update to kkitwriter (#458)

kkit: dangling reaction and enzyme are not saved, lsoda is added to solver

Author: hrani

python/moose/chemUtil/add_Delete_ChemicalSolver.py

@@ -50,6 +50,8 @@ def mooseDeleteChemSolver(modelRoot):
  return ("mooseDeleteChemSolver is only for deleting Chemical Model solver which has to be `CubeMesh` or `CylMesh` found ",list(set([x.className for x in compts]) - set(['CubeMesh',"CylMesh"])))
 
 def stdSolvertype(solverName):
+ if solverName.lower() in ["lsoda"]:
+ return "lsoda"
  if solverName.lower() in ["gssa","gillespie","stochastic","gsolve"]:
  return "gssa"
  elif solverName.lower() in ["gsl","runge kutta","deterministic","ksolve","rungekutta","rk5","rkf","rk"]:
@@ -75,7 +77,6 @@ def mooseAddChemSolver(modelRoot, solver):
 
  previousSolver = stdSolvertype(comptinfo.solver)
  currentSolver = stdSolvertype(solver)
-
  if previousSolver != currentSolver:
  comptinfo.solver = currentSolver
  if (moose.exists(compts[0].path + '/stoich')):

python/moose/genesis/writeKkit.py

@@ -60,7 +60,7 @@
 #Todo : To be written
 # --StimulusTable
 
-def mooseWriteKkit( modelpath, filename, sceneitems={}):
+def mooseWriteKkit( modelpath, filename, sceneitems={},deletedanglingObj=True):
  global foundmatplotlib_
  if not foundmatplotlib_:
  print('No maplotlib found.'
@@ -114,10 +114,10 @@ def mooseWriteKkit( modelpath, filename, sceneitems={}):
  error = writePool(modelpath,f,gtId_vol,sceneitems)
  errors = errors+error
 
- reacList,error= writeReac(modelpath,f,sceneitems)
+ reacList,error= writeReac(modelpath,f,sceneitems,deletedanglingObj)
  errors = errors+error
 
- enzList,error = writeEnz(modelpath,f,sceneitems)
+ enzList,error = writeEnz(modelpath,f,sceneitems,deletedanglingObj)
  errors = errors+error
 
  chanList, error = writeConcChan(modelpath,f,sceneitems)
@@ -287,9 +287,18 @@ def writeConcChan(modelpath,f,sceneitems):
  " " + str(int(x)) + " " + str(int(y)) + " "+str(int(0))+"\n")
 
  return concChanList,error
-def writeEnz( modelpath,f,sceneitems):
+def writeEnz( modelpath,f,sceneitems,deletedanglingObj):
  error = ""
  enzList = moose.wildcardFind(modelpath+'/##[0][ISA=EnzBase]')
+ enzListnew = []
+ if deletedanglingObj == True:
+ for enz in enzList:
+ if (enz.numSubstrates != 0 and enz.numProducts != 0):
+ enzListnew.append(enz)
+ else:
+
+ error = error+"\n"+enz.className+ " - "+enz.parent.parent.name +" - "+enz.name+" doesn't have substrate or product"
+ enzList = enzListnew
  for enz in enzList:
  if findCompartment(enz) == moose.element('/'):
  error = error + " \n "+enz.path+ " doesn't have compartment ignored to write to genesis"
@@ -392,9 +401,17 @@ def storeReacMsg(reacList,f):
  s = s + "addmsg /kinetics/" + reacPath + " /kinetics/" + trimPath( prd ) + " REAC B A\n";
  f.write( s)
 
-def writeReac(modelpath,f,sceneitems):
+def writeReac(modelpath,f,sceneitems,deletedanglingObj):
  error = ""
  reacList = moose.wildcardFind(modelpath+'/##[0][ISA=Reac]')
+ reacListnew = []
+ if deletedanglingObj == True:
+ for reac in reacList:
+ if (reac.numProducts != 0 and reac.numSubstrates != 0):
+ reacListnew.append(reac)
+ else:
+ error = error+"\n"+reac.className+" - "+reac.parent.name+ " - "+reac.name+" doesn't have substrate or product"
+ reacList = reacListnew 
  for reac in reacList:
  if findCompartment(reac) == moose.element('/'):
  error = error + " \n "+reac.path+ " doesn't have compartment ignored to write to genesis"