fixes

Author: TorkelE

docs/src/catalyst_functionality/constraint_equations.md

@@ -25,11 +25,12 @@ separate `ReactionSystem`s and `ODESystem`s with their respective components,
 and then extend the `ReactionSystem` with the `ODESystem`. Let's begin by
 creating these two systems. 
 
-Here, to create differentials with respect to time (for our differential equations), we must import the time differential operator from Catalyst. We do this through `import Catalyst: D_nounits as D` (calling it `D`). Here, `D(V)` denotes the differential of the variable `V` with respect to time.
+Here, to create differentials with respect to time (for our differential equations), we must import the time differential operator from Catalyst. We do this through `D = default_time_deriv()`. Here, `D(V)` denotes the differential of the variable `V` with respect to time.
 
 ```@example ceq1
 using Catalyst, DifferentialEquations, Plots
-t = default_t(), D_nounits as D
+t = default_t()
+D = default_time_deriv()
 
 # set the growth rate to 1.0
 @parameters λ = 1.0
@@ -72,7 +73,8 @@ As an alternative to the previous approach, we could have constructed our
 `ReactionSystem` all at once by directly using the symbolic interface:
 ```@example ceq2
 using Catalyst, DifferentialEquations, Plots
-t = default_t(), D_nounits as D
+t = default_t()
+D = default_time_deriv()
 
 @parameters λ = 1.0
 @variables V(t) = 1.0
@@ -104,7 +106,8 @@ advanced_simulations) tutorial.
 Let's first create our equations and unknowns/species again
 ```@example ceq3
 using Catalyst, DifferentialEquations, Plots
-t = default_t(), D_nounits as D
+t = default_t()
+D = default_time_deriv()
 
 @parameters λ = 1.0
 @variables V(t) = 1.0

docs/src/catalyst_functionality/example_networks/hodgkin_huxley_equation.md

@@ -15,7 +15,8 @@ We begin by importing some necessary packages.
 using ModelingToolkit, Catalyst, NonlinearSolve
 using DifferentialEquations, Symbolics
 using Plots
-t = default_t(), D_nounits as D
+t = default_t()
+D = default_time_deriv()
 ```
 
 We'll build a simple Hodgkin-Huxley model for a single neuron, with the voltage,

docs/src/catalyst_functionality/network_analysis.md

@@ -52,7 +52,7 @@ the reaction rate equation ODE model for the repressilator is
 ## Matrix-vector reaction rate equation representation
 In general, reaction rate equation (RRE) ODE models for chemical reaction networks can
 be represented as a first-order system of ODEs in a compact matrix-vector notation. Suppose
-we have a reaction network with ``K`` reactions and ``M`` species, labelled by the unknown vector
+we have a reaction network with ``K`` reactions and ``M`` species, labelled by the state vector
 ```math
 \mathbf{x}(t) = \begin{pmatrix} x_1(t) \\ \vdots \\ x_M(t)) \end{pmatrix}.
 ```
@@ -384,7 +384,7 @@ Recall that in the matrix-vector representation for the RRE ODEs, the entries,
 ``N_{m k}``, of the stoichiometry matrix, ``N``, give the net change in species
 ``m`` due to reaction ``k``. If we let ``\mathbf{N}_k`` denote the ``k``th
 column of this matrix, this vector corresponds to the change in the species
-unknown vector, ``\mathbf{x}(t)``, due to reaction ``k``, i.e. when reaction ``k``
+state vector, ``\mathbf{x}(t)``, due to reaction ``k``, i.e. when reaction ``k``
 occurs ``\mathbf{x}(t) \to \mathbf{x}(t) + \mathbf{N}_k``. Moreover, by
 integrating the ODE
 ```math

docs/src/catalyst_functionality/programmatic_CRN_construction.md

@@ -20,7 +20,7 @@ t = default_t()
 @species m₁(t) m₂(t) m₃(t) P₁(t) P₂(t) P₃(t)
 nothing    # hide
 ```
-Note: Each species is declared as a function of time. Here, we first import the *time independent variable using `t = default_t()`, and then use it to declare out species.
+Note: Each species is declared as a function of time. Here, we first import the *time independent variable*, and stores it in `t`, using `t = default_t()`, and then use it to declare out species.
 
 !!! note
        For users familiar with ModelingToolkit, chemical species must be declared

src/Catalyst.jl

@@ -43,12 +43,15 @@ import DataStructures: OrderedDict, OrderedSet
 import Parameters: @with_kw_noshow
 
 # globals for the modulate
+function default_time_deriv()
+    return ModelingToolkit.D_nounits
+end
 function default_t()
     return ModelingToolkit.t_nounits
 end
 const DEFAULT_t = default_t()
 const DEFAULT_IV_SYM = Symbol(DEFAULT_t)
-export default_t
+export default_t, default_time_deriv
 
 # as used in Catlab
 const USE_GV_JLL = Ref(false)

src/networkapi.jl

@@ -1403,7 +1403,7 @@ Notes:
 - `disablechecks` will disable checking for whether the passed in variable is
   already defined, which is useful when adding many new variables to the system.
   *Do not disable checks* unless you are sure the passed in variable is a new
-  variable, as this will potentially leave the system in an undefined unknown.
+  variable, as this will potentially leave the system in an undefined state.
 """
 function addspecies!(network::ReactionSystem, s::Symbolic; disablechecks = false)
     reset_networkproperties!(network)
@@ -1435,7 +1435,7 @@ integer id of the species within the system.
 - `disablechecks` will disable checking for whether the passed in variable is
   already defined, which is useful when adding many new variables to the system.
   *Do not disable checks* unless you are sure the passed in variable is a new
-  variable, as this will potentially leave the system in an undefined unknown.
+  variable, as this will potentially leave the system in an undefined state.
 """
 function addspecies!(network::ReactionSystem, s::Num; disablechecks = false)
     addspecies!(network, value(s), disablechecks = disablechecks)
@@ -1451,7 +1451,7 @@ id of the parameter within the system.
 - `disablechecks` will disable checking for whether the passed in variable is
   already defined, which is useful when adding many new variables to the system.
   *Do not disable checks* unless you are sure the passed in variable is a new
-  variable, as this will potentially leave the system in an undefined unknown.
+  variable, as this will potentially leave the system in an undefined state.
 """
 function addparam!(network::ReactionSystem, p::Symbolic; disablechecks = false)
     reset_networkproperties!(network)
@@ -1480,7 +1480,7 @@ integer id of the parameter within the system.
 - `disablechecks` will disable checking for whether the passed in variable is
   already defined, which is useful when adding many new variables to the system.
   *Do not disable checks* unless you are sure the passed in variable is a new
-  variable, as this will potentially leave the system in an undefined unknown.
+  variable, as this will potentially leave the system in an undefined state.
 """
 function addparam!(network::ReactionSystem, p::Num; disablechecks = false)
     addparam!(network, value(p); disablechecks = disablechecks)

test/miscellaneous_tests/events.jl

@@ -1,5 +1,6 @@
 using Test, Catalyst, ModelingToolkit, OrdinaryDiffEq
-t = default_t(), D_nounits as D
+t = default_t()
+D = default_time_deriv()
 
 # Test discrete event is propagated to ODE solver correctly.
 let