Merge branch 'main' into improve_auto_cut

Author: hwpang

Makefile

@@ -4,6 +4,9 @@
 #
 ################################################################################
 
+CC=gcc
+CXX=g++
+
 .PHONY : all minimal main solver check pycheck arkane clean install decython documentation test q2dtor
 
 all: pycheck main solver check

documentation/source/users/rmg/input.rst

@@ -49,7 +49,7 @@ by Benson's method.
 
 For example, if you wish to use the GRI-Mech 3.0 mechanism [GRIMech3.0]_ as a ThermoLibrary in your model, the syntax will be::
 
-	thermoLibraries = ['primaryThermoLibrary','GRI-Mech3.0']
+	thermoLibraries = ['primaryThermoLibrary', 'GRI-Mech3.0']
 
 .. [GRIMech3.0] Gregory P. Smith, David M. Golden, Michael Frenklach, Nigel W. Moriarty, Boris Eiteneer, Mikhail Goldenberg, C. Thomas Bowman, Ronald K. Hanson, Soonho Song, William C. Gardiner, Jr., Vitali V. Lissianski, and Zhiwei Qin http://combustion.berkeley.edu/gri-mech/
 
@@ -78,7 +78,7 @@ In the following example, the user has created
 a reaction library with a few additional reactions specific to n-butane, and these reactions
 are to be used in addition to the Glarborg C3 library::
 
-	reactionLibraries = [('Glarborg/C3',False)],
+	reactionLibraries = [('Glarborg/C3', False)],
 
 The keyword False/True permits user to append all unused reactions (= kept in the edge) from this library to the chemkin file.
 True means those reactions will be appended. Using just the string inputs would lead to
@@ -104,6 +104,23 @@ given in each mechanism, the different mechanisms can have different units.
 	Library.
 
 
+.. _externallib:
+
+External Libraries
+------------------
+Users may direct RMG to use thermo and/or kinetic libraries which are not included in the RMG database,
+e.g., a library a user created that was intentionally saved to a path different than the conventional
+RMG-database location. In such cases, the user can specify the full path to the library in the input file::
+
+    thermoLibraries = ['path/to/your/thermo/library/file.py']
+
+or::
+
+    reactionLibraries = [(path/to/your/kinetic/library/folder/']
+
+Combinations in any order of RMG's legacy libraries and users' external libraries are allowed,
+and the order in which the libraries are specified is the order in which they are loaded and given priority.
+
 .. _seedmechanism:
 
 Seed Mechanisms

environment.yml

@@ -81,13 +81,13 @@ dependencies:
   - conda-forge::gprof2dot
   - conda-forge::numdifftools
   - conda-forge::quantities
+  - conda-forge::muq
+  - conda-forge::lpsolve55
+  - conda-forge::ringdecomposerlib-python
 
 # packages we maintain
-  - rmg::lpsolve55
-  - rmg::muq2
   - rmg::pydas >=1.0.3
   - rmg::pydqed >=1.0.3
-  - rmg::pyrdl
   - rmg::pyrms
   - rmg::symmetry
 

rmgpy/data/kinetics/database.py

@@ -62,6 +62,7 @@ def __init__(self):
         self.recommended_families = {}
         self.families = {}
         self.libraries = {}
+        self.external_library_labels = {}
         self.library_order = []  # a list of tuples in the format ('library_label', LibraryType),
                                  # where LibraryType is set to either 'Reaction Library' or 'Seed'.
         self.local_context = {
@@ -227,17 +228,18 @@ def load_libraries(self, path, libraries=None):
         The `path` points to the folder of kinetics libraries in the database,
         and the libraries should be in files like :file:`<path>/<library>.py`.
         """
-
+        self.external_library_labels = dict()
         if libraries is not None:
             for library_name in libraries:
                 library_file = os.path.join(path, library_name, 'reactions.py')
                 if os.path.exists(library_name):
                     library_file = os.path.join(library_name, 'reactions.py')
-                    short_library_name = os.path.split(library_name)[-1]
+                    short_library_name = os.path.basename(library_name.rstrip(os.path.sep))
                     logging.info(f'Loading kinetics library {short_library_name} from {library_name}...')
                     library = KineticsLibrary(label=short_library_name)
                     library.load(library_file, self.local_context, self.global_context)
                     self.libraries[library.label] = library
+                    self.external_library_labels[library_name] = library.label
                 elif os.path.exists(library_file):
                     logging.info(f'Loading kinetics library {library_name} from {library_file}...')
                     library = KineticsLibrary(label=library_name)

rmgpy/reaction.py

@@ -1030,15 +1030,15 @@ def generate_reverse_rate_coefficient(self, network_kinetics=False, Tmin=None, T
             return self.reverse_arrhenius_rate(kf, kunits)
 
         elif isinstance(kf, Chebyshev):
-            Tlist = 1.0 / np.linspace(1.0 / kf.Tmax.value, 1.0 / kf.Tmin.value, 50)
-            Plist = np.linspace(kf.Pmin.value, kf.Pmax.value, 20)
+            Tlist = 1.0 / np.linspace(1.0 / kf.Tmax.value_si, 1.0 / kf.Tmin.value_si, 50)
+            Plist = np.linspace(kf.Pmin.value_si, kf.Pmax.value_si, 20)
             K = np.zeros((len(Tlist), len(Plist)), float)
             for Tindex, T in enumerate(Tlist):
                 for Pindex, P in enumerate(Plist):
                     K[Tindex, Pindex] = kf.get_rate_coefficient(T, P) / self.get_equilibrium_constant(T)
             kr = Chebyshev()
-            kr.fit_to_data(Tlist, Plist, K, kunits, kf.degreeT, kf.degreeP, kf.Tmin.value, kf.Tmax.value, kf.Pmin.value,
-                         kf.Pmax.value)
+            kr.fit_to_data(Tlist, Plist, K, kunits, kf.degreeT, kf.degreeP, kf.Tmin.value, kf.Tmax.value,
+                           kf.Pmin.value_si, kf.Pmax.value_si)
             return kr
 
         elif isinstance(kf, PDepArrhenius):

rmgpy/rmg/model.py

@@ -1722,7 +1722,12 @@ def add_reaction_library_to_edge(self, reaction_library):
         num_old_edge_reactions = len(self.edge.reactions)
 
         logging.info("Adding reaction library {0} to model edge...".format(reaction_library))
-        reaction_library = database.kinetics.libraries[reaction_library]
+        if reaction_library in database.kinetics.libraries:
+            reaction_library = database.kinetics.libraries[reaction_library]
+        elif reaction_library in database.kinetics.external_library_labels:
+            reaction_library = database.kinetics.libraries[database.kinetics.external_library_labels[reaction_library]]
+        else:
+            raise ValueError(f'Library {reaction_library} not found.')
 
         rxns = reaction_library.get_library_reactions()
         for rxn in rxns:

test/rmgpy/data/transportTest.py

@@ -151,9 +151,9 @@ def test_joback(self):
             [
                 "acetone",
                 "CC(=O)C",
-                Length(5.36421, "angstroms"),
+                Length(5.32979, "angstroms"),
                 Energy(3.20446, "kJ/mol"),
-                "Epsilon & sigma estimated with Tc=500.53 K, Pc=47.11 bar (from Joback method)",
+                "Epsilon & sigma estimated with Tc=500.53 K, Pc=48.02 bar (from Joback method)",
             ],
             [
                 "cyclopenta-1,2-diene",