Merge pull request #20 from PALEOtoolkit/paleoaqchem_updates

Update tests for PALEOaqchem v0.3.9

Project.toml

@@ -26,7 +26,7 @@ Documenter = "0.27, 1"
 Infiltrator = "1"
 Interpolations = "0.13, 0.14, 0.15"
 MAT = "0.10.4"
-PALEOaqchem = "0.3.1"
+PALEOaqchem = "0.3.9"
 PALEOboxes = "0.20.4, 0.21"
 PALEOcopse = "0.4.5"
 PALEOmodel = "0.15.8"

examples/PTBClarkson2014/PALEO_examples_PTB3box_cfg.yaml

@@ -438,12 +438,28 @@ ocean3box_oaopencarb_base:
                     variable_links:
                         # defaults OK for B_conc, BOH4_conc, B_delta, BOH4_delta
 
+                # [H+] primary species (as pHfree) for TAlk total
+                H_primary_species: 
+                    class: ReactionConstraintReservoir
+                    variable_links:
+                        Primary_pconc: pHfree
+                        Primary_conc: H_conc
+                        R*: TAlk*
+                    parameters:
+                        primary_total_stoich: 0.0 # ReactionCO2SYS adds H to TAlk_calc
+                        primary_variable: p_concentration # provide pHfree as state variable to solver
+                        constraint_variable: amount # provide TAlk_constraint (mol) as algebraic constraint to solver
+                    variable_attributes: 
+                        Primary_pconc%initial_value: 8.0
+                        Primary_pconc%norm_value: 1.0
+                        R_constraint%norm_value: 1.0
+
                 carbchem:
                     class: ReactionCO2SYS
                     parameters:
                         components: ["Ci", "B", "S", "F", "Omega", "H2S"]
                         defaultconcs: ["TF", "Ca"]
-                        solve_pH:   constraint # Hfree as DAE variable
+                        solve_pH:   speciationTAlk # Hfree as DAE variable
                         outputs:    ["pCO2", "xCO2dryinp", "CO2", "CO3", "OmegaCA", "OmegaAR", "BAlk", "TB"]
                     variable_links:
                         TCi_conc: DIC_conc