Merge branch 'ncc/FrozenKeyIdxBiMap' into ncc/refactor-GrainSpeciesInfo

Author: mabruzzo

.circleci/config.yml

@@ -187,7 +187,9 @@ commands:
                   echo "Answers already exist; skipping."
                 fi
               else
-                py.test --answer-dir=${ANSWER_DIR}
+                # we pass -vv, so that each test gets its own line of output
+                # (this can be helpful if we encounter a segfault)
+                py.test -vv --answer-dir=${ANSWER_DIR}
               fi
             fi
 
@@ -197,7 +199,7 @@ commands:
       gold-standard-tag:
         description: "The gold-standard to use for generating the answers"
         type: string
-        default: "gold-standard-nccv6"
+        default: "gold-standard-nccv7"
       cache-tag:
         description: "A unique tag to append to the cache name"
         type: string

.clang-format-ignore

@@ -40,15 +40,15 @@ src/clib/interp_table_utils.h
 src/clib/interpolate.hpp
 src/clib/phys_constants.h
 src/clib/rate_functions.c
-src/clib/set_default_chemistry_parameters.c
+src/clib/set_default_chemistry_parameters.cpp
 src/clib/solve_chemistry.cpp
 src/clib/solve_rate_cool_g-cpp.cpp
 src/clib/status_reporting.c
 src/clib/status_reporting.h
 src/clib/step_rate_gauss_seidel.hpp
 src/clib/step_rate_newton_raphson.hpp
 src/clib/time_deriv_0d.hpp
-src/clib/update_UVbackground_rates.c
+src/clib/update_UVbackground_rates.cpp
 src/clib/utils-cpp.cpp
 src/clib/utils-cpp.hpp
 src/clib/utils.c

src/clib/CMakeLists.txt

@@ -88,9 +88,7 @@ add_library(Grackle_Grackle
   initialize_cloudy_data.c initialize_cloudy_data.h
   initialize_UVbackground_data.c  initialize_UVbackground_data.h
   rate_functions.c
-  set_default_chemistry_parameters.c
   status_reporting.c status_reporting.h
-  update_UVbackground_rates.c
   utils.c
 
   # auto-generated C source files
@@ -112,6 +110,7 @@ add_library(Grackle_Grackle
   cool_multi_time_g.cpp cool_multi_time_g.h
   dust_props.hpp
   dust/grain_species_info.cpp dust/grain_species_info.hpp
+  dust/lookup_dust_rates1d.hpp
   init_misc_species_cool_rates.cpp init_misc_species_cool_rates.hpp
   initialize_chemistry_data.cpp
   initialize_dust_yields.cpp initialize_dust_yields.hpp
@@ -123,11 +122,13 @@ add_library(Grackle_Grackle
   rate_utils.cpp
   solve_chemistry.cpp
   scale_fields.cpp scale_fields.hpp
+  set_default_chemistry_parameters.cpp
   solve_rate_cool_g-cpp.cpp solve_rate_cool_g-cpp.h
   step_rate_gauss_seidel.hpp
   step_rate_newton_raphson.hpp
   support/FrozenKeyIdxBiMap.hpp
   time_deriv_0d.hpp
+  update_UVbackground_rates.cpp update_UVbackground_rates.hpp
   utils-cpp.cpp utils-cpp.hpp
   utils-field.hpp
   fortran_func_wrappers.hpp

src/clib/calculate_cooling_time.cpp

@@ -15,15 +15,9 @@
 #include "grackle.h"
 #include "cool_multi_time_g.h"
 #include "internal_units.h"
+#include "update_UVbackground_rates.hpp"
 #include "utils.h"
 
-/* function prototypes */
-
-extern "C" int update_UVbackground_rates(chemistry_data *my_chemistry,
-                                         chemistry_data_storage *my_rates,
-                                         photo_rate_storage *my_uvb_rates,
-                                         code_units *my_units);
- 
 extern "C" int local_calculate_cooling_time(chemistry_data *my_chemistry,
                                             chemistry_data_storage *my_rates,
                                             code_units *my_units,
@@ -47,8 +41,8 @@ extern "C" int local_calculate_cooling_time(chemistry_data *my_chemistry,
     my_uvb_rates.comp_xray = my_uvb_rates.temp_xray = 0.;
 
   if (my_chemistry->UVbackground == 1) {
-    if (update_UVbackground_rates(my_chemistry, my_rates,
-                                  &my_uvb_rates, my_units) != GR_SUCCESS) {
+    if (grackle::impl::update_UVbackground_rates(
+          my_chemistry, my_rates, &my_uvb_rates, my_units) != GR_SUCCESS) {
       std::fprintf(stderr, "Error in update_UVbackground_rates.\n");
       return GR_FAIL;
     }

src/clib/dust/grain_species_info.cpp

@@ -71,8 +71,9 @@ grackle::impl::GrainSpeciesInfoEntry mk_gsp_info_entry_helper_(
     // allocate and initialize the pointer
     out_ingredient_ptr =
         new grackle::impl::GrainGrowthIngredient[n_ingredients];
-    std::memcpy(out_ingredient_ptr, growth_ingredients,
-                (std::size_t)n_ingredients);
+    for (int i = 0; i < n_ingredients; i++) {
+      out_ingredient_ptr[i] = growth_ingredients[i];
+    }
   }
 
   return grackle::impl::GrainSpeciesInfoEntry{species_idx,