diff --git a/CMakeLists.txt b/CMakeLists.txt index eb0e6e050..2d45c424f 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -192,6 +192,9 @@ 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() ###################################################################### # partmc library diff --git a/src/gas_state.F90 b/src/gas_state.F90 index b32ad139f..a91e0a1a5 100644 --- a/src/gas_state.F90 +++ b/src/gas_state.F90 @@ -188,6 +188,20 @@ subroutine gas_state_mole_dens_to_ppb(gas_state, env_state) end subroutine gas_state_mole_dens_to_ppb +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Convert (ppb) to (mol m^{-3}). + subroutine gas_state_ppb_to_mole_dens(gas_state, env_state) + + !> Gas state. + type(gas_state_t), intent(inout) :: gas_state + !> Environment state. + type(env_state_t), intent(in) :: env_state + + call gas_state_scale(gas_state, env_state_air_molar_den(env_state) / 1e9) + + end subroutine gas_state_ppb_to_mole_dens + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! #ifdef PMC_USE_CAMP diff --git a/src/partmc.F90 b/src/partmc.F90 index 33e94e53c..667b0c814 100644 --- a/src/partmc.F90 +++ b/src/partmc.F90 @@ -511,6 +511,11 @@ subroutine partmc_part(file) #endif end if + if (run_part_opt%do_tchem) then + call pmc_tchem_initialize(tchem_config_filename, gas_data, & + aero_data) + 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, & @@ -524,11 +529,7 @@ subroutine partmc_part(file) call gas_data_initialize(gas_data, camp_core) #endif else if (run_part_opt%do_tchem) then - ! FIXME: Replacde with something else - 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) + print*, 'do nothing!' else call spec_file_read_string(file, 'gas_data', sub_filename) call spec_file_open(sub_filename, sub_file) @@ -752,10 +753,6 @@ subroutine partmc_part(file) #endif end if - if (run_part_opt%do_tchem) then - call pmc_tchem_initialize(tchem_config_filename, gas_data, gas_state_init, aero_data) - end if - ! re-initialize RNG with the given seed call pmc_rand_finalize() call pmc_srand(rand_init, pmc_mpi_rank()) diff --git a/src/tchem_interface.F90 b/src/tchem_interface.F90 index afd9c82f5..5ae91eb7e 100644 --- a/src/tchem_interface.F90 +++ b/src/tchem_interface.F90 @@ -11,15 +11,49 @@ module pmc_tchem_interface use pmc_aero_data use pmc_aero_particle use pmc_aero_state - use pmc_constants, only : dp + use pmc_constants use pmc_gas_data use pmc_gas_state #ifdef PMC_USE_TCHEM use iso_c_binding - use tchemdriver #endif use pmc_util, only : die_msg, warn_assert_msg, assert_msg +interface + subroutine initialize(arg_chemfile) bind(c, name="initialize") + use iso_c_binding + character(kind=c_char) :: arg_chemfile(*) + 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) bind(c, name="TChem_getStateVector") + use iso_c_binding + real(kind=c_double) :: array(*) + end subroutine + subroutine TChem_setStateVector(array) bind(c, name="TChem_setStateVector") + use iso_c_binding + real(kind=c_double) :: array(*) + 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() bind(C, name="TChem_doTimestep") + end subroutine +end interface + contains !