update

Author: TorkelE

docs/src/catalyst_functionality/chemistry_related_functionality.md

@@ -37,6 +37,16 @@ Finally, it is possible to check whether a species is a compound or not using th
 iscompound(CO2)
 ```
 
+!!! note
+    Currently, compounds with components that depend on variables that are not `t` are not supported. E.g. 
+    ```julia
+    @variables x y
+    @species O(x, y) 
+    @compound O2 ~ 2O
+    ```
+    will currently throw an error.
+
+
 Compound components that are also compounds are allowed, e.g. we can create a carbonic acid compound (H₂CO₃) that consists of CO₂ and H₂O:
 ```@example chem1
 @species H(t)

src/chemistry_functionality.jl

@@ -47,7 +47,7 @@ function make_compound(expr)
 
     # Extracts the composite species name, and a Vector{ReactantStruct} of its components.
     species_expr = expr.args[2]                                         # E.g. :(CO2(t))
-    species_expr = insert_independent_variable(species_expr, :t)        # Add independent variable (e.g. goes from `CO2` to `CO2(t)`).
+    species_expr = insert_independent_variable(species_expr, [:t])      # Add independent variable (e.g. goes from `CO2` to `CO2(t)`).
     species_name = find_varname_in_declaration(expr.args[2])            # E.g. :CO2
     composition = Catalyst.recursive_find_reactants!(expr.args[3], 1, Vector{ReactantStruct}(undef, 0))
 
@@ -61,13 +61,20 @@ function make_compound(expr)
 
     # Creates the found expressions that will create the compound species.
     # The `Expr(:escape, :(...))` is required so that teh expressions are evaluated in the scope the users use the macro in (to e.g. detect already exiting species).
+    non_t_iv_error_check_expr = Expr(:escape, :(@species $species_expr))                                                                                         # E.g. `@species CO2(t)`
     species_declaration_expr = Expr(:escape, :(@species $species_expr))                                                                                         # E.g. `@species CO2(t)`
     compound_designation_expr = Expr(:escape, :($species_name = ModelingToolkit.setmetadata($species_name, Catalyst.CompoundSpecies, true)))                    # E.g. `CO2 = ModelingToolkit.setmetadata(CO2, Catalyst.CompoundSpecies, true)`
     components_designation_expr = Expr(:escape, :($species_name = ModelingToolkit.setmetadata($species_name, Catalyst.CompoundComponents, $components)))        # E.g. `CO2 = ModelingToolkit.setmetadata(CO2, Catalyst.CompoundSpecies, [C, O])`
     coefficients_designation_expr = Expr(:escape, :($species_name = ModelingToolkit.setmetadata($species_name, Catalyst.CompoundCoefficients, $coefficients)))  # E.g. `CO2 = ModelingToolkit.setmetadata(CO2, Catalyst.CompoundSpecies, [1, 2])`
 
+    # Currently, non-t independent variables are not supported for compounds. If there are any like these, we throw an error:
+    non_t_iv_error_check_expr = Expr(:escape, :(issetequal(unique(reduce(vcat, arguments.(ModelingToolkit.unwrap.($components)))), [t]) || error("Currently, compounds depending on components that are not \"t\" are not supported.")))
+
+println(non_t_iv_error_check_expr)
+
     # Returns the rephrased expression.
     return quote
+        $non_t_iv_error_check_expr
         $species_declaration_expr
         $compound_designation_expr
         $components_designation_expr

src/expression_utils.jl

@@ -50,19 +50,23 @@ end
 # X(t), [metadata=true]
 # X(t) = 1.0, [metadata=true]
 # (In this example the independent variable t was inserted).
+# Extra dispatch is to ensure so that iv is a vector (so that we can handle both single or multiple iv insertion in one function). 
+#     - This way we don't have to make a check for how to create the final expression (which is different for symbol or vector of symbols).
 function insert_independent_variable(expr_in, iv)
+    # If iv is a symbol (e.g. :t), we convert to vector (e.g. [:t]). This way we can handle single and multiple ivs using the same code, without needing to check at the end.    
+    (iv isa Symbol) && (iv = [iv])
     # If expr is a symbol, just attach the iv. If not we have to create a new expr and mutate it. 
     # Because Symbols (a possible input) cannot be mutated, this function cannot mutate the input (would have been easier if Expr input was guaranteed).
-    (expr_in isa Symbol) && (return :($(expr_in)($iv)))
+    (expr_in isa Symbol) && (return Expr(:call, expr_in, iv...))
     expr = deepcopy(expr_in)
 
     if expr.head == :(=) # Case: :(X = 1.0)
-        expr.args[1] = :($(expr.args[1])($iv))
+        expr.args[1] = Expr(:call, expr.args[1], iv...)
     elseif expr.head == :tuple
         if expr.args[1] isa Symbol # Case: :(X, [metadata=true])
-            expr.args[1] = :($(expr.args[1])($iv))
+            expr.args[1] = Expr(:call, expr.args[1], iv...)
         elseif (expr.args[1].head == :(=)) && (expr.args[1].args[1] isa Symbol) # Case: :(X = 1.0, [metadata=true])
-            expr.args[1].args[1] = :($(expr.args[1].args[1])($iv))
+            expr.args[1].args[1] = Expr(:call, expr.args[1].args[1], iv...)
         end
     end
     (expr == expr_in) && error("Failed to add independent variable $(iv) to expression: $expr_in")

test/miscellaneous_tests/compound_macro.jl

@@ -67,6 +67,29 @@ let
     @test iscompound(rn.NH3_5)
 end
 
+### Test Various Independent Variables ###
+let
+    @variables t x y z
+    @species C(t) H(x) N(x) O(t) P(t,x) S(x,y)
+
+    @compound CO2 ~ C + 2O
+    @test issetequal(arguments(ModelingToolkit.unwrap(CO2)), [t])
+    
+    # These 4 tests checks currently non-supported feature.
+    @test_broken false
+    @test_broken false
+    @test_broken false
+    @test_broken false
+    # @compound NH4, [output=true] ~ N + 4H
+    # @compound (H2O = 2.0) ~ 2H + N
+    # @compound PH4 ~ P + 4H
+    # @compound SO2 ~ S + 2O
+    # @test issetequal(arguments(ModelingToolkit.unwrap(NH4)), [x])
+    # @test issetequal(arguments(ModelingToolkit.unwrap(H2O)), [t, x])
+    # @test issetequal(arguments(ModelingToolkit.unwrap(PH4)), [t, x])
+    # @test issetequal(arguments(ModelingToolkit.unwrap(SO2)), [t, x, y])
+end
+
 ### Other Minor Tests ###
 
 # Test base functionality in two cases.