Merge remote-tracking branch 'origin/master' into io

Author: shashi

Project.toml

@@ -1,7 +1,7 @@
 name = "ModelingToolkit"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
 authors = ["Chris Rackauckas <accounts@chrisrackauckas.com>"]
-version = "3.14.0"
+version = "3.14.1"
 
 [deps]
 ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"

src/systems/diffeqs/odesystem.jl

@@ -84,7 +84,7 @@ var_from_nested_derivative(x,i=0) = x.op isa Differential ? var_from_nested_deri
 iv_from_nested_derivative(x) = x.op isa Differential ? iv_from_nested_derivative(x.args[1]) : x.args[1].op
 iv_from_nested_derivative(x::Constant) = missing
 
-function ODESystem(eqs; kwargs...)
+function ODESystem(eqs, iv=nothing; kwargs...)
     # NOTE: this assumes that the order of algebric equations doesn't matter
     diffvars = OrderedSet{Variable}()
     allstates = OrderedSet{Variable}()
@@ -93,13 +93,15 @@ function ODESystem(eqs; kwargs...)
     diffeq = Equation[]
     algeeq = Equation[]
     # initial loop for finding `iv`
-    iv = nothing
-    for eq in eqs
-        if !(eq.lhs isa Constant) # assume eq.lhs is either Differential or Constant
-            iv = iv_from_nested_derivative(eq.lhs)
+    if iv === nothing
+        for eq in eqs
+            if !(eq.lhs isa Constant) # assume eq.lhs is either Differential or Constant
+                iv = iv_from_nested_derivative(eq.lhs)
+                break
+            end
         end
     end
-    iv === nothing && throw(ArgumentError("No differential variable detected."))
+    iv === nothing && throw(ArgumentError("Please pass in independent variables."))
     for eq in eqs
         for var in vars(eq.rhs for eq ∈ eqs)
             var isa Variable || continue

src/systems/reaction/reactionsystem.jl

@@ -213,7 +213,7 @@ function assemble_diffusion(rs, noise_scaling; combinatoric_ratelaws=true)
     species_to_idx = Dict((x => i for (i,x) in enumerate(rs.states)))
 
     for (j,rx) in enumerate(rs.eqs)
-        rlsqrt = sqrt(oderatelaw(rx; combinatoric_ratelaw=combinatoric_ratelaws))
+        rlsqrt = sqrt(abs(oderatelaw(rx; combinatoric_ratelaw=combinatoric_ratelaws)))
         (noise_scaling!==nothing) && (rlsqrt *= noise_scaling[j])
         for (spec,stoich) in rx.netstoich
             i            = species_to_idx[spec]

test/benchmark.jl

@@ -9,6 +9,7 @@ eqs = [D(y[1]) ~ -k[1]*y[1] + k[3]*y[2]*y[3],
        0 ~  y[1] + y[2] + y[3] - 1]
 
 sys = ODESystem(eqs,t,y,k)
+@test_throws ArgumentError ODESystem(eqs,y)
 M = calculate_massmatrix(sys)
 @test M == [1 0 0
             0 1 0