Restart attribute error

rmgpy/rmg/main.py

@@ -1558,11 +1558,11 @@ def initialize_reaction_threshold_and_react_flags(self):
 
                 # Load in the restart filter tensors
                 with h5py.File(self.filters_path, 'r') as f:
-                    try:
-                        unimolecular_threshold_restart = f.get('unimolecular_threshold').value
-                        bimolecular_threshold_restart = f.get('bimolecular_threshold').value
+                    if 'unimolecular_threshold' in f.keys():
+                        unimolecular_threshold_restart = f.get('unimolecular_threshold')[()]
+                        bimolecular_threshold_restart = f.get('bimolecular_threshold')[()]
                         if self.trimolecular:
-                            trimolecular_threshold_restart = f.get('trimolecular_threshold').value
+                            trimolecular_threshold_restart = f.get('trimolecular_threshold')[()]
 
                         # Expand Thresholds to match number of species in the current model.
                         # Note that we are about to reorder the core species to match the order in the restart seed
@@ -1581,7 +1581,7 @@ def initialize_reaction_threshold_and_react_flags(self):
 
                         filters_found = True
 
-                    except KeyError:  # If we can't find the filters then this is because filtering was not used
+                    else:  # If we can't find the filters then this is because filtering was not used
                         logging.warning('No filters were found in file {0}. This is to be expected if the restart '
                                         'files specified are from an RMG job without reaction filtering. Therefore, '
                                         'RMG will assume that all of the core species from the restart core seed have '

rmgpy/rmg/mainTest.py

@@ -27,13 +27,14 @@
 #                                                                             #
 ###############################################################################
 
+import logging
 import os
 import shutil
 import unittest
 
 from nose.plugins.attrib import attr
 
-from rmgpy.rmg.main import RMG
+from rmgpy.rmg.main import RMG, initialize_log
 from rmgpy.rmg.main import RMG_Memory
 from rmgpy import get_path
 from rmgpy import settings
@@ -183,6 +184,76 @@ def test_make_cantera_input_file(self):
                     self.fail('The output Cantera file is not loadable in Cantera.')
 
 
+@attr('functional')
+class TestRestartWithFilters(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        """A function that is run ONCE before all unit tests in this class."""
+        cls.testDir = os.path.join(originalPath, 'rmg', 'test_data', 'restartTest')
+        cls.outputDir = os.path.join(cls.testDir, 'output_w_filters')
+        cls.databaseDirectory = settings['database.directory']
+
+        os.mkdir(cls.outputDir)
+        initialize_log(logging.INFO, os.path.join(cls.outputDir, 'RMG.log'))
+
+        cls.rmg = RMG(input_file=os.path.join(cls.testDir, 'restart_w_filters.py'),
+                      output_directory=os.path.join(cls.outputDir))
+
+    def test_restart_with_filters(self):
+        """
+        Test that the RMG restart job with filters included completed without problems
+        """
+        self.rmg.execute()
+        with open(os.path.join(self.outputDir, 'RMG.log'), 'r') as f:
+            self.assertIn('MODEL GENERATION COMPLETED', f.read())
+
+    @classmethod
+    def tearDownClass(cls):
+        """A function that is run ONCE after all unit tests in this class."""
+        # Reset module level database
+        import rmgpy.data.rmg
+        rmgpy.data.rmg.database = None
+
+        # Remove output directory
+        shutil.rmtree(cls.outputDir)
+
+
+@attr('functional')
+class TestRestartNoFilters(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        """A function that is run ONCE before all unit tests in this class."""
+        cls.testDir = os.path.join(originalPath, 'rmg', 'test_data', 'restartTest')
+        cls.outputDir = os.path.join(cls.testDir, 'output_no_filters')
+        cls.databaseDirectory = settings['database.directory']
+
+        os.mkdir(cls.outputDir)
+        initialize_log(logging.INFO, os.path.join(cls.outputDir, 'RMG.log'))
+
+        cls.rmg = RMG(input_file=os.path.join(cls.testDir, 'restart_no_filters.py'),
+                      output_directory=os.path.join(cls.outputDir))
+
+    def test_restart_no_filters(self):
+        """
+        Test that the RMG restart job with no filters included completed without problems
+        """
+        self.rmg.execute()
+        with open(os.path.join(self.outputDir, 'RMG.log'), 'r') as f:
+            self.assertIn('MODEL GENERATION COMPLETED', f.read())
+
+    @classmethod
+    def tearDownClass(cls):
+        """A function that is run ONCE after all unit tests in this class."""
+        # Reset module level database
+        import rmgpy.data.rmg
+        rmgpy.data.rmg.database = None
+
+        # Remove output directory
+        shutil.rmtree(cls.outputDir)
+
+
 class TestCanteraOutput(unittest.TestCase):
 
     def setUp(self):

