Merge pull request #56 from ReactionMechanismGenerator/tst_lib

Iterate values of the ordered dict "entries" in the RMG thermo library

Author: kspieks

t3/main.py

@@ -1195,7 +1195,7 @@ def add_to_rmg_library(self):
                 for entry in arc_thermo_lib.entries.values():
                     entry_species = Species(molecule=[entry.item])
                     entry_species.generate_resonance_structures(keep_isomorphic=False, filter_structures=True)
-                    for existing_entry in rmg_thermo_lib.entries:
+                    for existing_entry in rmg_thermo_lib.entries.values():
                         if entry_species.is_isomorphic(existing_entry.item):
                             self.logger.warning(f"Not adding species {entry.label} to the "
                                                 f"{self.t3['options']['library_name']} thermo library, "

tests/data/restart/r6/species.yml

@@ -10,9 +10,11 @@
 import shutil
 
 from rmgpy import settings as rmg_settings
+from rmgpy.data.thermo import ThermoLibrary
 from rmgpy.rmg.pdep import PDepNetwork, PDepReaction
 from rmgpy.species import Species
-from rmgpy.thermo import NASA
+from rmgpy.thermo import NASA, ThermoData
+from rmgpy.statmech import Conformer, IdealGasTranslation, NonlinearRotor, HarmonicOscillator
 
 from arc.common import read_yaml_file
 from arc.species import ARCSpecies
@@ -551,7 +553,7 @@ def test_determine_species_based_on_sa():
 
 def test_determine_species_from_pdep_network():
     """Test determining species from pdep network"""
-    t3 = run_minimal(project_directory = os.path.join(DATA_BASE_PATH, 'pdep_network'),
+    t3 = run_minimal(project_directory=os.path.join(DATA_BASE_PATH, 'pdep_network'),
                      iteration=1,
                      set_paths=True,
                      )
@@ -761,6 +763,106 @@ def test_add_species():
     assert found_h2
 
