[newchem-cpp] convert some initialization files to C++

.clang-format-ignore

@@ -30,11 +30,11 @@ src/clib/grackle_units.c
 src/clib/index_helper.c
 src/clib/index_helper.h
 src/clib/initialize_UVbackground_data.c
-src/clib/initialize_chemistry_data.c
+src/clib/initialize_chemistry_data.cpp
 src/clib/initialize_cloudy_data.c
-src/clib/initialize_dust_yields.c
-src/clib/initialize_metal_chemistry_rates.c
-src/clib/initialize_rates.c
+src/clib/initialize_dust_yields.cpp
+src/clib/initialize_metal_chemistry_rates.cpp
+src/clib/initialize_rates.cpp
 src/clib/internal_types.hpp
 src/clib/internal_units.h
 src/clib/interp_table_utils.h

src/clib/CMakeLists.txt

@@ -90,17 +90,13 @@ add_library(Grackle_Grackle
   dynamic_api.c
   grackle_units.c
   index_helper.c
-  initialize_chemistry_data.c
   initialize_cloudy_data.c initialize_cloudy_data.h
-  initialize_rates.c initialize_rates.h
   initialize_UVbackground_data.c  initialize_UVbackground_data.h
   rate_functions.c
   set_default_chemistry_parameters.c
   solve_chemistry.c
   status_reporting.c status_reporting.h
   update_UVbackground_rates.c
-  initialize_dust_yields.c initialize_dust_yields.h
-  initialize_metal_chemistry_rates.c initialize_metal_chemistry_rates.h
   rate_utils.c
   utils.c
 
@@ -114,6 +110,10 @@ add_library(Grackle_Grackle
   calc_temp_cloudy_g.cpp calc_temp_cloudy_g.h
   cool_multi_time_g.cpp cool_multi_time_g.h
   dust_props.hpp
+  initialize_chemistry_data.cpp
+  initialize_dust_yields.cpp initialize_dust_yields.hpp
+  initialize_rates.cpp initialize_rates.hpp
+  initialize_metal_chemistry_rates.cpp initialize_metal_chemistry_rates.hpp
   internal_types.cpp internal_types.hpp
   scale_fields.hpp
   solve_rate_cool_g-cpp.cpp solve_rate_cool_g-cpp.h

src/clib/initialize_chemistry_data.c → src/clib/initialize_chemistry_data.cpp

@@ -21,9 +21,9 @@
 #include "auto_general.h"
 #include "interp_table_utils.h" // free_interp_grid_
 #include "initialize_cloudy_data.h"
-#include "initialize_dust_yields.h"
-#include "initialize_metal_chemistry_rates.h"
-#include "initialize_rates.h"
+#include "initialize_dust_yields.hpp"  // free_dust_yields
+#include "initialize_metal_chemistry_rates.hpp"  // free_metal_chemistry_rates
+#include "initialize_rates.hpp"
 #include "initialize_UVbackground_data.h"
 #include "phys_constants.h"
 
@@ -35,7 +35,7 @@
 #error "Sanity check failure: GR_SUCCESS must be consistent with SUCCESS and GR_FAIL must be consistent with FAIL"
 #endif
 
-void show_parameters(FILE *fp, chemistry_data *my_chemistry);
+static void show_parameters(FILE *fp, chemistry_data *my_chemistry);
 
 static void show_version(FILE *fp)
 {
@@ -65,7 +65,7 @@ static void initialize_empty_interp_grid_(gr_interp_grid* grid)
 /**
  * Initializes an empty #chemistry_data_storage struct with zeros and NULLs.
  */
-void initialize_empty_chemistry_data_storage_struct(chemistry_data_storage *my_rates)
+static void initialize_empty_chemistry_data_storage_struct(chemistry_data_storage *my_rates)
 {
 
   my_rates->k1 = NULL;
@@ -315,9 +315,9 @@ void initialize_empty_chemistry_data_storage_struct(chemistry_data_storage *my_r
   my_rates->cloudy_data_new = -1;
 }
 
-int local_initialize_chemistry_data(chemistry_data *my_chemistry,
-                                    chemistry_data_storage *my_rates,
-                                    code_units *my_units)
+extern "C" int local_initialize_chemistry_data(chemistry_data *my_chemistry,
+                                               chemistry_data_storage *my_rates,
+                                               code_units *my_units)
 {
 
   /* Better safe than sorry: Initialize everything to NULL/0 */
@@ -492,7 +492,8 @@ int local_initialize_chemistry_data(chemistry_data *my_chemistry,
   }
 
