[newchem-cpp] cppify interp_table_utils.{h->hpp}

.clang-format-ignore

@@ -21,7 +21,6 @@ src/clib/cie_thin_cooling_rate_tables.h
 src/clib/cool1d_multi_g-cpp.C
 src/clib/cool1d_multi_g-cpp.h
 src/clib/cool_multi_time_g.cpp
-src/clib/dust_props.hpp
 src/clib/dynamic_api.c
 src/clib/fortran_func_decls.h
 src/clib/fortran_func_wrappers.hpp
@@ -37,7 +36,6 @@ src/clib/initialize_dust_yields.cpp
 src/clib/initialize_rates.cpp
 src/clib/internal_types.hpp
 src/clib/internal_units.h
-src/clib/interp_table_utils.h
 src/clib/interpolate.hpp
 src/clib/phys_constants.h
 src/clib/rate_functions.c

src/clib/CMakeLists.txt

@@ -112,11 +112,13 @@ add_library(Grackle_Grackle
   cool1d_multi_g.cpp cool1d_multi_g.hpp
   cool_multi_time_g.cpp cool_multi_time_g.h
   dust_props.hpp
+  dust/grain_species_info.cpp dust/grain_species_info.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
   initialize_rates.cpp initialize_rates.hpp
   internal_types.cpp internal_types.hpp
+  interp_table_utils.hpp
   lookup_cool_rates1d.hpp
   make_consistent.cpp make_consistent.hpp
   opaque_storage.hpp
@@ -172,7 +174,6 @@ add_library(Grackle_Grackle
   grackle_chemistry_data_fields.def # <-- acts as a C header
   grackle_macros.h
   index_helper.h
-  interp_table_utils.h
   phys_constants.h
   collisional_rxn_rate_members.def # <-- acts as a C header
   utils.h

src/clib/LUT.hpp

@@ -99,12 +99,12 @@ struct OnlyGrainSpLUT {
   // XMacros provided in grackle_field_data_fdatamembers.def (or we may need to
   // slightly revise the system?)
   enum {
+    MgSiO3_dust,
+    AC_dust,
     SiM_dust,
     FeM_dust,
     Mg2SiO4_dust,
-    MgSiO3_dust,
     Fe3O4_dust,
-    AC_dust,
     SiO2_dust,
     MgO_dust,
     FeS_dust,

src/clib/Make.config.objects

@@ -25,6 +25,7 @@ OBJS_CONFIG_LIB = \
         cool1d_cloudy_old_tables_g.lo \
         cool1d_multi_g.lo \
         cool_multi_time_g.lo \
+        dust/grain_species_info.lo \
         dynamic_api.lo \
         grackle_units.lo \
 	index_helper.lo \

