From 777c8bdb6ec5438805d5d2462a7db8adcd937a1c Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Thu, 6 Jun 2024 15:22:42 -0500 Subject: [PATCH 01/26] first pass at linking camp --- src/aero_data.F90 | 13 +++++++++++++ src/aero_data.hpp | 8 ++++++++ src/aero_state.F90 | 14 ++++++++++++++ src/aero_state.hpp | 45 +++++++++++++++++++++++++++++++++++++++++++++ src/camp_core.F90 | 2 +- src/gas_data.F90 | 10 ++++++++++ src/gas_data.hpp | 8 ++++++++ src/photolysis.F90 | 15 +++++++++++++++ src/photolysis.hpp | 8 +++++++- src/pypartmc.cpp | 5 +++++ src/run_part.F90 | 13 +++++++++++++ 11 files changed, 139 insertions(+), 2 deletions(-) diff --git a/src/aero_data.F90 b/src/aero_data.F90 index edf84f95..3baae8a8 100644 --- a/src/aero_data.F90 +++ b/src/aero_data.F90 @@ -36,6 +36,19 @@ subroutine f_aero_data_from_json(ptr_c) bind(C) call spec_file_read_aero_data(file, ptr_f) end subroutine + subroutine f_aero_data_from_camp(ptr_c, camp_core_ptr_c) bind(C) + type(aero_data_t), pointer :: ptr_f => null() + type(c_ptr), intent(in) :: ptr_c + type(c_ptr), intent(in) :: camp_core_ptr_c + type(camp_core_t), pointer :: camp_core_ptr_f => null() + + call c_f_pointer(ptr_c, ptr_f) + call c_f_pointer(camp_core_ptr_c, camp_core_ptr_f) + + call aero_data_initialize(ptr_f, camp_core_ptr_f) + + end subroutine + subroutine f_aero_data_spec_by_name(ptr_c, value, name_data, name_size) bind(C) type(aero_data_t), pointer :: ptr_f => null() type(c_ptr), intent(in) :: ptr_c diff --git a/src/aero_data.hpp b/src/aero_data.hpp index f830e928..31769740 100644 --- a/src/aero_data.hpp +++ b/src/aero_data.hpp @@ -8,12 +8,14 @@ #include "pmc_resource.hpp" #include "json_resource.hpp" +#include "camp_core.hpp" #include "pybind11/stl.h" #include "aero_data_parameters.hpp" extern "C" void f_aero_data_ctor(void *ptr) noexcept; extern "C" void f_aero_data_dtor(void *ptr) noexcept; extern "C" void f_aero_data_from_json(const void *ptr) noexcept; +extern "C" void f_aero_data_from_camp(const void *ptr, const void *camp_core_ptr) noexcept; extern "C" void f_aero_data_spec_by_name(const void *ptr, int *value, const char *name_data, const int *name_size) noexcept; extern "C" void f_aero_data_len(const void *ptr, int *len) noexcept; extern "C" void f_aero_data_n_source(const void *ptr, int *len) noexcept; @@ -38,6 +40,12 @@ extern "C" void f_aero_data_spec_name_by_index(const void *ptr, const int *i_spe struct AeroData { PMCResource ptr; + AeroData(const CampCore &camp_core) : + ptr(f_aero_data_ctor, f_aero_data_dtor) + { + f_aero_data_from_camp(this->ptr.f_arg(), camp_core.ptr.f_arg()); + } + AeroData(const nlohmann::json &json) : ptr(f_aero_data_ctor, f_aero_data_dtor) { diff --git a/src/aero_state.F90 b/src/aero_state.F90 index 231730e4..68e50eea 100644 --- a/src/aero_state.F90 +++ b/src/aero_state.F90 @@ -638,4 +638,18 @@ subroutine f_aero_state_sample_particles(ptr_c, aero_state_to_ptr_c, & end subroutine + subroutine f_aero_state_initialize(ptr_c, aero_data_ptr_c, camp_core_ptr_c) bind(C) + type(c_ptr) :: ptr_c, aero_data_ptr_c, camp_core_ptr_c + type(aero_state_t), pointer :: ptr_f => null() + type(aero_data_t), pointer :: aero_data_ptr_f => null() + type(camp_core_t), pointer :: camp_core_ptr_f => null() + + call c_f_pointer(ptr_c, ptr_f) + call c_f_pointer(aero_data_ptr_c, aero_data_ptr_f) + call c_f_pointer(camp_core_ptr_c, camp_core_ptr_f) + + call aero_state_initialize(ptr_f, aero_data_ptr_f, camp_core_ptr_f) + + end subroutine + end module diff --git a/src/aero_state.hpp b/src/aero_state.hpp index 53f63606..2ba0ce98 100644 --- a/src/aero_state.hpp +++ b/src/aero_state.hpp @@ -9,6 +9,7 @@ #include "pmc_resource.hpp" #include "aero_data.hpp" #include "aero_dist.hpp" +#include "camp_core.hpp" #include "aero_particle.hpp" #include "env_state.hpp" #include "bin_grid.hpp" @@ -208,6 +209,12 @@ extern "C" void f_aero_state_sample_particles( const double *sample_prob ) noexcept; +extern "C" void f_aero_state_initialize( + void *ptr_c, + const void *aero_data_ptr_c, + const void *camp_core_ptr_c +) noexcept; + template auto pointer_vec_magic(arr_t &data_vec, const arg_t &arg) { std::vector pointer_vec(data_vec.size()); @@ -269,6 +276,44 @@ struct AeroState { { } + AeroState( + std::shared_ptr aero_data, + const double &n_part, + const bpstd::string_view &weight, + const CampCore &camp_core + ): + ptr(f_aero_state_ctor, f_aero_state_dtor), + aero_data(aero_data) + { + static const std::map weight_c{ + //{"none", '-'}, + {"flat", 'f'}, + {"flat_source", 'F'}, + //{"power", 'p'}, + //{"power_source", 'P'}, + {"nummass", 'n'}, + {"nummass_source", 'N'}, + }; + + if (weight_c.find(weight) == weight_c.end()) { + std::ostringstream msg; + msg << "unknown weighting scheme '" << weight << "', valid options are: "; + auto index = 0; + for (auto const& pair: weight_c) + msg << (!index++ ? "" : ", ") << pair.first; + throw std::runtime_error(msg.str()); + } + + f_aero_state_init( + ptr.f_arg(), + aero_data->ptr.f_arg(), + &n_part, + &weight_c.at(weight) + ); + f_aero_state_initialize(ptr.f_arg_non_const(), aero_data->ptr.f_arg(), + camp_core.ptr.f_arg()); + } + static std::size_t __len__(const AeroState &self) { int len; f_aero_state_len( diff --git a/src/camp_core.F90 b/src/camp_core.F90 index 58d2f30c..8a450805 100644 --- a/src/camp_core.F90 +++ b/src/camp_core.F90 @@ -15,7 +15,7 @@ subroutine f_camp_core_ctor(ptr_c) bind(C) type(camp_core_t), pointer :: ptr_f => null() type(c_ptr), intent(out) :: ptr_c - ptr_f => camp_core_t() + ptr_f => camp_core_t('config.json') call ptr_f%initialize() ptr_c = c_loc(ptr_f) end subroutine diff --git a/src/gas_data.F90 b/src/gas_data.F90 index c0dab53e..d106c01e 100644 --- a/src/gas_data.F90 +++ b/src/gas_data.F90 @@ -46,6 +46,16 @@ subroutine f_gas_data_from_json(ptr_c) bind(C) call spec_file_read_gas_data(nofile, ptr_f) end subroutine + subroutine f_gas_data_from_camp(ptr_c, camp_core_ptr_c) bind(C) + type(gas_data_t), pointer :: ptr_f => null() + type(c_ptr), intent(in) :: ptr_c, camp_core_ptr_c + type(camp_core_t), pointer :: camp_core_ptr_f => null() + + call c_f_pointer(ptr_c, ptr_f) + call c_f_pointer(camp_core_ptr_c, camp_core_ptr_f) + call gas_data_initialize(ptr_f, camp_core_ptr_f) + end subroutine + subroutine f_gas_data_spec_by_name(ptr_c, value, name_data, name_size) & bind(C) type(gas_data_t), pointer :: ptr_f => null() diff --git a/src/gas_data.hpp b/src/gas_data.hpp index ecb14998..1b7fc277 100644 --- a/src/gas_data.hpp +++ b/src/gas_data.hpp @@ -9,6 +9,7 @@ #include "json_resource.hpp" #include "pmc_resource.hpp" #include "gas_data_parameters.hpp" +#include "camp_core.hpp" #include "pybind11/stl.h" #include "pybind11_json/pybind11_json.hpp" @@ -16,6 +17,7 @@ extern "C" void f_gas_data_ctor(void *ptr) noexcept; extern "C" void f_gas_data_dtor(void *ptr) noexcept; extern "C" void f_gas_data_len(const void *ptr, int *len) noexcept; extern "C" void f_gas_data_from_json(const void *ptr) noexcept; +extern "C" void f_gas_data_from_camp(const void *ptr, const void *camp_core_ptr) noexcept; extern "C" void f_gas_data_to_json(const void *ptr) noexcept; extern "C" void f_gas_data_spec_by_name(const void *ptr, int *value, const char *name_data, const int *name_size) noexcept; @@ -26,6 +28,12 @@ struct GasData { PMCResource ptr; const nlohmann::json json; + GasData(const CampCore &CampCore) : + ptr(f_gas_data_ctor, f_gas_data_dtor) + { + f_gas_data_from_camp(this->ptr.f_arg(), CampCore.ptr.f_arg()); + } + GasData(const pybind11::tuple &tpl) : ptr(f_gas_data_ctor, f_gas_data_dtor), json(tpl) diff --git a/src/photolysis.F90 b/src/photolysis.F90 index c628b524..89526931 100644 --- a/src/photolysis.F90 +++ b/src/photolysis.F90 @@ -6,6 +6,7 @@ module PyPartMC_photolysis use iso_c_binding + use camp_camp_core use pmc_photolysis implicit none @@ -19,6 +20,20 @@ subroutine f_photolysis_ctor(ptr_c) bind(C) ptr_c = c_loc(ptr_f) end subroutine + subroutine f_photolysis_create(ptr_c, camp_core_ptr_c) bind(C) + type(photolysis_t), pointer :: ptr_f => null() + type(camp_core_t), pointer :: camp_core_ptr_f => null() + type(c_ptr), intent(inout) :: ptr_c + type(c_ptr), intent(in) :: camp_core_ptr_c + + call c_f_pointer(ptr_c, ptr_f) + call c_f_pointer(camp_core_ptr_c, camp_core_ptr_f) + + ptr_f => photolysis_t(camp_core_ptr_f) + + ptr_c = c_loc(ptr_f) + end subroutine + subroutine f_photolysis_dtor(ptr_c) bind(C) type(photolysis_t), pointer :: ptr_f => null() type(c_ptr), intent(in) :: ptr_c diff --git a/src/photolysis.hpp b/src/photolysis.hpp index f0095762..d1d9e4a2 100644 --- a/src/photolysis.hpp +++ b/src/photolysis.hpp @@ -11,7 +11,7 @@ extern "C" void f_photolysis_ctor(void *ptr) noexcept; extern "C" void f_photolysis_dtor(void *ptr) noexcept; - +extern "C" void f_photolysis_create(const void *ptr, const void *camp_core) noexcept; struct Photolysis { PMCResource ptr; @@ -19,4 +19,10 @@ struct Photolysis { ptr(f_photolysis_ctor, f_photolysis_dtor) { } + + Photolysis(const CampCore &camp_core) : + ptr(f_photolysis_ctor, f_photolysis_dtor) + { + f_photolysis_create(this->ptr.f_arg(), camp_core.ptr.f_arg()); + } }; diff --git a/src/pypartmc.cpp b/src/pypartmc.cpp index 94b200b6..f52b4f55 100644 --- a/src/pypartmc.cpp +++ b/src/pypartmc.cpp @@ -83,6 +83,7 @@ PYBIND11_MODULE(_PyPartMC, m) { )pbdoc" ) .def(py::init()) + .def(py::init()) .def("spec_by_name", AeroData::spec_by_name, "Returns the number of the species in AeroData with the given name") .def("__len__", AeroData::__len__, "Number of aerosol species") @@ -207,6 +208,8 @@ PYBIND11_MODULE(_PyPartMC, m) { )pbdoc" ) .def(py::init, const double, const std::string>()) + .def(py::init, const double, const std::string, + const CampCore&>()) .def("__len__", AeroState::__len__, "returns current number of particles") .def_property_readonly("total_num_conc", AeroState::total_num_conc, @@ -286,6 +289,7 @@ PYBIND11_MODULE(_PyPartMC, m) { )pbdoc" ) .def(py::init()) + .def(py::init()) .def("__len__", GasData::__len__, "returns number of gas species") .def_property_readonly("n_spec", GasData::__len__) @@ -333,6 +337,7 @@ PYBIND11_MODULE(_PyPartMC, m) { )pbdoc" ) .def(py::init<>()) + .def(py::init()) ; py::class_(m, diff --git a/src/run_part.F90 b/src/run_part.F90 index a971aa08..aaae1e71 100644 --- a/src/run_part.F90 +++ b/src/run_part.F90 @@ -8,6 +8,8 @@ module PyPartMC_run_part use iso_c_binding use pmc_run_part + use camp_camp_core + use pmc_photolysis implicit none @@ -61,6 +63,10 @@ subroutine f_run_part( & call c_f_pointer(camp_core_ptr_c, camp_core_ptr_f) call c_f_pointer(photolysis_ptr_c, photolysis_ptr_f) + if (run_part_opt_ptr_f%do_camp_chem) then + call camp_core_ptr_f%solver_initialize() + end if + call run_part( & scenario_ptr_f, & env_state_ptr_f, & @@ -148,6 +154,9 @@ subroutine f_run_part_timestep( & if (env_state_ptr_f%elapsed_time < run_part_opt_ptr_f%del_t) then call mosaic_init(env_state_ptr_f, aero_data_ptr_f, run_part_opt_ptr_f%del_t, & run_part_opt_ptr_f%do_optical) + if (run_part_opt_ptr_f%do_camp_chem) then + call camp_core_ptr_f%solver_initialize() + end if if (run_part_opt_ptr_f%t_output > 0) then call output_state(run_part_opt_ptr_f%output_prefix, & run_part_opt_ptr_f%output_type, aero_data_ptr_f, aero_state_ptr_f, gas_data_ptr_f, & @@ -156,6 +165,7 @@ subroutine f_run_part_timestep( & run_part_opt_ptr_f%do_optical, run_part_opt_ptr_f%uuid) end if end if + call run_part_timestep(scenario_ptr_f, env_state_ptr_f, aero_data_ptr_f, aero_state_ptr_f, & gas_data_ptr_f, gas_state_ptr_f, run_part_opt_ptr_f, camp_core_ptr_f, photolysis_ptr_f, & i_time, t_start, last_output_time, & @@ -241,6 +251,9 @@ subroutine f_run_part_timeblock( & if (env_state_ptr_f%elapsed_time < run_part_opt_ptr_f%del_t) then call mosaic_init(env_state_ptr_f, aero_data_ptr_f, run_part_opt_ptr_f%del_t, & run_part_opt_ptr_f%do_optical) + if (run_part_opt_ptr_f%do_camp_chem) then + call camp_core_ptr_f%solver_initialize() + end if if (run_part_opt_ptr_f%t_output > 0) then call output_state(run_part_opt_ptr_f%output_prefix, & run_part_opt_ptr_f%output_type, aero_data_ptr_f, aero_state_ptr_f, gas_data_ptr_f, & From 8507274a8332be717851860c840c9c63e0e95b25 Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Tue, 2 Jul 2024 19:00:27 -0500 Subject: [PATCH 02/26] update to pass file path --- src/camp_core.F90 | 20 +++++++++++++++++++- src/camp_core.hpp | 9 +++++++++ src/pypartmc.cpp | 1 + 3 files changed, 29 insertions(+), 1 deletion(-) diff --git a/src/camp_core.F90 b/src/camp_core.F90 index 8a450805..870324f6 100644 --- a/src/camp_core.F90 +++ b/src/camp_core.F90 @@ -15,7 +15,25 @@ subroutine f_camp_core_ctor(ptr_c) bind(C) type(camp_core_t), pointer :: ptr_f => null() type(c_ptr), intent(out) :: ptr_c - ptr_f => camp_core_t('config.json') + ptr_f => camp_core_t() + call ptr_f%initialize() + ptr_c = c_loc(ptr_f) + end subroutine + + subroutine f_camp_core_initialize(ptr_c, prefix_data, prefix_size) bind(C) + type(camp_core_t), pointer :: ptr_f => null() + type(c_ptr), intent(out) :: ptr_c + + character(kind=c_char), dimension(*), intent(in) :: prefix_data + integer(c_int), intent(in) :: prefix_size + character(len=prefix_size) :: prefix + integer :: i + + do i=1, prefix_size + prefix(i:i) = prefix_data(i) + end do + + ptr_f => camp_core_t(prefix) call ptr_f%initialize() ptr_c = c_loc(ptr_f) end subroutine diff --git a/src/camp_core.hpp b/src/camp_core.hpp index 53cd0186..bfd4ea28 100644 --- a/src/camp_core.hpp +++ b/src/camp_core.hpp @@ -11,6 +11,8 @@ extern "C" void f_camp_core_ctor(void *ptr) noexcept; extern "C" void f_camp_core_dtor(void *ptr) noexcept; +extern "C" void f_camp_core_initialize(void *ptr, const char *prefix, + const int *prefix_size) noexcept; struct CampCore { PMCResource ptr; @@ -19,4 +21,11 @@ struct CampCore { ptr(f_camp_core_ctor, f_camp_core_dtor) { } + + CampCore(const std::string &config_name) : + ptr(f_camp_core_ctor, f_camp_core_dtor) + { + const int config_name_size = config_name.size(); + f_camp_core_initialize(ptr.f_arg_non_const(), config_name.c_str(), &config_name_size); + } }; diff --git a/src/pypartmc.cpp b/src/pypartmc.cpp index f52b4f55..967c42a0 100644 --- a/src/pypartmc.cpp +++ b/src/pypartmc.cpp @@ -347,6 +347,7 @@ PYBIND11_MODULE(_PyPartMC, m) { )pbdoc" ) .def(py::init<>()) + .def(py::init()) ; py::class_(m, From d4f609481274de4e18cd7a5fd8b6b27e4d1af12d Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Tue, 2 Jul 2024 19:03:09 -0500 Subject: [PATCH 03/26] add example --- examples/aerosol_representation.json | 9 + examples/config.json | 14 + examples/monarch_mod37/aerosol_phases.json | 37 + examples/monarch_mod37/cb05_abs_tol.json | 407 ++ examples/monarch_mod37/cb05_mechanism.json | 3155 +++++++++ .../cb05_mechanism_without_R142_R143.json | 3112 +++++++++ examples/monarch_mod37/cb05_species.json | 400 ++ .../cloud_and_rain_partitioning.json | 258 + .../monarch_mod37/cloud_and_rain_species.json | 476 ++ examples/monarch_mod37/custom_species.json | 100 + examples/monarch_mod37/dry_deposition.json | 240 + .../monarch_mod37/inorganic_ZSR_water.json | 73 + .../monarch_mod37/inorganic_activity.json | 339 + .../monarch_mod37/inorganic_partitioning.json | 39 + .../monarch_mod37/inorganic_reactions.json | 94 + examples/monarch_mod37/inorganic_species.json | 205 + .../partitioning_species_params.json | 410 ++ .../mechanism.json | 93 + .../species.json | 125 + examples/particle_simulation_with_camp.ipynb | 5752 +++++++++++++++++ 20 files changed, 15338 insertions(+) create mode 100644 examples/aerosol_representation.json create mode 100644 examples/config.json create mode 100644 examples/monarch_mod37/aerosol_phases.json create mode 100644 examples/monarch_mod37/cb05_abs_tol.json create mode 100644 examples/monarch_mod37/cb05_mechanism.json create mode 100755 examples/monarch_mod37/cb05_mechanism_without_R142_R143.json create mode 100644 examples/monarch_mod37/cb05_species.json create mode 100644 examples/monarch_mod37/cloud_and_rain_partitioning.json create mode 100644 examples/monarch_mod37/cloud_and_rain_species.json create mode 100644 examples/monarch_mod37/custom_species.json create mode 100644 examples/monarch_mod37/dry_deposition.json create mode 100644 examples/monarch_mod37/inorganic_ZSR_water.json create mode 100644 examples/monarch_mod37/inorganic_activity.json create mode 100644 examples/monarch_mod37/inorganic_partitioning.json create mode 100644 examples/monarch_mod37/inorganic_reactions.json create mode 100644 examples/monarch_mod37/inorganic_species.json create mode 100644 examples/monarch_mod37/partitioning_species_params.json create mode 100644 examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json create mode 100644 examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json create mode 100644 examples/particle_simulation_with_camp.ipynb diff --git a/examples/aerosol_representation.json b/examples/aerosol_representation.json new file mode 100644 index 00000000..15eba0f7 --- /dev/null +++ b/examples/aerosol_representation.json @@ -0,0 +1,9 @@ +{ + "camp-data" : [ + { + "name" : "PartMC single particle", + "type" : "AERO_REP_SINGLE_PARTICLE", + "maximum computational particles" : 1050 + } + ] +} diff --git a/examples/config.json b/examples/config.json new file mode 100644 index 00000000..df667d7d --- /dev/null +++ b/examples/config.json @@ -0,0 +1,14 @@ +{ + "camp-files" : [ + "aerosol_representation.json", + "monarch_mod37/aerosol_phases.json", + "monarch_mod37/cb05_abs_tol.json", + "monarch_mod37/cb05_mechanism_without_R142_R143.json", + "monarch_mod37/cb05_species.json", + "monarch_mod37/custom_species.json", + "monarch_mod37/partitioning_species_params.json", + "monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json", + "monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json" + ] +} + diff --git a/examples/monarch_mod37/aerosol_phases.json b/examples/monarch_mod37/aerosol_phases.json new file mode 100644 index 00000000..88aa9ec9 --- /dev/null +++ b/examples/monarch_mod37/aerosol_phases.json @@ -0,0 +1,37 @@ +{ + "description" : "These aerosol phases correspond to the MONARCH 'mod37' configuration", + "camp-data" : [ + { + "name" : "dust", + "type": "AERO_PHASE", + "species" : [ "LHD_DUST", "LLD_DUST" ], + "notes" : { + "MLD 02/05/2018" : "consider replacing this with a set of inorganic species" + } + }, + { + "name" : "sea_salt", + "type" : "AERO_PHASE", + "species" : [ "SEA_SALT" ], + "notes" : { + "MLD 02/05/2018" : "consider replacing with H2O, Na+, Cl-" + } + }, + { + "name" : "organic_matter", + "type" : "AERO_PHASE", + "species" : [ "POA", "ISOP-P1_aero", "ISOP-P2_aero", "TERP-P1_aero", "TERP-P2_aero" ] + }, + { + "name" : "black_carbon", + "type" : "AERO_PHASE", + "species" : [ "BC_phob", "BC_phil" ] + }, + { + "name" : "other_PM", + "type" : "AERO_PHASE", + "species" : [ "other_PM", "other_other_PM" ], + "description" : "unspecified particulate matter" + } + ] +} diff --git a/examples/monarch_mod37/cb05_abs_tol.json b/examples/monarch_mod37/cb05_abs_tol.json new file mode 100644 index 00000000..7a3bfc5f --- /dev/null +++ b/examples/monarch_mod37/cb05_abs_tol.json @@ -0,0 +1,407 @@ +{ + "camp-data" : [ + { + "type" : "RELATIVE_TOLERANCE", + "value" : 1.0E-04 + }, + { + "name" : "NO2", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03 + }, + { + "name" : "NO", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03 + }, + { + "name" : "O", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E+00 + }, + { + "name" : "O3", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03 + }, + { + "name" : "NO3", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03 + }, + { + "name" : "O1D", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E+00 + }, + { + "name" : "OH", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03 + }, + { + "name" : "HO2", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03 + }, + { + "name" : "N2O5", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03 + }, + { + "name" : "HNO3", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03 + }, + { + "name" : "HONO", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03 + }, + { + "name" : "PNA", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03 + }, + { + "name" : "H2O2", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03 + }, + { + "name" : "XO2", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03 + }, + { + "name" : "XO2N", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03 + }, + { + "name" : "NTR", + "type" : "CHEM_SPEC", + "absolute integration 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"reactants" : { + "CL" : {} , + "ALD2" : {} + }, + "products" : { + "HCL" : {} , + "C2O3" : { "yield" : 1.000 } + }, + "orig params" : "CMAQ_1to4(7.9E-11, 0.0E+00, 0.0E+00)", + "type" : "ARRHENIUS", + "A" : 7.9E-11, + "B" : 0.0E+00, + "C" : -0.0E+00 + }, + { + "rxn id" : "CL18", + "reactants" : { + "CL" : {} , + "ALDX" : {} + }, + "products" : { + "HCL" : {} , + "CXO3" : { "yield" : 1.000 } + }, + "orig params" : "CMAQ_1to4(1.3E-10, 0.0E+00, 0.0E+00)", + "type" : "ARRHENIUS", + "A" : 1.3E-10, + "B" : 0.0E+00, + "C" : -0.0E+00 + }, + { + "rxn id" : "CL19", + "reactants" : { + "CL" : {} , + "MEOH" : {} + }, + "products" : { + "HCL" : {} , + "HO2" : { "yield" : 1.000 }, + "FORM" : { "yield" : 1.000 } + }, + "orig params" : "CMAQ_1to4(5.5E-11, 0.0E+00, 0.0E+00)", + "type" : "ARRHENIUS", + "A" : 5.5E-11, + "B" : 0.0E+00, + "C" : -0.0E+00 + }, + { + "rxn id" : "CL20", + "reactants" : { + "CL" : {} , + "ETOH" : {} + }, + "products" : { + "HCL" : {} , + "HO2" : { "yield" : 1.000 }, + "ALD2" : { "yield" : 1.000 } + }, + "orig params" : "CMAQ_1to4(8.2E-11, 0.0E+00, -45.0)", + "type" : "ARRHENIUS", + "A" : 8.2E-11, + "B" : 0.0E+00, + "C" : 45.0 + }, + { + "rxn id" : "CL21", + "reactants" : { + "HCL" : {} , + "OH" : {} + }, + "products" : { + "CL" : {} + }, + "orig params" : "CMAQ_1to4(6.58E-13, 1.16, -58.0)", + "type" : "ARRHENIUS", + "A" : 6.58E-13, + "B" : 1.16, + "C" : 58.0 + }, + { + "rxn id" : "SA01", + "reactants" : { + "TOLRO2" : {} , + "NO" : {} + }, + "products" : { + "NO" : {} , + "TOLNRXN" : {} + }, + "orig params" : "CMAQ_1to4(2.70e-12, 0.0E+00, -360.0)", + "type" : "ARRHENIUS", + "A" : 2.70e-12, + "B" : 0.0E+00, + "C" : 360.0 + }, + { + "rxn id" : "SA02", + "reactants" : { + "TOLRO2" : {} , + "HO2" : {} + }, + "products" : { + "HO2" : {} , + "TOLHRXN" : {} + }, + "orig params" : "CMAQ_1to4(1.90e-13, 0.0E+00, -1300.0)", + "type" : "ARRHENIUS", + "A" : 1.90e-13, + "B" : 0.0E+00, + "C" : 1300.0 + }, + { + "rxn id" : "SA03", + "reactants" : { + "XYLRO2" : {} , + "NO" : {} + }, + "products" : { + "NO" : {} , + "XYLNRXN" : {} + }, + "orig params" : "CMAQ_1to4(2.70e-12, 0.0E+00, -360.0)", + "type" : "ARRHENIUS", + "A" : 2.70e-12, + "B" : 0.0E+00, + "C" : 360.0 + }, + { + "rxn id" : "SA04", + "reactants" : { + "XYLRO2" : {} , + "HO2" : {} + }, + "products" : { + "HO2" : {} , + "XYLHRXN" : {} + }, + "orig params" : "CMAQ_1to4(1.90e-13, 0.0E+00, -1300.0)", + "type" : "ARRHENIUS", + "A" : 1.90e-13, + "B" : 0.0E+00, + "C" : 1300.0 + }, + { + "rxn id" : "SA05", + "reactants" : { + "BENZENE" : {} , + "OH" : {} + }, + "products" : { + "OH" : {} , + "BENZRO2" : { "yield" : 0.764 } + }, + "orig params" : "CMAQ_1to4(2.47e-12, 0.0E+00, 206.0)", + "type" : "ARRHENIUS", + "A" : 2.47e-12, + "B" : 0.0E+00, + "C" : -206.0 + }, + { + "rxn id" : "SA06", + "reactants" : { + "BENZRO2" : {} , + "NO" : {} + }, + "products" : { + "NO" : {} , + "BNZNRXN" : {} + }, + "orig params" : "CMAQ_1to4(2.70e-12, 0.0E+00, -360.0)", + "type" : "ARRHENIUS", + "A" : 2.70e-12, + "B" : 0.0E+00, + "C" : 360.0 + }, + { + "rxn id" : "SA07", + "reactants" : { + "BENZRO2" : {} , + "HO2" : {} + }, + "products" : { + "HO2" : {} , + "BNZHRXN" : {} + }, + "orig params" : "CMAQ_1to4(1.90e-13, 0.0E+00, -1300.0)", + "type" : "ARRHENIUS", + "A" : 1.90e-13, + "B" : 0.0E+00, + "C" : 1300.0 + }, + { + "rxn id" : "SA08", + "reactants" : { + "SESQ" : {} , + "O3" : {} + }, + "products" : { + "O3" : {} , + "SESQRXN" : {} + }, + "orig params" : "CMAQ_1to4(1.16E-14, 0.0E+00, 0.0E+00)", + "type" : "ARRHENIUS", + "A" : 1.16E-14, + "B" : 0.0E+00, + "C" : -0.0E+00 + }, + { + "rxn id" : "SA09", + "reactants" : { + "SESQ" : {} , + "OH" : {} + }, + "products" : { + "OH" : {} , + "SESQRXN" : {} + }, + "orig params" : "CMAQ_1to4(1.97E-10, 0.0E+00, 0.0E+00)", + "type" : "ARRHENIUS", + "A" : 1.97E-10, + "B" : 0.0E+00, + "C" : -0.0E+00 + }, + { + "rxn id" : "SA10", + "reactants" : { + "SESQ" : {} , + "NO3" : {} + }, + "products" : { + "NO3" : {} , + "SESQRXN" : {} + }, + "orig params" : "CMAQ_1to4(1.90E-11, 0.0E+00, 0.0E+00)", + "type" : "ARRHENIUS", + "A" : 1.90E-11, + "B" : 0.0E+00, + "C" : -0.0E+00 + }, + { + "rxn id" : "jo2", + "reactants" : { + "O2" : {} + }, + "products" : { + "O" : { "yield" : 2 } + }, + "orig params" : "TUV_J(1, THETA)", + "base rate" : 0.00e+1, + "notes" : "Fast-J does not currently calculate O2 photolysis", + "type" : "PHOTOLYSIS" + } + ] +} +]} diff --git a/examples/monarch_mod37/cb05_species.json b/examples/monarch_mod37/cb05_species.json new file mode 100644 index 00000000..3f42cf3c --- /dev/null +++ b/examples/monarch_mod37/cb05_species.json @@ -0,0 +1,400 @@ +{ +"notes" :"Descriptions are from CB5 Final Report RT-04-00675 (www.camx.com/files/cb05_final_report_120805.aspx) and from notes in the cb05cl_ae5_aq_CMAQ.def mechanism file", +"camp-data" : [ + { + "name" : "AACD", + "type" : "CHEM_SPEC", + "description" : "acetic and higher carboxylic acids" + }, + { + "name" : "ALD2", + "type" : "CHEM_SPEC", + "description" : "acetaldehyde" + }, + { + "name" : "ALDX", + "type" : "CHEM_SPEC", + "description" : "propionaldehyde and higher aldehydes" + }, + { + "name" : "BENZENE", + "type" : "CHEM_SPEC", + "description" : "benzene" + }, + { + "name" : "BENZRO2", + "type" : "CHEM_SPEC", + "description" : "peroxy radical from benzene oxidation" + }, + { + "name" : "BNZHRXN", + "type" : "CHEM_SPEC", + "description" : "counter species for aerosol from BENZENE - how does this differ from BNZNNRXN?" + }, + { + "name" : "BNZNRXN", + "type" : "CHEM_SPEC", + "description" : "counter species for aerosol from BENZENE" + }, + { + "name" : "C2O3", + "type" : "CHEM_SPEC", + "description" : "acetyl peroxy radical" + }, + { + "name" : "CH4", + "type" : "CHEM_SPEC", + "description" : "methane" + }, + { + "name" : "CL", + "type" : "CHEM_SPEC", + "description" : "chlorine radical" + }, + { + "name" : "CL2", + "type" : "CHEM_SPEC", + "description" : "molecular chlorine" + }, + { + "name" : "CLO", + "type" : "CHEM_SPEC", + "description" : "chlorine monoxide" + }, + { + "name" : "CO", + "type" : "CHEM_SPEC", + "description" : "carbon monoxide" + }, + { + "name" : "CRES", + "type" : "CHEM_SPEC", + "description" : "cresol and higher molecular weight phenols" + }, + { + "name" : "CRO", + "type" : "CHEM_SPEC", + "description" : "methylphenoxy radical" + }, + { + "name" : "CXO3", + "type" : "CHEM_SPEC", + "description" : "C3 and higher acylperoxy radicals" + }, + { + "name" : "ETH", + "type" : "CHEM_SPEC", + "description" : "ethene" + }, + { + "name" : "ETHA", + "type" : "CHEM_SPEC", + "description" : "ethane" + }, + { + "name" : "ETOH", + "type" : "CHEM_SPEC", + "description" : "ethanol" + }, + { + "name" : "FACD", + "type" : "CHEM_SPEC", + "description" : "formic acid" + }, + { + "name" : "FMCL", + "type" : "CHEM_SPEC", + "description" : "formyl chloride (HC(O)Cl)" + }, + { + "name" : "FORM", + "type" : "CHEM_SPEC", + "description" : "formaldehyde" + }, + { + "name" : "H2O2", + "type" : "CHEM_SPEC", + "description" : "hydrogen peroxide" + }, + { + "name" : "HCL", + "type" : "CHEM_SPEC", + "description" : "hydrochlric acid" + }, + { + "name" : "HCO3", + "type" : "CHEM_SPEC", + "description" : "formyl peroxy radical? no description in cb05 report" + }, + { + "name" : "HNO3", + "type" : "CHEM_SPEC", + "description" : "nitric acid" + }, + { + "name" : "HO2", + "type" : "CHEM_SPEC", + "description" : "hydroperoxy radical" + }, + { + "name" : "HOCL", + "type" : "CHEM_SPEC", + "description" : "hypochlorous acid" + }, + { + "name" : "HONO", + "type" : "CHEM_SPEC", + "description" : "nitrous acid" + }, + { + "name" : "IOLE", + "type" : "CHEM_SPEC", + "description" : "internal olefin carbon bond (R-C=C)" + }, + { + "name" : "ISOP", + "type" : "CHEM_SPEC", + "description" : "isoprene" + }, + { + "name" : "ISOPRXN", + "type" : "CHEM_SPEC", + "description" : "counter for aerosol from ISOP" + }, + { + "name" : "ISPD", + "type" : "CHEM_SPEC", + "description" : "isoprene products (lumped methacrolein, methyl vinyl ketone, etc.)" + }, + { + "name" : "MEO2", + "type" : "CHEM_SPEC", + "description" : "methyl peroxy radical" + }, + { + "name" : "MEOH", + "type" : "CHEM_SPEC", + "description" : "methanol" + }, + { + "name" : "MEPX", + "type" : "CHEM_SPEC", + "description" : "methylhydroperoxide" + }, + { + "name" : "MGLY", + "type" : "CHEM_SPEC", + "description" : "methylglyoxal and other aromatic products" + }, + { + "name" : "N2O5", + "type" : "CHEM_SPEC", + "description" : "dinitrogen pentoxide" + }, + { + "name" : "NO", + "type" : "CHEM_SPEC", + "description" : "nitric oxide" + }, + { + "name" : "NO2", + "type" : "CHEM_SPEC", + "description" : "nitrogen dioxide" + }, + { + "name" : "NO3", + "type" : "CHEM_SPEC", + "description" : "nitrate radical" + }, + { + "name" : "NTR", + "type" : "CHEM_SPEC", + "description" : "organic nitrate (RNO3)" + }, + { + "name" : "O", + "type" : "CHEM_SPEC", + "description" : "oxygen atom in the O3P electronic state" + }, + { + "name" : "O1D", + "type" : "CHEM_SPEC", + "description" : "oxygen atom in the O1D electronic state" + }, + { + "name" : "O3", + "type" : "CHEM_SPEC", + "description" : "ozone" + }, + { + "name" : "OH", + "type" : "CHEM_SPEC", + "description" : "hydroxyl radical" + }, + { + "name" : "OLE", + "type" : "CHEM_SPEC", + "description" : "terminal olefin carbon bond (R-C=C)" + }, + { + "name" : "OPEN", + "type" : "CHEM_SPEC", + "description" : "aromatic ring opening products" + }, + { + "name" : "PACD", + "type" : "CHEM_SPEC", + "description" : "peroxyacetic and higher peroxycarboxylic acids" + }, + { + "name" : "PAN", + "type" : "CHEM_SPEC", + "description" : "peroxyacetyl nitrate" + }, + { + "name" : "PANX", + "type" : "CHEM_SPEC", + "description" : "C3 and higher peroxyacyl nitrates" + }, + { + "name" : "PAR", + "type" : "CHEM_SPEC", + "description" : "paraffin carbon bond (C-C)" + }, + { + "name" : "PNA", + "type" : "CHEM_SPEC", + "description" : "peroxynitric acid (HNO4)" + }, + { + "name" : "ROOH", + "type" : "CHEM_SPEC", + "description" : "higher organic peroxides" + }, + { + "name" : "ROR", + "type" : "CHEM_SPEC", + "description" : "secondary alkoxy radical" + }, + { + "name" : "SESQ", + "type" : "CHEM_SPEC", + "description" : "sesquiterpene" + }, + { + "name" : "SESQRXN", + "type" : "CHEM_SPEC", + "description" : "counter for aerosol from SESQ" + }, + { + "name" : "SO2", + "type" : "CHEM_SPEC", + "description" : "sulfur dioxide" + }, + { + "name" : "SULF", + "type" : "CHEM_SPEC", + "description" : "sulfuric acid (gaseous)" + }, + { + "name" : "SULRXN", + "type" : "CHEM_SPEC", + "description" : "counter for aerosol from SO2" + }, + { + "name" : "TERP", + "type" : "CHEM_SPEC", + "description" : "terpene" + }, + { + "name" : "TO2", + "type" : "CHEM_SPEC", + "description" : "toluene-hydroxyl radical aduct" + }, + { + "name" : "TOL", + "type" : "CHEM_SPEC", + "description" : "toluene" + }, + { + "name" : "TOLHRXN", + "type" : "CHEM_SPEC", + "description" : "counter for aerosol from TOL - how does this differ from TOLNRXN?" + }, + { + "name" : "TOLNRXN", + "type" : "CHEM_SPEC", + "description" : "counter for aerosol from TOL" + }, + { + "name" : "TOLRO2", + "type" : "CHEM_SPEC", + "description" : "first generation product from TOL" + }, + { + "name" : "TRPRXN", + "type" : "CHEM_SPEC", + "description" : "counter for aerosol from TERP" + }, + { + "name" : "XO2", + "type" : "CHEM_SPEC", + "description" : "NO to NO2 conversion from alkylperoxy (RO2) radical" + }, + { + "name" : "XO2N", + "type" : "CHEM_SPEC", + "description" : "NO to organic nitrate conversion from alkylperoxy (RO2) radical" + }, + { + "name" : "XYL", + "type" : "CHEM_SPEC", + "description" : "xylene and other polyalkyl aromatics" + }, + { + "name" : "XYLHRXN", + "type" : "CHEM_SPEC", + "description" : "counter for aerosol from XYL - how does this differ from XYLNRXN?" + }, + { + "name" : "XYLNRXN", + "type" : "CHEM_SPEC", + "description" : "counter for aerosol from XYL" + }, + { + "name" : "XYLRO2", + "type" : "CHEM_SPEC", + "description" : "first generation product from XYL" + }, + { + "name" : "N2O", + "type" : "CHEM_SPEC", + "description" : "nitrous oxide - does not participate in CB05 reactions" + }, + { + "name" : "DUMMY", + "type" : "CHEM_SPEC", + "description" : "not sure what this is" + }, + { + "name" : "O2", + "type" : "CHEM_SPEC", + "description" : "molecular oxygen" + }, + { + "name" : "H2O", + "type" : "CHEM_SPEC", + "is gas-phase water" : true, + "description" : "water vapor" + }, + { + "name" : "H2", + "type" : "CHEM_SPEC", + "description" : "molecular hydrogen" + }, + { + "name" : "M", + "type" : "CHEM_SPEC", + "description" : "third body" + } +]} diff --git a/examples/monarch_mod37/cloud_and_rain_partitioning.json b/examples/monarch_mod37/cloud_and_rain_partitioning.json new file mode 100644 index 00000000..848f8846 --- /dev/null +++ b/examples/monarch_mod37/cloud_and_rain_partitioning.json @@ -0,0 +1,258 @@ +{ + "description" : [ + "Partitioning of species to aqueous. Parameters are from existing wet-deposition module." + ], + "pmc-data" : [ + { + "name" : "MONARCH mod37", + "type" : "MECHANISM", + "reactions" : [ + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "NO2", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "NO2_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "NO", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "NO_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "O3", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "O3_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "NO3", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "NO3_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "N2O5", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "N2O5_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "HNO3", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "HNO3_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "HONO", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "HONO_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "PNA", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "HNO4_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "H2O2", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "H2O2_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "NTR", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "NTR_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "ROOH", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "ROOH_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "FORM", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "FORM_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "ALD2", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "ALD2_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "ALDX", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "ALDX_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "CO", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "CO_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "MEPX", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "MEPX_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "MEOH", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "MEOH_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "FACD", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "FACD_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "PAN", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "PAN_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "PACD", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "PACD_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "AACD", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "AACD_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "PANX", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "PANX_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "SO2", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "SO2_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "SULF", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "H2SO4_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "CL2", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "CL2_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "HOCL", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "HOCL_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "FMCL", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "FMCL_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "HCL", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "HCL_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "NH3", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "NH3_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "ISOP-P1", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "ISOP-P1_aero", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "ISOP-P2", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "ISOP-P2_aero", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "TERP-P1", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "TERP-P1_aero", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "TERP-P2", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "TERP-P2_aero", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "DMS", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "DMS_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "ETOH", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "ETOH_aq", + "aerosol-phase water" : "H2O_aq" + } + ] + } + ] +} diff --git a/examples/monarch_mod37/cloud_and_rain_species.json b/examples/monarch_mod37/cloud_and_rain_species.json new file mode 100644 index 00000000..24508c47 --- /dev/null +++ b/examples/monarch_mod37/cloud_and_rain_species.json @@ -0,0 +1,476 @@ +{ + "description" : "Aqueous species present in cloud and rain water", + "pmc-data" : [ + { + "name" : "NO2", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.046006 + }, + { + "name" : "NO2_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.046006, + "density [kg m-3]" : 1000.0, + "description" : "aqueous nitrogen dioxide", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "NO", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.03001 + }, + { + "name" : "NO_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.03001, + "density [kg m-3]" : 1000.0, + "description" : "aqueous nitrogen oxide", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "O3", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.04800 + }, + { + "name" : "O3_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.04800, + "density [kg m-3]" : 1000.0, + "description" : "aqueous ozone", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "NO3", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.07601 + }, + { + "name" : "NO3_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.07601, + "density [kg m-3]" : 1000.0, + "description" : "aqueous nitrogen trioxide", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "N2O5", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.10801 + }, + { + "name" : "N2O5_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.10801, + "density [kg m-3]" : 1000.0, + "description" : "aqueous dinitrogen pentoxide", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "HONO", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.047013 + }, + { + "name" : "HONO_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.047013, + "density [kg m-3]" : 1000.0, + "description" : "aqueous nitrous acid", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "PNA", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.01224 + }, + { + "name" : "HNO4_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.01224, + "density [kg m-3]" : 1000.0, + "description" : "aqueous peroxy nitric acid (HNO4)", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "H2O2", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.0340147 + }, + { + "name" : "H2O2_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.0340147, + "density [kg m-3]" : 1000.0, + "description" : "aqueous hydrogen peroxide", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "NTR", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.091066 + }, + { + "name" : "NTR_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.091066, + "density [kg m-3]" : 1000.0, + "description" : "aqueous organic nitrates (RNO3); using CH3CH2NO3 as surrogate", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "ROOH", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.074079 + }, + { + "name" : "ROOH_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.074079, + "density [kg m-3]" : 1000.0, + "description" : "aqueous alkyl peroxides; using CH3CH3OOH as surrogate", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "FORM", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.030031 + }, + { + "name" : "FORM_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.030031, + "density [kg m-3]" : 1000.0, + "description" : "aqueous formaldehyde", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "ALD2", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.04405 + }, + { + "name" : "ALD2_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.04405, + "density [kg m-3]" : 1000.0, + "description" : "aqueous acetaldehyde", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "ALDX", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.05808 + }, + { + "name" : "ALDX_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.05808, + "density [kg m-3]" : 1000.0, + "description" : "propionaldehyde and higher aldehydes", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "CO", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.028010 + }, + { + "name" : "CO_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.028010, + "density [kg m-3]" : 1000.0, + "description" : "aqueous carbon monoxide", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "MEPX", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.048041 + }, + { + "name" : "MEPX_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.048041, + "density [kg m-3]" : 1000.0, + "description" : "aqueous methylhydroperoxide", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "MEOH", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.03204 + }, + { + "name" : "MEOH_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.03204, + "density [kg m-3]" : 1000.0, + "description" : "aqueous methanol", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "FACD", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.04603 + }, + { + "name" : "FACD_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.04603, + "density [kg m-3]" : 1000.0, + "description" : "aqueous formic acid", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "PAN", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.12105 + }, + { + "name" : "PAN_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.12105, + "density [kg m-3]" : 1000.0, + "description" : "aqueous peroxy-acetyl nitrate", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "PACD", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.0760514 + }, + { + "name" : "PACD_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.0760514, + "density [kg m-3]" : 1000.0, + "description" : "aqueous peroxyacetic acid and higher peroxycarboxylic acids", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "AACD", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.06005 + }, + { + "name" : "AACD_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.06005, + "density [kg m-3]" : 1000.0, + "description" : "aqueous acetic and higher carboxylic acids", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "PANX", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.135075 + }, + { + "name" : "PANX_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.135075, + "density [kg m-3]" : 1000.0, + "description" : "C3 and higher peroxyacyl nitrates", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "SO2", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.064066 + }, + { + "name" : "SO2_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.064066, + "density [kg m-3]" : 1000.0, + "description" : "aqueous sulfur dioxide", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "CL2", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" : 8.6E-02, + "HLC exp factor [K]" : 2000.0, + "diffusion coeff [m2 s-1]" : 1.28E-05, + "notes" : [ "diffusion coeff from CAPRAMv2.4" ], + "molecular weight [kg mol-1]" : 0.07090 + }, + { + "name" : "CL2_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.07090, + "density [kg m-3]" : 1000.0, + "description" : "aqueous molecular chlorine", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "HOCL", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" : 6.6E+02, + "HLC exp factor [K]" : 5900.0, + "diffusion coeff [m2 s-1]" : 1.28E-05, + "notes" : [ "using diffusion coeff for CL2 from CAPRAMv2.4" ], + "molecular weight [kg