diff --git a/2dtestcases.py b/2dtestcases.py
index 334aa9a48465e0d4281f565ccdc0b0a93a6cc22d..70bf2a5e209e2aaa4c54efcefb57099b6305a5b5 100755
--- a/2dtestcases.py
+++ b/2dtestcases.py
@@ -486,7 +486,13 @@ chemIntegrator = None
if chemtype == "ozoneco":
l = l + mechbib.leightonco_reacs()
mech = mechanism(l)
- chemIntegrator = "EulerBackward"
+ mech.define_integrator('EulerBackward',
+ errortarget_relative=1.0e-6,
+ nitersmax=10000
+ )
+else:
+ mech = mechanism(l)
+ mech.define_integrator('null')
#############################################################
@@ -554,13 +560,10 @@ myctm = ctm(
vts=vts,
dt=dt,
MassFluxFunc=MassFluxFunc,
- chemIntegrator=chemIntegrator,
split=split,
label=label,
prescset=defaults.prescset,
ndtchem=ndtchem,
- ebitolerance=1.0e-6,
- ebinitersmax=10000,
)
#############################################################
diff --git a/CItest-MRconservation.py b/CItest-MRconservation.py
index e6a76d7ad98b5d12e469a5d0dc5ac8ac5ab15c53..5651f9058b33566075cdd3ec7c77626933c7dc75 100755
--- a/CItest-MRconservation.py
+++ b/CItest-MRconservation.py
@@ -109,6 +109,7 @@ mrdiag = True
l = TRC_reacs()
mech = mechanism(l)
+mech.define_integrator('null')
# Grid creation
maxlat = 45.0
@@ -163,8 +164,7 @@ for tsname in tslist:
vts=defaults.vts,
prescset=defaults.prescset,
dt=dt,
- MassFluxFunc=MassFluxFunc,
- chemIntegrator=None,
+ MassFluxFunc=MassFluxFunc
)
masstest, mrtest = test(myctm)
if masstest and mrtest:
diff --git a/CItest-PrescEmi.py b/CItest-PrescEmi.py
index aea9efd26353afb1509601d390f783b686dd03b0..21cb9756b8e4ddf5c24cb36e70ce62b209f3cd6e 100755
--- a/CItest-PrescEmi.py
+++ b/CItest-PrescEmi.py
@@ -144,6 +144,7 @@ airdensity = 2.69e25
l = trop_ozone_reacs() + CO_hotwo_reacs() + TRC_reacs()
mech = mechanism(l)
+mech.define_integrator('EulerBackward')
# Initial concentrations
@@ -204,8 +205,7 @@ myctm = ctm(
ts=ts,
vts=defaults.vts,
dt=1200.0,
- MassFluxFunc=MassFluxFunc,
- chemIntegrator="EulerBackward",
+ MassFluxFunc=MassFluxFunc
)
# Some screen outputs to see if things go fine
diff --git a/CItest-chem.py b/CItest-chem.py
index 340f138edee2befc2891d92d49167b6deb215bad..8aba0f937bbaed01823df173b41810bf601d9ddb 100755
--- a/CItest-chem.py
+++ b/CItest-chem.py
@@ -75,6 +75,7 @@ ts_b_dict = {}
ts_c_dict = {}
for exp in experimentlist:
+ mech.define_integrator(exp[0])
myctm = ctm(
mech=mech,
finaltime=finaltime,
@@ -85,7 +86,6 @@ for exp in experimentlist:
tdgrid=defaults.tdgrid,
MassFluxFunc=defaults.MassFluxFunc,
dt=exp[1],
- chemIntegrator=exp[0],
)
ts_a = ((myctm.t, myctm.activeConc_ppb("A")[0, 0, 0]),)
ts_b = ((myctm.t, myctm.activeConc_ppb("B")[0, 0, 0]),)
diff --git a/CItest-compressible.py b/CItest-compressible.py
index d5fdcb9aab79998afe092862342eb40d654d8ae2..51597d75faf6ca19a3c5bf0f2569d044d69b6000 100755
--- a/CItest-compressible.py
+++ b/CItest-compressible.py
@@ -279,6 +279,8 @@ tdgrid = Threedimgrid("3d grid", myGrid, dzvector, vts.nneigh, vertperiod=False)
# Define mechanism
l = TRC_reacs()
mech = mechanism(l)
+mech.define_integrator('null')
+
#############################################################
#############################################################
@@ -311,7 +313,6 @@ myctm = ctm(
vts=vts,
dt=dt,
MassFluxFunc=MassFluxFunc,
- chemIntegrator=None,
prescset=defaults.prescset,
)
#############################################################
diff --git a/CItest-isopleth.py b/CItest-isopleth.py
index ddb119f37333d05c086d68240840ee01ab1f99f1..0d3dae48b34a27c34f3e88f991c8ab804ce2dda9 100755
--- a/CItest-isopleth.py
+++ b/CItest-isopleth.py
@@ -118,6 +118,7 @@ def add_standard_emi(dict, **kwargs):
l = trop_ozone_reacs() + hotwo_reacs() + NMVOC_reacs()
mech = mechanism(l)
+mech.define_integrator('EulerBackward')
tdgrid = defaults.tdgrid
MassFluxFunc = defaults.MassFluxFunc
@@ -164,7 +165,6 @@ for nox in noxvec:
ts=defaults.ts,
vts=defaults.vts,
dt=100.0,
- chemIntegrator="EulerBackward",
MassFluxFunc=MassFluxFunc,
)
diff --git a/CItest-leighton-radicals.py b/CItest-leighton-radicals.py
index efe19bde792d819ab9d0350febc7047ac6535a8c..fee9b89cbdf9e99012b2314b1252eeaa9b83b728 100755
--- a/CItest-leighton-radicals.py
+++ b/CItest-leighton-radicals.py
@@ -48,6 +48,9 @@ Mh2o = 0.018
# Chemical scheme creation
mech = mechanism(mechbib.leightonco_reacs())
+mech.define_integrator('EulerBackward',
+ nitersmax = 10000,
+ errortarget_relative=1.0e-6)
