diff --git a/.github/workflows/tchem.yml b/.github/workflows/tchem.yml new file mode 100644 index 000000000..e7abf74d1 --- /dev/null +++ b/.github/workflows/tchem.yml @@ -0,0 +1,15 @@ +name: TChem + +on: [push, pull_request] + +jobs: + build: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v1 + - name: Build the testing docker image + run: docker build -f Dockerfile.tchem -t partmc-test . + - name: Run the tests in the docker container + run: docker run -t partmc-test bash -c 'export CTEST_PARALLEL_LEVEL=4; cd /build; make test' diff --git a/CMakeLists.txt b/CMakeLists.txt index d43dc134e..788097ae3 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -3,7 +3,17 @@ cmake_minimum_required(VERSION 2.6.4) # http://www.cmake.org/Bug/view.php?id=8598 # http://gcc.gnu.org/bugzilla/show_bug.cgi?id=35707 # http://www.cmake.org/Bug/view.php?id=8408 -project(PARTMC Fortran C) +if (ENABLE_TCHEM) + # Use the wrapper to nvcc for the CXX compiler for GPU + if (ENABLE_TCHEM_GPU) + set(ENV{CXX} $ENV{KOKKOS_PATH}/bin/nvcc_wrapper) + project(PARTMC Fortran C CXX) + else() + project(PARTMC Fortran C) + endif() +else() + project(PARTMC Fortran C) +endif() set(PACKAGE_BUGREPORT "mwest@illinois.edu") set(PACKAGE_NAME "PartMC") @@ -17,6 +27,7 @@ set(PACKAGE_VERSION "2.8.0") option(ENABLE_GSL "Enable GSL library for random number generation" OFF) option(ENABLE_MOSAIC "Enable MOSAIC chemistry support" OFF) option(ENABLE_CAMP "Enable CAMP chemistry support" OFF) +option(ENABLE_TCHEM "Enable TChem chemistry support" OFF) option(ENABLE_MPI "Enable MPI parallel support" OFF) option(ENABLE_SUNDIALS "Enable SUNDIALS solver for condensation support" OFF) option(ENABLE_C_SORT "Enable C sorting routines" OFF) @@ -98,6 +109,50 @@ if(ENABLE_CAMP) add_definitions(-DPMC_USE_CAMP) endif() +###################################################################### + +if(ENABLE_TCHEM) + find_path(TCHEM_INCLUDE_DIR tchem_atm/TChem_Driver.hpp + DOC "TChem include directory" + PATHS $ENV{TCHEM_HOME}/include/) + find_library(TCHEM_LIB tchem_atm + DOC "TChem library" + PATHS $ENV{TCHEM_HOME}/lib64 $ENV{TCHEM_HOME}/lib) + add_definitions(-DPMC_USE_TCHEM) + include_directories(${TCHEM_INCLUDE_DIR}) + find_path(YAML_INCLUDE_DIR yaml-cpp/yaml.h + DOC "TChem include directory" + PATHS $ENV{YAML_PATH}/include/) + find_library(YAML_LIB yaml-cpp + PATHS $ENV{YAML_PATH}/lib) + include_directories(${YAML_INCLUDE_DIR}) + find_path(KOKKOS_INCLUDE_DIR Kokkos_Core.hpp + DOC "Kokkos include directory" + PATHS $ENV{KOKKOS_PATH}/include) + find_library(KOKKOS_LIB kokkoscore + PATHS $ENV{KOKKOS_PATH}/lib64 $ENV{KOKKOS_PATH}/lib) + include_directories(${KOKKOS_INCLUDE_DIR}) + find_path(KOKKOSKERNEL_INCLUDE_DIR KokkosKernels_Utils.hpp + DOC "Kokkos include directory" + PATHS $ENV{KOKKOSKERNEL_PATH}/include) + find_library(KOKKOSKERNEL_LIB kokkoskernels + PATHS $ENV{KOKKOSKERNEL_PATH}/lib64 $ENV{KOKKOSKERNEL_PATH}/lib) + find_path(TINES_INCLUDE_DIR tines/Tines.hpp + DOC "Tines include directory" + PATHS $ENV{TINES_PATH}/include) + find_library(TINES_LIB tines + PATHS $ENV{TINES_PATH}/lib64 $ENV{TINES_PATH}/lib) + include_directories(${TINES_INCLUDE_DIR}) + set(CPP_LIB -lstdc++) +# find_path(LAPACK_INCLUDE_DIR lapack.h +# DOC "LAPACK include directory" +# PATHS $ENV{LAPACK_PATH}/include) + find_library(LAPACK_LIB openblas + PATHS $ENV{LAPACK_PATH}/lib) +# include_directories(${LAPACK_INCLUDE_DIR}) + option(ENABLE_TCHEM_GPU "Enable TChem GPU chemistry support" OFF) +endif() + ###################################################################### # MPI @@ -154,6 +209,9 @@ if(ENABLE_MPI) endif() add_test(test_rand ${CMAKE_BINARY_DIR}/test_run/run_test_directory.sh rand) add_test(test_sedi ${CMAKE_BINARY_DIR}/test_run/run_test_directory.sh sedi) +if (ENABLE_TCHEM) + add_test(test_tchem ${CMAKE_BINARY_DIR}/test_run/run_test_directory.sh tchem) +endif() add_test(test_weighting ${CMAKE_BINARY_DIR}/test_run/run_test_directory.sh weighting) ###################################################################### @@ -176,14 +234,31 @@ add_library(partmclib src/aero_state.F90 src/integer_varray.F90 src/netcdf.F90 src/aero_info.F90 src/aero_info_array.F90 src/nucleate.F90 src/condense.F90 src/fractal.F90 src/chamber.F90 src/camp_interface.F90 src/photolysis.F90 src/sys.F90 + src/tchem_interface.F90 src/aero_component.F90 - ${SUNDIALS_SRC} ${GSL_SRC} + ${SUNDIALS_SRC} ${GSL_SRC} ${TCHEM_SRC} ${C_SORT_SRC}) target_link_libraries(partmclib ${NETCDF_LIBS} ${SUNDIALS_LIBS} - ${MOSAIC_LIB} ${GSL_LIBS} ${CAMP_LIB}) + ${MOSAIC_LIB} ${GSL_LIBS} ${CAMP_LIB} ${TCHEM_LIB} ${YAML_LIB} + ${KOKKOS_LIB} ${KOKKOSKERNEL_LIB} ${TINES_LIB} ${CPP_LIB} ${LAPACK_LIB}) + +if (ENABLE_TCHEM) + find_package(OpenMP REQUIRED) + if (ENABLE_TCHEM_GPU) + add_link_options(${OpenMP_CXX_FLAGS}) + else() + add_link_options(${OpenMP_Fortran_FLAGS}) + endif() + include(FindThreads) + target_link_libraries(partmclib ${CMAKE_THREAD_LIBS_INIT} ${CMAKE_DL_LIBS}) +endif() set_target_properties(partmclib PROPERTIES OUTPUT_NAME partmc) +if (ENABLE_TCHEM_GPU) + add_link_options(${OpenMP_CXX_FLAGS}) + set_target_properties(partmclib PROPERTIES LINKER_LANGUAGE CXX) +endif() ###################################################################### # partmc executable @@ -191,6 +266,9 @@ set_target_properties(partmclib PROPERTIES OUTPUT_NAME partmc) add_executable(partmc src/partmc.F90) target_link_libraries(partmc partmclib) +if (ENABLE_TCHEM_GPU) + set_property(TARGET partmc PROPERTY LINKER_LANGUAGE CXX) +endif() ###################################################################### # test_bidisperse_ode diff --git a/Dockerfile.tchem b/Dockerfile.tchem new file mode 100644 index 000000000..b34de0eb8 --- /dev/null +++ b/Dockerfile.tchem @@ -0,0 +1,177 @@ +FROM ubuntu:22.04 + +ARG BUILD_TYPE=RELEASE +ARG SACADO=ON +RUN echo "BUILD TYPE:" ${BUILD_TYPE} +RUN echo "SACADO:" ${SACADO} + +RUN apt-get update \ + && apt-get install -y --no-install-recommends \ + autoconf \ + clang-format \ + cmake \ + gcc \ + g++ \ + gfortran \ + git \ + lcov \ + make \ + libopenblas-dev \ + pkg-config \ + ca-certificates \ + less \ + tmux \ + libnetcdf-dev \ + libnetcdff-dev \ + libgsl-dev \ + openssh-client + +RUN git clone https://github.com/PCLAeroParams/TChem-atm.git /tchem_dir/ +WORKDIR /tchem_dir/ +RUN git submodule update --init --recursive + +RUN cmake -S /tchem_dir/external/Tines/ext/kokkos -B /build/kokkos_build \ + -DCMAKE_INSTALL_PREFIX="/install/kokkos_install" \ + -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \ + -DCMAKE_CXX_COMPILER=g++ \ + -DCMAKE_CXX_FLAGS="-fopenmp -g" \ + -DKokkos_ENABLE_SERIAL=ON \ + -DKokkos_ENABLE_OPENMP=ON \ + -DKokkos_ENABLE_CUDA=OFF \ + -DKokkos_ENABLE_CUDA_CONSTEXPR=OFF \ + -DKokkos_ENABLE_CUDA_LAMBDA=OFF +WORKDIR /build/kokkos_build/ +RUN make -j \ + && make install + +RUN cmake -S /tchem_dir/external/Tines/ext/gtest -B /build/gtest_build \ + -DCMAKE_INSTALL_PREFIX="/install/gtest_install" \ + -DCMAKE_CXX_COMPILER=g++ +WORKDIR /build/gtest_build +RUN make -j \ + && make install + +RUN cmake -S /tchem_dir/external/Tines/ext/yaml -B /build//yaml_build \ + -DCMAKE_INSTALL_PREFIX="/install/yaml_install" \ + -DCMAKE_CXX_COMPILER=g++ \ + -DCMAKE_C_COMPILER=gcc \ + -DCMAKE_CXX_FLAGS="-g -c" \ + -DCMAKE_EXE_LINKER_FLAGS="" \ + -DCMAKE_BUILD_TYPE=RELEASE +WORKDIR /build/yaml_build +RUN make -j \ + && make install + +RUN cmake -S /tchem_dir/external/Sundials -B /build/sundials_build \ + -DCMAKE_INSTALL_PREFIX="/install/sundials_install" \ + -DCMAKE_CXX_COMPILER=g++ \ + -DCMAKE_C_COMPILER=gcc \ + -DCMAKE_CXX_FLAGS="-g" \ + -DCMAKE_C_FLAGS="-g" \ + -DCMAKE_EXE_LINKER_FLAGS="" \ + -DENABLE_CALIPER:BOOL=OFF \ + -DCMAKE_BUILD_TYPE=RELEASE +WORKDIR /build/sundials_build +RUN make -j \ + && make install + +RUN cmake -S /tchem_dir/external/Skywalker -B /build/skywalker_build \ + -DCMAKE_INSTALL_PREFIX="/install/skywalker_install" \ + -DCMAKE_CXX_COMPILER=g++ \ + -DCMAKE_C_COMPILER=gcc \ + -DSKYWALKER_PRECISION=double \ + -DCMAKE_BUILD_TYPE=RELEASE +WORKDIR /build/skywalker_build +RUN make -j \ + && make install + +RUN cmake -S /tchem_dir/external/Tines/src -B /build/tines_build \ + -DCMAKE_INSTALL_PREFIX="/install/tines_install" \ + -DCMAKE_CXX_COMPILER=g++ \ + -DCMAKE_CXX_FLAGS="-g" \ + -DCMAKE_C_COMPILER=gcc \ + -DCMAKE_EXE_LINKER_FLAGS="-lgfortran" \ + -DTINES_ENABLE_DEBUG=OFF \ + -DTINES_ENABLE_VERBOSE=OFF \ + -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \ + -DTINES_ENABLE_TEST=OFF \ + -DTINES_ENABLE_EXAMPLE=OFF \ + -DSUNDIALS_INSTALL_PATH=/install/sundials_install \ + -DYAML_INSTALL_PATH=/install/yaml_install \ + -DKOKKOS_INSTALL_PATH=/install/kokkos_install \ + -DOPENBLAS_INSTALL_PATH=`/usr/lib64` \ + -DGTEST_INSTALL_PATH=/install/gtest_install +WORKDIR /build/tines_build +RUN make -j \ + && make install + +RUN cmake -S /tchem_dir/external/kokkos-kernels -B /build/kokkoskernels_build \ + -DCMAKE_INSTALL_PREFIX="/install/kokkoskernels_install" \ + -DCMAKE_CXX_COMPILER=g++ \ + -DCMAKE_CXX_FLAGS="-g" \ + -DCMAKE_EXE_LINKER_FLAGS="-lgfortran" \ + -DKokkosKernels_ENABLE_EXAMPLES=OFF \ + -DKokkosKernels_ENABLE_EXPERIMENTAL=OFF \ + -DKokkosKernels_ENABLE_TESTS=OFF \ + -DKokkosKernels_ENABLE_COMPONENT_BLAS=OFF \ + -DKokkosKernels_ENABLE_COMPONENT_GRAPH=OFF \ + -DKokkosKernels_ENABLE_COMPONENT_LAPACK=OFF \ + -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \ + -DKokkos_ROOT=/install/kokkos_install +WORKDIR /build/kokkoskernels_build +RUN make -j4 \ + && make install + + + +RUN cmake -S /tchem_dir/src -B /tchem_build \ + -DCMAKE_INSTALL_PREFIX=/tchem_install \ + -DCMAKE_CXX_COMPILER=g++ \ + -DCMAKE_CXX_FLAGS="-g" \ + -DCMAKE_C_COMPILER=gcc \ + -DCMAKE_EXE_LINKER_FLAGS="-lgfortran" \ + -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \ + -DTCHEM_ATM_ENABLE_VERBOSE=OFF \ + -DTCHEM_ATM_ENABLE_TEST=ON \ + -DTCHEM_ATM_ENABLE_EXAMPLE=ON \ + -DTCHEM_ATM_ENABLE_SACADO_JACOBIAN_ATMOSPHERIC_CHEMISTRY=${SACADO} \ + -DKOKKOS_INSTALL_PATH=/install/kokkos_install \ + -DTINES_INSTALL_PATH=/install/tines_install \ + -DTCHEM_ATM_ENABLE_SKYWALKER=ON \ + -DTCHEM_ATM_ENABLE_REAL_TYPE="double" \ + -DSKYWALKER_INSTALL_PATH=/install/skywalker_install \ + -DTCHEM_ATM_ENABLE_KOKKOSKERNELS=ON \ + -DKOKKOSKERNELS_INSTALL_PATH=/install/kokkoskernels_install \ + -DTCHEM_ATM_ENABLE_SKYWALKER=ON \ + -DGTEST_INSTALL_PATH=/install/gtest_install +WORKDIR /tchem_build +RUN make -j \ + && make install + +#RUN export FC=gfortran \ +# export CC=gcc \ +# export CXX=g++ + +COPY . /partmc/ +RUN cd /build \ + && export TCHEM_HOME="/tchem_install" \ + && export KOKKOS_PATH="/install/kokkos_install" \ + && export KOKKOSKERNEL_PATH="/install/kokkoskernels_install" \ + && export YAML_PATH="/install/yaml_install" \ + && export TINES_PATH="/install/tines_install" \ + && export LAPACK_PATH="/usr/" \ + && export SUNDIALS_HOME="/install/sundials_install/" \ + && export LD_LIBRARY_PATH="/usr/lib:/usr/lib64:$LD_LIBRARY_PATH" \ + && cmake -DCMAKE_BUILD_TYPE=release \ + -DCMAKE_C_COMPILER=gcc \ + -DCMAKE_Fortran_COMPILER=gfortran \ + -DCMAKE_C_FLAGS_RELEASE="-O2 -g -Werror -Wall -Wextra" \ + -DCMAKE_Fortran_FLAGS_RELEASE="-O2 -g -Werror -fimplicit-none -Wall -Wextra -Wconversion -Wunderflow -Wimplicit-interface -Wno-compare-reals -Wno-unused -Wno-unused-parameter -Wno-unused-dummy-argument -fbounds-check" \ + -D ENABLE_GSL:BOOL=TRUE \ + -D ENABLE_TCHEM:BOOL=TRUE \ + -D ENABLE_SUNDIALS:BOOL=TRUE \ + -DCMAKE_C_FLAGS="-lpthread -ldl -fopenmp" \ + -DCMAKE_Fortran_FLAGS="-lpthread -ldl -fopenmp" \ + /partmc \ + && make +WORKDIR /build diff --git a/scenarios/1_urban_plume/urban_plume.spec b/scenarios/1_urban_plume/urban_plume.spec index 82ae03aad..4f9290bbd 100644 --- a/scenarios/1_urban_plume/urban_plume.spec +++ b/scenarios/1_urban_plume/urban_plume.spec @@ -11,6 +11,7 @@ t_output 3600 # output interval (0 disables) (s) t_progress 600 # progress printing interval (0 disables) (s) do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas concentrations diff --git a/scenarios/2_urban_plume2/urban_plume2.spec b/scenarios/2_urban_plume2/urban_plume2.spec index 2b42f486a..6a22fa81e 100644 --- a/scenarios/2_urban_plume2/urban_plume2.spec +++ b/scenarios/2_urban_plume2/urban_plume2.spec @@ -11,6 +11,7 @@ t_output 3600 # output interval (0 disables) (s) t_progress 600 # progress printing interval (0 disables) (s) do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas concentrations diff --git a/scenarios/3_condense/cond_template.spec b/scenarios/3_condense/cond_template.spec index e9bf7389f..699fb6725 100644 --- a/scenarios/3_condense/cond_template.spec +++ b/scenarios/3_condense/cond_template.spec @@ -11,6 +11,7 @@ t_output 1 # output interval (0 disables) (s) t_progress 60 # progress printing interval (0 disables) (s) do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry temp_profile %%TEMP_PROFILE%% # temperature profile file pressure_profile pressure.dat # pressure profile file diff --git a/scenarios/4_chamber/chamber.spec b/scenarios/4_chamber/chamber.spec index 536d194dd..be35e8ed8 100644 --- a/scenarios/4_chamber/chamber.spec +++ b/scenarios/4_chamber/chamber.spec @@ -11,6 +11,7 @@ t_output 420 # output interval (0 disables) (s) t_progress 2520 # progress printing interval (0 disables) (s) do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/scenarios/5_coag_brownian/example.spec b/scenarios/5_coag_brownian/example.spec index 9e1f7d16a..fff0dae5c 100644 --- a/scenarios/5_coag_brownian/example.spec +++ b/scenarios/5_coag_brownian/example.spec @@ -11,6 +11,7 @@ t_output 3600 # output interval (0 disables) (s) t_progress 600 # progress printing interval (0 disables) (s) do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas concentrations diff --git a/scenarios/6_camp/camp.spec b/scenarios/6_camp/camp.spec index d66f3599a..e51383447 100644 --- a/scenarios/6_camp/camp.spec +++ b/scenarios/6_camp/camp.spec @@ -12,6 +12,7 @@ t_progress 600 # progress printing interval (0 disables) (s) do_camp_chem yes # whether to use CAMP for chemistry camp_config config.json +do_tchem no # whether to use TChem for chemistry gas_init gas_init.dat # initial gas concentrations diff --git a/src/camp_interface.F90 b/src/camp_interface.F90 index 20cb07ad4..59b7e7d20 100644 --- a/src/camp_interface.F90 +++ b/src/camp_interface.F90 @@ -68,7 +68,7 @@ subroutine pmc_camp_interface_solve(camp_core, camp_state, & call env_state_set_camp_env_state(env_state, camp_state) ! Set the CAMP gas-phase species concentrations - call gas_state_set_camp_conc(gas_state, camp_state, gas_data) + call gas_state_set_camp_conc(gas_state, env_state, camp_state, gas_data) ! Recalculate the photolysis rate constants call photolysis%update_rate_constants() diff --git a/src/env_state.F90 b/src/env_state.F90 index ef11f0f58..ce7dd9e28 100644 --- a/src/env_state.F90 +++ b/src/env_state.F90 @@ -197,6 +197,28 @@ real(kind=dp) function env_state_air_molar_den(env_state) end function env_state_air_molar_den +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Converts relative humidity (1) to water vapor mixing ratio (ppb). + !! + !! Uses equation (1.10) of Seinfeld and Pandis Atmospheric Chemistry and + !! Physics From Air Pollution to Climate Change Second Edition, 2006. + real(kind=dp) function env_state_rel_humid_to_mix_rat(env_state) + + !> Environment state. + type(env_state_t), intent(in) :: env_state + + real(kind=dp), parameter :: t_steam = 373.15 ! steam temperature (K) + real(kind=dp) :: a, water_vp + + a = 1.0 - t_steam / env_state%temp + a = (((-0.1299 * a - 0.6445) * a - 1.976) * a + 13.3185) * a + water_vp = 101325.0 * exp(a) ! (Pa) + env_state_rel_humid_to_mix_rat = env_state%rel_humid * water_vp * 1.0e9 & + / env_state%pressure ! (ppb) + + end function env_state_rel_humid_to_mix_rat + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !> Condensation \f$A\f$ parameter. diff --git a/src/gas_state.F90 b/src/gas_state.F90 index b32ad139f..f85caede8 100644 --- a/src/gas_state.F90 +++ b/src/gas_state.F90 @@ -177,7 +177,7 @@ end subroutine gas_state_ensure_nonnegative !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !> Convert (mol m^{-3}) to (ppb). - subroutine gas_state_mole_dens_to_ppb(gas_state, env_state) + subroutine gas_state_molar_conc_to_ppb(gas_state, env_state) !> Gas state. type(gas_state_t), intent(inout) :: gas_state @@ -186,40 +186,32 @@ subroutine gas_state_mole_dens_to_ppb(gas_state, env_state) call gas_state_scale(gas_state, 1d9 / env_state_air_molar_den(env_state)) - end subroutine gas_state_mole_dens_to_ppb + end subroutine gas_state_molar_conc_to_ppb !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! #ifdef PMC_USE_CAMP !> Set CAMP gas-phase species concentrations - subroutine gas_state_set_camp_conc(gas_state, camp_state, gas_data) + subroutine gas_state_set_camp_conc(gas_state, env_state, camp_state, & + gas_data) !> Gas state class(gas_state_t), intent(in) :: gas_state + ! Environmental state. + type(env_state_t), intent(in) :: env_state !> CAMP state type(camp_state_t), intent(inout) :: camp_state !> Gas data type(gas_data_t), intent(in) :: gas_data - real(kind=dp), parameter :: t_steam = 373.15 ! steam temperature (K) - real(kind=dp) :: a, water_vp + ! Convert relative humidity (1) to [H2O] (ppb) + camp_state%state_var(gas_data%i_camp_water) = & + env_state_rel_humid_to_mix_rat(env_state) + ! Convert from ppb to ppm camp_state%state_var(1:size(gas_state%mix_rat)) = gas_state%mix_rat(:) & / 1000.0d0 - ! Convert relative humidity (1) to [H2O] (ppm) - ! From MOSAIC code - reference to Seinfeld & Pandis page 181 - ! TODO Figure out how to have consistent RH<->ppm conversions - ! (There is only one environmental state for PartMC runs - call assert(590005048, associated(camp_state%env_states(1)%val)) - a = 1.0 - t_steam / camp_state%env_states(1)%val%temp - a = (((-0.1299 * a - 0.6445) * a - 1.976) * a + 13.3185) * a - water_vp = 101325.0 * exp(a) ! (Pa) - - camp_state%state_var(gas_data%i_camp_water) = & - camp_state%env_states(1)%val%rel_humid * water_vp * 1.0e6 & - / camp_state%env_states(1)%val%pressure ! (ppm) - end subroutine gas_state_set_camp_conc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! diff --git a/src/partmc.F90 b/src/partmc.F90 index 4a4076af1..d7d31cac5 100644 --- a/src/partmc.F90 +++ b/src/partmc.F90 @@ -486,7 +486,7 @@ subroutine partmc_part(file) call pmc_rand_finalize() call pmc_srand(rand_init, pmc_mpi_rank()) - call cpu_time(run_part_opt%t_wall_start) + run_part_opt%t_wall_start = system_clock_time() do i_repeat = 1,run_part_opt%n_repeat run_part_opt%i_repeat = i_repeat @@ -539,6 +539,12 @@ subroutine partmc_part(file) end do + if (run_part_opt%do_tchem) then +#ifdef PMC_USE_TCHEM + call pmc_tchem_cleanup() +#endif + end if + call pmc_rand_finalize() end subroutine partmc_part diff --git a/src/run_part.F90 b/src/run_part.F90 index 5bb673dcc..3793b01c8 100644 --- a/src/run_part.F90 +++ b/src/run_part.F90 @@ -25,6 +25,7 @@ module pmc_run_part use pmc_mpi use pmc_camp_interface use pmc_photolysis + use pmc_tchem_interface #ifdef PMC_USE_CAMP use camp_camp_core use camp_camp_state @@ -88,7 +89,7 @@ module pmc_run_part integer :: i_repeat !> Total number of repeats. integer :: n_repeat - !> Cpu_time() of start. + !> Wall clock time of start. real(kind=dp) :: t_wall_start !> Whether to record particle removal information. logical :: record_removals @@ -104,8 +105,10 @@ module pmc_run_part logical :: env_average !> Parallel coagulation method type. integer :: parallel_coag_type - !> Whether to run CAMP + !> Whether to run CAMP. logical :: do_camp_chem + !> Whether to run TChem. + logical :: do_tchem !> UUID for this simulation. character(len=PMC_UUID_LEN) :: uuid end type run_part_opt_t @@ -219,7 +222,7 @@ subroutine run_part(scenario, env_state, aero_data, aero_state, gas_data, & t_wall_elapsed = 0d0 t_wall_remain = 0d0 else - call cpu_time(t_wall_now) + t_wall_now = system_clock_time() prop_done = real(run_part_opt%i_repeat - 1, kind=dp) & / real(run_part_opt%n_repeat, kind=dp) t_wall_elapsed = t_wall_now - run_part_opt%t_wall_start @@ -332,6 +335,7 @@ integer function pmc_mpi_pack_size_run_part_opt(val) + pmc_mpi_pack_size_logical(val%env_average) & + pmc_mpi_pack_size_integer(val%parallel_coag_type) & + pmc_mpi_pack_size_logical(val%do_camp_chem) & + + pmc_mpi_pack_size_logical(val%do_tchem) & + pmc_mpi_pack_size_string(val%uuid) end function pmc_mpi_pack_size_run_part_opt @@ -382,6 +386,7 @@ subroutine pmc_mpi_pack_run_part_opt(buffer, position, val) call pmc_mpi_pack_logical(buffer, position, val%env_average) call pmc_mpi_pack_integer(buffer, position, val%parallel_coag_type) call pmc_mpi_pack_logical(buffer, position, val%do_camp_chem) + call pmc_mpi_pack_logical(buffer, position, val%do_tchem) call pmc_mpi_pack_string(buffer, position, val%uuid) call assert(946070052, & position - prev_position <= pmc_mpi_pack_size_run_part_opt(val)) @@ -435,6 +440,7 @@ subroutine pmc_mpi_unpack_run_part_opt(buffer, position, val) call pmc_mpi_unpack_logical(buffer, position, val%env_average) call pmc_mpi_unpack_integer(buffer, position, val%parallel_coag_type) call pmc_mpi_unpack_logical(buffer, position, val%do_camp_chem) + call pmc_mpi_unpack_logical(buffer, position, val%do_tchem) call pmc_mpi_unpack_string(buffer, position, val%uuid) call assert(480118362, & position - prev_position <= pmc_mpi_pack_size_run_part_opt(val)) @@ -495,7 +501,9 @@ subroutine spec_file_read_run_part(file, run_part_opt, aero_data, & real(kind=dp) :: dummy_time, dummy_del_t character(len=PMC_MAX_FILENAME_LEN) :: sub_filename type(spec_file_t) :: sub_file - character(len=PMC_MAX_FILENAME_LEN) :: camp_config_filename + character(len=PMC_MAX_FILENAME_LEN) :: camp_config_filename, & + tchem_gas_filename, tchem_aero_filename, tchem_numerics_filename + integer :: n_grid_cells call spec_file_read_string(file, 'output_prefix', & run_part_opt%output_prefix) @@ -541,6 +549,26 @@ subroutine spec_file_read_run_part(file, run_part_opt, aero_data, & #endif end if + call spec_file_read_logical(file, 'do_tchem', run_part_opt%do_tchem) + if (run_part_opt%do_tchem) then +#ifdef PMC_USE_TCHEM + call spec_file_read_string(file, 'tchem_gas_config', & + tchem_gas_filename) + call spec_file_read_string(file, 'tchem_aero_config', & + tchem_aero_filename) + call spec_file_read_string(file, 'tchem_numerics_config', & + tchem_numerics_filename) +#endif + end if + + if (run_part_opt%do_tchem) then +#ifdef PMC_USE_TCHEM + n_grid_cells = 1 + call pmc_tchem_initialize(tchem_gas_filename, tchem_aero_filename, & + tchem_numerics_filename, gas_data, aero_data, n_grid_cells) +#endif + end if + if (do_restart) then call input_state(restart_filename, dummy_index, dummy_time, & dummy_del_t, dummy_i_repeat, run_part_opt%uuid, aero_data, & @@ -549,12 +577,13 @@ subroutine spec_file_read_run_part(file, run_part_opt, aero_data, & if (.not. do_restart) then env_state_init%elapsed_time = 0d0 - if (.not. run_part_opt%do_camp_chem) then + + if (.not. (run_part_opt%do_camp_chem .or. run_part_opt%do_tchem)) then call spec_file_read_string(file, 'gas_data', sub_filename) call spec_file_open(sub_filename, sub_file) call spec_file_read_gas_data(sub_file, gas_data) call spec_file_close(sub_file) - else + else if (run_part_opt%do_camp_chem) then #ifdef PMC_USE_CAMP call gas_data_initialize(gas_data, camp_core) #endif @@ -569,6 +598,12 @@ subroutine spec_file_read_run_part(file, run_part_opt, aero_data, & call