src/clib/dust/grain_species_info.cpp

@@ -0,0 +1,314 @@
+//===----------------------------------------------------------------------===//
+//
+// See the LICENSE file for license and copyright information
+// SPDX-License-Identifier: NCSA AND BSD-3-Clause
+//
+//===----------------------------------------------------------------------===//
+///
+/// @file
+/// Implements functions associated with GrainSpeciesInfo (namely, the
+/// new_GrainSpeciesInfo function)
+///
+//===----------------------------------------------------------------------===//
+
+#include <cstring>  // memcpy
+
+#include "LUT.hpp"
+#include "grain_species_info.hpp"
+
+// The following logic effectively does 2 (related things):
+// 1. it serves as a human-readable registry of all known grain species and
+//    their associated properties.
+// 2. we must be able to use this information to construct an instance of the
+//    GrainSpeciesInfo data structure (so that the properties of each species
+//    can be queried programatically)
+
+// Encoding the gas-phase ingredients (for grain growth) of each grain species
+// poses a bit of an obstacle. Essentially, we need a way to specify a
+// variable-length list of ingredients and we should be able to infer the
+// length. Thus, similar to the way a c-string has a sentinel value signalling
+// the end of the list (i.e. the '\0' character), we use a sentinel for the
+// hardcoded ingredient lists. This is intended as a stopgap solution!
+//
+// Note: the version of the lists accessible through GrainSpeciesInfo NEVER
+// have the sentinel!
+
+/// Expands to an initializer list for initializing an instance of the
+/// GrainGrowthIngredient struct that is used to signal the termination of
+/// a variable length ingredient list (analogous to the role that '\0' plays
+/// in a c-string).
+#define GRIMPL_INGREDIENT_LIST_SENTINEL {-1, -1, -1.0}
+
+namespace {  // stuff inside an anonymous namespace is local to this file
+
+/// Constructs a GrainSpeciesInfoEntry instance
+///
+/// The primary work that this function must complete is determine the number
+/// of ingredients that a grain species has (if any) and then construct a
+/// heap-allocated copy of the ingredient list that is stored by the returned
+/// GrainSpeciesInfoEntry instance. Importantly:
+/// - the @p growth_ingredients argument is terminated by the sentinel
+/// - the ingredient list in the returned instance is **NOT** terminated by
+///   the sentinel
+grackle::impl::GrainSpeciesInfoEntry mk_gsp_info_entry_helper_(
+    int species_idx, int onlygrainsp_idx, const char* name,
+    bool h2dust_uses_carbonaceous_table, double sublimation_temperature,
+    double bulk_density_cgs,
+    const grackle::impl::GrainGrowthIngredient* growth_ingredients) {
+  using grackle::impl::GrainGrowthIngredient;
+
+  // the main "work" is to determine the number of specified growth_ingredients
+  // and copy them (if there are no ingredients, we use a nullptr)
+  GrainGrowthIngredient* out_ingredient_ptr = nullptr;
+  int n_ingredients = 0;
+
+  if (growth_ingredients != nullptr) {
+    n_ingredients = 0;
+    // increment the counter until we reach the sentinel
+    while (growth_ingredients[n_ingredients].coef != -1) {
+      n_ingredients++;
+    }
+    // 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);
+  }
+
+  return grackle::impl::GrainSpeciesInfoEntry{species_idx,
+                                              onlygrainsp_idx,
+                                              name,
+                                              h2dust_uses_carbonaceous_table,
+                                              sublimation_temperature,
+                                              bulk_density_cgs,
+                                              n_ingredients,
+                                              out_ingredient_ptr};
+}
+
+}  // anonymous namespace
+
+grackle::impl::GrainSpeciesInfo grackle::impl::new_GrainSpeciesInfo(
+    int dust_species_parameter) {
+  GrainSpeciesInfo out{-1, nullptr};  // indicates an error
+  out.n_species = get_n_grain_species(dust_species_parameter);
+
+  if (out.n_species <= 0) {
+    return out;
+  }
+
+  out.species_info = new GrainSpeciesInfoEntry[out.n_species];
+
+  // At the time of writing:
+  // - we **only** use h2rate_carbonaceous_coef_table for the AC_dust
+  //   species (amorphous carbon grains)
+  // - we use h2rate_silicate_coef_table for **ALL** other grain species
+  //   (including species that are obviously NOT silicates)
+  //
