         mol = Molecule().from_smiles("C1=CC=C2C=CC=CC2=C1")  # Naphthalene

From 370687091515a5505bc5ade512f0bb641f24c242 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Tue, 3 Dec 2024 12:28:02 -0500
Subject: [PATCH 161/162] fix literal comparison

---
 rmgpy/molecule/util.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rmgpy/molecule/util.py b/rmgpy/molecule/util.py
index d1093f4582..46f8c3504c 100644
--- a/rmgpy/molecule/util.py
+++ b/rmgpy/molecule/util.py
@@ -30,8 +30,8 @@
 import itertools
 import re
 
-from rmgpy.molecule.molecule import Molecule
 from rmgpy.molecule.fragment import Fragment
+from rmgpy.molecule.molecule import Molecule
 
 
 def get_element_count(obj):
@@ -47,7 +47,7 @@ def get_element_count(obj):
             match = re.match(r"([a-z]+)([0-9]*)", piece, re.I)
             if match:
                 element, count = match.groups()
-                if count is '':
+                if count == '':
                     count = 1
                 if element in element_count:
                     element_count[element] += int(count)

From c30809524c79da89bbbc1d31dfa77566d674a421 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Tue, 3 Dec 2024 13:07:30 -0500
Subject: [PATCH 162/162] squash as well

---
 rmgpy/molecule/resonance.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
index d3ef2d0a7b..3cb0bad9b8 100644
--- a/rmgpy/molecule/resonance.py
+++ b/rmgpy/molecule/resonance.py
@@ -1101,7 +1101,7 @@ def _clar_optimization(mol, recursion_constraints=None, clar_number=-1, save_ord
         if status == 2:  # infeasible
             raise RuntimeError("All valid Clar formulae have been enumerated!")
         else:
-            raise RuntimeError(f"Clar optimization failed (Exit Code {status}) for an unexpected reason: {result.message}")
+            raise RuntimeError(f"Optimization failed (Exit Code {status}) for an unexpected reason '{result.message}'")
 
     _clar_number, solution = -result.fun, result.x
 
@@ -1109,6 +1109,11 @@ def _clar_optimization(mol, recursion_constraints=None, clar_number=-1, save_ord
     if _clar_number == 0:
         return []
 
+    # on later runs, non-integer solutions occur - branching might be able to find actual solutions,
+    # but we just call it good enough here
+    if any([x != 1 and x != 0 for x in solution]):
+        raise RuntimeError("Optimization obtained a non-integer solution - no more formulae will be enumerated.")
+
     # first solution, so the result should be an upper limit
     if clar_number == -1:
         clar_number = _clar_number