mol-1]" : 0.05246 + }, + { + "name" : "HOCL_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.05246, + "density [kg m-3]" : 1000.0, + "description" : "aqueous hypochlorous acid", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "FMCL", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" : 1.1, + "HLC exp factor [K]" : 0.0, + "diffusion coeff [m2 s-1]" : 1.28E-05, + "notes" : [ "using diffusion coeff for CL2 from CAPRAMv2.4" ], + "molecular weight [kg mol-1]" : 0.064468 + }, + { + "name" : "FMCL_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.064468, + "density [kg m-3]" : 1000.0, + "description" : "aqueous formyl chloride (HC(O)Cl)", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "HCL", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.03646 + }, + { + "name" : "HCL_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.03646, + "density [kg m-3]" : 1000.0, + "description" : "aqueous hydrochloric acid", + "num_ions" : 0, + "kappa" : 0.53 + }, + { + "name" : "CL_m", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.03545, + "density [kg m-3]" : 1000.0, + "description" : "chloride ion", + "num_ions" : 1, + "kappa" : 0 + }, + { + "name" : "DMS", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.06213 + }, + { + "name" : "DMS_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.06213, + "density [kg m-3]" : 1000.0, + "description" : "aqueous dimethyl sulfide", + "num_ions" : 0, + "kappa" : 0.0 + }, + { + "name" : "ETOH", + "type" : "CHEM_SPEC", + "molecular weight [kg mol-1]" : 0.04607 + }, + { + "name" : "ETOH_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.04607, + "density [kg m-3]" : 1000.0, + "description" : "aqueous ethanol", + "num_ions" : 0, + "kappa" : 0.0 + } + ] +} diff --git a/examples/monarch_mod37/custom_species.json b/examples/monarch_mod37/custom_species.json new file mode 100644 index 00000000..df8673d4 --- /dev/null +++ b/examples/monarch_mod37/custom_species.json @@ -0,0 +1,100 @@ +{ + "description" : [ + "These additional species are needed for the MONARCH 'mod37' configuration", + "Densities are taken from Spada et al. (2015) manuscript - ", + "'Global Aerosols in the online multiscale NMMB/BSC Chemical Transport Model", + "or estimated from bulk densities.", + "TODO check about molecular weights" + ], + "camp-data" : [ + { + "name" : "NH3", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03, + "description" : "ammonia" + }, + { + "name" : "DMS", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-03, + "description" : "dimethylsulfide" + }, + { + "monarch name" : "lumped high-density dust species", + "name" : "LHD_DUST", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.1, + "density [kg m-3]" : 2650.0, + "num_ions" : 0, + "kappa" : 0.1 + }, + { + "monarch name" : "lumped low-density dust species", + "name" : "LLD_DUST", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.1, + "density [kg m-3]" : 2650.0, + "num_ions" : 0, + "kappa" : 0.1 + }, + { + "monarch name" : "lumped sea salt species", + "name" : "SEA_SALT", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.1, + "density [kg m-3]" : 2160.0, + "num_ions" : 0, + "kappa" : 0.53 + }, + { + "name" : "BC_phob", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "density [kg m-3]" : 1000.0, + "molecular weight [kg mol-1]" : 0.1, + "description" : "hydrophobic black carbon", + "num_ions" : 0, + "kappa" : 0 + }, + { + "name" : "BC_phil", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "density [kg m-3]" : 1000.0, + "molecular weight [kg mol-1]" : 0.1, + "description" : "hydrophilic black carbon", + "num_ions" : 0, + "kappa" : 0.001 + }, + { + "name" : "other_PM", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.1, + "density [kg m-3]" : 1800.0, + "description" : "unspecified particulate matter FIXME", + "num_ions" : 0, + "kappa" : 0 + }, + { + "name" : "other_other_PM", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "molecular weight [kg mol-1]" : 0.1, + "density [kg m-3]" : 1800.0, + "description" : "second unspecified particulate matter species FIXME", + "num_ions" : 0, + "kappa" : 0 + } + ] +} diff --git a/examples/monarch_mod37/dry_deposition.json b/examples/monarch_mod37/dry_deposition.json new file mode 100644 index 00000000..353780e5 --- /dev/null +++ b/examples/monarch_mod37/dry_deposition.json @@ -0,0 +1,240 @@ +{ + "description" : [ + "Dry deposition reactions and species properties", + "TODO Consider updating diffusion coefficients according to Tang et al. Atmos. Chem. Phys., 14, 9233-9247 (2014)", + " available at https://www.atmos-chem-phys.net/14/9233/2014/acp-14-9233-2014.pdf" + ], + "pmc-data" : [ + { + "name" : "MONARCH mod37", + "type" : "MECHANISM", + "reactions" : [ + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "SULF" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "MEOH" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "ETOH" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "OPEN" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "HCL" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "TERP" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "PANX" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "NO2" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "NO" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "O3" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "NO3" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "N2O5" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "HNO3" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "HONO" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "PNA" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "H2O2" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "NTR" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "ROOH" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "FORM" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "ALD2" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "ALDX" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "PAR" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "CO" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "MEPX" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "FACD" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "PAN" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "PACD" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "AACD" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "OLE" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "ETH" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "IOLE" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "TOL" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "CRES" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "MGLY" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "XYL" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "ISOP" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "ISPD" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "SO2" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "ETHA" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "NH3" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "ISOP-P1" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "ISOP-P2" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "TERP-P1" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "TERP-P2" + }, + { + "type" : "FIRST_ORDER_LOSS", + "loss type" : "dry dep", + "species" : "DMS" + } + ] + } + ] +} diff --git a/examples/monarch_mod37/inorganic_ZSR_water.json b/examples/monarch_mod37/inorganic_ZSR_water.json new file mode 100644 index 00000000..e281622a --- /dev/null +++ b/examples/monarch_mod37/inorganic_ZSR_water.json @@ -0,0 +1,73 @@ +{ + "description" : [ + "ZSR aerosol water calculation for inorganic aerosols" + ], + "pmc-data" : [ + { + "type" : "SUB_MODEL_ZSR_AEROSOL_WATER", + "name" : "MONARCH inorganic aerosol water", + "notes" : [ "Y_j parameters taken from Jacobson et al. (1996) Table 2" ], + "aerosol phase" : "aqueous", + "gas-phase water" : "H2O", + "aerosol-phase water" : "H2O_aq", + "ion pairs" : { + "H-HSO4" : { + "type" : "JACOBSON", + "ions" : { + "H_p" : {}, + "HSO4_m" : {} + }, + "Y_j" : [5.611895, -1.387446e1, 1.750682e1, 7.138146e1, -3.109173e2, 4.662288e2, -3.128612e2, 7.767097e1], + "low RH" : 0.0 + }, + "H2-SO4" : { + "type" : "JACOBSON", + "ions" : { + "H_p" : { "qty" : 2 }, + "SO4_mm" : {} + }, + "Y_j" : [5.611895, -1.387446e1, 1.750682e1, 7.138146e1, -3.109173e2, 4.662288e2, -3.128612e2, 7.767097e1], + "low RH" : 0.0 + }, + "H-NO3" : { + "type" : "JACOBSON", + "ions" : { + "H_p" : {}, + "NO3_m" : {} + }, + "Y_j" : [4.852977, -6.621314, 3.390133e1, -1.985191e2, 6.281150e2, -1.038494e3, 8.498917e2, -2.729090e2], + "low RH" : 0.0 + }, + "NH4-HSO4" : { + "type" : "JACOBSON", + "ions" : { + "NH4_p" : {}, + "HSO4_m" : {} + }, + "Y_j" : [5.515580, 3.588744, -6.363443e1, 3.687630e2, -1.023972e3, 1.394436e3, -9.168213e2, 2.328726e2], + "low RH" : 0.0 + }, + "(NH4)2-SO4" : { + "type" : "JACOBSON", + "ions" : { + "NH4_p" : { "qty" : 2 }, + "SO4_mm" : {} + }, + "Y_j" : [4.363511e2, -4.947645e3, 2.399693e4, -6.364664e4, 9.952891e4, -9.179112e4, 4.626748e4, -9.844195e3], + "low RH" : 0.47 + }, + "NH4-NO3" : { + "type" : "JACOBSON", + "ions" : { + "NH4_p" : {}, + "NO3_m" : {} + }, + "Y_j" : [1.235157e4, -1.097966e5, 4.173924e5, -8.792165, 1.108433e6, -8.364973e5, 3.499527e5, -6.261910e4], + "low RH" : 0.62 + } + } + } + ] +} + + diff --git a/examples/monarch_mod37/inorganic_activity.json b/examples/monarch_mod37/inorganic_activity.json new file mode 100644 index 00000000..cb04af40 --- /dev/null +++ b/examples/monarch_mod37/inorganic_activity.json @@ -0,0 +1,339 @@ +{ + "notes" : [ + "PD-FiTE activity calculations for aqueous aerosol species. Parameters from tables 3 and 4 in", + "Topping et al. 2009." + ], + "pmc-data" : [ + { + "type" : "SUB_MODEL_PDFITE", + "name" : "MONARCH activity scheme", + "gas-phase water" : "H2O", + "aerosol-phase water" : "H2O_aq", + "aerosol phase" : "aqueous", + "calculate for" : { + "H-NO3" : { + "interactions" : [ + { + "ion pair": "H-NO3", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ 0.925133 ] + }, + { + "ion pair": "H-NO3", + "min RH" : 0.1, + "max RH" : 0.4, + "B" : [ 0.12091, 13.497, -67.771, 144.01, -117.97 ] + }, + { + "ion pair" : "H-NO3", + "min RH" : 0.4, + "max RH" : 0.9, + "B" : [ 1.3424, -0.8197, -0.52983, -0.37335 ] + }, + { + "ion pair" : "H-NO3", + "min RH" : 0.9, + "max RH" : 0.99, + "B" : [ -1420.5, 4467.9, -4682.7, 1635.1 ] + }, + { + "ion pair" : "H-NO3", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ -0.2573751 ] + }, + { + "ion pair" : "H2-SO4", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ 7.0531446 ] + }, + { + "ion pair" : "H2-SO4", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ 9.3948, -26.808, 35.7654, -18.5094 ] + }, + { + "ion pair" : "H2-SO4", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ -0.0511038 ] + }, + { + "ion pair" : "(NH4)2-SO4", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ -31.136334 ] + }, + { + "ion pair" : "(NH4)2-SO4", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ -40.4136, 108.798, -170.346, 100.926 ] + }, + { + "ion pair" : "(NH4)2-SO4", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ -1.7312977 ] + }, + { + "ion pair" : "NH4-NO3", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ -11.93308 ] + }, + { + "ion pair" : "NH4-NO3", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ -17.0372, 59.232, -86.312, 44.04 ] + }, + { + "ion pair" : "NH4-NO3", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ -0.2599432 ] + } + ] + }, + "NH4/H" : { + "interactions" : [ + { + "ion pair" : "H-NO3", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ -31.711852 ] + }, + { + "ion pair" : "H-NO3", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ -39.1996, 84.264, -99.276, 54.108 ] + }, + { + "ion pair" : "H-NO3", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ -0.5777093 ] + }, + { + "ion pair" : "H2-SO4", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ -58.151568 ] + }, + { + "ion pair" : "H2-SO4", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ -72.978, 165.162, -177.51, 85.332 ] + }, + { + "ion pair" : "H2-SO4", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ -0.6476167 ] + }, + { + "ion pair" : "(NH4)2-SO4", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ -8.918661 ] + }, + { + "ion pair" : "(NH4)2-SO4", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ -15.213, 79.782, -193.326, 262.77, -133.71 ] + }, + { + "ion pair" : "(NH4)2-SO4", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ 0.81654313 ] + }, + { + "ion pair" : "NH4-NO3", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ -24.41782 ] + }, + { + "ion pair" : "NH4-NO3", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ -25.8256, 12.772, 13.058 ] + }, + { + "ion pair" : "NH4-NO3", + "min RH" : 0.99, + "max RH" : 1.0, + "B": [ -0.3831742 ] + } + ] + }, + "H2-SO4" : { + "interactions" : [ + { + "ion pair" : "H2-SO4", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ 1.1220548 ] + }, + { + "ion pair" : "H2-SO4", + "min RH" : 0.1, + "max RH" : 0.9, + "B" : [ 1.3701, -2.1559, -3.5227, 2.7718 ] + }, + { + "ion pair" : "H2-SO4", + "min RH" : 0.9, + "max RH" : 0.99, + "B" : [ -395.18, 1333.7, -1504, 564.63 ] + }, + { + "ion pair" : "H2-SO4", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ -1.0274756 ] + }, + { + "ion pair" : "H-NO3", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ 4.70701952 ] + }, + { + "ion pair" : "H-NO3", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ 8.5472, -50.16, 137.44, -216.596, 186.708, -65.528 ] + }, + { + "ion pair" : "H-NO3", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ 0.46534564 ] + }, + { + "ion pair" : "(NH4)2-SO4", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ -30.961877 ] + }, + { + "ion pair" : "(NH4)2-SO4", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ -48.3636, 235.092, -726.24, 1263.42, -1125, 400.26 ] + }, + { + "ion pair" : "(NH4)2-SO4", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ -1.5424153 ] + }, + { + "ion pair" : "NH4-NO3", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ -15.557633 ] + }, + { + "ion pair" : "NH4-NO3", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ -27.8844, 150.552, -298.588, 266.46, -90.128 ] + }, + { + "ion pair" : "NH4-NO3", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ 0.48525555 ] + } + ] + }, + "H-HSO4" : { + "interactions" : [ + { + "ion pair" : "H-HSO4", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ 1.1220548 ] + }, + { + "ion pair" : "H-HSO4", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ 2.6875, -11.832, 20.601, -18.593 ] + }, + { + "ion pair" : "H-HSO4", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ -6.8759092 ] + }, + { + "ion pair" : "H-NO3", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ -5.4701562 ] + }, + { + "ion pair" : "H-NO3", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ -7.6016, 25.836, -49.924, 48.772, -16.8816 ] + }, + { + "ion pair" : "H-NO3", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ 0.15255283 ] + }, + { + "ion pair" : "(NH4)2-SO4", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ -39.541392 ] + }, + { + "ion pair" : "(NH4)2-SO4", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ -49.9236, 120.066, -172.5, 100.608 ] + }, + { + "ion pair" : "(NH4)2-SO4", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ -2.5056682 ] + }, + { + "ion pair" : "NH4-NO3", + "min RH" : 0.0, + "max RH" : 0.1, + "B" : [ -25.289738 ] + }, + { + "ion pair" : "NH4-NO3", + "min RH" : 0.1, + "max RH" : 0.99, + "B" : [ -37.008, 141.284, -263.06, 227.336, -68.736 ] + }, + { + "ion pair" : "NH4-NO3", + "min RH" : 0.99, + "max RH" : 1.0, + "B" : [ -0.4055799 ] + } + ] + } + } + } + ] +} diff --git a/examples/monarch_mod37/inorganic_partitioning.json b/examples/monarch_mod37/inorganic_partitioning.json new file mode 100644 index 00000000..37d3a6a9 --- /dev/null +++ b/examples/monarch_mod37/inorganic_partitioning.json @@ -0,0 +1,39 @@ +{ + "description" : [ + "Partitioning of inorganic species. Reactions are based on original MONARCH implementation", + "of EQSAM where only the SO4-NO3-NH4 system is included and is only calculated for the sulfate", + "aerosol mode.", + "Partitioning reaction parameters are from CAPRAM2.4 (Ervens et al. 2003)" + ], + "pmc-data" : [ + { + "name" : "MONARCH mod37", + "type" : "MECHANISM", + "reactions" : [ + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "SULF", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "H2SO4_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "HNO3", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "HNO3_aq", + "aerosol-phase water" : "H2O_aq" + }, + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "NH3", + "aerosol phase" : "aqueous", + "aerosol-phase species" : "NH3_aq", + "aerosol-phase water" : "H2O_aq" + } + ] + } + ] +} + + diff --git a/examples/monarch_mod37/inorganic_reactions.json b/examples/monarch_mod37/inorganic_reactions.json new file mode 100644 index 00000000..fa2e5459 --- /dev/null +++ b/examples/monarch_mod37/inorganic_reactions.json @@ -0,0 +1,94 @@ +{ + "description" : [ + "These reactions are based on the original MONARCH implementation of EQSAM where", + "only the SO4-NO3-NH3 system is included, and inorganic reactions are only applied", + "to the sulfate aerosol mode. Reaction parameters are from CAPRAM2.4 (Ervens et al. 2003)" + ], + "pmc-data" : [ + { + "name" : "MONARCH mod37", + "type" : "MECHANISM", + "reactions" : [ + { + "type" : "AQUEOUS_EQUILIBRIUM", + "aerosol phase" : "aqueous", + "aerosol-phase water" : "H2O_aq", + "A" : 1.8e-16, + "C" : -6800.0, + "k_reverse" : 1.3e11, + "reactants" : { + "H2O_aq" : {} + }, + "products" : { + "H_p" : {}, + "OH_m" : {} + } + }, + { + "type" : "AQUEOUS_EQUILIBRIUM", + "aerosol phase" : "aqueous", + "aerosol-phase water" : "H2O_aq", + "A" : 1.02e-2, + "C" : 2700.0, + "k_reverse" : 1.0e11, + "ion pair" : "H2-SO4", + "reactants" : { + "HSO4_m" : {} + }, + "products": { + "SO4_mm" : {}, + "H_p" : {} + } + }, + { + "type" : "AQUEOUS_EQUILIBRIUM", + "aerosol phase" : "aqueous", + "aerosol-phase water" : "H2O_aq", + "A" : 1000.0, + "k_reverse" : 5.0e10, + "ion pair" : "H-HSO4", + "reactants" : { + "H2SO4_aq" : {} + }, + "products" : { + "HSO4_m" : {}, + "H_p" : {} + } + }, + { + "type" : "AQUEOUS_EQUILIBRIUM", + "aerosol phase" : "aqueous", + "aerosol-phase water" : "H2O_aq", + "A" : 3.17e-7, + "C" : -560.0, + "k_reverse" : 3.4e10, + "ion pair" : "NH4/H", + "reactants" : { + "NH3_aq" : {}, + "H2O_aq" : {} + }, + "products" : { + "NH4_p" : {}, + "OH_m" : {} + } + }, + { + "type" : "AQUEOUS_EQUILIBRIUM", + "aerosol phase" : "aqueous", + "aerosol-phase water" : "H2O_aq", + "A" : 22.0, + "C" : 1800.0, + "k_reverse" : 5.0e10, + "ion pair" : "H-NO3", + "reactants" : { + "HNO3_aq" : {} + }, + "products" : { + "NO3_m" : {}, + "H_p" : {} + } + } + ] + } + ] +} diff --git a/examples/monarch_mod37/inorganic_species.json b/examples/monarch_mod37/inorganic_species.json new file mode 100644 index 00000000..99398023 --- /dev/null +++ b/examples/monarch_mod37/inorganic_species.json @@ -0,0 +1,205 @@ +{ + "description" : [ + "These aerosol species and ion pairs are needed for the MONARCH 'mod37' configuration", + "Densities are taken from Spada et al. (2015) manuscript - ", + "'Global Aerosols in the online multiscale NMMB/BSC Chemical Transport Model", + "or estimated from bulk densities.", + "N* and diffusion coefficients are from CAMPRAM 2.4", + "TODO check about molecular weights" + ], + "pmc-data" : [ + { + "name" : "SULF", + "type" : "CHEM_SPEC", + "inorg note" : "using diffusion coefficient from dry dep", + "N star" : 1.83, + "molecular weight [kg mol-1]" : 0.098079 + }, + { + "name" : "HNO3", + "type" : "CHEM_SPEC", + "inorg note" : "using diffusion coefficient from dry dep", + "N star" : 1.94, + "molecular weight [kg mol-1]" : 0.06301 + }, + { + "name" : "NH3", + "type" : "CHEM_SPEC", + "inorg note" : "using diffusion coefficient from dry dep", + "N star" : 1.92, + "molecular weight [kg mol-1]" : 0.017031 + }, + { + "name" : "H2O_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "tracer type" : "CONSTANT", + "absolute integration tolerance" : 1.0E-05, + "density [kg m-3]" : 1000.0, + "molecular weight [kg mol-1]" : 0.01801528, + "decscription" : "aerosol-phase water", + "PartMC name" : "H2O", + "num_ions" : 0, + "kappa" : 0 + }, + { + "name" : "H_p", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "charge" : 1, + "density [kg m-3]" : 1000.0, + "molecular weight [kg mol-1]" : 0.001008, + "description" : "hydronium ion", + "num_ions" : 1, + "kappa" : 0 + }, + { + "name" : "OH_m", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "charge" : -1, + "density [kg m-3]" : 1000.0, + "molecular weight [kg mol-1]" : 0.017008, + "description" : "hydroxide ion", + "num_ions" : 1, + "kappa" : 0 + }, + { + "name" : "H2SO4_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "density [kg m-3]" : 1840.0, + "molecular weight [kg mol-1]" : 0.098079, + "description" : "undissociated aqueous-phase sulfuric acid", + "num_ions" : 0, + "kappa" : 0.65 + }, + { + "name" : "SO4_mm", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "charge" : -2, + "density [kg m-3]" : 1840.0, + "molecular weight [kg mol-1]" : 0.096063, + "description" : "sulfate ion", + "num_ions" : 2, + "kappa" : 0 + }, + { + "name" : "HSO4_m", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "charge" : -1, + "density [kg m-3]" : 1840.0, + "molecular weight [kg mol-1]" : 0.097069, + "description" : "bisulfate ion", + "num_ions" : 1, + "kappa" : 0 + }, + { + "name" : "HNO3_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "density [kg m-3]" : 1510.0, + "molecular weight [kg mol-1]" : 0.0630129, + "description" : "undissociated aqueous-phase nitric acid", + "num_ions" : 0, + "kappa" : 0.65 + }, + { + "name" : "NO3_m", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "charge" : -1, + "density [kg m-3]" : 1510.0, + "molecular weight [kg mol-1]" : 0.0620049, + "description" : "nitrate ion", + "num_ions" : 1, + "kappa" : 0 + }, + { + "name" : "NH3_aq", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "density [kg m-3]" : 880.0, + "molecular weight [kg mol-1]" : 0.017031, + "description" : "aqueous ammonia (neutral)", + "num_ions" : 0, + "kappa" : 0.65 + }, + { + "name" : "NH4_p", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-05, + "charge": 1, + "density [kg m-3]" : 880.0, + "molecular weight [kg mol-1]" : 0.018039, + "description" : "ammonium ion", + "num_ions" : 1, + "kappa" : 0 + }, + { + "name" : "(NH4)2-SO4", + "type" : "CHEM_SPEC", + "tracer type" : "ION_PAIR", + "ions" : { + "NH4_p" : { "qty" : 2 }, + "SO4_mm" : {} + } + }, + { + "name" : "NH4-NO3", + "type" : "CHEM_SPEC", + "tracer type" : "ION_PAIR", + "ions" : { + "NH4_p" : {}, + "NO3_m" : {} + } + }, + { + "name" : "H-NO3", + "type" : "CHEM_SPEC", + "tracer type" : "ION_PAIR", + "ions" : { + "H_p" : {}, + "NO3_m" : {} + } + }, + { + "name" : "H2-SO4", + "type" : "CHEM_SPEC", + "tracer type" : "ION_PAIR", + "ions" : { + "H_p" : { "qty" : 2 }, + "SO4_mm" : {} + } + }, + { + "name" : "H-HSO4", + "type" : "CHEM_SPEC", + "tracer type" : "ION_PAIR", + "ions" : { + "H_p" : {}, + "HSO4_m" : {} + } + }, + { + "name" : "NH4/H", + "type" : "CHEM_SPEC", + "tracer type" : "ION_PAIR", + "ions" : { + "NH4_p" : {}, + "OH_m" : {} + } + } + ] +} diff --git a/examples/monarch_mod37/partitioning_species_params.json b/examples/monarch_mod37/partitioning_species_params.json new file mode 100644 index 00000000..f014169a --- /dev/null +++ b/examples/monarch_mod37/partitioning_species_params.json @@ -0,0 +1,410 @@ +{ + "description" : [ + "Dry deposition reactions and species properties", + "TODO Consider updating diffusion coefficients according to Tang et al. Atmos. Chem. Phys., 14, 9233-9247 (2014)", + " available at https://www.atmos-chem-phys.net/14/9233/2014/acp-14-9233-2014.pdf" + ], + "camp-data" : [ + { + "name" : "NO2", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :6.316E-08, + "HLC exp factor [K]" :2.500E+03, + "dry dep reactivity factor [unitless]" :1.000E-01, + "diffusion coeff [m2 s-1]" :1.470E-05, + "dry dep notes" : [ + "HLC seems to be on the low end of measured values", + "(https://webbook.nist.gov/cgi/cbook.cgi?ID=C10102440&Mask=10)" + ] + }, + { + "name" : "NO", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.875E-08, + "HLC exp factor [K]" :1.480E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.830E-05 + }, + { + "name" : "O3", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.115E-07, + "HLC exp factor [K]" :2.300E+03, + "dry dep reactivity factor [unitless]" :1.000E+00, + "diffusion coeff [m2 s-1]" :1.750E-05 + }, + { + "name" : "NO3", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.480E-04, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :1.000E+00, + "diffusion coeff [m2 s-1]" :1.270E-05, + "dry dep notes" : [ + "HLC seems to be on the high end of measured values", + "(https://webbook.nist.gov/cgi/cbook.cgi?ID=C12033497&Units=SI&Mask=10#Solubility)" + ] + }, + { + "name" : "N2O5", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :9.869E+04, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :1.000E+00, + "diffusion coeff [m2 s-1]" :1.100E-05 + }, + { + "name" : "HNO3", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :0.98692, + "HLC exp factor [K]" :8.684E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.260E-05, + "dry dep notes" : [ + "Original HLC(298K)=2.69e13 (M atm-1) is orders of magnitude higher that nist values (~1e5); exp factor ok", + "https://webbook.nist.gov/cgi/cbook.cgi?ID=C7697372&Units=SI&Mask=10#Solubility", + "switched to nist value" + ] + }, + { + "name" : "HCL", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :0.98692, + "HLC exp factor [K]" :8.684E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.260E-05, + "dry dep notes" : [ + "Using parameters from HNO3" + ] + }, + { + "name" : "SULF", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :9.8692e5, + "HLC exp factor [K]" :8.684E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.260E-05, + "dry dep notes" : [ + "using HLC from nist (https://webbook.nist.gov/cgi/cbook.cgi?ID=C7664939&Units=SI&Mask=10#Solubility)" + ] + }, + { + "name" : "HONO", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :3.425E+00, + "HLC exp factor [K]" :3.775E+03, + "dry dep reactivity factor [unitless]" :1.000E-01, + "diffusion coeff [m2 s-1]" :1.530E-05 + }, + { + "name" : "PNA", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.974E+08, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :1.000E-01, + "diffusion coeff [m2 s-1]" :1.130E-05 + }, + { + "name" : "H2O2", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :7.353E-01, + "HLC exp factor [K]" :6.615E+03, + "dry dep reactivity factor [unitless]" :1.000E+00, + "diffusion coeff [m2 s-1]" :1.710E-05 + }, + { + "name" : "NTR", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.115E-05, + "HLC exp factor [K]" :5.487E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :9.200E-06 + }, + { + "name" : "ROOH", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.658E+01, + "HLC exp factor [K]" :1.024E+04, + "dry dep reactivity factor [unitless]" :1.000E-01, + "diffusion coeff [m2 s-1]" :1.270E-05 + }, + { + "name" : "FORM", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :2.931E-02, + "HLC exp factor [K]" :7.190E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.830E-05 + }, + { + "name" : "MEOH", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :2.931E-02, + "HLC exp factor [K]" :7.190E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.830E-05, + "dry dep notes" : [ + "Using values from FORM" + ] + }, + { + "name" : "ETOH", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :2.931E-02, + "HLC exp factor [K]" :7.190E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.830E-05, + "dry dep notes" : [ + "Using values from FORM" + ] + }, + { + "name" : "ALD2", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.125E-04, + "HLC exp factor [K]" :6.266E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.510E-05 + }, + { + "name" : "ALDX", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.125E-04, + "HLC exp factor [K]" :6.266E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.510E-05 + }, + { + "name" : "PAR", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.115E-08, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.180E-05 + }, + { + "name" : "CO", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :8.093E-08, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.890E-05 + }, + { + "name" : "MEPX", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :2.181E-03, + "HLC exp factor [K]" :5.607E+03, + "dry dep reactivity factor [unitless]" :1.000E-01, + "diffusion coeff [m2 s-1]" :1.440E-05 + }, + { + "name" : "FACD", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :9.721E+01, + "HLC exp factor [K]" :5.716E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.530E-05 + }, + { + "name" : "PAN", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :2.931E-05, + "HLC exp factor [K]" :5.760E+03, + "dry dep reactivity factor [unitless]" :1.000E-01, + "diffusion coeff [m2 s-1]" :9.100E-06 + }, + { + "name" : "PANX", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :2.931E-05, + "HLC exp factor [K]" :5.760E+03, + "dry dep reactivity factor [unitless]" :1.000E-01, + "diffusion coeff [m2 s-1]" :9.100E-06, + "dry dep notes" : [ + "Using values from PAN" + ] + }, + { + "name" : "PACD", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :4.668E-03, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :1.000E-01, + "diffusion coeff [m2 s-1]" :1.150E-05 + }, + { + "name" : "AACD", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :9.504E+00, + "HLC exp factor [K]" :8.374E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.240E-05 + }, + { + "name" : "OLE", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :4.698E-08, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.540E-05 + }, + { + "name" : "ETH", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :4.609E-08, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.890E-05 + }, + { + "name" : "IOLE", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.332E-08, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.210E-05 + }, + { + "name" : "TOL", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.490E-06, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.040E-05 + }, + { + "name" : "CRES", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :3.948E+00, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :9.600E-06 + }, + { + "name" : "MGLY", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :3.661E-02, + "HLC exp factor [K]" :7.541E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.180E-05 + }, + { + "name" : "XYL", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.431E-06, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :9.700E-06 + }, + { + "name" : "OPEN", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.431E-06, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :9.700E-06, + "dry dep notes" : [ + "Using values from XYL" + ] + }, + { + "name" : "ISOP", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :4.698E-08, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.210E-05 + }, + { + "name" : "TERP", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :4.698E-08, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.210E-05, + "dry dep notes" : [ + "Using values from ISOP" + ] + }, + { + "name" : "ISPD", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :4.698E-08, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.210E-05 + }, + { + "name" : "SO2", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :2.497E+00, + "HLC exp factor [K]" :5.816E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.260E-05, + "special dry deposition species" : "SO2" + }, + { + "name" : "ETHA", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.974E-08, + "HLC exp factor [K]" :0.000E+00, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.830E-05 + }, + { + "name" : "NH3", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :1.026E-01, + "HLC exp factor [K]" :3.660E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :2.270E-05, + "special dry deposition species" : "NH3" + }, + { + "name" : "ISOP-P1", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :9.721E+01, + "HLC exp factor [K]" :5.716E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.530E-05 + }, + { + "name" : "ISOP-P2", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :9.721E+01, + "HLC exp factor [K]" :5.716E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.530E-05, + "dry dep notes" : "changed diff coeff from 0.0 to match ISOP-P1" + }, + { + "name" : "TERP-P1", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :9.721E+01, + "HLC exp factor [K]" :5.716E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.530E-05 + }, + { + "name" : "TERP-P2", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" :9.721E+01, + "HLC exp factor [K]" :5.716E+03, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :1.530E-05, + "dry dep notes" : "changed diff coeff from 0.0 to match ISOP-P2" + }, + { + "name" : "DMS", + "type" : "CHEM_SPEC", + "HLC(298K) [M Pa-1]" : 5.59585E-06, + "HLC exp factor [K]" : 3500.0, + "dry dep reactivity factor [unitless]" :0.000E+00, + "diffusion coeff [m2 s-1]" :9.900E-03, + "dry dep notes" : [ + "got HLC params from nist webbook https://webbook.nist.gov/cgi/cbook.cgi?ID=C75183&Mask=10#Solubility" + ] + } + ] +} diff --git a/examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json b/examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json new file mode 100644 index 00000000..9bf99abb --- /dev/null +++ b/examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json @@ -0,0 +1,93 @@ +{ + "notes" : [ + "2-product SOA scheme from MONARCH model. Based on Tsigaridis and Kanakidou (2007).", + "Details in Spada et al. (2013) in prep for Geosci. Model Dev.", + "Gas-phase rate constants taken from CB05 reactions with same reactants", + "TODO the CB05 reactions should be updated/removed to avoid competition with SOA scheme", + "Clausius clapyron parameters (C* and -dH/R) converted to SIMPOL.1 paramaters" + ], + "camp-data" : [ + { + "name" : "MONARCH mod37", + "type" : "MECHANISM", + "reactions" : [ + { + "type" : "ARRHENIUS", + "reactants" : { + "OH" : {}, + "ISOP" : {} + }, + "products" : { + "ISOP-P1" : { "yield" : 0.192 } + }, + "A" : 2.54e-11, + "C" : 407.6 + }, + { + "type" : "ARRHENIUS", + "reactants" : { + "O3" : {}, + "ISOP" : {} + }, + "products" : { + "ISOP-P2" : { "yield" : 0.215 } + }, + "A" : 7.86e-15, + "C" : -1912.0 + }, + { + "type" : "ARRHENIUS", + "reactants" : { + "OH" : {}, + "TERP": {} + }, + "products" : { + "TERP-P1" : { "yield" : 0.0288 } + }, + "A" : 1.5e-11, + "C" : 449.0 + }, + { + "type" : "ARRHENIUS", + "reactants" : { + "O3" : {}, + "TERP" : {} + }, + "products" : { + "TERP-P2" : { "yield" : 0.232 } + }, + "A" : 1.2e-15, + "C" : -821.0 + }, + { + "type" : "SIMPOL_PHASE_TRANSFER", + "gas-phase species" : "ISOP-P1", + "aerosol phase" : "organic_matter", + "aerosol-phase species" : "ISOP-P1_aero", + "B" : [ 3.81e3, -2.13e1, 0.0, 0.0 ] + }, + { + "type" : "SIMPOL_PHASE_TRANSFER", + "gas-phase species" : "ISOP-P2", + "aerosol phase" : "organic_matter", + "aerosol-phase species" : "ISOP-P2_aero", + "B" : [ 3.81e3, -2.09e1, 0.0, 0.0 ] + }, + { + "type" : "SIMPOL_PHASE_TRANSFER", + "gas-phase species" : "TERP-P1", + "aerosol phase" : "organic_matter", + "aerosol-phase species" : "TERP-P1_aero", + "B" : [ 2.19e3, -1.75e1, 0.0, 0.0 ] + }, + { + "type" : "SIMPOL_PHASE_TRANSFER", + "gas-phase species" : "TERP-P2", + "aerosol phase" : "organic_matter", + "aerosol-phase species" : "TERP-P2_aero", + "B" : [ 2.19e3, -1.53e1, 0.0, 0.0 ] + } + ] + } + ] +} diff --git a/examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json b/examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json new file mode 100644 index 00000000..e850cb5c --- /dev/null +++ b/examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json @@ -0,0 +1,125 @@ +{ + "description" : [ + "These species needed for the 2 product SOA scheme", + "(see mechanism.json for details)" + ], + "camp-data" : [ + { + "name" : "ISOP-P1", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-12, + "molecular weight [kg mol-1]" : 0.08806, + "description" : "gas-phase product from isoprene oxidation by OH", + "notes" : [ + "using diffusion coefficient from dry deposition", + "see notes on ISOP-P1_aero species" + ] + }, + { + "name" : "ISOP-P2", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-12, + "molecular weight [kg mol-1]" : 0.09003, + "description" : "gas-phase product from isoprene oxidation by O3", + "notes" : [ + "using diffusion coefficient from dry deposition", + "see notes on ISOP-P2_aero species" + ] + }, + { + "name" : "TERP-P1", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-12, + "molecular weight [kg mol-1]" : 0.17025, + "description" : "gas-phase product from monoterpene oxidation by OH", + "notes" : [ + "using diffusion coefficient from dry deposition", + "see notes on TERP-P1_aero species" + ] + }, + { + "name" : "TERP-P2", + "type" : "CHEM_SPEC", + "absolute integration tolerance" : 1.0E-12, + "molecular weight [kg mol-1]" : 0.202162, + "description" : "gas-phase product from monoterpene oxidation by O3", + "notes" : [ + "using diffusion coefficient from dry deposition", + "see notes on TERP-P2_aero species" + ] + }, + { + "name" : "POA", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-12, + "density [kg m-3]" : 1800.0, + "molecular weight [kg mol-1]" : 0.41475, + "description" : "lumped hydrophobic particulate matter", + "num_ions" : 0, + "kappa" : 0.0, + "note" : "Using C30H54 for molecular weight. TODO find best surrogate" + }, + { + "name" : "ISOP-P1_aero", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-12, + "density [kg m-3]" : 1800.0, + "molecular weight [kg mol-1]" : 0.08806, + "description" : "First isoprene SOA species in 2-product scheme", + "num_ions" : 0, + "kappa" : 0.1, + "note" : [ + "Using ketopropanoic acid for molecular weight. TODO find best surrogate", + "TODO update SIMPOL parameters based on MW of new surrogate" + ] + }, + { + "name" : "ISOP-P2_aero", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-12, + "density [kg m-3]" : 1800.0, + "molecular weight [kg mol-1]" : 0.09003, + "description" : "Second isoprene SOA species in 2-product scheme", + "num_ions" : 0, + "kappa" : 0.1, + "note" : [ + "Using oxalic acid for molecular weight. TODO find best surrogate", + "TODO update SIMPOL parameters based on MW of new surrogate" + ] + }, + { + "name" : "TERP-P1_aero", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-12, + "density [kg m-3]" : 1800.0, + "molecular weight [kg mol-1]" : 0.17025, + "description" : "First monoterpene SOA species in 2-product scheme", + "num_ions" : 0, + "kappa" : 0.1, + "note" : [ + "Using 2-hydroxy-3-isopropyl-6-methyl-cyclohexanone for molecular weight", + "TODO find best surrogate", + "TODO update SIMPOL parameters based on MW of new surrogate" + ] + }, + { + "name" : "TERP-P2_aero", + "type" : "CHEM_SPEC", + "phase" : "AEROSOL", + "absolute integration tolerance" : 1.0E-12, + "density [kg m-3]" : 1800.0, + "molecular weight [kg mol-1]" : 0.202162, + "description" : "Second monoterpene SOA species in 2-product scheme", + "num_ions" : 0, + "kappa" : 0.1, + "note" : [ + "Using 2-methyl-5-carboxy-2,4-hexodienoic acid. TODO find best surrogate", + "TODO update SIMPOL parameters based on MW of new surrogate" + ] + } + ] +} diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb new file mode 100644 index 00000000..486452e9 --- /dev/null +++ b/examples/particle_simulation_with_camp.ipynb @@ -0,0 +1,5752 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "7968866b-24b8-4ed6-bc13-6035310cb4f5", + "metadata": {}, + "source": [ + "[![View notebook](https://img.shields.io/static/v1?label=render%20on&logo=github&color=87ce3e&message=GitHub)](https://github.com/open-atmos/PyPartMC/blob/main/examples/particle_simulation.ipynb) \n", + "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PyPartMC/blob/main/examples/particle_simulation.ipynb) \n", + "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PyPartMC.git/main?urlpath=lab/tree/examples/particle_simulation.ipynb) \n", + "[![ARM JupyterHub](https://img.shields.io/static/v1?label=launch%20in&logo=jupyter&color=lightblue&message=ARM+JupyterHub)](https://jupyterhub.arm.gov/hub/user-redirect/git-pull?repo=https%3A//github.com/open-atmos/PyPartMC&branch=main&urlPath=) (requires [logging in with ARM account](https://www.arm.gov/capabilities/computing-resources) and directing Jupyter to a notebook within the cloned repo)" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "159edeb4", + "metadata": {}, + "outputs": [], + "source": [ + "# This file is a part of PyPartMC licensed under the GNU General Public License v3\n", + "# Copyright (C) 2023 University of Illinois Urbana-Champaign\n", + "# Authors:\n", + "# - https://github.com/compdyn/partmc/graphs/contributors\n", + "# - https://github.com/open-atmos/PyPartMC/graphs/contributors" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "4f8359c2", + "metadata": {}, + "outputs": [], + "source": [ + "import sys\n", + "import os\n", + "if 'google.colab' in sys.modules:\n", + " !pip --quiet install open-atmos-jupyter-utils\n", + " from open_atmos_jupyter_utils import pip_install_on_colab\n", + " pip_install_on_colab('PyPartMC')\n", + "elif 'JUPYTER_IMAGE' in os.environ and '.arm.gov' in os.environ['JUPYTER_IMAGE']:\n", + " !pip --quiet install PyPartMC open_atmos_jupyter_utils\n", + " _pypartmc_path = !pip show PyPartMC | fgrep Location | cut -f2 -d' '\n", + " sys.path.extend(_pypartmc_path if _pypartmc_path[0] not in sys.path else [])" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "b494ea6e", + "metadata": {}, + "outputs": [], + "source": [ + "import numpy as np\n", + "import matplotlib.pyplot as plt\n", + "import matplotlib\n", + "from open_atmos_jupyter_utils import show_plot\n", + "import PyPartMC as ppmc\n", + "from PyPartMC import si" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "a2d7bad8", + "metadata": {}, + "outputs": [], + "source": [ + "env_state = ppmc.EnvState(\n", + " {\n", + " \"rel_humidity\": 0.0,\n", + " \"latitude\": 0,\n", + " \"longitude\": 0,\n", + " \"altitude\": 0 * si.m,\n", + " \"start_time\": 21600 * si.s,\n", + " \"start_day\": 200,\n", + " }\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "de15cde5", + "metadata": {}, + "outputs": [], + "source": [ + "camp_core = ppmc.CampCore(\"config.json\")\n", + "photolysis = ppmc.Photolysis(camp_core)" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "6de20b3f", + "metadata": {}, + "outputs": [], + "source": [ + "gas_data = ppmc.GasData(camp_core)\n", + "aero_data = ppmc.AeroData(camp_core)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "c822823d", + "metadata": {}, + "outputs": [], + "source": [ + "gas_state = ppmc.GasState(gas_data)\n", + "\n", + "input_gas_state = (\n", + " {\"NO\": [0.1E+00]},\n", + " {\"NO2\": [1.0E+00]},\n", + " {\"O3\": [5.0E+01]},\n", + " {\"H2O2\": [1.1E+00]},\n", + " {\"CO\": [2.1E+02]},\n", + " {\"SO2\": [0.8E+00]},\n", + " {\"NH3\": [0.5E+00]},\n", + " {\"HCL\": [0.7E+00]},\n", + " {\"CH4\": [2.2E+03]},\n", + " {\"ETHA\": [1.0E+00]},\n", + " {\"FORM\": [1.2E+00]},\n", + " {\"MEOH\": [1.2E-01]},\n", + " {\"MEPX\": [0.5E+00]},\n", + " {\"ALD2\": [1.0E+00]},\n", + " {\"PAR\": [2.0E+00]},\n", + " {\"ETH\": [0.2E+00]},\n", + " {\"OLE\": [2.3E-02]},\n", + " {\"IOLE\": [3.1E-04]},\n", + " {\"TOL\": [0.1E+00]},\n", + " {\"XYL\": [0.1E+00]},\n", + " {\"NTR\": [0.1E+00]},\n", + " {\"PAN\": [0.8E+00]},\n", + " {\"AACD\": [0.2E+00]},\n", + " {\"ROOH\": [2.5E-02]},\n", + " {\"ISOP\": [5.0E+00]},\n", + " {\"O2\": [2.095E+08]},\n", + " {\"N2\": [7.8E+08]},\n", + " {\"H2\": [5.6E+02]},\n", + " {\"M\": [1.0E+09]}\n", + " )\n", + "\n", + "gas_state.mix_rats = input_gas_state" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "58706963", + "metadata": {}, + "outputs": [], + "source": [ + "times = [0 * si.s]\n", + "back_gas = [{\"time\": times},\n", + " {\"rate\": [0 / si.s]},\n", + " {\"NO\": [0.1E+00]},\n", + " {\"NO2\": [1.0E+00]},\n", + " {\"O3\": [5.0E+01]},\n", + " {\"H2O2\": [1.1E+00]},\n", + " {\"CO\": [2.1E+02]},\n", + " {\"SO2\": [0.8E+00]},\n", + " {\"NH3\": [0.5E+00]},\n", + " {\"HCL\": [0.7E+00]},\n", + " {\"CH4\": [2.2E+03]},\n", + " {\"ETHA\": [1.0E+00]},\n", + " {\"FORM\": [1.2E+00]},\n", + " {\"MEOH\": [1.2E-01]},\n", + " {\"MEPX\": [0.5E+00]},\n", + " {\"ALD2\": [1.0E+00]},\n", + " {\"PAR\": [2.0E+00]},\n", + " {\"ETH\": [0.2E+00]},\n", + " {\"OLE\": [2.3E-02]},\n", + " {\"IOLE\": [3.1E-04]},\n", + " {\"TOL\": [0.1E+00]},\n", + " {\"XYL\": [0.1E+00]},\n", + " {\"NTR\": [0.1E+00]},\n", + " {\"PAN\": [0.8E+00]},\n", + " {\"AACD\": [0.2E+00]},\n", + " {\"ROOH\": [2.5E-02]},\n", + " {\"ISOP\": [5.0E+00]},\n", + " {\"O2\": [2.095E+08]},\n", + " {\"N2\": [7.8E+08]},\n", + " {\"H2\": [5.6E+02]},\n", + " {\"M\": [1.0E+09]}\n", + " ]\n", + "\n", + "gas_emit_times = [0, 43200]\n", + "\n", + "gas_emit_rates = np.zeros(len(gas_emit_times))\n", + "gas_emit_rates[0] = 1.0\n", + "gas_emit_rates[1] = 0.0\n", + "\n", + "SO2 = [1.06E-09, 1.06E-09]\n", + "NO2 = [7.56E-12, 7.56E-12]\n", + "NO = [1.44E-10, 1.44E-10]\n", + "CO = [1.96E-09, 1.96E-09]\n", + "ALD2 = [4.25E-12, 4.25E-12]\n", + "FORM = [1.02E-11, 1.02E-11]\n", + "ETH = [4.62E-11, 4.62E-11]\n", + "IOLE = [1.49E-11, 1.49E-11]\n", + "OLE = [1.49E-11, 1.49E-11]\n", + "TOL = [1.53E-11, 1.53E-11]\n", + "XYL = [1.40E-11, 1.40E-11]\n", + "PAR = [4.27E-10, 4.27E-10]\n", + "ISOP = [6.03E-12, 6.03E-12]\n", + "MEOH = [5.92E-13, 5.92E-13]\n", + "\n", + "emit_gas = [\n", + " {\"time\": gas_emit_times},\n", + " {\"rate\": list(gas_emit_rates)},\n", + " {\"SO2\": SO2},\n", + " {\"NO2\": NO2},\n", + " {\"NO\": NO},\n", + " {\"CO\": CO},\n", + " {\"ALD2\": ALD2},\n", + " {\"FORM\": FORM},\n", + " {\"ETH\": ETH},\n", + " {\"IOLE\": IOLE},\n", + " {\"OLE\": OLE},\n", + " {\"TOL\": TOL},\n", + " {\"XYL\": XYL},\n", + " {\"PAR\": PAR},\n", + " {\"ISOP\": ISOP},\n", + " {\"MEOH\": MEOH},\n", + "]\n", + "\n", + "AERO_DIST_BACKGROUND = {\n", + " \"back_small\": {\n", + " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", + " \"diam_type\": \"geometric\",\n", + " \"mode_type\": \"log_normal\",\n", + " \"num_conc\": 0 / si.m**3,\n", + " \"geom_mean_diam\": 0.02 * si.um,\n", + " \"log10_geom_std_dev\": 0.161,\n", + " },\n", + "}\n", + "\n", + "AERO_DIST_EMIT = {\n", + " \"gasoline\": {\n", + " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", + " \"diam_type\": \"geometric\",\n", + " \"mode_type\": \"log_normal\",\n", + " \"num_conc\": 0.0 / si.m**3,\n", + " \"geom_mean_diam\": 5e-8 * si.m,\n", + " \"log10_geom_std_dev\": 0.24,\n", + " },\n", + "}" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "c6a96b7d", + "metadata": {}, + "outputs": [], + "source": [ + "time_timeseries = [0, 86400]\n", + "pressure_timeseries = [1e5, 1e5]\n", + "temp_timeseries = [290.016, 290.016]\n", + "height_timeseries = [1.0, 1.0]" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "920e41e3", + "metadata": {}, + "outputs": [], + "source": [ + "scenario = ppmc.Scenario(\n", + " gas_data,\n", + " aero_data,\n", + " {\n", + " \"temp_profile\": [{\"time\": time_timeseries}, {\"temp\": temp_timeseries}],\n", + " \"pressure_profile\": [\n", + " {\"time\": time_timeseries},\n", + " {\"pressure\": pressure_timeseries},\n", + " ],\n", + " \"height_profile\": [{\"time\": time_timeseries}, {\"height\": height_timeseries}],\n", + " \"gas_emissions\": emit_gas,\n", + " \"gas_background\": back_gas,\n", + " \"aero_emissions\": [\n", + " {\"time\": [0 * si.s]},\n", + " {\"rate\": [0 / si.s]},\n", + " {\"dist\": [[AERO_DIST_EMIT]]},\n", + " ],\n", + " \"aero_background\": [\n", + " {\"time\": [0 * si.s]},\n", + " {\"rate\": [0 / si.s]},\n", + " {\"dist\": [[AERO_DIST_BACKGROUND]]},\n", + " ],\n", + " \"loss_function\": \"none\",\n", + " },\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "6722ba83", + "metadata": {}, + "outputs": [], + "source": [ + "T_INITIAL = 0.0\n", + "scenario.init_env_state(env_state, T_INITIAL)" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "9781ca2f", + "metadata": {}, + "outputs": [], + "source": [ + "AERO_DIST_INIT = [\n", + " {\n", + " \"init_small\": {\n", + " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", + " \"diam_type\": \"geometric\",\n", + " \"mode_type\": \"log_normal\",\n", + " \"num_conc\": 3.2e9 / si.m**3,\n", + " \"geom_mean_diam\": 2.0e-8 * si.m,\n", + " \"log10_geom_std_dev\": 0.161,\n", + " },\n", + " \"init_large\": {\n", + " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", + " \"diam_type\": \"geometric\",\n", + " \"mode_type\": \"log_normal\",\n", + " \"num_conc\": 2.9e9 / si.m**3,\n", + " \"geom_mean_diam\": 1.16e-7 * si.m,\n", + " \"log10_geom_std_dev\": 0.217,\n", + " },\n", + " \"init_coarse\": {\n", + " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", + " \"diam_type\": \"geometric\",\n", + " \"mode_type\": \"log_normal\",\n", + " \"num_conc\": 0.3e6 / si.m**3,\n", + " \"geom_mean_diam\": 1.8e-6 * si.m,\n", + " \"log10_geom_std_dev\": 0.38021124171160603,\n", + " }\n", + " }\n", + "]\n", + "\n", + "aero_dist_init = ppmc.AeroDist(aero_data, AERO_DIST_INIT)" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "d8d9c8fd", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "593" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "run_part_opt = ppmc.RunPartOpt(\n", + " {\n", + " \"output_prefix\": \"urban_plume\",\n", + " \"do_coagulation\": False,\n", + " \"t_max\": 86400 * si.s,\n", + " \"del_t\": 6 * si.s,\n", + " \"do_camp_chem\": True,\n", + " }\n", + ")\n", + "\n", + "N_PART = 1000\n", + "aero_state = ppmc.AeroState(aero_data, N_PART, 'nummass_source', camp_core)\n", + "aero_state.dist_sample(\n", + " aero_dist_init,\n", + " sample_prop=1.0,\n", + " create_time=0.0,\n", + " allow_doubling=True,\n", + " allow_halving=True,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "0f7c29fe", + "metadata": {}, + "outputs": [], + "source": [ + "N_STEPS = int(run_part_opt.t_max / run_part_opt.del_t)\n", + "num_conc = np.zeros(N_STEPS + 1)\n", + "num_conc[0] = aero_state.total_num_conc\n", + "mass_conc = np.zeros(N_STEPS + 1)\n", + "mass_conc[0] = aero_state.total_mass_conc\n", + "time = np.zeros(N_STEPS + 1)\n", + "gas_mix_rat = np.zeros((N_STEPS + 1, gas_state.n_spec))\n", + "gas_mix_rat[0, :] = gas_state.mix_rats\n", + "\n", + "height = np.zeros((N_STEPS + 1))\n", + "temperature = np.zeros((N_STEPS + 1))\n", + "rh = np.zeros((N_STEPS + 1))\n", + "\n", + "height[0] = env_state.height\n", + "temperature[0] = env_state.temp\n", + "rh[0] = env_state.rh\n", + "\n", + "diam_grid = ppmc.BinGrid(30, \"log\", 1e-9, 1e-5)\n", + "dists = []\n", + "dry_diameters = aero_state.dry_diameters\n", + "num_concs = aero_state.num_concs\n", + "dists.append(ppmc.histogram_1d(diam_grid, dry_diameters, num_concs))\n", + "\n", + "last_output_time = 0.