+  // It is not obvious at all why this is the case...
+  //
+  // TODO: we should add documentation clearly addressing each of the
+  // following questions and replace this todo-item with a reference to the
+  // part of the documentation that discusses this! The documentation
+  // should make sure to address:
+  // - if this choice physically motivated or a common convention? (or if
+  //   it was a quick & dirty choice because Gen didn't know what to do)
+  // - do we have a sense for how "wrong" the choice is? (e.g. will it
+  //   generally overpredict/underpredict?)
+  // - why don't we use the generic my_rates->h2dusta rate as a generic
+  //   fallback for non-silicate grains instead of using h2dustS? I realize
+  //   that h2dusta has very different units...
+
+  if (dust_species_parameter > 0) {
+    // growth rxn: "Mg + SiO + 2H2O -> MgSiO3_dust + 2H2I"
+    const GrainGrowthIngredient MgSiO3_dust_ingred[] = {
+        // {coef, species_idx, particle mass}
+        {1, SpLUT::Mg, 24.},
+        {1, SpLUT::SiOI, 44.},
+        {2, SpLUT::H2O, 18.},
+        GRIMPL_INGREDIENT_LIST_SENTINEL};
+    out.species_info[0] = mk_gsp_info_entry_helper_(
+        /* species_idx = */ SpLUT::MgSiO3_dust,
+        /* onlygrainsp_idx = */ OnlyGrainSpLUT::MgSiO3_dust,
+        /* name = */ "MgSiO3_dust",
+        /* h2dust_uses_carbonaceous_table = */ false,
+        /* sublimation_temperature = */ 1222.0,
+        /* bulk_density_cgs = */ 3.20185,
+        /* growth_ingredients = */ MgSiO3_dust_ingred);
+
+    // growth rxn: "C -> AC_dust"
+    const GrainGrowthIngredient AC_dust_ingred[] = {
+        // {coef, species_idx, particle mass}
+        {1, SpLUT::CI, 12.},
+        GRIMPL_INGREDIENT_LIST_SENTINEL};
+    out.species_info[1] = mk_gsp_info_entry_helper_(
+        /* species_idx = */ SpLUT::AC_dust,
+        /* onlygrainsp_idx = */ OnlyGrainSpLUT::AC_dust,
+        /* name = */ "AC_dust",
+        /* h2dust_uses_carbonaceous_table = */ true,
+        /* sublimation_temperature = */ 1800.0,
+        /* bulk_density_cgs = */ 2.27949,
+        /* growth_ingredients = */ AC_dust_ingred);
+  }
+
+  if (dust_species_parameter > 1) {
+    // growth rxn: "Si -> SiM_dust"
+    const GrainGrowthIngredient SiM_dust_ingred[] = {
+        // {coef, species_idx, particle mass}
+        {1, SpLUT::SiI, 28.},
+        GRIMPL_INGREDIENT_LIST_SENTINEL};
+    out.species_info[2] = mk_gsp_info_entry_helper_(
+        /* species_idx = */ SpLUT::SiM_dust,
+        /* onlygrainsp_idx = */ OnlyGrainSpLUT::SiM_dust,
+        /* name = */ "SiM_dust",
+        /* h2dust_uses_carbonaceous_table = */ false,
+        /* sublimation_temperature = */ 1500.0,
+        /* bulk_density_cgs = */ 2.34118,
+        /* growth_ingredients = */ SiM_dust_ingred);
+
+    // growth rxn: "Fe -> FeM_dust"
+    const GrainGrowthIngredient FeM_dust_ingred[] = {
+        // {coef, species_idx, particle mass}
+        {1, SpLUT::Fe, 56.},
+        GRIMPL_INGREDIENT_LIST_SENTINEL};
+    out.species_info[3] = mk_gsp_info_entry_helper_(
+        /* species_idx = */ SpLUT::FeM_dust,
+        /* onlygrainsp_idx = */ OnlyGrainSpLUT::FeM_dust,
+        /* name = */ "FeM_dust",
+        /* h2dust_uses_carbonaceous_table = */ false,
+        /* sublimation_temperature = */ 1500.0,
+        /* bulk_density_cgs = */ 7.95995,
+        /* growth_ingredients = */ FeM_dust_ingred);
+
+    // growth rxn: "2Mg + SiO + 3H2O -> Mg2SiO4_dust + 3H2I"
+    const GrainGrowthIngredient Mg2SiO4_dust_ingred[] = {
+        // {coef, species_idx, particle mass}
+        {2, SpLUT::Mg, 24.},
+        {1, SpLUT::SiOI, 44.},
+        {3, SpLUT::H2O, 18.},
+        GRIMPL_INGREDIENT_LIST_SENTINEL};
+    out.species_info[4] = mk_gsp_info_entry_helper_(
+        /* species_idx = */ SpLUT::Mg2SiO4_dust,
+        /* onlygrainsp_idx = */ OnlyGrainSpLUT::Mg2SiO4_dust,
+        /* name = */ "Mg2SiO4_dust",
+        /* h2dust_uses_carbonaceous_table = */ false,
+        /* sublimation_temperature = */ 1277.0,
+        /* bulk_density_cgs = */ 3.22133,
+        /* growth_ingredients = */ Mg2SiO4_dust_ingred);
+
+    // growth rxn: "3Fe + 4H2O -> Fe3O4_dust + 4H2I"
+    const GrainGrowthIngredient Fe3O4_dust_ingred[] = {
+        // {coef, species_idx, particle mass}
+        {3, SpLUT::Fe, 56.},
+        {4, SpLUT::H2O, 18.},
+        GRIMPL_INGREDIENT_LIST_SENTINEL};
+    out.species_info[5] = mk_gsp_info_entry_helper_(
+        /* species_idx = */ SpLUT::Fe3O4_dust,
+        /* onlygrainsp_idx = */ OnlyGrainSpLUT::Fe3O4_dust,
+        /* name = */ "Fe3O4_dust",
