changed path to reacSystemPath

snippets/changeFuncExpression.py

@@ -99,7 +99,7 @@ def main():
     stoich = moose.Stoich( '/model/compartment/stoich' )
     stoich.compartment = moose.element( '/model/compartment' )
     stoich.ksolve = ksolve
-    stoich.path = "/model/compartment/##"
+    stoich.reacSystemPath = "/model/compartment/##"
     #solver.method = "rk5"
     #mesh = moose.element( "/model/compartment/mesh" )
     #moose.connect( mesh, "remesh", solver, "remesh" )

snippets/chemDoseResponse.py

@@ -65,7 +65,7 @@ def main():
     stoich = moose.Stoich( '/model/compartment/stoich' )
     stoich.compartment = compartment
     stoich.ksolve = ksolve
-    stoich.path = "/model/compartment/##"
+    stoich.reacSystemPath = "/model/compartment/##"
     state = moose.SteadyState( '/model/compartment/state' )
 
     moose.reinit()

snippets/cspaceSteadyState.py

@@ -111,7 +111,7 @@ def main():
     stoich.compartment = compartment
     stoich.ksolve = ksolve
     #ksolve.stoich = stoich
-    stoich.path = "/model/compartment/##"
+    stoich.reacSystemPath = "/model/compartment/##"
     state = moose.SteadyState( '/model/compartment/state' )
 
     moose.reinit()

snippets/cylinderMotor.py

@@ -98,7 +98,7 @@ def makeModel():
     stoich.compartment = compartment
     stoich.ksolve = ksolve
     stoich.dsolve = dsolve
-    stoich.path = "/model/compartment/##"
+    stoich.reacSystemPath = "/model/compartment/##"
     assert( dsolve.numPools == 4 )
     a.vec[0].concInit = concA * 1
     b.vec[num-1].concInit = concA * 2

snippets/diffusion_using_Gillespie.py

@@ -70,7 +70,7 @@ def setup_solvers( ):
     k = moose.Ksolve( '%s/ksolve' % compt_.path )
     s.ksolve = k
     s.compartment = compt_
-    s.path = '%s/##' % compt_.path 
+    s.reacSystemPath = '%s/##' % compt_.path 
 
 
 def main( ):

snippets/findChemSteadyState.py

@@ -71,7 +71,7 @@ def main():
     stoich = moose.Stoich( '/model/compartment/stoich' )
     stoich.compartment = compartment
     stoich.ksolve = ksolve
-    stoich.path = "/model/compartment/##"
+    stoich.reacSystemPath = "/model/compartment/##"
     state = moose.SteadyState( '/model/compartment/state' )
 
     moose.reinit()

snippets/funcInputToPools.py

@@ -64,7 +64,7 @@ def makeModel():
     stoich = moose.Stoich( '/model/compartment/stoich' )
     stoich.compartment = compartment
     stoich.ksolve = gsolve
-    stoich.path = '/model/compartment/##'
+    stoich.reacSystemPath = '/model/compartment/##'
     '''
     '''
 

snippets/funcRateHarmonicOsc.py

@@ -87,7 +87,7 @@ def main():
     stoich = moose.Stoich( '/model/harmonic/stoich' )
     stoich.compartment = compt
     stoich.ksolve = ksolve
-    stoich.path = '/model/harmonic/##'
+    stoich.reacSystemPath = '/model/harmonic/##'
     for i in range( 11, 18 ):
         moose.setClock( i, 0.1 )
     moose.reinit()

snippets/funcReacLotkaVolterra.py

@@ -111,7 +111,7 @@ def main():
     stoich = moose.Stoich( '/model/lotka/stoich' )
     stoich.compartment = compt
     stoich.ksolve = ksolve
-    stoich.path = '/model/lotka/##'
+    stoich.reacSystemPath = '/model/lotka/##'
     moose.reinit()
     moose.start( runtime ) # Run the model
 

snippets/rxdFuncDiffusion.py

@@ -44,7 +44,7 @@ def main():
     stoich.ksolve = ksolve
     stoich.dsolve = dsolve
     stoich.compartment = compt
-    stoich.path = '/cylinder/##'
+    stoich.reacSystemPath = '/cylinder/##'
 
     #initialize
     x = numpy.arange( 0, compt.x1, compt.diffLength )

snippets/rxdFuncDiffusionStoch.py

@@ -44,7 +44,7 @@ def main():
     stoich.compartment = compt
     stoich.ksolve = ksolve
     stoich.dsolve = dsolve
-    stoich.path = '/cylinder/##'
+    stoich.reacSystemPath = '/cylinder/##'
 
     #for i in range( 10, 18 ):
     #    moose.setClock( i, dt )

snippets/rxdReacDiffusion.py

@@ -54,7 +54,7 @@ def main():
     stoich.compartment = compt
     stoich.ksolve = ksolve
     stoich.dsolve = dsolve
-    stoich.path = '/cylinder/##'
+    stoich.reacSystemPath = '/cylinder/##'
     for i in range( 10, 18 ):
         moose.setClock( i, dt )
 

snippets/savemodel.py

@@ -57,7 +57,7 @@ def main():
     file using moose 
     """
     model = moose.loadModel(os.path.join( cwd, '../genesis/reaction.g'), '/model')
-    written = moose.mooseWriteKkit('/model', 'testsave.g')
+    written = moose.writeKkit('/model', 'testsave.g')
     print( written )
 if __name__ == '__main__':
     main()

snippets/scaleVolumes.py

@@ -120,7 +120,7 @@ def main():
     compt = moose.element( '/model/compartment' );
     stoich.compartment = compt
     stoich.ksolve = gsolve
-    stoich.path = "/model/compartment/##"
+    stoich.reacSystemPath = "/model/compartment/##"
     #moose.setClock( 5, 1.0 ) # clock for the solver
     #moose.useClock( 5, '/model/compartment/gsolve', 'process' )
     a = moose.element( '/model/compartment/a' )

snippets/scriptGssaSolver.py

@@ -91,7 +91,7 @@ def main():
     stoich = moose.Stoich( '/model/compartment/stoich' )
     stoich.compartment = moose.element( '/model/compartment' )
     stoich.ksolve = gsolve
-    stoich.path = "/model/compartment/##"
+    stoich.reacSystemPath = "/model/compartment/##"
     #solver.method = "rk5"
     #mesh = moose.element( "/model/compartment/mesh" )
     #moose.connect( mesh, "remesh", solver, "remesh" )

snippets/stochasticLotkaVolterra.py

@@ -120,7 +120,7 @@ def main():
     stoich = moose.Stoich( '/model/lotka/stoich' )
     stoich.compartment = compt
     stoich.ksolve = ksolve
-    stoich.path = '/model/lotka/##'
+    stoich.reacSystemPath = '/model/lotka/##'
     moose.reinit()
     moose.start( runtime ) # Run the model
 

snippets/switchKineticSolvers.py

@@ -41,7 +41,7 @@ def switchSolvers(solver):
         stoich = moose.Stoich('/model/kinetics/stoich')
         stoich.compartment = compt
         stoich.ksolve = ksolve
-        stoich.path = "/model/kinetics/##"
+        stoich.reacSystemPath = "/model/kinetics/##"
 
 def main():
     """