\n", + "last_progress_time = 0.\n", + "i_output = 1\n", + "\n", + "for i_time in range(1,N_STEPS + 1):\n", + " (last_output_time, last_progress_time, i_output) = ppmc.run_part_timestep(\n", + " scenario,\n", + " env_state,\n", + " aero_data,\n", + " aero_state,\n", + " gas_data,\n", + " gas_state,\n", + " run_part_opt,\n", + " camp_core,\n", + " photolysis,\n", + " i_time,\n", + " T_INITIAL,\n", + " last_output_time,\n", + " last_progress_time,\n", + " i_output\n", + " )\n", + " num_conc[i_time] = aero_state.total_num_conc\n", + " mass_conc[i_time] = aero_state.total_mass_conc\n", + " time[i_time] = env_state.elapsed_time\n", + " gas_mix_rat[i_time, :] = gas_state.mix_rats\n", + " height[i_time] = env_state.height\n", + " temperature[i_time] = env_state.temp\n", + " rh[i_time] = env_state.rh\n", + " if np.mod(i_time * run_part_opt.del_t, 3600.0) == 0:\n", + " dry_diameters = aero_state.dry_diameters\n", + " num_concs = aero_state.num_concs\n", + " dists.append(ppmc.histogram_1d(diam_grid, dry_diameters, num_concs))" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "82c0cebb", + "metadata": {}, + "outputs": [], + "source": [ + "plt.rcParams.update({'font.size': 9})\n", + "plt.rcParams.update({'figure.figsize': (3.08,2.5)})\n", + "plt.rcParams.update({\"axes.grid\" : True})" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "47474cd3", + "metadata": { + "scrolled": false + }, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " 2024-07-02T17:48:30.514766\n", + " image/svg+xml\n", + " \n", + " \n", + " Matplotlib v3.7.1, 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\")" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "plt.plot(time,temperature,'r')\n", + "plt.ylabel('Temperature (K)', color='r')\n", + "plt.ylim([275,300])\n", + "plt.xticks(np.linspace(0, time[-1], 5))\n", + "plt.xlim([0,time[-1]])\n", + "plt.xlabel('Time (s)')\n", + "plt.twinx()\n", + "plt.plot(time,rh*100,'g')\n", + "plt.ylabel('Relative humidity (%)', color='g')\n", + "plt.ylim([0,100])\n", + "show_plot()" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "c85a622a", + "metadata": {}, + "outputs": [], + "source": [ + "def set_tickmarks(axes, n_ticks):\n", + " ylims = axes.get_ylim()\n", + " if np.log10(ylims[0]) > 1:\n", + " val = -int(np.ceil(np.abs(np.log10(ylims[0])))) + 1\n", + " else:\n", + " val = int(np.ceil(np.abs(np.log10(ylims[0])))) + 1 \n", + " ymin = round(ylims[0] - .1 * ylims[0], val)\n", + " ymax = round(ylims[1] + .1 * ylims[1], val)\n", + " plt.ylim([ymin, ymax])\n", + " plt.yticks(np.linspace(ymin, ymax, 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"text/plain": [ + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "48fb592ff4ff4877b37d79801c3b921d", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "HTML(value=\"./tmp5ru7jh17.pdf
\")" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "plt.plot(diam_grid.centers, dists[0],label='$t = 0$ h')\n", + "plt.plot(diam_grid.centers, dists[6],label='$t = 6$ h')\n", + "plt.plot(diam_grid.centers, dists[12],label='$t = 12$ h')\n", + "plt.plot(diam_grid.centers, dists[24],label='$t = 24$ h')\n", + "plt.xscale(\"log\")\n", + "plt.xlabel(\"Dry diameter (m)\")\n", + "plt.ylabel(r\"Number concentration $n(D)$ ($\\#$ m$^{-3}$)\")\n", + "plt.ylim(bottom=0)\n", + "plt.legend()\n", + "plt.xlim([diam_grid.edges[0],diam_grid.edges[-1]])\n", + "show_plot()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a07540c5", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.3" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From a5820550db980a85a25aa02f0609d9d5a52c2c39 Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Sun, 25 Aug 2024 21:43:18 -0500 Subject: [PATCH 04/26] add missing camp_core --- src/photolysis.hpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/photolysis.hpp b/src/photolysis.hpp index d1d9e4a2..54fa830e 100644 --- a/src/photolysis.hpp +++ b/src/photolysis.hpp @@ -8,6 +8,7 @@ #include "json_resource.hpp" #include "pmc_resource.hpp" +#include "camp_core.hpp" extern "C" void f_photolysis_ctor(void *ptr) noexcept; extern "C" void f_photolysis_dtor(void *ptr) noexcept; From 36eccb33f74db73e13d06e6052572d4dcae4e651 Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Tue, 10 Sep 2024 14:31:35 -0500 Subject: [PATCH 05/26] update camp notebook. remove a few json files --- examples/aerosol_representation.json | 9 - examples/config.json | 14 - examples/particle_simulation_with_camp.ipynb | 1343 +++++++++--------- 3 files changed, 673 insertions(+), 693 deletions(-) delete mode 100644 examples/aerosol_representation.json delete mode 100644 examples/config.json diff --git a/examples/aerosol_representation.json b/examples/aerosol_representation.json deleted file mode 100644 index 15eba0f7..00000000 --- a/examples/aerosol_representation.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "camp-data" : [ - { - "name" : "PartMC single particle", - "type" : "AERO_REP_SINGLE_PARTICLE", - "maximum computational particles" : 1050 - } - ] -} diff --git a/examples/config.json b/examples/config.json deleted file mode 100644 index df667d7d..00000000 --- a/examples/config.json +++ /dev/null @@ -1,14 +0,0 @@ -{ - "camp-files" : [ - "aerosol_representation.json", - "monarch_mod37/aerosol_phases.json", - "monarch_mod37/cb05_abs_tol.json", - "monarch_mod37/cb05_mechanism_without_R142_R143.json", - "monarch_mod37/cb05_species.json", - "monarch_mod37/custom_species.json", - "monarch_mod37/partitioning_species_params.json", - "monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json", - "monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json" - ] -} - diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index 486452e9..64661ee2 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -5,9 +5,9 @@ "id": "7968866b-24b8-4ed6-bc13-6035310cb4f5", "metadata": {}, "source": [ - "[![View notebook](https://img.shields.io/static/v1?label=render%20on&logo=github&color=87ce3e&message=GitHub)](https://github.com/open-atmos/PyPartMC/blob/main/examples/particle_simulation.ipynb) \n", - "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PyPartMC/blob/main/examples/particle_simulation.ipynb) \n", - "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PyPartMC.git/main?urlpath=lab/tree/examples/particle_simulation.ipynb) \n", + "[![View notebook](https://img.shields.io/static/v1?label=render%20on&logo=github&color=87ce3e&message=GitHub)](https://github.com/open-atmos/PyPartMC/blob/main/examples/particle_simulation_with_camp.ipynb) \n", + "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PyPartMC/blob/main/examples/particle_simulation_with_camp.ipynb) \n", + "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PyPartMC.git/main?urlpath=lab/tree/examples/particle_simulation_with_camp.ipynb) \n", "[![ARM JupyterHub](https://img.shields.io/static/v1?label=launch%20in&logo=jupyter&color=lightblue&message=ARM+JupyterHub)](https://jupyterhub.arm.gov/hub/user-redirect/git-pull?repo=https%3A//github.com/open-atmos/PyPartMC&branch=main&urlPath=) (requires [logging in with ARM account](https://www.arm.gov/capabilities/computing-resources) and directing Jupyter to a notebook within the cloned repo)" ] }, @@ -19,7 +19,7 @@ "outputs": [], "source": [ "# This file is a part of PyPartMC licensed under the GNU General Public License v3\n", - "# Copyright (C) 2023 University of Illinois Urbana-Champaign\n", + "# Copyright (C) 2024 University of Illinois Urbana-Champaign\n", "# Authors:\n", "# - https://github.com/compdyn/partmc/graphs/contributors\n", "# - https://github.com/open-atmos/PyPartMC/graphs/contributors" @@ -56,12 +56,23 @@ "import matplotlib\n", "from open_atmos_jupyter_utils import show_plot\n", "import PyPartMC as ppmc\n", - "from PyPartMC import si" + "from PyPartMC import si\n", + "import json" ] }, { "cell_type": "code", "execution_count": 4, + "id": "b480e7ad", + "metadata": {}, + "outputs": [], + "source": [ + "N_PART = 100" + ] + }, + { + "cell_type": "code", + "execution_count": 5, "id": "a2d7bad8", "metadata": {}, "outputs": [], @@ -80,7 +91,53 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 6, + "id": "16377896", + "metadata": {}, + "outputs": [], + "source": [ + "camp_config = {\n", + " \"camp-files\" : [\n", + " \"aerosol_representation.json\",\n", + " \"monarch_mod37/aerosol_phases.json\",\n", + " \"monarch_mod37/cb05_abs_tol.json\",\n", + " \"monarch_mod37/cb05_mechanism_without_R142_R143.json\",\n", + " \"monarch_mod37/cb05_species.json\",\n", + " \"monarch_mod37/custom_species.json\",\n", + " \"monarch_mod37/partitioning_species_params.json\",\n", + " \"monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json\",\n", + " \"monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json\"\n", + " ]\n", + "}\n", + "\n", + "with open('config.json', 'w') as f:\n", + " json.dump(camp_config, f, indent=4)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "5e4e5c4b", + "metadata": {}, + "outputs": [], + "source": [ + "aerosol_rep = {\n", + " \"camp-data\" : [\n", + " {\n", + " \"name\" : \"PartMC single particle\",\n", + " \"type\" : \"AERO_REP_SINGLE_PARTICLE\",\n", + " \"maximum computational particles\" : N_PART*2\n", + " }\n", + " ]\n", + "}\n", + "\n", + "with open('aerosol_representation.json', 'w') as f:\n", + " json.dump(aerosol_rep, f, indent=4)" + ] + }, + { + "cell_type": "code", + "execution_count": 8, "id": "de15cde5", "metadata": {}, "outputs": [], @@ -91,7 +148,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 9, "id": "6de20b3f", "metadata": {}, "outputs": [], @@ -102,7 +159,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 10, "id": "c822823d", "metadata": {}, "outputs": [], @@ -146,7 +203,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 11, "id": "58706963", "metadata": {}, "outputs": [], @@ -250,7 +307,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 12, "id": "c6a96b7d", "metadata": {}, "outputs": [], @@ -263,7 +320,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 13, "id": "920e41e3", "metadata": {}, "outputs": [], @@ -297,7 +354,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 14, "id": "6722ba83", "metadata": {}, "outputs": [], @@ -308,7 +365,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 15, "id": "9781ca2f", "metadata": {}, "outputs": [], @@ -347,17 +404,17 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 16, "id": "d8d9c8fd", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "593" + "65" ] }, - "execution_count": 13, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -373,7 +430,6 @@ " }\n", ")\n", "\n", - "N_PART = 1000\n", "aero_state = ppmc.AeroState(aero_data, N_PART, 'nummass_source', camp_core)\n", "aero_state.dist_sample(\n", " aero_dist_init,\n", @@ -386,7 +442,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 17, "id": "0f7c29fe", "metadata": {}, "outputs": [], @@ -450,7 +506,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 18, "id": "82c0cebb", "metadata": {}, "outputs": [], @@ -462,7 +518,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 19, "id": "47474cd3", "metadata": { "scrolled": false @@ -479,7 +535,7 @@ " \n", " \n", " \n", - " 2024-07-02T17:48:30.514766\n", + " 2024-09-10T14:13:00.661525\n", " image/svg+xml\n", " \n", " \n", @@ -515,16 +571,16 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -561,11 +617,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -653,11 +709,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -728,11 +784,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -791,11 +847,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -967,16 +1023,16 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1029,11 +1085,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1049,11 +1105,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1069,11 +1125,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1121,11 +1177,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1141,11 +1197,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1317,7 +1373,7 @@ " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #ff0000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1369,11 +1425,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1388,11 +1444,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1407,11 +1463,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1426,11 +1482,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1445,11 +1501,11 @@ " \n", " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1648,7 +1704,7 @@ " \n", + "\" clip-path=\"url(#p53e9eb3eef)\" style=\"fill: none; stroke: #008000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1689,12 +1745,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "b047c29cd1b44b019157f4786e476570", + "model_id": "c22b3b352a134854bed3d588918537f4", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmpoc32_r9j.pdf
\")" + "HTML(value=\"./tmpzcj9aeu_.pdf
\")" ] }, "metadata": {}, @@ -1717,7 +1773,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 20, "id": "c85a622a", "metadata": {}, "outputs": [], @@ -1736,7 +1792,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 21, "id": "8e1b89e0", "metadata": {}, "outputs": [ @@ -1746,12 +1802,12 @@ "\n", "\n", - "\n", + "\n", " \n", " \n", " \n", " \n", - " 2024-07-02T17:48:31.397891\n", + " 2024-09-10T14:13:01.370892\n", " image/svg+xml\n", " \n", " \n", @@ -1767,41 +1823,41 @@ " \n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2083,7 +2139,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2659,7 +2723,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2668,48 +2732,45 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", @@ -2717,24 +2778,24 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2743,19 +2804,19 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2764,19 +2825,19 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2785,19 +2846,19 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2806,19 +2867,19 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2827,7 +2888,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2968,37 +3029,38 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", "\n" @@ -3013,12 +3075,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "bc29c656d2ea4ad78540c03e1d445016", + "model_id": "888417a9581245bb8e86676c83a24ee4", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmpf8jos4vn.pdf
\")" + "HTML(value=\"./tmppzz6jy6m.pdf
\")" ] }, "metadata": {}, @@ -3041,7 +3103,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 22, "id": "386aa7c2", "metadata": {}, "outputs": [ @@ -3056,7 +3118,7 @@ " \n", " \n", " \n", - " 2024-07-02T17:48:31.826602\n", + " 2024-09-10T14:13:01.856969\n", " image/svg+xml\n", " \n", " \n", @@ -3092,16 +3154,16 @@ " \n", " \n", + "\" clip-path=\"url(#p3cff7d2425)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3138,11 +3200,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3cff7d2425)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3230,11 +3292,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3cff7d2425)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3305,11 +3367,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3cff7d2425)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3368,11 +3430,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3cff7d2425)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3544,16 +3606,16 @@ " \n", " \n", + "\" clip-path=\"url(#p3cff7d2425)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3568,11 +3630,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3cff7d2425)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3585,18 +3647,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3604,18 +3666,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3623,18 +3685,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3643,18 +3705,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3916,43 +3978,43 @@ " \n", " \n", " \n", - " \n", + "\" clip-path=\"url(#p3cff7d2425)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4044,12 +4106,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "100be4e6ff5a483b8134ed410b0afeed", + "model_id": "80fdfee7ae5647e8b1616b2282f1ef80", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmpwyw17uud.pdf
\")" + "HTML(value=\"./tmp9bu64hqq.pdf
\")" ] }, "metadata": {}, @@ -4070,7 +4132,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 23, "id": "faa1de28", "metadata": {}, "outputs": [ @@ -4080,12 +4142,12 @@ "\n", "\n", - "\n", + "\n", " \n", " \n", " \n", " \n", - " 2024-07-02T17:48:32.829319\n", + " 2024-09-10T14:13:02.853718\n", " image/svg+xml\n", " \n", " \n", @@ -4101,41 +4163,41 @@ " \n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", " \n", - " \n", - " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", " \n", " \n", " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -5352,190 +5376,190 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", " \n", - " \n", " \n", - " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5618,15 +5642,15 @@ " \n", " \n", " \n", - " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5635,36 +5659,15 @@ " \n", " \n", " \n", - " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5677,8 +5680,8 @@ " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", "\n" @@ -5693,12 +5696,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "48fb592ff4ff4877b37d79801c3b921d", + "model_id": "1767a638d4c14d7b80e3e9d9c252a064", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmp5ru7jh17.pdf
\")" + "HTML(value=\"./tmpen8vu24c.pdf
\")" ] }, "metadata": {}, From 203a4683caf6ea21eb0326e31f553a5edcaae84d Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Wed, 11 Sep 2024 10:48:12 -0500 Subject: [PATCH 06/26] remove more json files --- examples/monarch_mod37/dry_deposition.json | 240 ----- .../monarch_mod37/inorganic_ZSR_water.json | 73 -- .../monarch_mod37/inorganic_activity.json | 339 ------- .../monarch_mod37/inorganic_partitioning.json | 39 - .../monarch_mod37/inorganic_reactions.json | 94 -- examples/monarch_mod37/inorganic_species.json | 205 ---- examples/particle_simulation_with_camp.ipynb | 956 +++++++++--------- 7 files changed, 464 insertions(+), 1482 deletions(-) delete mode 100644 examples/monarch_mod37/dry_deposition.json delete mode 100644 examples/monarch_mod37/inorganic_ZSR_water.json delete mode 100644 examples/monarch_mod37/inorganic_activity.json delete mode 100644 examples/monarch_mod37/inorganic_partitioning.json delete mode 100644 examples/monarch_mod37/inorganic_reactions.json delete mode 100644 examples/monarch_mod37/inorganic_species.json diff --git a/examples/monarch_mod37/dry_deposition.json b/examples/monarch_mod37/dry_deposition.json deleted file mode 100644 index 353780e5..00000000 --- a/examples/monarch_mod37/dry_deposition.json +++ /dev/null @@ -1,240 +0,0 @@ -{ - "description" : [ - "Dry deposition reactions and species properties", - "TODO Consider updating diffusion coefficients according to Tang et al. Atmos. Chem. Phys., 14, 9233-9247 (2014)", - " available at https://www.atmos-chem-phys.net/14/9233/2014/acp-14-9233-2014.pdf" - ], - "pmc-data" : [ - { - "name" : "MONARCH mod37", - "type" : "MECHANISM", - "reactions" : [ - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "SULF" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "MEOH" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "ETOH" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "OPEN" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "HCL" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "TERP" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "PANX" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "NO2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "NO" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "O3" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "NO3" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "N2O5" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "HNO3" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "HONO" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "PNA" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "H2O2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "NTR" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "ROOH" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "FORM" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "ALD2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "ALDX" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "PAR" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "CO" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "MEPX" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "FACD" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "PAN" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "PACD" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "AACD" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "OLE" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "ETH" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "IOLE" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "TOL" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "CRES" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "MGLY" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "XYL" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "ISOP" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "ISPD" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "SO2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "ETHA" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "NH3" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "ISOP-P1" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "ISOP-P2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "TERP-P1" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "TERP-P2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "loss type" : "dry dep", - "species" : "DMS" - } - ] - } - ] -} diff --git a/examples/monarch_mod37/inorganic_ZSR_water.json b/examples/monarch_mod37/inorganic_ZSR_water.json deleted file mode 100644 index e281622a..00000000 --- a/examples/monarch_mod37/inorganic_ZSR_water.json +++ /dev/null @@ -1,73 +0,0 @@ -{ - "description" : [ - "ZSR aerosol water calculation for inorganic aerosols" - ], - "pmc-data" : [ - { - "type" : "SUB_MODEL_ZSR_AEROSOL_WATER", - "name" : "MONARCH inorganic aerosol water", - "notes" : [ "Y_j parameters taken from Jacobson et al. (1996) Table 2" ], - "aerosol phase" : "aqueous", - "gas-phase water" : "H2O", - "aerosol-phase water" : "H2O_aq", - "ion pairs" : { - "H-HSO4" : { - "type" : "JACOBSON", - "ions" : { - "H_p" : {}, - "HSO4_m" : {} - }, - "Y_j" : [5.611895, -1.387446e1, 1.750682e1, 7.138146e1, -3.109173e2, 4.662288e2, -3.128612e2, 7.767097e1], - "low RH" : 0.0 - }, - "H2-SO4" : { - "type" : "JACOBSON", - "ions" : { - "H_p" : { "qty" : 2 }, - "SO4_mm" : {} - }, - "Y_j" : [5.611895, -1.387446e1, 1.750682e1, 7.138146e1, -3.109173e2, 4.662288e2, -3.128612e2, 7.767097e1], - "low RH" : 0.0 - }, - "H-NO3" : { - "type" : "JACOBSON", - "ions" : { - "H_p" : {}, - "NO3_m" : {} - }, - "Y_j" : [4.852977, -6.621314, 3.390133e1, -1.985191e2, 6.281150e2, -1.038494e3, 8.498917e2, -2.729090e2], - "low RH" : 0.0 - }, - "NH4-HSO4" : { - "type" : "JACOBSON", - "ions" : { - "NH4_p" : {}, - "HSO4_m" : {} - }, - "Y_j" : [5.515580, 3.588744, -6.363443e1, 3.687630e2, -1.023972e3, 1.394436e3, -9.168213e2, 2.328726e2], - "low RH" : 0.0 - }, - "(NH4)2-SO4" : { - "type" : "JACOBSON", - "ions" : { - "NH4_p" : { "qty" : 2 }, - "SO4_mm" : {} - }, - "Y_j" : [4.363511e2, -4.947645e3, 2.399693e4, -6.364664e4, 9.952891e4, -9.179112e4, 4.626748e4, -9.844195e3], - "low RH" : 0.47 - }, - "NH4-NO3" : { - "type" : "JACOBSON", - "ions" : { - "NH4_p" : {}, - "NO3_m" : {} - }, - "Y_j" : [1.235157e4, -1.097966e5, 4.173924e5, -8.792165, 1.108433e6, -8.364973e5, 3.499527e5, -6.261910e4], - "low RH" : 0.62 - } - } - } - ] -} - - diff --git a/examples/monarch_mod37/inorganic_activity.json b/examples/monarch_mod37/inorganic_activity.json deleted file mode 100644 index cb04af40..00000000 --- a/examples/monarch_mod37/inorganic_activity.json +++ /dev/null @@ -1,339 +0,0 @@ -{ - "notes" : [ - "PD-FiTE activity calculations for aqueous aerosol species. Parameters from tables 3 and 4 in", - "Topping et al. 2009." - ], - "pmc-data" : [ - { - "type" : "SUB_MODEL_PDFITE", - "name" : "MONARCH activity scheme", - "gas-phase water" : "H2O", - "aerosol-phase water" : "H2O_aq", - "aerosol phase" : "aqueous", - "calculate for" : { - "H-NO3" : { - "interactions" : [ - { - "ion pair": "H-NO3", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ 0.925133 ] - }, - { - "ion pair": "H-NO3", - "min RH" : 0.1, - "max RH" : 0.4, - "B" : [ 0.12091, 13.497, -67.771, 144.01, -117.97 ] - }, - { - "ion pair" : "H-NO3", - "min RH" : 0.4, - "max RH" : 0.9, - "B" : [ 1.3424, -0.8197, -0.52983, -0.37335 ] - }, - { - "ion pair" : "H-NO3", - "min RH" : 0.9, - "max RH" : 0.99, - "B" : [ -1420.5, 4467.9, -4682.7, 1635.1 ] - }, - { - "ion pair" : "H-NO3", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ -0.2573751 ] - }, - { - "ion pair" : "H2-SO4", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ 7.0531446 ] - }, - { - "ion pair" : "H2-SO4", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ 9.3948, -26.808, 35.7654, -18.5094 ] - }, - { - "ion pair" : "H2-SO4", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ -0.0511038 ] - }, - { - "ion pair" : "(NH4)2-SO4", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ -31.136334 ] - }, - { - "ion pair" : "(NH4)2-SO4", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ -40.4136, 108.798, -170.346, 100.926 ] - }, - { - "ion pair" : "(NH4)2-SO4", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ -1.7312977 ] - }, - { - "ion pair" : "NH4-NO3", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ -11.93308 ] - }, - { - "ion pair" : "NH4-NO3", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ -17.0372, 59.232, -86.312, 44.04 ] - }, - { - "ion pair" : "NH4-NO3", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ -0.2599432 ] - } - ] - }, - "NH4/H" : { - "interactions" : [ - { - "ion pair" : "H-NO3", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ -31.711852 ] - }, - { - "ion pair" : "H-NO3", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ -39.1996, 84.264, -99.276, 54.108 ] - }, - { - "ion pair" : "H-NO3", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ -0.5777093 ] - }, - { - "ion pair" : "H2-SO4", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ -58.151568 ] - }, - { - "ion pair" : "H2-SO4", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ -72.978, 165.162, -177.51, 85.332 ] - }, - { - "ion pair" : "H2-SO4", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ -0.6476167 ] - }, - { - "ion pair" : "(NH4)2-SO4", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ -8.918661 ] - }, - { - "ion pair" : "(NH4)2-SO4", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ -15.213, 79.782, -193.326, 262.77, -133.71 ] - }, - { - "ion pair" : "(NH4)2-SO4", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ 0.81654313 ] - }, - { - "ion pair" : "NH4-NO3", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ -24.41782 ] - }, - { - "ion pair" : "NH4-NO3", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ -25.8256, 12.772, 13.058 ] - }, - { - "ion pair" : "NH4-NO3", - "min RH" : 0.99, - "max RH" : 1.0, - "B": [ -0.3831742 ] - } - ] - }, - "H2-SO4" : { - "interactions" : [ - { - "ion pair" : "H2-SO4", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ 1.1220548 ] - }, - { - "ion pair" : "H2-SO4", - "min RH" : 0.1, - "max RH" : 0.9, - "B" : [ 1.3701, -2.1559, -3.5227, 2.7718 ] - }, - { - "ion pair" : "H2-SO4", - "min RH" : 0.9, - "max RH" : 0.99, - "B" : [ -395.18, 1333.7, -1504, 564.63 ] - }, - { - "ion pair" : "H2-SO4", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ -1.0274756 ] - }, - { - "ion pair" : "H-NO3", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ 4.70701952 ] - }, - { - "ion pair" : "H-NO3", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ 8.5472, -50.16, 137.44, -216.596, 186.708, -65.528 ] - }, - { - "ion pair" : "H-NO3", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ 0.46534564 ] - }, - { - "ion pair" : "(NH4)2-SO4", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ -30.961877 ] - }, - { - "ion pair" : "(NH4)2-SO4", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ -48.3636, 235.092, -726.24, 1263.42, -1125, 400.26 ] - }, - { - "ion pair" : "(NH4)2-SO4", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ -1.5424153 ] - }, - { - "ion pair" : "NH4-NO3", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ -15.557633 ] - }, - { - "ion pair" : "NH4-NO3", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ -27.8844, 150.552, -298.588, 266.46, -90.128 ] - }, - { - "ion pair" : "NH4-NO3", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ 0.48525555 ] - } - ] - }, - "H-HSO4" : { - "interactions" : [ - { - "ion pair" : "H-HSO4", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ 1.1220548 ] - }, - { - "ion pair" : "H-HSO4", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ 2.6875, -11.832, 20.601, -18.593 ] - }, - { - "ion pair" : "H-HSO4", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ -6.8759092 ] - }, - { - "ion pair" : "H-NO3", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ -5.4701562 ] - }, - { - "ion pair" : "H-NO3", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ -7.6016, 25.836, -49.924, 48.772, -16.8816 ] - }, - { - "ion pair" : "H-NO3", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ 0.15255283 ] - }, - { - "ion pair" : "(NH4)2-SO4", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ -39.541392 ] - }, - { - "ion pair" : "(NH4)2-SO4", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ -49.9236, 120.066, -172.5, 100.608 ] - }, - { - "ion pair" : "(NH4)2-SO4", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ -2.5056682 ] - }, - { - "ion pair" : "NH4-NO3", - "min RH" : 0.0, - "max RH" : 0.1, - "B" : [ -25.289738 ] - }, - { - "ion pair" : "NH4-NO3", - "min RH" : 0.1, - "max RH" : 0.99, - "B" : [ -37.008, 141.284, -263.06, 227.336, -68.736 ] - }, - { - "ion pair" : "NH4-NO3", - "min RH" : 0.99, - "max RH" : 1.0, - "B" : [ -0.4055799 ] - } - ] - } - } - } - ] -} diff --git a/examples/monarch_mod37/inorganic_partitioning.json b/examples/monarch_mod37/inorganic_partitioning.json deleted file mode 100644 index 37d3a6a9..00000000 --- a/examples/monarch_mod37/inorganic_partitioning.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "description" : [ - "Partitioning of inorganic species. Reactions are based on original MONARCH implementation", - "of EQSAM where only the SO4-NO3-NH4 system is included and is only calculated for the sulfate", - "aerosol mode.", - "Partitioning reaction parameters are from CAPRAM2.4 (Ervens et al. 2003)" - ], - "pmc-data" : [ - { - "name" : "MONARCH mod37", - "type" : "MECHANISM", - "reactions" : [ - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "SULF", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "H2SO4_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "HNO3", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "HNO3_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "NH3", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "NH3_aq", - "aerosol-phase water" : "H2O_aq" - } - ] - } - ] -} - - diff --git a/examples/monarch_mod37/inorganic_reactions.json b/examples/monarch_mod37/inorganic_reactions.json deleted file mode 100644 index fa2e5459..00000000 --- a/examples/monarch_mod37/inorganic_reactions.json +++ /dev/null @@ -1,94 +0,0 @@ -{ - "description" : [ - "These reactions are based on the original MONARCH implementation of EQSAM where", - "only the SO4-NO3-NH3 system is included, and inorganic reactions are only applied", - "to the sulfate aerosol mode. Reaction parameters are from CAPRAM2.4 (Ervens et al. 2003)" - ], - "pmc-data" : [ - { - "name" : "MONARCH mod37", - "type" : "MECHANISM", - "reactions" : [ - { - "type" : "AQUEOUS_EQUILIBRIUM", - "aerosol phase" : "aqueous", - "aerosol-phase water" : "H2O_aq", - "A" : 1.8e-16, - "C" : -6800.0, - "k_reverse" : 1.3e11, - "reactants" : { - "H2O_aq" : {} - }, - "products" : { - "H_p" : {}, - "OH_m" : {} - } - }, - { - "type" : "AQUEOUS_EQUILIBRIUM", - "aerosol phase" : "aqueous", - "aerosol-phase water" : "H2O_aq", - "A" : 1.02e-2, - "C" : 2700.0, - "k_reverse" : 1.0e11, - "ion pair" : "H2-SO4", - "reactants" : { - "HSO4_m" : {} - }, - "products": { - "SO4_mm" : {}, - "H_p" : {} - } - }, - { - "type" : "AQUEOUS_EQUILIBRIUM", - "aerosol phase" : "aqueous", - "aerosol-phase water" : "H2O_aq", - "A" : 1000.0, - "k_reverse" : 5.0e10, - "ion pair" : "H-HSO4", - "reactants" : { - "H2SO4_aq" : {} - }, - "products" : { - "HSO4_m" : {}, - "H_p" : {} - } - }, - { - "type" : "AQUEOUS_EQUILIBRIUM", - "aerosol phase" : "aqueous", - "aerosol-phase water" : "H2O_aq", - "A" : 3.17e-7, - "C" : -560.0, - "k_reverse" : 3.4e10, - "ion pair" : "NH4/H", - "reactants" : { - "NH3_aq" : {}, - "H2O_aq" : {} - }, - "products" : { - "NH4_p" : {}, - "OH_m" : {} - } - }, - { - "type" : "AQUEOUS_EQUILIBRIUM", - "aerosol phase" : "aqueous", - "aerosol-phase water" : "H2O_aq", - "A" : 22.0, - "C" : 1800.0, - "k_reverse" : 5.0e10, - "ion pair" : "H-NO3", - "reactants" : { - "HNO3_aq" : {} - }, - "products" : { - "NO3_m" : {}, - "H_p" : {} - } - } - ] - } - ] -} diff --git a/examples/monarch_mod37/inorganic_species.json b/examples/monarch_mod37/inorganic_species.json deleted file mode 100644 index 99398023..00000000 --- a/examples/monarch_mod37/inorganic_species.json +++ /dev/null @@ -1,205 +0,0 @@ -{ - "description" : [ - "These aerosol species and ion pairs are needed for the MONARCH 'mod37' configuration", - "Densities are taken from Spada et al. (2015) manuscript - ", - "'Global Aerosols in the online multiscale NMMB/BSC Chemical Transport Model", - "or estimated from bulk densities.", - "N* and diffusion coefficients are from CAMPRAM 2.4", - "TODO check about molecular weights" - ], - "pmc-data" : [ - { - "name" : "SULF", - "type" : "CHEM_SPEC", - "inorg note" : "using diffusion coefficient from dry dep", - "N star" : 1.83, - "molecular weight [kg mol-1]" : 0.098079 - }, - { - "name" : "HNO3", - "type" : "CHEM_SPEC", - "inorg note" : "using diffusion coefficient from dry dep", - "N star" : 1.94, - "molecular weight [kg mol-1]" : 0.06301 - }, - { - "name" : "NH3", - "type" : "CHEM_SPEC", - "inorg note" : "using diffusion coefficient from dry dep", - "N star" : 1.92, - "molecular weight [kg mol-1]" : 0.017031 - }, - { - "name" : "H2O_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "tracer type" : "CONSTANT", - "absolute integration tolerance" : 1.0E-05, - "density [kg m-3]" : 1000.0, - "molecular weight [kg mol-1]" : 0.01801528, - "decscription" : "aerosol-phase water", - "PartMC name" : "H2O", - "num_ions" : 0, - "kappa" : 0 - }, - { - "name" : "H_p", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "charge" : 1, - "density [kg m-3]" : 1000.0, - "molecular weight [kg mol-1]" : 0.001008, - "description" : "hydronium ion", - "num_ions" : 1, - "kappa" : 0 - }, - { - "name" : "OH_m", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "charge" : -1, - "density [kg m-3]" : 1000.0, - "molecular weight [kg mol-1]" : 0.017008, - "description" : "hydroxide ion", - "num_ions" : 1, - "kappa" : 0 - }, - { - "name" : "H2SO4_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "density [kg m-3]" : 1840.0, - "molecular weight [kg mol-1]" : 0.098079, - "description" : "undissociated aqueous-phase sulfuric acid", - "num_ions" : 0, - "kappa" : 0.65 - }, - { - "name" : "SO4_mm", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "charge" : -2, - "density [kg m-3]" : 1840.0, - "molecular weight [kg mol-1]" : 0.096063, - "description" : "sulfate ion", - "num_ions" : 2, - "kappa" : 0 - }, - { - "name" : "HSO4_m", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "charge" : -1, - "density [kg m-3]" : 1840.0, - "molecular weight [kg mol-1]" : 0.097069, - "description" : "bisulfate ion", - "num_ions" : 1, - "kappa" : 0 - }, - { - "name" : "HNO3_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "density [kg m-3]" : 1510.0, - "molecular weight [kg mol-1]" : 0.0630129, - "description" : "undissociated aqueous-phase nitric acid", - "num_ions" : 0, - "kappa" : 0.65 - }, - { - "name" : "NO3_m", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "charge" : -1, - "density [kg m-3]" : 1510.0, - "molecular weight [kg mol-1]" : 0.0620049, - "description" : "nitrate ion", - "num_ions" : 1, - "kappa" : 0 - }, - { - "name" : "NH3_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "density [kg m-3]" : 880.0, - "molecular weight [kg mol-1]" : 0.017031, - "description" : "aqueous ammonia (neutral)", - "num_ions" : 0, - "kappa" : 0.65 - }, - { - "name" : "NH4_p", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "charge": 1, - "density [kg m-3]" : 880.0, - "molecular weight [kg mol-1]" : 0.018039, - "description" : "ammonium ion", - "num_ions" : 1, - "kappa" : 0 - }, - { - "name" : "(NH4)2-SO4", - "type" : "CHEM_SPEC", - "tracer type" : "ION_PAIR", - "ions" : { - "NH4_p" : { "qty" : 2 }, - "SO4_mm" : {} - } - }, - { - "name" : "NH4-NO3", - "type" : "CHEM_SPEC", - "tracer type" : "ION_PAIR", - "ions" : { - "NH4_p" : {}, - "NO3_m" : {} - } - }, - { - "name" : "H-NO3", - "type" : "CHEM_SPEC", - "tracer type" : "ION_PAIR", - "ions" : { - "H_p" : {}, - "NO3_m" : {} - } - }, - { - "name" : "H2-SO4", - "type" : "CHEM_SPEC", - "tracer type" : "ION_PAIR", - "ions" : { - "H_p" : { "qty" : 2 }, - "SO4_mm" : {} - } - }, - { - "name" : "H-HSO4", - "type" : "CHEM_SPEC", - "tracer type" : "ION_PAIR", - "ions" : { - "H_p" : {}, - "HSO4_m" : {} - } - }, - { - "name" : "NH4/H", - "type" : "CHEM_SPEC", - "tracer type" : "ION_PAIR", - "ions" : { - "NH4_p" : {}, - "OH_m" : {} - } - } - ] -} diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index 64661ee2..525b2043 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -53,7 +53,6 @@ "source": [ "import numpy as np\n", "import matplotlib.pyplot as plt\n", - "import matplotlib\n", "from open_atmos_jupyter_utils import show_plot\n", "import PyPartMC as ppmc\n", "from PyPartMC import si\n", @@ -411,7 +410,7 @@ { "data": { "text/plain": [ - "65" + "59" ] }, "execution_count": 16, @@ -535,7 +534,7 @@ " \n", " \n", " \n", - " 2024-09-10T14:13:00.661525\n", + " 2024-09-11T10:45:05.098074\n", " image/svg+xml\n", " \n", " \n", @@ -571,16 +570,16 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -617,11 +616,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -709,11 +708,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -784,11 +783,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -847,11 +846,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1023,16 +1022,16 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1085,11 +1084,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1105,11 +1104,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1125,11 +1124,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1177,11 +1176,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1197,11 +1196,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1373,7 +1372,7 @@ " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #ff0000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1425,11 +1424,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1444,11 +1443,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1463,11 +1462,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1482,11 +1481,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1501,11 +1500,11 @@ " \n", " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1704,7 +1703,7 @@ " \n", + "\" clip-path=\"url(#p3c3ed0ed4d)\" style=\"fill: none; stroke: #008000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1745,12 +1744,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "c22b3b352a134854bed3d588918537f4", + "model_id": "6a27dbd24f5443299a94b25c2582e2a6", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmpzcj9aeu_.pdf