+        /* h2dust_uses_carbonaceous_table = */ false,
+        /* sublimation_temperature = */ 1500.0,
+        /* bulk_density_cgs = */ 5.25096,
+        /* growth_ingredients = */ Fe3O4_dust_ingred);
+
+    // growth rxn: "SiO2 -> SiO2_dust"
+    const GrainGrowthIngredient SiO2_dust_ingred[] = {
+        // {coef, species_idx, particle mass}
+        {1, SpLUT::SiO2I, 60.},
+        GRIMPL_INGREDIENT_LIST_SENTINEL};
+    out.species_info[6] = mk_gsp_info_entry_helper_(
+        /* species_idx = */ SpLUT::SiO2_dust,
+        /* onlygrainsp_idx = */ OnlyGrainSpLUT::SiO2_dust,
+        /* name = */ "SiO2_dust",
+        /* h2dust_uses_carbonaceous_table = */ false,
+        /* sublimation_temperature = */ 1500.0,
+        /* bulk_density_cgs = */ 2.66235,
+        /* growth_ingredients = */ SiO2_dust_ingred);
+
+    // growth rxn: "Mg + H2O -> MgO_dust + H2I"
+    const GrainGrowthIngredient MgO_dust_ingred[] = {
+        // {coef, species_idx, particle mass}
+        {1, SpLUT::Mg, 24.},
+        {1, SpLUT::H2O, 18.},
+        GRIMPL_INGREDIENT_LIST_SENTINEL};
+    out.species_info[7] = mk_gsp_info_entry_helper_(
+        /* species_idx = */ SpLUT::MgO_dust,
+        /* onlygrainsp_idx = */ OnlyGrainSpLUT::MgO_dust,
+        /* name = */ "MgO_dust",
+        /* h2dust_uses_carbonaceous_table = */ false,
+        /* sublimation_temperature = */ 1500.0,
+        /* bulk_density_cgs = */ 3.58157,
+        /* growth_ingredients = */ MgO_dust_ingred);
+
+    // growth rxn: "Fe + S -> FeS_dust"
+    const GrainGrowthIngredient FeS_dust_ingred[] = {
+        // {coef, species_idx, particle mass}
+        {1, SpLUT::Fe, 56.},
+        {1, SpLUT::S, 32.},
+        GRIMPL_INGREDIENT_LIST_SENTINEL};
+    out.species_info[8] = mk_gsp_info_entry_helper_(
+        /* species_idx = */ SpLUT::FeS_dust,
+        /* onlygrainsp_idx = */ OnlyGrainSpLUT::FeS_dust,
+        /* name = */ "FeS_dust",
+        /* h2dust_uses_carbonaceous_table = */ false,
+        /* sublimation_temperature = */ 680.0,
+        /* bulk_density_cgs = */ 4.87265,
+        /* growth_ingredients = */ FeS_dust_ingred);
+
+    // growth rxn: "2Al + 3H2O -> Al2O3_dust + 3H2I"
+    const GrainGrowthIngredient Al2O3_dust_ingred[] = {
+        // {coef, species_idx, particle mass}
+        {2, SpLUT::Al, 27.},
+        {3, SpLUT::H2O, 18.},
+        GRIMPL_INGREDIENT_LIST_SENTINEL};
+    out.species_info[9] = mk_gsp_info_entry_helper_(
+        /* species_idx = */ SpLUT::Al2O3_dust,
+        /* onlygrainsp_idx = */ OnlyGrainSpLUT::Al2O3_dust,
+        /* name = */ "Al2O3_dust",
+        /* h2dust_uses_carbonaceous_table = */ false,
+        /* sublimation_temperature = */ 1500.0,
+        /* bulk_density_cgs = */ 4.01610,
+        /* growth_ingredients = */ Al2O3_dust_ingred);
+  }
+
+  if (dust_species_parameter > 2) {
+    // We do not consider the growth of refractory organics, volatile
+    // organics, and water ice because their sublimation temperatures
+    // are low (100-600 K). They sublimate before the growth occurs.
+
+    // nominal growth rxn: "0.5CO + 0.5CH2 + 1.2N -> ref_org_dust"
+    // nuclide ratios: C:H:O:N = 1:1:0.5:1.2
+    out.species_info[10] = mk_gsp_info_entry_helper_(
+        /* species_idx = */ SpLUT::ref_org_dust,
+        /* onlygrainsp_idx = */ OnlyGrainSpLUT::ref_org_dust,
+        /* name = */ "ref_org_dust",
+        /* h2dust_uses_carbonaceous_table = */ false,
+        /* sublimation_temperature = */ 575.0,
+        /* bulk_density_cgs = */ 1.5,
+        /* growth_ingredients = */ nullptr);
+
+    // nominal growth rxn: "CO + 2H2I -> vol_org_dust"
+    // effective formula: CH3OH
+    out.species_info[11] = mk_gsp_info_entry_helper_(
+        /* species_idx = */ SpLUT::vol_org_dust,
+        /* onlygrainsp_idx = */ OnlyGrainSpLUT::vol_org_dust,
+        /* name = */ "vol_org_dust",
+        /* h2dust_uses_carbonaceous_table = */ false,
+        /* sublimation_temperature = */ 375.0,
+        /* bulk_density_cgs = */ 1.0,
+        /* growth_ingredients = */ nullptr);
+
+    // nominal growth rxn: "H2O -> H2O_ice_dust"
+    out.species_info[12] = mk_gsp_info_entry_helper_(
+        /* species_idx = */ SpLUT::H2O_ice_dust,
+        /* onlygrainsp_idx = */ OnlyGrainSpLUT::H2O_ice_dust,
+        /* name = */ "H2O_ice_dust",
+        /* h2dust_uses_carbonaceous_table = */ false,
+        /* sublimation_temperature = */ 153.0,
+        /* bulk_density_cgs = */ 0.92,
+        /* growth_ingredients = */ nullptr);
+  }
+
+  return out;
+}
+
+#undef GRIMPL_INGREDIENT_LIST_SENTINEL