diff --git a/snippets/changeFuncExpression.py b/snippets/changeFuncExpression.py index 343dc23d..d6111c2f 100644 --- a/snippets/changeFuncExpression.py +++ b/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" ) diff --git a/snippets/chemDoseResponse.py b/snippets/chemDoseResponse.py index 671015b6..e24882b4 100644 --- a/snippets/chemDoseResponse.py +++ b/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() diff --git a/snippets/cspaceSteadyState.py b/snippets/cspaceSteadyState.py index e24b06cc..1fdcdb0b 100644 --- a/snippets/cspaceSteadyState.py +++ b/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() diff --git a/snippets/cylinderMotor.py b/snippets/cylinderMotor.py index 1f0cf281..650f702f 100644 --- a/snippets/cylinderMotor.py +++ b/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 diff --git a/snippets/diffusion_using_Gillespie.py b/snippets/diffusion_using_Gillespie.py index cdb5dba5..023f5afd 100644 --- a/snippets/diffusion_using_Gillespie.py +++ b/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( ): diff --git a/snippets/findChemSteadyState.py b/snippets/findChemSteadyState.py index 008af946..acd3cdbf 100644 --- a/snippets/findChemSteadyState.py +++ b/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() diff --git a/snippets/funcInputToPools.py b/snippets/funcInputToPools.py index 4a92032a..6bc07537 100644 --- a/snippets/funcInputToPools.py +++ b/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/##' ''' ''' diff --git a/snippets/funcRateHarmonicOsc.py b/snippets/funcRateHarmonicOsc.py index 66207881..83b19f77 100644 --- a/snippets/funcRateHarmonicOsc.py +++ b/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() diff --git a/snippets/funcReacLotkaVolterra.py b/snippets/funcReacLotkaVolterra.py index acd4c285..f540237b 100644 --- a/snippets/funcReacLotkaVolterra.py +++ b/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 diff --git a/snippets/rxdFuncDiffusion.py b/snippets/rxdFuncDiffusion.py index c9c9d058..5ee63036 100644 --- a/snippets/rxdFuncDiffusion.py +++ b/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 ) diff --git a/snippets/rxdFuncDiffusionStoch.py b/snippets/rxdFuncDiffusionStoch.py index e19c1170..fcb90efe 100644 --- a/snippets/rxdFuncDiffusionStoch.py +++ b/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 ) diff --git a/snippets/rxdReacDiffusion.py b/snippets/rxdReacDiffusion.py index 84c3f8bf..7e0d75c3 100644 --- a/snippets/rxdReacDiffusion.py +++ b/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 ) diff --git a/snippets/savemodel.py b/snippets/savemodel.py index 7c106cbd..a8b044a8 100644 --- a/snippets/savemodel.py +++ b/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() diff --git a/snippets/scaleVolumes.py b/snippets/scaleVolumes.py index 25b4c236..d9320633 100644 --- a/snippets/scaleVolumes.py +++ b/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' ) diff --git a/snippets/scriptGssaSolver.py b/snippets/scriptGssaSolver.py index 281adddd..6ddce913 100644 --- a/snippets/scriptGssaSolver.py +++ b/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" ) diff --git a/snippets/stochasticLotkaVolterra.py b/snippets/stochasticLotkaVolterra.py index 0f97bc93..6535841d 100644 --- a/snippets/stochasticLotkaVolterra.py +++ b/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 diff --git a/snippets/switchKineticSolvers.py b/snippets/switchKineticSolvers.py index 0be72c2d..cda41049 100644 --- a/snippets/switchKineticSolvers.py +++ b/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(): """