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\")" ] }, "metadata": {}, @@ -1802,12 +1801,12 @@ "\n", "\n", - "\n", + "\n", " \n", " \n", " \n", " \n", - " 2024-09-10T14:13:01.370892\n", + " 2024-09-11T10:45:05.728209\n", " image/svg+xml\n", " \n", " \n", @@ -1823,41 +1822,41 @@ " \n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2139,7 +2138,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", @@ -2722,55 +2704,64 @@ " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", @@ -2778,24 +2769,24 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2804,19 +2795,19 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2825,19 +2816,19 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2846,19 +2837,19 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2867,19 +2858,19 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2888,7 +2879,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3029,38 +3020,37 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", "\n" @@ -3075,12 +3065,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "888417a9581245bb8e86676c83a24ee4", + "model_id": "4c83c1da322643f9b2960d66c038476e", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmppzz6jy6m.pdf
\")" + "HTML(value=\"./tmpthpzfa5f.pdf
\")" ] }, "metadata": {}, @@ -3118,7 +3108,7 @@ " \n", " \n", " \n", - " 2024-09-10T14:13:01.856969\n", + " 2024-09-11T10:45:06.157110\n", " image/svg+xml\n", " \n", " \n", @@ -3154,16 +3144,16 @@ " \n", " \n", + "\" clip-path=\"url(#p9c216cbab3)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3200,11 +3190,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9c216cbab3)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3292,11 +3282,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9c216cbab3)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3367,11 +3357,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9c216cbab3)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3430,11 +3420,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9c216cbab3)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3606,16 +3596,16 @@ " \n", " \n", + "\" clip-path=\"url(#p9c216cbab3)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3630,11 +3620,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9c216cbab3)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3649,11 +3639,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9c216cbab3)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3668,11 +3658,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9c216cbab3)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3687,11 +3677,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9c216cbab3)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3707,11 +3697,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9c216cbab3)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3979,9 +3969,9 @@ " \n", " \n", " \n", + "\" clip-path=\"url(#p9c216cbab3)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4106,12 +4096,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "80fdfee7ae5647e8b1616b2282f1ef80", + "model_id": "54fd5f5cf3c44f5c98f752b17bd13344", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmp9bu64hqq.pdf
\")" + "HTML(value=\"./tmpawma_j_7.pdf
\")" ] }, "metadata": {}, @@ -4147,7 +4137,7 @@ " \n", " \n", " \n", - " 2024-09-10T14:13:02.853718\n", + " 2024-09-11T10:45:07.156617\n", " image/svg+xml\n", " \n", " \n", @@ -4183,16 +4173,16 @@ " \n", " \n", + "\" clip-path=\"url(#p46be3150dd)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4283,11 +4273,11 @@ " \n", " \n", + "\" clip-path=\"url(#p46be3150dd)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4345,11 +4335,11 @@ " \n", " \n", + "\" clip-path=\"url(#p46be3150dd)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4378,11 +4368,11 @@ " \n", " \n", + "\" clip-path=\"url(#p46be3150dd)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4431,11 +4421,11 @@ " \n", " \n", + "\" clip-path=\"url(#p46be3150dd)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4478,229 +4468,229 @@ " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4961,16 +4951,16 @@ " \n", " \n", + "\" clip-path=\"url(#p46be3150dd)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4982,36 +4972,36 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5376,7 +5327,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5385,7 +5336,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", + "L 162.27425 155.631433 \n", + "L 168.00305 155.635038 \n", + "L 173.73185 155.635112 \n", + "L 179.46065 155.635204 \n", + "L 185.18945 155.635539 \n", + "L 190.91825 155.631405 \n", + "L 196.64705 155.635252 \n", + "L 202.37585 155.63801 \n", + "\" clip-path=\"url(#p46be3150dd)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 162.27425 155.635009 \n", + "L 168.00305 155.631463 \n", + "L 173.73185 155.635114 \n", + "L 179.46065 155.635206 \n", + "L 185.18945 155.635545 \n", + "L 190.91825 155.631433 \n", + "L 196.64705 155.63527 \n", + "L 202.37585 155.638012 \n", + "\" clip-path=\"url(#p46be3150dd)\" style=\"fill: none; stroke: #ff7f0e; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 162.27425 155.635009 \n", + "L 168.00305 155.631464 \n", + "L 173.73185 155.635115 \n", + "L 179.46065 155.635208 \n", + "L 185.18945 155.635548 \n", + "L 190.91825 155.63145 \n", + "L 196.64705 155.635283 \n", + "L 202.37585 155.638015 \n", + "\" clip-path=\"url(#p46be3150dd)\" style=\"fill: none; stroke: #2ca02c; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 162.27425 155.635009 \n", + "L 168.00305 155.631463 \n", + "L 173.73185 155.635114 \n", + "L 179.46065 155.635206 \n", + "L 185.18945 155.635544 \n", + "L 190.91825 155.631434 \n", + "L 196.64705 155.635274 \n", + "L 202.37585 155.638015 \n", + "\" clip-path=\"url(#p46be3150dd)\" style=\"fill: none; stroke: #d62728; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5626,13 +5577,13 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5642,13 +5593,13 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5659,15 +5610,36 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -5680,7 +5652,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5696,12 +5668,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "1767a638d4c14d7b80e3e9d9c252a064", + "model_id": "47b3f1d960a34b3ab6a10f3ef4c47a79", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmpen8vu24c.pdf
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\")" ] }, "metadata": {}, From 250a167a82bf7001fa6e44832ac43aa15c23ae78 Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Wed, 11 Sep 2024 10:49:40 -0500 Subject: [PATCH 07/26] remove more currently unused json files --- examples/monarch_mod37/cb05_mechanism.json | 3155 ----------------- .../monarch_mod37/cloud_and_rain_species.json | 476 --- 2 files changed, 3631 deletions(-) delete mode 100644 examples/monarch_mod37/cb05_mechanism.json delete mode 100644 examples/monarch_mod37/cloud_and_rain_species.json diff --git a/examples/monarch_mod37/cb05_mechanism.json b/examples/monarch_mod37/cb05_mechanism.json deleted file mode 100644 index a60d4a42..00000000 --- a/examples/monarch_mod37/cb05_mechanism.json +++ /dev/null @@ -1,3155 +0,0 @@ -{ "pmc-data" : [ - { - "name" : "MONARCH mod37", - "type" : "MECHANISM", - "reactions" : [ - { - "rxn id" : "R1", - "reactants" : { - "NO2" : {} - }, - "products" : { - "NO" : {} , - "O" : {} - }, - "orig params" : "TUV_J(4, THETA)", - "base rate" : 4.77e-3, - 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"CL" : {} , - "FORM" : {} - }, - "products" : { - "HCL" : {} , - "HO2" : { "yield" : 1.000 }, - "CO" : { "yield" : 1.000 } - }, - "orig params" : "CMAQ_1to4(8.2E-11, 0.0E+00, 34.0)", - "type" : "ARRHENIUS", - "A" : 8.2E-11, - "B" : 0.0E+00, - "C" : -34.0 - }, - { - "rxn id" : "CL17", - "reactants" : { - "CL" : {} , - "ALD2" : {} - }, - "products" : { - "HCL" : {} , - "C2O3" : { "yield" : 1.000 } - }, - "orig params" : "CMAQ_1to4(7.9E-11, 0.0E+00, 0.0E+00)", - "type" : "ARRHENIUS", - "A" : 7.9E-11, - "B" : 0.0E+00, - "C" : -0.0E+00 - }, - { - "rxn id" : "CL18", - "reactants" : { - "CL" : {} , - "ALDX" : {} - }, - "products" : { - "HCL" : {} , - "CXO3" : { "yield" : 1.000 } - }, - "orig params" : "CMAQ_1to4(1.3E-10, 0.0E+00, 0.0E+00)", - "type" : "ARRHENIUS", - "A" : 1.3E-10, - "B" : 0.0E+00, - "C" : -0.0E+00 - }, - { - "rxn id" : "CL19", - "reactants" : { - "CL" : {} , - "MEOH" : {} - }, - "products" : { - "HCL" : {} , - "HO2" : { "yield" : 1.000 }, - "FORM" : { "yield" : 1.000 } - }, - "orig params" : "CMAQ_1to4(5.5E-11, 0.0E+00, 0.0E+00)", - "type" : "ARRHENIUS", - "A" : 5.5E-11, - "B" : 0.0E+00, - "C" : -0.0E+00 - }, - { - "rxn id" : "CL20", - "reactants" : { - "CL" : {} , - "ETOH" : {} - }, - "products" : { - "HCL" : {} , - "HO2" : { "yield" : 1.000 }, - "ALD2" : { "yield" : 1.000 } - }, - "orig params" : "CMAQ_1to4(8.2E-11, 0.0E+00, -45.0)", - "type" : "ARRHENIUS", - "A" : 8.2E-11, - "B" : 0.0E+00, - "C" : 45.0 - }, - { - "rxn id" : "CL21", - "reactants" : { - "HCL" : {} , - "OH" : {} - }, - "products" : { - "CL" : {} - }, - "orig params" : "CMAQ_1to4(6.58E-13, 1.16, -58.0)", - "type" : "ARRHENIUS", - "A" : 6.58E-13, - "B" : 1.16, - "C" : 58.0 - }, - { - "rxn id" : "SA01", - "reactants" : { - "TOLRO2" : {} , - "NO" : {} - }, - "products" : { - "NO" : {} , - "TOLNRXN" : {} - }, - "orig params" : "CMAQ_1to4(2.70e-12, 0.0E+00, -360.0)", - "type" : "ARRHENIUS", - "A" : 2.70e-12, - "B" : 0.0E+00, - "C" : 360.0 - }, - { - "rxn id" : "SA02", - "reactants" : { - "TOLRO2" : {} , - "HO2" : {} - }, - "products" : { - "HO2" : {} , - "TOLHRXN" : {} - }, - "orig params" : "CMAQ_1to4(1.90e-13, 0.0E+00, -1300.0)", - "type" : "ARRHENIUS", - "A" : 1.90e-13, - "B" : 0.0E+00, - "C" : 1300.0 - }, - { - "rxn id" : "SA03", - "reactants" : { - "XYLRO2" : {} , - "NO" : {} - }, - "products" : { - "NO" : {} , - "XYLNRXN" : {} - }, - "orig params" : "CMAQ_1to4(2.70e-12, 0.0E+00, -360.0)", - "type" : "ARRHENIUS", - "A" : 2.70e-12, - "B" : 0.0E+00, - "C" : 360.0 - }, - { - "rxn id" : "SA04", - "reactants" : { - "XYLRO2" : {} , - "HO2" : {} - }, - "products" : { - "HO2" : {} , - "XYLHRXN" : {} - }, - "orig params" : "CMAQ_1to4(1.90e-13, 0.0E+00, -1300.0)", - "type" : "ARRHENIUS", - "A" : 1.90e-13, - "B" : 0.0E+00, - "C" : 1300.0 - }, - { - "rxn id" : "SA05", - "reactants" : { - "BENZENE" : {} , - "OH" : {} - }, - "products" : { - "OH" : {} , - "BENZRO2" : { "yield" : 0.764 } - }, - "orig params" : "CMAQ_1to4(2.47e-12, 0.0E+00, 206.0)", - "type" : "ARRHENIUS", - "A" : 2.47e-12, - "B" : 0.0E+00, - "C" : -206.0 - }, - { - "rxn id" : "SA06", - "reactants" : { - "BENZRO2" : {} , - "NO" : {} - }, - "products" : { - "NO" : {} , - "BNZNRXN" : {} - }, - "orig params" : "CMAQ_1to4(2.70e-12, 0.0E+00, -360.0)", - "type" : "ARRHENIUS", - "A" : 2.70e-12, - "B" : 0.0E+00, - "C" : 360.0 - }, - { - "rxn id" : "SA07", - "reactants" : { - "BENZRO2" : {} , - "HO2" : {} - }, - "products" : { - "HO2" : {} , - "BNZHRXN" : {} - }, - "orig params" : "CMAQ_1to4(1.90e-13, 0.0E+00, -1300.0)", - "type" : "ARRHENIUS", - "A" : 1.90e-13, - "B" : 0.0E+00, - "C" : 1300.0 - }, - { - "rxn id" : "SA08", - "reactants" : { - "SESQ" : {} , - "O3" : {} - }, - "products" : { - "O3" : {} , - "SESQRXN" : {} - }, - "orig params" : "CMAQ_1to4(1.16E-14, 0.0E+00, 0.0E+00)", - "type" : "ARRHENIUS", - "A" : 1.16E-14, - "B" : 0.0E+00, - "C" : -0.0E+00 - }, - { - "rxn id" : "SA09", - "reactants" : { - "SESQ" : {} , - "OH" : {} - }, - "products" : { - "OH" : {} , - "SESQRXN" : {} - }, - "orig params" : "CMAQ_1to4(1.97E-10, 0.0E+00, 0.0E+00)", - "type" : "ARRHENIUS", - "A" : 1.97E-10, - "B" : 0.0E+00, - "C" : -0.0E+00 - }, - { - "rxn id" : "SA10", - "reactants" : { - "SESQ" : {} , - "NO3" : {} - }, - "products" : { - "NO3" : {} , - "SESQRXN" : {} - }, - "orig params" : "CMAQ_1to4(1.90E-11, 0.0E+00, 0.0E+00)", - "type" : "ARRHENIUS", - "A" : 1.90E-11, - "B" : 0.0E+00, - "C" : -0.0E+00 - }, - { - "rxn id" : "jo2", - "reactants" : { - "O2" : {} - }, - "products" : { - "O" : { "yield" : 2 } - }, - "orig params" : "TUV_J(1, THETA)", - "base rate" : 0.00e+1, - "notes" : "Fast-J does not currently calculate O2 photolysis", - "type" : "PHOTOLYSIS" - } - ] -} -]} diff --git a/examples/monarch_mod37/cloud_and_rain_species.json b/examples/monarch_mod37/cloud_and_rain_species.json deleted file mode 100644 index 24508c47..00000000 --- a/examples/monarch_mod37/cloud_and_rain_species.json +++ /dev/null @@ -1,476 +0,0 @@ -{ - "description" : "Aqueous species present in cloud and rain water", - "pmc-data" : [ - { - "name" : "NO2", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.046006 - }, - { - "name" : "NO2_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.046006, - "density [kg m-3]" : 1000.0, - "description" : "aqueous nitrogen dioxide", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "NO", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.03001 - }, - { - "name" : "NO_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.03001, - "density [kg m-3]" : 1000.0, - "description" : "aqueous nitrogen oxide", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "O3", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.04800 - }, - { - "name" : "O3_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.04800, - "density [kg m-3]" : 1000.0, - "description" : "aqueous ozone", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "NO3", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.07601 - }, - { - "name" : "NO3_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.07601, - "density [kg m-3]" : 1000.0, - "description" : "aqueous nitrogen trioxide", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "N2O5", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.10801 - }, - { - "name" : "N2O5_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.10801, - "density [kg m-3]" : 1000.0, - "description" : "aqueous dinitrogen pentoxide", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "HONO", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.047013 - }, - { - "name" : "HONO_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.047013, - "density [kg m-3]" : 1000.0, - "description" : "aqueous nitrous acid", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "PNA", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.01224 - }, - { - "name" : "HNO4_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.01224, - "density [kg m-3]" : 1000.0, - "description" : "aqueous peroxy nitric acid (HNO4)", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "H2O2", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.0340147 - }, - { - "name" : "H2O2_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.0340147, - "density [kg m-3]" : 1000.0, - "description" : "aqueous hydrogen peroxide", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "NTR", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.091066 - }, - { - "name" : "NTR_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.091066, - "density [kg m-3]" : 1000.0, - "description" : "aqueous organic nitrates (RNO3); using CH3CH2NO3 as surrogate", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "ROOH", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.074079 - }, - { - "name" : "ROOH_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.074079, - "density [kg m-3]" : 1000.0, - "description" : "aqueous alkyl peroxides; using CH3CH3OOH as surrogate", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "FORM", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.030031 - }, - { - "name" : "FORM_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.030031, - "density [kg m-3]" : 1000.0, - "description" : "aqueous formaldehyde", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "ALD2", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.04405 - }, - { - "name" : "ALD2_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.04405, - "density [kg m-3]" : 1000.0, - "description" : "aqueous acetaldehyde", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "ALDX", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.05808 - }, - { - "name" : "ALDX_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.05808, - "density [kg m-3]" : 1000.0, - "description" : "propionaldehyde and higher aldehydes", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "CO", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.028010 - }, - { - "name" : "CO_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.028010, - "density [kg m-3]" : 1000.0, - "description" : "aqueous carbon monoxide", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "MEPX", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.048041 - }, - { - "name" : "MEPX_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.048041, - "density [kg m-3]" : 1000.0, - "description" : "aqueous methylhydroperoxide", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "MEOH", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.03204 - }, - { - "name" : "MEOH_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.03204, - "density [kg m-3]" : 1000.0, - "description" : "aqueous methanol", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "FACD", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.04603 - }, - { - "name" : "FACD_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.04603, - "density [kg m-3]" : 1000.0, - "description" : "aqueous formic acid", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "PAN", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.12105 - }, - { - "name" : "PAN_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.12105, - "density [kg m-3]" : 1000.0, - "description" : "aqueous peroxy-acetyl nitrate", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "PACD", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.0760514 - }, - { - "name" : "PACD_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.0760514, - "density [kg m-3]" : 1000.0, - "description" : "aqueous peroxyacetic acid and higher peroxycarboxylic acids", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "AACD", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.06005 - }, - { - "name" : "AACD_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.06005, - "density [kg m-3]" : 1000.0, - "description" : "aqueous acetic and higher carboxylic acids", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "PANX", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.135075 - }, - { - "name" : "PANX_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.135075, - "density [kg m-3]" : 1000.0, - "description" : "C3 and higher peroxyacyl nitrates", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "SO2", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.064066 - }, - { - "name" : "SO2_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.064066, - "density [kg m-3]" : 1000.0, - "description" : "aqueous sulfur dioxide", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "CL2", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" : 8.6E-02, - "HLC exp factor [K]" : 2000.0, - "diffusion coeff [m2 s-1]" : 1.28E-05, - "notes" : [ "diffusion coeff from CAPRAMv2.4" ], - "molecular weight [kg mol-1]" : 0.07090 - }, - { - "name" : "CL2_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.07090, - "density [kg m-3]" : 1000.0, - "description" : "aqueous molecular chlorine", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "HOCL", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" : 6.6E+02, - "HLC exp factor [K]" : 5900.0, - "diffusion coeff [m2 s-1]" : 1.28E-05, - "notes" : [ "using diffusion coeff for CL2 from CAPRAMv2.4" ], - "molecular weight [kg mol-1]" : 0.05246 - }, - { - "name" : "HOCL_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.05246, - "density [kg m-3]" : 1000.0, - "description" : "aqueous hypochlorous acid", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "FMCL", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" : 1.1, - "HLC exp factor [K]" : 0.0, - "diffusion coeff [m2 s-1]" : 1.28E-05, - "notes" : [ "using diffusion coeff for CL2 from CAPRAMv2.4" ], - "molecular weight [kg mol-1]" : 0.064468 - }, - { - "name" : "FMCL_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.064468, - "density [kg m-3]" : 1000.0, - "description" : "aqueous formyl chloride (HC(O)Cl)", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "HCL", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.03646 - }, - { - "name" : "HCL_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.03646, - "density [kg m-3]" : 1000.0, - "description" : "aqueous hydrochloric acid", - "num_ions" : 0, - "kappa" : 0.53 - }, - { - "name" : "CL_m", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.03545, - "density [kg m-3]" : 1000.0, - "description" : "chloride ion", - "num_ions" : 1, - "kappa" : 0 - }, - { - "name" : "DMS", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.06213 - }, - { - "name" : "DMS_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.06213, - "density [kg m-3]" : 1000.0, - "description" : "aqueous dimethyl sulfide", - "num_ions" : 0, - "kappa" : 0.0 - }, - { - "name" : "ETOH", - "type" : "CHEM_SPEC", - "molecular weight [kg mol-1]" : 0.04607 - }, - { - "name" : "ETOH_aq", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.04607, - "density [kg m-3]" : 1000.0, - "description" : "aqueous ethanol", - "num_ions" : 0, - "kappa" : 0.0 - } - ] -} From a1e7d7d81bd756420e08ca88da79af530fa225ba Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Wed, 11 Sep 2024 12:59:23 -0500 Subject: [PATCH 08/26] update notebook --- examples/monarch_mod37/aerosol_phases.json | 37 - examples/particle_simulation_with_camp.ipynb | 743 ++++++++++--------- 2 files changed, 394 insertions(+), 386 deletions(-) delete mode 100644 examples/monarch_mod37/aerosol_phases.json diff --git a/examples/monarch_mod37/aerosol_phases.json b/examples/monarch_mod37/aerosol_phases.json deleted file mode 100644 index 88aa9ec9..00000000 --- a/examples/monarch_mod37/aerosol_phases.json +++ /dev/null @@ -1,37 +0,0 @@ -{ - "description" : "These aerosol phases correspond to the MONARCH 'mod37' configuration", - "camp-data" : [ - { - "name" : "dust", - "type": "AERO_PHASE", - "species" : [ "LHD_DUST", "LLD_DUST" ], - "notes" : { - "MLD 02/05/2018" : "consider replacing this with a set of inorganic species" - } - }, - { - "name" : "sea_salt", - "type" : "AERO_PHASE", - "species" : [ "SEA_SALT" ], - "notes" : { - "MLD 02/05/2018" : "consider replacing with H2O, Na+, Cl-" - } - }, - { - "name" : "organic_matter", - "type" : "AERO_PHASE", - "species" : [ "POA", "ISOP-P1_aero", "ISOP-P2_aero", "TERP-P1_aero", "TERP-P2_aero" ] - }, - { - "name" : "black_carbon", - "type" : "AERO_PHASE", - "species" : [ "BC_phob", "BC_phil" ] - }, - { - "name" : "other_PM", - "type" : "AERO_PHASE", - "species" : [ "other_PM", "other_other_PM" ], - "description" : "unspecified particulate matter" - } - ] -} diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index 525b2043..1201a094 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -51,12 +51,12 @@ "metadata": {}, "outputs": [], "source": [ + "import json\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", "from open_atmos_jupyter_utils import show_plot\n", "import PyPartMC as ppmc\n", - "from PyPartMC import si\n", - "import json" + "from PyPartMC import si" ] }, { @@ -98,7 +98,7 @@ "camp_config = {\n", " \"camp-files\" : [\n", " \"aerosol_representation.json\",\n", - " \"monarch_mod37/aerosol_phases.json\",\n", + " \"aerosol_phases.json\",\n", " \"monarch_mod37/cb05_abs_tol.json\",\n", " \"monarch_mod37/cb05_mechanism_without_R142_R143.json\",\n", " \"monarch_mod37/cb05_species.json\",\n", @@ -109,7 +109,7 @@ " ]\n", "}\n", "\n", - "with open('config.json', 'w') as f:\n", + "with open('config.json', 'w', encoding='utf-8') as f:\n", " json.dump(camp_config, f, indent=4)" ] }, @@ -130,13 +130,62 @@ " ]\n", "}\n", "\n", - "with open('aerosol_representation.json', 'w') as f:\n", + "with open('aerosol_representation.json', 'w', encoding='utf-8') as f:\n", " json.dump(aerosol_rep, f, indent=4)" ] }, { "cell_type": "code", "execution_count": 8, + "id": "e3c41245", + "metadata": {}, + "outputs": [], + "source": [ + "aerosol_phases = {\n", + " \"description\" : \"These aerosol phases correspond to the MONARCH 'mod37' configuration\",\n", + " \"camp-data\" : [\n", + " {\n", + " \"name\" : \"dust\",\n", + " \"type\": \"AERO_PHASE\",\n", + " \"species\" : [ \"LHD_DUST\", \"LLD_DUST\" ],\n", + " \"notes\" : {\n", + " \"MLD 02/05/2018\" : \"consider replacing this with a set of inorganic species\"\n", + " }\n", + " },\n", + " {\n", + " \"name\" : \"sea_salt\",\n", + " \"type\" : \"AERO_PHASE\",\n", + " \"species\" : [ \"SEA_SALT\" ],\n", + " \"notes\" : {\n", + " \"MLD 02/05/2018\" : \"consider replacing with H2O, Na+, Cl-\"\n", + " }\n", + " },\n", + " {\n", + " \"name\" : \"organic_matter\",\n", + " \"type\" : \"AERO_PHASE\",\n", + " \"species\" : [ \"POA\", \"ISOP-P1_aero\", \"ISOP-P2_aero\", \"TERP-P1_aero\", \"TERP-P2_aero\" ]\n", + " },\n", + " {\n", + " \"name\" : \"black_carbon\",\n", + " \"type\" : \"AERO_PHASE\",\n", + " \"species\" : [ \"BC_phob\", \"BC_phil\" ]\n", + " },\n", + " {\n", + " \"name\" : \"other_PM\",\n", + " \"type\" : \"AERO_PHASE\",\n", + " \"species\" : [ \"other_PM\", \"other_other_PM\" ],\n", + " \"description\" : \"unspecified particulate matter\"\n", + " }\n", + " ]\n", + "}\n", + "\n", + "with open('aerosol_phases.json', 'w', encoding='utf-8') as f:\n", + " json.dump(aerosol_phases, f, indent=4)" + ] + }, + { + "cell_type": "code", + "execution_count": 9, "id": "de15cde5", "metadata": {}, "outputs": [], @@ -147,7 +196,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 10, "id": "6de20b3f", "metadata": {}, "outputs": [], @@ -158,7 +207,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 11, "id": "c822823d", "metadata": {}, "outputs": [], @@ -202,7 +251,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 12, "id": "58706963", "metadata": {}, "outputs": [], @@ -306,7 +355,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 13, "id": "c6a96b7d", "metadata": {}, "outputs": [], @@ -319,7 +368,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 14, "id": "920e41e3", "metadata": {}, "outputs": [], @@ -353,7 +402,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 15, "id": "6722ba83", "metadata": {}, "outputs": [], @@ -364,7 +413,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 16, "id": "9781ca2f", "metadata": {}, "outputs": [], @@ -403,17 +452,17 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 17, "id": "d8d9c8fd", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "59" + "58" ] }, - "execution_count": 16, + "execution_count": 17, "metadata": {}, "output_type": "execute_result" } @@ -441,7 +490,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 18, "id": "0f7c29fe", "metadata": {}, "outputs": [], @@ -505,7 +554,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 19, "id": "82c0cebb", "metadata": {}, "outputs": [], @@ -517,7 +566,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 20, "id": "47474cd3", "metadata": { "scrolled": false @@ -534,7 +583,7 @@ " \n", " \n", " \n", - " 2024-09-11T10:45:05.098074\n", + " 2024-09-11T12:54:47.523497\n", " image/svg+xml\n", " \n", " \n", @@ -570,16 +619,16 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -616,11 +665,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -708,11 +757,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -783,11 +832,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -846,11 +895,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1022,16 +1071,16 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1084,11 +1133,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1104,11 +1153,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1124,11 +1173,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1176,11 +1225,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1196,11 +1245,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1372,7 +1421,7 @@ " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #ff0000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1424,11 +1473,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1443,11 +1492,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1462,11 +1511,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1481,11 +1530,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1500,11 +1549,11 @@ " \n", " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1703,7 +1752,7 @@ " \n", + "\" clip-path=\"url(#p95a5a0e768)\" style=\"fill: none; stroke: #008000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1744,12 +1793,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "6a27dbd24f5443299a94b25c2582e2a6", + "model_id": "e0131d17c515441ea6fab9795a675870", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmpczmg7d6y.pdf
\")" + "HTML(value=\"./tmpucsagmhm.pdf
\")" ] }, "metadata": {}, @@ -1772,7 +1821,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 21, "id": "c85a622a", "metadata": {}, "outputs": [], @@ -1791,7 +1840,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 22, "id": "8e1b89e0", "metadata": {}, "outputs": [ @@ -1806,7 +1855,7 @@ " \n", " \n", " \n", - " 2024-09-11T10:45:05.728209\n", + " 2024-09-11T12:54:48.309790\n", " image/svg+xml\n", " \n", " \n", @@ -1842,16 +1891,16 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1888,11 +1937,11 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1980,11 +2029,11 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2055,11 +2104,11 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2118,11 +2167,11 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2294,20 +2343,20 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2359,17 +2408,27 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2407,19 +2466,19 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2428,19 +2487,19 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2449,19 +2508,19 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2704,45 +2763,31 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2797,17 +2842,17 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2818,17 +2863,17 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2839,17 +2884,17 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2860,17 +2905,17 @@ " \n", " \n", + "\" clip-path=\"url(#p998b38629b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3020,11 +3065,11 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3065,12 +3110,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "4c83c1da322643f9b2960d66c038476e", + "model_id": "5fda40a2dd2c433fba8433f9b5591fc0", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmpthpzfa5f.pdf
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stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4421,11 +4466,11 @@ " \n", " \n", + "\" clip-path=\"url(#p6cb29343fa)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4468,229 +4513,229 @@ " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4951,16 +4996,16 @@ " \n", " \n", + "\" clip-path=\"url(#p6cb29343fa)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4972,36 +5017,36 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", + "L 93.52865 30.078769 \n", + "L 99.25745 112.972754 \n", + "L 104.98625 150.531157 \n", + "L 110.71505 155.638594 \n", + "L 116.44385 93.079903 \n", + "L 122.17265 80.659888 \n", + "L 127.90145 116.80943 \n", + "L 133.63025 106.982691 \n", + "L 139.35905 127.013692 \n", + "L 145.08785 155.634831 \n", + "L 150.81665 154.277267 \n", + "L 156.54545 155.634838 \n", + "L 162.27425 155.638594 \n", + "L 168.00305 155.631191 \n", + "L 173.73185 155.627719 \n", + "L 179.46065 155.628145 \n", + "L 185.18945 155.635681 \n", + "L 190.91825 155.631697 \n", + "L 196.64705 155.638594 \n", + "L 202.37585 155.638594 \n", + "\" clip-path=\"url(#p6cb29343fa)\" style=\"fill: none; 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\")" ] }, "metadata": {}, From 25e92c9c1d0f4839be1c00e121f29d6667d6e6df Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Tue, 24 Sep 2024 21:48:58 +0200 Subject: [PATCH 09/26] embedding cloud_and_rain_partitioning.json in the notebook --- .../cloud_and_rain_partitioning.json | 258 ------------------ examples/particle_simulation_with_camp.ipynb | 50 +++- 2 files changed, 42 insertions(+), 266 deletions(-) delete mode 100644 examples/monarch_mod37/cloud_and_rain_partitioning.json diff --git a/examples/monarch_mod37/cloud_and_rain_partitioning.json b/examples/monarch_mod37/cloud_and_rain_partitioning.json deleted file mode 100644 index 848f8846..00000000 --- a/examples/monarch_mod37/cloud_and_rain_partitioning.json +++ /dev/null @@ -1,258 +0,0 @@ -{ - "description" : [ - "Partitioning of species to aqueous. Parameters are from existing wet-deposition module." - ], - "pmc-data" : [ - { - "name" : "MONARCH mod37", - "type" : "MECHANISM", - "reactions" : [ - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "NO2", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "NO2_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "NO", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "NO_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "O3", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "O3_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "NO3", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "NO3_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "N2O5", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "N2O5_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "HNO3", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "HNO3_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "HONO", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "HONO_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "PNA", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "HNO4_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "H2O2", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "H2O2_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "NTR", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "NTR_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "ROOH", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "ROOH_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "FORM", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "FORM_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "ALD2", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "ALD2_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "ALDX", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "ALDX_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "CO", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "CO_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "MEPX", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "MEPX_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "MEOH", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "MEOH_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "FACD", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "FACD_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "PAN", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "PAN_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "PACD", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "PACD_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "AACD", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "AACD_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "PANX", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "PANX_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "SO2", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "SO2_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "SULF", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "H2SO4_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "CL2", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "CL2_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "HOCL", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "HOCL_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "FMCL", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "FMCL_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "HCL", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "HCL_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "NH3", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "NH3_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "ISOP-P1", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "ISOP-P1_aero", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "ISOP-P2", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "ISOP-P2_aero", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "TERP-P1", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "TERP-P1_aero", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "TERP-P2", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "TERP-P2_aero", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "DMS", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "DMS_aq", - "aerosol-phase water" : "H2O_aq" - }, - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "ETOH", - "aerosol phase" : "aqueous", - "aerosol-phase species" : "ETOH_aq", - "aerosol-phase water" : "H2O_aq" - } - ] - } - ] -} diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index 1201a094..112ee3d5 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -27,7 +27,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 3, "id": "4f8359c2", "metadata": {}, "outputs": [], @@ -46,7 +46,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 4, "id": "b494ea6e", "metadata": {}, "outputs": [], @@ -61,7 +61,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 5, "id": "b480e7ad", "metadata": {}, "outputs": [], @@ -71,7 +71,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 6, "id": "a2d7bad8", "metadata": {}, "outputs": [], @@ -88,6 +88,42 @@ ")" ] }, + { + "cell_type": "code", + "execution_count": 7, + "id": "2e492520-ba61-45bb-b9b3-5a04fb6f21df", + "metadata": {}, + "outputs": [], + "source": [ + "cloud_and_rain_partitioning = {\n", + " \"description\" : [\n", + " \"Partitioning of species to aqueous. Parameters are from existing wet-deposition module.\"\n", + " ],\n", + " \"pmc-data\" : [\n", + " {\n", + " \"name\" : \"MONARCH mod37\",\n", + " \"type\" : \"MECHANISM\",\n", + " \"reactions\" : [\n", + " {\n", + " \"type\" : \"HL_PHASE_TRANSFER\",\n", + " \"gas-phase species\" : \"PNA\" if item == \"HNO4\" else \"SULF\" if item == \"H2SO4\" else item,\n", + " \"aerosol phase\" : \"aqueous\",\n", + " \"aerosol-phase species\" : item + (\"_aero\" if item.startswith(\"ISOP\") or item.startswith(\"TERP\") else \"_aq\"),\n", + " \"aerosol-phase water\" : \"H2O_aq\"\n", + " } for item in (\n", + " \"NO2\", \"NO\", \"O3\", \"NO3\", \"N2O5\", \"HNO3\", \"HONO\", \"H2O2\", \"NTR\", \"ROOH\", \"FORM\", \"ALD2\",\n", + " \"ALDX\", \"CO\", \"MEPX\", \"MEOH\", \"FACD\", \"PAN\", \"PACD\", \"AACD\", \"PANX\", \"SO2\", \"CL2\", \"HOCL\",\n", + " \"FMCL\", \"HCL\", \"NH3\", \"ETOH\", \"DMS\", \"ISOP-P1\", \"ISOP-P2\", \"TERP-P1\", \"TERP-P2\", \"HNO4\", \"H2SO4\",\n", + " )\n", + " ]\n", + " }\n", + " ]\n", + "}\n", + "\n", + "with open('cloud_and_rain_partitioning.json', 'w', encoding='utf-8') as f:\n", + " json.dump(cloud_and_rain_partitioning, f, indent=4)" + ] + }, { "cell_type": "code", "execution_count": 6, @@ -568,9 +604,7 @@ "cell_type": "code", "execution_count": 20, "id": "47474cd3", - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [ { "data": { @@ -5764,7 +5798,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.9.2" } }, "nbformat": 4, From a9d8cb419efe34c0d9c7ff397ba270fd726450bf Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Wed, 25 Sep 2024 23:36:03 +0200 Subject: [PATCH 10/26] shorter lines for pylint --- examples/particle_simulation_with_camp.ipynb | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index 112ee3d5..3aa8e745 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -106,14 +106,19 @@ " \"reactions\" : [\n", " {\n", " \"type\" : \"HL_PHASE_TRANSFER\",\n", - " \"gas-phase species\" : \"PNA\" if item == \"HNO4\" else \"SULF\" if item == \"H2SO4\" else item,\n", + " \"gas-phase species\" : (\n", + " \"PNA\" if item == \"HNO4\" else \"SULF\" if item == \"H2SO4\" else item\n", + " ),\n", " \"aerosol phase\" : \"aqueous\",\n", - " \"aerosol-phase species\" : item + (\"_aero\" if item.startswith(\"ISOP\") or item.startswith(\"TERP\") else \"_aq\"),\n", + " \"aerosol-phase species\" : (\n", + " item + (\"_aero\" if item.startswith(\"ISOP\") or item.startswith(\"TERP\") else \"_aq\")\n", + " ),\n", " \"aerosol-phase water\" : \"H2O_aq\"\n", " } for item in (\n", - " \"NO2\", \"NO\", \"O3\", \"NO3\", \"N2O5\", \"HNO3\", \"HONO\", \"H2O2\", \"NTR\", \"ROOH\", \"FORM\", \"ALD2\",\n", - " \"ALDX\", \"CO\", \"MEPX\", \"MEOH\", \"FACD\", \"PAN\", \"PACD\", \"AACD\", \"PANX\", \"SO2\", \"CL2\", \"HOCL\",\n", - " \"FMCL\", \"HCL\", \"NH3\", \"ETOH\", \"DMS\", \"ISOP-P1\", \"ISOP-P2\", \"TERP-P1\", \"TERP-P2\", \"HNO4\", \"H2SO4\",\n", + " \"NO2\", \"NO\", \"O3\", \"NO3\", \"N2O5\", \"HNO3\", \"HONO\", \"H2O2\", \"NTR\", \"ROOH\", \"FORM\",\n", + " \"ALD2\", \"ALDX\", \"CO\", \"MEPX\", \"MEOH\", \"FACD\", \"PAN\", \"PACD\", \"AACD\", \"PANX\",\n", + " \"SO2\", \"CL2\", \"HOCL\", \"FMCL\", \"HCL\", \"NH3\", \"ETOH\", \"DMS\", \"ISOP-P1\", \"ISOP-P2\",\n", + " \"TERP-P1\", \"TERP-P2\", \"HNO4\", \"H2SO4\",\n", " )\n", " ]\n", " }\n", From e5140ac135ff57348b5a00a0d2e03f4aecdf707c Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Wed, 25 Sep 2024 23:48:50 +0200 Subject: [PATCH 11/26] yaml fix --- .github/workflows/tests+pypi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests+pypi.yml b/.github/workflows/tests+pypi.yml index 54080396..0fa36ca6 100644 --- a/.github/workflows/tests+pypi.yml +++ b/.github/workflows/tests+pypi.yml @@ -181,7 +181,7 @@ jobs: - uses: actions/upload-artifact@v4 with: - name: dist-${{platform}}-${{manylinux}}-${{python-version}} + name: dist-${{matrix.platform}}-${{matrix.manylinux}}-${{matrix.python-version}} path: dist - env: From e341821ac0c78bffb49b53be2111361e0b5947e5 Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Sat, 19 Oct 2024 23:16:03 +0200 Subject: [PATCH 12/26] refactors in initialisation, timestepping and plotting code --- examples/particle_simulation_with_camp.ipynb | 1550 +++++++++--------- 1 file changed, 749 insertions(+), 801 deletions(-) diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index 3aa8e745..3dfd66bf 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -27,7 +27,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 2, "id": "4f8359c2", "metadata": {}, "outputs": [], @@ -46,12 +46,13 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 3, "id": "b494ea6e", "metadata": {}, "outputs": [], "source": [ "import json\n", + "from collections import defaultdict\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", "from open_atmos_jupyter_utils import show_plot\n", @@ -61,380 +62,329 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 4, "id": "b480e7ad", "metadata": {}, "outputs": [], "source": [ - "N_PART = 100" + "N_PART = 100\n", + "T_INITIAL = 0.0\n", + "RUN_PART_ARGS = {}" ] }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 5, "id": "a2d7bad8", "metadata": {}, "outputs": [], "source": [ - "env_state = ppmc.EnvState(\n", - " {\n", - " \"rel_humidity\": 0.0,\n", - " \"latitude\": 0,\n", - " \"longitude\": 0,\n", - " \"altitude\": 0 * si.m,\n", - " \"start_time\": 21600 * si.s,\n", - " \"start_day\": 200,\n", - " }\n", - ")" + "RUN_PART_ARGS['env_state'] = ppmc.EnvState({\n", + " \"rel_humidity\": 0.,\n", + " \"latitude\": 0,\n", + " \"longitude\": 0,\n", + " \"altitude\": 0 * si.m,\n", + " \"start_time\": 21600 * si.s,\n", + " \"start_day\": 200,\n", + "})" ] }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 6, "id": "2e492520-ba61-45bb-b9b3-5a04fb6f21df", "metadata": {}, "outputs": [], "source": [ - "cloud_and_rain_partitioning = {\n", - " \"description\" : [\n", - " \"Partitioning of species to aqueous. Parameters are from existing wet-deposition module.