Merge pull request #35 from PALEOtoolkit/setup_fixes

Fix setup of constant (non-state) Variables

Project.toml

@@ -1,7 +1,7 @@
 name = "PALEOboxes"
 uuid = "804b410e-d900-4b2a-9ecd-f5a06d4c1fd4"
 authors = ["Stuart Daines <[email protected]>"]
-version = "0.19.1"
+version = "0.19.2"
 
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"

src/VariableReaction.jl

@@ -361,7 +361,7 @@ function create_accessors(va::VarList_components, modeldata::AbstractModelData)
             if va.allow_unlinked
                 append!(accessors_generic, fill(nothing, num_components(v)))
             else
-                error("create_accessors(::VarList_components, ) - unlinked variable $(v.reaction.name).$(v.localname) $v")
+                error("create_accessors(::VarList_components, ) - unlinked variable $(fullname(v)) $v")
             end
         else
             append!(accessors_generic, a)

src/reactioncatalog/Reservoirs.jl

@@ -88,7 +88,12 @@ function PB.register_methods!(rj::ReactionReservoirScalar)
 
     if rj.pars.const.v
         R            = PB.VarPropScalar(      "R", "mol", "scalar constant reservoir", attributes=(:field_data =>rj.pars.field_data.v,))
-        PB.add_method_setup_initialvalue_vars_default!(rj, [R], filterfn = v->true, setup_callback=setup_callback)  # force setup even though R is not a state Variable
+        PB.add_method_setup_initialvalue_vars_default!(
+            rj, [R], 
+            filterfn = v->true, # force setup even though R is not a state Variable
+            force_initial_norm_value=true, # setup :norm_value, :initial_value to get norm_value callback, even though R is not a state Variable
+            setup_callback=setup_callback
+        )  
         # no _sms variable
     else        
         R        = PB.VarStateExplicitScalar("R", "mol", "scalar reservoir", attributes=(:field_data =>rj.pars.field_data.v,))

src/reactionmethods/SetupInitializeUtilityMethods.jl

@@ -6,10 +6,19 @@
     add_method_setup_initialvalue_vars_default!(react::AbstractReaction, variables [; kwargs...])
 
 Create and add a default method to initialize Variables matching `filterfn` (defaults to state Variables)
-from Attributes `:initial_value`, `:norm_value` at beginning of integration.
-
+at beginning of integration.
+
+# Setup callbacks used
+- State Variables and similar (`:vfunction != VF_Undefined`) are initialized in a setup callback with 
+  `attribute_name in (:initial_value, :norm_value)`, with values from those Variable attributes.
+- If `force_state_norm_value=false`, other Variables (with `:vfunction == VF_Undefined`) are initialized in a setup callback with 
+  `attribute_name=:setup`, with values from the `:initial_value` Variable attribute. NB: `filterfn` must be set to include these Variables.
+- If `force_initial_norm_value=true`, all Variables (including those with `:vfunction == VF_Undefined`) are initialised as state Variables
+  
 # Keywords
-- `filterfn`: set to f(var)::Bool to override the default selection on :vfunction for state variables.
+- `filterfn`: set to f(var)::Bool to override the default selection for state variables only
+  (Variables with `:vfunction in (VF_StateExplicit, VF_State, VF_Total, VF_Constraint)`)
+- `force_initial_norm_value=false`: `true` to always use `:initial_value`, `:norm_value`, even for variables with `:vfunction=VF_Undefined`
 - `transfer_attribute_vars=[]`: Set to a list of the same length as `variables` to initialise `variables`
   from attributes of `transfer_attribute_vars`.
 - `setup_callback=(method, attribute_name, var, vardata) -> nothing`: Set to a function that is called 
@@ -33,6 +42,7 @@ Example: To interpret `:initial_value` as a concentration-like quantity:
 function add_method_setup_initialvalue_vars_default!(
     react::AbstractReaction, variables;
     filterfn=var -> get_attribute(var, :vfunction) in (VF_StateExplicit, VF_State, VF_Total, VF_Constraint),
+    force_initial_norm_value=false,
     transfer_attribute_vars = [],
     convertvars = [],
     convertfn = (convertvars_tuple, i) -> 1.0, 
@@ -58,7 +68,7 @@ function add_method_setup_initialvalue_vars_default!(
         react,
         setup_initialvalue_vars_default,
         (VarList_fields(setup_vars), VarList_tuple(setup_transfer_vars), VarList_tuple(convertvars)),
-        p = (convertfn, convertinfo, setup_callback),
+        p = (force_initial_norm_value, convertfn, convertinfo, setup_callback),
     )
 
     return nothing
@@ -75,11 +85,8 @@ function setup_initialvalue_vars_default(
     cellrange::AbstractCellRange,
     attribute_name
 )    
-    attribute_name in (:norm_value, :initial_value) || return
-
-    (convertfn, convertinfo, setup_callback) = m.p
-
-    @info "$(fullname(m)):"
+    (force_initial_norm_value, convertfn, convertinfo, setup_callback) = m.p
+
     # VariableReactions corresponding to (vardata, transfervardata, convertvarsdata)
     vars, transfer_attribute_vars, convertvars = get_variables_tuple(m)
 
@@ -90,16 +97,32 @@ function setup_initialvalue_vars_default(
         attrbvars = [v.linkvar for v in transfer_attribute_vars]
     end
 
-    for (rv, v, attrbv, vfield) in IteratorUtils.zipstrict(vars, domvars, attrbvars, varfields)
-
+    first_var = true
+    for (rv, v, attrbv, vfield) in IteratorUtils.zipstrict(vars, domvars, attrbvars, varfields)        
+        vfunction = get_attribute(v, :vfunction, VF_Undefined)
+        if vfunction == VF_Undefined && !force_initial_norm_value
+            # non-state Variables are initialized in :setup, from :initial_value attribute
+            attribute_name == :setup || continue
+            attribute_to_read = :initial_value
+        else
+            # state Variables etc are initialized in :initial_value, :norm_value, from that attribute
+            attribute_name in (:initial_value, :norm_value) || continue
+            attribute_to_read = attribute_name
+        end
+
+        if first_var
+            @info "$(fullname(m)):"
+            first_var = false
+        end
+
         if v === attrbv
             trsfrinfo = ""
         else
             trsfrinfo = " [from $(fullname(attrbv))]"
         end
 
         init_field!(
-            vfield, attribute_name, attrbv, convertfn, convertvarsdata, cellrange, (fullname(v), convertinfo, trsfrinfo)
+            vfield, attribute_to_read, attrbv, convertfn, convertvarsdata, cellrange, (fullname(v), convertinfo, trsfrinfo)
         )
 
         setup_callback(m, attribute_name, rv, vfield.values)