[newchem-cpp] Cleanup initialization of kcol_rate_tables

.clang-format-ignore

@@ -10,7 +10,7 @@
 # - No new files should be added to this list
 
 src/clib/c_wrappers/wrap_interpolators_g.c
-src/clib/calc_tdust_3d.C
+src/clib/calc_tdust_3d.cpp
 src/clib/calculate_cooling_time.c
 src/clib/calculate_dust_temperature.c
 src/clib/calculate_gamma.c
@@ -20,8 +20,7 @@ src/clib/chemistry_solver_funcs.hpp
 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.C
-src/clib/cool_multi_time_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
@@ -30,12 +29,12 @@ src/clib/grackle_macros.h
 src/clib/grackle_units.c
 src/clib/index_helper.c
 src/clib/index_helper.h
+src/clib/init_misc_species_cool_rates.cpp
 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_rates.cpp
 src/clib/internal_types.hpp
 src/clib/internal_units.h
 src/clib/interp_table_utils.h
@@ -44,14 +43,13 @@ src/clib/phys_constants.h
 src/clib/rate_functions.c
 src/clib/set_default_chemistry_parameters.c
 src/clib/solve_chemistry.c
-src/clib/solve_rate_cool_g-cpp.C
-src/clib/solve_rate_cool_g-cpp.h
+src/clib/solve_rate_cool_g-cpp.cpp
 src/clib/status_reporting.c
 src/clib/status_reporting.h
 src/clib/step_rate_newton_raphson.hpp
 src/clib/time_deriv_0d.hpp
 src/clib/update_UVbackground_rates.c
-src/clib/utils-cpp.C
+src/clib/utils-cpp.cpp
 src/clib/utils-cpp.hpp
 src/clib/utils.c
 src/clib/utils.h

src/clib/CMakeLists.txt

@@ -90,34 +90,38 @@ add_library(Grackle_Grackle
   dynamic_api.c
   grackle_units.c
   index_helper.c
-  initialize_chemistry_data.c
-  initialize_cloudy_data.c
-  initialize_rates.c
-  initialize_UVbackground_data.c
+  initialize_cloudy_data.c initialize_cloudy_data.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_metal_chemistry_rates.c
-  rate_utils.c
   utils.c
 
   # auto-generated C source files
   ${CMAKE_CURRENT_BINARY_DIR}/auto_general.c
+  # here is the companion header file (not generated)
+  auto_general.h
 
   # C++ Source (and Private Header Files)
-  calc_temp_cloudy_g-cpp.C calc_temp_cloudy_g-cpp.h
-  calc_tdust_3d.C calc_tdust_3d.h
-  cool_multi_time_g-cpp.C cool_multi_time_g-cpp.h
+  calc_tdust_3d.cpp calc_tdust_3d.h
+  calc_temp_cloudy_g.cpp calc_temp_cloudy_g.h
+  collisional_rate_props.cpp collisional_rate_props.hpp
+  cool_multi_time_g.cpp cool_multi_time_g.h
   dust_props.hpp
-  internal_types.C internal_types.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
+  opaque_storage.hpp
+  rate_utils.cpp
   scale_fields.hpp
-  solve_rate_cool_g-cpp.C solve_rate_cool_g-cpp.h
+  solve_rate_cool_g-cpp.cpp solve_rate_cool_g-cpp.h
   step_rate_newton_raphson.hpp
   time_deriv_0d.hpp
-  utils-cpp.C utils-cpp.hpp
+  utils-cpp.cpp utils-cpp.hpp
   utils-field.hpp
   fortran_func_wrappers.hpp
   visitor/common.hpp

src/clib/LUT.hpp

@@ -118,6 +118,11 @@ struct OnlyGrainSpLUT {
 };  // struct OnlyGrainSpLUT
 
 /// Defines the LUT for Standard Collisional reaction rates
+///
+/// @note
+/// If we ever make changes, we should consider how the changes will affect
+/// `get_CollisionalRxn_rateprop_`. If necessary, we could always refactor
+/// `get_CollisionalRxn_rateprop_` to not use this enum
 struct CollisionalRxnLUT {
   enum {
 #define ENTRY(NAME) NAME,

src/clib/Make.config.objects

@@ -19,18 +19,19 @@ OBJS_CONFIG_LIB = \
         calculate_pressure.lo \
         calculate_temperature.lo \
         calc_temp1d_cloudy_g.lo \
-        calc_temp_cloudy_g-cpp.lo \
+        calc_temp_cloudy_g.lo \
+        collisional_rate_props.lo \
         cool1d_cloudy_g.lo \
         cool1d_cloudy_old_tables_g.lo \
         cool1d_multi_g.lo \
-        cool_multi_time_g-cpp.lo \
+        cool_multi_time_g.lo \
         dynamic_api.lo \
         grackle_units.lo \
 	index_helper.lo \
         initialize_chemistry_data.lo \
         initialize_cloudy_data.lo \
         initialize_dust_yields.lo \
-        initialize_metal_chemistry_rates.lo \
+        init_misc_species_cool_rates.lo \
         initialize_rates.lo \
         initialize_UVbackground_data.lo \
         interpolators_g.lo \

src/clib/Makefile

@@ -138,11 +138,11 @@ verbose: VERBOSE = 1
 # Implicit rules
 #-----------------------------------------------------------------------
 