# Initial concentrations
inidict = {}
@@ -95,8 +98,6 @@ myctm = ctm(
ts=defaults.ts,
vts=defaults.vts,
prescset=defaults.prescset,
- ebitolerance=1.0e-6,
- ebinitersmax=10000,
)
o3 = myctm.centerConc("O3")
no = myctm.centerConc("NO")
diff --git a/CItest-xz.py b/CItest-xz.py
index 687ccb97165eb6103ff62144395ec26ca33b69e5..10ad8c202c063270b351fe19fbdec6e6f0055b47 100755
--- a/CItest-xz.py
+++ b/CItest-xz.py
@@ -473,6 +473,7 @@ print("dt", dt)
l = tracer_reacs()
mech = mechanism(l) # These two lines create fake chemistry with one inert tracer
+mech.define_integrator('null')
# No emissions
emidict = {}
@@ -642,8 +643,7 @@ myctm = ctm(
prescset=defaults.prescset,
inidict=inidict,
lagdict=lagdict,
- label=label,
- chemIntegrator=None,
+ label=label
)
if myctm.vts.name == "ppmSL":
diff --git a/toyctm/toyctm.py b/toyctm/toyctm.py
index 451c26c6277ae40deb31573c73c09dfe1c713f45..40f0a509ab8351b6fc781409172f67783ea37c20 100644
--- a/toyctm/toyctm.py
+++ b/toyctm/toyctm.py
@@ -62,8 +62,6 @@ class ctm:
- MassFluxFunc : Instance of the MassFluxGenerator class (examples in threedmassfluxes.py)
- lagdict : defaults to {}
- label : string tha gives a name to the simulation
- - chemIntegrator : time scheme for chemistry. So far available,
- EulerBackward (strongly recommended) and EulerForward
"""
# read Mandatory arguments
@@ -94,6 +92,14 @@ class ctm:
"toyctm.py ERROR: Please provide a chemical mechanism with mech= when calling ctm()"
)
sys.exit(1)
+ if self.mech.integrator_name is None:
+ print(
+ """toyctm.py ERROR: Please initialize the chemical integrator
+ with mech.define_integrator(). If no chemistry integration
+ is needed please use mech.define_integrator('null')"""
+ )
+ sys.exit(1)
+
if self.tdgrid is None:
print(
"toyctm.py ERROR: Please provide a grid with tdgrid= when calling ctm()"
@@ -133,10 +139,18 @@ class ctm:
sys.exit(1)
# read optional arguments
- self.chemIntegrator = kwargs.get(
- "chemIntegrator", "EulerBackward"
- ) # Chemical integrator. 'EulerBackward', 'EulerForward' or None are supported.
- # 'EulerBackward' is strongly recommended if you have chemistry.
+
+ # Deprecated arguments produce an error
+ if 'chemIntegrator' in kwargs :
+ print('ERROR: chemIntegrator is deprecated, please use mech.define_integrator')
+ sys.exit(1)
+ if 'ebitolerance' in kwargs :
+ print('ERROR: ebitolerance is deprecated, please use mech.define_integrator')
+ sys.exit(1)
+ if 'ebinitersmax' in kwargs :
+ print('ERROR: ebinitersmax is deprecated, please use mech.define_integrator')
+ sys.exit(1)
+
inidict = kwargs.get(
"inidict", {}
) # Dictionnary associating an instance of the initialization class to each model species.
@@ -166,8 +180,6 @@ class ctm:
"split", "lie"
) # splitting strategy, so far 'strang' or 'lie'
self.ndtchem = kwargs.get("ndtchem", None)
- self.ebitolerance = kwargs.get("ebitolerance", 1.0e-2)
- self.ebinitersmax = kwargs.get("ebinitersmax", 1000)
# End of arguments read
@@ -216,11 +228,6 @@ class ctm:
self.zdconc = np.zeros(self.conc.shape)
self.mdconc = np.zeros(self.conc.shape)
- # Initialize the chemistry solver
- if self.chemIntegrator is not None :
- self.mech.define_integrator(self.chemIntegrator,
- errortarget_relative = self.ebitolerance,
- nitersmax = self.ebinitersmax)
# Misc initializations
self.niters = -999
self.vdconc = 0.
@@ -693,7 +700,7 @@ class ctm:
self.emi()
# dtchem for chemistry
- if self.chemIntegrator is not None:
+ if self.mech.integrator is not None:
# CHEMISTRY
self.chemstep()
for sp in self.species:
@@ -706,7 +713,7 @@ class ctm:
def chemupdate_reverse(self):
""" Everything except transport on time dtchem in reverse order
during time dtchem"""
- if self.chemIntegrator is not None:
+ if self.mech.integrator is not None:
# CHEMISTRY
self.chemstep()
for sp in self.species:
diff --git a/toyctm_addons/chemistry.py b/toyctm_addons/chemistry.py
index 51459ae1b24ecfc7446ce051df8dcf443184f387..04f108f9e8c15311564159e50bc865a569b307b7 100644
--- a/toyctm_addons/chemistry.py
+++ b/toyctm_addons/chemistry.py
@@ -309,6 +309,8 @@ class mechanism:
self.errortarget_absolute = self.minimalconcentration
elif integrator_name == 'EulerForward' :
self.integrator = self.eulerForwardTimestep
+ elif integrator_name == 'null' :
+ self.integrator = None
else :
print('ERROR : integrator', integrator_name, 'not available')
sys.exit(1)