def main():
"""
This example illustrates loading, running of an SBML model defined in XML format.
Default this file load's 00001-sbml-l3v1.xml which is taken from l3v1 SBML testcase.
Plots are setup.
Model is run for 20sec.
As a general rule we created model under '/path/model' and plots under '/path/graphs'.
If someone wants to load anyother file then
`python loadSbmlmodel filepath runtime`
"""
dfilepath = "../genesis/00001-sbml-l3v1.xml"
druntime = 20.0
msg = ""
try:
sys.argv[1]
except IndexError:
filepath = dfilepath
else:
filepath = sys.argv[1]
if not os.path.exists(filepath):
msg = "Filename or path does not exist", filepath, "loading default file", dfilepath
filepath = dfilepath
try:
sys.argv[2]
except:
runtime = druntime
else:
runtime = float(sys.argv[2])
sbmlId = moose.element('/')
# Loading the sbml file into MOOSE, models are loaded in path/model
sbmlId = moose.mooseReadSBML(filepath, '/sbml')
if isinstance(sbmlId, (list, tuple)):
print(sbmlId)
elif sbmlId.path != '/':
s1 = moose.element('/sbml/model/compartment/S1')
s2 = moose.element('/sbml/model/compartment/S2')
# Creating MOOSE Table, Table2 is for the chemical model
graphs = moose.Neutral('/sbml/graphs')
outputs1 = moose.Table2('/sbml/graphs/concS1')
outputs2 = moose.Table2('/sbml/graphs/concS2')
# connect up the tables
moose.connect(outputs1, 'requestOut', s1, 'getConc')
moose.connect(outputs2, 'requestOut', s2, 'getConc')
# gsl solver is added, default is ee
moose.mooseAddChemSolver(sbmlId.path, "ee")
# Reset and Run
moose.reinit()
moose.start(runtime)
return sbmlId, True, msg
return sbmlId, False, msg
def main():
"""
This example illustrates loading, running of an SBML model defined in XML format.
Default this file load's 00001-sbml-l3v1.xml which is taken from l3v1 SBML testcase.
Plots are setup.
Model is run for 20sec.
As a general rule we created model under '/path/model' and plots under '/path/graphs'.
If someone wants to load anyother file then
`python loadSbmlmodel filepath runtime`
"""
dfilepath = "../genesis/00001-sbml-l3v1.xml"
druntime = 20.0
msg = ""
try:
sys.argv[1]
except IndexError:
filepath = dfilepath
else:
filepath = sys.argv[1]
if not os.path.exists(filepath):
msg = "Filename or path does not exist",filepath,"loading default file",dfilepath
filepath = dfilepath
try:
sys.argv[2]
except :
runtime = druntime
else:
runtime = float(sys.argv[2])
sbmlId = moose.element('/')
# Loading the sbml file into MOOSE, models are loaded in path/model
sbmlId = moose.mooseReadSBML(filepath,'/sbml')
if isinstance(sbmlId, (list, tuple)):
print(sbmlId)
elif sbmlId.path != '/':
s1 = moose.element('/sbml/model/compartment/S1')
s2= moose.element('/sbml/model/compartment/S2')
# Creating MOOSE Table, Table2 is for the chemical model
graphs = moose.Neutral( '/sbml/graphs' )
outputs1 = moose.Table2 ( '/sbml/graphs/concS1')
outputs2 = moose.Table2 ( '/sbml/graphs/concS2')
# connect up the tables
moose.connect( outputs1,'requestOut', s1, 'getConc' );
moose.connect( outputs2,'requestOut', s2, 'getConc' );
# gsl solver is added, default is ee
moose.mooseAddChemSolver(sbmlId.path,"ee")
# Reset and Run
moose.reinit()
moose.start(runtime)
return sbmlId,True,msg
return sbmlId,False,msg
def main():
"""
This example illustrates loading, running, and saving a kinetic
model defined in kkit format. It uses a default kkit model but
you can specify another using the command line
``python filename runtime solver``.
We use the gsl solver here.
The model already defines a couple of plots and sets the runtime 20 secs.
"""
solver = "gsl" # Pick any of gsl, gssa, ee..
mfile = os.path.join( scriptDir, './genesis/acc11.g' )
runtime = 1000.0
if ( len( sys.argv ) >= 3 ):
if sys.argv[1][0] == '/':
mfile = sys.argv[1]
else:
mfile = sys.argv[1]
runtime = float( sys.argv[2] )
if ( len( sys.argv ) == 4 ):
solver = sys.argv[3]
modelId = moose.loadModel( mfile, 'model')
moose.mooseAddChemSolver('model',solver)
moose.element( '/model/kinetics/neuroNOS/nNOS.arg' ).concInit = 0.1
moose.reinit()
moose.start( runtime )
# Display all plots.
for x in moose.wildcardFind( '/model/#graphs/conc#/#' ):
t = np.arange( 0, x.vector.size, 1 ) * x.dt
print( x.vector )
if x.vector.size > 0:
assert min( x.vector ) >= 0.0, min(x.vector)
assert x.vector.size in [0, 10001], x.vector.size
########################################################
# Run it again with negative values allowed
moose.element( '/model/kinetics/stoich' ).allowNegative = True
moose.reinit()
moose.start( runtime )
oneValIsBelowZero = False
allVals = [ ]
for x in moose.wildcardFind( '/model/#graphs/conc#/#' ):
t = np.arange( 0, x.vector.size, 1 ) * x.dt
if x.vector.size > 0:
allVals.append( min( x.vector ) )
if min( x.vector ) <= 0.0:
oneValIsBelowZero = True
if allVals:
assert oneValIsBelowZero, "No value is negative: %s" % allVals
assert x.vector.size in [0, 10001], x.vector.size
def main():
""" This example illustrates loading, running, and saving a kinetic model
defined in kkit format. It uses a default kkit model but you can specify another using the command line ``python filename runtime solver``. We use the gsl solver here. The model already defines a couple of plots and sets the runtime to 20 seconds.
