Merge branch 'development' into jacobian_correction

.github/workflows/burn_cell_metal_chem.yml

@@ -33,20 +33,22 @@ jobs:
           cd unit_test/burn_cell_metal_chem
           make -j 2
 
-      - name: Run and compare outputs for different Z values
+      - name: Run and compare outputs for different Z values, also including cosmic ray ionization
         run: |
           set -e
           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"]="4463 4465 4467 4469 4470 4473 4474 4477 4483 4488"
+            ["Z=1_cr"]="652 654 656 658 659 662 663 666 672 677"
+            ["Z=1e-4_cr"]="652 654 656 658 659 662 663 666 672 677"
           )
 
           declare -A ref_map=(
@@ -58,6 +60,8 @@ jobs:
             ["Z=1e-4"]="reference_solution_1e-4.out"
             ["Z=1e-5"]="reference_solution_1e-5.out"
             ["Z=1e-6"]="reference_solution_1e-6.out"
+            ["Z=1_cr"]="reference_solution_1_cr.out"
+            ["Z=1e-4_cr"]="reference_solution_1e-4_cr.out"
           )
 
           ref_line_number_z10=(1 2 3 5 7 10 17 23 28)
@@ -66,19 +70,31 @@ jobs:
           original_input_file="inputs_metal_chem_1"
           modified_input_file="inputs_metal_chem_modified"
 
-          for Z in "Z=1" "Z=1_z10" "Z=1e-1" "Z=1e-2" "Z=1e-3" "Z=1e-4" "Z=1e-5" "Z=1e-6"; do
+          for Z in "Z=1" "Z=1_z10" "Z=1e-1" "Z=1e-2" "Z=1e-3" "Z=1e-4" "Z=1e-5" "Z=1e-6" "Z=1_cr" "Z=1e-4_cr"; do
             cp $original_input_file $modified_input_file
             Z_val=${Z//Z=/}
 
             if [[ "$Z" == "Z=1_z10" ]]; then
               # Modify the redshift line for Z=1_z10
               sed -i 's/network.redshift = 0.0/network.redshift = 10.0/g' $modified_input_file
-            else
+            elif [[ "$Z" != "Z=1_cr" && "$Z" != "Z=1e-4_cr" ]]; then
               # Replace the metallicity and dust2gas_ratio values for other Z values
               sed -i 's/network.metallicity = .*/network.metallicity = '"$Z_val"'/g' $modified_input_file
               sed -i 's/network.dust2gas_ratio = .*/network.dust2gas_ratio = '"$Z_val"'/g' $modified_input_file
             fi
 
+            if [[ "$Z" == "Z=1_cr" || "$Z" == "Z=1e-4_cr" ]]; then
+              # Modify the number of steps, since CRs impact lowest densities
+              sed -i 's/unit_test.nsteps = 100000/unit_test.nsteps = 600/g' $modified_input_file
+              # Modify the crate line for Z=1_cr
+              sed -i 's/network.crate = 0.0/network.crate = 3e-17/g' $modified_input_file
+              if [[ "$Z" == "Z=1e-4_cr" ]]; then
+                 # Replace the metallicity and dust2gas_ratio values for other Z values
+                 sed -i 's/network.metallicity = 1/network.metallicity = 1e-4/g' $modified_input_file
+                 sed -i 's/network.dust2gas_ratio = 1/network.dust2gas_ratio = 1e-4/g' $modified_input_file
+              fi
+           fi
+
             output_file="test_${Z_val}.out"
             ./main1d.gnu.DEBUG.ex $modified_input_file amrex.fpe_trap_{invalid,zero,overflow}=1 > $output_file
 
@@ -92,9 +108,13 @@ 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 - 4462))
+              elif [[ "$Z" == "Z=1_cr" || "$Z" == "Z=1e-4_cr" ]]; then
+                reference_line_number=$((line_number - 651))
               else
                 reference_line_number=$((line_number - 4437))
               fi

CHANGES.md

@@ -1,3 +1,11 @@
+# 24.10
+
+  * metal chemistry updates (#1648) with ices (#1650) and cosmic rays (#1651)
+
+  * added dust to primordial chemistry (#1649)
+
+  * doc updates (#1652)
+
 # 24.09
 
   * Improvements to the primordial chemistry network and the addition

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
 

README.md

@@ -2,7 +2,7 @@
 
 # Microphysics
 
-*A collection of astrophysical microphysics routines for stellar explosions*
+*A collection of astrophysical microphysics routines for stellar explosions and interstellar medium chemistry (including primordial chemistry)*
 
 There are several core types of microphysics routines hosted here:
 
@@ -25,7 +25,9 @@ There are several core types of microphysics routines hosted here:
 
 * `networks/`: these are the reaction networks. They serve both to
   define the composition and its properties, as well as describe the
-  reactions and energy release when reactions occur.
+  reactions and energy release when reactions occur. For ISM chemistry,
+  network contains the differentials of the number density of various
+  chemical species and the gas specific internal energy.
 
 * `neutrinos/`: this holds the plasma neutrino cooling routines used
   in the reaction networks.
@@ -57,7 +59,7 @@ There are several core types of microphysics routines hosted here:
 # AMReX-Astro Codes
 
 At the moment, these routines are written to be compatible with
-the AMReX-Astro codes, Maestro and Castro.
+the AMReX-Astro codes, Maestro, Castro and Quokka.
 
 * Castro: http://amrex-astro.github.io/Castro/
 

networks/metal_chem/_parameters

@@ -9,8 +9,6 @@ redshift                          real               0e0
 metallicity                          real               1e0
 # dust to gas ratio relative to solar
 dust2gas_ratio                 real               1e0
-# starting index for gas-phase species (after the ices)
-idx_gas_species                int                2
 
 # Cosmic ray ionization rate (per s)
 crate                          real               0e0