spec_file_open(sub_filename, sub_file) call spec_file_read_aero_data(sub_file, aero_data) call spec_file_close(sub_file) + ! FIXME: Temporary to run PartMC. Replace with initialization from TChem + else if (run_part_opt%do_tchem) then + call spec_file_read_string(file, 'aerosol_data', sub_filename) + call spec_file_open(sub_filename, sub_file) + call spec_file_read_aero_data(sub_file, aero_data) + call spec_file_close(sub_file) else #ifdef PMC_USE_CAMP call aero_data_initialize(aero_data, camp_core) @@ -848,6 +883,13 @@ subroutine run_part_timestep(scenario, env_state, aero_data, aero_state, & #endif end if + if (run_part_opt%do_tchem) then +#ifdef PMC_USE_TCHEM + call pmc_tchem_interface_solve(env_state, aero_data, aero_state, & + gas_data, gas_state, run_part_opt%del_t) +#endif + end if + if (run_part_opt%do_mosaic) then call mosaic_timestep(env_state, aero_data, aero_state, gas_data, & gas_state, run_part_opt%do_optical, run_part_opt%uuid) @@ -905,7 +947,7 @@ subroutine run_part_timestep(scenario, env_state, aero_data, aero_state, & call pmc_mpi_reduce_sum_integer(progress_n_nuc, global_n_nuc) if (pmc_mpi_rank() == 0) then ! progress only printed from root process - call cpu_time(t_wall_now) + t_wall_now = system_clock_time() prop_done = (real(run_part_opt%i_repeat - 1, kind=dp) & + time / run_part_opt%t_max) & / real(run_part_opt%n_repeat, kind=dp) diff --git a/src/scenario.F90 b/src/scenario.F90 index dc62a5202..ead729f94 100644 --- a/src/scenario.F90 +++ b/src/scenario.F90 @@ -228,7 +228,7 @@ subroutine scenario_update_gas_state(scenario, delta_t, env_state, & call gas_state_interp_1d(scenario%gas_emission, & scenario%gas_emission_time, scenario%gas_emission_rate_scale, & env_state%elapsed_time, emissions, emission_rate_scale) - call gas_state_mole_dens_to_ppb(emissions, env_state) + call gas_state_molar_conc_to_ppb(emissions, env_state) p = emission_rate_scale * delta_t / env_state%height call gas_state_add_scaled(gas_state, emissions, p) end if diff --git a/src/tchem_interface.F90 b/src/tchem_interface.F90 new file mode 100644 index 000000000..136f75856 --- /dev/null +++ b/src/tchem_interface.F90 @@ -0,0 +1,309 @@ +! Copyright (C) 2024 Jeff Curtis +! Licensed under the GNU General Public License version 2 or (at your +! option) any later version. See the file COPYING for details. + +!> \file +!> The pmc_tchem_interface module. + +!> An interface between PartMC and TChem +module pmc_tchem_interface + + use pmc_aero_data + use pmc_aero_particle + use pmc_aero_state + use pmc_constants + use pmc_gas_data + use pmc_gas_state +#ifdef PMC_USE_TCHEM + use iso_c_binding +#endif + use pmc_util, only : die_msg, warn_assert_msg, assert_msg + +interface + subroutine initialize(arg_chemfile, arg_aerofile, arg_numericsfile, & + n_batch) & + bind(c, name="initialize") + use iso_c_binding + character(kind=c_char), intent(in) :: arg_chemfile(*) + character(kind=c_char), intent(in) :: arg_aerofile(*) + character(kind=c_char), intent(in) :: arg_numericsfile(*) + integer(c_int), intent(in), value :: n_batch + end subroutine initialize + subroutine finalize() bind(c, name="finalize") + end subroutine finalize + function TChem_getNumberOfSpecies() bind(c, name="TChem_getNumberOfSpecies") + use iso_c_binding + integer(kind=c_int) :: TChem_getNumberOfSpecies + end function + function TChem_getLengthOfStateVector() bind(c, & + name="TChem_getLengthOfStateVector") + use iso_c_binding + integer(kind=c_int) :: TChem_getLengthOfStateVector + end function + subroutine TChem_getStateVector(array, i_batch) bind(c, & + name="TChem_getStateVector") + use iso_c_binding + real(kind=c_double) :: array(*) + integer(c_int), value :: i_batch + end subroutine + subroutine TChem_setStateVector(array, i_batch) bind(c, & + name="TChem_setStateVector") + use iso_c_binding + real(kind=c_double) :: array(*) + integer(c_int), value :: i_batch + end subroutine + integer(kind=c_size_t) function TChem_getSpeciesName(index, result, & + buffer_size) bind(C, name="TChem_getSpeciesName") + use iso_c_binding + integer(kind=c_int), intent(in) :: index + character(kind=c_char), intent(out) :: result(*) + integer(kind=c_size_t), intent(in), value :: buffer_size + end function + subroutine TChem_doTimestep(del_t) bind(C, name="TChem_doTimestep") + use iso_c_binding + real(kind=c_double), intent(in) :: del_t + end subroutine +end interface + +contains + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +#ifdef PMC_USE_TCHEM + !> Run the CAMP module for the current PartMC state + subroutine pmc_tchem_interface_solve(env_state, aero_data, aero_state, & + gas_data, gas_state, del_t) + + !> Environment data. + type(env_state_t), intent(in) :: env_state + !> Aerosol data. + type(aero_data_t), intent(in) :: aero_data + !> Aerosol state. + type(aero_state_t), intent(inout) :: aero_state + !> Gas data. + type(gas_data_t), intent(in) :: gas_data + !> Gas state. + type(gas_state_t), intent(inout) :: gas_state + !> Time step (s). + real(kind=dp), intent(in) :: del_t + + call tchem_from_partmc(aero_data, aero_state, gas_data, gas_state, & + env_state) + + call tchem_timestep(del_t) + + call tchem_to_partmc(aero_data, aero_state, gas_data, gas_state, env_state) + + end subroutine pmc_tchem_interface_solve + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Initialize TChem and PartMC gas and aerosol data. + subroutine pmc_tchem_initialize(gas_config_filename, aero_config_filename, & + solver_config_filename, gas_data, aero_data, n_grid_cells) + use iso_c_binding + + !> Gas configuration filename. + character(len=*), intent(in) :: gas_config_filename + !> Aerosol configuration filename. + character(len=*), intent(in) :: aero_config_filename + !> Numerical configuration filename. + character(len=*), intent(in) :: solver_config_filename + !> Gas data. + type(gas_data_t), intent(inout) :: gas_data + !> Aerosol data. + type(aero_data_t), intent(inout) :: aero_data + !> Number of cells to solve. + integer, intent(in) :: n_grid_cells + + integer(kind=c_int) :: nSpec, nAeroSpec + integer :: n_species + integer :: i + real(kind=c_double), dimension(:), allocatable :: array + character(:), allocatable :: val + + ! initialize the model + call TChem_initialize(trim(gas_config_filename), & + trim(aero_config_filename), trim(solver_config_filename), & + n_grid_cells) + + ! Get size that gas_data should be + nSpec = TChem_getNumberOfSpecies() + call ensure_string_array_size(gas_data%name, nSpec) + + ! Populate gas_data with gas species from TChem + do i = 1,nSpec + val = TChem_species_name(i-1) + gas_data%name(i) = trim(val) + end do + + ! For output and MPI, this needs to be allocated (for now) + allocate(gas_data%mosaic_index(gas_data_n_spec(gas_data))) + gas_data%mosaic_index(:) = 0 + + ! TODO: Create aero_data based on TChem input. + ! From TChem we need: + ! Species names + ! Species properties - density, kappa, molecular weight + ! n_species = 10 + ! call ensure_string_array_size(aero_data%name, n_species) + ! call ensure_integer_array_size(aero_data%mosaic_index, n_species) + ! call ensure_real_array_size(aero_data%wavelengths, n_swbands) + ! call ensure_real_array_size(aero_data%density, n_species) + ! call ensure_integer_array_size(aero_data%num_ions, n_species) + ! call ensure_real_array_size(aero_data%molec_weight, n_species) + ! call ensure_real_array_size(aero_data%kappa, n_species) + !do i = 1,n_species + !end do + + end subroutine pmc_tchem_initialize + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Clean up TChem. + subroutine pmc_tchem_cleanup() + + call finalize() + + end subroutine pmc_tchem_cleanup + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Map all data TChem -> PartMC. + subroutine tchem_to_partmc(aero_data, aero_state, gas_data, gas_state, & + env_state) + + !> Aerosol data. + type(aero_data_t), intent(in) :: aero_data + !> Aerosol state. + type(aero_state_t), intent(inout) :: aero_state + !> Gas data. + type(gas_data_t), intent(in) :: gas_data + !> Gas state. + type(gas_state_t), intent(inout) :: gas_state + !> Environment state. + type(env_state_t), intent(in) :: env_state + + integer(c_int) :: nSpec, stateVecDim + integer :: i_part + real(kind=c_double), dimension(:), allocatable :: stateVector + + ! Get gas array + stateVecDim = TChem_getLengthOfStateVector() + nSpec = TChem_getNumberOfSpecies() + allocate(stateVector(stateVecDim)) + call TChem_getStateVector(stateVector, 0) + + gas_state%mix_rat = 0.0 + ! Convert from ppm to ppb. + gas_state%mix_rat = stateVector(4:nSpec+3) * 1000.d0 + + ! Map aerosols + do i_part = 1,aero_state_n_part(aero_state) + + end do + + end subroutine tchem_to_partmc + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Map all data PartMC -> TChem. + subroutine tchem_from_partmc(aero_data, aero_state, gas_data, gas_state, & + env_state) + + !> Aerosol data. + type(aero_data_t), intent(in) :: aero_data + !> Aerosol state. + type(aero_state_t), intent(in) :: aero_state + !> Gas data. + type(gas_data_t), intent(in) :: gas_data + !> Gas State. + type(gas_state_t), intent(inout) :: gas_state + !> Environment state. + type(env_state_t), intent(in) :: env_state + + real(kind=dp), allocatable :: stateVector(:) + integer :: stateVecDim + integer :: i_part + integer :: i_water + + ! Get size of stateVector + stateVecDim = TChem_getLengthOfStateVector() + allocate(stateVector(stateVecDim)) + ! First three elements are density, pressure and temperature + stateVector(1) = env_state_air_den(env_state) + stateVector(2) = env_state%pressure + stateVector(3) = env_state%temp + + ! PartMC uses relative humidity and not H2O mixing ratio. + ! Equation 1.10 from Seinfeld and Pandis - Second Edition. + i_water = gas_data_spec_by_name(gas_data, "H2O") + gas_state%mix_rat(i_water) = env_state_rel_humid_to_mix_rat(env_state) + ! Add gas species to state vector. Convert from ppb to ppm. + stateVector(4:gas_data_n_spec(gas_data)+3) = gas_state%mix_rat / 1000.d0 + + ! TODO: Map aerosols + do i_part = 1,aero_state_n_part(aero_state) + + end do + + call TChem_setStateVector(stateVector, 0) + + end subroutine tchem_from_partmc + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Do a single timestep of TChem chemistry. + subroutine TChem_timestep(del_t) + use iso_c_binding + + !> Time step (s). + real(kind=c_double) :: del_t + + call TChem_doTimestep(del_t) + + end subroutine TChem_timestep + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Initialize TChem. + subroutine TChem_initialize(chemFile, aeroFile, NumericsFile, n_batch) + use iso_c_binding + + !> Chemistry configuration file. + character(kind=c_char,len=*), intent(in) :: chemFile + !> Chemistry configuration file. + character(kind=c_char,len=*), intent(in) :: aeroFile + !> Chemistry configuration file. + character(kind=c_char,len=*), intent(in) :: numericsFile + !> Number of systems to solve. + integer(kind=c_int), intent(in) :: n_batch + + call initialize(chemFile//c_null_char, aeroFile//c_null_char, & + numericsFile//c_null_char, n_batch) + + end subroutine TChem_initialize + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Get species name from TChem for a given index. + function TChem_species_name(i_spec) result(species_name) + use iso_c_binding + + ! Species name. + character(:), allocatable :: species_name + + integer(kind=c_int), intent(in) :: i_spec + character(kind=c_char, len=:), allocatable :: cbuf + integer(kind=c_size_t) :: N + + allocate(character(256) :: cbuf) + N = len(cbuf) + N = TChem_getSpeciesName(i_spec, cbuf, N) + allocate(character(N) :: species_name) + species_name = cbuf(:N) + + end function TChem_species_name +#endif +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +end module pmc_tchem_interface diff --git a/src/util.F90 b/src/util.F90 index ccaa9020b..1380794c4 100644 --- a/src/util.F90 +++ b/src/util.F90 @@ -1970,6 +1970,19 @@ integer function pow2_above(n) end function pow2_above +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Returns the current system clock time in seconds. + real(kind=dp) function system_clock_time() + + ! 