   //* Call initialise_rates to compute rate tables.
-  initialize_rates(my_chemistry, my_rates, my_units, co_length_units, co_density_units);
+  grackle::impl::initialize_rates(
+    my_chemistry, my_rates, my_units, co_length_units, co_density_units);
 
   /* Initialize Cloudy cooling. */
   my_rates->cloudy_data_new = 1;
@@ -573,7 +574,7 @@ int local_initialize_chemistry_data(chemistry_data *my_chemistry,
   return GR_SUCCESS;
 }
 
-int initialize_chemistry_data(code_units *my_units)
+extern "C" int initialize_chemistry_data(code_units *my_units)
 {
   if (local_initialize_chemistry_data(grackle_data, &grackle_rates,
                                       my_units) == GR_FAIL) {
@@ -586,31 +587,31 @@ int initialize_chemistry_data(code_units *my_units)
 // Define helpers for the show_parameters function
 // NOTE: it's okay that these functions all begin with an underscore since they
 //       each have internal linkage (i.e. they are each declared static)
-static void _show_field_INT(FILE *fp, const char* field, int val)
+static void show_field_INT(FILE *fp, const char* field, int val)
 { fprintf(fp, "%-33s = %d\n", field, val); }
-static void _show_field_DOUBLE(FILE *fp, const char* field, double val)
+static void show_field_DOUBLE(FILE *fp, const char* field, double val)
 { fprintf(fp, "%-33s = %g\n", field, val); }
-static void _show_field_STRING(FILE *fp, const char* field, const char* val)
+static void show_field_STRING(FILE *fp, const char* field, const char* val)
 { fprintf(fp, "%-33s = %s\n", field, val); }
 
 // this function writes each field of my_chemistry to fp
-void show_parameters(FILE *fp, chemistry_data *my_chemistry){
+static void show_parameters(FILE *fp, chemistry_data *my_chemistry){
   #define ENTRY(FIELD, TYPE, DEFAULT_VAL) \
-    _show_field_ ## TYPE (fp, #FIELD, my_chemistry->FIELD);
+    show_field_ ## TYPE (fp, #FIELD, my_chemistry->FIELD);
   #include "grackle_chemistry_data_fields.def"
   #undef ENTRY
 }
 
-int free_chemistry_data(void){
+extern "C" int free_chemistry_data(void){
   if (local_free_chemistry_data(grackle_data, &grackle_rates) == GR_FAIL) {
     fprintf(stderr, "Error in local_free_chemistry_data.\n");
     return GR_FAIL;
   }
   return GR_SUCCESS;
 }
 
-int local_free_chemistry_data(chemistry_data *my_chemistry,
-                              chemistry_data_storage *my_rates) {
+extern "C" int local_free_chemistry_data(chemistry_data *my_chemistry,
+                                         chemistry_data_storage *my_rates) {
   if (my_chemistry->primordial_chemistry > 0) {
     GRACKLE_FREE(my_rates->ceHI);
     GRACKLE_FREE(my_rates->ceHeI);
@@ -722,20 +723,20 @@ int local_free_chemistry_data(chemistry_data *my_chemistry,
     GRACKLE_FREE(my_rates->UVbackground_table.crsHeI);
   }
 
-  if (local_free_metal_chemistry_rates(my_chemistry, my_rates) == FAIL) {
-    fprintf(stderr, "Error in local_free_metal_chemistry_rates.\n");
+  if (grackle::impl::free_metal_chemistry_rates(my_chemistry, my_rates) == FAIL) {
+    fprintf(stderr, "Error in free_metal_chemistry_rates.\n");
     return FAIL;
   }
 
-  if (local_free_dust_yields(my_chemistry, my_rates) == FAIL) {
+  if (grackle::impl::free_dust_yields(my_chemistry, my_rates) == FAIL) {
     fprintf(stderr, "Error in local_free_dust_yields.\n");
     return FAIL;
   }
 
   return GR_SUCCESS;
 }
 
-int grimpl_check_consistency_(int gr_float_hdrsize) {
+extern "C" int grimpl_check_consistency_(int gr_float_hdrsize) {
   if (gr_float_hdrsize != ((int)sizeof(gr_float))) {
     fprintf(stderr, "ERROR: Inconsistent floating-point precisions.\n"
                     "       size of gr_float in the headers used during compilation = %d\n"

src/clib/initialize_cloudy_data.c

@@ -41,7 +41,7 @@ void initialize_empty_cloudy_data_struct(cloudy_data *my_cloudy)
 // initialize cloudy cooling data
 int initialize_cloudy_data(chemistry_data *my_chemistry,
                            chemistry_data_storage *my_rates,
-                           cloudy_data *my_cloudy, char *group_name,
+                           cloudy_data *my_cloudy, const char *group_name,
                            code_units *my_units, int read_data)
 {
 

