include solvent information in the .rms file

ReactionMechanismGenerator · Jun 17, 2019 · c71800e · c71800e
1 parent e77f98b
commit c71800e
Showing 1 changed file with 15 additions and 9 deletions.
diff --git a/rmgpy/yml.py b/rmgpy/yml.py
@@ -18,18 +18,20 @@ def convertchemkin2yml(chemkinpath,spcdictpath=None,output="chem.rms"):
         spcs,rxns = loadChemkinFile(chemkinpath)
     writeyml(spcs,rxns,path=output)
 
-def writeyml(spcs,rxns,path="chem.yml"):
-    D = getmechdict(spcs,rxns)
+def writeyml(spcs,rxns,solvent=None,solventData=None,path="chem.yml"):
+    D = getmechdict(spcs,rxns,solvent=solvent,solventData=solventData)
     yaml.dump(D,stream=file(path,'w'))
 
-def getmechdict(spcs,rxns):
+def getmechdict(spcs,rxns,solvent='solvent',solventData=None):
     D = dict()
     D["Units"] = dict()
     D["Reactions"] = []
     D["Phases"] = [dict()]
     D["Phases"][0]["name"] = "phase"
     D["Phases"][0]["Species"] = [obj2dict(x,spcs) for x in spcs]
     D["Reactions"] = [obj2dict(x,spcs) for x in rxns]
+    if solventData:
+        D["Solvents"]= [obj2dict(solventData,spcs,label=solvent)]
     return D
 
 def getradicals(spc):
@@ -119,11 +121,11 @@ def obj2dict(obj,spcs,label="solvent"):
         D["name"] = label
         dsub = dict()
         dsub["type"] = "RiedelViscosity"
-        dsub["A"] = obj.A.value_si
-        dsub["B"] = obj.B.value_si
-        dsub["C"] = obj.C.value_si
-        dsub["D"] = obj.D.value_si
-        dsub["E"] = obj.E.value_si
+        dsub["A"] = float(obj.A)
+        dsub["B"] = float(obj.B)
+        dsub["C"] = float(obj.C)
+        dsub["D"] = float(obj.D)
+        dsub["E"] = float(obj.E)
         D["mu"] = dsub
     elif obj is None:
         return None
@@ -159,4 +161,8 @@ def __init__(self, outputDirectory=''):
         makeOutputSubdirectory(outputDirectory, 'rms')
 
     def update(self, rmg):
-        writeyml(rmg.reactionModel.core.species,rmg.reactionModel.core.reactions,os.path.join(self.outputDirectory,'rms','chem{}.rms').format(len(rmg.reactionModel.core.species)))
+        solventData = None
+        if rmg.solvent:
+            solventData = rmg.database.solvation.getSolventData(rmg.solvent)
+        writeyml(rmg.reactionModel.core.species,rmg.reactionModel.core.reactions,solvent=rmg.solvent,solventData=solventData,
+                 path=os.path.join(self.outputDirectory,'rms','chem{}.rms').format(len(rmg.reactionModel.core.species)))