Add enabling of CAMP for chemistry

[jcurtis2]

• Add CampCore() that takes a filename argument
• Add alternative initializations for GasData, AeroData to accept CampCore
• Example notebook of partmc/scenarios/5_camp
• Handle json input files in notebook

[slayoo]

@jcurtis2, in the recent commits, there are:

• a refactor of the time-stepping logic making the code shorter and a bit more Pythoni
• a workaround for the JSON files issue (inability to ship seperate files with notebooks) by downloading them from github.com

Still, the new CAMP notebook fails for a variety of reasons:

• on Windows:

ERROR (PartMC-592148911): Solver failed for aerosol-phase with code -6
terminate called after throwing an instance of 'std::runtime_error'
  what():  845183800

• on macos-14 (Apple Silicon):

libc++abi: terminating due to uncaught exception of type std::runtime_error: to_json not implemented for this type of object: <_PyPartMC.CampCore object at 0x109d731b0>

• on Linux:

free(): double free detected in tcache 2

Could you please check on your machine? Thanks

[slayoo]

OK, managed to get a backtrace for the macOS error (libc++abi: terminating due to uncaught exception of type std::runtime_error: to_json not implemented for this type of object: <_PyPartMC.CampCore object at 0x109d731b0>):

    frame #1: 0x0000000106601f00 _PyPartMC.cpython-310-darwin.so`pyjson::to_json(obj=0x000000016fdfbfb0) at pybind11_json.hpp:137:9
    frame #2: 0x000000010660136c _PyPartMC.cpython-310-darwin.so`pybind11::detail::type_caster<nlohmann::basic_json<std::__1::map, std::__1::vector, std::__1::basic_string<char, std::__1::char_traits<char>, std:
:__1::allocator<char> >, bool, long long, unsigned long long, double, std::__1::allocator, nlohmann::adl_serializer, std::__1::vector<unsigned char, std::__1::allocator<unsigned char> > >, void>::load(this=0x000
000016fdfc0f8, src=handle @ 0x000000016fdfbfb0, (null)=false) at pybind11_json.hpp:206:29
    frame #3: 0x0000000106601240 _PyPartMC.cpython-310-darwin.so`bool pybind11::detail::argument_loader<pybind11::detail::value_and_holder&, nlohmann::basic_json<std::__1::map, std::__1::vector, std::__1::basic_
string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool, long long, unsigned long long, double, std::__1::allocator, nlohmann::adl_serializer, std::__1::vector<unsigned char, std::__1::alloca
tor<unsigned char> > > const&>::load_impl_sequence<0ul, 1ul>(this=0x000000016fdfc0f0, call=0x000000016fdfc7b0, (null)=std::__1::index_sequence<0UL, 1UL> @ 0x000000016fdfc04e) at cast.h:1415:47
    frame #4: 0x00000001065fdc14 _PyPartMC.cpython-310-darwin.so`pybind11::detail::argument_loader<pybind11::detail::value_and_holder&, nlohmann::basic_json<std::__1::map, std::__1::vector, std::__1::basic_strin
g<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool, long long, unsigned long long, double, std::__1::allocator, nlohmann::adl_serializer, std::__1::vector<unsigned char, std::__1::allocator<u
nsigned char> > > const&>::load_args(this=0x000000016fdfc0f0, call=0x000000016fdfc7b0) at cast.h:1393:50
    frame #5: 0x00000001065fdac4 _PyPartMC.cpython-310-darwin.so`void pybind11::cpp_function::initialize<void pybind11::detail::initimpl::constructor<nlohmann::basic_json<std::__1::map, std::__1::vector, std::__
1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool, long long, unsigned long long, double, std::__1::allocator, nlohmann::adl_serializer, std::__1::vector<unsigned char, std::__
1::allocator<unsigned char> > > const&>::execute<pybind11::class_<AeroData, std::__1::shared_ptr<AeroData> >, 0>(pybind11::class_<AeroData, std::__1::shared_ptr<AeroData> >&)::'lambda'(pybind11::detail::value_an
d_holder&, nlohmann::basic_json<std::__1::map, std::__1::vector, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool, long long, unsigned long long, double, std::__1::allo
cator, nlohmann::adl_serializer, std::__1::vector<unsigned char, std::__1::allocator<unsigned char> > > const&), void, pybind11::detail::value_and_holder&, nlohmann::basic_json<std::__1::map, std::__1::vector, s
td::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool, long long, unsigned long long, double, std::__1::allocator, nlohmann::adl_serializer, std::__1::vector<unsigned char, s
td::__1::allocator<unsigned char> > > const&, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::detail::is_new_style_constructor>(this=0x000000016fdfc7b0, call=0x000000016fdfc7b0)(pybind11::detai
l::value_and_holder&, nlohmann::basic_json<std::__1::map, std::__1::vector, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool, long long, unsigned long long, double, std
::__1::allocator, nlohmann::adl_serializer, std::__1::vector<unsigned char, std::__1::allocator<unsigned char> > > const&), pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::
detail::is_new_style_constructor const&)::'lambda'(pybind11::detail::function_call&)::operator()(pybind11::detail::function_call&) const at pybind11.h:228:33
    frame #6: 0x00000001065fda7c _PyPartMC.cpython-310-darwin.so`void pybind11::cpp_function::initialize<void pybind11::detail::initimpl::constructor<nlohmann::basic_json<std::__1::map, std::__1::vector, std::__
1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool, long long, unsigned long long, double, std::__1::allocator, nlohmann::adl_serializer, std::__1::vector<unsigned char, std::__
1::allocator<unsigned char> > > const&>::execute<pybind11::class_<AeroData, std::__1::shared_ptr<AeroData> >, 0>(pybind11::class_<AeroData, std::__1::shared_ptr<AeroData> >&)::'lambda'(pybind11::detail::value_an
d_holder&, nlohmann::basic_json<std::__1::map, std::__1::vector, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool, long long, unsigned long long, double, std::__1::allo
cator, nlohmann::adl_serializer, std::__1::vector<unsigned char, std::__1::allocator<unsigned char> > > const&), void, pybind11::detail::value_and_holder&, nlohmann::basic_json<std::__1::map, std::__1::vector, s
td::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool, long long, unsigned long long, double, std::__1::allocator, nlohmann::adl_serializer, std::__1::vector<unsigned char, s
td::__1::allocator<unsigned char> > > const&, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::detail::is_new_style_constructor>(call=0x000000016fdfc7b0)(pybind11::detail::value_and_holder&, nlo
hmann::basic_json<std::__1::map, std::__1::vector, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool, long long, unsigned long long, double, std::__1::allocator, nlohman
n::adl_serializer, std::__1::vector<unsigned char, std::__1::allocator<unsigned char> > > const&), pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::detail::is_new_style_cons
tructor const&)::'lambda'(pybind11::detail::function_call&)::__invoke(pybind11::detail::function_call&) at pybind11.h:224:21
    frame #7: 0x00000001065bd59c _PyPartMC.cpython-310-darwin.so`pybind11::cpp_function::dispatcher(self=0x000000010453f9f0, args_in=0x0000000104353900, kwargs_in=0x0000000000000000) at pybind11.h:929:30
    frame #8: 0x0000000100e8832c Python`cfunction_call + 60
    frame #9: 0x0000000100e20cf8 Python`_PyObject_MakeTpCall + 136
    frame #10: 0x0000000100e24dc0 Python`method_vectorcall + 636
    frame #11: 0x0000000100eb57fc Python`slot_tp_init + 480
    frame #12: 0x0000000100eac4e0 Python`type_call + 312
    frame #13: 0x0000000100d6f644 _c_internal_utils.cpython-310-darwin.so`pybind11_meta_call + 40
    frame #14: 0x0000000100e20cf8 Python`_PyObject_MakeTpCall + 136
    frame #15: 0x0000000100f57238 Python`call_function + 380
    frame #16: 0x0000000100f4f470 Python`_PyEval_EvalFrameDefault + 23772
    frame #17: 0x0000000100f47f28 Python`_PyEval_Vector + 360
    frame #18: 0x0000000100fb2c54 Python`pyrun_file + 308
    frame #19: 0x0000000100fb2398 Python`_PyRun_SimpleFileObject + 336
    frame #20: 0x0000000100fb19e4 Python`_PyRun_AnyFileObject + 216
    frame #21: 0x0000000100fdddd0 Python`pymain_run_file_obj + 180
    frame #22: 0x0000000100fdd470 Python`pymain_run_file + 72
    frame #23: 0x0000000100fdca58 Python`pymain_run_python + 300
    frame #24: 0x0000000100fdc8ec Python`Py_RunMain + 24
    frame #25: 0x0000000100fddf78 Python`pymain_main + 56
    frame #26: 0x0000000100fde23c Python`Py_BytesMain + 40
    frame #27: 0x0000000192be7154 dyld`start + 2476

