Merge pull request #1669 from ReactionMechanismGenerator/simulate_MB_…

…sampled_reactor

Created a new reactor type MBSampledReactor for modeling laser lab Mass-Spec experiments

rmgpy/chemkin.pyx

@@ -1411,7 +1411,11 @@ def getSpeciesIdentifier(species):
             # Try the chemical formula
             name = '{0}({1:d})'.format(species.molecule[0].getFormula(), species.index)
             if len(name) <= 10:
-                return name
+                if 'obs' in label:
+                    # For MBSampledReactor, keep observed species tag
+                    return name + '_obs'
+                else:
+                    return name
 
         # As a last resort, just use the index
         if species.index >= 0:
@@ -1421,7 +1425,11 @@ def getSpeciesIdentifier(species):
             else:
                 name = 'S({0:d})'.format(species.index)
             if len(name) <= 10:
-                return name
+                if 'obs' in label:
+                    # For MBSampledReactor, keep observed species tag
+                    return name + '_obs'
+                else:
+                    return name
 
     # If we're here then we just can't come up with a valid Chemkin name
     # for this species, so raise an exception

rmgpy/rmg/input.py

@@ -38,10 +38,11 @@
 from rmgpy import settings
 
 from rmgpy.molecule import Molecule
-from rmgpy.quantity import Quantity, Energy, SurfaceConcentration
+from rmgpy.quantity import Quantity, Energy, RateCoefficient, SurfaceConcentration
 from rmgpy.solver.base import TerminationTime, TerminationConversion, TerminationRateRatio
 from rmgpy.solver.simple import SimpleReactor
 from rmgpy.solver.liquid import LiquidReactor
+from rmgpy.solver.mbSampled import MBSampledReactor
 from rmgpy.solver.surface import SurfaceReactor
 from rmgpy.rmg.settings import ModelSettings, SimulatorSettings
 from model import CoreEdgeReactionModel
@@ -447,6 +448,69 @@ def surfaceReactor(temperature,
     rmg.reactionSystems.append(system)
     system.log_initial_conditions(number=len(rmg.reactionSystems))
 
+
+# Reaction systems
+def mbsampledReactor(temperature,
+                     pressure,
+                     initialMoleFractions,
+                     mbsamplingRate,
+                     terminationConversion=None,
+                     terminationTime=None,
+                     sensitivity=None,
+                     sensitivityThreshold=1e-3,
+                     constantSpecies=None,
+                     ):
+    logging.debug('Found MBSampledReactor reaction system')
+
+    for value in initialMoleFractions.values():
+        if value < 0:
+            raise InputError('Initial mole fractions cannot be negative.')
+
+    for spec in initialMoleFractions:
+        initialMoleFractions[spec] = float(initialMoleFractions[spec])
+
+    totalInitialMoles = sum(initialMoleFractions.values())
+    if totalInitialMoles != 1:
+        logging.warning('Initial mole fractions do not sum to one; normalizing.')
+        logging.info('')
+        logging.info('Original composition:')
+        for spec, molfrac in initialMoleFractions.iteritems():
+            logging.info("{0} = {1}".format(spec, molfrac))
+        for spec in initialMoleFractions:
+            initialMoleFractions[spec] /= totalInitialMoles
+        logging.info('')
+        logging.info('Normalized mole fractions:')
+        for spec, molfrac in initialMoleFractions.iteritems():
+            logging.info("{0} = {1}".format(spec, molfrac))
+
+    T = Quantity(temperature)
+    P = Quantity(pressure)
+
+    k_sampling = RateCoefficient(mbsamplingRate, 's^-1')
+
+    constantSpeciesList = []
+
+    for spec in constantSpecies:
+        constantSpeciesList.append(speciesDict[spec])
+
+    termination = []
+    if terminationConversion is not None:
+        for spec, conv in terminationConversion.iteritems():
+            termination.append(TerminationConversion(speciesDict[spec], conv))
+    if terminationTime is not None:
+        termination.append(TerminationTime(Quantity(terminationTime)))
+    if len(termination) == 0:
+        raise InputError(
+            'No termination conditions specified for reaction system #{0}.'.format(len(rmg.reactionSystems) + 2))
+
+    sensitiveSpecies = []
+    if sensitivity:
+        if isinstance(sensitivity, str): sensitivity = [sensitivity]
+        for spec in sensitivity:
+            sensitiveSpecies.append(speciesDict[spec])
+    system = MBSampledReactor(T, P, initialMoleFractions, k_sampling, constantSpeciesList, termination, sensitiveSpecies, sensitivityThreshold)
+    rmg.reactionSystems.append(system)
+
 def simulator(atol, rtol, sens_atol=1e-6, sens_rtol=1e-4):
     rmg.simulatorSettingsList.append(SimulatorSettings(atol, rtol, sens_atol, sens_rtol))
 
@@ -756,6 +820,7 @@ def readInputFile(path, rmg0):
         'simpleReactor': simpleReactor,
         'liquidReactor': liquidReactor,
         'surfaceReactor': surfaceReactor,
+        'mbsampledReactor': mbsampledReactor,
         'simulator': simulator,
         'solvation': solvation,
         'model': model,