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! @@ -28,63 +62,67 @@ module pmc_tchem_interface subroutine pmc_tchem_interface_solve(env_state, aero_data, aero_state, & gas_data, gas_state) + !> 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 - call tchem_from_partmc(gas_data, gas_state) - call timestep() - call tchem_to_partmc(gas_data, gas_state) + call tchem_from_partmc(gas_data, gas_state, env_state) + call tchem_timestep() + call tchem_to_partmc(gas_data, gas_state, env_state) end subroutine pmc_tchem_interface_solve !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - subroutine pmc_tchem_initialize(config_filename, gas_data, gas_state, aero_data) - + !> Initialize TChem and PartMC gas and aerosol data. + subroutine pmc_tchem_initialize(config_filename, gas_data, aero_data) use iso_c_binding + !> character(len=*), intent(in) :: config_filename + !> Gas data. type(gas_data_t), intent(inout) :: gas_data - type(gas_state_t), intent(inout) :: gas_state + !> Aerosol data. type(aero_data_t), intent(inout) :: aero_data - integer(c_int) :: nSpec - integer :: i, j - character(len=5) :: name - character(kind=c_char), dimension(5) :: name_data + integer(kind=c_int) :: nSpec + integer :: i real(kind=c_double), dimension(:), allocatable :: array + character(:), allocatable :: val ! initialize the model call TChem_initialize(trim(config_filename)) - ! feedback to PartMC ! what we need: - ! - number of gas species + ! - number of gas species for gas_data ! - name of gas species to set gas_data - ! - set the size of gas_state nSpec = TChem_getNumberOfSpecies() call ensure_string_array_size(gas_data%name, nSpec) - call gas_state_set_size(gas_state, nSpec) - - - call TChem_getSpeciesNames() ! name of gas species - !do i = 1,nSpec - ! gas_data%name(i) = "H2O" - !end do + do i = 1,nSpec + val = TChem_species_name(i-1) + gas_data%name(i) = trim(val) + end do + + ! We need this + allocate(gas_data%mosaic_index(gas_data_n_spec(gas_data))) + gas_data%mosaic_index(:) = 0 print*, 'in partmc', nSpec, trim(config_filename), gas_data_n_spec(gas_data) - - call tchem_to_partmc(gas_data, gas_state) - print*, 'in partmc' - print*, gas_state%mix_rat -end subroutine + end subroutine +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Clean up TChem. subroutine pmc_tchem_cleanup() call finalize() @@ -93,41 +131,112 @@ end subroutine pmc_tchem_cleanup !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - !> - subroutine tchem_to_partmc(gas_data, gas_state) + !