Implement ISM chemistry including metals and dust

CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.20)
 
 project(Microphysics
     VERSION 1.0.0
-    DESCRIPTION "building primordial_chemistry network in Microphysics with CMake"
+    DESCRIPTION "building primordial_chemistry or metal_chemistry networks in Microphysics with CMake"
     LANGUAGES CXX C)
 
 #----------------------------------------------------------------------------------------------------------------------
@@ -23,11 +23,11 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
   set(integrationparamfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/_parameters")
   set(unittestparamfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/unit_test/_parameters")
 
-  set(networkpropfile "${output_dir}/network_properties.H")
 
   if (${network_name} STREQUAL "gamma_law")
     set(EOSparamfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS/gamma_law/_parameters")
 
+    set(networkpropfile "${output_dir}/network_properties.H")
     set(networkfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/gammalaw.net")
     set(networkdir "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/")
     set(networkheadertemplatefile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/network_header.template")
@@ -44,6 +44,7 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
     set(gamma_law_sources ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces/eos_data.cpp
                           ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces/network_initialization.cpp
                           ${output_dir}/extern_parameters.cpp PARENT_SCOPE)
+    execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/write_network.py" --header_template "${networkheadertemplatefile}" --header_output "${networkpropfile}" -s "${networkfile}" WORKING_DIRECTORY ${output_dir}/)
 
   elseif (${network_name} STREQUAL "primordial_chem")
     #need these to write extern_parameters.H
@@ -52,6 +53,7 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
     set(networkpcparamfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/primordial_chem/_parameters")
 
     #similarly, we want network_properties.H
+    set(networkpropfile "${output_dir}/network_properties.H")
     set(networkfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/primordial_chem/pynucastro.net")
     set(networkdir "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/primordial_chem/")
     set(networkheadertemplatefile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/network_header.template")
@@ -71,7 +73,7 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
     #so, if any of the _parameter files are changed, one needs to re-run 'cmake'
     #to generate updated header files
 
-    if(BUILD_UNIT_TEST)
+    if(BUILD_UNIT_TEST_PC)
       execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${paramfile} ${EOSparamfile}
                       ${networkpcparamfile} ${networkparamfile} ${VODEparamfile} ${integrationparamfile} ${unittestparamfile}" --use_namespace WORKING_DIRECTORY ${output_dir}/)
     else()
@@ -88,13 +90,59 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
 
     #below for NAUX
     execute_process(COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${PYTHONPATH}:${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null" python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/get_naux.py" --net "${networkdir}" --microphysics_path "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/" WORKING_DIRECTORY ${output_dir}/)
+    execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/write_network.py" --header_template "${networkheadertemplatefile}" --header_output "${networkpropfile}" -s "${networkfile}" WORKING_DIRECTORY ${output_dir}/)
+
+  elseif (${network_name} STREQUAL "metal_chem")
+    #need these to write extern_parameters.H
+    set(paramfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/unit_test/burn_cell_metal_chem/_parameters")
+    set(EOSparamfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS/metal_chem/_parameters")
+    set(networkpcparamfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/metal_chem/_parameters")
+
+    #similarly, we want network_properties.H
+    set(networkpropfile "${output_dir}/network_properties.H")
+    set(networkfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/metal_chem/pynucastro.net")
+    set(networkdir "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/metal_chem/")
+    set(networkheadertemplatefile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/network_header.template")
+
+    #DO NOT change the order of the directories below!
+    set (metal_chem_dirs ${CMAKE_BINARY_DIR} ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/gcem/include
+                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/VODE ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/utils
+                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces
+                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS/metal_chem
+                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/metal_chem ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks
+                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/constants
+                             PARENT_SCOPE)
+
+    #we need to have extern_parameters.cpp be available at configure time
+    #the script write_probin.py writes this .cpp file so we call it here
+    #note, execute_process only works on 'cmake' and not 'make'
+    #so, if any of the _parameter files are changed, one needs to re-run 'cmake'
+    #to generate updated header files
+
+    if(BUILD_UNIT_TEST_MC)
+      execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${paramfile} ${EOSparamfile}
+                      ${networkpcparamfile} ${networkparamfile} ${VODEparamfile} ${integrationparamfile} ${unittestparamfile}" --use_namespace WORKING_DIRECTORY ${output_dir}/)
+    else()
+      #do not need paramfile and unittestparamfile
+      execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${EOSparamfile} ${networkpcparamfile}
+                      ${networkparamfile} ${VODEparamfile} ${integrationparamfile} " --use_namespace WORKING_DIRECTORY ${output_dir}/)
+    endif()
+
+    set(primordial_chem_sources ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces/eos_data.cpp
+                                ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces/network_initialization.cpp
+                                ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS/metal_chem/actual_eos_data.cpp
+                                ${output_dir}/extern_parameters.cpp PARENT_SCOPE)
+
+
+    #below for NAUX
+    execute_process(COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${PYTHONPATH}:${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null" python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/get_naux.py" --net "${networkdir}" --microphysics_path "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/" WORKING_DIRECTORY ${output_dir}/)
+    execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/write_network.py" --header_template "${networkheadertemplatefile}" --header_output "${networkpropfile}" -s "${networkfile}" WORKING_DIRECTORY ${output_dir}/)
 
