Add thermo_models.jl, refactor and fix bugs

Author: jfbarthelemy

.github/workflows/CI.yml

@@ -43,6 +43,7 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       actions: write # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      pull-requests: read
       contents: write
       statuses: write
     steps:

.github/workflows/TagBot.yml

@@ -7,19 +7,19 @@ on:
     inputs:
       lookback:
         default: "3"
-permissions:
-  actions: read
-  checks: read
-  contents: write
-  deployments: read
-  issues: read
-  discussions: read
-  packages: read
-  pages: read
-  pull-requests: read
-  repository-projects: read
-  security-events: read
-  statuses: read
+# permissions:
+#   actions: read
+#   checks: read
+#   contents: write
+#   deployments: read
+#   issues: read
+#   discussions: read
+#   packages: read
+#   pages: read
+#   pull-requests: read
+#   repository-projects: read
+#   security-events: read
+#   statuses: read
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'

README.md

@@ -141,7 +141,7 @@ aggregate_state: AS_AQUEOUS
                  ΔfH⁰ = -1.417243319379807e6 - 104.60063934326T ♢ unit=[m² kg s⁻² mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
                  S⁰ = 616.8922592448816 - 104.60063934326log(T) ♢ unit=[m² kg s⁻² K⁻¹ mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
                  ΔfG⁰ = -1.27295402135706e6 - 721.4928985881417T + 104.60063934326T*log(T) ♢ unit=[m² kg s⁻² mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
-                 Vm = 4.700633883476301e-6 ♢ unit=[m³ mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
+                 V⁰ = 4.700633883476301e-6 ♢ unit=[m³ mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
 
 julia> Ca²⁺ = dict_species["Ca+2"]
 Species{Int64}
@@ -159,7 +159,7 @@ aggregate_state: AS_AQUEOUS
                  ΔfH⁰ = -533849.4518936157 - 30.922515869141T ♢ unit=[m² kg s⁻² mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
                  S⁰ = 119.70002369348362 - 30.922515869141log(T) ♢ unit=[m² kg s⁻² K⁻¹ mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
                  ΔfG⁰ = -560411.1568393706 - 150.6225395626246T + 30.922515869141T*log(T) ♢ unit=[m² kg s⁻² mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
-                 Vm = -1.8438742160797e-5 ♢ unit=[m³ mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
+                 V⁰ = -1.8438742160797e-5 ♢ unit=[m³ mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
 
 julia> SO₄²⁻ = dict_species["SO4-2"]
 Species{Int64}
@@ -177,7 +177,7 @@ aggregate_state: AS_AQUEOUS
                  ΔfH⁰ = -830362.0492202746 - 266.09072875977T ♢ unit=[m² kg s⁻² mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
                  S⁰ = 1534.9056613400478 - 266.09072875977log(T) ♢ unit=[m² kg s⁻² K⁻¹ mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
                  ΔfG⁰ = -659510.4812841403 - 1800.9963900998177T + 266.09072875977T*log(T) ♢ unit=[m² kg s⁻² mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
-                 Vm = 1.2917655706406e-5 ♢ unit=[m³ mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
+                 V⁰ = 1.2917655706406e-5 ♢ unit=[m³ mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
 
 julia> r = Reaction([CaSO₄, Ca²⁺, SO₄²⁻])
   equation: CaSO₄@ = Ca²⁺ + SO₄²⁻
@@ -188,7 +188,7 @@ properties: ΔrCp⁰ = -192.412605285651 ♢ unit=[m² kg s⁻² K⁻¹ mol⁻¹
             ΔrS⁰ = 1037.7134257886498 - 192.412605285651log(T) ♢ unit=[m² kg s⁻² K⁻¹ mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
             ΔrH⁰ = 53031.81826591678 - 192.412605285651T ♢ unit=[m² kg s⁻² mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
             ΔrG⁰ = 53032.38323354907 - 1230.1260310743007T + 192.412605285651T*log(T) ♢ unit=[m² kg s⁻² mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
-            ΔrV = -1.02217203378673e-5 ♢ unit=[m³ mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
+            ΔrV⁰ = -1.02217203378673e-5 ♢ unit=[m³ mol⁻¹] ♢ ref=[T=298.15 K, P=100000.0 m⁻¹ kg s⁻²]
 ```
 
 ## Installation

data/aq17-thermofun.jls

@@ -9,12 +9,13 @@ pages = [
         "man/stoich_matrices.md",
         "man/reactions.md",
     ],
-    "Examples" => ["example/bogue_calculation.md",
-                   "example/example_stoich_matrix.md"],
+    "Examples" => ["examples/bogue_calculation.md",
+                   "examples/example_stoich_matrix.md"],
     "API" => Any[
+    "Thermodynamical functions" => "api/thermo_functions.md",
+    "Thermodynamical models" => "api/thermo_models.md",
     "Element order" => "api/element_order.md",
     "Parsing tools" => "api/parsing_tools.md",
-    "Thermodynamical functions" => "api/thermo_functions.md",
     "Formulas" => "api/formulas.md",
     "Species" => "api/species.md",
     "Stoichiometric Matrix" => "api/stoich_matrices.md",

data/cemdata18-merged.jls

@@ -13,7 +13,6 @@ ThermoFunction(
     vars=[:T, :P, :t];
     ref=[:T => 298.15u"K", :P => 1u"bar", :t => 0u"s"],
 )
-thermo_function_library
 ∂
 ∫
 calculate_molar_mass

data/psinagra-12-07-thermofun.jls

@@ -0,0 +1,11 @@
+# Thermodynamical models
+
+```@index
+Pages = ["thermo_models.md"]
+```
+
+```@docs
+dict_cp_ft_equation
+thermo_functions_cp_ft_equation
+thermo_functions_generic_cp_ft
+```