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[newchem-cpp] hdf5 io refactor #455

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[newchem-cpp] hdf5 io refactor #455

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d5ff24e
Initial conversion initialize_cloudy_data.{c->cpp}
mabruzzo Nov 24, 2025
ec0b5c6
a small tweak
mabruzzo Nov 24, 2025
5435b76
Replace sprintf with snprintf
mabruzzo Nov 24, 2025
978187c
mv `(initialize|free)_cloudy_data` into namespace
mabruzzo Nov 24, 2025
41c3f94
rename and mv declaration of MAX_LINE_LENGTH_MACRO
mabruzzo Nov 24, 2025
d9708c4
change handling of temp_int_arr
mabruzzo Nov 24, 2025
8cbbe48
Remove a use of malloc & free while reading in a parameter grid
mabruzzo Nov 24, 2025
abf852b
replace another use of malloc & free with new & delete
mabruzzo Nov 24, 2025
2ac76b8
replace a 3rd use of malloc & free with new & delete
mabruzzo Nov 24, 2025
15cd75d
remove remaining occurrences of malloc from initialize_cloudy_data
mabruzzo Nov 24, 2025
3bc8649
cleanup include directives of initialize_cloudy_data.cpp
mabruzzo Nov 24, 2025
11964ff
initial conversion of `initialize_UVbackground_data.{c->cpp}`
mabruzzo Nov 24, 2025
c131973
mv UVBtable methods into grackle::impl and factor out cleanup logic
mabruzzo Nov 24, 2025
ad8388d
initialize_UVbackground_data: replace malloc with new
mabruzzo Nov 24, 2025
dfd1a87
initialize_UVbackground_data: more cppification
mabruzzo Nov 24, 2025
597f9cf
initialize_UVbackground_data: use std::vector instead of a C++ compil…
mabruzzo Nov 24, 2025
303a3ad
call initialize_empty_UVBtable_struct within initialize_UVbackground_…
mabruzzo Nov 24, 2025
e3e915a
introduce h5io utility file
mabruzzo Nov 24, 2025
bcd3074
start using read_dataset in initialize_cloudy_data
mabruzzo Nov 24, 2025
6854adf
another use of read_dataset in initialize_cloudy_data
mabruzzo Nov 24, 2025
76e5f3a
the last commit in the sequence
mabruzzo Nov 24, 2025
70fe333
fix the failing build
mabruzzo Nov 25, 2025
9498310
introduce abstractions to load the shape of hdf5 datasets
mabruzzo Nov 25, 2025
0ed1ef3
more explicitly verify shapes when loading UVbackground data
mabruzzo Nov 25, 2025
619da6c
Overhauled parsing of the table-axes for interpolation
mabruzzo Nov 26, 2025
62ac9c5
remove unused variables
mabruzzo Nov 26, 2025
753eb9c
fixup get_num_attrs
mabruzzo Nov 26, 2025
fb25a6b
more meaningful error message
mabruzzo Nov 30, 2025
0859fb8
address compiler warnings
mabruzzo Dec 1, 2025
34f5a33
move a bunch of hdf5-specific macros out of grackle_macros.h
mabruzzo Dec 1, 2025
75b6873
add a few docstrings
mabruzzo Dec 1, 2025
c11ddea
light refactor of read_str_attribute
mabruzzo Dec 1, 2025
fdc3c72
wrap the logic for loading a string dataset
mabruzzo Dec 1, 2025
fa4f0e8
add a consistency check
mabruzzo Dec 2, 2025
4454a61
light refactor
mabruzzo Dec 2, 2025
88e56f8
a last change
mabruzzo Dec 3, 2025
34bdcf6
adjust a comment
mabruzzo Dec 4, 2025
b6966a2
move utils/h5io.[ch]pp -> support/h5io.[ch]pp
mabruzzo Dec 12, 2025
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4 changes: 2 additions & 2 deletions .clang-format-ignore
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Original file line number Diff line number Diff line change
Expand Up @@ -30,9 +30,9 @@ 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_UVbackground_data.cpp
src/clib/initialize_chemistry_data.cpp
src/clib/initialize_cloudy_data.c
src/clib/initialize_cloudy_data.cpp
src/clib/initialize_dust_yields.cpp
src/clib/initialize_rates.cpp
src/clib/internal_types.hpp
Expand Down
5 changes: 3 additions & 2 deletions src/clib/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -90,8 +90,6 @@ add_library(Grackle_Grackle
dynamic_api.c
grackle_units.c
index_helper.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
Expand All @@ -114,8 +112,10 @@ add_library(Grackle_Grackle
dust_props.hpp
init_misc_species_cool_rates.cpp init_misc_species_cool_rates.hpp
initialize_chemistry_data.cpp
initialize_cloudy_data.cpp initialize_cloudy_data.hpp
initialize_dust_yields.cpp initialize_dust_yields.hpp
initialize_rates.cpp initialize_rates.hpp
initialize_UVbackground_data.cpp initialize_UVbackground_data.hpp
internal_types.cpp internal_types.hpp
lookup_cool_rates1d.hpp
make_consistent.cpp make_consistent.hpp
Expand All @@ -124,6 +124,7 @@ add_library(Grackle_Grackle
scale_fields.cpp scale_fields.hpp
solve_rate_cool_g-cpp.cpp solve_rate_cool_g-cpp.h
step_rate_newton_raphson.hpp
support/h5io.cpp support/h5io.hpp
time_deriv_0d.hpp
utils-cpp.cpp utils-cpp.hpp
utils-field.hpp
Expand Down
1 change: 1 addition & 0 deletions src/clib/Make.config.objects
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@ OBJS_CONFIG_LIB = \
rate_functions.lo \
rate_utils.lo \
gaussj_g.lo \
support/h5io.lo \
utils.lo \
utils-cpp.lo \
internal_types.lo
15 changes: 0 additions & 15 deletions src/clib/grackle_macros.h
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Original file line number Diff line number Diff line change
Expand Up @@ -82,20 +82,6 @@
#define GRFLOAT_C(DBL_LITERAL) ( DBL_LITERAL )
#endif

/* HDF5 definitions */

#define HDF5_FILE_I4 H5T_STD_I32BE
#define HDF5_FILE_I8 H5T_STD_I64BE
#define HDF5_FILE_R4 H5T_IEEE_F32BE
#define HDF5_FILE_R8 H5T_IEEE_F64BE
#define HDF5_FILE_B8 H5T_STD_B8BE

#define HDF5_I4 H5T_NATIVE_INT
#define HDF5_I8 H5T_NATIVE_LLONG
#define HDF5_R4 H5T_NATIVE_FLOAT
#define HDF5_R8 H5T_NATIVE_DOUBLE
#define HDF5_R16 H5T_NATIVE_LDOUBLE

/* Precision-dependent definitions */

#ifdef GRACKLE_FLOAT_4
Expand Down Expand Up @@ -129,7 +115,6 @@

#define FLOAT_UNDEFINED -99999.0
#define INT_UNDEFINED -99999
#define MAX_LINE_LENGTH 512

#ifndef tiny
#define tiny 1.0e-20
Expand Down
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