   else()
     message(FATAL_ERROR "Given network_name " ${network_name} " currently not supported. Use either 'gamma_law' or 'primordial_chem' ")
 
   endif()
 
-  execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/write_network.py" --header_template "${networkheadertemplatefile}" --header_output "${networkpropfile}" -s "${networkfile}" WORKING_DIRECTORY ${output_dir}/)
 
 endfunction()
 
@@ -126,8 +174,11 @@ endif()
 
 #set a cache variable that controls whether
 #we want to build the unit test or not
-set(BUILD_UNIT_TEST false CACHE BOOL "Do you want to build the unit test? (true/false)")
-message("Building unit test -- ${BUILD_UNIT_TEST}")
+set(BUILD_UNIT_TEST_PC false CACHE BOOL "Do you want to build the primordial chem unit test? (true/false)")
+message("Building unit test -- ${BUILD_UNIT_TEST_PC}")
+
+set(BUILD_UNIT_TEST_MC false CACHE BOOL "Do you want to build the metal chem unit test? (true/false)")
+message("Building unit test -- ${BUILD_UNIT_TEST_MC}")
 
 add_compile_options(-Werror -Wall -Wextra)
 
@@ -140,12 +191,12 @@ add_compile_options(-Werror -Wall -Wextra)
 #this will generate a warning but it will build successfully
 #do not need unit_test paramfiles when unit_test is not built
 
-if(BUILD_UNIT_TEST)
+if(BUILD_UNIT_TEST_PC)
+  #Build primordial chem unit test
   setup_target_for_microphysics_compilation("primordial_chem" ${CMAKE_BINARY_DIR})
-
   include_directories(${primordial_chem_dirs})
 
-  #adding unit_test as subdirectories
+  #adding unit_tests as subdirectories
   add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/unit_test)
   message("Building primordial chem unit test")
 
@@ -155,4 +206,19 @@ else()
 endif()
 
 
+if(BUILD_UNIT_TEST_MC)
+  #Build metal chem unit test
+  setup_target_for_microphysics_compilation("metal_chem" ${CMAKE_BINARY_DIR})
+  include_directories(${metal_chem_dirs})
+
+  #adding unit_tests as subdirectories
+  add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/unit_test)
+  message("Building metal chem unit test")
+
+else()
+
+  message("Not building metal chem unit test")
+endif()
+
+
 

EOS/metal_chem/Make.package

@@ -0,0 +1,3 @@
+CEXE_headers += actual_eos.H
+CEXE_headers += actual_eos_data.H
+CEXE_sources += actual_eos_data.cpp