[slayoo]

OK, one more hint from the logs: this is a minimal 2-line reproducer of the Linux double free or corruption (fasttop) error:

import PyPartMC as ppmc
ppmc.Photolysis(ppmc.CampCore())

[github-actions]

Stale pull request message

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 12.50000% with 49 lines in your changes missing coverage. Please review.

Project coverage is 89.04%. Comparing base (13827e2) to head (a557a9e).

Files with missing lines	Patch %	Lines
src/aero_state.hpp	0.00%	13 Missing ⚠️
src/camp_core.F90	0.00%	8 Missing ⚠️
src/aero_state.F90	0.00%	6 Missing ⚠️
src/run_part.F90	0.00%	3 Missing and 3 partials ⚠️
src/aero_data.F90	0.00%	5 Missing ⚠️
src/gas_data.F90	0.00%	5 Missing ⚠️
src/camp_core.hpp	0.00%	3 Missing ⚠️
src/gas_data.hpp	0.00%	2 Missing ⚠️
src/aero_data.hpp	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #368      +/-   ##
==========================================
- Coverage   90.76%   89.04%   -1.73%     
==========================================
  Files          55       55              
  Lines        2491     2547      +56     
  Branches      135      140       +5     
==========================================
+ Hits         2261     2268       +7     
- Misses        158      204      +46     
- Partials       72       75       +3     

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