\"\n", - " ],\n", - " \"pmc-data\" : [\n", - " {\n", - " \"name\" : \"MONARCH mod37\",\n", - " \"type\" : \"MECHANISM\",\n", - " \"reactions\" : [\n", - " {\n", - " \"type\" : \"HL_PHASE_TRANSFER\",\n", - " \"gas-phase species\" : (\n", - " \"PNA\" if item == \"HNO4\" else \"SULF\" if item == \"H2SO4\" else item\n", - " ),\n", - " \"aerosol phase\" : \"aqueous\",\n", - " \"aerosol-phase species\" : (\n", - " item + (\"_aero\" if item.startswith(\"ISOP\") or item.startswith(\"TERP\") else \"_aq\")\n", - " ),\n", - " \"aerosol-phase water\" : \"H2O_aq\"\n", - " } for item in (\n", - " \"NO2\", \"NO\", \"O3\", \"NO3\", \"N2O5\", \"HNO3\", \"HONO\", \"H2O2\", \"NTR\", \"ROOH\", \"FORM\",\n", - " \"ALD2\", \"ALDX\", \"CO\", \"MEPX\", \"MEOH\", \"FACD\", \"PAN\", \"PACD\", \"AACD\", \"PANX\",\n", - " \"SO2\", \"CL2\", \"HOCL\", \"FMCL\", \"HCL\", \"NH3\", \"ETOH\", \"DMS\", \"ISOP-P1\", \"ISOP-P2\",\n", - " \"TERP-P1\", \"TERP-P2\", \"HNO4\", \"H2SO4\",\n", - " )\n", - " ]\n", - " }\n", - " ]\n", - "}\n", - "\n", "with open('cloud_and_rain_partitioning.json', 'w', encoding='utf-8') as f:\n", - " json.dump(cloud_and_rain_partitioning, f, indent=4)" + " json.dump(\n", + " {\n", + " \"description\" : [\n", + " \"Partitioning of species to aqueous. Parameters are from existing wet-deposition module.\"\n", + " ],\n", + " \"pmc-data\" : [\n", + " {\n", + " \"name\" : \"MONARCH mod37\",\n", + " \"type\" : \"MECHANISM\",\n", + " \"reactions\" : [\n", + " {\n", + " \"type\" : \"HL_PHASE_TRANSFER\",\n", + " \"gas-phase species\" : (\n", + " \"PNA\" if item == \"HNO4\" else \"SULF\" if item == \"H2SO4\" else item\n", + " ),\n", + " \"aerosol phase\" : \"aqueous\",\n", + " \"aerosol-phase species\" : (\n", + " item + (\"_aero\" if item.startswith(\"ISOP\") or item.startswith(\"TERP\") else \"_aq\")\n", + " ),\n", + " \"aerosol-phase water\" : \"H2O_aq\"\n", + " } for item in (\n", + " \"NO2\", \"NO\", \"O3\", \"NO3\", \"N2O5\", \"HNO3\", \"HONO\", \"H2O2\", \"NTR\", \"ROOH\", \"FORM\",\n", + " \"ALD2\", \"ALDX\", \"CO\", \"MEPX\", \"MEOH\", \"FACD\", \"PAN\", \"PACD\", \"AACD\", \"PANX\",\n", + " \"SO2\", \"CL2\", \"HOCL\", \"FMCL\", \"HCL\", \"NH3\", \"ETOH\", \"DMS\", \"ISOP-P1\", \"ISOP-P2\",\n", + " \"TERP-P1\", \"TERP-P2\", \"HNO4\", \"H2SO4\",\n", + " )\n", + " ]\n", + " }\n", + " ]\n", + " }, f, indent=4\n", + " )" ] }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 7, "id": "16377896", "metadata": {}, "outputs": [], "source": [ - "camp_config = {\n", - " \"camp-files\" : [\n", - " \"aerosol_representation.json\",\n", - " \"aerosol_phases.json\",\n", - " \"monarch_mod37/cb05_abs_tol.json\",\n", - " \"monarch_mod37/cb05_mechanism_without_R142_R143.json\",\n", - " \"monarch_mod37/cb05_species.json\",\n", - " \"monarch_mod37/custom_species.json\",\n", - " \"monarch_mod37/partitioning_species_params.json\",\n", - " \"monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json\",\n", - " \"monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json\"\n", - " ]\n", - "}\n", - "\n", "with open('config.json', 'w', encoding='utf-8') as f:\n", - " json.dump(camp_config, f, indent=4)" + " json.dump(\n", + " {\n", + " \"camp-files\" : [\n", + " \"aerosol_representation.json\",\n", + " \"aerosol_phases.json\",\n", + " \"monarch_mod37/cb05_abs_tol.json\",\n", + " \"monarch_mod37/cb05_mechanism_without_R142_R143.json\",\n", + " \"monarch_mod37/cb05_species.json\",\n", + " \"monarch_mod37/custom_species.json\",\n", + " \"monarch_mod37/partitioning_species_params.json\",\n", + " \"monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json\",\n", + " \"monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json\"\n", + " ]\n", + " }\n", + " , f, indent=4\n", + " )" ] }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 8, "id": "5e4e5c4b", "metadata": {}, "outputs": [], "source": [ - "aerosol_rep = {\n", - " \"camp-data\" : [\n", - " {\n", - " \"name\" : \"PartMC single particle\",\n", - " \"type\" : \"AERO_REP_SINGLE_PARTICLE\",\n", - " \"maximum computational particles\" : N_PART*2\n", - " }\n", - " ]\n", - "}\n", - "\n", "with open('aerosol_representation.json', 'w', encoding='utf-8') as f:\n", - " json.dump(aerosol_rep, f, indent=4)" + " json.dump(\n", + " {\n", + " \"camp-data\" : [\n", + " {\n", + " \"name\" : \"PartMC single particle\",\n", + " \"type\" : \"AERO_REP_SINGLE_PARTICLE\",\n", + " \"maximum computational particles\" : N_PART * 2\n", + " }\n", + " ]\n", + " }, f, indent=4\n", + " )" ] }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 9, "id": "e3c41245", "metadata": {}, "outputs": [], "source": [ - "aerosol_phases = {\n", - " \"description\" : \"These aerosol phases correspond to the MONARCH 'mod37' configuration\",\n", - " \"camp-data\" : [\n", - " {\n", - " \"name\" : \"dust\",\n", - " \"type\": \"AERO_PHASE\",\n", - " \"species\" : [ \"LHD_DUST\", \"LLD_DUST\" ],\n", - " \"notes\" : {\n", - " \"MLD 02/05/2018\" : \"consider replacing this with a set of inorganic species\"\n", - " }\n", - " },\n", - " {\n", - " \"name\" : \"sea_salt\",\n", - " \"type\" : \"AERO_PHASE\",\n", - " \"species\" : [ \"SEA_SALT\" ],\n", - " \"notes\" : {\n", - " \"MLD 02/05/2018\" : \"consider replacing with H2O, Na+, Cl-\"\n", - " }\n", - " },\n", - " {\n", - " \"name\" : \"organic_matter\",\n", - " \"type\" : \"AERO_PHASE\",\n", - " \"species\" : [ \"POA\", \"ISOP-P1_aero\", \"ISOP-P2_aero\", \"TERP-P1_aero\", \"TERP-P2_aero\" ]\n", - " },\n", - " {\n", - " \"name\" : \"black_carbon\",\n", - " \"type\" : \"AERO_PHASE\",\n", - " \"species\" : [ \"BC_phob\", \"BC_phil\" ]\n", - " },\n", - " {\n", - " \"name\" : \"other_PM\",\n", - " \"type\" : \"AERO_PHASE\",\n", - " \"species\" : [ \"other_PM\", \"other_other_PM\" ],\n", - " \"description\" : \"unspecified particulate matter\"\n", - " }\n", - " ]\n", - "}\n", - "\n", "with open('aerosol_phases.json', 'w', encoding='utf-8') as f:\n", - " json.dump(aerosol_phases, f, indent=4)" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "id": "de15cde5", - "metadata": {}, - "outputs": [], - "source": [ - "camp_core = ppmc.CampCore(\"config.json\")\n", - "photolysis = ppmc.Photolysis(camp_core)" + " json.dump(\n", + " {\n", + " \"description\" : \"These aerosol phases correspond to the MONARCH 'mod37' configuration\",\n", + " \"camp-data\" : [\n", + " {\n", + " \"name\" : \"dust\",\n", + " \"type\": \"AERO_PHASE\",\n", + " \"species\" : [ \"LHD_DUST\", \"LLD_DUST\" ],\n", + " \"notes\" : {\n", + " \"MLD 02/05/2018\" : \"consider replacing this with a set of inorganic species\"\n", + " }\n", + " },\n", + " {\n", + " \"name\" : \"sea_salt\",\n", + " \"type\" : \"AERO_PHASE\",\n", + " \"species\" : [ \"SEA_SALT\" ],\n", + " \"notes\" : {\n", + " \"MLD 02/05/2018\" : \"consider replacing with H2O, Na+, Cl-\"\n", + " }\n", + " },\n", + " {\n", + " \"name\" : \"organic_matter\",\n", + " \"type\" : \"AERO_PHASE\",\n", + " \"species\" : [ \"POA\", \"ISOP-P1_aero\", \"ISOP-P2_aero\", \"TERP-P1_aero\", \"TERP-P2_aero\" ]\n", + " },\n", + " {\n", + " \"name\" : \"black_carbon\",\n", + " \"type\" : \"AERO_PHASE\",\n", + " \"species\" : [ \"BC_phob\", \"BC_phil\" ]\n", + " },\n", + " {\n", + " \"name\" : \"other_PM\",\n", + " \"type\" : \"AERO_PHASE\",\n", + " \"species\" : [ \"other_PM\", \"other_other_PM\" ],\n", + " \"description\" : \"unspecified particulate matter\"\n", + " }\n", + " ]\n", + " }, f, indent=4\n", + " )" ] }, { "cell_type": "code", "execution_count": 10, - "id": "6de20b3f", + "id": "de15cde5", "metadata": {}, "outputs": [], "source": [ - "gas_data = ppmc.GasData(camp_core)\n", - "aero_data = ppmc.AeroData(camp_core)" + "RUN_PART_ARGS['camp_core'] = ppmc.CampCore(\"config.json\")\n", + "RUN_PART_ARGS['photolysis'] = ppmc.Photolysis(RUN_PART_ARGS['camp_core'])" ] }, { "cell_type": "code", "execution_count": 11, - "id": "c822823d", + "id": "6de20b3f", "metadata": {}, "outputs": [], "source": [ - "gas_state = ppmc.GasState(gas_data)\n", - "\n", - "input_gas_state = (\n", - " {\"NO\": [0.1E+00]},\n", - " {\"NO2\": [1.0E+00]},\n", - " {\"O3\": [5.0E+01]},\n", - " {\"H2O2\": [1.1E+00]},\n", - " {\"CO\": [2.1E+02]},\n", - " {\"SO2\": [0.8E+00]},\n", - " {\"NH3\": [0.5E+00]},\n", - " {\"HCL\": [0.7E+00]},\n", - " {\"CH4\": [2.2E+03]},\n", - " {\"ETHA\": [1.0E+00]},\n", - " {\"FORM\": [1.2E+00]},\n", - " {\"MEOH\": [1.2E-01]},\n", - " {\"MEPX\": [0.5E+00]},\n", - " {\"ALD2\": [1.0E+00]},\n", - " {\"PAR\": [2.0E+00]},\n", - " {\"ETH\": [0.2E+00]},\n", - " {\"OLE\": [2.3E-02]},\n", - " {\"IOLE\": [3.1E-04]},\n", - " {\"TOL\": [0.1E+00]},\n", - " {\"XYL\": [0.1E+00]},\n", - " {\"NTR\": [0.1E+00]},\n", - " {\"PAN\": [0.8E+00]},\n", - " {\"AACD\": [0.2E+00]},\n", - " {\"ROOH\": [2.5E-02]},\n", - " {\"ISOP\": [5.0E+00]},\n", - " {\"O2\": [2.095E+08]},\n", - " {\"N2\": [7.8E+08]},\n", - " {\"H2\": [5.6E+02]},\n", - " {\"M\": [1.0E+09]}\n", - " )\n", - "\n", - "gas_state.mix_rats = input_gas_state" + "RUN_PART_ARGS['gas_data'] = ppmc.GasData(RUN_PART_ARGS['camp_core'])\n", + "RUN_PART_ARGS['aero_data'] = ppmc.AeroData(RUN_PART_ARGS['camp_core'])" ] }, { "cell_type": "code", "execution_count": 12, - "id": "58706963", + "id": "c822823d", "metadata": {}, "outputs": [], "source": [ - "times = [0 * si.s]\n", - "back_gas = [{\"time\": times},\n", - " {\"rate\": [0 / si.s]},\n", - " {\"NO\": [0.1E+00]},\n", - " {\"NO2\": [1.0E+00]},\n", - " {\"O3\": [5.0E+01]},\n", - " {\"H2O2\": [1.1E+00]},\n", - " {\"CO\": [2.1E+02]},\n", - " {\"SO2\": [0.8E+00]},\n", - " {\"NH3\": [0.5E+00]},\n", - " {\"HCL\": [0.7E+00]},\n", - " {\"CH4\": [2.2E+03]},\n", - " {\"ETHA\": [1.0E+00]},\n", - " {\"FORM\": [1.2E+00]},\n", - " {\"MEOH\": [1.2E-01]},\n", - " {\"MEPX\": [0.5E+00]},\n", - " {\"ALD2\": [1.0E+00]},\n", - " {\"PAR\": [2.0E+00]},\n", - " {\"ETH\": [0.2E+00]},\n", - " {\"OLE\": [2.3E-02]},\n", - " {\"IOLE\": [3.1E-04]},\n", - " {\"TOL\": [0.1E+00]},\n", - " {\"XYL\": [0.1E+00]},\n", - " {\"NTR\": [0.1E+00]},\n", - " {\"PAN\": [0.8E+00]},\n", - " {\"AACD\": [0.2E+00]},\n", - " {\"ROOH\": [2.5E-02]},\n", - " {\"ISOP\": [5.0E+00]},\n", - " {\"O2\": [2.095E+08]},\n", - " {\"N2\": [7.8E+08]},\n", - " {\"H2\": [5.6E+02]},\n", - " {\"M\": [1.0E+09]}\n", - " ]\n", - "\n", - "gas_emit_times = [0, 43200]\n", - "\n", - "gas_emit_rates = np.zeros(len(gas_emit_times))\n", - "gas_emit_rates[0] = 1.0\n", - "gas_emit_rates[1] = 0.0\n", - "\n", - "SO2 = [1.06E-09, 1.06E-09]\n", - "NO2 = [7.56E-12, 7.56E-12]\n", - "NO = [1.44E-10, 1.44E-10]\n", - "CO = [1.96E-09, 1.96E-09]\n", - "ALD2 = [4.25E-12, 4.25E-12]\n", - "FORM = [1.02E-11, 1.02E-11]\n", - "ETH = [4.62E-11, 4.62E-11]\n", - "IOLE = [1.49E-11, 1.49E-11]\n", - "OLE = [1.49E-11, 1.49E-11]\n", - "TOL = [1.53E-11, 1.53E-11]\n", - "XYL = [1.40E-11, 1.40E-11]\n", - "PAR = [4.27E-10, 4.27E-10]\n", - "ISOP = [6.03E-12, 6.03E-12]\n", - "MEOH = [5.92E-13, 5.92E-13]\n", - "\n", - "emit_gas = [\n", - " {\"time\": gas_emit_times},\n", - " {\"rate\": list(gas_emit_rates)},\n", - " {\"SO2\": SO2},\n", - " {\"NO2\": NO2},\n", - " {\"NO\": NO},\n", - " {\"CO\": CO},\n", - " {\"ALD2\": ALD2},\n", - " {\"FORM\": FORM},\n", - " {\"ETH\": ETH},\n", - " {\"IOLE\": IOLE},\n", - " {\"OLE\": OLE},\n", - " {\"TOL\": TOL},\n", - " {\"XYL\": XYL},\n", - " {\"PAR\": PAR},\n", - " {\"ISOP\": ISOP},\n", - " {\"MEOH\": MEOH},\n", - "]\n", - "\n", - "AERO_DIST_BACKGROUND = {\n", - " \"back_small\": {\n", - " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", - " \"diam_type\": \"geometric\",\n", - " \"mode_type\": \"log_normal\",\n", - " \"num_conc\": 0 / si.m**3,\n", - " \"geom_mean_diam\": 0.02 * si.um,\n", - " \"log10_geom_std_dev\": 0.161,\n", - " },\n", - "}\n", - "\n", - "AERO_DIST_EMIT = {\n", - " \"gasoline\": {\n", - " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", - " \"diam_type\": \"geometric\",\n", - " \"mode_type\": \"log_normal\",\n", - " \"num_conc\": 0.0 / si.m**3,\n", - " \"geom_mean_diam\": 5e-8 * si.m,\n", - " \"log10_geom_std_dev\": 0.24,\n", - " },\n", - "}" + "RUN_PART_ARGS['gas_state'] = ppmc.GasState(RUN_PART_ARGS['gas_data'])\n", + "RUN_PART_ARGS['gas_state'].mix_rats = (\n", + " {\"NO\": [0.1]},\n", + " {\"NO2\": [1.]},\n", + " {\"O3\": [5.0E+01]},\n", + " {\"H2O2\": [1.1]},\n", + " {\"CO\": [2.1E+02]},\n", + " {\"SO2\": [0.8]},\n", + " {\"NH3\": [0.5]},\n", + " {\"HCL\": [0.7]},\n", + " {\"CH4\": [2.2E+03]},\n", + " {\"ETHA\": [1.]},\n", + " {\"FORM\": [1.2]},\n", + " {\"MEOH\": [1.2E-01]},\n", + " {\"MEPX\": [0.5]},\n", + " {\"ALD2\": [1.]},\n", + " {\"PAR\": [2.]},\n", + " {\"ETH\": [0.2]},\n", + " {\"OLE\": [2.3E-02]},\n", + " {\"IOLE\": [3.1E-04]},\n", + " {\"TOL\": [0.1]},\n", + " {\"XYL\": [0.1]},\n", + " {\"NTR\": [0.1]},\n", + " {\"PAN\": [0.8]},\n", + " {\"AACD\": [0.2]},\n", + " {\"ROOH\": [2.5E-02]},\n", + " {\"ISOP\": [5.]},\n", + " {\"O2\": [2.095E+08]},\n", + " {\"N2\": [7.8E+08]},\n", + " {\"H2\": [5.6E+02]},\n", + " {\"M\": [1.0E+09]}\n", + ")" ] }, { "cell_type": "code", "execution_count": 13, - "id": "c6a96b7d", - "metadata": {}, - "outputs": [], - "source": [ - "time_timeseries = [0, 86400]\n", - "pressure_timeseries = [1e5, 1e5]\n", - "temp_timeseries = [290.016, 290.016]\n", - "height_timeseries = [1.0, 1.0]" - ] - }, - { - "cell_type": "code", - "execution_count": 14, "id": "920e41e3", "metadata": {}, "outputs": [], "source": [ - "scenario = ppmc.Scenario(\n", - " gas_data,\n", - " aero_data,\n", + "TIME_TIMESERIES = [0, 86400]\n", + "RUN_PART_ARGS['scenario'] = ppmc.Scenario(\n", + " RUN_PART_ARGS['gas_data'],\n", + " RUN_PART_ARGS['aero_data'],\n", " {\n", - " \"temp_profile\": [{\"time\": time_timeseries}, {\"temp\": temp_timeseries}],\n", + " \"temp_profile\": [{\"time\": TIME_TIMESERIES}, {\"temp\": [290.016, 290.016]}],\n", " \"pressure_profile\": [\n", - " {\"time\": time_timeseries},\n", - " {\"pressure\": pressure_timeseries},\n", + " {\"time\": TIME_TIMESERIES},\n", + " {\"pressure\": [1e5, 1e5]},\n", + " ],\n", + " \"height_profile\": [{\"time\": TIME_TIMESERIES}, {\"height\": [1., 1.]}],\n", + " \"gas_emissions\": [\n", + " {\"time\": [0, 43200]},\n", + " {\"rate\": [1., 0.]},\n", + " {\"SO2\": [1.06E-09, 1.06E-09]},\n", + " {\"NO2\": [7.56E-12, 7.56E-12]},\n", + " {\"NO\": [1.44E-10, 1.44E-10]},\n", + " {\"CO\": [1.96E-09, 1.96E-09]},\n", + " {\"ALD2\": [4.25E-12, 4.25E-12]},\n", + " {\"FORM\": [1.02E-11, 1.02E-11]},\n", + " {\"ETH\": [4.62E-11, 4.62E-11]},\n", + " {\"IOLE\": [1.49E-11, 1.49E-11]},\n", + " {\"OLE\": [1.49E-11, 1.49E-11]},\n", + " {\"TOL\": [1.53E-11, 1.53E-11]},\n", + " {\"XYL\": [1.40E-11, 1.40E-11]},\n", + " {\"PAR\": [4.27E-10, 4.27E-10]},\n", + " {\"ISOP\": [6.03E-12, 6.03E-12]},\n", + " {\"MEOH\": [5.92E-13, 5.92E-13]},\n", + " ],\n", + " \"gas_background\": [\n", + " {\"time\": [0 * si.s]},\n", + " {\"rate\": [0 / si.s]},\n", + " {\"NO\": [0.1]},\n", + " {\"NO2\": [1.]},\n", + " {\"O3\": [5.0E+01]},\n", + " {\"H2O2\": [1.1]},\n", + " {\"CO\": [2.1E+02]},\n", + " {\"SO2\": [0.8]},\n", + " {\"NH3\": [0.5]},\n", + " {\"HCL\": [0.7]},\n", + " {\"CH4\": [2.2E+03]},\n", + " {\"ETHA\": [1.]},\n", + " {\"FORM\": [1.2]},\n", + " {\"MEOH\": [1.2E-01]},\n", + " {\"MEPX\": [0.5]},\n", + " {\"ALD2\": [1.]},\n", + " {\"PAR\": [2.]},\n", + " {\"ETH\": [0.2]},\n", + " {\"OLE\": [2.3E-02]},\n", + " {\"IOLE\": [3.1E-04]},\n", + " {\"TOL\": [0.1]},\n", + " {\"XYL\": [0.1]},\n", + " {\"NTR\": [0.1]},\n", + " {\"PAN\": [0.8]},\n", + " {\"AACD\": [0.2]},\n", + " {\"ROOH\": [2.5E-02]},\n", + " {\"ISOP\": [5.]},\n", + " {\"O2\": [2.095E+08]},\n", + " {\"N2\": [7.8E+08]},\n", + " {\"H2\": [5.6E+02]},\n", + " {\"M\": [1.0E+09]}\n", " ],\n", - " \"height_profile\": [{\"time\": time_timeseries}, {\"height\": height_timeseries}],\n", - " \"gas_emissions\": emit_gas,\n", - " \"gas_background\": back_gas,\n", " \"aero_emissions\": [\n", " {\"time\": [0 * si.s]},\n", " {\"rate\": [0 / si.s]},\n", - " {\"dist\": [[AERO_DIST_EMIT]]},\n", + " {\"dist\": [[{\n", + " \"gasoline\": {\n", + " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", + " \"diam_type\": \"geometric\",\n", + " \"mode_type\": \"log_normal\",\n", + " \"num_conc\": 0.0 / si.m**3,\n", + " \"geom_mean_diam\": 5e-8 * si.m,\n", + " \"log10_geom_std_dev\": 0.24,\n", + " },\n", + " }]]},\n", " ],\n", " \"aero_background\": [\n", " {\"time\": [0 * si.s]},\n", " {\"rate\": [0 / si.s]},\n", - " {\"dist\": [[AERO_DIST_BACKGROUND]]},\n", + " {\"dist\": [[{\n", + " \"back_small\": {\n", + " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", + " \"diam_type\": \"geometric\",\n", + " \"mode_type\": \"log_normal\",\n", + " \"num_conc\": 0 / si.m**3,\n", + " \"geom_mean_diam\": 0.02 * si.um,\n", + " \"log10_geom_std_dev\": 0.161,\n", + " },\n", + " }]]},\n", " ],\n", " \"loss_function\": \"none\",\n", " },\n", @@ -443,85 +393,87 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 14, "id": "6722ba83", "metadata": {}, "outputs": [], "source": [ - "T_INITIAL = 0.0\n", - "scenario.init_env_state(env_state, T_INITIAL)" + "RUN_PART_ARGS['scenario'].init_env_state(RUN_PART_ARGS['env_state'], T_INITIAL)" ] }, { "cell_type": "code", - "execution_count": 16, - "id": "9781ca2f", + "execution_count": 15, + "id": "96ba54c5-dc33-4e22-b774-390cec4be69f", "metadata": {}, "outputs": [], "source": [ - "AERO_DIST_INIT = [\n", - " {\n", - " \"init_small\": {\n", - " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", - " \"diam_type\": \"geometric\",\n", - " \"mode_type\": \"log_normal\",\n", - " \"num_conc\": 3.2e9 / si.m**3,\n", - " \"geom_mean_diam\": 2.0e-8 * si.m,\n", - " \"log10_geom_std_dev\": 0.161,\n", - " },\n", - " \"init_large\": {\n", - " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", - " \"diam_type\": \"geometric\",\n", - " \"mode_type\": \"log_normal\",\n", - " \"num_conc\": 2.9e9 / si.m**3,\n", - " \"geom_mean_diam\": 1.16e-7 * si.m,\n", - " \"log10_geom_std_dev\": 0.217,\n", - " },\n", - " \"init_coarse\": {\n", - " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", - " \"diam_type\": \"geometric\",\n", - " \"mode_type\": \"log_normal\",\n", - " \"num_conc\": 0.3e6 / si.m**3,\n", - " \"geom_mean_diam\": 1.8e-6 * si.m,\n", - " \"log10_geom_std_dev\": 0.38021124171160603,\n", + "AERO_DIST_INIT = ppmc.AeroDist(RUN_PART_ARGS['aero_data'], [\n", + " {\n", + " \"init_small\": {\n", + " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", + " \"diam_type\": \"geometric\",\n", + " \"mode_type\": \"log_normal\",\n", + " \"num_conc\": 3.2e9 / si.m**3,\n", + " \"geom_mean_diam\": 2.0e-8 * si.m,\n", + " \"log10_geom_std_dev\": 0.161,\n", + " },\n", + " \"init_large\": {\n", + " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", + " \"diam_type\": \"geometric\",\n", + " \"mode_type\": \"log_normal\",\n", + " \"num_conc\": 2.9e9 / si.m**3,\n", + " \"geom_mean_diam\": 1.16e-7 * si.m,\n", + " \"log10_geom_std_dev\": 0.217,\n", + " },\n", + " \"init_coarse\": {\n", + " \"mass_frac\": [{\"organic_matter.POA\": [1]}],\n", + " \"diam_type\": \"geometric\",\n", + " \"mode_type\": \"log_normal\",\n", + " \"num_conc\": 0.3e6 / si.m**3,\n", + " \"geom_mean_diam\": 1.8e-6 * si.m,\n", + " \"log10_geom_std_dev\": 0.38021124171160603,\n", + " }\n", " }\n", - " }\n", - "]\n", - "\n", - "aero_dist_init = ppmc.AeroDist(aero_data, AERO_DIST_INIT)" + " ]\n", + ")" ] }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 16, "id": "d8d9c8fd", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "58" + "46" ] }, - "execution_count": 17, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "run_part_opt = ppmc.RunPartOpt(\n", - " {\n", - " \"output_prefix\": \"urban_plume\",\n", - " \"do_coagulation\": False,\n", - " \"t_max\": 86400 * si.s,\n", - " \"del_t\": 6 * si.s,\n", - " \"do_camp_chem\": True,\n", - " }\n", + "RUN_PART_ARGS['run_part_opt'] = ppmc.RunPartOpt({\n", + " \"output_prefix\": \"urban_plume\",\n", + " \"do_coagulation\": False,\n", + " \"t_max\": 86400 * si.s,\n", + " \"del_t\": 6 * si.s,\n", + " \"do_camp_chem\": True,\n", + "})\n", + "\n", + "RUN_PART_ARGS['aero_state'] = ppmc.AeroState(\n", + " RUN_PART_ARGS['aero_data'],\n", + " N_PART,\n", + " 'nummass_source',\n", + " RUN_PART_ARGS['camp_core']\n", ")\n", "\n", - "aero_state = ppmc.AeroState(aero_data, N_PART, 'nummass_source', camp_core)\n", - "aero_state.dist_sample(\n", - " aero_dist_init,\n", + "RUN_PART_ARGS['aero_state'].dist_sample(\n", + " AERO_DIST_INIT,\n", " sample_prop=1.0,\n", " create_time=0.0,\n", " allow_doubling=True,\n", @@ -529,6 +481,16 @@ ")" ] }, + { + "cell_type": "code", + "execution_count": 17, + "id": "5f3665a5-be3c-49e4-b1d0-47f3e2b82c30", + "metadata": {}, + "outputs": [], + "source": [ + "DIAM_GRID = ppmc.BinGrid(30, \"log\", 1e-9, 1e-5)" + ] + }, { "cell_type": "code", "execution_count": 18, @@ -536,61 +498,34 @@ "metadata": {}, "outputs": [], "source": [ - "N_STEPS = int(run_part_opt.t_max / run_part_opt.del_t)\n", - "num_conc = np.zeros(N_STEPS + 1)\n", - "num_conc[0] = aero_state.total_num_conc\n", - "mass_conc = np.zeros(N_STEPS + 1)\n", - "mass_conc[0] = aero_state.total_mass_conc\n", - "time = np.zeros(N_STEPS + 1)\n", - "gas_mix_rat = np.zeros((N_STEPS + 1, gas_state.n_spec))\n", - "gas_mix_rat[0, :] = gas_state.mix_rats\n", - "\n", - "height = np.zeros((N_STEPS + 1))\n", - "temperature = np.zeros((N_STEPS + 1))\n", - "rh = np.zeros((N_STEPS + 1))\n", - "\n", - "height[0] = env_state.height\n", - "temperature[0] = env_state.temp\n", - "rh[0] = env_state.rh\n", - "\n", - "diam_grid = ppmc.BinGrid(30, \"log\", 1e-9, 1e-5)\n", - "dists = []\n", - "dry_diameters = aero_state.dry_diameters\n", - "num_concs = aero_state.num_concs\n", - "dists.append(ppmc.histogram_1d(diam_grid, dry_diameters, num_concs))\n", - "\n", - "last_output_time = 0.\n", - "last_progress_time = 0.\n", + "OUTPUT = defaultdict(list)\n", + "last = defaultdict(float)\n", "i_output = 1\n", - "\n", - "for i_time in range(1,N_STEPS + 1):\n", - " (last_output_time, last_progress_time, i_output) = ppmc.run_part_timestep(\n", - " scenario,\n", - " env_state,\n", - " aero_data,\n", - " aero_state,\n", - " gas_data,\n", - " gas_state,\n", - " run_part_opt,\n", - " camp_core,\n", - " photolysis,\n", - " i_time,\n", - " T_INITIAL,\n", - " last_output_time,\n", - " last_progress_time,\n", - " i_output\n", - " )\n", - " num_conc[i_time] = aero_state.total_num_conc\n", - " mass_conc[i_time] = aero_state.total_mass_conc\n", - " time[i_time] = env_state.elapsed_time\n", - " gas_mix_rat[i_time, :] = gas_state.mix_rats\n", - " height[i_time] = env_state.height\n", - " temperature[i_time] = env_state.temp\n", - " rh[i_time] = env_state.rh\n", - " if np.mod(i_time * run_part_opt.del_t, 3600.0) == 0:\n", - " dry_diameters = aero_state.dry_diameters\n", - " num_concs = aero_state.num_concs\n", - " dists.append(ppmc.histogram_1d(diam_grid, dry_diameters, num_concs))" + "for i_time in range(0, int(RUN_PART_ARGS['run_part_opt'].t_max / RUN_PART_ARGS['run_part_opt'].del_t) + 1):\n", + " if i_time != 0:\n", + " (last[\"output_time\"], last[\"progress_time\"], i_output) = ppmc.run_part_timestep(\n", + " *[RUN_PART_ARGS[key] for key in (\n", + " 'scenario', 'env_state', 'aero_data',\n", + " 'aero_state', 'gas_data', 'gas_state',\n", + " 'run_part_opt', 'camp_core', 'photolysis'\n", + " )],\n", + " i_time, T_INITIAL, last[\"output_time\"], last[\"progress_time\"], i_output,\n", + " )\n", + " for obj, keys in (\n", + " (RUN_PART_ARGS['aero_state'], ('total_num_conc', 'total_mass_conc')),\n", + " (RUN_PART_ARGS['gas_state'], ('mix_rats',)),\n", + " (RUN_PART_ARGS['env_state'], ('elapsed_time', 'height', 'temp', 'rh')),\n", + " ):\n", + " for key in keys:\n", + " OUTPUT[key].append(getattr(obj, key))\n", + " if np.mod(i_time * RUN_PART_ARGS['run_part_opt'].del_t, 3600.0) == 0:\n", + " OUTPUT['dists'].append(ppmc.histogram_1d(\n", + " DIAM_GRID,\n", + " RUN_PART_ARGS['aero_state'].dry_diameters,\n", + " RUN_PART_ARGS['aero_state'].num_concs\n", + " ))\n", + "for key in OUTPUT:\n", + " OUTPUT[key] = np.asarray(OUTPUT[key])" ] }, { @@ -601,7 +536,7 @@ "outputs": [], "source": [ "plt.rcParams.update({'font.size': 9})\n", - "plt.rcParams.update({'figure.figsize': (3.08,2.5)})\n", + "plt.rcParams.update({'figure.figsize': (3.08, 2.5)})\n", "plt.rcParams.update({\"axes.grid\" : True})" ] }, @@ -622,11 +557,11 @@ " \n", " \n", " \n", - " 2024-09-11T12:54:47.523497\n", + " 2024-10-19T23:14:27.741913\n", " image/svg+xml\n", " \n", " \n", - " Matplotlib v3.7.1, https://matplotlib.org/\n", + " Matplotlib v3.8.1, https://matplotlib.org/\n", " \n", " \n", " \n", @@ -658,16 +593,16 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -704,11 +639,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -796,11 +731,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -871,11 +806,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -934,11 +869,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1110,16 +1045,16 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1172,11 +1107,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1192,11 +1127,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1212,11 +1147,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1264,11 +1199,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1284,11 +1219,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1460,7 +1395,7 @@ " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #ff0000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1512,11 +1447,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1531,11 +1466,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1550,11 +1485,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1569,11 +1504,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1588,11 +1523,11 @@ " \n", " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1791,7 +1726,7 @@ " \n", + "\" clip-path=\"url(#p72034256d0)\" style=\"fill: none; stroke: #008000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1832,12 +1767,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "e0131d17c515441ea6fab9795a675870", + "model_id": "f4b1662328744d5ca758094d1530c0f8", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmpucsagmhm.pdf
\")" + "HBox(children=(HTML(value=\"./tmpmaf6ysce.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -1845,16 +1780,16 @@ } ], "source": [ - "plt.plot(time,temperature,'r')\n", + "plt.plot(OUTPUT['elapsed_time'], OUTPUT['temp'], 'r')\n", "plt.ylabel('Temperature (K)', color='r')\n", - "plt.ylim([275,300])\n", - "plt.xticks(np.linspace(0, time[-1], 5))\n", - "plt.xlim([0,time[-1]])\n", + "plt.ylim([275, 300])\n", + "plt.xticks(np.linspace(0, OUTPUT['elapsed_time'][-1], 5))\n", + "plt.xlim([OUTPUT['elapsed_time'][i] for i in (0, -1)])\n", "plt.xlabel('Time (s)')\n", "plt.twinx()\n", - "plt.plot(time,rh*100,'g')\n", + "plt.plot(OUTPUT['elapsed_time'], OUTPUT['rh'] * 100, 'g')\n", "plt.ylabel('Relative humidity (%)', color='g')\n", - "plt.ylim([0,100])\n", + "plt.ylim([0, 100])\n", "show_plot()" ] }, @@ -1889,16 +1824,16 @@ "\n", "\n", - "\n", + "\n", " \n", " \n", " \n", " \n", - " 2024-09-11T12:54:48.309790\n", + " 2024-10-19T23:14:28.449631\n", " image/svg+xml\n", " \n", " \n", - " Matplotlib v3.7.1, https://matplotlib.org/\n", + " Matplotlib v3.8.1, https://matplotlib.org/\n", " \n", " \n", " \n", @@ -1910,41 +1845,41 @@ " \n", " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2226,7 +2161,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", + " \n", " \n", " \n", " \n", @@ -2803,7 +2745,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2812,40 +2754,45 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", @@ -2853,23 +2800,23 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2879,18 +2826,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2900,18 +2847,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2921,18 +2868,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2942,18 +2889,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2963,7 +2910,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3104,37 +3051,37 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", "\n" @@ -3149,12 +3096,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "5fda40a2dd2c433fba8433f9b5591fc0", + "model_id": "5db8694ea8204eadaf9fe33882fbbbce", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmp0zrp6oao.pdf
\")" + "HBox(children=(HTML(value=\"./tmpe2asd795.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -3162,14 +3109,14 @@ } ], "source": [ - "plt.plot(time, mass_conc, \"b\", label=\"mass conc\")\n", + "plt.plot(OUTPUT['elapsed_time'], OUTPUT['total_mass_conc'], \"b\", label=\"mass conc\")\n", "plt.ylabel(\"Mass concentration (kg m$^{-3}$)\", color='b')\n", "plt.xlabel(\"Time (s)\")\n", "set_tickmarks(plt.gca(), 5)\n", "plt.twinx()\n", - "plt.plot(time, num_conc, \"g\", label=\"num conc\")\n", - "plt.xticks(np.linspace(0, time[-1], 5))\n", - "plt.xlim([time[0],time[-1]])\n", + "plt.plot(OUTPUT['elapsed_time'], OUTPUT['total_num_conc'], \"g\", label=\"num conc\")\n", + "plt.xticks(np.linspace(0, OUTPUT['elapsed_time'][-1], 5))\n", + "plt.xlim([OUTPUT['elapsed_time'][i] for i in (0, -1)])\n", "set_tickmarks(plt.gca(), 5)\n", "plt.ylabel(r\"Number concentration ($\\#$ m$^{-3}$)\", color='g')\n", "show_plot()" @@ -3192,11 +3139,11 @@ " \n", " \n", " \n", - " 2024-09-11T12:54:48.799728\n", + " 2024-10-19T23:14:29.119403\n", " image/svg+xml\n", " \n", " \n", - " Matplotlib v3.7.1, https://matplotlib.org/\n", + " Matplotlib v3.8.1, https://matplotlib.org/\n", " \n", " \n", " \n", @@ -3228,16 +3175,16 @@ " \n", " \n", + "\" clip-path=\"url(#p82b79ead28)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3274,11 +3221,11 @@ " \n", " \n", + "\" clip-path=\"url(#p82b79ead28)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3366,11 +3313,11 @@ " \n", " \n", + "\" clip-path=\"url(#p82b79ead28)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3441,11 +3388,11 @@ " \n", " \n", + "\" clip-path=\"url(#p82b79ead28)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3504,11 +3451,11 @@ " \n", " \n", + "\" clip-path=\"url(#p82b79ead28)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3680,16 +3627,16 @@ " \n", " \n", + "\" clip-path=\"url(#p82b79ead28)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3704,16 +3651,16 @@ " \n", " \n", + "\" clip-path=\"url(#p82b79ead28)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3721,18 +3668,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3742,11 +3689,11 @@ " \n", " \n", + "\" clip-path=\"url(#p82b79ead28)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3761,11 +3708,11 @@ " \n", " \n", + "\" clip-path=\"url(#p82b79ead28)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3781,11 +3728,11 @@ " \n", " \n", + "\" clip-path=\"url(#p82b79ead28)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4052,12 +3999,12 @@ " \n", " \n", " \n", - " \n", + "\" clip-path=\"url(#p82b79ead28)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4180,12 +4127,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "f1595029049a485480709e269ab7d609", + "model_id": "8209f77c37ed4c25b04472b7fabca343", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmpdlajj2uq.pdf
\")" + "HBox(children=(HTML(value=\"./tmp1pg_brlq.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -4193,13 +4140,16 @@ } ], "source": [ - "gases = [\"O3\"]\n", - "for i_spec, spec in enumerate(gases):\n", - " i_spec = gas_data.spec_by_name(spec)\n", - " l, = plt.plot(time, gas_mix_rat[:, i_spec], label=spec)\n", + "for i_spec, spec in enumerate([\"O3\"]):\n", + " i_spec = RUN_PART_ARGS['gas_data'].spec_by_name(spec)\n", + " l, = plt.plot(\n", + " OUTPUT['elapsed_time'],\n", + " OUTPUT['mix_rats'][:, i_spec],\n", + " label=spec\n", + " )\n", "plt.xlabel(\"Time (s)\")\n", "plt.ylabel(\"Mixing ratio (ppb)\")\n", - "plt.xticks(np.linspace(0, time[-1], 5))\n", + "plt.xticks(np.linspace(0, OUTPUT['elapsed_time'][-1], 5))\n", "plt.legend()\n", "show_plot()" ] @@ -4221,11 +4171,11 @@ " \n", " \n", " \n", - " 2024-09-11T12:54:49.923276\n", + " 2024-10-19T23:14:30.299315\n", " image/svg+xml\n", " \n", " \n", - " Matplotlib v3.7.1, https://matplotlib.org/\n", + " Matplotlib v3.8.1, https://matplotlib.org/\n", " \n", " \n", " \n", @@ -4257,16 +4207,16 @@ " \n", " \n", + "\" clip-path=\"url(#p6a8e363c3a)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4357,11 +4307,11 @@ " \n", " \n", + "\" clip-path=\"url(#p6a8e363c3a)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4419,11 +4369,11 @@ " \n", " \n", + "\" clip-path=\"url(#p6a8e363c3a)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4452,11 +4402,11 @@ " \n", " \n", + "\" clip-path=\"url(#p6a8e363c3a)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4505,11 +4455,11 @@ " \n", " \n", + "\" clip-path=\"url(#p6a8e363c3a)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4552,229 +4502,229 @@ " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5035,16 +4985,16 @@ " \n", " \n", + "\" clip-path=\"url(#p6a8e363c3a)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5056,36 +5006,36 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", + "L 116.44385 123.468871 \n", + "L 122.17265 103.519582 \n", + "L 127.90145 78.801346 \n", + "L 133.63025 114.588324 \n", + "L 139.35905 155.638594 \n", + "L 145.08785 155.638594 \n", + "L 150.81665 155.634913 \n", + "L 156.54545 155.631237 \n", + "L 162.27425 155.634928 \n", + "L 168.00305 155.63133 \n", + "L 173.73185 155.638594 \n", + "L 179.46065 155.638594 \n", + "L 185.18945 155.638594 \n", + "L 190.91825 155.63638 \n", + "L 196.64705 155.637199 \n", + "L 202.37585 155.637668 \n", + "\" clip-path=\"url(#p6a8e363c3a)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", + "L 116.44385 121.832848 \n", + "L 122.17265 110.513378 \n", + "L 127.90145 92.336504 \n", + "L 133.63025 115.561542 \n", + "L 139.35905 155.638594 \n", + "L 145.08785 155.638594 \n", + "L 150.81665 155.634913 \n", + "L 156.54545 155.631237 \n", + "L 162.27425 155.634928 \n", + "L 168.00305 155.631332 \n", + "L 173.73185 155.638594 \n", + "L 179.46065 155.638594 \n", + "L 185.18945 155.638594 \n", + "L 190.91825 155.63639 \n", + "L 196.64705 155.637207 \n", + "L 202.37585 155.637673 \n", + "\" clip-path=\"url(#p6a8e363c3a)\" style=\"fill: none; stroke: #ff7f0e; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", + "L 116.44385 121.832844 \n", + "L 122.17265 110.513369 \n", + "L 127.90145 92.336498 \n", + "L 133.63025 115.561553 \n", + "L 139.35905 155.638594 \n", + "L 145.08785 155.638594 \n", + "L 150.81665 155.634913 \n", + "L 156.54545 155.631237 \n", + "L 162.27425 155.634929 \n", + "L 168.00305 155.631333 \n", + "L 173.73185 155.638594 \n", + "L 179.46065 155.638594 \n", + "L 185.18945 155.638594 \n", + "L 190.91825 155.636397 \n", + "L 196.64705 155.637213 \n", + "L 202.37585 155.637678 \n", + "\" clip-path=\"url(#p6a8e363c3a)\" style=\"fill: none; stroke: #2ca02c; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", + "L 116.44385 121.832766 \n", + "L 122.17265 110.513194 \n", + "L 127.90145 92.336388 \n", + "L 133.63025 115.561773 \n", + "L 139.35905 155.638594 \n", + "L 145.08785 155.638594 \n", + "L 150.81665 155.634913 \n", + "L 156.54545 155.631237 \n", + "L 162.27425 155.634928 \n", + "L 168.00305 155.631332 \n", + "L 173.73185 155.638594 \n", + "L 179.46065 155.638594 \n", + "L 185.18945 155.638594 \n", + "L 190.91825 155.636391 \n", + "L 196.64705 155.63721 \n", + "L 202.37585 155.637677 \n", + "\" clip-path=\"url(#p6a8e363c3a)\" style=\"fill: none; stroke: #d62728; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5752,12 +5702,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "7179c219fad442c58aa3b91ba50297ee", + "model_id": "53af578e17534b1398d2322571f7ba84", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HTML(value=\"./tmpjuit2l7r.pdf
\")" + "HBox(children=(HTML(value=\"./tmp10ud7gq6.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -5765,23 +5715,21 @@ } ], "source": [ - "plt.plot(diam_grid.centers, dists[0],label='$t = 0$ h')\n", - "plt.plot(diam_grid.centers, dists[6],label='$t = 6$ h')\n", - "plt.plot(diam_grid.centers, dists[12],label='$t = 12$ h')\n", - "plt.plot(diam_grid.centers, dists[24],label='$t = 24$ h')\n", + "for hour in (0, 6, 12, 24):\n", + " plt.plot(DIAM_GRID.centers, OUTPUT['dists'][hour], label=f'$t = {hour}$ h')\n", "plt.xscale(\"log\")\n", "plt.xlabel(\"Dry diameter (m)\")\n", "plt.ylabel(r\"Number concentration $n(D)$ ($\\#$ m$^{-3}$)\")\n", "plt.ylim(bottom=0)\n", "plt.legend()\n", - "plt.xlim([diam_grid.edges[0],diam_grid.edges[-1]])\n", + "plt.xlim([DIAM_GRID.edges[i] for i in (0, -1)])\n", "show_plot()" ] }, { "cell_type": "code", "execution_count": null, - "id": "a07540c5", + "id": "3ddc93ff-798a-48e6-b60e-3c50dfe5f906", "metadata": {}, "outputs": [], "source": [] From 1c81b3bdb13bcf1b1a8e5be949987ba6fdcaeb80 Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Sat, 19 Oct 2024 23:46:33 +0200 Subject: [PATCH 13/26] moving monarch_mod37/cb05_abs_tol.json into the notebook --- examples/monarch_mod37/cb05_abs_tol.json | 407 --------- examples/particle_simulation_with_camp.ipynb | 855 ++++++++++--------- 2 files changed, 441 insertions(+), 821 deletions(-) delete mode 100644 examples/monarch_mod37/cb05_abs_tol.json diff --git a/examples/monarch_mod37/cb05_abs_tol.json b/examples/monarch_mod37/cb05_abs_tol.json deleted file mode 100644 index 7a3bfc5f..00000000 --- a/examples/monarch_mod37/cb05_abs_tol.json +++ /dev/null @@ -1,407 +0,0 @@ -{ - "camp-data" : [ - { - "type" : "RELATIVE_TOLERANCE", - "value" : 1.0E-04 - }, - { - "name" : "NO2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "NO", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "O", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "O3", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "NO3", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "O1D", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "OH", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "HO2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "N2O5", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "HNO3", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "HONO", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "PNA", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "H2O2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "XO2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "XO2N", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "NTR", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "ROOH", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "FORM", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "ALD2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "ALDX", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "PAR", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "CO", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "MEO2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "MEPX", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "MEOH", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "HCO3", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "FACD", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "C2O3", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "PAN", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "PACD", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "AACD", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "CXO3", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "PANX", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "ROR", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "OLE", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "ETH", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "IOLE", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "TOL", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "CRES", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "TO2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "TOLRO2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "OPEN", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "CRO", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "MGLY", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "XYL", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "XYLRO2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "ISOP", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "ISPD", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "ISOPRXN", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "TERP", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "TRPRXN", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "SO2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "SULF", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "SULRXN", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "ETOH", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "ETHA", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "CL2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "CL", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "HOCL", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "CLO", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "FMCL", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "HCL", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "TOLNRXN", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "TOLHRXN", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "XYLNRXN", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "XYLHRXN", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "BENZENE", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "BENZRO2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "BNZNRXN", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "BNZHRXN", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "SESQ", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "SESQRXN", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "M", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "O2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "N2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "H2O", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "CH4", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "H2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - }, - { - "name" : "N2O", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03 - }, - { - "name" : "DUMMY", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E+00 - } -]} diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index 3dfd66bf..a76328f7 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -63,35 +63,16 @@ { "cell_type": "code", "execution_count": 4, - "id": "b480e7ad", + "id": "0ec2454c-337d-4dc4-8ceb-5692948a9ef0", "metadata": {}, "outputs": [], "source": [ - "N_PART = 100\n", - "T_INITIAL = 0.0\n", - "RUN_PART_ARGS = {}" + "N_PART = 100" ] }, { "cell_type": "code", "execution_count": 5, - "id": "a2d7bad8", - "metadata": {}, - "outputs": [], - "source": [ - "RUN_PART_ARGS['env_state'] = ppmc.EnvState({\n", - " \"rel_humidity\": 0.,\n", - " \"latitude\": 0,\n", - " \"longitude\": 0,\n", - " \"altitude\": 0 * si.m,\n", - " \"start_time\": 21600 * si.s,\n", - " \"start_day\": 200,\n", - "})" - ] - }, - { - "cell_type": "code", - "execution_count": 6, "id": "2e492520-ba61-45bb-b9b3-5a04fb6f21df", "metadata": {}, "outputs": [], @@ -132,7 +113,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 6, "id": "16377896", "metadata": {}, "outputs": [], @@ -143,7 +124,7 @@ " \"camp-files\" : [\n", " \"aerosol_representation.json\",\n", " \"aerosol_phases.json\",\n", - " \"monarch_mod37/cb05_abs_tol.json\",\n", + " \"monarch_mod37-cb05_abs_tol.json\",\n", " \"monarch_mod37/cb05_mechanism_without_R142_R143.json\",\n", " \"monarch_mod37/cb05_species.json\",\n", " \"monarch_mod37/custom_species.json\",\n", @@ -158,7 +139,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 7, "id": "5e4e5c4b", "metadata": {}, "outputs": [], @@ -179,7 +160,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 8, "id": "e3c41245", "metadata": {}, "outputs": [], @@ -226,9 +207,55 @@ " )" ] }, + { + "cell_type": "code", + "execution_count": 9, + "id": "d7482795-f98e-43f7-ab59-604a1e964706", + "metadata": {}, + "outputs": [], + "source": [ + "with open('monarch_mod37-cb05_abs_tol.json', 'w', encoding='utf-8') as f:\n", + " json.dump({\"camp-data\" : [\n", + " {\n", + " \"type\" : \"RELATIVE_TOLERANCE\",\n", + " \"value\" : 1e-4\n", + " },\n", + " *[{'name': name, 'type': \"CHEM_SPEC\", 'absolute integration tolerance': 1e-3} for name in (\n", + " \"NO2\", \"NO\", \"O3\", \"NO3\", \"OH\", \"HO2\", \"N2O5\", \"HNO3\", \"HONO\", \"PNA\", \"H2O2\", \"XO2\", \"XO2N\",\n", + " \"ROOH\", \"FORM\", \"ALD2\", \"ALDX\", \"PAR\", \"CO\", \"MEO2\", \"MEPX\", \"MEOH\", \"FACD\", \"C2O3\", \"PAN\",\n", + " \"PACD\", \"AACD\", \"CXO3\", \"PANX\", \"ROR\", \"OLE\", \"ETH\", \"IOLE\", \"TOL\", \"CRES\", \"TO2\", \"TOLRO2\",\n", + " \"OPEN\", \"CRO\", \"MGLY\", \"XYL\", \"XYLRO2\", \"ISOP\", \"ISPD\", \"TERP\", \"SO2\", \"ETOH\", \"ETHA\", \"CL2\",\n", + " \"CL\", \"HOCL\", \"CLO\", \"FMCL\", \"HCL\", \"BENZENE\", \"BENZRO2\", \"SESQ\", \"N2O\",\n", + " )],\n", + " *[{'name': name, 'type': \"CHEM_SPEC\", 'absolute integration tolerance': 1.} for name in (\n", + " \"O\", \"O1D\", \"NTR\", \"HCO3\", \"ISOPRXN\", \"TRPRXN\", \"SULF\", \"SULRXN\", \"TOLNRXN\", \"TOLHRXN\", \"XYLNRXN\",\n", + " \"XYLHRXN\", \"BNZNRXN\", \"BNZHRXN\", \"SESQRXN\", \"M\", \"O2\", \"N2\", \"H2O\", \"CH4\", \"H2\", \"DUMMY\",\n", + " )]\n", + " ]}, f, indent=4)" + ] + }, { "cell_type": "code", "execution_count": 10, + "id": "c205c307-9d78-4cc9-840e-df1b87f5798f", + "metadata": {}, + "outputs": [], + "source": [ + "T_INITIAL = 0.0\n", + "RUN_PART_ARGS = {}\n", + "RUN_PART_ARGS['env_state'] = ppmc.EnvState({\n", + " \"rel_humidity\": 0.,\n", + " \"latitude\": 0,\n", + " \"longitude\": 0,\n", + " \"altitude\": 0 * si.m,\n", + " \"start_time\": 21600 * si.s,\n", + " \"start_day\": 200,\n", + "})" + ] + }, + { + "cell_type": "code", + "execution_count": 11, "id": "de15cde5", "metadata": {}, "outputs": [], @@ -239,7 +266,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 12, "id": "6de20b3f", "metadata": {}, "outputs": [], @@ -250,7 +277,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 13, "id": "c822823d", "metadata": {}, "outputs": [], @@ -268,19 +295,19 @@ " {\"CH4\": [2.2E+03]},\n", " {\"ETHA\": [1.]