EOS/metal_chem/_parameters

@@ -0,0 +1,140 @@
+@namespace: eos
+
+eos_gamma_default       real          1.4
+
+# define the specie names, and their masses and gammas
+species_1_name          string     "co_ice"
+species_1_gamma         real          5./3.
+species_1_mass          real          0.0
+
+species_2_name          string     "h2o_ice"
+species_2_gamma         real          5./3.
+species_2_mass          real          0.0
+
+species_3_name          string     "elec"
+species_3_gamma         real          5./3.
+species_3_mass          real          9.10938188e-28
+
+species_4_name          string     "hp"
+species_4_gamma         real          5./3.
+species_4_mass          real          1.67262158e-24
+
+species_5_name          string     "h"
+species_5_gamma         real          5./3.
+species_5_mass          real          1.67353251819e-24
+
+species_6_name          string     "hm"
+species_6_gamma         real          5./3.
+species_6_mass          real          1.67444345638e-24
+
+species_7_name          string     "dp"
+species_7_gamma         real          5./3.
+species_7_mass          real          3.34512158e-24
+
+species_8_name          string     "d"
+species_8_gamma         real          5./3.
+species_8_mass          real          3.34603251819e-24
+
+species_9_name          string     "h2p"
+species_9_gamma         real          1.4
+species_9_mass          real          3.34615409819e-24
+
+species_10_name          string     "dm"
+species_10_gamma         real          5./3.
+species_10_mass          real          3.34694345638e-24
+
+species_11_name          string     "h2"
+species_11_gamma         real          1.4
+species_11_mass          real          3.34706503638e-24
+
+species_12_name          string     "hdp"
+species_12_gamma         real          1.4
+species_12_mass          real          5.01865409819e-24
+
+species_13_name          string     "hd"
+species_13_gamma         real          1.4
+species_13_mass          real          5.01956503638e-24
+
+species_14_name          string     "hepp"
+species_14_gamma         real          5./3.
+species_14_mass          real          6.69024316e-24
+
+species_15_name          string     "hep"
+species_15_gamma         real          5./3.
+species_15_mass          real          6.69115409819e-24
+
+species_16_name          string     "he"
+species_16_gamma         real          5./3.
+species_16_mass          real          6.69206503638e-24
+
+species_17_name          string     "cp"
+species_17_gamma         real          5./3.
+species_17_mass          real          2.007528417094e-23
+
+species_18_name          string     "c"
+species_18_gamma         real          5./3.
+species_18_mass          real          2.0076195109128e-23
+
+species_19_name          string     "ch"
+species_19_gamma         real          1.4
+species_19_mass          real          2.1749727627316e-23
+
+species_20_name          string     "ch2"
+species_20_gamma         real          1.4
+species_20_mass          real          2.3423260145503998e-23
+
+species_21_name          string     "ch3"
+species_21_gamma         real          1.4
+species_21_mass          real          .5096792663692e-23
+
+species_22_name          string     "op"
+species_22_gamma         real          5./3.
+species_22_mass          real          2.6767349207316e-23
+
+species_23_name          string     "o"
+species_23_gamma         real          5./3.
+species_23_mass          real          2.6768260145504e-23
+
+species_24_name          string     "ch4"
+species_24_gamma         real          1.4
+species_24_mass          real          2.677032518188e-23
+
+species_25_name          string     "ohp"
+species_25_gamma         real          1.4
+species_25_mass          real          2.8440881725504e-23
+
+species_26_name          string     "oh"
+species_26_gamma         real          1.4
+species_26_mass          real          2.8441792663692003e-23
+
+species_27_name          string     "h2op"
+species_27_gamma         real          1.4
+species_27_mass          real          3.0114414243692e-23
+
+species_28_name          string     "h2o"
+species_28_gamma         real          1.4
+species_28_mass          real          3.011532518188e-23
+
+species_29_name          string     "h3op"
+species_29_gamma         real          1.4
+species_29_mass          real          3.178794676188e-23
+
+species_30_name          string     "cop"
+species_30_gamma         real          1.4
+species_30_mass          real          4.6843544316444e-23
+
+species_31_name          string     "co"
+species_31_gamma         real          1.4
+species_31_mass          real          4.6844455254632e-23
+
+species_32_name          string     "o2p"
+species_32_gamma         real          1.4
+species_32_mass          real          5.353560935282e-23
+
+species_33_name          string     "o2"
+species_33_gamma         real          1.4
+species_33_mass          real          5.3536520291008e-23
+
+species_34_name          string     "co2"
+species_34_gamma         real          1.4
+species_34_mass          real          7.3612715400136e-23