Correctly handle ices in metal chemistry (#1650)

Minor modifications to ensure we handle ices correctly in the metal chemistry network (following the methodology used in KROME - Grassi et al. 2014). Also updates the reference solution outputs (minor differences from what we already have).
AMReX-Astro · Sep 17, 2024 · 01cc637 · 01cc637
1 parent 1e1dc14
commit 01cc637
Show file tree

Hide file tree

Showing 11 changed files with 800 additions and 798 deletions.
diff --git a/.github/workflows/burn_cell_metal_chem.yml b/.github/workflows/burn_cell_metal_chem.yml
@@ -39,14 +39,14 @@ jobs:
           cd unit_test/burn_cell_metal_chem
 
           declare -A line_numbers_map=(
-            ["Z=1"]="4461 4463 4465 4467 4468 4471 4472 4475 4481 4486"
+            ["Z=1"]="4450 4452 4454 4456 4457 4460 4461 4464 4470 4475"
             ["Z=1_z10"]="1613 1615 4456 4458 4460 4463 4470 4476 4481"
             ["Z=1e-1"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463"
             ["Z=1e-2"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463"
             ["Z=1e-3"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463"
             ["Z=1e-4"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463"
             ["Z=1e-5"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463"
-            ["Z=1e-6"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463"
+            ["Z=1e-6"]="4451 4453 4455 4457 4458 4461 4462 4465 4471 4476"
           )
 
           declare -A ref_map=(
@@ -92,9 +92,11 @@ jobs:
 
               # Adjust the line number for the reference file
               if [[ "$Z" == "Z=1" ]]; then
-                reference_line_number=$((line_number - 4460))
+                reference_line_number=$((line_number - 4449))
               elif [[ "$Z" == "Z=1_z10" ]]; then
                 reference_line_number=${ref_line_number_z10[$index]}
+              elif [[ "$Z" == "Z=1e-6" ]]; then
+                reference_line_number=$((line_number - 4450))
               else
                 reference_line_number=$((line_number - 4437))
               fi

diff --git a/EOS/metal_chem/_parameters b/EOS/metal_chem/_parameters
@@ -3,11 +3,11 @@
 eos_gamma_default       real          1.4
 
 # define the specie names, and their masses and gammas
-species_1_name          string     "co_ice"
+species_1_name          string     "co_total"
 species_1_gamma         real          5./3.
 species_1_mass          real          0.0
 
-species_2_name          string     "h2o_ice"
+species_2_name          string     "h2o_total"
 species_2_gamma         real          5./3.
 species_2_mass          real          0.0