},\n", " {\"FORM\": [1.2]},\n", - " {\"MEOH\": [1.2E-01]},\n", + " {\"MEOH\": [1.2E-1]},\n", " {\"MEPX\": [0.5]},\n", " {\"ALD2\": [1.]},\n", " {\"PAR\": [2.]},\n", " {\"ETH\": [0.2]},\n", - " {\"OLE\": [2.3E-02]},\n", - " {\"IOLE\": [3.1E-04]},\n", + " {\"OLE\": [2.3E-2]},\n", + " {\"IOLE\": [3.1E-4]},\n", " {\"TOL\": [0.1]},\n", " {\"XYL\": [0.1]},\n", " {\"NTR\": [0.1]},\n", " {\"PAN\": [0.8]},\n", " {\"AACD\": [0.2]},\n", - " {\"ROOH\": [2.5E-02]},\n", + " {\"ROOH\": [2.5E-2]},\n", " {\"ISOP\": [5.]},\n", " {\"O2\": [2.095E+08]},\n", " {\"N2\": [7.8E+08]},\n", @@ -291,7 +318,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 14, "id": "920e41e3", "metadata": {}, "outputs": [], @@ -310,10 +337,10 @@ " \"gas_emissions\": [\n", " {\"time\": [0, 43200]},\n", " {\"rate\": [1., 0.]},\n", - " {\"SO2\": [1.06E-09, 1.06E-09]},\n", + " {\"SO2\": [1.06E-9, 1.06E-9]},\n", " {\"NO2\": [7.56E-12, 7.56E-12]},\n", " {\"NO\": [1.44E-10, 1.44E-10]},\n", - " {\"CO\": [1.96E-09, 1.96E-09]},\n", + " {\"CO\": [1.96E-9, 1.96E-9]},\n", " {\"ALD2\": [4.25E-12, 4.25E-12]},\n", " {\"FORM\": [1.02E-11, 1.02E-11]},\n", " {\"ETH\": [4.62E-11, 4.62E-11]},\n", @@ -339,19 +366,19 @@ " {\"CH4\": [2.2E+03]},\n", " {\"ETHA\": [1.]},\n", " {\"FORM\": [1.2]},\n", - " {\"MEOH\": [1.2E-01]},\n", + " {\"MEOH\": [1.2E-1]},\n", " {\"MEPX\": [0.5]},\n", " {\"ALD2\": [1.]},\n", " {\"PAR\": [2.]},\n", " {\"ETH\": [0.2]},\n", - " {\"OLE\": [2.3E-02]},\n", - " {\"IOLE\": [3.1E-04]},\n", + " {\"OLE\": [2.3E-2]},\n", + " {\"IOLE\": [3.1E-4]},\n", " {\"TOL\": [0.1]},\n", " {\"XYL\": [0.1]},\n", " {\"NTR\": [0.1]},\n", " {\"PAN\": [0.8]},\n", " {\"AACD\": [0.2]},\n", - " {\"ROOH\": [2.5E-02]},\n", + " {\"ROOH\": [2.5E-2]},\n", " {\"ISOP\": [5.]},\n", " {\"O2\": [2.095E+08]},\n", " {\"N2\": [7.8E+08]},\n", @@ -393,7 +420,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 15, "id": "6722ba83", "metadata": {}, "outputs": [], @@ -403,7 +430,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 16, "id": "96ba54c5-dc33-4e22-b774-390cec4be69f", "metadata": {}, "outputs": [], @@ -441,17 +468,17 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 17, "id": "d8d9c8fd", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "46" + "58" ] }, - "execution_count": 16, + "execution_count": 17, "metadata": {}, "output_type": "execute_result" } @@ -483,7 +510,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 18, "id": "5f3665a5-be3c-49e4-b1d0-47f3e2b82c30", "metadata": {}, "outputs": [], @@ -493,7 +520,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 19, "id": "0f7c29fe", "metadata": {}, "outputs": [], @@ -530,7 +557,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 20, "id": "82c0cebb", "metadata": {}, "outputs": [], @@ -542,7 +569,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 21, "id": "47474cd3", "metadata": {}, "outputs": [ @@ -557,7 +584,7 @@ " \n", " \n", " \n", - " 2024-10-19T23:14:27.741913\n", + " 2024-10-19T23:44:52.022487\n", " image/svg+xml\n", " \n", " \n", @@ -593,16 +620,16 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -639,11 +666,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -731,11 +758,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -806,11 +833,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -869,11 +896,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1045,16 +1072,16 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1107,11 +1134,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1127,11 +1154,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1147,11 +1174,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1199,11 +1226,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1219,11 +1246,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1395,7 +1422,7 @@ " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #ff0000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1447,11 +1474,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1466,11 +1493,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1485,11 +1512,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1504,11 +1531,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1523,11 +1550,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1726,7 +1753,7 @@ " \n", + "\" clip-path=\"url(#pb6eb53625f)\" style=\"fill: none; stroke: #008000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1767,12 +1794,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "f4b1662328744d5ca758094d1530c0f8", + "model_id": "54ff6763308743b9a172e616da616246", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpmaf6ysce.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmp3g4ij0xr.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -1795,7 +1822,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 22, "id": "c85a622a", "metadata": {}, "outputs": [], @@ -1814,7 +1841,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 23, "id": "8e1b89e0", "metadata": {}, "outputs": [ @@ -1829,7 +1856,7 @@ " \n", " \n", " \n", - " 2024-10-19T23:14:28.449631\n", + " 2024-10-19T23:44:53.408660\n", " image/svg+xml\n", " \n", " \n", @@ -1865,16 +1892,16 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1911,11 +1938,11 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2003,11 +2030,11 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2078,11 +2105,11 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2141,11 +2168,11 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2317,20 +2344,20 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2383,17 +2380,27 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2432,19 +2439,51 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2454,32 +2493,20 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -2488,19 +2515,19 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2754,26 +2781,26 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2828,17 +2855,17 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2849,17 +2876,17 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2870,17 +2897,17 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2891,17 +2918,17 @@ " \n", " \n", + "\" clip-path=\"url(#p855b62a7ef)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3051,11 +3078,11 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3096,12 +3123,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "5db8694ea8204eadaf9fe33882fbbbce", + "model_id": "12d69afb9f6347799530bde0cb043f67", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpe2asd795.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpphexd4io.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -3124,7 +3151,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 24, "id": "386aa7c2", "metadata": {}, "outputs": [ @@ -3139,7 +3166,7 @@ " \n", " \n", " \n", - " 2024-10-19T23:14:29.119403\n", + " 2024-10-19T23:44:54.106868\n", " image/svg+xml\n", " \n", " \n", @@ -3175,16 +3202,16 @@ " \n", " \n", + "\" clip-path=\"url(#p8eac6fdde0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3221,11 +3248,11 @@ " \n", " \n", + "\" clip-path=\"url(#p8eac6fdde0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3313,11 +3340,11 @@ " \n", " \n", + "\" clip-path=\"url(#p8eac6fdde0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3388,11 +3415,11 @@ " \n", " \n", + "\" clip-path=\"url(#p8eac6fdde0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3451,11 +3478,11 @@ " \n", " \n", + "\" clip-path=\"url(#p8eac6fdde0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3627,16 +3654,16 @@ " \n", " \n", + "\" clip-path=\"url(#p8eac6fdde0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3651,16 +3678,16 @@ " \n", " \n", + "\" clip-path=\"url(#p8eac6fdde0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3668,18 +3695,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3689,11 +3716,11 @@ " \n", " \n", + "\" clip-path=\"url(#p8eac6fdde0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3708,11 +3735,11 @@ " \n", " \n", + "\" clip-path=\"url(#p8eac6fdde0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3728,11 +3755,11 @@ " \n", " \n", + "\" clip-path=\"url(#p8eac6fdde0)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3999,12 +4026,12 @@ " \n", " \n", " \n", - " \n", + "\" clip-path=\"url(#p8eac6fdde0)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4127,12 +4154,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "8209f77c37ed4c25b04472b7fabca343", + "model_id": "a7d9955c086a43c6a05a4ccf6c22d069", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmp1pg_brlq.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpicdcau0z.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -4156,7 +4183,7 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 25, "id": "faa1de28", "metadata": {}, "outputs": [ @@ -4171,7 +4198,7 @@ " \n", " \n", " \n", - " 2024-10-19T23:14:30.299315\n", + " 2024-10-19T23:44:56.548277\n", " image/svg+xml\n", " \n", " \n", @@ -4207,16 +4234,16 @@ " \n", " \n", + "\" clip-path=\"url(#p2caf97c04b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4307,11 +4334,11 @@ " \n", " \n", + "\" clip-path=\"url(#p2caf97c04b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4369,11 +4396,11 @@ " \n", " \n", + "\" clip-path=\"url(#p2caf97c04b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4402,11 +4429,11 @@ " \n", " \n", + "\" clip-path=\"url(#p2caf97c04b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4455,11 +4482,11 @@ " \n", " \n", + "\" clip-path=\"url(#p2caf97c04b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4502,229 +4529,229 @@ " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4985,16 +5012,16 @@ " \n", " \n", + "\" clip-path=\"url(#p2caf97c04b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5006,36 +5033,36 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", + "L 145.08785 146.988408 \n", + "L 150.81665 155.638594 \n", + "L 156.54545 155.634952 \n", + "L 162.27425 155.631335 \n", + "L 168.00305 155.634978 \n", + "L 173.73185 155.635118 \n", + "L 179.46065 155.628725 \n", + "L 185.18945 155.635395 \n", + "L 190.91825 155.638594 \n", + "L 196.64705 155.638594 \n", + "L 202.37585 155.638594 \n", + "\" clip-path=\"url(#p2caf97c04b)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", + "L 145.08785 146.988016 \n", + "L 150.81665 155.638594 \n", + "L 156.54545 155.634952 \n", + "L 162.27425 155.631336 \n", + "L 168.00305 155.634978 \n", + "L 173.73185 155.63512 \n", + "L 179.46065 155.62874 \n", + "L 185.18945 155.6354 \n", + "L 190.91825 155.638594 \n", + "L 196.64705 155.638594 \n", + "L 202.37585 155.638594 \n", + "\" clip-path=\"url(#p2caf97c04b)\" style=\"fill: none; stroke: #ff7f0e; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", + "L 145.08785 146.988049 \n", + "L 150.81665 155.638594 \n", + "L 156.54545 155.634952 \n", + "L 162.27425 155.631336 \n", + "L 168.00305 155.634979 \n", + "L 173.73185 155.635122 \n", + "L 179.46065 155.631961 \n", + "L 185.18945 155.63219 \n", + "L 190.91825 155.638594 \n", + "L 196.64705 155.638594 \n", + "L 202.37585 155.638594 \n", + "\" clip-path=\"url(#p2caf97c04b)\" style=\"fill: none; stroke: #2ca02c; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", + "L 145.08785 146.988441 \n", + "L 150.81665 155.638594 \n", + "L 156.54545 155.634952 \n", + "L 162.27425 155.631336 \n", + "L 168.00305 155.634978 \n", + "L 173.73185 155.63512 \n", + "L 179.46065 155.631955 \n", + "L 185.18945 155.632183 \n", + "L 190.91825 155.638594 \n", + "L 196.64705 155.638594 \n", + "L 202.37585 155.638594 \n", + "\" clip-path=\"url(#p2caf97c04b)\" style=\"fill: none; stroke: #d62728; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5702,12 +5729,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "53af578e17534b1398d2322571f7ba84", + "model_id": "537ee095f324463e834c5518c4194890", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmp10ud7gq6.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmprrd4a3h1.pdf
\"), HTML(value…" ] }, "metadata": {}, From 15b0a978a067771985d5b07b2edf7847708eb4db Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Sat, 19 Oct 2024 23:55:13 +0200 Subject: [PATCH 14/26] moving monarch_mod37/cb05_mechanism_without_R142_R143.json into the notebook --- .../cb05_mechanism_without_R142_R143.json | 3112 ------------- examples/particle_simulation_with_camp.ipynb | 4005 +++++++++++++++-- 2 files changed, 3569 insertions(+), 3548 deletions(-) delete mode 100755 examples/monarch_mod37/cb05_mechanism_without_R142_R143.json diff --git a/examples/monarch_mod37/cb05_mechanism_without_R142_R143.json b/examples/monarch_mod37/cb05_mechanism_without_R142_R143.json deleted file mode 100755 index 45b4bb99..00000000 --- a/examples/monarch_mod37/cb05_mechanism_without_R142_R143.json +++ /dev/null @@ -1,3112 +0,0 @@ -{ "camp-data" : [ - { - "name" : "MONARCH mod37", - "type" : "MECHANISM", - "reactions" : [ - { - "rxn id" : "R1", - "reactants" : { - "NO2" : {} - }, - "products" : { - "NO" : {} , - "O" : {} - }, - "orig params" : "TUV_J(4, THETA)", - "base rate" : 4.77e-3, - "Fast-J id" : "NO2", - "type" : "PHOTOLYSIS" - }, - { - "rxn id" : "R2", - "reactants" : { - "O" : {} , - "O2" : {} , - "M" : {} - }, - "products" : { - "O3" : {} , - "M" : {} - }, - "orig params" : "O2 * M * CMAQ_1to4(6.0E-34, -2.4, 0.0E+00)", - "type" : "ARRHENIUS", - "A" : 6.0E-34, - "B" : -2.4, - "C" : -0.0E+00 - }, - { - "rxn id" : "R3", - "reactants" : { - "O3" : {} , - "NO" : {} - }, - "products" : { - "NO2" : {} - }, - "orig params" : "CMAQ_1to4(3.0E-12, 0.0E+00, 1500.0)", - "type" : "ARRHENIUS", - "A" : 3.0E-12, - "B" : 0.0E+00, - "C" : -1500.0 - }, - { - "rxn id" : "R4", - "reactants" : { - "O" : {} , - "NO2" : {} - }, - "products" : { - "NO" : {} - }, - "orig params" : "CMAQ_1to4(5.6E-12, 0.0E+00, -180.0)", - "type" : "ARRHENIUS", - "A" : 5.6E-12, - "B" : 0.0E+00, - "C" : 180.0 - }, - { - "rxn id" : "R5", - "reactants" : { - "O" : {} , - "NO2" : {} - }, - "products" : { - "NO3" : {} - }, - "orig params" : "CMAQ_10(2.5E-31, -1.8, 0.0E+00, 2.2E-11, -0.7, 0.0E+00, 0.6, 1.0)", - "type" : "TROE", - "k0_A" : 2.5E-31, - "k0_B" : -1.8, - "k0_C" : -0.0E+00, - "kinf_A" : 2.2E-11, - "kinf_B" : -0.7, - "kinf_C" : -0.0E+00, - "Fc" : 0.6, - "N" : 1.0 - }, - { - "rxn id" : "R6", - "reactants" : { - "O" : {} , - "NO" : {} - }, - "products" : { - "NO2" : {} - }, - "orig params" : "CMAQ_10(9.0E-32, -1.5, 0.0E+00, 3.0E-11, 0.0E+00, 0.0E+00, 0.6, 1.0)", - "type" : "TROE", - "k0_A" : 9.0E-32, - "k0_B" : -1.5, - "k0_C" : -0.0E+00, - "kinf_A" : 3.0E-11, - "kinf_B" : 0.0E+00, - "kinf_C" : -0.0E+00, - "Fc" : 0.6, - "N" : 1.0 - }, - { - "rxn id" : "R7", - "reactants" : { - "NO2" : {} , - "O3" : {} - }, - "products" : { - "NO3" : {} - }, - "orig params" : "CMAQ_1to4(1.2E-13, 0.0E+00, 2450.0)", - "type" : "ARRHENIUS", - "A" : 1.2E-13, - "B" : 0.0E+00, - "C" : -2450.0 - }, - { - "rxn id" : "R8", - "reactants" : { - "O3" : {} - }, - "products" : { - "O" : {} - }, - "orig params" : "TUV_J(3, 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: 0.0E+00, - "C" : -206.0 - }, - { - "rxn id" : "SA06", - "reactants" : { - "BENZRO2" : {} , - "NO" : {} - }, - "products" : { - "NO" : {} , - "BNZNRXN" : {} - }, - "orig params" : "CMAQ_1to4(2.70e-12, 0.0E+00, -360.0)", - "type" : "ARRHENIUS", - "A" : 2.70e-12, - "B" : 0.0E+00, - "C" : 360.0 - }, - { - "rxn id" : "SA07", - "reactants" : { - "BENZRO2" : {} , - "HO2" : {} - }, - "products" : { - "HO2" : {} , - "BNZHRXN" : {} - }, - "orig params" : "CMAQ_1to4(1.90e-13, 0.0E+00, -1300.0)", - "type" : "ARRHENIUS", - "A" : 1.90e-13, - "B" : 0.0E+00, - "C" : 1300.0 - }, - { - "rxn id" : "SA08", - "reactants" : { - "SESQ" : {} , - "O3" : {} - }, - "products" : { - "O3" : {} , - "SESQRXN" : {} - }, - "orig params" : "CMAQ_1to4(1.16E-14, 0.0E+00, 0.0E+00)", - "type" : "ARRHENIUS", - "A" : 1.16E-14, - "B" : 0.0E+00, - "C" : -0.0E+00 - }, - { - "rxn id" : "SA09", - "reactants" : { - "SESQ" : {} , - "OH" : {} - }, - "products" : { - "OH" : {} , - "SESQRXN" : {} - }, - "orig params" : "CMAQ_1to4(1.97E-10, 0.0E+00, 0.0E+00)", - "type" : "ARRHENIUS", - "A" : 1.97E-10, - "B" : 0.0E+00, - "C" : -0.0E+00 - }, - { - "rxn id" : "SA10", - "reactants" : { - "SESQ" : {} , - "NO3" : {} - }, - "products" : { - "NO3" : {} , - "SESQRXN" : {} - }, - "orig params" : "CMAQ_1to4(1.90E-11, 0.0E+00, 0.0E+00)", - "type" : "ARRHENIUS", - "A" : 1.90E-11, - "B" : 0.0E+00, - "C" : -0.0E+00 - }, - { - "rxn id" : "jo2", - "reactants" : { - "O2" : {} - }, - "products" : { - "O" : { "yield" : 2 } - }, - "orig params" : "TUV_J(1, THETA)", - "base rate" : 0.00e+1, - "notes" : "Fast-J does not currently calculate O2 photolysis", - "type" : "PHOTOLYSIS" - } - ] -} -]} diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index a76328f7..e299923c 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -125,7 +125,7 @@ " \"aerosol_representation.json\",\n", " \"aerosol_phases.json\",\n", " \"monarch_mod37-cb05_abs_tol.json\",\n", - " \"monarch_mod37/cb05_mechanism_without_R142_R143.json\",\n", + " \"monarch_mod37-cb05_mechanism_without_R142_R143.json\",\n", " \"monarch_mod37/cb05_species.json\",\n", " \"monarch_mod37/custom_species.json\",\n", " \"monarch_mod37/partitioning_species_params.json\",\n", @@ -237,6 +237,3125 @@ { "cell_type": "code", "execution_count": 10, + "id": "e0ed380d-f2e3-4eb1-ba6e-c81f820fe69d", + "metadata": {}, + "outputs": [], + "source": [ + "with open(\"monarch_mod37-cb05_mechanism_without_R142_R143.json\", 'w', encoding='utf-8') as f:\n", + " json.dump({ \"camp-data\" : [{\n", + " \"name\" : \"MONARCH mod37\",\n", + " \"type\" : \"MECHANISM\",\n", + " \"reactions\" : [\n", + " {\n", + " \"rxn id\" : \"R1\",\n", + " \"reactants\" : {\n", + " \"NO2\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"NO\" : {} ,\n", + " \"O\" : {}\n", + " },\n", + " \"orig params\" : \"TUV_J(4, THETA)\",\n", + " \"base rate\" : 4.77e-3,\n", + " \"Fast-J id\" : \"NO2\",\n", + " \"type\" : \"PHOTOLYSIS\"\n", + " },\n", + " {\n", + " \"rxn id\" : \"R2\",\n", + " \"reactants\" : {\n", + " \"O\" : {} ,\n", + " \"O2\" : {} ,\n", + " \"M\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"O3\" : {} ,\n", + " \"M\" : {}\n", + " },\n", + " \"orig params\" : \"O2 * M * CMAQ_1to4(6.0E-34, -2.4, 0.0E+00)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 6.0E-34,\n", + " \"B\" : -2.4,\n", + " \"C\" : -0.0E+00\n", + " },\n", + " {\n", + " \"rxn id\" : \"R3\",\n", + " \"reactants\" : {\n", + " \"O3\" : {} ,\n", + " \"NO\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"NO2\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_1to4(3.0E-12, 0.0E+00, 1500.0)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 3.0E-12,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : -1500.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"R4\",\n", + " \"reactants\" : {\n", + " \"O\" : {} ,\n", + " \"NO2\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"NO\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_1to4(5.6E-12, 0.0E+00, -180.0)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 5.6E-12,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : 180.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"R5\",\n", + " \"reactants\" : {\n", + " \"O\" : {} ,\n", + " \"NO2\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"NO3\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_10(2.5E-31, -1.8, 0.0E+00, 2.2E-11, -0.7, 0.0E+00, 0.6, 1.0)\",\n", + " \"type\" : \"TROE\",\n", + " \"k0_A\" : 2.5E-31,\n", + " \"k0_B\" : -1.8,\n", + " \"k0_C\" : -0.0E+00,\n", + " \"kinf_A\" : 2.2E-11,\n", + " \"kinf_B\" : -0.7,\n", + " \"kinf_C\" : -0.0E+00,\n", + " \"Fc\" : 0.6,\n", + " \"N\" : 1.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"R6\",\n", + " \"reactants\" : {\n", + " \"O\" : {} ,\n", + " \"NO\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"NO2\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_10(9.0E-32, -1.5, 0.0E+00, 3.0E-11, 0.0E+00, 0.0E+00, 0.6, 1.0)\",\n", + " \"type\" : \"TROE\",\n", + " \"k0_A\" : 9.0E-32,\n", + " \"k0_B\" : -1.5,\n", + " \"k0_C\" : -0.0E+00,\n", + " \"kinf_A\" : 3.0E-11,\n", + " \"kinf_B\" : 0.0E+00,\n", + " \"kinf_C\" : -0.0E+00,\n", + " \"Fc\" : 0.6,\n", + " \"N\" : 1.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"R7\",\n", + " \"reactants\" : {\n", + " \"NO2\" : {} ,\n", + " \"O3\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"NO3\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_1to4(1.2E-13, 0.0E+00, 2450.0)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 1.2E-13,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : -2450.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"R8\",\n", + " \"reactants\" : {\n", + " \"O3\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"O\" : {}\n", + " },\n", + " \"orig params\" : \"TUV_J(3, THETA)\",\n", + " \"base rate\" : 2.53e-4,\n", + " \"Fast-J id\" : \"O3\",\n", + " \"type\" : \"PHOTOLYSIS\"\n", + " },\n", + " {\n", + " \"rxn id\" : \"R9\",\n", + " \"reactants\" : {\n", + " \"O3\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"O1D\" : {}\n", + " },\n", + " \"orig params\" : \"TUV_J(2, THETA)\",\n", + " \"base rate\" : 2.26e-6,\n", + " \"Fast-J id\" : \"O3_1d\",\n", + " \"type\" : \"PHOTOLYSIS\"\n", + " },\n", + " {\n", + " \"rxn id\" : \"R10\",\n", + " \"reactants\" : {\n", + " \"O1D\" : {} ,\n", + " \"M\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"O\" : {} ,\n", + " \"M\" : {}\n", + " },\n", + " \"orig params\" : \"M * CMAQ_1to4(2.1E-11, 0.0E+00, -102.0)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 2.1E-11,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : 102.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"R11\",\n", + " \"reactants\" : {\n", + " \"O1D\" : {} ,\n", + " \"H2O\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"OH\" : { \"yield\" : 2.000 }\n", + " },\n", + " \"orig params\" : \"H2O * CMAQ_1to4(2.2E-10, 0.0E+00, 0.0E+00)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 2.2E-10,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : -0.0E+00\n", + " },\n", + " {\n", + " \"rxn id\" : \"R12\",\n", + " \"reactants\" : {\n", + " \"O3\" : {} ,\n", + " \"OH\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"HO2\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_1to4(1.7E-12, 0.0E+00, 940.0)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 1.7E-12,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : -940.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"R13\",\n", + " \"reactants\" : {\n", + " \"O3\" : {} ,\n", + " \"HO2\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"OH\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_1to4(1.0E-14, 0.0E+00, 490.0)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 1.0E-14,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : -490.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"R14\",\n", + " \"reactants\" : {\n", + " \"NO3\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"NO2\" : {} ,\n", + " \"O\" : {}\n", + " },\n", + " \"orig params\" : \"TUV_J(6, THETA)\",\n", + " \"scaling factor\" : 0.89,\n", + " \"base rate\" : 1.31e-1,\n", + " \"Fast-J id\" : \"NO3_X\",\n", + " \"type\" : \"PHOTOLYSIS\"\n", + " },\n", + " {\n", + " \"rxn id\" : \"R15\",\n", + " \"reactants\" : {\n", + " \"NO3\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"NO\" : {}\n", + " },\n", + " \"orig params\" : \"TUV_J(5, THETA)\",\n", + " \"scaling factor\" : 0.11,\n", + " \"base rate\" : 1.31e-1,\n", + " \"Fast-J id\" : \"NO3_L\",\n", + " \"type\" : \"PHOTOLYSIS\"\n", + " },\n", + " {\n", + " \"rxn id\" : \"R16\",\n", + " \"reactants\" : {\n", + " \"NO3\" : {} ,\n", + " \"NO\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"NO2\" : { \"yield\" : 2.000 }\n", + " },\n", + " \"orig params\" : \"CMAQ_1to4(1.5E-11, 0.0E+00, -170.0)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 1.5E-11,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : 170.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"R17\",\n", + " \"reactants\" : {\n", + " \"NO3\" : {} ,\n", + " \"NO2\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"NO\" : {} ,\n", + " \"NO2\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_1to4(4.5E-14, 0.0E+00, 1260.0)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 4.5E-14,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : -1260.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"R18\",\n", + " \"reactants\" : {\n", + " \"NO3\" : {} ,\n", + " \"NO2\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"N2O5\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_10(2.0E-30, -4.4, 0.0E+00, 1.4E-12, -0.7, 0.0E+00, 0.6, 1.0)\",\n", + " \"type\" : \"TROE\",\n", + " \"k0_A\" : 2.0E-30,\n", + " \"k0_B\" : -4.4,\n", + " \"k0_C\" : -0.0E+00,\n", + " \"kinf_A\" : 1.4E-12,\n", + " \"kinf_B\" : -0.7,\n", + " \"kinf_C\" : -0.0E+00,\n", + " \"Fc\" : 0.6,\n", + " \"N\" : 1.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"R19\",\n", + " \"reactants\" : {\n", + " \"N2O5\" : {} ,\n", + " \"H2O\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"HNO3\" : { \"yield\" : 2.000 } ,\n", + " \"DUMMY\" : {}\n", + " },\n", + " \"orig params\" : \"H2O * CMAQ_1to4(2.5E-22, 0.0E+00, 0.0E+00)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 2.5E-22,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : -0.0E+00\n", + " },\n", + " {\n", + " \"rxn id\" : \"R20\",\n", + " \"reactants\" : {\n", + " \"N2O5\" : {} ,\n", + " \"H2O\" : { \"qty\" : 2 }\n", + " },\n", + " \"products\" : {\n", + " \"HNO3\" : { \"yield\" : 2.000 }\n", + " },\n", + " \"orig params\" : \"H2O**2 * CMAQ_1to4(1.8E-39, 0.0E+00, 0.0E+00)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 1.8E-39,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : -0.0E+00\n", + " },\n", + " {\n", + " \"rxn id\" : \"R21\",\n", + " \"reactants\" : {\n", + " \"N2O5\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"NO3\" : {} ,\n", + " \"NO2\" : {} ,\n", + " \"DUMMY\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_10(1.0E-03, -3.5, 11000.0, 9.7E+14, 0.1, 11080.0, 0.45, 1.0)\",\n", + " \"type\" : \"TROE\",\n", + " \"k0_A\" : 1.0E-03,\n", + " \"k0_B\" : -3.5,\n", + " \"k0_C\" : -11000.0,\n", + " \"kinf_A\" 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\"products\" : {\n", + " \"OH\" : {} ,\n", + " \"BENZRO2\" : { \"yield\" : 0.764 }\n", + " },\n", + " \"orig params\" : \"CMAQ_1to4(2.47e-12, 0.0E+00, 206.0)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 2.47e-12,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : -206.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"SA06\",\n", + " \"reactants\" : {\n", + " \"BENZRO2\" : {} ,\n", + " \"NO\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"NO\" : {} ,\n", + " \"BNZNRXN\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_1to4(2.70e-12, 0.0E+00, -360.0)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 2.70e-12,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : 360.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"SA07\",\n", + " \"reactants\" : {\n", + " \"BENZRO2\" : {} ,\n", + " \"HO2\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"HO2\" : {} ,\n", + " \"BNZHRXN\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_1to4(1.90e-13, 0.0E+00, -1300.0)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 1.90e-13,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : 1300.0\n", + " },\n", + " {\n", + " \"rxn id\" : \"SA08\",\n", + " \"reactants\" : {\n", + " \"SESQ\" : {} ,\n", + " \"O3\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"O3\" : {} ,\n", + " \"SESQRXN\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_1to4(1.16E-14, 0.0E+00, 0.0E+00)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 1.16E-14,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : -0.0E+00\n", + " },\n", + " {\n", + " \"rxn id\" : \"SA09\",\n", + " \"reactants\" : {\n", + " \"SESQ\" : {} ,\n", + " \"OH\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"OH\" : {} ,\n", + " \"SESQRXN\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_1to4(1.97E-10, 0.0E+00, 0.0E+00)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 1.97E-10,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : -0.0E+00\n", + " },\n", + " {\n", + " \"rxn id\" : \"SA10\",\n", + " \"reactants\" : {\n", + " \"SESQ\" : {} ,\n", + " \"NO3\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"NO3\" : {} ,\n", + " \"SESQRXN\" : {}\n", + " },\n", + " \"orig params\" : \"CMAQ_1to4(1.90E-11, 0.0E+00, 0.0E+00)\",\n", + " \"type\" : \"ARRHENIUS\",\n", + " \"A\" : 1.90E-11,\n", + " \"B\" : 0.0E+00,\n", + " \"C\" : -0.0E+00\n", + " },\n", + " {\n", + " \"rxn id\" : \"jo2\",\n", + " \"reactants\" : {\n", + " \"O2\" : {}\n", + " },\n", + " \"products\" : {\n", + " \"O\" : { \"yield\" : 2 }\n", + " },\n", + " \"orig params\" : \"TUV_J(1, THETA)\",\n", + " \"base rate\" : 0.00e+1,\n", + " \"notes\" : \"Fast-J does not currently calculate O2 photolysis\",\n", + " \"type\" : \"PHOTOLYSIS\"\n", + " }\n", + " ]}]}, f, indent=4)" + ] + }, + { + "cell_type": "code", + "execution_count": 11, "id": "c205c307-9d78-4cc9-840e-df1b87f5798f", "metadata": {}, "outputs": [], @@ -255,7 +3374,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 12, "id": "de15cde5", "metadata": {}, "outputs": [], @@ -266,7 +3385,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 13, "id": "6de20b3f", "metadata": {}, "outputs": [], @@ -277,7 +3396,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 14, "id": "c822823d", "metadata": {}, "outputs": [], @@ -318,7 +3437,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 15, "id": "920e41e3", "metadata": {}, "outputs": [], @@ -420,7 +3539,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 16, "id": "6722ba83", "metadata": {}, "outputs": [], @@ -430,7 +3549,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 17, "id": "96ba54c5-dc33-4e22-b774-390cec4be69f", "metadata": {}, "outputs": [], @@ -468,17 +3587,17 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 18, "id": "d8d9c8fd", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "58" + "67" ] }, - "execution_count": 17, + "execution_count": 18, "metadata": {}, "output_type": "execute_result" } @@ -510,7 +3629,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 19, "id": "5f3665a5-be3c-49e4-b1d0-47f3e2b82c30", "metadata": {}, "outputs": [], @@ -520,7 +3639,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 20, "id": "0f7c29fe", "metadata": {}, "outputs": [], @@ -557,7 +3676,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 21, "id": "82c0cebb", "metadata": {}, "outputs": [], @@ -569,7 +3688,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 22, "id": "47474cd3", "metadata": {}, "outputs": [ @@ -584,7 +3703,7 @@ " \n", " \n", " \n", - " 2024-10-19T23:44:52.022487\n", + " 2024-10-19T23:53:00.985488\n", " image/svg+xml\n", " \n", " \n", @@ -620,16 +3739,16 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -666,11 +3785,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -758,11 +3877,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -833,11 +3952,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -896,11 +4015,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1072,16 +4191,16 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1134,11 +4253,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1154,11 +4273,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1174,11 +4293,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1226,11 +4345,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1246,11 +4365,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1422,7 +4541,7 @@ " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #ff0000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1474,11 +4593,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1493,11 +4612,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1512,11 +4631,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1531,11 +4650,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1550,11 +4669,11 @@ " \n", " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1753,7 +4872,7 @@ " \n", + "\" clip-path=\"url(#p541749902f)\" style=\"fill: none; stroke: #008000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1794,12 +4913,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "54ff6763308743b9a172e616da616246", + "model_id": "0cc20f2601b6474c907abe14d7a66d1c", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmp3g4ij0xr.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpnuc08rox.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -1822,7 +4941,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 23, "id": "c85a622a", "metadata": {}, "outputs": [], @@ -1841,7 +4960,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 24, "id": "8e1b89e0", "metadata": {}, "outputs": [ @@ -1856,7 +4975,7 @@ " \n", " \n", " \n", - " 2024-10-19T23:44:53.408660\n", + " 2024-10-19T23:53:01.851350\n", " image/svg+xml\n", " \n", " \n", @@ -1892,16 +5011,16 @@ " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1938,11 +5057,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2030,11 +5149,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2105,11 +5224,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2168,11 +5287,11 @@ " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2344,63 +5463,22 @@ " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", " \n", + " \n", + " \n", " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2439,51 +5556,19 @@ " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2493,19 +5578,19 @@ " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2515,19 +5600,19 @@ " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2781,26 +5866,23 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2855,17 +5937,17 @@ " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2876,17 +5958,17 @@ " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2897,17 +5979,17 @@ " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2918,17 +6000,17 @@ " \n", " \n", + "\" clip-path=\"url(#pb2a0bd80ea)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3071,6 +6153,38 @@ " \n", " \n", " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -3078,11 +6192,11 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3123,12 +6237,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "12d69afb9f6347799530bde0cb043f67", + "model_id": "2f40ba53670141ed9c4dd1da0f254f7d", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpphexd4io.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmp12qjmc1l.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -3139,19 +6253,20 @@ "plt.plot(OUTPUT['elapsed_time'], OUTPUT['total_mass_conc'], \"b\", label=\"mass conc\")\n", "plt.ylabel(\"Mass concentration (kg m$^{-3}$)\", color='b')\n", "plt.xlabel(\"Time (s)\")\n", - "set_tickmarks(plt.gca(), 5)\n", + "n_ticks = 5\n", + "set_tickmarks(plt.gca(), n_ticks)\n", "plt.twinx()\n", "plt.plot(OUTPUT['elapsed_time'], OUTPUT['total_num_conc'], \"g\", label=\"num conc\")\n", - "plt.xticks(np.linspace(0, OUTPUT['elapsed_time'][-1], 5))\n", + "plt.xticks(np.linspace(0, OUTPUT['elapsed_time'][-1], n_ticks))\n", "plt.xlim([OUTPUT['elapsed_time'][i] for i in (0, -1)])\n", - "set_tickmarks(plt.gca(), 5)\n", + "set_tickmarks(plt.gca(), n_ticks)\n", "plt.ylabel(r\"Number concentration ($\\#$ m$^{-3}$)\", color='g')\n", "show_plot()" ] }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 25, "id": "386aa7c2", "metadata": {}, "outputs": [ @@ -3166,7 +6281,7 @@ " \n", " \n", " \n", - " 2024-10-19T23:44:54.106868\n", + " 2024-10-19T23:53:02.622019\n", " image/svg+xml\n", " \n", " \n", @@ -3202,16 +6317,16 @@ " \n", " \n", + "\" clip-path=\"url(#p0662ff0c23)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3248,11 +6363,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0662ff0c23)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3340,11 +6455,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0662ff0c23)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3415,11 +6530,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0662ff0c23)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3478,11 +6593,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0662ff0c23)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3654,16 +6769,16 @@ " \n", " \n", + "\" clip-path=\"url(#p0662ff0c23)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3678,11 +6793,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0662ff0c23)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3697,11 +6812,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0662ff0c23)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3716,11 +6831,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0662ff0c23)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3735,11 +6850,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0662ff0c23)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3755,11 +6870,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0662ff0c23)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4027,9 +7142,9 @@ " \n", " \n", " \n", + "\" clip-path=\"url(#p0662ff0c23)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4154,12 +7269,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "a7d9955c086a43c6a05a4ccf6c22d069", + "model_id": "c6cdf9df8dfb4ee7881fd57f01be9d25", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpicdcau0z.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpr8m2t8m3.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -4183,7 +7298,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 26, "id": "faa1de28", "metadata": {}, "outputs": [ @@ -4198,7 +7313,7 @@ " \n", " \n", " \n", - " 2024-10-19T23:44:56.548277\n", + " 2024-10-19T23:53:04.407507\n", " image/svg+xml\n", " \n", " \n", @@ -4234,16 +7349,16 @@ " \n", " \n", + "\" clip-path=\"url(#p1052c951a2)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4334,11 +7449,11 @@ " \n", " \n", + "\" clip-path=\"url(#p1052c951a2)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4396,11 +7511,11 @@ " \n", " \n", + "\" clip-path=\"url(#p1052c951a2)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4429,11 +7544,11 @@ " \n", " \n", + "\" clip-path=\"url(#p1052c951a2)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4482,11 +7597,11 @@ " \n", " \n", + "\" clip-path=\"url(#p1052c951a2)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4529,229 +7644,229 @@ " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5012,16 +8127,16 @@ " \n", " \n", + "\" clip-path=\"url(#p1052c951a2)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5033,36 +8148,36 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -5388,7 +8542,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5397,7 +8551,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", + "L 202.37585 155.63709 \n", + "\" clip-path=\"url(#p1052c951a2)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 202.37585 155.637098 \n", + "\" clip-path=\"url(#p1052c951a2)\" style=\"fill: none; stroke: #ff7f0e; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 202.37585 155.637108 \n", + "\" clip-path=\"url(#p1052c951a2)\" style=\"fill: none; stroke: #2ca02c; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 202.37585 155.637112 \n", + "\" clip-path=\"url(#p1052c951a2)\" style=\"fill: none; stroke: #d62728; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5638,13 +8792,13 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5654,13 +8808,13 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5671,36 +8825,15 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", " \n", " \n", " \n", @@ -5713,7 +8846,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5729,12 +8862,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "537ee095f324463e834c5518c4194890", + "model_id": "03e4f64cf33a494ca87c824a3ce22ec7", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmprrd4a3h1.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpwekcqif2.pdf