src/clib/initialize_cloudy_data.h

@@ -25,7 +25,7 @@ void initialize_empty_cloudy_data_struct(cloudy_data* my_cloudy);
 // initialize cloudy cooling data
 int initialize_cloudy_data(chemistry_data* my_chemistry,
                            chemistry_data_storage* my_rates,
-                           cloudy_data* my_cloudy, char* group_name,
+                           cloudy_data* my_cloudy, const char* group_name,
                            code_units* my_units, int read_data);
 
 int free_cloudy_data(cloudy_data* my_cloudy, chemistry_data* my_chemistry,

src/clib/initialize_dust_yields.c → src/clib/initialize_dust_yields.cpp

@@ -1,8 +1,25 @@
+//===----------------------------------------------------------------------===//
+//
+// See the LICENSE file for license and copyright information
+// SPDX-License-Identifier: NCSA AND BSD-3-Clause
+//
+//===----------------------------------------------------------------------===//
+///
+/// @file
+/// Implements the functions to initialize the dust yields
+///
+//===----------------------------------------------------------------------===//
+
 #include <stdlib.h> 
 #include <stdio.h>
 #include <math.h>
 #include "grackle_macros.h"
 #include "grackle_chemistry_data.h"
+#include "initialize_dust_yields.hpp" // forward declarations
+
+// forward declare some functions
+
+namespace {  // stuff inside an anonymous namespace is local to this file
 
 int calc_rates_dust_loc(int iSN, chemistry_data *my_chemistry, chemistry_data_storage *my_rates);
 int calc_rates_dust_C13(int iSN, chemistry_data *my_chemistry, chemistry_data_storage *my_rates);
@@ -17,11 +34,13 @@ int calc_rates_dust_P170(int iSN, chemistry_data *my_chemistry, chemistry_data_s
 int calc_rates_dust_P200(int iSN, chemistry_data *my_chemistry, chemistry_data_storage *my_rates);
 int calc_rates_dust_Y19(int iSN, chemistry_data *my_chemistry, chemistry_data_storage *my_rates);
 
+}  // anonymous namespace
+
 typedef int calc_yield_rate_fn(int, chemistry_data*, chemistry_data_storage*);
 
-int initialize_dust_yields(chemistry_data *my_chemistry,
-                           chemistry_data_storage *my_rates,
-                           code_units *my_units)
+int grackle::impl::initialize_dust_yields(chemistry_data *my_chemistry,
+                                          chemistry_data_storage *my_rates,
+                                          code_units *my_units)
 {
 
   if (my_chemistry->metal_chemistry == 0)
@@ -50,35 +69,35 @@ int initialize_dust_yields(chemistry_data *my_chemistry,
       NSN = 12;
       my_rates->SN0_N = NSN;
 
-      my_rates->SN0_XC  = malloc(NSN * sizeof(double));
-      my_rates->SN0_XO  = malloc(NSN * sizeof(double));
-      my_rates->SN0_XMg = malloc(NSN * sizeof(double));
-      my_rates->SN0_XAl = malloc(NSN * sizeof(double));
-      my_rates->SN0_XSi = malloc(NSN * sizeof(double));
-      my_rates->SN0_XS  = malloc(NSN * sizeof(double));
-      my_rates->SN0_XFe = malloc(NSN * sizeof(double));
-
-      my_rates->SN0_fC  = malloc(NSN * sizeof(double));
-      my_rates->SN0_fO  = malloc(NSN * sizeof(double));
-      my_rates->SN0_fMg = malloc(NSN * sizeof(double));
-      my_rates->SN0_fAl = malloc(NSN * sizeof(double));
-      my_rates->SN0_fSi = malloc(NSN * sizeof(double));
-      my_rates->SN0_fS  = malloc(NSN * sizeof(double));
-      my_rates->SN0_fFe = malloc(NSN * sizeof(double));
-
-      my_rates->SN0_fSiM      = malloc(NSN * sizeof(double));
-      my_rates->SN0_fFeM      = malloc(NSN * sizeof(double));
-      my_rates->SN0_fMg2SiO4  = malloc(NSN * sizeof(double));
-      my_rates->SN0_fMgSiO3   = malloc(NSN * sizeof(double));
-      my_rates->SN0_fFe3O4    = malloc(NSN * sizeof(double));
-      my_rates->SN0_fAC       = malloc(NSN * sizeof(double));
-      my_rates->SN0_fSiO2D    = malloc(NSN * sizeof(double));
-      my_rates->SN0_fMgO      = malloc(NSN * sizeof(double));
-      my_rates->SN0_fFeS      = malloc(NSN * sizeof(double));
-      my_rates->SN0_fAl2O3    = malloc(NSN * sizeof(double));
-      my_rates->SN0_freforg   = malloc(NSN * sizeof(double));
-      my_rates->SN0_fvolorg   = malloc(NSN * sizeof(double));
-      my_rates->SN0_fH2Oice   = malloc(NSN * sizeof(double));
+      my_rates->SN0_XC  = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_XO  = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_XMg = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_XAl = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_XSi = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_XS  = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_XFe = (double*)malloc(NSN * sizeof(double));
+
+      my_rates->SN0_fC  = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fO  = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fMg = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fAl = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fSi = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fS  = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fFe = (double*)malloc(NSN * sizeof(double));
+
+      my_rates->SN0_fSiM      = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fFeM      = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fMg2SiO4  = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fMgSiO3   = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fFe3O4    = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fAC       = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fSiO2D    = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fMgO      = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fFeS      = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fAl2O3    = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_freforg   = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fvolorg   = (double*)malloc(NSN * sizeof(double));
+      my_rates->SN0_fH2Oice   = (double*)malloc(NSN * sizeof(double));
 
