up

Author: TorkelE

src/Catalyst.jl

@@ -34,7 +34,6 @@ import ModelingToolkit: get_variables, namespace_expr, namespace_equation, get_v
 import ModelingToolkit: check_variables,
                         check_parameters, _iszero, _merge, check_units,
                         get_unit, check_equations
-import ModelingToolkit: D_nounits
 
 import Base: (==), hash, size, getindex, setindex, isless, Sort.defalg, length, show
 import MacroTools, Graphs

test/dsl/dsl_basics.jl

@@ -299,7 +299,7 @@ let
         k, A + 2*B --> 2*B
     end
     @unpack A,B = rn2
-    D = Catalyst.D_nounits
+    D = default_time_deriv()
     eq = D(B) ~ -B
     @named osys = ODESystem([eq], t)
     @named rn2 = extend(osys, rn2)

test/programmatic_model_creation/component_based_model_creation.jl

@@ -340,7 +340,7 @@ let
     @parameters a, b
     @unpack A = rn
     @variables C(t)
-    D = Catalyst.D_nounits
+    D = default_time_deriv()
     eqs = [D(C) ~ -b * C + a * A]
     @named osys = ODESystem(eqs, t, [A, C], [a, b])
     rn2 = extend(osys, rn)
@@ -387,7 +387,7 @@ let
         @parameters k
         k/$V, A + B --> C
     end
-    Dt = Catalyst.D_nounits
+    Dt = default_time_deriv()
     @named csys = ODESystem([Dt(V) ~ -b * V], t)
     @named fullrn = extend(csys, rn)
     setdefaults!(fullrn, [:b => 2.0])
@@ -424,7 +424,7 @@ let
     @parameters k1 k2 k3
     @variables V1(t) V2(t) V3(t)
     @species A1(t) A2(t) A3(t) B1(t) B2(t) B3(t)
-    D = Catalyst.D_nounits
+    D = default_time_deriv()
     rx1 = Reaction(k1*V1, [A1], [B1])
     eq1 = D(V1) ~ -V1
     @named rs1 = ReactionSystem([rx1, eq1], t)

test/reactionsystem_structure/reactionsystem.jl

@@ -456,7 +456,7 @@ end
 let
     @parameters k1 k2 A [isconstantspecies = true]
     @species B(t) C(t) [isbcspecies = true] D(t) E(t)
-    Dt = Catalyst.D_nounits
+    Dt = default_time_deriv()
     eqs = [(@reaction k1, $A --> B),
         (@reaction k2, B --> $A),
         (@reaction k1, $C + D --> E + $C),
@@ -567,7 +567,7 @@ let
     @parameters k1 k2 S2 [isconstantspecies = true]
     @species S1(t) S3(t)
     rx = Reaction(k2, [S1], nothing)
-    ∂ₜ = Catalyst.D_nounits
+    ∂ₜ = default_time_deriv()
     eq = ∂ₜ(S3) ~ k1 * S2
     @named osys = ODESystem([eq], t)
     @named rs = ReactionSystem([rx, eq], t)
@@ -581,7 +581,7 @@ let
     @parameters k1 k2 S2 [isconstantspecies = true]
     @species S1(t) S3(t) [isbcspecies = true]
     rx = Reaction(k2, [S1], nothing)
-    ∂ₜ = Catalyst.D_nounits
+    ∂ₜ = default_time_deriv()
     eq = S3 ~ k1 * S2
     @named rs = ReactionSystem([rx, eq], t)
     @test issetequal(unknowns(rs), [S1, S3])
@@ -599,7 +599,7 @@ let
     @variables S3(t)
     @species S1(t)
     rx = Reaction(k2, [S1], nothing)
-    ∂ₜ = Catalyst.D_nounits
+    ∂ₜ = default_time_deriv()
     eq = S3 ~ k1 * S2
     @named rs = ReactionSystem([rx, eq], t)
     @test issetequal(unknowns(rs), [S1, S3])
@@ -694,7 +694,7 @@ let
     @variables V(t)
     @species A(t) B(t)
     rx = Reaction(k1, [A], [B], [k2], [2])
-    D = Catalyst.D_nounits
+    D = default_time_deriv()
     eq = D(V) ~ -k1 * k2 * V + A
     @named rs = ReactionSystem([eq, rx], t)
     @test length(unknowns(rs)) == 3

test/spatial_reaction_systems/simulate_PDEs.jl

@@ -51,7 +51,7 @@ let
     @test bpm == bpm2
 
     # Check we can build a PDESystem.
-    ∂t = Catalyst.D_nounits
+    ∂t = default_time_deriv()
     ∂x = Differential(x)
     ∂y = Differential(y)
     Δ(u) = (∂x^2)(u) + (∂y^2)(u)