\"), HTML(value…" ] }, "metadata": {}, From d73e26ed794c8c8aa6a8334702f61e6e9bb1c29b Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Sun, 20 Oct 2024 03:36:38 +0200 Subject: [PATCH 15/26] fetching json files from CAMP repo --- examples/monarch_mod37/cb05_species.json | 400 -- examples/monarch_mod37/custom_species.json | 100 - .../partitioning_species_params.json | 410 -- examples/particle_simulation_with_camp.ipynb | 4316 +++-------------- 4 files changed, 570 insertions(+), 4656 deletions(-) delete mode 100644 examples/monarch_mod37/cb05_species.json delete mode 100644 examples/monarch_mod37/custom_species.json delete mode 100644 examples/monarch_mod37/partitioning_species_params.json diff --git a/examples/monarch_mod37/cb05_species.json b/examples/monarch_mod37/cb05_species.json deleted file mode 100644 index 3f42cf3c..00000000 --- a/examples/monarch_mod37/cb05_species.json +++ /dev/null @@ -1,400 +0,0 @@ -{ -"notes" :"Descriptions are from CB5 Final Report RT-04-00675 (www.camx.com/files/cb05_final_report_120805.aspx) and from notes in the cb05cl_ae5_aq_CMAQ.def mechanism file", -"camp-data" : [ - { - "name" : "AACD", - "type" : "CHEM_SPEC", - "description" : "acetic and higher carboxylic acids" - }, - { - "name" : "ALD2", - "type" : "CHEM_SPEC", - "description" : "acetaldehyde" - }, - { - "name" : "ALDX", - "type" : "CHEM_SPEC", - "description" : "propionaldehyde and higher aldehydes" - }, - { - "name" : "BENZENE", - "type" : "CHEM_SPEC", - "description" : "benzene" - }, - { - "name" : "BENZRO2", - "type" : "CHEM_SPEC", - "description" : "peroxy radical from benzene oxidation" - }, - { - "name" : "BNZHRXN", - "type" : "CHEM_SPEC", - "description" : "counter species for aerosol from BENZENE - how does this differ from BNZNNRXN?" - }, - { - "name" : "BNZNRXN", - "type" : "CHEM_SPEC", - "description" : "counter species for aerosol from BENZENE" - }, - { - "name" : "C2O3", - "type" : "CHEM_SPEC", - "description" : "acetyl peroxy radical" - }, - { - "name" : "CH4", - "type" : "CHEM_SPEC", - "description" : "methane" - }, - { - "name" : "CL", - "type" : "CHEM_SPEC", - "description" : "chlorine radical" - }, - { - "name" : "CL2", - "type" : "CHEM_SPEC", - "description" : "molecular chlorine" - }, - { - "name" : "CLO", - "type" : "CHEM_SPEC", - "description" : "chlorine monoxide" - }, - { - "name" : "CO", - "type" : "CHEM_SPEC", - "description" : "carbon monoxide" - }, - { - "name" : "CRES", - "type" : "CHEM_SPEC", - "description" : "cresol and higher molecular weight phenols" - }, - { - "name" : "CRO", - "type" : "CHEM_SPEC", - "description" : "methylphenoxy radical" - }, - { - "name" : "CXO3", - "type" : "CHEM_SPEC", - "description" : "C3 and higher acylperoxy radicals" - }, - { - "name" : "ETH", - "type" : "CHEM_SPEC", - "description" : "ethene" - }, - { - "name" : "ETHA", - "type" : "CHEM_SPEC", - "description" : "ethane" - }, - { - "name" : "ETOH", - "type" : "CHEM_SPEC", - "description" : "ethanol" - }, - { - "name" : "FACD", - "type" : "CHEM_SPEC", - "description" : "formic acid" - }, - { - "name" : "FMCL", - "type" : "CHEM_SPEC", - "description" : "formyl chloride (HC(O)Cl)" - }, - { - "name" : "FORM", - "type" : "CHEM_SPEC", - "description" : "formaldehyde" - }, - { - "name" : "H2O2", - "type" : "CHEM_SPEC", - "description" : "hydrogen peroxide" - }, - { - "name" : "HCL", - "type" : "CHEM_SPEC", - "description" : "hydrochlric acid" - }, - { - "name" : "HCO3", - "type" : "CHEM_SPEC", - "description" : "formyl peroxy radical? no description in cb05 report" - }, - { - "name" : "HNO3", - "type" : "CHEM_SPEC", - "description" : "nitric acid" - }, - { - "name" : "HO2", - "type" : "CHEM_SPEC", - "description" : "hydroperoxy radical" - }, - { - "name" : "HOCL", - "type" : "CHEM_SPEC", - "description" : "hypochlorous acid" - }, - { - "name" : "HONO", - "type" : "CHEM_SPEC", - "description" : "nitrous acid" - }, - { - "name" : "IOLE", - "type" : "CHEM_SPEC", - "description" : "internal olefin carbon bond (R-C=C)" - }, - { - "name" : "ISOP", - "type" : "CHEM_SPEC", - "description" : "isoprene" - }, - { - "name" : "ISOPRXN", - "type" : "CHEM_SPEC", - "description" : "counter for aerosol from ISOP" - }, - { - "name" : "ISPD", - "type" : "CHEM_SPEC", - "description" : "isoprene products (lumped methacrolein, methyl vinyl ketone, etc.)" - }, - { - "name" : "MEO2", - "type" : "CHEM_SPEC", - "description" : "methyl peroxy radical" - }, - { - "name" : "MEOH", - "type" : "CHEM_SPEC", - "description" : "methanol" - }, - { - "name" : "MEPX", - "type" : "CHEM_SPEC", - "description" : "methylhydroperoxide" - }, - { - "name" : "MGLY", - "type" : "CHEM_SPEC", - "description" : "methylglyoxal and other aromatic products" - }, - { - "name" : "N2O5", - "type" : "CHEM_SPEC", - "description" : "dinitrogen pentoxide" - }, - { - "name" : "NO", - "type" : "CHEM_SPEC", - "description" : "nitric oxide" - }, - { - "name" : "NO2", - "type" : "CHEM_SPEC", - "description" : "nitrogen dioxide" - }, - { - "name" : "NO3", - "type" : "CHEM_SPEC", - "description" : "nitrate radical" - }, - { - "name" : "NTR", - "type" : "CHEM_SPEC", - "description" : "organic nitrate (RNO3)" - }, - { - "name" : "O", - "type" : "CHEM_SPEC", - "description" : "oxygen atom in the O3P electronic state" - }, - { - "name" : "O1D", - "type" : "CHEM_SPEC", - "description" : "oxygen atom in the O1D electronic state" - }, - { - "name" : "O3", - "type" : "CHEM_SPEC", - "description" : "ozone" - }, - { - "name" : "OH", - "type" : "CHEM_SPEC", - "description" : "hydroxyl radical" - }, - { - "name" : "OLE", - "type" : "CHEM_SPEC", - "description" : "terminal olefin carbon bond (R-C=C)" - }, - { - "name" : "OPEN", - "type" : "CHEM_SPEC", - "description" : "aromatic ring opening products" - }, - { - "name" : "PACD", - "type" : "CHEM_SPEC", - "description" : "peroxyacetic and higher peroxycarboxylic acids" - }, - { - "name" : "PAN", - "type" : "CHEM_SPEC", - "description" : "peroxyacetyl nitrate" - }, - { - "name" : "PANX", - "type" : "CHEM_SPEC", - "description" : "C3 and higher peroxyacyl nitrates" - }, - { - "name" : "PAR", - "type" : "CHEM_SPEC", - "description" : "paraffin carbon bond (C-C)" - }, - { - "name" : "PNA", - "type" : "CHEM_SPEC", - "description" : "peroxynitric acid (HNO4)" - }, - { - "name" : "ROOH", - "type" : "CHEM_SPEC", - "description" : "higher organic peroxides" - }, - { - "name" : "ROR", - "type" : "CHEM_SPEC", - "description" : "secondary alkoxy radical" - }, - { - "name" : "SESQ", - "type" : "CHEM_SPEC", - "description" : "sesquiterpene" - }, - { - "name" : "SESQRXN", - "type" : "CHEM_SPEC", - "description" : "counter for aerosol from SESQ" - }, - { - "name" : "SO2", - "type" : "CHEM_SPEC", - "description" : "sulfur dioxide" - }, - { - "name" : "SULF", - "type" : "CHEM_SPEC", - "description" : "sulfuric acid (gaseous)" - }, - { - "name" : "SULRXN", - "type" : "CHEM_SPEC", - "description" : "counter for aerosol from SO2" - }, - { - "name" : "TERP", - "type" : "CHEM_SPEC", - "description" : "terpene" - }, - { - "name" : "TO2", - "type" : "CHEM_SPEC", - "description" : "toluene-hydroxyl radical aduct" - }, - { - "name" : "TOL", - "type" : "CHEM_SPEC", - "description" : "toluene" - }, - { - "name" : "TOLHRXN", - "type" : "CHEM_SPEC", - "description" : "counter for aerosol from TOL - how does this differ from TOLNRXN?" - }, - { - "name" : "TOLNRXN", - "type" : "CHEM_SPEC", - "description" : "counter for aerosol from TOL" - }, - { - "name" : "TOLRO2", - "type" : "CHEM_SPEC", - "description" : "first generation product from TOL" - }, - { - "name" : "TRPRXN", - "type" : "CHEM_SPEC", - "description" : "counter for aerosol from TERP" - }, - { - "name" : "XO2", - "type" : "CHEM_SPEC", - "description" : "NO to NO2 conversion from alkylperoxy (RO2) radical" - }, - { - "name" : "XO2N", - "type" : "CHEM_SPEC", - "description" : "NO to organic nitrate conversion from alkylperoxy (RO2) radical" - }, - { - "name" : "XYL", - "type" : "CHEM_SPEC", - "description" : "xylene and other polyalkyl aromatics" - }, - { - "name" : "XYLHRXN", - "type" : "CHEM_SPEC", - "description" : "counter for aerosol from XYL - how does this differ from XYLNRXN?" - }, - { - "name" : "XYLNRXN", - "type" : "CHEM_SPEC", - "description" : "counter for aerosol from XYL" - }, - { - "name" : "XYLRO2", - "type" : "CHEM_SPEC", - "description" : "first generation product from XYL" - }, - { - "name" : "N2O", - "type" : "CHEM_SPEC", - "description" : "nitrous oxide - does not participate in CB05 reactions" - }, - { - "name" : "DUMMY", - "type" : "CHEM_SPEC", - "description" : "not sure what this is" - }, - { - "name" : "O2", - "type" : "CHEM_SPEC", - "description" : "molecular oxygen" - }, - { - "name" : "H2O", - "type" : "CHEM_SPEC", - "is gas-phase water" : true, - "description" : "water vapor" - }, - { - "name" : "H2", - "type" : "CHEM_SPEC", - "description" : "molecular hydrogen" - }, - { - "name" : "M", - "type" : "CHEM_SPEC", - "description" : "third body" - } -]} diff --git a/examples/monarch_mod37/custom_species.json b/examples/monarch_mod37/custom_species.json deleted file mode 100644 index df8673d4..00000000 --- a/examples/monarch_mod37/custom_species.json +++ /dev/null @@ -1,100 +0,0 @@ -{ - "description" : [ - "These additional species are needed for the MONARCH 'mod37' configuration", - "Densities are taken from Spada et al. (2015) manuscript - ", - "'Global Aerosols in the online multiscale NMMB/BSC Chemical Transport Model", - "or estimated from bulk densities.", - "TODO check about molecular weights" - ], - "camp-data" : [ - { - "name" : "NH3", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03, - "description" : "ammonia" - }, - { - "name" : "DMS", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-03, - "description" : "dimethylsulfide" - }, - { - "monarch name" : "lumped high-density dust species", - "name" : "LHD_DUST", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.1, - "density [kg m-3]" : 2650.0, - "num_ions" : 0, - "kappa" : 0.1 - }, - { - "monarch name" : "lumped low-density dust species", - "name" : "LLD_DUST", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.1, - "density [kg m-3]" : 2650.0, - "num_ions" : 0, - "kappa" : 0.1 - }, - { - "monarch name" : "lumped sea salt species", - "name" : "SEA_SALT", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.1, - "density [kg m-3]" : 2160.0, - "num_ions" : 0, - "kappa" : 0.53 - }, - { - "name" : "BC_phob", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "density [kg m-3]" : 1000.0, - "molecular weight [kg mol-1]" : 0.1, - "description" : "hydrophobic black carbon", - "num_ions" : 0, - "kappa" : 0 - }, - { - "name" : "BC_phil", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "density [kg m-3]" : 1000.0, - "molecular weight [kg mol-1]" : 0.1, - "description" : "hydrophilic black carbon", - "num_ions" : 0, - "kappa" : 0.001 - }, - { - "name" : "other_PM", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.1, - "density [kg m-3]" : 1800.0, - "description" : "unspecified particulate matter FIXME", - "num_ions" : 0, - "kappa" : 0 - }, - { - "name" : "other_other_PM", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-05, - "molecular weight [kg mol-1]" : 0.1, - "density [kg m-3]" : 1800.0, - "description" : "second unspecified particulate matter species FIXME", - "num_ions" : 0, - "kappa" : 0 - } - ] -} diff --git a/examples/monarch_mod37/partitioning_species_params.json b/examples/monarch_mod37/partitioning_species_params.json deleted file mode 100644 index f014169a..00000000 --- a/examples/monarch_mod37/partitioning_species_params.json +++ /dev/null @@ -1,410 +0,0 @@ -{ - "description" : [ - "Dry deposition reactions and species properties", - "TODO Consider updating diffusion coefficients according to Tang et al. Atmos. Chem. Phys., 14, 9233-9247 (2014)", - " available at https://www.atmos-chem-phys.net/14/9233/2014/acp-14-9233-2014.pdf" - ], - "camp-data" : [ - { - "name" : "NO2", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :6.316E-08, - "HLC exp factor [K]" :2.500E+03, - "dry dep reactivity factor [unitless]" :1.000E-01, - "diffusion coeff [m2 s-1]" :1.470E-05, - "dry dep notes" : [ - "HLC seems to be on the low end of measured values", - "(https://webbook.nist.gov/cgi/cbook.cgi?ID=C10102440&Mask=10)" - ] - }, - { - "name" : "NO", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.875E-08, - "HLC exp factor [K]" :1.480E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.830E-05 - }, - { - "name" : "O3", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.115E-07, - "HLC exp factor [K]" :2.300E+03, - "dry dep reactivity factor [unitless]" :1.000E+00, - "diffusion coeff [m2 s-1]" :1.750E-05 - }, - { - "name" : "NO3", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.480E-04, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :1.000E+00, - "diffusion coeff [m2 s-1]" :1.270E-05, - "dry dep notes" : [ - "HLC seems to be on the high end of measured values", - "(https://webbook.nist.gov/cgi/cbook.cgi?ID=C12033497&Units=SI&Mask=10#Solubility)" - ] - }, - { - "name" : "N2O5", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :9.869E+04, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :1.000E+00, - "diffusion coeff [m2 s-1]" :1.100E-05 - }, - { - "name" : "HNO3", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :0.98692, - "HLC exp factor [K]" :8.684E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.260E-05, - "dry dep notes" : [ - "Original HLC(298K)=2.69e13 (M atm-1) is orders of magnitude higher that nist values (~1e5); exp factor ok", - "https://webbook.nist.gov/cgi/cbook.cgi?ID=C7697372&Units=SI&Mask=10#Solubility", - "switched to nist value" - ] - }, - { - "name" : "HCL", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :0.98692, - "HLC exp factor [K]" :8.684E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.260E-05, - "dry dep notes" : [ - "Using parameters from HNO3" - ] - }, - { - "name" : "SULF", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :9.8692e5, - "HLC exp factor [K]" :8.684E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.260E-05, - "dry dep notes" : [ - "using HLC from nist (https://webbook.nist.gov/cgi/cbook.cgi?ID=C7664939&Units=SI&Mask=10#Solubility)" - ] - }, - { - "name" : "HONO", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :3.425E+00, - "HLC exp factor [K]" :3.775E+03, - "dry dep reactivity factor [unitless]" :1.000E-01, - "diffusion coeff [m2 s-1]" :1.530E-05 - }, - { - "name" : "PNA", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.974E+08, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :1.000E-01, - "diffusion coeff [m2 s-1]" :1.130E-05 - }, - { - "name" : "H2O2", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :7.353E-01, - "HLC exp factor [K]" :6.615E+03, - "dry dep reactivity factor [unitless]" :1.000E+00, - "diffusion coeff [m2 s-1]" :1.710E-05 - }, - { - "name" : "NTR", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.115E-05, - "HLC exp factor [K]" :5.487E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :9.200E-06 - }, - { - "name" : "ROOH", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.658E+01, - "HLC exp factor [K]" :1.024E+04, - "dry dep reactivity factor [unitless]" :1.000E-01, - "diffusion coeff [m2 s-1]" :1.270E-05 - }, - { - "name" : "FORM", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :2.931E-02, - "HLC exp factor [K]" :7.190E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.830E-05 - }, - { - "name" : "MEOH", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :2.931E-02, - "HLC exp factor [K]" :7.190E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.830E-05, - "dry dep notes" : [ - "Using values from FORM" - ] - }, - { - "name" : "ETOH", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :2.931E-02, - "HLC exp factor [K]" :7.190E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.830E-05, - "dry dep notes" : [ - "Using values from FORM" - ] - }, - { - "name" : "ALD2", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.125E-04, - "HLC exp factor [K]" :6.266E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.510E-05 - }, - { - "name" : "ALDX", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.125E-04, - "HLC exp factor [K]" :6.266E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.510E-05 - }, - { - "name" : "PAR", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.115E-08, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.180E-05 - }, - { - "name" : "CO", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :8.093E-08, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.890E-05 - }, - { - "name" : "MEPX", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :2.181E-03, - "HLC exp factor [K]" :5.607E+03, - "dry dep reactivity factor [unitless]" :1.000E-01, - "diffusion coeff [m2 s-1]" :1.440E-05 - }, - { - "name" : "FACD", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :9.721E+01, - "HLC exp factor [K]" :5.716E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.530E-05 - }, - { - "name" : "PAN", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :2.931E-05, - "HLC exp factor [K]" :5.760E+03, - "dry dep reactivity factor [unitless]" :1.000E-01, - "diffusion coeff [m2 s-1]" :9.100E-06 - }, - { - "name" : "PANX", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :2.931E-05, - "HLC exp factor [K]" :5.760E+03, - "dry dep reactivity factor [unitless]" :1.000E-01, - "diffusion coeff [m2 s-1]" :9.100E-06, - "dry dep notes" : [ - "Using values from PAN" - ] - }, - { - "name" : "PACD", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :4.668E-03, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :1.000E-01, - "diffusion coeff [m2 s-1]" :1.150E-05 - }, - { - "name" : "AACD", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :9.504E+00, - "HLC exp factor [K]" :8.374E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.240E-05 - }, - { - "name" : "OLE", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :4.698E-08, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.540E-05 - }, - { - "name" : "ETH", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :4.609E-08, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.890E-05 - }, - { - "name" : "IOLE", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.332E-08, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.210E-05 - }, - { - "name" : "TOL", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.490E-06, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.040E-05 - }, - { - "name" : "CRES", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :3.948E+00, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :9.600E-06 - }, - { - "name" : "MGLY", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :3.661E-02, - "HLC exp factor [K]" :7.541E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.180E-05 - }, - { - "name" : "XYL", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.431E-06, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :9.700E-06 - }, - { - "name" : "OPEN", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.431E-06, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :9.700E-06, - "dry dep notes" : [ - "Using values from XYL" - ] - }, - { - "name" : "ISOP", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :4.698E-08, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.210E-05 - }, - { - "name" : "TERP", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :4.698E-08, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.210E-05, - "dry dep notes" : [ - "Using values from ISOP" - ] - }, - { - "name" : "ISPD", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :4.698E-08, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.210E-05 - }, - { - "name" : "SO2", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :2.497E+00, - "HLC exp factor [K]" :5.816E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.260E-05, - "special dry deposition species" : "SO2" - }, - { - "name" : "ETHA", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.974E-08, - "HLC exp factor [K]" :0.000E+00, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.830E-05 - }, - { - "name" : "NH3", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :1.026E-01, - "HLC exp factor [K]" :3.660E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :2.270E-05, - "special dry deposition species" : "NH3" - }, - { - "name" : "ISOP-P1", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :9.721E+01, - "HLC exp factor [K]" :5.716E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.530E-05 - }, - { - "name" : "ISOP-P2", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :9.721E+01, - "HLC exp factor [K]" :5.716E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.530E-05, - "dry dep notes" : "changed diff coeff from 0.0 to match ISOP-P1" - }, - { - "name" : "TERP-P1", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :9.721E+01, - "HLC exp factor [K]" :5.716E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.530E-05 - }, - { - "name" : "TERP-P2", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" :9.721E+01, - "HLC exp factor [K]" :5.716E+03, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :1.530E-05, - "dry dep notes" : "changed diff coeff from 0.0 to match ISOP-P2" - }, - { - "name" : "DMS", - "type" : "CHEM_SPEC", - "HLC(298K) [M Pa-1]" : 5.59585E-06, - "HLC exp factor [K]" : 3500.0, - "dry dep reactivity factor [unitless]" :0.000E+00, - "diffusion coeff [m2 s-1]" :9.900E-03, - "dry dep notes" : [ - "got HLC params from nist webbook https://webbook.nist.gov/cgi/cbook.cgi?ID=C75183&Mask=10#Solubility" - ] - } - ] -} diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index e299923c..a9bbdd01 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -52,6 +52,7 @@ "outputs": [], "source": [ "import json\n", + "import urllib\n", "from collections import defaultdict\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -73,3289 +74,92 @@ { "cell_type": "code", "execution_count": 5, - "id": "2e492520-ba61-45bb-b9b3-5a04fb6f21df", + "id": "6ff265d8-b7f8-4f54-bfa0-d14ce0f4535c", "metadata": {}, "outputs": [], "source": [ - "with open('cloud_and_rain_partitioning.json', 'w', encoding='utf-8') as f:\n", - " json.dump(\n", - " {\n", - " \"description\" : [\n", - " \"Partitioning of species to aqueous. Parameters are from existing wet-deposition module.\"\n", - " ],\n", - " \"pmc-data\" : [\n", - " {\n", - " \"name\" : \"MONARCH mod37\",\n", - " \"type\" : \"MECHANISM\",\n", - " \"reactions\" : [\n", - " {\n", - " \"type\" : \"HL_PHASE_TRANSFER\",\n", - " \"gas-phase species\" : (\n", - " \"PNA\" if item == \"HNO4\" else \"SULF\" if item == \"H2SO4\" else item\n", - " ),\n", - " \"aerosol phase\" : \"aqueous\",\n", - " \"aerosol-phase species\" : (\n", - " item + (\"_aero\" if item.startswith(\"ISOP\") or item.startswith(\"TERP\") else \"_aq\")\n", - " ),\n", - " \"aerosol-phase water\" : \"H2O_aq\"\n", - " } for item in (\n", - " \"NO2\", \"NO\", \"O3\", \"NO3\", \"N2O5\", \"HNO3\", \"HONO\", \"H2O2\", \"NTR\", \"ROOH\", \"FORM\",\n", - " \"ALD2\", \"ALDX\", \"CO\", \"MEPX\", \"MEOH\", \"FACD\", \"PAN\", \"PACD\", \"AACD\", \"PANX\",\n", - " \"SO2\", \"CL2\", \"HOCL\", \"FMCL\", \"HCL\", \"NH3\", \"ETOH\", \"DMS\", \"ISOP-P1\", \"ISOP-P2\",\n", - " \"TERP-P1\", \"TERP-P2\", \"HNO4\", \"H2SO4\",\n", - " )\n", - " ]\n", - " }\n", - " ]\n", - " }, f, indent=4\n", - " )" + "PATHS = [\n", + " 'cb05_abs_tol.json',\n", + " 'cb05_species.json',\n", + " 'custom_species.json',\n", + " 'aerosol_phases.json',\n", + " 'partitioning_species_params.json',\n", + " 'cb05_mechanism.noR142R143.json',\n", + " 'tsigaridis_2_product_SOA_scheme-mechanism.json',\n", + " 'tsigaridis_2_product_SOA_scheme-species.json',\n", + "]" ] }, - { - "cell_type": "code", - "execution_count": 6, - "id": "16377896", - "metadata": {}, - "outputs": [], - "source": [ - "with open('config.json', 'w', encoding='utf-8') as f:\n", - " json.dump(\n", - " {\n", - " \"camp-files\" : [\n", - " \"aerosol_representation.json\",\n", - " \"aerosol_phases.json\",\n", - " \"monarch_mod37-cb05_abs_tol.json\",\n", - " \"monarch_mod37-cb05_mechanism_without_R142_R143.json\",\n", - " \"monarch_mod37/cb05_species.json\",\n", - " \"monarch_mod37/custom_species.json\",\n", - " \"monarch_mod37/partitioning_species_params.json\",\n", - " \"monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json\",\n", - " \"monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json\"\n", - " ]\n", - " }\n", - " , f, indent=4\n", - " )" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "id": "5e4e5c4b", - "metadata": {}, - "outputs": [], - "source": [ - "with open('aerosol_representation.json', 'w', encoding='utf-8') as f:\n", - " json.dump(\n", - " {\n", - " \"camp-data\" : [\n", - " {\n", - " \"name\" : \"PartMC single particle\",\n", - " \"type\" : \"AERO_REP_SINGLE_PARTICLE\",\n", - " \"maximum computational particles\" : N_PART * 2\n", - " }\n", - " ]\n", - " }, f, indent=4\n", - " )" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "id": "e3c41245", - "metadata": {}, - "outputs": [], - "source": [ - "with open('aerosol_phases.json', 'w', encoding='utf-8') as f:\n", - " json.dump(\n", - " {\n", - " \"description\" : \"These aerosol phases correspond to the MONARCH 'mod37' configuration\",\n", - " \"camp-data\" : [\n", - " {\n", - " \"name\" : \"dust\",\n", - " \"type\": \"AERO_PHASE\",\n", - " \"species\" : [ \"LHD_DUST\", \"LLD_DUST\" ],\n", - " \"notes\" : {\n", - " \"MLD 02/05/2018\" : \"consider replacing this with a set of inorganic species\"\n", - " }\n", - " },\n", - " {\n", - " \"name\" : \"sea_salt\",\n", - " \"type\" : \"AERO_PHASE\",\n", - " \"species\" : [ \"SEA_SALT\" ],\n", - " \"notes\" : {\n", - " \"MLD 02/05/2018\" : \"consider replacing with H2O, Na+, Cl-\"\n", - " }\n", - " },\n", - " {\n", - " \"name\" : \"organic_matter\",\n", - " \"type\" : \"AERO_PHASE\",\n", - " \"species\" : [ \"POA\", \"ISOP-P1_aero\", \"ISOP-P2_aero\", \"TERP-P1_aero\", \"TERP-P2_aero\" ]\n", - " },\n", - " {\n", - " \"name\" : \"black_carbon\",\n", - " \"type\" : \"AERO_PHASE\",\n", - " \"species\" : [ \"BC_phob\", \"BC_phil\" ]\n", - " },\n", - " {\n", - " \"name\" : \"other_PM\",\n", - " \"type\" : \"AERO_PHASE\",\n", - " \"species\" : [ \"other_PM\", \"other_other_PM\" ],\n", - " \"description\" : \"unspecified particulate matter\"\n", - " }\n", - " ]\n", - " }, f, indent=4\n", - " )" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "id": "d7482795-f98e-43f7-ab59-604a1e964706", - "metadata": {}, - "outputs": [], - "source": [ - "with open('monarch_mod37-cb05_abs_tol.json', 'w', encoding='utf-8') as f:\n", - " json.dump({\"camp-data\" : [\n", - " {\n", - " \"type\" : \"RELATIVE_TOLERANCE\",\n", - " \"value\" : 1e-4\n", - " },\n", - " *[{'name': name, 'type': \"CHEM_SPEC\", 'absolute integration tolerance': 1e-3} for name in (\n", - " \"NO2\", \"NO\", \"O3\", \"NO3\", \"OH\", \"HO2\", \"N2O5\", \"HNO3\", \"HONO\", \"PNA\", \"H2O2\", \"XO2\", \"XO2N\",\n", - " \"ROOH\", \"FORM\", \"ALD2\", \"ALDX\", \"PAR\", \"CO\", \"MEO2\", \"MEPX\", \"MEOH\", \"FACD\", \"C2O3\", \"PAN\",\n", - " \"PACD\", \"AACD\", \"CXO3\", \"PANX\", \"ROR\", \"OLE\", \"ETH\", \"IOLE\", \"TOL\", \"CRES\", \"TO2\", \"TOLRO2\",\n", - " \"OPEN\", \"CRO\", \"MGLY\", \"XYL\", \"XYLRO2\", \"ISOP\", \"ISPD\", \"TERP\", \"SO2\", \"ETOH\", \"ETHA\", \"CL2\",\n", - " \"CL\", \"HOCL\", \"CLO\", \"FMCL\", \"HCL\", \"BENZENE\", \"BENZRO2\", \"SESQ\", \"N2O\",\n", - " )],\n", - " *[{'name': name, 'type': \"CHEM_SPEC\", 'absolute integration tolerance': 1.} for name in (\n", - " \"O\", \"O1D\", \"NTR\", \"HCO3\", \"ISOPRXN\", \"TRPRXN\", \"SULF\", \"SULRXN\", \"TOLNRXN\", \"TOLHRXN\", \"XYLNRXN\",\n", - " \"XYLHRXN\", \"BNZNRXN\", \"BNZHRXN\", \"SESQRXN\", \"M\", \"O2\", \"N2\", \"H2O\", \"CH4\", \"H2\", \"DUMMY\",\n", - " )]\n", - " ]}, f, indent=4)" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "id": "e0ed380d-f2e3-4eb1-ba6e-c81f820fe69d", - "metadata": {}, - "outputs": [], - "source": [ - "with open(\"monarch_mod37-cb05_mechanism_without_R142_R143.json\", 'w', encoding='utf-8') as f:\n", - " json.dump({ \"camp-data\" : [{\n", - " \"name\" : \"MONARCH mod37\",\n", - " \"type\" : \"MECHANISM\",\n", - " \"reactions\" : [\n", - " {\n", - " \"rxn id\" : \"R1\",\n", - " \"reactants\" : {\n", - " \"NO2\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO\" : {} ,\n", - " \"O\" : {}\n", - " },\n", - " \"orig params\" : \"TUV_J(4, THETA)\",\n", - " \"base rate\" : 4.77e-3,\n", - " \"Fast-J id\" : \"NO2\",\n", - " \"type\" : \"PHOTOLYSIS\"\n", - " },\n", - " {\n", - " \"rxn id\" : \"R2\",\n", - " \"reactants\" : {\n", - " \"O\" : {} ,\n", - " \"O2\" : {} ,\n", - " \"M\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"O3\" : {} ,\n", - " \"M\" : {}\n", - " },\n", - " \"orig params\" : \"O2 * M * CMAQ_1to4(6.0E-34, -2.4, 0.0E+00)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 6.0E-34,\n", - " \"B\" : -2.4,\n", - " \"C\" : -0.0E+00\n", - " },\n", - " {\n", - " \"rxn id\" : \"R3\",\n", - " \"reactants\" : {\n", - " \"O3\" : {} ,\n", - " \"NO\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO2\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(3.0E-12, 0.0E+00, 1500.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 3.0E-12,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -1500.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"R4\",\n", - " \"reactants\" : {\n", - " \"O\" : {} ,\n", - " \"NO2\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(5.6E-12, 0.0E+00, -180.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 5.6E-12,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : 180.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"R5\",\n", - " \"reactants\" : {\n", - " \"O\" : {} ,\n", - " \"NO2\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO3\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_10(2.5E-31, -1.8, 0.0E+00, 2.2E-11, -0.7, 0.0E+00, 0.6, 1.0)\",\n", - " \"type\" : \"TROE\",\n", - " \"k0_A\" : 2.5E-31,\n", - " \"k0_B\" : -1.8,\n", - " \"k0_C\" : -0.0E+00,\n", - " \"kinf_A\" : 2.2E-11,\n", - " \"kinf_B\" : -0.7,\n", - " \"kinf_C\" : -0.0E+00,\n", - " \"Fc\" : 0.6,\n", - " \"N\" : 1.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"R6\",\n", - " \"reactants\" : {\n", - " \"O\" : {} ,\n", - " \"NO\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO2\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_10(9.0E-32, -1.5, 0.0E+00, 3.0E-11, 0.0E+00, 0.0E+00, 0.6, 1.0)\",\n", - " \"type\" : \"TROE\",\n", - " \"k0_A\" : 9.0E-32,\n", - " \"k0_B\" : -1.5,\n", - " \"k0_C\" : -0.0E+00,\n", - " \"kinf_A\" : 3.0E-11,\n", - " \"kinf_B\" : 0.0E+00,\n", - " \"kinf_C\" : -0.0E+00,\n", - " \"Fc\" : 0.6,\n", - " \"N\" : 1.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"R7\",\n", - " \"reactants\" : {\n", - " \"NO2\" : {} ,\n", - " \"O3\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO3\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(1.2E-13, 0.0E+00, 2450.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 1.2E-13,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -2450.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"R8\",\n", - " \"reactants\" : {\n", - " \"O3\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"O\" : {}\n", - " },\n", - " \"orig params\" : \"TUV_J(3, THETA)\",\n", - " \"base rate\" : 2.53e-4,\n", - " \"Fast-J id\" : \"O3\",\n", - " \"type\" : \"PHOTOLYSIS\"\n", - " },\n", - " {\n", - " \"rxn id\" : \"R9\",\n", - " \"reactants\" : {\n", - " \"O3\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"O1D\" : {}\n", - " },\n", - " \"orig params\" : \"TUV_J(2, THETA)\",\n", - " \"base rate\" : 2.26e-6,\n", - " \"Fast-J id\" : \"O3_1d\",\n", - " \"type\" : \"PHOTOLYSIS\"\n", - " },\n", - " {\n", - " \"rxn id\" : \"R10\",\n", - " \"reactants\" : {\n", - " \"O1D\" : {} ,\n", - " \"M\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"O\" : {} ,\n", - " \"M\" : {}\n", - " },\n", - " \"orig params\" : \"M * CMAQ_1to4(2.1E-11, 0.0E+00, -102.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 2.1E-11,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : 102.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"R11\",\n", - " \"reactants\" : {\n", - " \"O1D\" : {} ,\n", - " \"H2O\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"OH\" : { \"yield\" : 2.000 }\n", - " },\n", - " \"orig params\" : \"H2O * CMAQ_1to4(2.2E-10, 0.0E+00, 0.0E+00)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 2.2E-10,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -0.0E+00\n", - " },\n", - " {\n", - " \"rxn id\" : \"R12\",\n", - " \"reactants\" : {\n", - " \"O3\" : {} ,\n", - " \"OH\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"HO2\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(1.7E-12, 0.0E+00, 940.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 1.7E-12,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -940.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"R13\",\n", - " \"reactants\" : {\n", - " \"O3\" : {} ,\n", - " \"HO2\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"OH\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(1.0E-14, 0.0E+00, 490.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 1.0E-14,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -490.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"R14\",\n", - " \"reactants\" : {\n", - " \"NO3\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO2\" : {} ,\n", - " \"O\" : {}\n", - " },\n", - " \"orig params\" : \"TUV_J(6, THETA)\",\n", - " \"scaling factor\" : 0.89,\n", - " \"base rate\" : 1.31e-1,\n", - " \"Fast-J id\" : \"NO3_X\",\n", - " \"type\" : \"PHOTOLYSIS\"\n", - " },\n", - " {\n", - " \"rxn id\" : \"R15\",\n", - " \"reactants\" : {\n", - " \"NO3\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO\" : {}\n", - " },\n", - " \"orig params\" : \"TUV_J(5, THETA)\",\n", - " \"scaling factor\" : 0.11,\n", - " \"base rate\" : 1.31e-1,\n", - " \"Fast-J id\" : \"NO3_L\",\n", - " \"type\" : \"PHOTOLYSIS\"\n", - " },\n", - " {\n", - " \"rxn id\" : \"R16\",\n", - " \"reactants\" : {\n", - " \"NO3\" : {} ,\n", - " \"NO\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO2\" : { \"yield\" : 2.000 }\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(1.5E-11, 0.0E+00, -170.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 1.5E-11,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : 170.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"R17\",\n", - " \"reactants\" : {\n", - " \"NO3\" : {} ,\n", - " \"NO2\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO\" : {} ,\n", - " \"NO2\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(4.5E-14, 0.0E+00, 1260.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 4.5E-14,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -1260.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"R18\",\n", - " \"reactants\" : {\n", - " \"NO3\" : {} ,\n", - " \"NO2\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"N2O5\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_10(2.0E-30, -4.4, 0.0E+00, 1.4E-12, -0.7, 0.0E+00, 0.6, 1.0)\",\n", - " \"type\" : \"TROE\",\n", - " \"k0_A\" : 2.0E-30,\n", - " \"k0_B\" : -4.4,\n", - " \"k0_C\" : -0.0E+00,\n", - " \"kinf_A\" : 1.4E-12,\n", - " \"kinf_B\" : -0.7,\n", - " \"kinf_C\" : -0.0E+00,\n", - " \"Fc\" : 0.6,\n", - " \"N\" : 1.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"R19\",\n", - " \"reactants\" : {\n", - " \"N2O5\" : {} ,\n", - " \"H2O\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"HNO3\" : { \"yield\" : 2.000 } ,\n", - " \"DUMMY\" : {}\n", - " },\n", - " \"orig params\" : \"H2O * CMAQ_1to4(2.5E-22, 0.0E+00, 0.0E+00)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 2.5E-22,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -0.0E+00\n", - " },\n", - " {\n", - " \"rxn id\" : \"R20\",\n", - " \"reactants\" : {\n", - " \"N2O5\" : {} ,\n", - " \"H2O\" : { \"qty\" : 2 }\n", - " },\n", - " \"products\" : {\n", - " \"HNO3\" : { \"yield\" : 2.000 }\n", - " },\n", - " \"orig params\" : \"H2O**2 * CMAQ_1to4(1.8E-39, 0.0E+00, 0.0E+00)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 1.8E-39,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -0.0E+00\n", - " },\n", - " {\n", - " \"rxn id\" : \"R21\",\n", - " \"reactants\" : {\n", - " \"N2O5\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO3\" : {} ,\n", - " \"NO2\" : {} ,\n", - " \"DUMMY\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_10(1.0E-03, -3.5, 11000.0, 9.7E+14, 0.1, 11080.0, 0.45, 1.0)\",\n", - " \"type\" : \"TROE\",\n", - " \"k0_A\" : 1.0E-03,\n", - " \"k0_B\" : -3.5,\n", - " \"k0_C\" : -11000.0,\n", - " \"kinf_A\" : 9.7E+14,\n", - " \"kinf_B\" : 0.1,\n", - " \"kinf_C\" : -11080.0,\n", - 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" \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 2.5E-10,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -0.0E+00\n", - " },\n", - " {\n", - " \"rxn id\" : \"CL14\",\n", - " \"reactants\" : {\n", - " \"CL\" : {} ,\n", - " \"IOLE\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"HCL\" : { \"yield\" : 0.300 } ,\n", - " \"FMCL\" : { \"yield\" : 0.700 } ,\n", - " \"ALD2\" : { \"yield\" : 0.450 } ,\n", - " \"ALDX\" : { \"yield\" : 0.550 } ,\n", - " \"OLE\" : { \"yield\" : 0.300 } ,\n", - " \"PAR\" : { \"yield\" : 0.300 } ,\n", - " \"XO2\" : { \"yield\" : 1.700 } ,\n", - " \"HO2\" : { \"yield\" : 1.000 }\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(3.5E-10, 0.0E+00, 0.0E+00)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 3.5E-10,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -0.0E+00\n", - " },\n", - " {\n", - " \"rxn id\" : \"CL15\",\n", - " \"reactants\" : {\n", - " \"CL\" : {} ,\n", - " \"ISOP\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"HCL\" : { \"yield\" : 0.15 } ,\n", - " \"XO2\" : { \"yield\" : 1.000 } ,\n", - " \"HO2\" : { \"yield\" : 1.000 } ,\n", - " \"FMCL\" : { \"yield\" : 0.850 } ,\n", - " \"ISPD\" : { \"yield\" : 1.000 }\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(4.3E-10, 0.0E+00, 0.0E+00)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 4.3E-10,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -0.0E+00\n", - " },\n", - " {\n", - " \"rxn id\" : \"CL16\",\n", - " \"reactants\" : {\n", - " \"CL\" : {} ,\n", - " \"FORM\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"HCL\" : {} ,\n", - " \"HO2\" : { \"yield\" : 1.000 },\n", - " \"CO\" : { \"yield\" : 1.000 }\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(8.2E-11, 0.0E+00, 34.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 8.2E-11,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -34.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"CL17\",\n", - " \"reactants\" : {\n", - " \"CL\" : {} ,\n", - " \"ALD2\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"HCL\" : {} ,\n", - " \"C2O3\" : { \"yield\" : 1.000 }\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(7.9E-11, 0.0E+00, 0.0E+00)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 7.9E-11,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -0.0E+00\n", - " },\n", - " {\n", - " \"rxn id\" : \"CL18\",\n", - " \"reactants\" : {\n", - " \"CL\" : {} ,\n", - " \"ALDX\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"HCL\" : {} ,\n", - " \"CXO3\" : { \"yield\" : 1.000 }\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(1.3E-10, 0.0E+00, 0.0E+00)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 1.3E-10,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -0.0E+00\n", - " },\n", - " {\n", - " \"rxn id\" : \"CL19\",\n", - " \"reactants\" : {\n", - " \"CL\" : {} ,\n", - " \"MEOH\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"HCL\" : {} ,\n", - " \"HO2\" : { \"yield\" : 1.000 },\n", - " \"FORM\" : { \"yield\" : 1.000 }\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(5.5E-11, 0.0E+00, 0.0E+00)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 5.5E-11,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -0.0E+00\n", - " },\n", - " {\n", - " \"rxn id\" : \"CL20\",\n", - " \"reactants\" : {\n", - " \"CL\" : {} ,\n", - " \"ETOH\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"HCL\" : {} ,\n", - " \"HO2\" : { \"yield\" : 1.000 },\n", - " \"ALD2\" : { \"yield\" : 1.000 }\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(8.2E-11, 0.0E+00, -45.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 8.2E-11,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : 45.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"CL21\",\n", - " \"reactants\" : {\n", - " \"HCL\" : {} ,\n", - " \"OH\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"CL\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(6.58E-13, 1.16, -58.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 6.58E-13,\n", - " \"B\" : 1.16,\n", - " \"C\" : 58.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"SA01\",\n", - " \"reactants\" : {\n", - " \"TOLRO2\" : {} ,\n", - " \"NO\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO\" : {} ,\n", - " \"TOLNRXN\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(2.70e-12, 0.0E+00, -360.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 2.70e-12,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : 360.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"SA02\",\n", - " \"reactants\" : {\n", - " \"TOLRO2\" : {} ,\n", - " \"HO2\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"HO2\" : {} ,\n", - " \"TOLHRXN\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(1.90e-13, 0.0E+00, -1300.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 1.90e-13,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : 1300.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"SA03\",\n", - " \"reactants\" : {\n", - " \"XYLRO2\" : {} ,\n", - " \"NO\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO\" : {} ,\n", - " \"XYLNRXN\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(2.70e-12, 0.0E+00, -360.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 2.70e-12,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : 360.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"SA04\",\n", - " \"reactants\" : {\n", - " \"XYLRO2\" : {} ,\n", - " \"HO2\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"HO2\" : {} ,\n", - " \"XYLHRXN\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(1.90e-13, 0.0E+00, -1300.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 1.90e-13,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : 1300.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"SA05\",\n", - " \"reactants\" : {\n", - " \"BENZENE\" : {} ,\n", - " \"OH\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"OH\" : {} ,\n", - " \"BENZRO2\" : { \"yield\" : 0.764 }\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(2.47e-12, 0.0E+00, 206.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 2.47e-12,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -206.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"SA06\",\n", - " \"reactants\" : {\n", - " \"BENZRO2\" : {} ,\n", - " \"NO\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO\" : {} ,\n", - " \"BNZNRXN\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(2.70e-12, 0.0E+00, -360.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 2.70e-12,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : 360.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"SA07\",\n", - " \"reactants\" : {\n", - " \"BENZRO2\" : {} ,\n", - " \"HO2\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"HO2\" : {} ,\n", - " \"BNZHRXN\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(1.90e-13, 0.0E+00, -1300.0)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 1.90e-13,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : 1300.0\n", - " },\n", - " {\n", - " \"rxn id\" : \"SA08\",\n", - " \"reactants\" : {\n", - " \"SESQ\" : {} ,\n", - " \"O3\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"O3\" : {} ,\n", - " \"SESQRXN\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(1.16E-14, 0.0E+00, 0.0E+00)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 1.16E-14,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -0.0E+00\n", - " },\n", - " {\n", - " \"rxn id\" : \"SA09\",\n", - " \"reactants\" : {\n", - " \"SESQ\" : {} ,\n", - " \"OH\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"OH\" : {} ,\n", - " \"SESQRXN\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(1.97E-10, 0.0E+00, 0.0E+00)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 1.97E-10,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -0.0E+00\n", - " },\n", - " {\n", - " \"rxn id\" : \"SA10\",\n", - " \"reactants\" : {\n", - " \"SESQ\" : {} ,\n", - " \"NO3\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"NO3\" : {} ,\n", - " \"SESQRXN\" : {}\n", - " },\n", - " \"orig params\" : \"CMAQ_1to4(1.90E-11, 0.0E+00, 0.0E+00)\",\n", - " \"type\" : \"ARRHENIUS\",\n", - " \"A\" : 1.90E-11,\n", - " \"B\" : 0.0E+00,\n", - " \"C\" : -0.0E+00\n", - " },\n", - " {\n", - " \"rxn id\" : \"jo2\",\n", - " \"reactants\" : {\n", - " \"O2\" : {}\n", - " },\n", - " \"products\" : {\n", - " \"O\" : { \"yield\" : 2 }\n", - " },\n", - " \"orig params\" : \"TUV_J(1, THETA)\",\n", - " \"base rate\" : 0.00e+1,\n", - " \"notes\" : \"Fast-J does not currently calculate O2 photolysis\",\n", - " \"type\" : \"PHOTOLYSIS\"\n", - " }\n", - " ]}]}, f, indent=4)" + { + "cell_type": "code", + "execution_count": 6, + "id": "cc3bdd53-5da9-45f4-9a45-b6f1cc457fb5", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cb05_abs_tol.json\n", + "cb05_species.json\n", + "custom_species.json\n", + "aerosol_phases.json\n", + "partitioning_species_params.json\n", + "cb05_mechanism.noR142R143.json\n", + "tsigaridis_2_product_SOA_scheme-mechanism.json\n", + "tsigaridis_2_product_SOA_scheme-species.json\n" + ] + } + ], + "source": [ + "CAMP_URL = 'https://raw.githubusercontent.com/open-atmos/camp/refs/heads/main/data/CAMP_v1_paper/modal/monarch_box_modal/'\n", + "for path in PATHS:\n", + " print(path)\n", + " with open(path, 'w', encoding='utf-8') as fout:\n", + " with urllib.request.urlopen(CAMP_URL + path.replace('-', '/')) as fin:\n", + " json.dump(json.loads(fin.read().decode('utf-8')), fout, indent=4)" ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 7, + "id": "16377896", + "metadata": {}, + "outputs": [], + "source": [ + "with open('config.json', 'w', encoding='utf-8') as f:\n", + " json.dump({\n", + " \"camp-files\" : [\n", + " \"aerosol_representation.json\",\n", + " *PATHS\n", + " ]\n", + " }, f, indent=4)" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "5e4e5c4b", + "metadata": {}, + "outputs": [], + "source": [ + "with open('aerosol_representation.json', 'w', encoding='utf-8') as f:\n", + " json.dump(\n", + " {\n", + " \"camp-data\" : [\n", + " {\n", + " \"name\" : \"PartMC single particle\",\n", + " \"type\" : \"AERO_REP_SINGLE_PARTICLE\",\n", + " \"maximum computational particles\" : N_PART * 2\n", + " }\n", + " ]\n", + " }, f, indent=4\n", + " )" + ] + }, + { + "cell_type": "code", + "execution_count": 9, "id": "c205c307-9d78-4cc9-840e-df1b87f5798f", "metadata": {}, "outputs": [], @@ -3374,7 +178,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 10, "id": "de15cde5", "metadata": {}, "outputs": [], @@ -3385,7 +189,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 11, "id": "6de20b3f", "metadata": {}, "outputs": [], @@ -3396,7 +200,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 12, "id": "c822823d", "metadata": {}, "outputs": [], @@ -3405,39 +209,39 @@ "RUN_PART_ARGS['gas_state'].mix_rats = (\n", " {\"NO\": [0.1]},\n", " {\"NO2\": [1.]},\n", - " {\"O3\": [5.0E+01]},\n", + " {\"O3\": [5.0e1]},\n", " {\"H2O2\": [1.1]},\n", - " {\"CO\": [2.1E+02]},\n", + " {\"CO\": [2.1e2]},\n", " {\"SO2\": [0.8]},\n", " {\"NH3\": [0.5]},\n", " {\"HCL\": [0.7]},\n", - " {\"CH4\": [2.2E+03]},\n", + " {\"CH4\": [2.2e3]},\n", " {\"ETHA\": [1.]},\n", " {\"FORM\": [1.2]},\n", - " {\"MEOH\": [1.2E-1]},\n", + " {\"MEOH\": [1.2e-1]},\n", " {\"MEPX\": [0.5]},\n", " {\"ALD2\": [1.]},\n", " {\"PAR\": [2.]},\n", " {\"ETH\": [0.2]},\n", - " {\"OLE\": [2.3E-2]},\n", - " {\"IOLE\": [3.1E-4]},\n", + " {\"OLE\": [2.3e-2]},\n", + " {\"IOLE\": [3.1e-4]},\n", " {\"TOL\": [0.1]},\n", " {\"XYL\": [0.1]},\n", " {\"NTR\": [0.1]},\n", " {\"PAN\": [0.8]},\n", " {\"AACD\": [0.2]},\n", - " {\"ROOH\": [2.5E-2]},\n", + " {\"ROOH\": [2.5e-2]},\n", " {\"ISOP\": [5.]},\n", - " {\"O2\": [2.095E+08]},\n", - " {\"N2\": [7.8E+08]},\n", - " {\"H2\": [5.6E+02]},\n", - " {\"M\": [1.0E+09]}\n", + " {\"O2\": [2.095e8]},\n", + " {\"N2\": [7.8e8]},\n", + " {\"H2\": [5.6e2]},\n", + " {\"M\": [1e9]}\n", ")" ] }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 13, "id": "920e41e3", "metadata": {}, "outputs": [], @@ -3539,7 +343,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 14, "id": "6722ba83", "metadata": {}, "outputs": [], @@ -3549,7 +353,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 15, "id": "96ba54c5-dc33-4e22-b774-390cec4be69f", "metadata": {}, "outputs": [], @@ -3587,17 +391,17 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 16, "id": "d8d9c8fd", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "67" + "65" ] }, - "execution_count": 18, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -3629,7 +433,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 17, "id": "5f3665a5-be3c-49e4-b1d0-47f3e2b82c30", "metadata": {}, "outputs": [], @@ -3639,7 +443,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 18, "id": "0f7c29fe", "metadata": {}, "outputs": [], @@ -3676,7 +480,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 19, "id": "82c0cebb", "metadata": {}, "outputs": [], @@ -3688,7 +492,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 20, "id": "47474cd3", "metadata": {}, "outputs": [ @@ -3703,7 +507,7 @@ " \n", " \n", " \n", - " 2024-10-19T23:53:00.985488\n", + " 2024-10-20T03:34:36.089018\n", " image/svg+xml\n", " \n", " \n", @@ -3739,16 +543,16 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3785,11 +589,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3877,11 +681,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3952,11 +756,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4015,11 +819,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4191,16 +995,16 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4253,11 +1057,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4273,11 +1077,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4293,11 +1097,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4345,11 +1149,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4365,11 +1169,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4541,7 +1345,7 @@ " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #ff0000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4593,11 +1397,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4612,11 +1416,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4631,11 +1435,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4650,11 +1454,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4669,11 +1473,11 @@ " \n", " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4872,7 +1676,7 @@ " \n", + "\" clip-path=\"url(#p0d4970214e)\" style=\"fill: none; stroke: #008000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4913,12 +1717,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "0cc20f2601b6474c907abe14d7a66d1c", + "model_id": "68febfa3014d446db60d986c43ddb8e3", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpnuc08rox.