       for(iSN = 0; iSN < NSN; iSN++) {
         my_rates->SN0_XC [iSN] = 0.0;
@@ -112,19 +131,19 @@ int initialize_dust_yields(chemistry_data *my_chemistry,
         my_rates->SN0_fH2Oice  [iSN] = 0.0;
       }
 
-      my_rates->SN0_r0SiM      = malloc(NSN * 3 * sizeof(double));
-      my_rates->SN0_r0FeM      = malloc(NSN * 3 * sizeof(double));
-      my_rates->SN0_r0Mg2SiO4  = malloc(NSN * 3 * sizeof(double));
-      my_rates->SN0_r0MgSiO3   = malloc(NSN * 3 * sizeof(double));
-      my_rates->SN0_r0Fe3O4    = malloc(NSN * 3 * sizeof(double));
-      my_rates->SN0_r0AC       = malloc(NSN * 3 * sizeof(double));
-      my_rates->SN0_r0SiO2D    = malloc(NSN * 3 * sizeof(double));
-      my_rates->SN0_r0MgO      = malloc(NSN * 3 * sizeof(double));
-      my_rates->SN0_r0FeS      = malloc(NSN * 3 * sizeof(double));
-      my_rates->SN0_r0Al2O3    = malloc(NSN * 3 * sizeof(double));
-      my_rates->SN0_r0reforg   = malloc(NSN * 3 * sizeof(double));
-      my_rates->SN0_r0volorg   = malloc(NSN * 3 * sizeof(double));
-      my_rates->SN0_r0H2Oice   = malloc(NSN * 3 * sizeof(double));
+      my_rates->SN0_r0SiM      = (double*)malloc(NSN * 3 * sizeof(double));
+      my_rates->SN0_r0FeM      = (double*)malloc(NSN * 3 * sizeof(double));
+      my_rates->SN0_r0Mg2SiO4  = (double*)malloc(NSN * 3 * sizeof(double));
+      my_rates->SN0_r0MgSiO3   = (double*)malloc(NSN * 3 * sizeof(double));
+      my_rates->SN0_r0Fe3O4    = (double*)malloc(NSN * 3 * sizeof(double));
+      my_rates->SN0_r0AC       = (double*)malloc(NSN * 3 * sizeof(double));
+      my_rates->SN0_r0SiO2D    = (double*)malloc(NSN * 3 * sizeof(double));
+      my_rates->SN0_r0MgO      = (double*)malloc(NSN * 3 * sizeof(double));
+      my_rates->SN0_r0FeS      = (double*)malloc(NSN * 3 * sizeof(double));
+      my_rates->SN0_r0Al2O3    = (double*)malloc(NSN * 3 * sizeof(double));
+      my_rates->SN0_r0reforg   = (double*)malloc(NSN * 3 * sizeof(double));
+      my_rates->SN0_r0volorg   = (double*)malloc(NSN * 3 * sizeof(double));
+      my_rates->SN0_r0H2Oice   = (double*)malloc(NSN * 3 * sizeof(double));
 
       itab = 0;
       for(iSN = 0; iSN < NSN; iSN++) {
@@ -151,27 +170,27 @@ int initialize_dust_yields(chemistry_data *my_chemistry,
       dTd =     0.1000000;
      Nmom =             4;
 
