save user input concentration as quantity

We want to preserve the units specified in the input file as much as
possible to avoid the ambiguity of saving just floats in memory

Author: sevyharris

rmgpy/rmg/input.py

@@ -656,10 +656,7 @@ def liquid_cat_reactor(temperature,
                    constantSpecies=[]):
     for spec, conc in initialConcentrations.items():
         if not isinstance(conc, list):
-            concentration = Quantity(conc)
-            # check the dimensions are ok
-            # convert to mol/m^3 (or something numerically nice? or must it be SI)
-            initialConcentrations[spec] = concentration.value_si
+            initialConcentrations[spec] = Quantity(conc)
         else:
             if len(conc) != 2:
                 raise InputError("Concentration values must either be in the form of (number,units) or a list with 2 "
@@ -715,14 +712,14 @@ def liquid_cat_reactor(temperature,
 
     initialCondLiq = dict()
     V = 1.0
-    A = V*Quantity(surfaceVolumeRatio).value_si
-    for key,item in initialConcentrations.items():
-        initialCondLiq[key] = item*V
+    A = V * Quantity(surfaceVolumeRatio).value_si
+    for key, conc in initialConcentrations.items():
+        initialCondLiq[key] = conc.value_si * V
     initialCondLiq["T"] = T
     initialCondLiq["V"] = V
     initialCondSurf = dict()
-    for key,item in initialSurfaceCoverages.items():
-        initialCondSurf[key] = item*rmg.surface_site_density.value_si*A
+    for key, surf_cov in initialSurfaceCoverages.items():
+        initialCondSurf[key] = surf_cov * rmg.surface_site_density.value_si * A
     initialCondSurf["T"] = T
     initialCondSurf["A"] = A
     initialCondSurf["d"] = 0.0
@@ -771,8 +768,7 @@ def constant_T_V_liquid_reactor(temperature,
 
     for spec, conc in initialConcentrations.items():
         if not isinstance(conc, list):
-            concentration = Quantity(conc)
-            initialConcentrations[spec] = concentration.value_si
+            initialConcentrations[spec] = Quantity(conc)
         else:
             raise InputError("Condition ranges not supported for this reaction type")
             if len(conc) != 2:
@@ -880,16 +876,16 @@ def constant_T_V_liquid_reactor(temperature,
     ############################################### process inputs ##############################################
 
     initial_conditions = dict()
-    for key, item in initialConcentrations.items():
-        initial_conditions[key] = item*V
+    for key, conc in initialConcentrations.items():
+        initial_conditions[key] = conc.value_si * V
     initial_conditions["T"] = T
     initial_conditions["V"] = V
 
     inlet_conditions = dict()
     if inletConcentrations:
         total_molar_flow_rate = 0
-        for key, item in inletConcentrations.items():
-            inlet_conditions[key] = item*inlet_volumetric_flow_rate
+        for key, inlet_conc in inletConcentrations.items():
+            inlet_conditions[key] = inlet_conc.value_si * inlet_volumetric_flow_rate
             total_molar_flow_rate += inlet_conditions[key]
         for key, item in inlet_conditions.items():
             inlet_conditions[key] = item/total_molar_flow_rate #molar fraction for each species
@@ -946,10 +942,7 @@ def liquid_reactor(temperature,
 
     for spec, conc in initialConcentrations.items():
         if not isinstance(conc, list):
-            concentration = Quantity(conc)
-            # check the dimensions are ok
-            # convert to mol/m^3 (or something numerically nice? or must it be SI)
-            initialConcentrations[spec] = concentration.value_si
+            initialConcentrations[spec] = Quantity(conc)
         else:
             if len(conc) != 2:
                 raise InputError("Concentration values must either be in the form of (number,units) or a list with 2 "