Add flag in RMG input for restarting from a seed mechanism

examples/rmg/commented/input.py

@@ -1,3 +1,15 @@
+# Uncomment either of the blocks below to restart from a seed mechanism
+#
+# # Option 1: Specify the path to an RMG (version > 2.4.1) generated seed mechanism folder, which contains all of the
+# # required files (core and edge seed, filters and mappings) in their default locations and names in the seed folder.
+# restartFromSeed(path='seed')  # Location of the seed mechanism (with `Filters` subfolder) to load for restarting
+#
+# # Option 2: Specify the paths of each of the required files individually.
+# restartFromSeed(coreSeed='seed/Seed'  # Path to core seed folder. Must contain `reactions.py` and `dictionary.txt`
+#                 edgeSeed='seed/Seed_edge'  # Path to edge seed folder containing `reactions.py` and `dictionary.txt`
+#                 filters='seed/Filters/filters.h5',
+#                 speciesMap='seed/Filters/species_map.yml')
+
 # Data sources
 database(
     # overrides RMG thermo calculation of RMG with these values.

rmgpy/rmg/input.py

@@ -770,6 +770,50 @@ def uncertainty(localAnalysis=False, globalAnalysis=False, uncorrelated=True, co
     }
 
 
+def restartFromSeed(path=None, coreSeed=None, edgeSeed=None, filters=None, speciesMap=None):
+    parentDir = os.path.dirname(rmg.inputFile)
+    rmg.restart = True
+    docLink = 'http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/input.html#restarting-from-a-seed-mechanism.'
+
+    if path:
+        if any((coreSeed, edgeSeed, filters, speciesMap)):
+            raise InputError('For restarting an RMG job from a seed mechanism, either the path to the RMG generated '
+                             'seed mechanism should be given as `path`, or the path for each of the required files '
+                             'should be explicitly given, but not both. Please take one approach or the other. For '
+                             'further information see the RMG documentation on restarting from a seed mechanism at '
+                             '{0}.'.format(docLink))
+
+        if not os.path.isabs(path):
+            path = os.path.join(parentDir, path)
+
+        if not os.path.exists(path):
+            raise ValueError('Unable to find the path to the restart seed folder. {0} does not exist'.format(path))
+
+        # Try to find the paths for all of the required modules
+        rmg.coreSeedPath = os.path.join(path, 'Seed')
+        rmg.edgeSeedPath = os.path.join(path, 'Seed_edge')
+        rmg.filtersPath = os.path.join(path, 'Filters', 'filters.h5')
+        rmg.speciesMapPath = os.path.join(path, 'Filters', 'species_map.yml')
+
+    else:  # The user has specified each of the paths individually
+        rmg.coreSeedPath = coreSeed
+        rmg.edgeSeedPath = edgeSeed
+        rmg.filtersPath = filters
+        rmg.speciesMapPath = speciesMap
+
+    rmgPaths = [rmg.coreSeedPath, rmg.edgeSeedPath, rmg.filtersPath, rmg.speciesMapPath]
+    pathErrors = [filePath for filePath in rmgPaths if not os.path.exists(filePath)]
+
+    if pathErrors:
+        if path:
+            raise InputError('Could not find one or more of the required files/directories for restarting from a seed ' 
+                             'mechanism: {0}. Try specifying the file paths individually. See the RMG documentation '
+                             'at {1} for more information'.format(pathErrors, docLink))
+        else:
+            raise InputError('Could not find one or more of the required files/directories for restarting from a seed '
+                             'mechanism: {0}. See the RMG documentation at {1} for more information'.format(pathErrors,
+                                                                                                            docLink))
+
 ################################################################################
 
 def setGlobalRMG(rmg0):
@@ -831,6 +875,7 @@ def readInputFile(path, rmg0):
         'generatedSpeciesConstraints': generatedSpeciesConstraints,
         'thermoCentralDatabase': thermoCentralDatabase,
         'uncertainty': uncertainty,
+        'restartFromSeed': restartFromSeed,
     }
 
     try:

rmgpy/rmg/main.py

@@ -219,6 +219,11 @@ def clear(self):
         self.wallTime = '00:00:00:00'
         self.initializationTime = 0
         self.kineticsdatastore = None
+        self.restart = False
+        self.coreSeedPath = None
+        self.edgeSeedPath = None
+        self.filtersPath = None
+        self.speciesMapPath = None
 
         self.name = 'Seed'
         self.generateSeedEachIteration = True