64 bit integer enables hi-resolution time. + integer(kind=8) :: clock_count, clock_count_rate + + call system_clock(clock_count, clock_count_rate) + system_clock_time = real(clock_count, kind=dp) / clock_count_rate + + end function system_clock_time + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! end module pmc_util diff --git a/test/additive/run_part.spec b/test/additive/run_part.spec index bd86e3efd..2c0cb2487 100644 --- a/test/additive/run_part.spec +++ b/test/additive/run_part.spec @@ -11,7 +11,8 @@ del_t 1 # timestep (s) t_output 60 # output interval (0 disables) (s) t_progress 60 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/average/run_part.spec b/test/average/run_part.spec index 7e762a611..22a7fb06e 100644 --- a/test/average/run_part.spec +++ b/test/average/run_part.spec @@ -10,7 +10,8 @@ del_t 600 # timestep (s) t_output 600 # output interval (0 disables) (s) t_progress 600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/bidisperse/run_part.spec b/test/bidisperse/run_part.spec index 845740b9d..260689cd6 100644 --- a/test/bidisperse/run_part.spec +++ b/test/bidisperse/run_part.spec @@ -10,7 +10,8 @@ del_t 1 # timestep (s) t_output 10 # output interval (0 disables) (s) t_progress 60 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/brownian/run_part.spec b/test/brownian/run_part.spec index 8d92b6439..a2ba909fe 100644 --- a/test/brownian/run_part.spec +++ b/test/brownian/run_part.spec @@ -10,7 +10,8 @@ del_t 600 # timestep (s) t_output 3600 # output interval (0 disables) (s) t_progress 21600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/camp/camp.spec b/test/camp/camp.spec index dcdb4fed2..f563bbbf9 100644 --- a/test/camp/camp.spec +++ b/test/camp/camp.spec @@ -12,6 +12,7 @@ t_progress 3600 # progress printing interval (0 disables) (s) do_camp_chem yes # whether to use CAMP for chemistry camp_config config.json +do_tchem no # whether to use TChem for chemistry gas_init gas_init.dat # initial gas concentrations diff --git a/test/condense/run_part.spec b/test/condense/run_part.spec index 86cd321c2..23cf93f4b 100644 --- a/test/condense/run_part.spec +++ b/test/condense/run_part.spec @@ -10,7 +10,8 @@ del_t 10 # timestep (s) t_output 10 # output interval (0 disables) (s) t_progress 60 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/emission/run_part.spec b/test/emission/run_part.spec index 8c8564030..016496f3a 100644 --- a/test/emission/run_part.spec +++ b/test/emission/run_part.spec @@ -10,7 +10,8 @@ del_t 60 # timestep (s) t_output 1200 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/fractal/run_part_brown_cont_df_1_8_restart.spec b/test/fractal/run_part_brown_cont_df_1_8_restart.spec index e8a9c04e5..173d16530 100644 --- a/test/fractal/run_part_brown_cont_df_1_8_restart.spec +++ b/test/fractal/run_part_brown_cont_df_1_8_restart.spec @@ -10,7 +10,8 @@ del_t 100 # timestep (s) t_output 5000 # output interval (0 disables) (s) t_progress 1000 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry temp_profile temp_cont.dat # temperature profile file pressure_profile pressure.dat # pressure profile file diff --git a/test/fractal/run_part_brown_cont_df_1_8_upto1000s.spec b/test/fractal/run_part_brown_cont_df_1_8_upto1000s.spec index bc8ce6607..6df294249 100644 --- a/test/fractal/run_part_brown_cont_df_1_8_upto1000s.spec +++ b/test/fractal/run_part_brown_cont_df_1_8_upto1000s.spec @@ -10,7 +10,8 @@ del_t 10 # timestep (s) t_output 50 # output interval (0 disables) (s) t_progress 10 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/fractal/run_part_brown_free_df_2_4_restart.spec b/test/fractal/run_part_brown_free_df_2_4_restart.spec index 0e60f2a2b..fb5356fbd 100644 --- a/test/fractal/run_part_brown_free_df_2_4_restart.spec +++ b/test/fractal/run_part_brown_free_df_2_4_restart.spec @@ -10,7 +10,8 @@ del_t 100 # timestep (s) t_output 5000 # output interval (0 disables) (s) t_progress 1000 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry temp_profile temp_free.dat # temperature profile file pressure_profile pressure.dat # pressure profile file diff --git a/test/fractal/run_part_brown_free_df_2_4_upto1000s.spec b/test/fractal/run_part_brown_free_df_2_4_upto1000s.spec index 59a431a9a..1051a29e3 100644 --- a/test/fractal/run_part_brown_free_df_2_4_upto1000s.spec +++ b/test/fractal/run_part_brown_free_df_2_4_upto1000s.spec @@ -10,7 +10,8 @@ del_t 10 # timestep (s) t_output 50 # output interval (0 disables) (s) t_progress 10 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/loss/run_chamber_part.spec b/test/loss/run_chamber_part.spec index 89bbce0e5..3675a6872 100644 --- a/test/loss/run_chamber_part.spec +++ b/test/loss/run_chamber_part.spec @@ -10,7 +10,8 @@ del_t 600 # timestep (s) t_output 3600 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/loss/run_constant_part.spec b/test/loss/run_constant_part.spec index dafd4bd8a..cc469ed6c 100644 --- a/test/loss/run_constant_part.spec +++ b/test/loss/run_constant_part.spec @@ -10,7 +10,8 @@ del_t 60 # timestep (s) t_output 600 # output interval (0 disables) (s) t_progress 600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/loss/run_drydep_part.spec b/test/loss/run_drydep_part.spec index 234b8ad16..54c24a261 100644 --- a/test/loss/run_drydep_part.spec +++ b/test/loss/run_drydep_part.spec @@ -10,7 +10,8 @@ del_t 3600 # timestep (s) t_output 21600 # output interval (0 disables) (s) t_progress 14400 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/loss/run_volume_part.spec b/test/loss/run_volume_part.spec index 84c4d5bc6..864127e09 100644 --- a/test/loss/run_volume_part.spec +++ b/test/loss/run_volume_part.spec @@ -10,7 +10,8 @@ del_t 60 # timestep (s) t_output 60 # output interval (0 disables) (s) t_progress 60 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/mixing_state/run_part.spec b/test/mixing_state/run_part.spec index 1f8eb8afe..f4832e215 100644 --- a/test/mixing_state/run_part.spec +++ b/test/mixing_state/run_part.spec @@ -10,7 +10,8 @@ del_t 1 # timestep (s) t_output 1 # output interval (0 disables) (s) t_progress 1 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas concentrations diff --git a/test/mosaic/run_part.spec b/test/mosaic/run_part.spec index 5e3e54763..6d5426ec8 100644 --- a/test/mosaic/run_part.spec +++ b/test/mosaic/run_part.spec @@ -10,7 +10,8 @@ del_t 300 # timestep (s) t_output 3600 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/mosaic/run_part_restarted.spec b/test/mosaic/run_part_restarted.spec index 338af7f41..c6f2c5986 100644 --- a/test/mosaic/run_part_restarted.spec +++ b/test/mosaic/run_part_restarted.spec @@ -10,7 +10,8 @@ del_t 300 # timestep (s) t_output 3600 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry temp_profile temp.dat # temperature profile file pressure_profile pressure.dat # pressure profile file diff --git a/test/nucleate/run_part.spec b/test/nucleate/run_part.spec index 91a566801..b806c2b81 100644 --- a/test/nucleate/run_part.spec +++ b/test/nucleate/run_part.spec @@ -10,7 +10,8 @@ del_t 1 # timestep (s) t_output 60 # output interval (0 disables) (s) t_progress 600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/parallel/run_part_parallel_dist.spec b/test/parallel/run_part_parallel_dist.spec index 29f4f3927..210e729ad 100644 --- a/test/parallel/run_part_parallel_dist.spec +++ b/test/parallel/run_part_parallel_dist.spec @@ -11,7 +11,8 @@ del_t 600 # timestep (s) t_output 3600 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/parallel/run_part_parallel_dist_single.spec b/test/parallel/run_part_parallel_dist_single.spec index 15fbe0ba7..b1a803233 100644 --- a/test/parallel/run_part_parallel_dist_single.spec +++ b/test/parallel/run_part_parallel_dist_single.spec @@ -11,7 +11,8 @@ del_t 600 # timestep (s) t_output 3600 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/parallel/run_part_parallel_mix.spec b/test/parallel/run_part_parallel_mix.spec index 9d5d9da7f..819299b18 100644 --- a/test/parallel/run_part_parallel_mix.spec +++ b/test/parallel/run_part_parallel_mix.spec @@ -10,7 +10,8 @@ del_t 600 # timestep (s) t_output 3600 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/parallel/run_part_serial.spec b/test/parallel/run_part_serial.spec index 44aff6c1d..c9fb42ea0 100644 --- a/test/parallel/run_part_serial.spec +++ b/test/parallel/run_part_serial.spec @@ -10,7 +10,8 @@ del_t 600 # timestep (s) t_output 3600 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/sedi/run_part.spec b/test/sedi/run_part.spec index f280f2376..53e565105 100644 --- a/test/sedi/run_part.spec +++ b/test/sedi/run_part.spec @@ -10,7 +10,8 @@ del_t 5 # timestep (s) t_output 300 # output interval (0 disables) (s) t_progress 60 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/tchem/README b/test/tchem/README new file mode 100644 index 000000000..348ebc9dd --- /dev/null +++ b/test/tchem/README @@ -0,0 +1,8 @@ + +TChemn Test-case +=========================================== + +- test_tchem_1.sh tests PartMC-TChem Chapman mechanism against a standalone output +from TChem that is interpolated to the output timestep of PartMC. +- test_test_2.s tests the cb05cl_ae5 mechanism against a standalone output from +TChem that is interpolated to the output timestep of PartMC. diff --git a/test/tchem/aero_back.dat b/test/tchem/aero_back.dat new file mode 100644 index 000000000..6688101c7 --- /dev/null +++ b/test/tchem/aero_back.dat @@ -0,0 +1,6 @@ +# time (s) +# rate (s^{-1}) +# aerosol distribution filename +time 0 +rate 0e-5 +dist aero_back_dist.dat diff --git a/test/tchem/aero_back_comp.dat b/test/tchem/aero_back_comp.dat new file mode 100644 index 000000000..405053758 --- /dev/null +++ b/test/tchem/aero_back_comp.dat @@ -0,0 +1,2 @@ +# mass fractions +SB 1 diff --git a/test/tchem/aero_back_dist.dat b/test/tchem/aero_back_dist.dat new file mode 100644 index 000000000..e69de29bb diff --git a/test/tchem/aero_data.dat b/test/tchem/aero_data.dat new file mode 100644 index 000000000..83d7a7091 --- /dev/null +++ b/test/tchem/aero_data.dat @@ -0,0 +1,4 @@ +# dens (kg/m^3) ions in soln (1) molec wght (kg/mole) kappa (1) +SI 10000 0 18d-3 0 +SB 100 0 18d-3 0 +SE 1500 0 18d-3 0 diff --git a/test/tchem/aero_emit.dat b/test/tchem/aero_emit.dat new file mode 100644 index 000000000..ab813ec2a --- /dev/null +++ b/test/tchem/aero_emit.dat @@ -0,0 +1,6 @@ +# time (s) +# rate (s^{-1}) +# aerosol distribution filename +time 0 +rate 0e-5 +dist aero_emit_dist.dat diff --git a/test/tchem/aero_emit_comp.dat b/test/tchem/aero_emit_comp.dat new file mode 100644 index 000000000..ce8d06eca --- /dev/null +++ b/test/tchem/aero_emit_comp.dat @@ -0,0 +1,2 @@ +# mass fractions +SE 1 diff --git a/test/tchem/aero_emit_dist.dat b/test/tchem/aero_emit_dist.dat new file mode 100644 index 000000000..e69de29bb diff --git a/test/tchem/aero_init_comp.dat b/test/tchem/aero_init_comp.dat new file mode 100644 index 000000000..ef33bcba8 --- /dev/null +++ b/test/tchem/aero_init_comp.dat @@ -0,0 +1,2 @@ +# mass fractions +SI 1 diff --git a/test/tchem/aero_init_dist.dat b/test/tchem/aero_init_dist.dat new file mode 100644 index 000000000..3f7104900 --- /dev/null +++ b/test/tchem/aero_init_dist.dat @@ -0,0 +1,6 @@ +mode_name init1 # name of mode source +mass_frac aero_init_comp.dat # species mass fractions +diam_type geometric # type of diameter specified +mode_type mono # type of distribution +num_conc 1e9 # particle number concentration (#/m^3) +diam 3.03e-5 # diameter (m) diff --git a/test/tchem/chem.yaml b/test/tchem/chem.yaml new file mode 100644 index 000000000..06307e83c --- /dev/null +++ b/test/tchem/chem.yaml @@ -0,0 +1,2614 @@ +NCAR-version: v1.0 +environmental_conditions: + pressure: + evolving: false + initial_value: [101325.0] + units: Pa + temperature: + evolving: false + initial_value: [298.15] + units: K +model_info: + chemistry_time_step: + units: min + value: 1.0 + evolving_conditions: + exist: false + output_time_step: + units: min + value: 1.0 + simulation_length: + units: hr + value: 3.0 +reactions: +- MUSICA_name: NO2 + coefficients: + A: 0.00477 + note: PHOTOLYSIS (A := photolysis rate) + products: + NO: 1.0 + O: 1.0 + reactants: + NO2: 1.0 + type: ARRHENIUS +- coefficients: + A: 6.0e-34 + B: -2.4 + C: -0.0 + products: + M: 1.0 + O3: 1.0 + reactants: + M: 1.0 + O: 1.0 + O2: 1.0 + rxn_id: R2 + type: ARRHENIUS +- coefficients: + A: 3.0e-12 + B: 0.0 + C: -1500.0 + products: + NO2: 1.0 + reactants: + NO: 1.0 + O3: 1.0 + rxn_id: R3 + type: ARRHENIUS +- coefficients: + A: 5.6e-12 + B: 0.0 + C: 180.0 + products: + NO: 1.0 + reactants: + NO2: 1.0 + O: 1.0 + rxn_id: R4 + type: ARRHENIUS +- coefficients: + Fc: 0.6 + N: 1.0 + k0_A: 2.5e-31 + k0_B: -1.8 + k0_C: -0.0 + kinf_A: 2.2e-11 + kinf_B: -0.7 + kinf_C: -0.0 + products: + NO3: 1.0 + reactants: + NO2: 1.0 + O: 1.0 + rxn_id: R5 + type: TROE +- coefficients: + Fc: 0.6 + N: 1.0 + k0_A: 9.0e-32 + k0_B: -1.5 + k0_C: -0.0 + kinf_A: 3.0e-11 + kinf_B: 0.0 + kinf_C: -0.0 + products: + NO2: 1.0 + reactants: + NO: 1.0 + O: 1.0 + rxn_id: R6 + type: TROE +- coefficients: + A: 1.2e-13 + B: 0.0 + C: -2450.0 + products: + NO3: 1.0 + reactants: + NO2: 1.0 + O3: 1.0 + rxn_id: R7 + type: ARRHENIUS +- MUSICA_name: O3->O3P + coefficients: + A: 0.000253 + note: PHOTOLYSIS (A := photolysis rate) + products: + O: 1.0 + reactants: + O3: 1.0 + type: ARRHENIUS +- MUSICA_name: O3->O1D + coefficients: + A: 2.26e-06 + note: PHOTOLYSIS (A := photolysis rate) + products: + O1D: 1.0 + reactants: + O3: 1.0 + type: ARRHENIUS +- coefficients: + A: 2.1e-11 + B: 0.0 + C: 102.0 + products: + M: 1.0 + O: 1.0 + reactants: + M: 1.0 + O1D: 1.0 + rxn_id: R10 + type: ARRHENIUS +- coefficients: + A: 2.2e-10 + B: 0.0 + C: -0.0 + products: + OH: 2.0 + reactants: + H2O: 1.0 + O1D: 1.0 + rxn_id: R11 + type: ARRHENIUS +- coefficients: + A: 1.7e-12 + B: 0.0 + C: -940.0 + products: + HO2: 1.0 + reactants: + O3: 1.0 + OH: 1.0 + rxn_id: R12 + type: ARRHENIUS +- coefficients: + A: 1.0e-14 + B: 0.0 + C: -490.0 + products: + OH: 1.0 + reactants: + HO2: 1.0 + O3: 1.0 + rxn_id: R13 + type: ARRHENIUS +- MUSICA_name: NO3->NO2 + coefficients: + A: 0.117 + note: PHOTOLYSIS (A := photolysis rate) + products: + NO2: 1.0 + O: 1.0 + reactants: + NO3: 1.0 + type: ARRHENIUS +- MUSICA_name: NO3->NO + coefficients: + A: 0.0144 + note: PHOTOLYSIS (A := photolysis rate) + products: + NO: 1.0 + reactants: + NO3: 1.0 + type: ARRHENIUS +- coefficients: + A: 1.5e-11 + B: 0.0 + C: 170.0 + products: + NO2: 2.0 + reactants: + NO: 1.0 + NO3: 1.0 + rxn_id: R16 + type: ARRHENIUS +- coefficients: + A: 4.5e-14 + B: 0.0 + C: -1260.0 + products: + NO: 1.0 + NO2: 1.0 + reactants: + NO2: 1.0 + NO3: 1.0 + rxn_id: R17 + type: ARRHENIUS +- coefficients: + Fc: 0.6 + N: 1.0 + k0_A: 2.0e-30 + k0_B: -4.4 + k0_C: -0.0 + kinf_A: 1.4e-12 + kinf_B: -0.7 + kinf_C: -0.0 + products: + N2O5: 1.0 + reactants: + NO2: 1.0 + NO3: 1.0 + rxn_id: R18 + type: TROE +- coefficients: + A: 2.5e-22 + B: 0.0 + C: -0.0 + products: + HNO3: 2.0 + reactants: + H2O: 1.0 + N2O5: 1.0 + rxn_id: R19 + type: ARRHENIUS +- coefficients: + A: 1.8e-39 + B: 0.0 + C: -0.0 + products: + HNO3: 2.0 + reactants: + H2O: 2 + N2O5: 1.0 + rxn_id: R20 + type: ARRHENIUS +- coefficients: + Fc: 0.45 + N: 1.0 + k0_A: 0.001 + k0_B: -3.5 + k0_C: -11000.0 + kinf_A: 970000000000000.0 + kinf_B: 0.1 + kinf_C: -11080.0 + products: + NO2: 1.0 + NO3: 1.0 + reactants: + N2O5: 1.0 + rxn_id: R21 + type: TROE +- coefficients: + A: 3.3e-39 + B: 0.0 + C: 530.0 + products: + NO2: 2.0 + reactants: + NO: 2 + O2: 1.0 + rxn_id: R22 + type: ARRHENIUS +- coefficients: + A: 5.0e-40 + B: 0.0 + C: -0.0 + products: + HONO: 2.0 + reactants: + H2O: 1.0 + NO: 1.0 + NO2: 1.0 + rxn_id: R23 + type: ARRHENIUS +- coefficients: + Fc: 0.6 + N: 1.0 + k0_A: 7.0e-31 + k0_B: -2.6 + k0_C: -0.0 + kinf_A: 3.6e-11 + kinf_B: -0.1 + kinf_C: -0.0 + products: + HONO: 1.0 + reactants: + NO: 1.0 + OH: 1.0 + rxn_id: R24 + type: TROE +- MUSICA_name: HONO + coefficients: + A: 0.000918 + note: PHOTOLYSIS (A := photolysis rate) + products: + NO: 1.0 + OH: 1.0 + reactants: + HONO: 1.0 + type: ARRHENIUS +- coefficients: + A: 1.8e-11 + B: 0.0 + C: -390.0 + products: + NO2: 1.0 + reactants: + HONO: 1.0 + OH: 1.0 + rxn_id: R26 + type: ARRHENIUS +- coefficients: + A: 1.0e-20 + B: 0.0 + C: -0.0 + products: + NO: 1.0 + NO2: 1.0 + reactants: + HONO: 2 + rxn_id: R27 + type: ARRHENIUS +- coefficients: + Fc: 0.6 + N: 1.0 + k0_A: 2.0e-30 + k0_B: -3.0 + k0_C: -0.0 + kinf_A: 2.5e-11 + kinf_B: 0.0 + kinf_C: -0.0 + products: + HNO3: 1.0 + reactants: + NO2: 1.0 + OH: 1.0 + rxn_id: R28 + type: TROE +- coefficients: + A: 2.4e-14 + C: 460.0 + note: CMAQ_OH_HNO3 + products: + NO3: 1.0 + reactants: + HNO3: 1.0 + OH: 1.0 + type: ARRHENIUS 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1.0 + rxn_id: SA05 + type: ARRHENIUS +- coefficients: + A: 2.7e-12 + B: 0.0 + C: 360.0 + products: + NO: 1.0 + reactants: + BENZRO2: 1.0 + NO: 1.0 + rxn_id: SA06 + type: ARRHENIUS +- coefficients: + A: 1.9e-13 + B: 0.0 + C: 1300.0 + products: + HO2: 1.0 + reactants: + BENZRO2: 1.0 + HO2: 1.0 + rxn_id: SA07 + type: ARRHENIUS +- coefficients: + A: 1.16e-14 + B: 0.0 + C: -0.0 + products: + O3: 1.0 + reactants: + O3: 1.0 + SESQ: 1.0 + rxn_id: SA08 + type: ARRHENIUS +- coefficients: + A: 1.97e-10 + B: 0.0 + C: -0.0 + products: + OH: 1.0 + reactants: + OH: 1.0 + SESQ: 1.0 + rxn_id: SA09 + type: ARRHENIUS +- coefficients: + A: 1.9e-11 + B: 0.0 + C: -0.0 + products: + NO3: 1.0 + reactants: + NO3: 1.0 + SESQ: 1.0 + rxn_id: SA10 + type: ARRHENIUS +- MUSICA_name: O2 + coefficients: + A: 0.0 + note: PHOTOLYSIS (A := photolysis rate) + products: + O: 2 + reactants: + O2: 1.0 + type: ARRHENIUS +sources: +- MUSICA_name: NO + coefficients: + emission_rate: 1.44e-10 + species: NO + type: EMISSION +- MUSICA_name: NO2 + coefficients: + emission_rate: 7.56e-12 + species: NO2 + type: EMISSION +- MUSICA_name: CO + coefficients: + emission_rate: 1.96e-09 + species: CO + type: EMISSION +- MUSICA_name: SO2 + coefficients: + emission_rate: 1.06e-09 + species: SO2 + type: EMISSION +- MUSICA_name: FORM + coefficients: + emission_rate: 1.02e-11 + species: FORM + type: EMISSION +- MUSICA_name: MEOH + coefficients: + emission_rate: 5.92e-13 + species: MEOH + type: EMISSION +- MUSICA_name: ALD2 + coefficients: + emission_rate: 4.25e-12 + species: ALD2 + type: EMISSION +- MUSICA_name: PAR + coefficients: + emission_rate: 4.27e-10 + species: PAR + type: EMISSION +- MUSICA_name: ETH + coefficients: + emission_rate: 4.62e-11 + species: ETH + type: EMISSION +- MUSICA_name: OLE + coefficients: + emission_rate: 1.49e-11 + species: OLE + type: EMISSION +- MUSICA_name: IOLE + coefficients: + emission_rate: 1.49e-11 + species: IOLE + type: EMISSION +- MUSICA_name: TOL + coefficients: + emission_rate: 1.53e-11 + species: TOL + type: EMISSION +- MUSICA_name: XYL + coefficients: + emission_rate: 1.4e-11 + species: XYL + type: EMISSION +- MUSICA_name: ISOP + coefficients: + emission_rate: 6.03e-12 + species: ISOP + type: EMISSION +constant_species: +- description: third body + name: M +species: +- description: acetic and higher carboxylic acids + name: AACD +- description: acetaldehyde + name: ALD2 +- description: propionaldehyde and higher aldehydes + name: ALDX +- description: benzene + name: BENZENE +- description: peroxy radical from benzene oxidation + name: BENZRO2 +- description: acetyl peroxy radical + name: C2O3 +- description: methane + name: CH4 +- description: chlorine radical + name: CL +- description: molecular chlorine + name: CL2 +- description: chlorine monoxide + name: CLO +- description: carbon monoxide + name: CO +- description: cresol and higher molecular weight phenols + name: CRES +- description: methylphenoxy radical + name: CRO +- description: C3 and higher acylperoxy radicals + name: CXO3 +- description: ethene + name: ETH +- description: ethane + name: ETHA +- description: ethanol + name: ETOH +- description: formic acid + name: FACD +- description: formyl chloride (HC(O)Cl) + name: FMCL +- description: formaldehyde + name: FORM +- description: molecular hydrogen + name: H2 +- description: water + name: H2O +- description: hydrogen peroxide + name: H2O2 +- description: hydrochlric acid + name: HCL +- description: formyl peroxy radical + name: HCO3 +- description: nitric acid + name: HNO3 +- description: hydroperoxy radical + name: HO2 +- description: hypochlorous acid + name: HOCL +- description: nitrous acid + name: HONO +- description: internal olefin carbon bond (R-C=C) + name: IOLE +- description: isoprene + name: ISOP +- description: isoprene products (lumped methacrolein, methyl vinyl ketone, etc.) + name: ISPD +- description: methyl peroxy radical + name: MEO2 +- description: methanol + name: MEOH +- description: methylhydroperoxide + name: MEPX +- description: methylglyoxal and other aromatic products + name: MGLY +- description: dinitrogen pentoxide + name: N2O5 +- description: nitric oxide + name: NO +- description: nitrogen dioxide + name: NO2 +- description: nitrate radical + name: NO3 +- description: organic nitrates (RNO3) + name: NTR +- description: oxygen atom in the O3P electronic state + name: O +- description: oxygen atom in the O1D electronic state + name: O1D +- description: ozone + name: O3 +- description: hydroxyl radical + name: OH +- description: molecular oxygen + name: O2 +- description: terminal olefin carbon bond (R-C=C) + name: OLE +- description: aromatic ring opening products + name: OPEN +- description: peroxyacetic and higher peroxycarboxylic acids + name: PACD +- description: peroxyacetyl nitrate + name: PAN +- description: C3 and higher peroxyacyl nitrates + name: PANX +- description: paraffin carbon bond (C-C) + name: PAR +- description: peroxynitric acid (HNO4) + name: PNA +- description: higher organic peroxides + name: ROOH +- description: secondary alkoxy radical + name: ROR +- description: sesquiterpene + name: SESQ +- description: sulfur dioxide + name: SO2 +- description: sulfuric acid (gaseous) + name: SULF +- description: terpenes + name: TERP +- description: toluene-hydroxyl radical aduct + name: TO2 +- description: toluene + name: TOL +- description: first generation product from TOL oxidation + name: TOLRO2 +- description: NO to NO2 conversion from alkylperoxy (RO2) radical + name: XO2 +- description: NO to organic nitrate conversion from alkylperoxy (RO2) radical + name: XO2N +- description: xylene and other polyalkyl aromatics + name: XYL +- description: first generation product from XYL oxidation + name: XYLRO2 diff --git a/test/tchem/config_cb05cl_ae5.yaml b/test/tchem/config_cb05cl_ae5.yaml new file mode 100755 index 000000000..51216b042 --- /dev/null +++ b/test/tchem/config_cb05cl_ae5.yaml @@ -0,0 +1,2840 @@ +NCAR-version: v1.0 +environmental_conditions: + pressure: + evolving: 'false' + initial_value: [81060] + units: Pa + temperature: + evolving: 'false' + initial_value: [272.5] + units: K +model_info: + chemistry_time_step: + units: min + value: 1.0 + evolving_conditions: + exist: 'false' + output_time_step: + units: min + value: 1.0 + simulation_length: + units: hr + value: 3.0 +initial_state: + AACD: + initial_value: [0.001] + units: mol m-3 + ALD2: + initial_value: [0.005] + units: mol m-3 + ALDX: + initial_value: [0.001] + units: mol m-3 + BENZENE: + initial_value: [0.001] + units: mol m-3 + BENZRO2: + initial_value: [0.0] + units: mol m-3 + BNZHRXN: + initial_value: [0.0] + units: mol m-3 + BNZNRXN: + initial_value: [0.0] + units: mol m-3 + C2O3: + initial_value: [0.0] + units: mol m-3 + CH4: + initial_value: [1.85] + units: mol m-3 + CL: + initial_value: [0.0] + units: mol m-3 + CL2: + initial_value: [0.02] + units: mol m-3 + CLO: + initial_value: [0.0] + units: mol m-3 + CO: + initial_value: [20.0] + units: mol m-3 + CRES: + initial_value: [5e-06] + units: mol m-3 + CRO: + initial_value: [0.0] + units: mol m-3 + CXO3: + initial_value: [0.0] + units: mol m-3 + ETH: + initial_value: [0.01] + units: mol m-3 + ETHA: + initial_value: [0.0005] + units: mol m-3 + ETOH: + initial_value: [0.1] + units: mol m-3 + FACD: + initial_value: [1.0] + units: mol m-3 + FMCL: + initial_value: [0.0] + units: mol m-3 + FORM: + initial_value: [0.015] + units: mol m-3 + H2O2: + initial_value: [8e-05] + units: mol m-3 + HCL: + initial_value: [0.0] + units: mol m-3 + HCO3: + initial_value: [0.0] + units: mol m-3 + HNO3: + initial_value: [0.002] + units: mol m-3 + HO2: + initial_value: [0.0001] + units: mol m-3 + HOCL: + initial_value: [0.0] + units: mol m-3 + HONO: + initial_value: [0.001] + units: mol m-3 + IOLE: + initial_value: [0.0005] + units: mol m-3 + ISOP: + initial_value: [0.001] + units: mol m-3 + ISOPRXN: + initial_value: [0.0] + units: mol m-3 + ISPD: + initial_value: [0.0] + units: mol m-3 + MEO2: + initial_value: [0.0] + units: mol m-3 + MEOH: + initial_value: [0.002] + units: mol m-3 + MEPX: + initial_value: [0.0] + units: mol m-3 + MGLY: + initial_value: [0.0] + units: mol m-3 + N2O5: + initial_value: [0.0] + units: mol m-3 + NO: + initial_value: [0.002] + units: mol m-3 + NO2: + initial_value: [0.018] + units: mol m-3 + NO3: + initial_value: [0.0] + units: mol m-3 + NTR: + initial_value: [0.0] + units: mol m-3 + O: + initial_value: [0.0] + units: mol m-3 + O1D: + initial_value: [0.0] + units: mol m-3 + O3: + initial_value: [0.06] + units: mol m-3 + OH: + initial_value: [1e-06] + units: mol m-3 + OLE: + initial_value: [0.003] + units: mol m-3 + OPEN: + initial_value: [0.0] + units: mol m-3 + PACD: + initial_value: [0.0] + units: mol m-3 + PAN: + initial_value: [0.0] + units: mol m-3 + PANX: + initial_value: [0.0] + units: mol m-3 + PAR: + initial_value: [0.001] + units: mol m-3 + PNA: + initial_value: [0.0] + units: mol m-3 + ROOH: + initial_value: [0.0] + units: mol m-3 + ROR: + initial_value: [0.0] + units: mol m-3 + SESQ: + initial_value: [0.0001] + units: mol m-3 + SESQRXN: + initial_value: [0.0] + units: mol m-3 + SO2: + initial_value: [0.004] + units: mol m-3 + SULF: + initial_value: [0.0] + units: mol m-3 + SULRXN: + initial_value: [0.0] + units: mol m-3 + TERP: + initial_value: [0.04] + units: mol m-3 + TO2: + initial_value: [0.0] + units: mol m-3 + TOL: + initial_value: [0.0083] + units: mol m-3 + TOLHRXN: + initial_value: [0.0] + units: mol m-3 + TOLNRXN: + initial_value: [0.0] + units: mol m-3 + TOLRO2: + initial_value: [0.0] + units: mol m-3 + TRPRXN: + initial_value: [0.0] + units: mol m-3 + XO2: + initial_value: [0.0] + units: mol m-3 + XO2N: + initial_value: [0.0] + units: mol m-3 + XYL: + initial_value: [0.003] + units: mol m-3 + XYLHRXN: + initial_value: [0.0] + units: mol m-3 + XYLNRXN: + initial_value: [0.0] + units: mol m-3 + XYLRO2: + initial_value: [0.0] + units: mol m-3 + N2O: + initial_value: [0.3] + units: mol m-3 + DUMMY: + initial_value: [0.0] + units: mol m-3 + O2: + initial_value: [209500.0] + units: mol m-3 + H2O: + initial_value: [1000.0] + units: mol m-3 + H2: + initial_value: [0.56] + units: mol m-3 + M: + initial_value: [1000000.0] + units: mol m-3 + N2: + initial_value: [780800.0] + units: mol m-3 +constant_species: +- description: methane + name: CH4 +- description: M + name: M +- description: molecular oxygen + name: O2 +- description: water vapor + name: H2O +- description: molecular hydrogen + name: H2 +- description: third body + name: M +- description: N2 + name: N2 +species: +- description: acetic and higher carboxylic acids + name: AACD +- description: acetaldehyde + name: ALD2 +- description: propionaldehyde and higher aldehydes + name: ALDX +- description: benzene + name: BENZENE +- description: peroxy radical from benzene oxidation + name: BENZRO2 +- description: counter species for aerosol from BENZENE - how does this + differ from BNZNNRXN? + name: BNZHRXN +- description: counter species for aerosol from BENZENE + name: BNZNRXN +- description: acetyl peroxy radical + name: C2O3 +- description: chlorine radical + name: CL +- description: molecular chlorine + name: CL2 +- description: chlorine monoxide + name: CLO +- description: carbon monoxide + name: CO +- description: cresol and higher molecular weight phenols + name: CRES +- description: methylphenoxy radical + name: CRO +- description: C3 and higher acylperoxy radicals + name: CXO3 +- description: ethene + name: ETH +- description: ethane + name: ETHA +- description: ethanol + name: ETOH +- description: formic acid + name: FACD +- description: formyl chloride (HC(O)Cl) + name: FMCL +- description: formaldehyde + name: FORM +- description: hydrogen peroxide + name: H2O2 +- description: hydrochlric acid + name: HCL +- description: formyl peroxy radical? no description in cb05 report + name: HCO3 +- description: nitric acid + name: HNO3 +- description: hydroperoxy radical + name: HO2 +- description: hypochlorous acid + name: HOCL +- description: nitrous acid + name: HONO +- description: internal olefin carbon bond (R-C=C) + name: IOLE +- description: isoprene + name: ISOP +- description: counter for aerosol from ISOP + name: ISOPRXN +- description: isoprene products (lumped methacrolein, methyl vinyl ketone, + etc.) + name: ISPD +- description: methyl peroxy radical + name: MEO2 +- description: methanol + name: MEOH +- description: methylhydroperoxide + name: MEPX +- description: methylglyoxal and other aromatic products + name: MGLY +- description: dinitrogen pentoxide + name: N2O5 +- description: nitric oxide + name: NO +- description: nitrogen dioxide + name: NO2 +- description: nitrate radical + name: NO3 +- description: organic nitrate (RNO3) + name: NTR +- description: oxygen atom in the O3P electronic state + name: O +- description: oxygen atom in the O1D electronic state + name: O1D +- description: ozone + name: O3 +- description: hydroxyl radical + name: OH +- description: terminal olefin carbon bond (R-C=C) + name: OLE +- description: aromatic ring opening products + name: OPEN +- description: peroxyacetic and higher peroxycarboxylic acids + name: PACD +- description: peroxyacetyl nitrate + name: PAN +- description: C3 and higher peroxyacyl nitrates + name: PANX +- description: paraffin carbon bond (C-C) + name: PAR +- description: peroxynitric acid (HNO4) + name: PNA +- description: higher organic peroxides + name: ROOH +- description: secondary alkoxy radical + name: ROR +- description: sesquiterpene + name: SESQ +- description: counter for aerosol from SESQ + name: SESQRXN +- description: sulfur dioxide + name: SO2 +- description: sulfuric acid (gaseous) + name: SULF +- description: counter for aerosol from SO2 + name: SULRXN +- description: terpene + name: TERP +- description: toluene-hydroxyl radical aduct + name: TO2 +- description: toluene + name: TOL +- description: counter for aerosol from TOL - how does this differ from + TOLNRXN? + name: TOLHRXN +- description: counter for aerosol from TOL + name: TOLNRXN +- description: first generation product from TOL + name: TOLRO2 +- description: counter for aerosol from TERP + name: TRPRXN +- description: NO to NO2 conversion from alkylperoxy (RO2) radical + name: XO2 +- description: NO to organic nitrate conversion from alkylperoxy (RO2) radical + name: XO2N +- description: xylene and other polyalkyl aromatics + name: XYL +- description: counter for aerosol from XYL - how does this differ from + XYLNRXN? + name: XYLHRXN +- description: counter for aerosol from XYL + name: XYLNRXN +- description: first generation product from XYL + name: XYLRO2 +- description: nitrous oxide - does not participate in CB05 reactions + name: N2O +- description: not sure what this is + name: DUMMY +reactions: +- MUSICA_name: R1 + reactants: + NO2: 1 + products: + NO: 1 + O: 1 + type: ARRHENIUS + coefficients: + A: 0.0001 + note: PHOTOLYSIS (A := photolysis rate) +- MUSICA_name: R2 + reactants: + O: 1 + O2: 1 + M: 1 + products: + O3: 1 + M: 1 + type: ARRHENIUS + coefficients: + A: 6e-34 + B: -2.4 + C: -0.0 +- MUSICA_name: R3 + reactants: + O3: 1 + NO: 1 + products: + NO2: 1 + type: ARRHENIUS + coefficients: + A: 3e-12 + B: 0.0 + C: -1500.0 +- MUSICA_name: R4 + reactants: + O: 1 + NO2: 1 + products: + NO: 1 + type: ARRHENIUS + coefficients: + A: 5.6e-12 + B: 0.0 + C: 180.0 +- MUSICA_name: R5 + reactants: + O: 1 + NO2: 1 + products: + NO3: 1 + type: TROE + coefficients: + k0_A: 2.5e-31 + k0_B: -1.8 + k0_C: -0.0 + kinf_A: 2.2e-11 + kinf_B: -0.7 + kinf_C: -0.0 + Fc: 0.6 + N: 1.0 +- MUSICA_name: R6 + reactants: + O: 1 + NO: 1 + products: + NO2: 1 + type: TROE + coefficients: + k0_A: 9e-32 + k0_B: -1.5 + k0_C: -0.0 + kinf_A: 3e-11 + kinf_B: 0.0 + kinf_C: -0.0 + Fc: 0.6 + N: 1.0 +- MUSICA_name: R7 + reactants: + NO2: 1 + O3: 1 + products: + NO3: 1 + type: ARRHENIUS + coefficients: + A: 1.2e-13 + B: 0.0 + C: -2450.0 +- MUSICA_name: R8 + reactants: + O3: 1 + products: + O: 1 + type: ARRHENIUS + coefficients: + A: 0.0001 + note: PHOTOLYSIS (A := photolysis rate) +- MUSICA_name: R9 + reactants: + O3: 1 + products: + O1D: 1 + type: ARRHENIUS + coefficients: + A: 0.0001 + note: PHOTOLYSIS (A := photolysis rate) +- MUSICA_name: R10 + reactants: + O1D: 1 + M: 1 + products: + O: 1 + M: 1 + type: ARRHENIUS + coefficients: + A: 2.1e-11 + B: 0.0 + C: 102.0 +- MUSICA_name: R11 + reactants: + O1D: 1 + H2O: 1 + products: + OH: 2.0 + type: ARRHENIUS + coefficients: + A: 2.2e-10 + B: 0.0 + C: -0.0 +- MUSICA_name: R12 + reactants: + O3: 1 + OH: 1 + products: + HO2: 1 + type: ARRHENIUS + coefficients: + A: 1.7e-12 + B: 0.0 + C: -940.0 +- MUSICA_name: R13 + reactants: + O3: 1 + HO2: 1 + products: + OH: 1 + type: ARRHENIUS + coefficients: + A: 1e-14 + B: 0.0 + C: -490.0 +- MUSICA_name: R14 + reactants: + NO3: 1 + products: + NO2: 1 + O: 1 + type: ARRHENIUS + coefficients: + A: 0.0001 + note: PHOTOLYSIS (A := photolysis rate) +- MUSICA_name: R15 + reactants: + NO3: 1 + products: + NO: 1 + type: ARRHENIUS + coefficients: + A: 0.0001 + note: PHOTOLYSIS (A := photolysis rate) +- MUSICA_name: R16 + reactants: + NO3: 1 + NO: 1 + products: + NO2: 2.0 + type: ARRHENIUS + coefficients: + A: 1.5e-11 + B: 0.0 + C: 170.0 +- MUSICA_name: R17 + reactants: + NO3: 1 + NO2: 1 + products: + NO: 1 + NO2: 1 + type: ARRHENIUS + coefficients: + A: 4.5e-14 + B: 0.0 + C: -1260.0 +- MUSICA_name: R18 + reactants: + NO3: 1 + NO2: 1 + products: + N2O5: 1 + type: TROE + coefficients: + k0_A: 2e-30 + k0_B: -4.4 + k0_C: -0.0 + kinf_A: 1.4e-12 + kinf_B: -0.7 + kinf_C: -0.0 + Fc: 0.6 + N: 1.0 +- MUSICA_name: R19 + reactants: + N2O5: 1 + H2O: 1 + products: + HNO3: 2.0 + DUMMY: 1 + type: ARRHENIUS + coefficients: + A: 2.5e-22 + B: 0.0 + C: -0.0 +- MUSICA_name: R20 + reactants: + N2O5: 1 + H2O: 2 + products: + HNO3: 2.0 + type: ARRHENIUS + coefficients: + A: 1.8e-39 + B: 0.0 + C: -0.0 +- MUSICA_name: R21 + reactants: + N2O5: 1 + products: + NO3: 1 + NO2: 1 + DUMMY: 1 + type: TROE + coefficients: + k0_A: 0.001 + k0_B: -3.5 + k0_C: -11000.0 + kinf_A: 970000000000000.0 + kinf_B: 0.1 + kinf_C: -11080.0 + Fc: 0.45 + N: 1.0 +- MUSICA_name: R22 + reactants: + NO: 2 + O2: 1 + products: + NO2: 2.0 + type: ARRHENIUS + coefficients: + A: 3.3e-39 + B: 0.0 + C: 530.0 +- MUSICA_name: R23 + reactants: + NO: 1 + NO2: 1 + H2O: 1 + products: + HONO: 2.0 + type: ARRHENIUS + coefficients: + A: 5e-40 + B: 0.0 + C: -0.0 +- MUSICA_name: R24 + reactants: + NO: 1 + OH: 1 + products: + HONO: 1 + type: TROE + coefficients: + k0_A: 7e-31 + k0_B: -2.6 + k0_C: -0.0 + kinf_A: 3.6e-11 + kinf_B: -0.1 + kinf_C: -0.0 + Fc: 0.6 + N: 1.0 +- MUSICA_name: R25 + reactants: + HONO: 1 + products: + NO: 1 + OH: 1 + type: ARRHENIUS + coefficients: + A: 0.0001 + note: PHOTOLYSIS (A := photolysis rate) +- MUSICA_name: R26 + reactants: + OH: 1 + HONO: 1 + products: + NO2: 1 + type: ARRHENIUS + coefficients: + A: 1.8e-11 + B: 0.0 + C: -390.0 +- MUSICA_name: R27 + reactants: + HONO: 2 + products: + NO: 1 + NO2: 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coefficients: + A: 2.54e-11 + B: 0.0 + C: 407.6 +- MUSICA_name: R143 + reactants: + O3: 1 + ISOP: 1 + products: + ISPD: 0.65 + FORM: 0.6 + XO2: 0.2 + HO2: 0.066 + OH: 0.266 + CXO3: 0.2 + ALDX: 0.15 + PAR: 0.35 + CO: 0.066 + type: ARRHENIUS + coefficients: + A: 7.86e-15 + B: 0.0 + C: -1912.0 +- MUSICA_name: R144 + reactants: + NO3: 1 + ISOP: 1 + products: + ISPD: 0.2 + NTR: 0.8 + XO2: 1 + HO2: 0.8 + NO2: 0.2 + ALDX: 0.8 + PAR: 2.4 + type: ARRHENIUS + coefficients: + A: 3.03e-12 + B: 0.0 + C: -448.0 +- MUSICA_name: R145 + reactants: + OH: 1 + ISPD: 1 + products: + PAR: 1.565 + FORM: 0.167 + XO2: 0.713 + HO2: 0.503 + CO: 0.334 + MGLY: 0.168 + ALD2: 0.252 + C2O3: 0.21 + CXO3: 0.25 + ALDX: 0.12 + type: ARRHENIUS + coefficients: + A: 3.36e-11 + B: 0.0 + C: -0.0 +- MUSICA_name: R146 + reactants: + O3: 1 + ISPD: 1 + products: + C2O3: 0.114 + FORM: 0.15 + MGLY: 0.85 + HO2: 0.154 + OH: 0.268 + XO2: 0.064 + ALD2: 0.02 + PAR: 0.36 + CO: 0.225 + type: ARRHENIUS + coefficients: + A: 7.1e-18 + B: 0.0 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+ CO: 0.001 + PAR: 7.0 + ALDX: 0.21 + CXO3: 0.39 + TRPRXN: 1 + type: ARRHENIUS + coefficients: + A: 1.2e-15 + B: 0.0 + C: -821.0 +- MUSICA_name: R152 + reactants: + TERP: 1 + NO3: 1 + products: + NO2: 0.47 + HO2: 0.28 + XO2: 1.03 + XO2N: 0.25 + ALDX: 0.47 + NTR: 0.53 + TRPRXN: 1 + type: ARRHENIUS + coefficients: + A: 3.7e-12 + B: 0.0 + C: 175.0 +- MUSICA_name: R153 + reactants: + SO2: 1 + OH: 1 + products: + SULF: 1 + HO2: 1 + SULRXN: 1 + type: TROE + coefficients: + k0_A: 3e-31 + k0_B: -3.3 + k0_C: -0.0 + kinf_A: 1.5e-12 + kinf_B: 0.0 + kinf_C: -0.0 + Fc: 0.6 + N: 1.0 +- MUSICA_name: R154 + reactants: + OH: 1 + ETOH: 1 + products: + HO2: 1 + ALD2: 0.9 + ALDX: 0.05 + FORM: 0.1 + XO2: 0.1 + type: ARRHENIUS + coefficients: + A: 6.9e-12 + B: 0.0 + C: -230.0 +- MUSICA_name: R155 + reactants: + OH: 1 + ETHA: 1 + products: + ALD2: 0.991 + XO2: 0.991 + XO2N: 0.009 + HO2: 1 + type: ARRHENIUS + coefficients: + A: 8.7e-12 + B: 0.0 + C: -1070.0 +- MUSICA_name: R156 + reactants: + NO2: 1 + ISOP: 1 + products: + ISPD: 0.2 + NTR: 0.8 + XO2: 1 + HO2: 0.8 + NO: 0.2 + ALDX: 0.8 + PAR: 2.4 + type: ARRHENIUS + coefficients: + A: 1.5e-19 + B: 0.0 + C: -0.0 +- MUSICA_name: CL1 + reactants: + CL2: 1 + products: + CL: 2.0 + type: ARRHENIUS + coefficients: + A: 0.0001 + note: PHOTOLYSIS (A := photolysis rate) +- MUSICA_name: CL3 + reactants: + CL: 1 + O3: 1 + products: + CLO: 1 + type: ARRHENIUS + coefficients: + A: 2.3e-11 + B: 0.0 + C: -200.0 +- MUSICA_name: CL4 + reactants: + CLO: 2 + products: + CL2: 0.3 + CL: 1.4 + type: ARRHENIUS + coefficients: + A: 1.63e-14 + B: 0.0 + C: -0.0 +- MUSICA_name: CL5 + reactants: + CLO: 1 + NO: 1 + products: + CL: 1 + NO2: 1 + type: ARRHENIUS + coefficients: + A: 6.4e-12 + B: 0.0 + C: 290.0 +- MUSICA_name: CL6 + reactants: + CLO: 1 + HO2: 1 + products: + HOCL: 1 + type: ARRHENIUS + coefficients: + A: 2.7e-12 + B: 0.0 + C: 220.0 +- MUSICA_name: CL7 + reactants: + OH: 1 + FMCL: 1 + products: + CL: 1 + CO: 1 + type: ARRHENIUS + coefficients: + A: 5e-13 + B: 0.0 + C: -0.0 +- MUSICA_name: CL9 + reactants: + CL: 1 + CH4: 1 + products: + HCL: 1 + MEO2: 1 + type: ARRHENIUS + coefficients: + A: 6.6e-12 + B: 0.0 + C: -1240.0 +- MUSICA_name: CL10 + reactants: + CL: 1 + PAR: 1 + products: + HCL: 1 + XO2: 0.87 + XO2N: 0.13 + HO2: 0.11 + ALD2: 0.06 + PAR: -0.11 + ROR: 0.76 + ALDX: 0.05 + type: ARRHENIUS + coefficients: + A: 5e-11 + B: 0.0 + C: -0.0 +- MUSICA_name: CL11 + reactants: + CL: 1 + ETHA: 1 + products: + HCL: 1 + ALD2: 0.991 + XO2: 0.991 + XO2N: 0.009 + HO2: 1 + type: ARRHENIUS + coefficients: + A: 8.3e-11 + B: 0.0 + C: -100.0 +- MUSICA_name: CL12 + reactants: + CL: 1 + ETH: 1 + products: + FMCL: 1 + XO2: 2.0 + HO2: 1.0 + FORM: 1.0 + type: ARRHENIUS + coefficients: + A: 1.07e-10 + B: 0.0 + C: -0.0 +- MUSICA_name: CL13 + reactants: + CL: 1 + OLE: 1 + products: + FMCL: 1 + ALD2: 0.33 + ALDX: 0.67 + XO2: 2.0 + HO2: 1.0 + PAR: -1.0 + type: ARRHENIUS + coefficients: + A: 2.5e-10 + B: 0.0 + C: -0.0 +- MUSICA_name: CL14 + reactants: + CL: 1 + IOLE: 1 + products: + HCL: 0.3 + FMCL: 0.7 + ALD2: 0.45 + ALDX: 0.55 + OLE: 0.3 + PAR: 0.3 + XO2: 1.7 + HO2: 1.0 + type: ARRHENIUS + coefficients: + A: 3.5e-10 + B: 0.0 + C: -0.0 +- MUSICA_name: CL15 + reactants: + CL: 1 + ISOP: 1 + products: + HCL: 0.15 + XO2: 1.0 + HO2: 1.0 + FMCL: 0.85 + ISPD: 1.0 + type: ARRHENIUS + coefficients: + A: 4.3e-10 + B: 0.0 + C: -0.0 +- MUSICA_name: CL16 + reactants: + CL: 1 + FORM: 1 + products: + HCL: 1 + HO2: 1.0 + CO: 1.0 + type: ARRHENIUS + coefficients: + A: 8.2e-11 + B: 0.0 + C: -34.0 +- MUSICA_name: CL17 + reactants: + CL: 1 + ALD2: 1 + products: + HCL: 1 + C2O3: 1.0 + type: ARRHENIUS + coefficients: + A: 7.9e-11 + B: 0.0 + C: -0.0 +- MUSICA_name: CL18 + reactants: + CL: 1 + ALDX: 1 + products: + HCL: 1 + CXO3: 1.0 + type: ARRHENIUS + coefficients: + A: 1.3e-10 + B: 0.0 + C: -0.0 +- MUSICA_name: CL19 + reactants: + CL: 1 + MEOH: 1 + products: + HCL: 1 + HO2: 1.0 + FORM: 1.0 + type: ARRHENIUS + coefficients: + A: 5.5e-11 + B: 0.0 + C: -0.0 +- MUSICA_name: CL20 + reactants: + CL: 1 + ETOH: 1 + products: + HCL: 1 + HO2: 1.0 + ALD2: 1.0 + type: ARRHENIUS + coefficients: + A: 8.2e-11 + B: 0.0 + C: 45.0 +- MUSICA_name: CL21 + reactants: + HCL: 1 + OH: 1 + products: + CL: 1 + type: ARRHENIUS + coefficients: + A: 6.58e-13 + B: 1.16 + C: 58.0 +- MUSICA_name: SA01 + reactants: + TOLRO2: 1 + NO: 1 + products: + NO: 1 + TOLNRXN: 1 + type: ARRHENIUS + coefficients: + A: 2.7e-12 + B: 0.0 + C: 360.0 +- MUSICA_name: SA02 + reactants: + TOLRO2: 1 + HO2: 1 + products: + HO2: 1 + TOLHRXN: 1 + type: ARRHENIUS + coefficients: + A: 1.9e-13 + B: 0.0 + C: 1300.0 +- MUSICA_name: SA03 + reactants: + XYLRO2: 1 + NO: 1 + products: + NO: 1 + XYLNRXN: 1 + type: ARRHENIUS + coefficients: + A: 2.7e-12 + B: 0.0 + C: 360.0 +- MUSICA_name: SA04 + reactants: + XYLRO2: 1 + HO2: 1 + products: + HO2: 1 + XYLHRXN: 1 + type: ARRHENIUS + coefficients: + A: 1.9e-13 + B: 0.0 + C: 1300.0 +- MUSICA_name: SA05 + reactants: + BENZENE: 1 + OH: 1 + products: + OH: 1 + BENZRO2: 0.764 + type: ARRHENIUS + coefficients: + A: 2.47e-12 + B: 0.0 + C: -206.0 +- MUSICA_name: SA06 + reactants: + BENZRO2: 1 + NO: 1 + products: + NO: 1 + BNZNRXN: 1 + type: ARRHENIUS + coefficients: + A: 2.7e-12 + B: 0.0 + C: 360.0 +- MUSICA_name: SA07 + reactants: + BENZRO2: 1 + HO2: 1 + products: + HO2: 1 + BNZHRXN: 1 + type: ARRHENIUS + coefficients: + A: 1.9e-13 + B: 0.0 + C: 1300.0 +- MUSICA_name: SA08 + reactants: + SESQ: 1 + O3: 1 + products: + O3: 1 + SESQRXN: 1 + type: ARRHENIUS + coefficients: + A: 1.16e-14 + B: 0.0 + C: -0.0 +- MUSICA_name: SA09 + reactants: + SESQ: 1 + OH: 1 + products: + OH: 1 + SESQRXN: 1 + type: ARRHENIUS + coefficients: + A: 1.97e-10 + B: 0.0 + C: -0.0 +- MUSICA_name: SA10 + reactants: + SESQ: 1 + NO3: 1 + products: + NO3: 1 + SESQRXN: 1 + type: ARRHENIUS + coefficients: + A: 1.9e-11 + B: 0.0 + C: -0.0 +- MUSICA_name: jo2 + reactants: + O2: 1 + products: + O: 2 + type: ARRHENIUS + coefficients: + A: 0.0 + note: PHOTOLYSIS (A := photolysis rate) +- coefficients: + A: 2.4e-14 + C: 460.0 + note: CMAQ_OH_HNO3 + products: + NO3: 1.0 + reactants: + HNO3: 1.0 + OH: 1.0 + type: ARRHENIUS +- coefficients: + k0_A: 6.5e-34 + k0_C: 1335.0 + kinf_A: 2.7e-17 + kinf_C: 2199.0 + Fc : 1 + note: CMAQ_OH_HNO3 + products: + NO3: 1.0 + reactants: + HNO3: 1.0 + OH: 1.0 + type: TROE diff --git a/test/tchem/config_chapman.yaml b/test/tchem/config_chapman.yaml new file mode 100755 index 000000000..35f36aa2b --- /dev/null +++ b/test/tchem/config_chapman.yaml @@ -0,0 +1,129 @@ +NCAR-version: v1.0 +environmental_conditions: + pressure: + evolving: false + initial_value: [6152.049805] + units: Pa + temperature: + evolving: false + initial_value: [206.6374207] + units: K +initial_state: + Ar: + initial_value: [0.0334] + units: mol m-3 + CO2: + initial_value: [0.00146] + units: mol m-3 + H2O: + initial_value: [1.19e-05] + units: mol m-3 + N2: + initial_value: [2.8] + units: mol m-3 + O2: + initial_value: [0.75] + units: mol m-3 + O3: + initial_value: [8.1e-06] + units: mol m-3 + M: + initial_value: [1] ## mol/mol + units: molecules m-3 +model_info: + chemistry_time_step: + units: sec + value: 1.0 + evolving_conditions: + exist: false + output_time_step: + units: sec + value: 1.0 + simulation_length: + units: sec + value: 100.0 + cells: 5 +reactions: +- coefficients: + A: 2.42E-17 # time 0 photolysis O2_1 + products: + O: 2.0 + reactants: + O2: 1.0 + type: ARRHENIUS +- coefficients: + A: 6.61E-09 # time 0 photolysis O3_1 + products: + O1D: 1.0 + O2: 1.0 + reactants: + O3: 1.0 + type: ARRHENIUS +- coefficients: + A: 1.15E-05 # time 0 photolysis O3_2 + products: + O: 1.0 + O2: 1.0 + reactants: + O3: 1.0 + type: ARRHENIUS +- coefficients: + A: 2.15e-11 + Ea: -1.518e-21 + products: + N2: 1.0 + O: 1.0 + reactants: + O1D: 1.0 + N2: 1.0 + type: ARRHENIUS +- coefficients: + A: 3.3e-11 + Ea: -7.59e-22 + products: + O2: 1.0 + O: 1.0 + reactants: + O1D: 1.0 + O2: 1.0 + type: ARRHENIUS +- coefficients: + A: 8e-12 + Ea: 2.8428e-20 + products: + O2: 2.0 + reactants: + O3: 1.0 + O: 1.0 + type: ARRHENIUS +- coefficients: + A: 6e-34 + B: -2.4 + products: + O3: 1.0 + M: 1.0 + reactants: + M: 1.0 + O2: 1.0 + O: 1.0 + type: ARRHENIUS +constant_species: +- description: "Third-body molecule. This is any molecule present in the system." + name: M +species: +- description: Ar + name: Ar +- description: CO2 + name: CO2 +- description: H2O + name: H2O +- description: N2 + name: N2 +- description: O1D + name: O1D +- description: O + name: O +- description: O2 + name: O2 +- description: O3 + name: O3 diff --git a/test/tchem/gas_back.dat b/test/tchem/gas_back.dat new file mode 100644 index 000000000..e36d355a4 --- /dev/null +++ b/test/tchem/gas_back.dat @@ -0,0 +1,7 @@ +# time (s) +# rate (s^{-1}) +# mixing ratios (ppb) +time 0 +rate 0 +# these lines intentionally left empty +# to serve as an empty gas state diff --git a/test/tchem/gas_data.dat b/test/tchem/gas_data.dat new file mode 100644 index 000000000..5bf86180b --- /dev/null +++ b/test/tchem/gas_data.dat @@ -0,0 +1,7 @@ +# list of gas species +H2SO4 +HNO3 +HCl +NH3 +NO +NO2 diff --git a/test/tchem/gas_emit_empty.dat b/test/tchem/gas_emit_empty.dat new file mode 100644 index 000000000..f9c5d452c --- /dev/null +++ b/test/tchem/gas_emit_empty.dat @@ -0,0 +1,5 @@ +# time (s) +# rate = scaling parameter +# emissions (mol m^{-2} s^{-1}) +time 0 43200 +rate 1.0 0.0 diff --git a/test/tchem/gas_init_cb05cl_ae5.dat b/test/tchem/gas_init_cb05cl_ae5.dat new file mode 100644 index 000000000..2b5b6ed0b --- /dev/null +++ b/test/tchem/gas_init_cb05cl_ae5.dat @@ -0,0 +1,37 @@ +# species initial concentration (ppb) +AACD 1.0 +ALD2 5.0 +ALDX 1.0 +BENZENE 1.0 +CH4 1.85e3 +CL2 0.02e3 +CO 20.0e3 +CRES 5e-03 +ETH 0.01e3 +ETHA 0.5 +ETOH 0.1e3 +FACD 1.0e3 +FORM 0.015e3 +H2O2 8e-02 +HNO3 2.0 +HO2 0.1 +HONO 1.0 +IOLE 0.0005e3 +ISOP 1.0 +MEOH 2.0 +NO 2.0 +NO2 0.018e3 +O3 0.06e3 +OH 1e-3 +OLE 0.003e3 +PAR 0.001e3 +SESQ 0.0001e3 +SO2 0.004e3 +TERP 0.04e3 +TOL 0.0083e3 +XYL 0.003e3 +N2O 0.3e3 +O2 209500.0e3 +H2 0.56e3 +M 1000000.0e3 +N2 780800.0e3 diff --git a/test/tchem/gas_init_chapman.dat b/test/tchem/gas_init_chapman.dat new file mode 100644 index 000000000..66d1c6ab5 --- /dev/null +++ b/test/tchem/gas_init_chapman.dat @@ -0,0 +1,7 @@ +# species initial concentration (ppb) +Ar 33.4 +CO2 1.46 +N2 2.8e3 +O2 0.75e3 +O3 8.1e-3 +M 4.6373815300000007e-10 diff --git a/test/tchem/height.dat b/test/tchem/height.dat new file mode 100644 index 000000000..7bc7287cd --- /dev/null +++ b/test/tchem/height.dat @@ -0,0 +1,4 @@ +# time (s) +# height (m) +time 0 +height 1 diff --git a/test/tchem/pressure_cb05cl_ae5.dat b/test/tchem/pressure_cb05cl_ae5.dat new file mode 100644 index 000000000..f288eca62 --- /dev/null +++ b/test/tchem/pressure_cb05cl_ae5.dat @@ -0,0 +1,4 @@ +# time (s) +# pressure (Pa) +time 0 +pressure 81060 diff --git a/test/tchem/pressure_chapman.dat b/test/tchem/pressure_chapman.dat new file mode 100644 index 000000000..03d132842 --- /dev/null +++ b/test/tchem/pressure_chapman.dat @@ -0,0 +1,4 @@ +# time (s) +# pressure (Pa) +time 0 +pressure 6152.049805 diff --git a/test/tchem/run_part_cb05cl_ae5.spec b/test/tchem/run_part_cb05cl_ae5.spec new file mode 100644 index 000000000..296463b2e --- /dev/null +++ b/test/tchem/run_part_cb05cl_ae5.spec @@ -0,0 +1,50 @@ +run_type particle # particle-resolved run +output_prefix out/tchem_cb05cl_ae5 # prefix of output files +n_repeat 1 # number of Monte Carlo repeats +n_part 100 # total number of particles +restart no # whether to restart from saved state (yes/no) +do_select_weighting no # whether to select weighting explicitly (yes/no) + +t_max 600 # total simulation time (s) +del_t 60 # timestep (s) +t_output 60 # output interval (0 disables) (s) +t_progress 60 # progress printing interval (0 disables) (s) + +do_camp_chem no # whether to use CAMP for chemistry +do_tchem yes # whether to use TChem for chemistry +tchem_gas_config config_cb05cl_ae5.yaml +tchem_aero_config config_cb05cl_ae5.yaml +tchem_numerics_config solver_cb05cl_ae5.yaml + +gas_init gas_init_cb05cl_ae5.dat # initial gas mixing ratios + +aerosol_data aero_data.dat # file containing aerosol data +do_fractal no # whether to do fractal treatment +aerosol_init aero_init_dist.dat # aerosol initial condition file + +temp_profile temp_cb05cl_ae5.dat # temperature profile file +pressure_profile pressure_cb05cl_ae5.dat # pressure profile file +height_profile height.dat # height profile file +gas_emissions gas_emit_empty.dat # gas emissions file +gas_background gas_back.dat # background gas mixing ratios file +aero_emissions aero_emit.dat # aerosol emissions file +aero_background aero_back.dat # aerosol background file +loss_function none # particle loss function + +rel_humidity 0.13916579011880265 # initial relative humidity (1) +latitude 40 # latitude (degrees, -90 to 90) +longitude 0 # longitude (degrees, -180 to 180) +altitude 0 # altitude (m) +start_time 0 # start time (s since 00:00 UTC) +start_day 1 # start day of year (UTC) + +do_coagulation no # whether to do coagulation (yes/no) +do_condensation no # whether to do condensation (yes/no) +do_mosaic no # whether to do MOSAIC (yes/no) +do_nucleation no # whether to do nucleation (yes/no) + +rand_init 0 # random initialization (0 to auto-generate) +allow_doubling yes # whether to allow doubling (yes/no) +allow_halving yes # whether to allow halving (yes/no) +record_removals no # whether to record particle removals (yes/no) +do_parallel no # whether to run in parallel (yes/no) diff --git a/test/tchem/run_part_chapman.spec b/test/tchem/run_part_chapman.spec new file mode 100644 index 000000000..e28a9dae5 --- /dev/null +++ b/test/tchem/run_part_chapman.spec @@ -0,0 +1,50 @@ +run_type particle # particle-resolved run +output_prefix out/tchem_chapman # prefix of output files +n_repeat 1 # number of Monte Carlo repeats +n_part 100 # total number of particles +restart no # whether to restart from saved state (yes/no) +do_select_weighting no # whether to select weighting explicitly (yes/no) + +t_max 1000000 # total simulation time (s) +del_t 100 # timestep (s) +t_output 1000 # output interval (0 disables) (s) +t_progress 10000 # progress printing interval (0 disables) (s) + +do_camp_chem no # whether to use CAMP for chemistry +do_tchem yes # whether to use TChem for chemistry +tchem_gas_config config_chapman.yaml +tchem_aero_config config_chapman.yaml +tchem_numerics_config solver_chapman.yaml + +gas_init gas_init_chapman.dat # initial gas mixing ratios + +aerosol_data aero_data.dat # file containing aerosol data +do_fractal no # whether to do fractal treatment +aerosol_init aero_init_dist.dat # aerosol initial condition file + +temp_profile temp_chapman.dat # temperature profile file +pressure_profile pressure_chapman.dat # pressure profile file +height_profile height.dat # height profile file +gas_emissions gas_emit_empty.dat # gas emissions file +gas_background gas_back.dat # background gas mixing ratios file +aero_emissions aero_emit.dat # aerosol emissions file +aero_background aero_back.dat # aerosol background file +loss_function none # particle loss function + +rel_humidity 9.0034351828398e-08 # initial relative humidity (1) +latitude 40 # latitude (degrees, -90 to 90) +longitude 0 # longitude (degrees, -180 to 180) +altitude 0 # altitude (m) +start_time 0 # start time (s since 00:00 UTC) +start_day 1 # start day of year (UTC) + +do_coagulation no # whether to do coagulation (yes/no) +do_condensation no # whether to do condensation (yes/no) +do_mosaic no # whether to do MOSAIC (yes/no) +do_nucleation no # whether to do nucleation (yes/no) + +rand_init 0 # random initialization (0 to auto-generate) +allow_doubling yes # whether to allow doubling (yes/no) +allow_halving yes # whether to allow halving (yes/no) +record_removals no # whether to record particle removals (yes/no) +do_parallel no # whether to run in parallel (yes/no) diff --git a/test/tchem/solver_cb05cl_ae5.yaml b/test/tchem/solver_cb05cl_ae5.yaml new file mode 100644 index 000000000..6afc253e2 --- /dev/null +++ b/test/tchem/solver_cb05cl_ae5.yaml @@ -0,0 +1,9 @@ +solver_info: + atol_time: 1e-6 + rtol_time: 1e-6 + dtmin: 1e-20 + atol_newton: 1e-18 + rtol_newton: 1e-8 + max_newton_iterations: 100 + max_time_iterations: 1000000 + jacobian_interval: 100 diff --git a/test/tchem/solver_chapman.yaml b/test/tchem/solver_chapman.yaml new file mode 100644 index 000000000..96bab04ee --- /dev/null +++ b/test/tchem/solver_chapman.yaml @@ -0,0 +1,9 @@ +solver_info: + atol_time: 1e-6 + rtol_time: 1e-6 + dtmin: 1e-20 + atol_newton: 1e-3 + rtol_newton: 1e-6 + max_newton_iterations: 100 + max_time_iterations: 100000 + jacobian_interval: 100 diff --git a/test/tchem/tchem_cb05cl_ae5_gas_saved.txt b/test/tchem/tchem_cb05cl_ae5_gas_saved.txt new file mode 100644 index 000000000..bfb60d4bb --- /dev/null +++ b/test/tchem/tchem_cb05cl_ae5_gas_saved.txt @@ -0,0 +1,11 @@ +0.000000000000000000e+00 1.000000000000000000e+00 5.000000000000000000e+00 1.000000000000000000e+00 1.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 2.000000000000000000e+01 0.000000000000000000e+00 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2.002249635400000000e-18 8.095324278299998594e-03 7.500081022100000609e+02 8.803968327999998991e-08 4.637381530000000577e-10 diff --git a/test/tchem/temp_cb05cl_ae5.dat b/test/tchem/temp_cb05cl_ae5.dat new file mode 100644 index 000000000..a8582b2cd --- /dev/null +++ b/test/tchem/temp_cb05cl_ae5.dat @@ -0,0 +1,4 @@ +# time (s) +# temp (K) +time 0 +temp 272.5 diff --git a/test/tchem/temp_chapman.dat b/test/tchem/temp_chapman.dat new file mode 100644 index 000000000..41070eb73 --- /dev/null +++ b/test/tchem/temp_chapman.dat @@ -0,0 +1,4 @@ +# time (s) +# temp (K) +time 0 +temp 206.6374207 diff --git a/test/tchem/test_tchem_1.sh b/test/tchem/test_tchem_1.sh new file mode 100755 index 000000000..ecdcb3c8c --- /dev/null +++ b/test/tchem/test_tchem_1.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +# exit on error +set -e +# turn on command echoing +set -v +# make sure that the current directory is the one where this script is +cd ${0%/*} +# make the output directory if it doesn't exist +mkdir -p out + +../../partmc run_part_chapman.spec +../../extract_gas out/tchem_chapman_0001 +../../numeric_diff --by col --rel-tol 0.4 out/tchem_chapman_0001_gas.txt tchem_chapman_gas_saved.txt diff --git a/test/tchem/test_tchem_2.sh b/test/tchem/test_tchem_2.sh new file mode 100755 index 000000000..15c2dce2b --- /dev/null +++ b/test/tchem/test_tchem_2.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +# exit on error +set -e +# turn on command echoing +set -v +# make sure that the current directory is the one where this script is +cd ${0%/*} +# make the output directory if it doesn't exist +mkdir -p out + +../../partmc run_part_cb05cl_ae5.spec +../../extract_gas out/tchem_cb05cl_ae5_0001 +../../numeric_diff --by col --rel-tol 0.4 out/tchem_cb05cl_ae5_0001_gas.txt tchem_cb05cl_ae5_gas_saved.txt diff --git a/test/weighting/run_part_flat.spec b/test/weighting/run_part_flat.spec index e3734b7e6..4ae85f318 100644 --- a/test/weighting/run_part_flat.spec +++ b/test/weighting/run_part_flat.spec @@ -11,7 +11,8 @@ del_t 60 # timestep (s) t_output 1200 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/weighting/run_part_flat_source.spec b/test/weighting/run_part_flat_source.spec index 28209ad99..5ff999a45 100644 --- a/test/weighting/run_part_flat_source.spec +++ b/test/weighting/run_part_flat_source.spec @@ -11,7 +11,8 @@ del_t 60 # timestep (s) t_output 1200 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/weighting/run_part_flat_specified.spec b/test/weighting/run_part_flat_specified.spec index 750d87ff9..3bb804688 100644 --- a/test/weighting/run_part_flat_specified.spec +++ b/test/weighting/run_part_flat_specified.spec @@ -11,7 +11,8 @@ del_t 60 # timestep (s) t_output 1200 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/weighting/run_part_nummass.spec b/test/weighting/run_part_nummass.spec index ec4e62737..eb6a5d208 100644 --- a/test/weighting/run_part_nummass.spec +++ b/test/weighting/run_part_nummass.spec @@ -11,7 +11,8 @@ del_t 60 # timestep (s) t_output 1200 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/weighting/run_part_nummass_source.spec b/test/weighting/run_part_nummass_source.spec index 5c6f08358..fd107ebab 100644 --- a/test/weighting/run_part_nummass_source.spec +++ b/test/weighting/run_part_nummass_source.spec @@ -11,7 +11,8 @@ del_t 60 # timestep (s) t_output 1200 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios diff --git a/test/weighting/run_part_nummass_specified.spec b/test/weighting/run_part_nummass_specified.spec index ea57afdc0..0dc3e5cca 100644 --- a/test/weighting/run_part_nummass_specified.spec +++ b/test/weighting/run_part_nummass_specified.spec @@ -11,7 +11,8 @@ del_t 60 # timestep (s) t_output 1200 # output interval (0 disables) (s) t_progress 3600 # progress printing interval (0 disables) (s) -do_camp_chem no # whether to run the campible chemistry module +do_camp_chem no # whether to use CAMP for chemistry +do_tchem no # whether to use TChem for chemistry gas_data gas_data.dat # file containing gas data gas_init gas_init.dat # initial gas mixing ratios