rmgpy/rmg/test_data/restartTest/restart_no_filters.py

@@ -0,0 +1,57 @@
+restartFromSeed(path='seed_no_filters')
+
+# Data sources
+database(
+    thermoLibraries = ['primaryThermoLibrary'],
+    reactionLibraries = [],
+    seedMechanisms = [],
+    kineticsDepositories = ['training'],
+    kineticsFamilies = ['H_Abstraction','Disproportionation','R_Recombination',
+                        'Birad_recombination', 'Birad_R_Recombination'],
+    kineticsEstimator = 'rate rules',
+)
+
+# List of species
+species(
+    label='H2',
+    reactive=True,
+    structure=SMILES("[H][H]"),
+)
+species(
+   label='O2',
+   reactive=True,
+   structure=SMILES("[O][O]"),
+)
+
+# Reaction systems
+simpleReactor(
+    temperature=(1000,'K'),
+    pressure=(1.0,'bar'),
+    initialMoleFractions={
+        'H2':.67, 'O2':.33,
+    },
+    terminationConversion={
+        'H2': 0.9,
+    },
+    terminationTime=(1e6,'s'),
+)
+
+simulator(
+    atol=1e-16,
+    rtol=1e-8,
+)
+
+model(
+    toleranceKeepInEdge=0.0,
+    toleranceMoveToCore=0.001,
+    toleranceInterruptSimulation=0.001,
+    maximumEdgeSpecies=100000,
+)
+
+options(
+    units='si',
+    generateOutputHTML=True,
+    generatePlots=False,
+    saveEdgeSpecies=True,
+    saveSimulationProfiles=True,
+)

rmgpy/rmg/test_data/restartTest/restart_w_filters.py

@@ -0,0 +1,52 @@
+restartFromSeed(path='seed_w_filters')
+
+# Data sources
+database(
+    thermoLibraries = ['primaryThermoLibrary'],
+    reactionLibraries = [],
+    seedMechanisms = [],
+    kineticsDepositories = ['training'],
+    kineticsFamilies = 'default',
+    kineticsEstimator = 'rate rules',
+)
+
+# List of species
+species(
+    label='ethane',
+    reactive=True,
+    structure=SMILES("CC"),
+)
+
+# Reaction systems
+simpleReactor(
+    temperature=(1350,'K'),
+    pressure=(1.0,'bar'),
+    initialMoleFractions={
+        "ethane": 1.0,
+    },
+    terminationConversion={
+        'ethane': 0.9,
+    },
+    terminationTime=(1e6,'s'),
+)
+
+simulator(
+    atol=1e-16,
+    rtol=1e-8,
+)
+
+model(
+    toleranceKeepInEdge=0.0,
+    toleranceMoveToCore=0.1,
+    toleranceInterruptSimulation=0.1,
+    maximumEdgeSpecies=100000,
+    filterReactions=True,
+)
+
+options(
+    units='si',
+    generateOutputHTML=True,
+    generatePlots=False,
+    saveEdgeSpecies=True,
+    saveSimulationProfiles=True,
+)

rmgpy/rmg/test_data/restartTest/seed_no_filters/filters/species_map.yml

@@ -0,0 +1,49 @@
+- '1 Ar u0 p4 c0
+
+  '
+- '1 He u0 p1 c0
+
+  '
+- '1 Ne u0 p4 c0
+
+  '
+- '1 N u0 p1 c0 {2,T}
+
+  2 N u0 p1 c0 {1,T}
+
+  '
+- '1 H u0 p0 c0 {2,S}
+
+  2 H u0 p0 c0 {1,S}
+
+  '
+- 'multiplicity 3
+
+  1 O u1 p2 c0 {2,S}
+
+  2 O u1 p2 c0 {1,S}
+
+  '
+- 'multiplicity 2
+
+  1 H u1 p0 c0
+
+  '
+- 'multiplicity 2
+
+  1 O u0 p2 c0 {2,S} {3,S}
+
+  2 O u1 p2 c0 {1,S}
+
+  3 H u0 p0 c0 {1,S}
+
+  '
+- '1 O u0 p2 c0 {2,S} {3,S}
+
+  2 O u0 p2 c0 {1,S} {4,S}
+
+  3 H u0 p0 c0 {1,S}
+
+  4 H u0 p0 c0 {2,S}
+
+  '

rmgpy/rmg/test_data/restartTest/seed_no_filters/seed/dictionary.txt

@@ -0,0 +1,25 @@
+H
+multiplicity 2
+1 H u1 p0 c0
+
+H2
+1 H u0 p0 c0 {2,S}
+2 H u0 p0 c0 {1,S}
+
+O2
+multiplicity 3
+1 O u1 p2 c0 {2,S}
+2 O u1 p2 c0 {1,S}
+
+[O]O
+multiplicity 2
+1 O u0 p2 c0 {2,S} {3,S}
+2 O u1 p2 c0 {1,S}
+3 H u0 p0 c0 {1,S}
+
+OO
+1 O u0 p2 c0 {2,S} {3,S}
+2 O u0 p2 c0 {1,S} {4,S}
+3 H u0 p0 c0 {1,S}
+4 H u0 p0 c0 {2,S}
+