 
+def test_add_to_rmg_library():
+    """Test adding thermo calculations to an existing thermo library"""
+    libraries_path = os.path.join(DATA_BASE_PATH, 'libraries')
+    if not os.path.isdir(libraries_path):
+        os.makedirs(libraries_path)
+
+    spc_1 = Species(
+        index=1,
+        label='C2H4',
+        thermo=ThermoData(
+            Tdata=([300.0, 400.0, 500.0, 600.0, 800.0, 1000.0, 1500.0], 'K'),
+            Cpdata=([3.0, 4.0, 5.0, 6.0, 8.0, 10.0, 15.0], 'cal/(mol*K)'),
+            H298=(-20.0, 'kcal/mol'),
+            S298=(50.0, 'cal/(mol*K)'),
+            Tmin=(300.0, 'K'),
+            Tmax=(2000.0, 'K'),
+        ),
+        conformer=Conformer(
+            E0=(0.0, 'kJ/mol'),
+            modes=[
+                IdealGasTranslation(mass=(28.03, 'amu')),
+                NonlinearRotor(inertia=([5.6952e-47, 2.7758e-46, 3.3454e-46], 'kg*m^2'), symmetry=1),
+                HarmonicOscillator(frequencies=([834.50, 973.31, 975.37, 1067.1, 1238.5, 1379.5, 1472.3, 1691.3,
+                                                 3121.6, 3136.7, 3192.5, 3221.0], 'cm^-1')),
+            ],
+            spin_multiplicity=1,
+            optical_isomers=1,
+        ),
+        smiles='C=C',
+    )
+
+    spc_2 = Species(
+        index=2,
+        label='CH4',
+        thermo=ThermoData(
+            Tdata=([300.0, 400.0, 500.0, 600.0, 800.0, 1000.0, 1500.0], 'K'),
+            Cpdata=([3.0, 4.0, 5.0, 6.0, 8.0, 10.0, 15.0], 'cal/(mol*K)'),
+            H298=(-50.0, 'kcal/mol'),
+            S298=(100.0, 'cal/(mol*K)'),
+            Tmin=(300.0, 'K'),
+            Tmax=(2000.0, 'K'),
+        ),
+        conformer=Conformer(
+            E0=(0.0, 'kJ/mol'),
+            modes=[
+                IdealGasTranslation(mass=(28.03, 'amu')),
+                NonlinearRotor(inertia=([5.6952e-47, 2.7758e-46, 3.3454e-46], 'kg*m^2'), symmetry=1),
+            ],
+            spin_multiplicity=1,
+            optical_isomers=1,
+        ),
+        smiles='C',
+    )
+
+    spc_3 = Species(
+        index=2,
+        label='CH4',
+        thermo=ThermoData(
+            Tdata=([300.0, 400.0, 500.0, 600.0, 800.0, 1000.0, 1500.0], 'K'),
+            Cpdata=([3.0, 4.0, 5.0, 6.0, 8.0, 10.0, 15.0], 'cal/(mol*K)'),
+            H298=(-92.0, 'kcal/mol'),  # this is different
+            S298=(12.0, 'cal/(mol*K)'),  # this is different
+            Tmin=(300.0, 'K'),
+            Tmax=(2000.0, 'K'),
+        ),
+        conformer=Conformer(
+            E0=(0.0, 'kJ/mol'),
+            modes=[
+                IdealGasTranslation(mass=(28.03, 'amu')),
+                NonlinearRotor(inertia=([5.6952e-47, 2.7758e-46, 3.3454e-46], 'kg*m^2'), symmetry=1),
+            ],
+            spin_multiplicity=1,
+            optical_isomers=1,
+        ),
+        smiles='C',
+    )
+
+    for lib_name, spc_list in [('RMG_library', [spc_1, spc_2]), ('ARC_library', [spc_3])]:
+        thermo_library = ThermoLibrary(name=lib_name, long_desc=lib_name)
+        for i, spc in enumerate(spc_list):
+            thermo_library.load_entry(index=i,
+                                      label=spc.label,
+                                      molecule=spc.to_adjacency_list(),
+                                      thermo=spc.thermo,
+                                      shortDesc=spc.label,
+                                      longDesc=spc.label)
+        thermo_library.save(os.path.join(libraries_path, f'{lib_name}.py'))
+
+    t3 = run_minimal()
+    t3.paths['ARC thermo lib'] = os.path.join(libraries_path, 'ARC_library.py')
+    t3.paths['RMG T3 thermo lib'] = os.path.join(libraries_path, 'RMG_library.py')
+    t3.add_to_rmg_library()
+    with open(t3.paths['RMG T3 thermo lib'], 'r') as f:
+        lines = f.readlines()
+    for line in ["        H298 = (-92,'kcal/mol'),\n",
+                 "        S298 = (12,'cal/(mol*K)'),\n",
+                 ]:
+        assert line in lines
+
+
 def test_dump_species():
     """Test dump species for restart purposes"""
     # create an empty `iteration_5` directory
@@ -860,6 +962,7 @@ def test_check_overtime():
 
 def teardown_module():
     """teardown any state that was previously setup with a setup_module method."""
+
     # delete log files
     for i in range(10):
         directory = os.path.join(restart_base_path, f'r{i}')
@@ -870,11 +973,25 @@ def teardown_module():
             log_archive = os.path.join(directory, 'log_archive')
             if os.path.isdir(log_archive):
                 shutil.rmtree(log_archive)
-    os.remove(os.path.join(restart_base_path, 'r6', 'iteration_6', 'ARC', 'T3_ARC_restart_test.info'))
+
+    # other files to delete
+    files = [os.path.join(restart_base_path, 'r6', 'iteration_6', 'ARC', 'T3_ARC_restart_test.info'),
+             os.path.join(restart_base_path, 'r6', 'iteration_6', 'ARC', 'input.yml'),
+             os.path.join(restart_base_path, 'r6', 'species.yml'),
+             os.path.join(DATA_BASE_PATH, 'process_arc', 'species.yml'),
+             ]
+    for file in files:
+        if os.path.isfile(file):
+            os.remove(file)
+
     # delete folders
     for directory in [test_minimal_project_directory,
                       dump_species_path,
                       os.path.join(DATA_BASE_PATH, 'minimal_data', 'log_archive'),
+                      os.path.join(DATA_BASE_PATH, 'determine_species', 'log_archive'),
+                      os.path.join(DATA_BASE_PATH, 'pdep_network', 'log_archive'),
+                      os.path.join(DATA_BASE_PATH, 'process_arc', 'log_archive'),
+                      os.path.join(DATA_BASE_PATH, 'libraries'),
                       os.path.join(restart_base_path, 'r6', 'iteration_6', 'ARC', 'output'),
                       os.path.join(restart_base_path, 'r6', 'iteration_6', 'ARC', 'log_and_restart_archive'),
                       ]: