renaming jacobian methods

CliMA · Jul 2, 2024 · 332a73b · 332a73b
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diff --git a/NEWS.md b/NEWS.md
@@ -11,7 +11,9 @@ Add base global soil canopy run to benchmark and experiments
 - PR [#669] adds topmodel runoff
 Soil implicit solver
 - PR [#678] updates Jacobian for soil energy
-
+Misc
+- PR [#685] Renames jacobian update functions to align with our convention
+            for tendency functions
 v0.12.4
 --------
 - Fix various canopy flux bugs

diff --git a/docs/src/APIs/shared_utilities.md b/docs/src/APIs/shared_utilities.md
@@ -60,8 +60,8 @@ ClimaLand.diffusive_flux
 ClimaLand.boundary_vars
 ClimaLand.boundary_var_domain_names
 ClimaLand.boundary_var_types
-ClimaLand.make_tendency_jacobian
-ClimaLand.make_update_jacobian
+ClimaLand.make_jacobian
+ClimaLand.make_compute_jacobian
 ClimaLand.set_dfluxBCdY!
 ClimaLand.get_drivers
 ```

diff --git a/docs/tutorials/integrated/soil_canopy_tutorial.jl b/docs/tutorials/integrated/soil_canopy_tutorial.jl
@@ -327,11 +327,9 @@ land = SoilCanopyModel{FT}(;
 Y, p, coords = initialize(land);
 exp_tendency! = make_exp_tendency(land);
 imp_tendency! = make_imp_tendency(land);
-tendency_jacobian! = make_tendency_jacobian(land);
-jac_kwargs = (;
-    jac_prototype = ClimaLand.ImplicitEquationJacobian(Y),
-    Wfact = tendency_jacobian!,
-);
+jacobian! = make_jacobian(land);
+jac_kwargs =
+    (; jac_prototype = ClimaLand.ImplicitEquationJacobian(Y), Wfact = jacobian!);
 
 # We need to provide initial conditions for the soil and canopy hydraulics
 # models:

diff --git a/docs/tutorials/standalone/Soil/evaporation.jl b/docs/tutorials/standalone/Soil/evaporation.jl
@@ -181,9 +181,8 @@ set_initial_cache!(p, Y, t0);
 # Define the tendency functions
 exp_tendency! = make_exp_tendency(soil)
 imp_tendency! = make_imp_tendency(soil);
-tendency_jacobian! = ClimaLand.make_tendency_jacobian(soil);
-jac_kwargs =
-    (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = tendency_jacobian!);
+jacobian! = ClimaLand.make_jacobian(soil);
+jac_kwargs = (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!);
 
 timestepper = CTS.ARS111();
 ode_algo = CTS.IMEXAlgorithm(

diff --git a/docs/tutorials/standalone/Soil/evaporation_gilat_loess.jl b/docs/tutorials/standalone/Soil/evaporation_gilat_loess.jl
@@ -168,9 +168,8 @@ set_initial_cache!(p, Y, t0);
 # Timestepping:
 exp_tendency! = make_exp_tendency(soil)
 imp_tendency! = make_imp_tendency(soil);
-tendency_jacobian! = ClimaLand.make_tendency_jacobian(soil);
-jac_kwargs =
-    (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = tendency_jacobian!);
+jacobian! = ClimaLand.make_jacobian(soil);
+jac_kwargs = (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!);
 
 timestepper = CTS.ARS111();
 ode_algo = CTS.IMEXAlgorithm(
@@ -224,7 +223,7 @@ set_initial_cache!(p, Y, t0)
 soil_exp_tendency! = make_exp_tendency(soil)
 exp_tendency! = make_exp_tendency(soil)
 imp_tendency! = make_imp_tendency(soil);
-tendency_jacobian! = ClimaLand.make_tendency_jacobian(soil);
+jacobian! = ClimaLand.make_jacobian(soil);
 timestepper = CTS.ARS111();
 ode_algo = CTS.IMEXAlgorithm(
     timestepper,
@@ -233,8 +232,7 @@ ode_algo = CTS.IMEXAlgorithm(
         update_j = CTS.UpdateEvery(CTS.NewNewtonIteration),
     ),
 );
-jac_kwargs =
-    (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = tendency_jacobian!);
+jac_kwargs = (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!);
 prob = SciMLBase.ODEProblem(
     CTS.ClimaODEFunction(
         T_exp! = exp_tendency!,
@@ -290,7 +288,7 @@ set_initial_cache! = make_set_initial_cache(soil)
 set_initial_cache!(p, Y, t0)
 exp_tendency! = make_exp_tendency(soil)
 imp_tendency! = make_imp_tendency(soil);
-tendency_jacobian! = ClimaLand.make_tendency_jacobian(soil);
+jacobian! = ClimaLand.make_jacobian(soil);
 timestepper = CTS.ARS111();
 ode_algo = CTS.IMEXAlgorithm(
     timestepper,
@@ -299,8 +297,7 @@ ode_algo = CTS.IMEXAlgorithm(
         update_j = CTS.UpdateEvery(CTS.NewNewtonIteration),
     ),
 );
-jac_kwargs =
-    (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = tendency_jacobian!);
+jac_kwargs = (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!);
 prob = SciMLBase.ODEProblem(
     CTS.ClimaODEFunction(
         T_exp! = exp_tendency!,

diff --git a/docs/tutorials/standalone/Soil/freezing_front.jl b/docs/tutorials/standalone/Soil/freezing_front.jl
@@ -211,9 +211,8 @@ set_initial_cache!(p, Y, t0);
 # Create the tendency function, and choose a timestep, and timestepper:
 exp_tendency! = make_exp_tendency(soil)
 imp_tendency! = make_imp_tendency(soil);
-tendency_jacobian! = ClimaLand.make_tendency_jacobian(soil);
-jac_kwargs =
-    (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = tendency_jacobian!);
+jacobian! = ClimaLand.make_jacobian(soil);
+jac_kwargs = (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!);
 
 dt = Float64(100)
 

diff --git a/docs/tutorials/standalone/Soil/layered_soil.jl b/docs/tutorials/standalone/Soil/layered_soil.jl
@@ -123,10 +123,9 @@ ode_algo = CTS.IMEXAlgorithm(
 )
 exp_tendency! = make_exp_tendency(soil)
 imp_tendency! = make_imp_tendency(soil)
-tendency_jacobian! = make_tendency_jacobian(soil)
+jacobian! = make_jacobian(soil)
 
-jac_kwargs =
-    (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = tendency_jacobian!)
+jac_kwargs = (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!)
 prob = SciMLBase.ODEProblem(
     CTS.ClimaODEFunction(
         T_exp! = exp_tendency!,

diff --git a/docs/tutorials/standalone/Soil/richards_equation.jl b/docs/tutorials/standalone/Soil/richards_equation.jl
@@ -140,7 +140,7 @@ soil = Soil.RichardsModel{FT}(;
 # We also create the function which is used to update our Jacobian.
 exp_tendency! = make_exp_tendency(soil);
 imp_tendency! = ClimaLand.make_imp_tendency(soil);
-tendency_jacobian! = ClimaLand.make_tendency_jacobian(soil);
+jacobian! = ClimaLand.make_jacobian(soil);
 
 # # Set up the simulation
 # We can now initialize the prognostic and auxiliary variable vectors, and take
@@ -185,8 +185,7 @@ ode_algo = CTS.IMEXAlgorithm(
 );
 
 # Here we set up the information used for our Jacobian.
-jac_kwargs =
-    (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = tendency_jacobian!);
+jac_kwargs = (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!);
 
 # And then we can solve the system of equations, using
 # [SciMLBase.jl](https://github.com/SciML/SciMLBase.jl) and

diff --git a/docs/tutorials/standalone/Soil/soil_energy_hydrology.jl b/docs/tutorials/standalone/Soil/soil_energy_hydrology.jl
@@ -185,7 +185,7 @@ soil = Soil.EnergyHydrology{FT}(;
 # We also create the function which is used to update our Jacobian.
 exp_tendency! = make_exp_tendency(soil);
 imp_tendency! = make_imp_tendency(soil);
-tendency_jacobian! = ClimaLand.make_tendency_jacobian(soil);
+jacobian! = ClimaLand.make_jacobian(soil);
 
 # # Set up the simulation
 # We can now initialize the prognostic and auxiliary variable vectors, and take
@@ -261,8 +261,7 @@ ode_algo = CTS.IMEXAlgorithm(
     ),
 );
 
-jac_kwargs =
-    (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = tendency_jacobian!);
+jac_kwargs = (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!);
 
 prob = SciMLBase.ODEProblem(
     CTS.ClimaODEFunction(

diff --git a/docs/tutorials/standalone/Soil/sublimation.jl b/docs/tutorials/standalone/Soil/sublimation.jl
@@ -167,9 +167,8 @@ set_initial_cache!(p, Y, t0);
 # Timestepping functions:
 exp_tendency! = make_exp_tendency(soil)
 imp_tendency! = make_imp_tendency(soil)
-tendency_jacobian! = ClimaLand.make_tendency_jacobian(soil)
-jac_kwargs =
-    (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = tendency_jacobian!)
+jacobian! = ClimaLand.make_jacobian(soil)
+jac_kwargs = (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!)
 
 timestepper = CTS.ARS111()
 ode_algo = CTS.IMEXAlgorithm(

diff --git a/experiments/benchmarks/land.jl b/experiments/benchmarks/land.jl
@@ -577,14 +577,12 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     set_initial_cache! = make_set_initial_cache(land)
     exp_tendency! = make_exp_tendency(land)
     imp_tendency! = ClimaLand.make_imp_tendency(land)
-    tendency_jacobian! = ClimaLand.make_tendency_jacobian(land)
+    jacobian! = ClimaLand.make_jacobian(land)
     set_initial_cache!(p, Y, t0)
 
     # set up jacobian info
-    jac_kwargs = (;
-        jac_prototype = ImplicitEquationJacobian(Y),
-        Wfact = tendency_jacobian!,
-    )
+    jac_kwargs =
+        (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!)
 
     prob = SciMLBase.ODEProblem(
         CTS.ClimaODEFunction(

diff --git a/experiments/benchmarks/richards.jl b/experiments/benchmarks/richards.jl
@@ -44,7 +44,7 @@ using ClimaLand:
     make_update_aux,
     make_exp_tendency,
     make_imp_tendency,
-    make_tendency_jacobian,
+    make_jacobian,
     make_set_initial_cache
 
 import Profile, ProfileCanvas
@@ -256,14 +256,14 @@ function setup_prob(t0, tf, Δt; nelements = (101, 15))
     set_initial_cache! = make_set_initial_cache(model)
     exp_tendency! = make_exp_tendency(model)
     imp_tendency! = make_imp_tendency(model)
-    tendency_jacobian! = make_tendency_jacobian(model)
+    jacobian! = make_jacobian(model)
 
     set_initial_cache!(p, Y, t0)
 
     # set up jacobian info
     jac_kwargs = (;
         jac_prototype = ClimaLand.Soil.ImplicitEquationJacobian(Y),
-        Wfact = tendency_jacobian!,
+        Wfact = jacobian!,
     )
 
     prob = SciMLBase.ODEProblem(

diff --git a/experiments/integrated/fluxnet/ozark_pft.jl b/experiments/integrated/fluxnet/ozark_pft.jl
@@ -256,11 +256,9 @@ land = SoilCanopyModel{FT}(;
 Y, p, cds = initialize(land)
 exp_tendency! = make_exp_tendency(land)
 imp_tendency! = make_imp_tendency(land);
-tendency_jacobian! = make_tendency_jacobian(land);
-jac_kwargs = (;
-    jac_prototype = ClimaLand.ImplicitEquationJacobian(Y),
-    Wfact = tendency_jacobian!,
-);
+jacobian! = make_jacobian(land);
+jac_kwargs =
+    (; jac_prototype = ClimaLand.ImplicitEquationJacobian(Y), Wfact = jacobian!);
 
 #Initial conditions
 Y.soil.ϑ_l =

diff --git a/experiments/integrated/fluxnet/run_fluxnet.jl b/experiments/integrated/fluxnet/run_fluxnet.jl
@@ -213,11 +213,9 @@ land = SoilCanopyModel{FT}(;
 Y, p, cds = initialize(land)
 exp_tendency! = make_exp_tendency(land)
 imp_tendency! = make_imp_tendency(land)
-tendency_jacobian! = make_tendency_jacobian(land);
-jac_kwargs = (;
-    jac_prototype = ClimaLand.ImplicitEquationJacobian(Y),
-    Wfact = tendency_jacobian!,
-);
+jacobian! = make_jacobian(land);
+jac_kwargs =
+    (; jac_prototype = ClimaLand.ImplicitEquationJacobian(Y), Wfact = jacobian!);
 
 #Initial conditions
 Y.soil.ϑ_l =

diff --git a/experiments/integrated/global/global_soil_canopy.jl b/experiments/integrated/global/global_soil_canopy.jl
@@ -338,7 +338,7 @@ evaluate!(Y.canopy.energy.T, atmos.T, t0)
 set_initial_cache! = make_set_initial_cache(land)
 exp_tendency! = make_exp_tendency(land);
 imp_tendency! = ClimaLand.make_imp_tendency(land);
-tendency_jacobian! = ClimaLand.make_tendency_jacobian(land);
+jacobian! = ClimaLand.make_jacobian(land);
 set_initial_cache!(p, Y, t0)
 stepper = CTS.ARS343()
 ode_algo = CTS.IMEXAlgorithm(
@@ -350,8 +350,7 @@ ode_algo = CTS.IMEXAlgorithm(
 )
 
 # set up jacobian info
-jac_kwargs =
-    (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = tendency_jacobian!)
+jac_kwargs = (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!)
 
 prob = SciMLBase.ODEProblem(
     CTS.ClimaODEFunction(

diff --git a/experiments/integrated/performance/conservation/ozark_conservation_setup.jl b/experiments/integrated/performance/conservation/ozark_conservation_setup.jl
@@ -193,13 +193,11 @@ land = SoilCanopyModel{FT}(;
 )
 exp_tendency! = make_exp_tendency(land)
 imp_tendency! = make_imp_tendency(land);
-tendency_jacobian! = make_tendency_jacobian(land);
+jacobian! = make_jacobian(land);
 set_initial_cache! = make_set_initial_cache(land)
 Y, p, cds = initialize(land)
-jac_kwargs = (;
-    jac_prototype = ClimaLand.ImplicitEquationJacobian(Y),
-    Wfact = tendency_jacobian!,
-);
+jac_kwargs =
+    (; jac_prototype = ClimaLand.ImplicitEquationJacobian(Y), Wfact = jacobian!);
 
 #Initial conditions
 Y.soil.ϑ_l = drivers.SWC.values[1 + Int(round(t0 / 1800))] # Get soil water content at t0

diff --git a/experiments/integrated/performance/profile_allocations.jl b/experiments/integrated/performance/profile_allocations.jl
@@ -330,7 +330,7 @@ land = SoilCanopyModel{FT}(;
 # Define explicit and implicit tendencies, and the jacobian
 exp_tendency! = make_exp_tendency(land)
 imp_tendency! = make_imp_tendency(land);
-tendency_jacobian! = make_tendency_jacobian(land);
+jacobian! = make_jacobian(land);
 
 # Set up timestepping and simulation callbacks
 dt = Float64(150)
@@ -352,10 +352,8 @@ driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc)
 Y, p = set_initial_conditions(land, t0)
 
 # Set up jacobian info
-jac_kwargs = (;
-    jac_prototype = ClimaLand.ImplicitEquationJacobian(Y),
-    Wfact = tendency_jacobian!,
-);
+jac_kwargs =
+    (; jac_prototype = ClimaLand.ImplicitEquationJacobian(Y), Wfact = jacobian!);
 
 # Solve simulation
 prob = SciMLBase.ODEProblem(

diff --git a/experiments/standalone/Soil/richards_comparison.jl b/experiments/standalone/Soil/richards_comparison.jl
@@ -77,7 +77,7 @@ outdir = joinpath(
         Y.soil.ϑ_l .= FT(0.24)
         exp_tendency! = make_exp_tendency(soil)
         imp_tendency! = ClimaLand.make_imp_tendency(soil)
-        tendency_jacobian! = ClimaLand.make_tendency_jacobian(soil)
+        jacobian! = ClimaLand.make_jacobian(soil)
         set_initial_cache!(p, Y, t0)
 
         stepper = CTS.ARS111()
@@ -93,10 +93,8 @@ outdir = joinpath(
         )
 
         # set up jacobian info
-        jac_kwargs = (;
-            jac_prototype = ImplicitEquationJacobian(Y),
-            Wfact = tendency_jacobian!,
-        )
+        jac_kwargs =
+            (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!)
 
         prob = SciMLBase.ODEProblem(
             CTS.ClimaODEFunction(
@@ -173,7 +171,7 @@ end
         Y.soil.ϑ_l .= FT(0.1)
         exp_tendency! = make_exp_tendency(soil)
         imp_tendency! = ClimaLand.make_imp_tendency(soil)
-        tendency_jacobian! = ClimaLand.make_tendency_jacobian(soil)
+        jacobian! = ClimaLand.make_jacobian(soil)
         set_initial_cache!(p, Y, t0)
 
         stepper = CTS.ARS111()
@@ -188,10 +186,8 @@ end
             ),
         )
         # set up jacobian info
-        jac_kwargs = (;
-            jac_prototype = ImplicitEquationJacobian(Y),
-            Wfact = tendency_jacobian!,
-        )
+        jac_kwargs =
+            (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!)
 
         prob = SciMLBase.ODEProblem(
             CTS.ClimaODEFunction(

diff --git a/experiments/standalone/Soil/richards_runoff.jl b/experiments/standalone/Soil/richards_runoff.jl
@@ -216,7 +216,7 @@ Y.soil.ϑ_l .= hydrostatic_profile.(lat, z, ν, θ_r, vg_α, vg_n, S_s, f_max)
 set_initial_cache! = make_set_initial_cache(model)
 exp_tendency! = make_exp_tendency(model);
 imp_tendency! = ClimaLand.make_imp_tendency(model);
-tendency_jacobian! = ClimaLand.make_tendency_jacobian(model);
+jacobian! = ClimaLand.make_jacobian(model);
 
 set_initial_cache!(p, Y, t0)
 stepper = CTS.ARS111()
@@ -229,8 +229,7 @@ ode_algo = CTS.IMEXAlgorithm(
 )
 
 # set up jacobian info
-jac_kwargs =
-    (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = tendency_jacobian!)
+jac_kwargs = (; jac_prototype = ImplicitEquationJacobian(Y), Wfact = jacobian!)
 
 prob = SciMLBase.ODEProblem(
     CTS.ClimaODEFunction(