-.SUFFIXES: .c .C .F .lo .o
+.SUFFIXES: .c .cpp .C .F .lo .o
 
 # Inhibit removing any *.o files after compiling
 
-.PRECIOUS: %.o %.lo %.c %.C %.F
+.PRECIOUS: %.o %.lo %.c %.cpp %.C %.F
 
 .F.lo:
 	@rm -f $@
@@ -163,6 +163,37 @@ verbose: VERBOSE = 1
 	  fi ; \
 	fi)
 
+# Keep this synchronized with the .C.lo implicit rule
+# -> the historic convention in the Grackle project was to use .C as the suffix
+#    for C++ source files. Thus, when we began transcribing files, we used the
+#    .C suffix (even though it is a less common choice than .cpp)
+# -> however, it turns out that converting a file named `<prefix>.c` to
+#    `<prefix>.C` causes lots of issues performing Git operations when your
+#    machine has a case-insensitive file-system (common on macOS).
+# -> consequently, we will be transitioning to the .cpp suffix
+.cpp.lo:
+	@rm -f $@
+	@(if [ $(VERBOSE) -eq 0 ]; then \
+	  echo "Compiling $<" ; \
+	  $(LIBTOOL) --mode=compile --tag=CXX $(CXX) -c $(DEFINES) $(CXXFLAGS) $(INCLUDES) $*.cpp -o $@ \
+	    >& $(OUTPUT) ; \
+	  if [ ! -e $@ ]; then \
+             echo; \
+	     echo "Compiling $< failed!"; \
+	     echo "See $(OUTPUT) for error messages."; \
+             echo; \
+             exit 1; \
+          fi ; \
+	else \
+	  $(LIBTOOL) --mode=compile --tag=CXX $(CXX) -c $(DEFINES) $(CXXFLAGS) $(INCLUDES) $*.cpp -o $@; \
+	  if [ ! -e $@ ]; then \
+	     exit 1; \
+	  fi ; \
+	fi)
+
+# Keep this synchronized with the .cpp.lo implicit rule. This is mostly for
+# legacy purposes. We'll be transitioning to "just" .cpp.lo in the future.
+# Justification for why we have both .cpp.lo AND .C.lo is provided up above
 .C.lo:
 	@rm -f $@
 	@(if [ $(VERBOSE) -eq 0 ]; then \
@@ -251,7 +282,7 @@ clean_autogen:
 .PHONY: dep
 dep:
 	@echo "Updating DEPEND"
-	-@(makedepend $(DEFINES) $(INCLUDES) -a -fDEPEND -o.o -m -- -- *.C) >> out.make.DEPEND 2>&1
+	-@(makedepend $(DEFINES) $(INCLUDES) -a -fDEPEND -o.o -m -- -- *.cpp *.C) >> out.make.DEPEND 2>&1
 	-@(makedepend $(DEFINES) $(INCLUDES) -a -fDEPEND -o.o -m -- -- *.c) >> out.make.DEPEND 2>&1
 	-@(makedepend $(DEFINES) $(INCLUDES) -a -fDEPEND -o.o -m -- -- *.F) >> out.make.DEPEND 2>&1
 	-@(makedepend $(DEFINES) $(INCLUDES) -a -fDEPEND -o.o -m -- -- *.h) >> out.make.DEPEND 2>&1

src/clib/auto_general.c.in

@@ -1,5 +1,6 @@
 #include <stdio.h>
 #include "grackle.h"
+#include "auto_general.h"
 
 grackle_version get_grackle_version(void) {
   grackle_version out;

src/clib/auto_general.h

@@ -0,0 +1,33 @@
+//===----------------------------------------------------------------------===//
+//
+// See the LICENSE file for license and copyright information
+// SPDX-License-Identifier: NCSA AND BSD-3-Clause
+//
+//===----------------------------------------------------------------------===//
+///
+/// @file
+/// Declares the general auto-generated functions
+///
+//===----------------------------------------------------------------------===//
+
+#ifndef AUTO_GENERAL_H
+#define AUTO_GENERAL_H
+
+#include <stdio.h>    // <- declares FILE
+#include "grackle.h"  // <- declares get_grackle_version
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+/// writes compilation flags to `fp`
+void auto_show_flags(FILE* fp);
+
+/// writes configuration information to `fp`
+void auto_show_config(FILE* fp);
+
+#ifdef __cplusplus
+}  // extern "C"
+#endif /* __cplusplus */
+
+#endif /* AUTO_GENERAL_H */

src/clib/calc_tdust_3d.C → src/clib/calc_tdust_3d.cpp

@@ -1,7 +1,14 @@
-// See LICENSE file for license and copyright information
-
-/// @file calc_tdust_3d.C
-/// @brief Declares signature of calc_tdust_3d_g
+//===----------------------------------------------------------------------===//
+//
+// See the LICENSE file for license and copyright information
+// SPDX-License-Identifier: NCSA AND BSD-3-Clause
+//
+//===----------------------------------------------------------------------===//
+///
+/// @file
+/// Implements the calc_tdust_3d_g function
+///
+//===----------------------------------------------------------------------===//
 