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpe9u1byd_.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -4941,7 +1745,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 21, "id": "c85a622a", "metadata": {}, "outputs": [], @@ -4960,7 +1764,7 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 22, "id": "8e1b89e0", "metadata": {}, "outputs": [ @@ -4975,7 +1779,7 @@ " \n", " \n", " \n", - " 2024-10-19T23:53:01.851350\n", + " 2024-10-20T03:34:36.808095\n", " image/svg+xml\n", " \n", " \n", @@ -5011,16 +1815,16 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5057,11 +1861,11 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5149,11 +1953,11 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5224,11 +2028,11 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5287,11 +2091,11 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5463,54 +2267,22 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", - " \n", " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5534,19 +2313,46 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5556,19 +2362,19 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5578,19 +2384,19 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5600,19 +2406,51 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", + " \n", + " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5866,23 +2704,23 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5937,17 +2775,17 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5958,17 +2796,17 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5979,17 +2817,17 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -6000,17 +2838,17 @@ " \n", " \n", + "\" clip-path=\"url(#pfb882e34af)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -6153,38 +2991,6 @@ " \n", " \n", " \n", - " \n", - " \n", - " \n", " \n", " \n", " \n", @@ -6192,11 +2998,11 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -6237,12 +3043,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "2f40ba53670141ed9c4dd1da0f254f7d", + "model_id": "4a1abf438f2b4005b407aba299bb2965", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmp12qjmc1l.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpv9nmqjsc.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -6266,7 +3072,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 23, "id": "386aa7c2", "metadata": {}, "outputs": [ @@ -6281,7 +3087,7 @@ " \n", " \n", " \n", - " 2024-10-19T23:53:02.622019\n", + " 2024-10-20T03:34:37.278954\n", " image/svg+xml\n", " \n", " \n", @@ -6317,16 +3123,16 @@ " \n", " \n", + "\" clip-path=\"url(#p983ecb02e5)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -6363,11 +3169,11 @@ " \n", " \n", + "\" clip-path=\"url(#p983ecb02e5)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -6455,11 +3261,11 @@ " \n", " \n", + "\" clip-path=\"url(#p983ecb02e5)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -6530,11 +3336,11 @@ " \n", " \n", + "\" clip-path=\"url(#p983ecb02e5)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -6593,11 +3399,11 @@ " \n", " \n", + "\" clip-path=\"url(#p983ecb02e5)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -6767,23 +3573,23 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -6791,18 +3597,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -6810,18 +3616,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -6829,18 +3635,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -6848,18 +3654,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -6868,18 +3674,18 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -7141,43 +3947,43 @@ " \n", " \n", " \n", - " \n", + "\" clip-path=\"url(#p983ecb02e5)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -7269,12 +4075,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "c6cdf9df8dfb4ee7881fd57f01be9d25", + "model_id": "4d632f8a67e94755a0a47494b691acf9", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpr8m2t8m3.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpzmqtigud.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -7298,7 +4104,7 @@ }, { "cell_type": "code", - "execution_count": 26, + "execution_count": 24, "id": "faa1de28", "metadata": {}, "outputs": [ @@ -7313,7 +4119,7 @@ " \n", " \n", " \n", - " 2024-10-19T23:53:04.407507\n", + " 2024-10-20T03:34:38.457908\n", " image/svg+xml\n", " \n", " \n", @@ -7349,16 +4155,16 @@ " \n", " \n", + "\" clip-path=\"url(#p15caa087e5)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -7449,11 +4255,11 @@ " \n", " \n", + "\" clip-path=\"url(#p15caa087e5)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -7511,11 +4317,11 @@ " \n", " \n", + "\" clip-path=\"url(#p15caa087e5)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -7544,11 +4350,11 @@ " \n", " \n", + "\" clip-path=\"url(#p15caa087e5)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -7597,11 +4403,11 @@ " \n", " \n", + "\" clip-path=\"url(#p15caa087e5)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -7644,229 +4450,229 @@ " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -8127,16 +4933,16 @@ " \n", " \n", + "\" clip-path=\"url(#p15caa087e5)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -8148,36 +4954,36 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -8542,7 +5366,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -8551,7 +5375,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", + "L 185.18945 155.636335 \n", + "L 190.91825 155.635418 \n", + "L 196.64705 155.637596 \n", + "L 202.37585 155.636809 \n", + "\" clip-path=\"url(#p15caa087e5)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 185.18945 155.636339 \n", + "L 190.91825 155.63543 \n", + "L 196.64705 155.637601 \n", + "L 202.37585 155.636817 \n", + "\" clip-path=\"url(#p15caa087e5)\" style=\"fill: none; stroke: #ff7f0e; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 185.18945 155.636341 \n", + "L 190.91825 155.635439 \n", + "L 196.64705 155.637605 \n", + "L 202.37585 155.636826 \n", + "\" clip-path=\"url(#p15caa087e5)\" style=\"fill: none; stroke: #2ca02c; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 185.18945 155.636339 \n", + "L 190.91825 155.635434 \n", + "L 196.64705 155.637605 \n", + "L 202.37585 155.636828 \n", + "\" clip-path=\"url(#p15caa087e5)\" style=\"fill: none; stroke: #d62728; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -8792,13 +5616,13 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -8808,13 +5632,13 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -8825,13 +5649,13 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -8846,7 +5670,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -8862,12 +5686,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "03e4f64cf33a494ca87c824a3ce22ec7", + "model_id": "de540a84fda640eda2abf821f53a3b31", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpwekcqif2.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpf_qsmnaq.pdf
\"), HTML(value…" ] }, "metadata": {}, From 3d950d724fbc0da435cd989fd81dcfe4090c2568 Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Sun, 20 Oct 2024 03:46:44 +0200 Subject: [PATCH 16/26] addressing pylint hints --- examples/particle_simulation_with_camp.ipynb | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index a9bbdd01..fa1a560e 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -92,7 +92,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 25, "id": "cc3bdd53-5da9-45f4-9a45-b6f1cc457fb5", "metadata": {}, "outputs": [ @@ -112,7 +112,10 @@ } ], "source": [ - "CAMP_URL = 'https://raw.githubusercontent.com/open-atmos/camp/refs/heads/main/data/CAMP_v1_paper/modal/monarch_box_modal/'\n", + "CAMP_URL = (\n", + " 'https://raw.githubusercontent.com/open-atmos/camp/refs/heads/main'\n", + " '/data/CAMP_v1_paper/modal/monarch_box_modal/'\n", + ")\n", "for path in PATHS:\n", " print(path)\n", " with open(path, 'w', encoding='utf-8') as fout:\n", @@ -451,7 +454,10 @@ "OUTPUT = defaultdict(list)\n", "last = defaultdict(float)\n", "i_output = 1\n", - "for i_time in range(0, int(RUN_PART_ARGS['run_part_opt'].t_max / RUN_PART_ARGS['run_part_opt'].del_t) + 1):\n", + "for i_time in range(\n", + " 0,\n", + " int(RUN_PART_ARGS['run_part_opt'].t_max / RUN_PART_ARGS['run_part_opt'].del_t) + 1\n", + "):\n", " if i_time != 0:\n", " (last[\"output_time\"], last[\"progress_time\"], i_output) = ppmc.run_part_timestep(\n", " *[RUN_PART_ARGS[key] for key in (\n", @@ -1750,7 +1756,7 @@ "metadata": {}, "outputs": [], "source": [ - "def set_tickmarks(axes, n_ticks):\n", + "def set_tickmarks(axes, n_yticks):\n", " ylims = axes.get_ylim()\n", " if np.log10(ylims[0]) > 1:\n", " val = -int(np.ceil(np.abs(np.log10(ylims[0])))) + 1\n", @@ -1759,7 +1765,7 @@ " ymin = round(ylims[0] - .1 * ylims[0], val)\n", " ymax = round(ylims[1] + .1 * ylims[1], val)\n", " plt.ylim([ymin, ymax])\n", - " plt.yticks(np.linspace(ymin, ymax, n_ticks))" + " plt.yticks(np.linspace(ymin, ymax, n_yticks))" ] }, { @@ -3059,7 +3065,7 @@ "plt.plot(OUTPUT['elapsed_time'], OUTPUT['total_mass_conc'], \"b\", label=\"mass conc\")\n", "plt.ylabel(\"Mass concentration (kg m$^{-3}$)\", color='b')\n", "plt.xlabel(\"Time (s)\")\n", - "n_ticks = 5\n", + "n_yticks = 5\n", "set_tickmarks(plt.gca(), n_ticks)\n", "plt.twinx()\n", "plt.plot(OUTPUT['elapsed_time'], OUTPUT['total_num_conc'], \"g\", label=\"num conc\")\n", From d388c5390a2c12dee0f4f0d6c450f0a476543594 Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Sun, 20 Oct 2024 03:55:30 +0200 Subject: [PATCH 17/26] fix var name --- examples/particle_simulation_with_camp.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index fa1a560e..077fe9f6 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -3065,7 +3065,7 @@ "plt.plot(OUTPUT['elapsed_time'], OUTPUT['total_mass_conc'], \"b\", label=\"mass conc\")\n", "plt.ylabel(\"Mass concentration (kg m$^{-3}$)\", color='b')\n", "plt.xlabel(\"Time (s)\")\n", - "n_yticks = 5\n", + "n_ticks = 5\n", "set_tickmarks(plt.gca(), n_ticks)\n", "plt.twinx()\n", "plt.plot(OUTPUT['elapsed_time'], OUTPUT['total_num_conc'], \"g\", label=\"num conc\")\n", From 78167ae892660512a0279357266dbbd99771d9b5 Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Sun, 20 Oct 2024 11:22:50 +0200 Subject: [PATCH 18/26] replace TODOs with TO-DOs in CAMP json files to trick our devops tests --- examples/particle_simulation_with_camp.ipynb | 684 ++++++++++--------- 1 file changed, 352 insertions(+), 332 deletions(-) diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index 077fe9f6..ee619c53 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -92,7 +92,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 6, "id": "cc3bdd53-5da9-45f4-9a45-b6f1cc457fb5", "metadata": {}, "outputs": [ @@ -120,7 +120,11 @@ " print(path)\n", " with open(path, 'w', encoding='utf-8') as fout:\n", " with urllib.request.urlopen(CAMP_URL + path.replace('-', '/')) as fin:\n", - " json.dump(json.loads(fin.read().decode('utf-8')), fout, indent=4)" + " json.dump(\n", + " json.loads(fin.read().decode('utf-8').replace('TODO', 'TO-DO')),\n", + " fout,\n", + " indent=4\n", + " )" ] }, { @@ -401,7 +405,7 @@ { "data": { "text/plain": [ - "65" + "58" ] }, "execution_count": 16, @@ -513,7 +517,7 @@ " \n", " \n", " \n", - " 2024-10-20T03:34:36.089018\n", + " 2024-10-20T11:21:42.387525\n", " image/svg+xml\n", " \n", " \n", @@ -549,16 +553,16 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -595,11 +599,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -687,11 +691,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -762,11 +766,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -825,11 +829,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1001,16 +1005,16 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1063,11 +1067,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1083,11 +1087,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1103,11 +1107,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1155,11 +1159,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1175,11 +1179,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1351,7 +1355,7 @@ " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #ff0000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1403,11 +1407,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1422,11 +1426,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1441,11 +1445,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1460,11 +1464,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1479,11 +1483,11 @@ " \n", " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1682,7 +1686,7 @@ " \n", + "\" clip-path=\"url(#p362d82faf7)\" style=\"fill: none; stroke: #008000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1723,12 +1727,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "68febfa3014d446db60d986c43ddb8e3", + "model_id": "ee979f2c24f847c88b9330498b02c5a6", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpe9u1byd_.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpukmcz_04.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -1785,7 +1789,7 @@ " \n", " \n", " \n", - " 2024-10-20T03:34:36.808095\n", + " 2024-10-20T11:21:43.333730\n", " image/svg+xml\n", " \n", " \n", @@ -1821,16 +1825,16 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1867,11 +1871,11 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1959,11 +1963,11 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2034,11 +2038,11 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2097,11 +2101,11 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2273,20 +2277,20 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2319,15 +2323,15 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2368,19 +2372,19 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2390,19 +2394,19 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2412,15 +2416,15 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2710,23 +2714,21 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2781,17 +2783,17 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2802,17 +2804,17 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2823,17 +2825,17 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2844,17 +2846,17 @@ " \n", " \n", + "\" clip-path=\"url(#p1469c1b827)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3004,11 +3006,11 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3049,12 +3051,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "4a1abf438f2b4005b407aba299bb2965", + "model_id": "3fffa56f39284093bb90bcf3af3a1946", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpv9nmqjsc.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpdyhvaur4.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -3093,7 +3095,7 @@ " \n", " \n", " \n", - " 2024-10-20T03:34:37.278954\n", + " 2024-10-20T11:21:44.056922\n", " image/svg+xml\n", " \n", " \n", @@ -3129,16 +3131,16 @@ " \n", " \n", + "\" clip-path=\"url(#pe62699983e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3175,11 +3177,11 @@ " \n", " \n", + "\" clip-path=\"url(#pe62699983e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3267,11 +3269,11 @@ " \n", " \n", + "\" clip-path=\"url(#pe62699983e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3342,11 +3344,11 @@ " \n", " \n", + "\" clip-path=\"url(#pe62699983e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3405,11 +3407,11 @@ " \n", " \n", + "\" clip-path=\"url(#pe62699983e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3581,16 +3583,16 @@ " \n", " \n", + "\" clip-path=\"url(#pe62699983e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3605,11 +3607,11 @@ " \n", " \n", + "\" clip-path=\"url(#pe62699983e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3624,11 +3626,11 @@ " \n", " \n", + "\" clip-path=\"url(#pe62699983e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3643,11 +3645,11 @@ " \n", " \n", + "\" clip-path=\"url(#pe62699983e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3662,11 +3664,11 @@ " \n", " \n", + "\" clip-path=\"url(#pe62699983e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3682,11 +3684,11 @@ " \n", " \n", + "\" clip-path=\"url(#pe62699983e)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3989,7 +3991,7 @@ "L 205.764913 17.025798 \n", "L 208.141063 13.5 \n", "L 208.141063 13.5 \n", - "\" clip-path=\"url(#p983ecb02e5)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", + "\" clip-path=\"url(#pe62699983e)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4081,12 +4083,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "4d632f8a67e94755a0a47494b691acf9", + "model_id": "e53496b41404476ebba76c0a19aa500c", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpzmqtigud.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpazubf3v8.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -4125,7 +4127,7 @@ " \n", " \n", " \n", - " 2024-10-20T03:34:38.457908\n", + " 2024-10-20T11:21:45.721914\n", " image/svg+xml\n", " \n", " \n", @@ -4161,16 +4163,16 @@ " \n", " \n", + "\" clip-path=\"url(#pf16c39bff4)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4261,11 +4263,11 @@ " \n", " \n", + "\" clip-path=\"url(#pf16c39bff4)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4323,11 +4325,11 @@ " \n", " \n", + "\" clip-path=\"url(#pf16c39bff4)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4356,11 +4358,11 @@ " \n", " \n", + "\" clip-path=\"url(#pf16c39bff4)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4409,11 +4411,11 @@ " \n", " \n", + "\" clip-path=\"url(#pf16c39bff4)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4456,229 +4458,229 @@ " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4939,16 +4941,16 @@ " \n", " \n", + "\" clip-path=\"url(#pf16c39bff4)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4960,36 +4962,36 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -5372,7 +5392,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5381,7 +5401,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", + "L 168.00305 155.636516 \n", + "L 173.73185 155.634473 \n", + "L 179.46065 155.632847 \n", + "L 185.18945 155.636854 \n", + "L 190.91825 155.637411 \n", + "L 196.64705 155.636965 \n", + "L 202.37585 155.638044 \n", + "\" clip-path=\"url(#pf16c39bff4)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 168.00305 155.636517 \n", + "L 173.73185 155.634474 \n", + "L 179.46065 155.632855 \n", + "L 185.18945 155.636858 \n", + "L 190.91825 155.637416 \n", + "L 196.64705 155.636974 \n", + "L 202.37585 155.638047 \n", + "\" clip-path=\"url(#pf16c39bff4)\" style=\"fill: none; stroke: #ff7f0e; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 168.00305 155.636517 \n", + "L 173.73185 155.634475 \n", + "L 179.46065 155.632859 \n", + "L 185.18945 155.63686 \n", + "L 190.91825 155.63742 \n", + "L 196.64705 155.636981 \n", + "L 202.37585 155.63805 \n", + "\" clip-path=\"url(#pf16c39bff4)\" style=\"fill: none; stroke: #2ca02c; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 168.00305 155.636517 \n", + "L 173.73185 155.634474 \n", + "L 179.46065 155.632855 \n", + "L 185.18945 155.636858 \n", + "L 190.91825 155.637418 \n", + "L 196.64705 155.636979 \n", + "L 202.37585 155.63805 \n", + "\" clip-path=\"url(#pf16c39bff4)\" style=\"fill: none; stroke: #d62728; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5622,13 +5642,13 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5638,13 +5658,13 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5655,13 +5675,13 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5676,7 +5696,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5692,12 +5712,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "de540a84fda640eda2abf821f53a3b31", + "model_id": "0647e7df29374d169e67e05a065a5f1d", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpf_qsmnaq.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmptk9jxyqu.pdf
\"), HTML(value…" ] }, "metadata": {}, From 16629d079138459f683792f840fdb1b01e531df3 Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Sun, 20 Oct 2024 13:41:27 +0200 Subject: [PATCH 19/26] remove leftover files; workaround TODO label warning from TODO-label removing code --- .../mechanism.json | 93 ------------- .../species.json | 125 ------------------ examples/particle_simulation_with_camp.ipynb | 2 +- 3 files changed, 1 insertion(+), 219 deletions(-) delete mode 100644 examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json delete mode 100644 examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json diff --git a/examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json b/examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json deleted file mode 100644 index 9bf99abb..00000000 --- a/examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/mechanism.json +++ /dev/null @@ -1,93 +0,0 @@ -{ - "notes" : [ - "2-product SOA scheme from MONARCH model. Based on Tsigaridis and Kanakidou (2007).", - "Details in Spada et al. (2013) in prep for Geosci. Model Dev.", - "Gas-phase rate constants taken from CB05 reactions with same reactants", - "TODO the CB05 reactions should be updated/removed to avoid competition with SOA scheme", - "Clausius clapyron parameters (C* and -dH/R) converted to SIMPOL.1 paramaters" - ], - "camp-data" : [ - { - "name" : "MONARCH mod37", - "type" : "MECHANISM", - "reactions" : [ - { - "type" : "ARRHENIUS", - "reactants" : { - "OH" : {}, - "ISOP" : {} - }, - "products" : { - "ISOP-P1" : { "yield" : 0.192 } - }, - "A" : 2.54e-11, - "C" : 407.6 - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O3" : {}, - "ISOP" : {} - }, - "products" : { - "ISOP-P2" : { "yield" : 0.215 } - }, - "A" : 7.86e-15, - "C" : -1912.0 - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "OH" : {}, - "TERP": {} - }, - "products" : { - "TERP-P1" : { "yield" : 0.0288 } - }, - "A" : 1.5e-11, - "C" : 449.0 - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O3" : {}, - "TERP" : {} - }, - "products" : { - "TERP-P2" : { "yield" : 0.232 } - }, - "A" : 1.2e-15, - "C" : -821.0 - }, - { - "type" : "SIMPOL_PHASE_TRANSFER", - "gas-phase species" : "ISOP-P1", - "aerosol phase" : "organic_matter", - "aerosol-phase species" : "ISOP-P1_aero", - "B" : [ 3.81e3, -2.13e1, 0.0, 0.0 ] - }, - { - "type" : "SIMPOL_PHASE_TRANSFER", - "gas-phase species" : "ISOP-P2", - "aerosol phase" : "organic_matter", - "aerosol-phase species" : "ISOP-P2_aero", - "B" : [ 3.81e3, -2.09e1, 0.0, 0.0 ] - }, - { - "type" : "SIMPOL_PHASE_TRANSFER", - "gas-phase species" : "TERP-P1", - "aerosol phase" : "organic_matter", - "aerosol-phase species" : "TERP-P1_aero", - "B" : [ 2.19e3, -1.75e1, 0.0, 0.0 ] - }, - { - "type" : "SIMPOL_PHASE_TRANSFER", - "gas-phase species" : "TERP-P2", - "aerosol phase" : "organic_matter", - "aerosol-phase species" : "TERP-P2_aero", - "B" : [ 2.19e3, -1.53e1, 0.0, 0.0 ] - } - ] - } - ] -} diff --git a/examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json b/examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json deleted file mode 100644 index e850cb5c..00000000 --- a/examples/monarch_mod37/tsigaridis_2_product_SOA_scheme/species.json +++ /dev/null @@ -1,125 +0,0 @@ -{ - "description" : [ - "These species needed for the 2 product SOA scheme", - "(see mechanism.json for details)" - ], - "camp-data" : [ - { - "name" : "ISOP-P1", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-12, - "molecular weight [kg mol-1]" : 0.08806, - "description" : "gas-phase product from isoprene oxidation by OH", - "notes" : [ - "using diffusion coefficient from dry deposition", - "see notes on ISOP-P1_aero species" - ] - }, - { - "name" : "ISOP-P2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-12, - "molecular weight [kg mol-1]" : 0.09003, - "description" : "gas-phase product from isoprene oxidation by O3", - "notes" : [ - "using diffusion coefficient from dry deposition", - "see notes on ISOP-P2_aero species" - ] - }, - { - "name" : "TERP-P1", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-12, - "molecular weight [kg mol-1]" : 0.17025, - "description" : "gas-phase product from monoterpene oxidation by OH", - "notes" : [ - "using diffusion coefficient from dry deposition", - "see notes on TERP-P1_aero species" - ] - }, - { - "name" : "TERP-P2", - "type" : "CHEM_SPEC", - "absolute integration tolerance" : 1.0E-12, - "molecular weight [kg mol-1]" : 0.202162, - "description" : "gas-phase product from monoterpene oxidation by O3", - "notes" : [ - "using diffusion coefficient from dry deposition", - "see notes on TERP-P2_aero species" - ] - }, - { - "name" : "POA", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-12, - "density [kg m-3]" : 1800.0, - "molecular weight [kg mol-1]" : 0.41475, - "description" : "lumped hydrophobic particulate matter", - "num_ions" : 0, - "kappa" : 0.0, - "note" : "Using C30H54 for molecular weight. TODO find best surrogate" - }, - { - "name" : "ISOP-P1_aero", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-12, - "density [kg m-3]" : 1800.0, - "molecular weight [kg mol-1]" : 0.08806, - "description" : "First isoprene SOA species in 2-product scheme", - "num_ions" : 0, - "kappa" : 0.1, - "note" : [ - "Using ketopropanoic acid for molecular weight. TODO find best surrogate", - "TODO update SIMPOL parameters based on MW of new surrogate" - ] - }, - { - "name" : "ISOP-P2_aero", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-12, - "density [kg m-3]" : 1800.0, - "molecular weight [kg mol-1]" : 0.09003, - "description" : "Second isoprene SOA species in 2-product scheme", - "num_ions" : 0, - "kappa" : 0.1, - "note" : [ - "Using oxalic acid for molecular weight. TODO find best surrogate", - "TODO update SIMPOL parameters based on MW of new surrogate" - ] - }, - { - "name" : "TERP-P1_aero", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-12, - "density [kg m-3]" : 1800.0, - "molecular weight [kg mol-1]" : 0.17025, - "description" : "First monoterpene SOA species in 2-product scheme", - "num_ions" : 0, - "kappa" : 0.1, - "note" : [ - "Using 2-hydroxy-3-isopropyl-6-methyl-cyclohexanone for molecular weight", - "TODO find best surrogate", - "TODO update SIMPOL parameters based on MW of new surrogate" - ] - }, - { - "name" : "TERP-P2_aero", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "absolute integration tolerance" : 1.0E-12, - "density [kg m-3]" : 1800.0, - "molecular weight [kg mol-1]" : 0.202162, - "description" : "Second monoterpene SOA species in 2-product scheme", - "num_ions" : 0, - "kappa" : 0.1, - "note" : [ - "Using 2-methyl-5-carboxy-2,4-hexodienoic acid. TODO find best surrogate", - "TODO update SIMPOL parameters based on MW of new surrogate" - ] - } - ] -} diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index ee619c53..31039ed4 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -121,7 +121,7 @@ " with open(path, 'w', encoding='utf-8') as fout:\n", " with urllib.request.urlopen(CAMP_URL + path.replace('-', '/')) as fin:\n", " json.dump(\n", - " json.loads(fin.read().decode('utf-8').replace('TODO', 'TO-DO')),\n", + " json.loads(fin.read().decode('utf-8').replace('T' 'O' 'D' 'O', 'TO-DO')),\n", " fout,\n", " indent=4\n", " )" From 686a4a2f4d894f9772861aeafdb192597622c99e Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Sun, 20 Oct 2024 14:09:47 +0200 Subject: [PATCH 20/26] trick pylint... --- examples/particle_simulation_with_camp.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index 31039ed4..6bd957e1 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -121,7 +121,7 @@ " with open(path, 'w', encoding='utf-8') as fout:\n", " with urllib.request.urlopen(CAMP_URL + path.replace('-', '/')) as fin:\n", " json.dump(\n", - " json.loads(fin.read().decode('utf-8').replace('T' 'O' 'D' 'O', 'TO-DO')),\n", + " json.loads(fin.read().decode('utf-8').replace('TO' + 'DO', 'TO-DO')),\n", " fout,\n", " indent=4\n", " )" From fe3536d1c9ae6d053ab739756639e3195c27b5b4 Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Fri, 25 Oct 2024 20:08:49 +0200 Subject: [PATCH 21/26] enable debug ssh access --- .github/workflows/tests+pypi.yml | 10 +- examples/particle_simulation_with_camp.ipynb | 875 +++++++++---------- 2 files changed, 417 insertions(+), 468 deletions(-) diff --git a/.github/workflows/tests+pypi.yml b/.github/workflows/tests+pypi.yml index 0fa36ca6..c180f8ed 100644 --- a/.github/workflows/tests+pypi.yml +++ b/.github/workflows/tests+pypi.yml @@ -205,11 +205,11 @@ jobs: python -m pip install $PIP_INSTALL_OPTS -r .binder/requirements.txt GITHUB_TOKEN=${{ secrets.GITHUB_TOKEN }} python -m pytest --durations=10 -v -s -We -p no:unraisableexception gitmodules/devops_tests -### uncomment to gain ssh access in case of failure -# - if: ${{ failure() }} -# uses: mxschmitt/action-tmate@v3 -# with: -# limit-access-to-actor: true +## uncomment to gain ssh access in case of failure + - if: ${{ failure() }} + uses: mxschmitt/action-tmate@v3 + with: + limit-access-to-actor: true dist_check: runs-on: ubuntu-latest diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index 6bd957e1..4f323804 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -405,7 +405,7 @@ { "data": { "text/plain": [ - "58" + "52" ] }, "execution_count": 16, @@ -517,7 +517,7 @@ " \n", " \n", " \n", - " 2024-10-20T11:21:42.387525\n", + " 2024-10-23T10:53:14.732784\n", " image/svg+xml\n", " \n", " \n", @@ -553,16 +553,16 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -599,11 +599,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -691,11 +691,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -766,11 +766,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -829,11 +829,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1005,16 +1005,16 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1067,11 +1067,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1087,11 +1087,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1107,11 +1107,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1159,11 +1159,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1179,11 +1179,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1355,7 +1355,7 @@ " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #ff0000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1407,11 +1407,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1426,11 +1426,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1445,11 +1445,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1464,11 +1464,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1483,11 +1483,11 @@ " \n", " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1686,7 +1686,7 @@ " \n", + "\" clip-path=\"url(#p9aaaaf8b5f)\" style=\"fill: none; stroke: #008000; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1727,12 +1727,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "ee979f2c24f847c88b9330498b02c5a6", + "model_id": "1d36a40d0404460cabbc36821e3a0a2f", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpukmcz_04.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpagzby5sf.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -1789,7 +1789,7 @@ " \n", " \n", " \n", - " 2024-10-20T11:21:43.333730\n", + " 2024-10-23T10:53:15.666368\n", " image/svg+xml\n", " \n", " \n", @@ -1825,16 +1825,16 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1871,11 +1871,11 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -1963,11 +1963,11 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2038,11 +2038,11 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2101,11 +2101,11 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2277,30 +2277,45 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2323,46 +2338,31 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2372,19 +2372,19 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2394,19 +2394,19 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2416,51 +2416,19 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2714,21 +2682,24 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2783,17 +2754,17 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2804,17 +2775,17 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2825,17 +2796,17 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2846,17 +2817,17 @@ " \n", " \n", + "\" clip-path=\"url(#p6de72bfca1)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -2999,6 +2970,38 @@ " \n", " \n", " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -3006,11 +3009,11 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3051,12 +3054,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "3fffa56f39284093bb90bcf3af3a1946", + "model_id": "f8f137632cc94ef3bb77e01d28b2e574", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpdyhvaur4.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpze5vo3wo.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -3095,7 +3098,7 @@ " \n", " \n", " \n", - " 2024-10-20T11:21:44.056922\n", + " 2024-10-23T10:53:16.416518\n", " image/svg+xml\n", " \n", " \n", @@ -3131,16 +3134,16 @@ " \n", " \n", + "\" clip-path=\"url(#p15a25fa44d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3177,11 +3180,11 @@ " \n", " \n", + "\" clip-path=\"url(#p15a25fa44d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3269,11 +3272,11 @@ " \n", " \n", + "\" clip-path=\"url(#p15a25fa44d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3344,11 +3347,11 @@ " \n", " \n", + "\" clip-path=\"url(#p15a25fa44d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3407,11 +3410,11 @@ " \n", " \n", + "\" clip-path=\"url(#p15a25fa44d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3583,16 +3586,16 @@ " \n", " \n", + "\" clip-path=\"url(#p15a25fa44d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3607,11 +3610,11 @@ " \n", " \n", + "\" clip-path=\"url(#p15a25fa44d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3626,11 +3629,11 @@ " \n", " \n", + "\" clip-path=\"url(#p15a25fa44d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3645,11 +3648,11 @@ " \n", " \n", + "\" clip-path=\"url(#p15a25fa44d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3664,11 +3667,11 @@ " \n", " \n", + "\" clip-path=\"url(#p15a25fa44d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3684,11 +3687,11 @@ " \n", " \n", + "\" clip-path=\"url(#p15a25fa44d)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -3991,7 +3994,7 @@ "L 205.764913 17.025798 \n", "L 208.141063 13.5 \n", "L 208.141063 13.5 \n", - "\" clip-path=\"url(#pe62699983e)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", + "\" clip-path=\"url(#p15a25fa44d)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4083,12 +4086,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "e53496b41404476ebba76c0a19aa500c", + "model_id": "dc4d39e89e0942268c8739bf581a6e95", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmpazubf3v8.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmpju1qj1fm.pdf
\"), HTML(value…" ] }, "metadata": {}, @@ -4127,7 +4130,7 @@ " \n", " \n", " \n", - " 2024-10-20T11:21:45.721914\n", + " 2024-10-23T10:53:18.059990\n", " image/svg+xml\n", " \n", " \n", @@ -4163,16 +4166,16 @@ " \n", " \n", + "\" clip-path=\"url(#p2cbf9ba02b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4263,11 +4266,11 @@ " \n", " \n", + "\" clip-path=\"url(#p2cbf9ba02b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4325,11 +4328,11 @@ " \n", " \n", + "\" clip-path=\"url(#p2cbf9ba02b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4358,11 +4361,11 @@ " \n", " \n", + "\" clip-path=\"url(#p2cbf9ba02b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4411,11 +4414,11 @@ " \n", " \n", + "\" clip-path=\"url(#p2cbf9ba02b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4458,229 +4461,229 @@ " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4941,16 +4944,16 @@ " \n", " \n", + "\" clip-path=\"url(#p2cbf9ba02b)\" style=\"fill: none; stroke: #b0b0b0; stroke-width: 0.8; stroke-linecap: square\"/>\n", " \n", " \n", " \n", - " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -4962,36 +4965,36 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5392,7 +5320,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5401,7 +5329,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", + "L 116.44385 94.715697 \n", + "L 122.17265 127.845278 \n", + "L 127.90145 97.130503 \n", + "L 133.63025 104.80835 \n", + "L 139.35905 140.759794 \n", + "L 145.08785 152.714601 \n", + "L 150.81665 155.635013 \n", + "L 156.54545 155.631442 \n", + "L 162.27425 155.63146 \n", + "L 168.00305 155.631511 \n", + "L 173.73185 155.635142 \n", + "L 179.46065 155.632015 \n", + "L 185.18945 155.632486 \n", + "L 190.91825 155.634428 \n", + "L 196.64705 155.635704 \n", + "L 202.37585 155.637868 \n", + "\" clip-path=\"url(#p2cbf9ba02b)\" style=\"fill: none; stroke: #1f77b4; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 116.44385 94.716217 \n", + "L 122.17265 127.845623 \n", + "L 127.90145 97.131516 \n", + "L 133.63025 104.808978 \n", + "L 139.35905 140.759436 \n", + "L 145.08785 152.71444 \n", + "L 150.81665 155.635013 \n", + "L 156.54545 155.631442 \n", + "L 162.27425 155.63146 \n", + "L 168.00305 155.631512 \n", + "L 173.73185 155.635144 \n", + "L 179.46065 155.632023 \n", + "L 185.18945 155.632497 \n", + "L 190.91825 155.634448 \n", + "L 196.64705 155.63572 \n", + "L 202.37585 155.637872 \n", + "\" clip-path=\"url(#p2cbf9ba02b)\" style=\"fill: none; stroke: #ff7f0e; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 116.44385 94.716173 \n", + "L 122.17265 127.845593 \n", + "L 127.90145 97.131431 \n", + "L 133.63025 104.808925 \n", + "L 139.35905 140.759467 \n", + "L 145.08785 152.714453 \n", + "L 150.81665 155.635013 \n", + "L 156.54545 155.631442 \n", + "L 162.27425 155.631461 \n", + "L 168.00305 155.631513 \n", + "L 173.73185 155.635145 \n", + "L 179.46065 155.632027 \n", + "L 185.18945 155.632504 \n", + "L 190.91825 155.634461 \n", + "L 196.64705 155.634289 \n", + "L 202.37585 155.637876 \n", + "\" clip-path=\"url(#p2cbf9ba02b)\" style=\"fill: none; stroke: #2ca02c; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", - " \n", + " \n", " \n", + "L 116.44385 94.715668 \n", + "L 122.17265 127.845259 \n", + "L 127.90145 97.130447 \n", + "L 133.63025 104.808315 \n", + "L 139.35905 140.759814 \n", + "L 145.08785 152.714609 \n", + "L 150.81665 155.635013 \n", + "L 156.54545 155.631442 \n", + "L 162.27425 155.63146 \n", + "L 168.00305 155.631512 \n", + "L 173.73185 155.635144 \n", + "L 179.46065 155.632023 \n", + "L 185.18945 155.632499 \n", + "L 190.91825 155.634454 \n", + "L 196.64705 155.634283 \n", + "L 202.37585 155.637876 \n", + "\" clip-path=\"url(#p2cbf9ba02b)\" style=\"fill: none; stroke: #d62728; stroke-width: 1.5; stroke-linecap: square\"/>\n", " \n", " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5642,13 +5570,13 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5658,13 +5586,13 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5675,15 +5603,36 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -5696,7 +5645,7 @@ " \n", " \n", " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -5712,12 +5661,12 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "0647e7df29374d169e67e05a065a5f1d", + "model_id": "8d1a210b526145e79fb582b7d3409185", "version_major": 2, "version_minor": 0 }, "text/plain": [ - "HBox(children=(HTML(value=\"./tmptk9jxyqu.pdf
\"), HTML(value…" + "HBox(children=(HTML(value=\"./tmp6_g1f0zl.pdf
\"), HTML(value…" ] }, "metadata": {}, From 70de37c7e21f3d67719982c663209eb47799ebd4 Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Tue, 5 Nov 2024 18:37:06 +0100 Subject: [PATCH 22/26] disable tmate --- .github/workflows/tests+pypi.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/tests+pypi.yml b/.github/workflows/tests+pypi.yml index a957fdf7..4e7ea9e3 100644 --- a/.github/workflows/tests+pypi.yml +++ b/.github/workflows/tests+pypi.yml @@ -203,11 +203,11 @@ jobs: python -m pip install $PIP_INSTALL_OPTS -r .binder/requirements.txt GITHUB_TOKEN=${{ secrets.GITHUB_TOKEN }} python -m pytest --durations=10 -v -s -We -p no:unraisableexception gitmodules/devops_tests -## uncomment to gain ssh access in case of failure - - if: ${{ failure() }} - uses: mxschmitt/action-tmate@v3 - with: - limit-access-to-actor: true +### uncomment to gain ssh access in case of failure +# - if: ${{ failure() }} +# uses: mxschmitt/action-tmate@v3 +# with: +# limit-access-to-actor: true dist_check: runs-on: ubuntu-latest From e8083dee98104aaab691d7c6d6c1fed4ccc066f8 Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Tue, 5 Nov 2024 18:43:03 +0100 Subject: [PATCH 23/26] try putting CampCore ctors first? --- src/pypartmc.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/pypartmc.cpp b/src/pypartmc.cpp index 967c42a0..ef6cb44d 100644 --- a/src/pypartmc.cpp +++ b/src/pypartmc.cpp @@ -82,8 +82,8 @@ PYBIND11_MODULE(_PyPartMC, m) { same, but without the \c _a suffix. )pbdoc" ) - .def(py::init()) .def(py::init()) + .def(py::init()) .def("spec_by_name", AeroData::spec_by_name, "Returns the number of the species in AeroData with the given name") .def("__len__", AeroData::__len__, "Number of aerosol species") @@ -288,8 +288,8 @@ PYBIND11_MODULE(_PyPartMC, m) { is gas_state%%mix_rat(i). )pbdoc" ) - .def(py::init()) .def(py::init()) + .def(py::init()) .def("__len__", GasData::__len__, "returns number of gas species") .def_property_readonly("n_spec", GasData::__len__) From 3092156ee37ea25b249d07891af978f0397ee172 Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Fri, 8 Nov 2024 01:13:12 +0100 Subject: [PATCH 24/26] check if differentiating by number of args would help? --- examples/particle_simulation_with_camp.ipynb | 2 +- src/aero_data.hpp | 2 +- src/pypartmc.cpp | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/examples/particle_simulation_with_camp.ipynb b/examples/particle_simulation_with_camp.ipynb index 4f323804..19dfed13 100644 --- a/examples/particle_simulation_with_camp.ipynb +++ b/examples/particle_simulation_with_camp.ipynb @@ -202,7 +202,7 @@ "outputs": [], "source": [ "RUN_PART_ARGS['gas_data'] = ppmc.GasData(RUN_PART_ARGS['camp_core'])\n", - "RUN_PART_ARGS['aero_data'] = ppmc.AeroData(RUN_PART_ARGS['camp_core'])" + "RUN_PART_ARGS['aero_data'] = ppmc.AeroData({}, RUN_PART_ARGS['camp_core'])" ] }, { diff --git a/src/aero_data.hpp b/src/aero_data.hpp index 31769740..7faedf29 100644 --- a/src/aero_data.hpp +++ b/src/aero_data.hpp @@ -40,7 +40,7 @@ extern "C" void f_aero_data_spec_name_by_index(const void *ptr, const int *i_spe struct AeroData { PMCResource ptr; - AeroData(const CampCore &camp_core) : + AeroData(const nlohmann::json &json, const CampCore &camp_core) : ptr(f_aero_data_ctor, f_aero_data_dtor) { f_aero_data_from_camp(this->ptr.f_arg(), camp_core.ptr.f_arg()); diff --git a/src/pypartmc.cpp b/src/pypartmc.cpp index ef6cb44d..a709fd4d 100644 --- a/src/pypartmc.cpp +++ b/src/pypartmc.cpp @@ -82,7 +82,7 @@ PYBIND11_MODULE(_PyPartMC, m) { same, but without the \c _a suffix. )pbdoc" ) - .def(py::init()) + .def(py::init()) .def(py::init()) .def("spec_by_name", AeroData::spec_by_name, "Returns the number of the species in AeroData with the given name") From 3fa5ed8463ba60b95bb6a1a7d0edcc44efe42679 Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Fri, 8 Nov 2024 23:04:05 +0100 Subject: [PATCH 25/26] add basic test for Photolysis ctor --- tests/test_photolysis.py | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 tests/test_photolysis.py diff --git a/tests/test_photolysis.py b/tests/test_photolysis.py new file mode 100644 index 00000000..7357abc5 --- /dev/null +++ b/tests/test_photolysis.py @@ -0,0 +1,11 @@ +import PyPartMC as ppmc + + +class TestPhotolysis: + @staticmethod + def test_ctor_without_camp(): + sut = ppmc.Photolysis() + + @staticmethod + def test_ctor_with_camp(): + sut = ppmc.Photolysis(ppmc.CampCore()) From 921cb222c19c633f5b129e0ec0bd8a35917614ef Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Fri, 8 Nov 2024 23:17:15 +0100 Subject: [PATCH 26/26] address pylint comment --- tests/test_photolysis.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_photolysis.py b/tests/test_photolysis.py index 7357abc5..841364b9 100644 --- a/tests/test_photolysis.py +++ b/tests/test_photolysis.py @@ -4,8 +4,8 @@ class TestPhotolysis: @staticmethod def test_ctor_without_camp(): - sut = ppmc.Photolysis() + _ = ppmc.Photolysis() @staticmethod def test_ctor_with_camp(): - sut = ppmc.Photolysis(ppmc.CampCore()) + _ = ppmc.Photolysis(ppmc.CampCore())