"""
solver = "gsl" # Pick any of gsl, gssa, ee..
mfile = os.path.join(scriptdir, 'genesis/kkit_objects_example.g')
runtime = 20.0
if (len(sys.argv) >= 3):
if sys.argv[1][0] == '/':
mfile = sys.argv[1]
else:
mfile = './genesis/' + sys.argv[1]
runtime = float(sys.argv[2])
if (len(sys.argv) == 4):
solver = sys.argv[3]
modelId = moose.loadModel(mfile, 'model')
moose.mooseAddChemSolver('model', solver)
# Increase volume so that the stochastic solver gssa
# gives an interesting output
#compt = moose.element( '/model/kinetics' )
#compt.volume = 1e-19
moose.reinit()
moose.start(runtime)
# Report parameters
'''
for x in moose.wildcardFind( '/model/kinetics/##[ISA=PoolBase]' ):
print x.name, x.nInit, x.concInit
for x in moose.wildcardFind( '/model/kinetics/##[ISA=ReacBase]' ):
print x.name, 'num: (', x.numKf, ', ', x.numKb, '), conc: (', x.Kf, ', ', x.Kb, ')'
for x in moose.wildcardFind('/model/kinetics/##[ISA=EnzBase]'):
print x.name, '(', x.Km, ', ', x.numKm, ', ', x.kcat, ')'
'''
# Display all plots.
for x in moose.wildcardFind('/model/#graphs/conc#/#'):
t = numpy.arange(0, x.vector.size, 1) * x.dt
vals = x.vector
stats = [vals.min(), vals.max(), vals.mean(), vals.std()]
expected = [0.0, 0.00040464, 0.0001444, 0.00013177]
assert numpy.allclose(stats, expected,
rtol=1e-4), 'Got %s expected %s' % (stats, expected)
def test_kkit():
"""This example illustrates loading, running, and saving a kinetic model
defined in kkit format. It uses a default kkit model but you can
specify another using the command line ``python filename runtime
solver``. We use the gsl solver here. The model already defines a
couple of plots and sets the runtime to 20 seconds.
"""
solver = "gsl" # Pick any of gsl, gssa, ee..
mfile = os.path.join(scriptdir, '..', 'data', 'kkit_objects_example.g')
runtime = 20.0
modelId = moose.loadModel(mfile, 'model')
moose.mooseAddChemSolver('model', solver)
moose.reinit()
moose.start(runtime)
for x in moose.wildcardFind('/model/#graphs/conc#/#'):
t = numpy.arange(0, x.vector.size, 1) * x.dt
vals = x.vector
stats = [vals.min(), vals.max(), vals.mean(), vals.std()]
expected = [0.0, 0.00040464, 0.0001444, 0.00013177]
assert numpy.allclose(stats, expected,
rtol=1e-4), 'Got %s expected %s' % (stats, expected)
def loadModel(filename, target, method=None):
solverClass = 'Neutral'
if method != None:
solverClass = method
try:
f = open(filename, 'r')
f.close()
except IOError as e:
print(e)
return
else:
file_name, extension = splitext(filename)
if extension in [".swc", ".p"]:
ret = moose._moose.loadModel(filename, target, "Neutral")
elif extension in [".g", ".cspace"]:
#only if genesis or cspace file, then mooseAddChemSolver is called
ret = moose._moose.loadModel(filename, target, "ee")
method = "ee"
if solverClass.lower() in [
"gssa", "gillespie", "stochastic", "gsolve"
]:
method = "gssa"
elif solverClass.lower() in [
"gsl", "runge kutta", "deterministic", "ksolve",
"rungekutta", "rk5", "rkf", "rk"
]:
method = "gsl"
elif solverClass.lower() in [
"exponential euler", "exponentialeuler", "neutral"
]:
method = "ee"
if method != 'ee':
moose.mooseAddChemSolver(target, method)
return ret
def loadModel(filename, target, method="ee"):
moose.loadModel(filename, target)
moose.mooseAddChemSolver(target, method)
if moose.exists(target + "/kinetics/info"):
moose.element(target + "/kinetics/info").solver = method
initiexpr = function.expr
#S1 connected to function
numVariables = function.numVars
expr = ""
expr = (function.expr + '+' + 'x' + str(numVariables))
expr = expr.lstrip("0 +")
expr = expr.replace(" ", "")
function.expr = expr
s1msg = moose.connect(S1, 'nOut', function.x[numVariables], 'input')
#S2 connected to function
numVariables = function.numVars
expr = ""
expr = (function.expr + '+' + 'x' + str(numVariables))
expr = expr.lstrip("0 +")
expr = expr.replace(" ", "")
function.expr = expr
s2msg = moose.connect(S2, 'nOut', function.x[numVariables], 'input')
compts = moose.wildcardFind(modelRoot.path + '/##[ISA=ChemCompt]')
solver = 'gsl'
moose.mooseAddChemSolver('/model', solver)
moose.mooseDeleteChemSolver('/model')
#moose.delete(s1msg)
#moose.delete(s2msg)
#deleting the function
#moose.delete(function) #deleting this will not cause seg fault
print(function.expr
) #function's expr still has the expression which is causing the problem