 // This file was initially generated automatically during conversion of the
 // calc_tdust_3d_g function from FORTRAN to C++

src/clib/calc_tdust_3d.h

@@ -1,13 +1,20 @@
-// See LICENSE file for license and copyright information
-
-/// @file calc_tdust_3d.h
-/// @brief Declares signature of calc_tdust_3d_g
+//===----------------------------------------------------------------------===//
+//
+// See the LICENSE file for license and copyright information
+// SPDX-License-Identifier: NCSA AND BSD-3-Clause
+//
+//===----------------------------------------------------------------------===//
+///
+/// @file
+/// Declares signature of calc_tdust_3d_g
+///
+//===----------------------------------------------------------------------===//
 
 // This file was initially generated automatically during conversion of the
 // calc_tdust_3d_g function from FORTRAN to C++
 
-#ifndef MY_FILE_CPP_H
-#define MY_FILE_CPP_H
+#ifndef CALC_TDUST_3D_H
+#define CALC_TDUST_3D_H
 
 #include "grackle.h"  // gr_float
 #include "internal_units.h"
@@ -30,4 +37,4 @@ void calc_tdust_3d_g(gr_float* gas_temp_data_, gr_float* dust_temp_data_,
 }  // extern "C"
 #endif /* __cplusplus */
 
-#endif /* MY_FILE_CPP_H */
+#endif /* CALC_TDUST_3D_H */

src/clib/calc_temp_cloudy_g-cpp.C → src/clib/calc_temp_cloudy_g.cpp

@@ -1,7 +1,14 @@
-// See LICENSE file for license and copyright information
-
-/// @file calc_temp_cloudy_g-cpp.C
-/// @brief Declares signature of calc_temp_cloudy_g
+//===----------------------------------------------------------------------===//
+//
+// See the LICENSE file for license and copyright information
+// SPDX-License-Identifier: NCSA AND BSD-3-Clause
+//
+//===----------------------------------------------------------------------===//
+///
+/// @file
+/// Implements the calc_temp_cloudy_g function
+///
+//===----------------------------------------------------------------------===//
 
 // This file was initially generated automatically during conversion of the
 // calc_temp_cloudy_g function from FORTRAN to C++
@@ -16,7 +23,7 @@
 #include "scale_fields.hpp"
 #include "utils-cpp.hpp"
 
-#include "calc_temp_cloudy_g-cpp.h"
+#include "calc_temp_cloudy_g.h"
 
 #ifdef __cplusplus
 extern "C" {

src/clib/calc_temp_cloudy_g-cpp.h → src/clib/calc_temp_cloudy_g.h

@@ -1,13 +1,23 @@
-// See LICENSE file for license and copyright information
+//===----------------------------------------------------------------------===//
+//
+// See the LICENSE file for license and copyright information
+// SPDX-License-Identifier: NCSA AND BSD-3-Clause
+//
+//===----------------------------------------------------------------------===//
+///
+/// @file
+/// Declares the calc_temp_cloudy_g function
+///
+//===----------------------------------------------------------------------===//
 
 /// @file calc_temp_cloudy_g-cpp.h
 /// @brief Declares signature of calc_temp_cloudy_g
 
 // This file was initially generated automatically during conversion of the
 // calc_temp_cloudy_g function from FORTRAN to C++
 
-#ifndef MY_FILE_CPP_H
-#define MY_FILE_CPP_H
+#ifndef CALC_TEMP_CLOUDY_G_H
+#define CALC_TEMP_CLOUDY_G_H
 
 #include "grackle.h"  // gr_float
 #include "internal_units.h"
@@ -42,4 +52,4 @@ void calc_temp_cloudy_g(gr_float* temperature_data_, int imetal,
 }  // extern "C"
 #endif /* __cplusplus */
 
-#endif /* MY_FILE_CPP_H */
+#endif /* CALC_TEMP_CLOUDY_G_H */

src/clib/calculate_cooling_time.c

@@ -16,7 +16,7 @@
 #include <math.h>
 #include "grackle.h"
 #include "grackle_macros.h"
-#include "cool_multi_time_g-cpp.h"
+#include "cool_multi_time_g.h"
 #include "grackle_types.h"
 #include "internal_units.h"
 #include "phys_constants.h"

src/clib/calculate_temperature.c

@@ -14,7 +14,7 @@
 #include <stdlib.h>
 #include <stdio.h>
 #include <math.h>
-#include "calc_temp_cloudy_g-cpp.h"
+#include "calc_temp_cloudy_g.h"
 #include "grackle.h"
 #include "index_helper.h"
 #include "internal_units.h"