-      my_rates->gr_Td = malloc(NTd * Nmom * sizeof(double));
+      my_rates->gr_Td = (double*)malloc(NTd * Nmom * sizeof(double));
       my_rates->gr_Size = NTd * Nmom;
       my_rates->gr_N[0] = Nmom;
       my_rates->gr_N[1] = NTd;
       my_rates->gr_dT   = dTd;
       for(iTd = 0; iTd < NTd; iTd++)
         my_rates->gr_Td[iTd] = Td0 + (double)iTd * dTd;
 
-      my_rates->SN0_kpSiM      = malloc(NSN * Nmom * NTd * sizeof(double));
-      my_rates->SN0_kpFeM      = malloc(NSN * Nmom * NTd * sizeof(double));
-      my_rates->SN0_kpMg2SiO4  = malloc(NSN * Nmom * NTd * sizeof(double));
-      my_rates->SN0_kpMgSiO3   = malloc(NSN * Nmom * NTd * sizeof(double));
-      my_rates->SN0_kpFe3O4    = malloc(NSN * Nmom * NTd * sizeof(double));
-      my_rates->SN0_kpAC       = malloc(NSN * Nmom * NTd * sizeof(double));
-      my_rates->SN0_kpSiO2D    = malloc(NSN * Nmom * NTd * sizeof(double));
-      my_rates->SN0_kpMgO      = malloc(NSN * Nmom * NTd * sizeof(double));
-      my_rates->SN0_kpFeS      = malloc(NSN * Nmom * NTd * sizeof(double));
-      my_rates->SN0_kpAl2O3    = malloc(NSN * Nmom * NTd * sizeof(double));
-      my_rates->SN0_kpreforg   = malloc(NSN * Nmom * NTd * sizeof(double));
-      my_rates->SN0_kpvolorg   = malloc(NSN * Nmom * NTd * sizeof(double));
-      my_rates->SN0_kpH2Oice   = malloc(NSN * Nmom * NTd * sizeof(double));
+      my_rates->SN0_kpSiM      = (double*)malloc(NSN * Nmom * NTd * sizeof(double));
+      my_rates->SN0_kpFeM      = (double*)malloc(NSN * Nmom * NTd * sizeof(double));
+      my_rates->SN0_kpMg2SiO4  = (double*)malloc(NSN * Nmom * NTd * sizeof(double));
+      my_rates->SN0_kpMgSiO3   = (double*)malloc(NSN * Nmom * NTd * sizeof(double));
+      my_rates->SN0_kpFe3O4    = (double*)malloc(NSN * Nmom * NTd * sizeof(double));
+      my_rates->SN0_kpAC       = (double*)malloc(NSN * Nmom * NTd * sizeof(double));
+      my_rates->SN0_kpSiO2D    = (double*)malloc(NSN * Nmom * NTd * sizeof(double));
+      my_rates->SN0_kpMgO      = (double*)malloc(NSN * Nmom * NTd * sizeof(double));
+      my_rates->SN0_kpFeS      = (double*)malloc(NSN * Nmom * NTd * sizeof(double));
+      my_rates->SN0_kpAl2O3    = (double*)malloc(NSN * Nmom * NTd * sizeof(double));
+      my_rates->SN0_kpreforg   = (double*)malloc(NSN * Nmom * NTd * sizeof(double));
+      my_rates->SN0_kpvolorg   = (double*)malloc(NSN * Nmom * NTd * sizeof(double));
+      my_rates->SN0_kpH2Oice   = (double*)malloc(NSN * Nmom * NTd * sizeof(double));
 
       itab = 0;
       for(iSN = 0; iSN < NSN; iSN++) {
@@ -212,8 +231,8 @@ int initialize_dust_yields(chemistry_data *my_chemistry,
   return SUCCESS;
 }
 
-int local_free_dust_yields(chemistry_data *my_chemistry,
-                           chemistry_data_storage *my_rates)
+int grackle::impl::free_dust_yields(chemistry_data *my_chemistry,
+                                    chemistry_data_storage *my_rates)
 {
 
   if (my_chemistry->metal_chemistry == 0)
@@ -282,6 +301,8 @@ int local_free_dust_yields(chemistry_data *my_chemistry,
   return SUCCESS;
 }
 
+namespace {  // stuff inside an anonymous namespace is local to this file
+
 int calc_rates_dust_loc(int iSN, chemistry_data *my_chemistry, chemistry_data_storage *my_rates)
 {
 
@@ -4367,3 +4388,5 @@ int calc_rates_dust_Y19(int iSN, chemistry_data *my_chemistry, chemistry_data_st
 
   return SUCCESS;
 }
+
+}  // anonymous namespace