> Map all data TChem -> PartMC. + subroutine tchem_to_partmc(gas_data, gas_state, env_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 - real(kind=c_double), dimension(:), allocatable :: array + integer(c_int) :: nSpec, stateVecDim + real(kind=c_double), dimension(:), allocatable :: stateVector ! Get gas array + stateVecDim = TChem_getLengthOfStateVector() nSpec = TChem_getNumberOfSpecies() - allocate(array(nSpec)) + allocate(stateVector(stateVecDim)) array = 0.0d0 - call TChem_getStateVector(array) - gas_state%mix_rat = array + call TChem_getStateVector(stateVector) + + ! FIXME: adjust this range later + gas_state%mix_rat = stateVector(4:nSpec+3) + ! Convert gas_state from mol m^-3 to ppb. + call gas_state_mole_dens_to_ppb(gas_state, env_state) end subroutine tchem_to_partmc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - !> - subroutine tchem_from_partmc(gas_data, gas_state) + !> Map all data PartMC -> TChem. + subroutine tchem_from_partmc(gas_data, gas_state, env_state) - !> + !> Gas data. type(gas_data_t), intent(in) :: gas_data - ! FIXME: Fix intent later + !> 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 + + ! Make a state vector + ! Density + ! Pressure + ! Temperature + ! Concentrations + ! get size of stateVector + stateVecDim = TChem_getLengthOfStateVector() + allocate(stateVector(stateVecDim)) + stateVector(1) = env_state_air_den(env_state) + stateVector(2) = env_state%pressure + stateVector(3) = env_state%temp + + call gas_state_ppb_to_mole_dens(gas_state, env_state) + stateVector(4:gas_data_n_spec(gas_data)+3) = gas_state%mix_rat - call TChem_setStateVector(gas_state%mix_rat) + call TChem_setStateVector(stateVector) end subroutine tchem_from_partmc -#endif +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Do a single timestep of TChem chemistry. + subroutine TChem_timestep() + use iso_c_binding + + call TChem_doTimestep() + + end subroutine TChem_timestep + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Initialize TChem. + subroutine TChem_initialize(chemFile) + use iso_c_binding + + !> Chemistry configuration file. + character(kind=c_char,len=*), intent(in) :: chemFile + + print*, 'in TChemDriver: ', chemFile + + call initialize(chemFile//c_null_char) + + end subroutine TChem_initialize + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + !> Get i_spec species name from TChem. + 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/test/tchem/README b/test/tchem/README new file mode 100644 index 000000000..5e8432024 --- /dev/null +++ b/test/tchem/README @@ -0,0 +1,3 @@ + +TChemn Test-case +=========================================== diff --git a/test/tchem/aero_back.dat b/test/tchem/aero_back.dat new file mode 100644 index 000000000..524982c94 --- /dev/null +++ b/test/tchem/aero_back.dat @@ -0,0 +1,6 @@ +# time (s) +# rate (s^{-1}) +# aerosol distribution filename +time 0 +rate 3e-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..99436c308 --- /dev/null +++ b/test/tchem/aero_back_dist.dat @@ -0,0 +1,6 @@ +mode_name back1 # name of mode source +mass_frac aero_back_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 1e-4 # diameter (m) 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..2c9d1cc02 --- /dev/null +++ b/test/tchem/aero_emit.dat @@ -0,0 +1,6 @@ +# time (s) +# rate (s^{-1}) +# aerosol distribution filename +time 0 +rate 1.5e-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..b68de68d2 --- /dev/null +++ b/test/tchem/aero_emit_dist.dat @@ -0,0 +1,6 @@ +mode_name emit1 # name of mode source +mass_frac aero_emit_comp.dat # species mass fractions +diam_type geometric # type of diameter specified +mode_type mono # type of distribution +num_conc 1e12 # particle number concentration (#/m^2) +diam 6.03e-5 # diameter (m) 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 +- 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 +- coefficients: + A: 3.5e-12 + B: 0.0 + C: 250.0 + products: + NO2: 1.0 + OH: 1.0 + reactants: + HO2: 1.0 + NO: 1.0 + rxn_id: R30 + type: ARRHENIUS +- coefficients: + Fc: 0.6 + N: 1.0 + k0_A: 1.8e-31 + k0_B: -3.2 + k0_C: -0.0 + kinf_A: 4.7e-12 + kinf_B: 0.0 + kinf_C: -0.0 + products: + PNA: 1.0 + reactants: + HO2: 1.0 + NO2: 1.0 + rxn_id: R31 + type: TROE +- coefficients: + Fc: 0.6 + N: 1.0 + k0_A: 4.1e-05 + k0_B: 0.0 + k0_C: -10650.0 + kinf_A: 4800000000000000.0 + kinf_B: 0.0 + kinf_C: -11170.0 + products: + HO2: 1.0 + NO2: 1.0 + reactants: + PNA: 1.0 + rxn_id: R32 + type: TROE +- coefficients: + A: 1.3e-12 + B: 0.0 + C: 380.0 + products: + NO2: 1.0 + reactants: + OH: 1.0 + PNA: 1.0 + rxn_id: R33 + type: ARRHENIUS +- coefficients: + k1_A: 2.3e-13 + k1_C: 600.0 + k2_A: 1.7e-33 + k2_C: 1000.0 + products: + H2O2: 1.0 + reactants: + HO2: 2 + rxn_id: R34 + type: CMAQ_H2O2 +- coefficients: + k1_A: 3.22e-34 + k1_C: 2800.0 + k2_A: 2.38e-54 + 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-0.8 + k0_C: -0.0 + kinf_A: 8.8e-12 + kinf_B: 0.0 + kinf_C: -0.0 + products: + ALDX: 0.22 + FORM: 1.56 + HO2: 1.0 + XO2: 1.0 + reactants: + ETH: 1.0 + OH: 1.0 + rxn_id: R121 + type: TROE +- coefficients: + A: 1.2e-14 + B: 0.0 + C: -2630.0 + products: + CO: 0.63 + FACD: 0.37 + FORM: 1.0 + HO2: 0.13 + OH: 0.13 + reactants: + ETH: 1.0 + O3: 1.0 + rxn_id: R122 + type: ARRHENIUS +- coefficients: + A: 3.3e-12 + B: 0.0 + C: -2880.0 + products: + FORM: 2.0 + NO2: 1.0 + XO2: 1.0 + reactants: + ETH: 1.0 + NO3: 1.0 + rxn_id: R123 + type: ARRHENIUS +- coefficients: + A: 2.3e-11 + B: 0.0 + C: -0.0 + products: + ALD2: 1.24 + ALDX: 0.66 + CO: 0.1 + HO2: 0.1 + PAR: 0.1 + XO2: 0.1 + reactants: + IOLE: 1.0 + O: 1.0 + rxn_id: R124 + type: ARRHENIUS +- coefficients: + A: 1.0e-11 + B: 0.0 + C: 550.0 + products: + ALD2: 1.3 + ALDX: 0.7 + HO2: 1.0 + XO2: 1.0 + reactants: + IOLE: 1.0 + OH: 1.0 + rxn_id: R125 + type: ARRHENIUS +- coefficients: + A: 8.4e-15 + B: 0.0 + C: -1100.0 + products: + ALD2: 0.65 + ALDX: 0.35 + CO: 0.25 + FORM: 0.25 + HO2: 0.5 + O: 0.5 + OH: 0.5 + reactants: + IOLE: 1.0 + O3: 1.0 + rxn_id: R126 + type: ARRHENIUS +- coefficients: + A: 9.6e-13 + B: 0.0 + C: -270.0 + products: + ALD2: 1.18 + ALDX: 0.64 + HO2: 1.0 + NO2: 1.0 + reactants: + IOLE: 1.0 + NO3: 1.0 + rxn_id: R127 + type: ARRHENIUS +- coefficients: + A: 1.8e-12 + B: 0.0 + C: 355.0 + products: + CRES: 0.36 + HO2: 0.44 + TO2: 0.56 + TOLRO2: 0.765 + XO2: 0.08 + reactants: + OH: 1.0 + TOL: 1.0 + rxn_id: R128 + type: ARRHENIUS +- coefficients: + A: 8.1e-12 + B: 0.0 + C: -0.0 + products: + HO2: 0.9 + NO2: 0.9 + NTR: 0.1 + OPEN: 0.9 + reactants: + NO: 1.0 + TO2: 1.0 + rxn_id: R129 + type: ARRHENIUS +- coefficients: + A: 4.2 + B: 0.0 + C: -0.0 + products: + CRES: 1.0 + HO2: 1.0 + reactants: + TO2: 1.0 + rxn_id: R130 + type: ARRHENIUS +- coefficients: + A: 4.1e-11 + B: 0.0 + C: -0.0 + products: + CRO: 0.4 + HO2: 0.6 + OPEN: 0.3 + XO2: 0.6 + reactants: + CRES: 1.0 + OH: 1.0 + rxn_id: R131 + type: ARRHENIUS +- coefficients: + A: 2.2e-11 + B: 0.0 + C: -0.0 + products: + CRO: 1.0 + HNO3: 1.0 + reactants: + CRES: 1.0 + NO3: 1.0 + rxn_id: R132 + type: ARRHENIUS +- coefficients: + A: 1.4e-11 + B: 0.0 + C: -0.0 + products: + NTR: 1.0 + reactants: + CRO: 1.0 + NO2: 1.0 + rxn_id: R133 + type: ARRHENIUS +- coefficients: + A: 5.5e-12 + B: 0.0 + C: -0.0 + products: + CRES: 1.0 + reactants: + CRO: 1.0 + HO2: 1.0 + rxn_id: R134 + type: ARRHENIUS +- MUSICA_name: OPEN + coefficients: + A: 0.000645 + note: PHOTOLYSIS (A := photolysis rate) + products: + C2O3: 1.0 + CO: 1.0 + HO2: 1.0 + reactants: + OPEN: 1.0 + type: ARRHENIUS +- coefficients: + A: 3.0e-11 + B: 0.0 + C: -0.0 + products: + C2O3: 1.0 + CO: 2.0 + FORM: 1.0 + HO2: 2.0 + XO2: 1.0 + reactants: + OH: 1.0 + OPEN: 1.0 + rxn_id: R136 + type: ARRHENIUS +- coefficients: + A: 5.4e-17 + B: 0.0 + C: -500.0 + products: + ALDX: 0.03 + C2O3: 0.62 + CO: 0.69 + FORM: 0.7 + HO2: 0.76 + MGLY: 0.2 + OH: 0.08 + XO2: 0.03 + reactants: + O3: 1.0 + OPEN: 1.0 + rxn_id: R137 + type: ARRHENIUS +- coefficients: + A: 1.7e-11 + B: 0.0 + C: 116.0 + products: + CRES: 0.2 + HO2: 0.7 + MGLY: 0.8 + PAR: 1.1 + TO2: 0.3 + XO2: 0.5 + XYLRO2: 0.804 + reactants: + OH: 1.0 + XYL: 1.0 + rxn_id: R138 + type: ARRHENIUS +- coefficients: + A: 1.8e-11 + B: 0.0 + C: -0.0 + products: + C2O3: 1.0 + XO2: 1.0 + reactants: + MGLY: 1.0 + OH: 1.0 + rxn_id: R139 + type: ARRHENIUS +- MUSICA_name: MGLY + coefficients: + A: 7.64e-05 + note: PHOTOLYSIS (A := photolysis rate) + products: + C2O3: 1.0 + CO: 1.0 + HO2: 1.0 + reactants: + MGLY: 1.0 + type: ARRHENIUS +- coefficients: + A: 3.6e-11 + B: 0.0 + C: -0.0 + products: + CXO3: 0.25 + FORM: 0.5 + HO2: 0.25 + ISPD: 0.75 + PAR: 0.25 + XO2: 0.25 + reactants: + ISOP: 1.0 + O: 1.0 + rxn_id: R141 + type: ARRHENIUS +- coefficients: + A: 2.54e-11 + B: 0.0 + C: 407.6 + products: + FORM: 0.629 + HO2: 0.912 + ISPD: 0.912 + XO2: 0.991 + XO2N: 0.088 + reactants: + ISOP: 1.0 + OH: 1.0 + rxn_id: R142 + type: ARRHENIUS +- coefficients: + A: 7.86e-15 + B: 0.0 + C: -1912.0 + products: + ALDX: 0.15 + CO: 0.066 + CXO3: 0.2 + FORM: 0.6 + HO2: 0.066 + ISPD: 0.65 + OH: 0.266 + PAR: 0.35 + XO2: 0.2 + reactants: + ISOP: 1.0 + O3: 1.0 + rxn_id: R143 + type: ARRHENIUS +- coefficients: + A: 3.03e-12 + B: 0.0 + C: -448.0 + products: + ALDX: 0.8 + HO2: 0.8 + ISPD: 0.2 + NO2: 0.2 + NTR: 0.8 + PAR: 2.4 + XO2: 1.0 + reactants: + ISOP: 1.0 + NO3: 1.0 + rxn_id: R144 + type: ARRHENIUS +- coefficients: + A: 3.36e-11 + B: 0.0 + C: -0.0 + products: + ALD2: 0.252 + ALDX: 0.12 + C2O3: 0.21 + CO: 0.334 + CXO3: 0.25 + FORM: 0.167 + HO2: 0.503 + MGLY: 0.168 + PAR: 1.565 + XO2: 0.713 + reactants: + ISPD: 1.0 + OH: 1.0 + rxn_id: R145 + type: ARRHENIUS +- coefficients: + A: 7.1e-18 + B: 0.0 + C: -0.0 + products: + ALD2: 0.02 + C2O3: 0.114 + CO: 0.225 + FORM: 0.15 + HO2: 0.154 + MGLY: 0.85 + OH: 0.268 + PAR: 0.36 + XO2: 0.064 + reactants: + ISPD: 1.0 + O3: 1.0 + rxn_id: R146 + type: ARRHENIUS +- coefficients: + A: 1.0e-15 + B: 0.0 + C: -0.0 + products: + ALDX: 0.357 + CO: 0.643 + CXO3: 0.075 + FORM: 0.282 + HNO3: 0.15 + HO2: 0.925 + NTR: 0.85 + PAR: 1.282 + XO2: 0.075 + reactants: + ISPD: 1.0 + NO3: 1.0 + rxn_id: R147 + type: ARRHENIUS +- MUSICA_name: ISPD + coefficients: + A: 1.98e-09 + note: PHOTOLYSIS (A := photolysis rate) + products: + ALD2: 0.067 + C2O3: 0.967 + CO: 0.333 + FORM: 0.9 + HO2: 1.033 + PAR: 0.832 + XO2: 0.7 + reactants: + ISPD: 1.0 + type: ARRHENIUS +- coefficients: + A: 3.6e-11 + B: 0.0 + C: -0.0 + products: + ALDX: 0.15 + PAR: 5.12 + reactants: + O: 1.0 + TERP: 1.0 + rxn_id: R149 + type: ARRHENIUS +- coefficients: + A: 1.5e-11 + B: 0.0 + C: 449.0 + products: + ALDX: 0.47 + FORM: 0.28 + HO2: 0.75 + PAR: 1.66 + XO2: 1.25 + XO2N: 0.25 + reactants: + OH: 1.0 + TERP: 1.0 + rxn_id: R150 + type: ARRHENIUS +- coefficients: + A: 1.2e-15 + B: 0.0 + C: -821.0 + products: + ALDX: 0.21 + CO: 0.001 + CXO3: 0.39 + FORM: 0.24 + HO2: 0.07 + OH: 0.57 + PAR: 7.0 + XO2: 0.76 + XO2N: 0.18 + reactants: + O3: 1.0 + TERP: 1.0 + rxn_id: R151 + type: ARRHENIUS +- coefficients: + A: 3.7e-12 + B: 0.0 + C: 175.0 + products: + ALDX: 0.47 + HO2: 0.28 + NO2: 0.47 + NTR: 0.53 + XO2: 1.03 + XO2N: 0.25 + reactants: + NO3: 1.0 + TERP: 1.0 + rxn_id: R152 + type: ARRHENIUS +- coefficients: + Fc: 0.6 + N: 1.0 + k0_A: 3.0e-31 + k0_B: -3.3 + k0_C: -0.0 + kinf_A: 1.5e-12 + kinf_B: 0.0 + kinf_C: -0.0 + products: + HO2: 1.0 + SULF: 1.0 + reactants: + OH: 1.0 + SO2: 1.0 + rxn_id: R153 + type: TROE +- coefficients: + A: 6.9e-12 + B: 0.0 + C: -230.0 + products: + ALD2: 0.9 + ALDX: 0.05 + FORM: 0.1 + HO2: 1.0 + XO2: 0.1 + reactants: + ETOH: 1.0 + OH: 1.0 + rxn_id: R154 + type: ARRHENIUS +- coefficients: + A: 8.7e-12 + B: 0.0 + C: -1070.0 + products: + ALD2: 0.991 + HO2: 1.0 + XO2: 0.991 + XO2N: 0.009 + reactants: + ETHA: 1.0 + OH: 1.0 + rxn_id: R155 + type: ARRHENIUS +- coefficients: + A: 1.5e-19 + B: 0.0 + C: -0.0 + products: + ALDX: 0.8 + HO2: 0.8 + ISPD: 0.2 + NO: 0.2 + NTR: 0.8 + PAR: 2.4 + XO2: 1.0 + reactants: + ISOP: 1.0 + NO2: 1.0 + rxn_id: R156 + type: ARRHENIUS +- MUSICA_name: CL2 + coefficients: + A: 0.0 + note: PHOTOLYSIS (A := photolysis rate) + products: + CL: 2 + reactants: + CL2: 1.0 + type: ARRHENIUS +- coefficients: + A: 2.3e-11 + B: 0.0 + C: -200.0 + products: + CLO: 1.0 + reactants: + CL: 1.0 + O3: 1.0 + rxn_id: CL3 + type: ARRHENIUS +- coefficients: + A: 1.63e-14 + B: 0.0 + C: -0.0 + products: + CL: 1.4 + CL2: 0.3 + reactants: + CLO: 2 + rxn_id: CL4 + type: ARRHENIUS +- coefficients: + A: 6.4e-12 + B: 0.0 + C: 290.0 + products: + CL: 1.0 + NO2: 1.0 + reactants: + CLO: 1.0 + NO: 1.0 + rxn_id: CL5 + type: ARRHENIUS +- coefficients: + A: 2.7e-12 + B: 0.0 + C: 220.0 + products: + HOCL: 1.0 + reactants: + CLO: 1.0 + HO2: 1.0 + rxn_id: CL6 + type: ARRHENIUS +- coefficients: + A: 5.0e-13 + B: 0.0 + C: -0.0 + products: + CL: 1.0 + CO: 1.0 + reactants: + FMCL: 1.0 + OH: 1.0 + rxn_id: CL7 + type: ARRHENIUS +- coefficients: + A: 6.6e-12 + B: 0.0 + C: -1240.0 + products: + HCL: 1.0 + MEO2: 1.0 + reactants: + CH4: 1.0 + CL: 1.0 + rxn_id: CL9 + type: ARRHENIUS +- coefficients: + A: 5.0e-11 + B: 0.0 + C: -0.0 + products: + ALD2: 0.06 + ALDX: 0.05 + HCL: 1.0 + HO2: 0.11 + PAR: -0.11 + ROR: 0.76 + XO2: 0.87 + XO2N: 0.13 + reactants: + CL: 1.0 + PAR: 1.0 + rxn_id: CL10 + type: ARRHENIUS +- coefficients: + A: 8.3e-11 + B: 0.0 + C: -100.0 + products: + ALD2: 0.991 + HCL: 1.0 + HO2: 1.0 + XO2: 0.991 + XO2N: 0.009 + reactants: + CL: 1.0 + ETHA: 1.0 + rxn_id: CL11 + type: ARRHENIUS +- coefficients: + A: 1.07e-10 + B: 0.0 + C: -0.0 + products: + FMCL: 1.0 + FORM: 1.0 + HO2: 1.0 + XO2: 2.0 + reactants: + CL: 1.0 + ETH: 1.0 + rxn_id: CL12 + type: ARRHENIUS +- coefficients: + A: 2.5e-10 + B: 0.0 + C: -0.0 + products: + ALD2: 0.33 + ALDX: 0.67 + FMCL: 1.0 + HO2: 1.0 + PAR: -1.0 + XO2: 2.0 + reactants: + CL: 1.0 + OLE: 1.0 + rxn_id: CL13 + type: ARRHENIUS +- coefficients: + A: 3.5e-10 + B: 0.0 + C: -0.0 + products: + ALD2: 0.45 + ALDX: 0.55 + FMCL: 0.7 + HCL: 0.3 + HO2: 1.0 + OLE: 0.3 + PAR: 0.3 + XO2: 1.7 + reactants: + CL: 1.0 + IOLE: 1.0 + rxn_id: CL14 + type: ARRHENIUS +- coefficients: + A: 4.3e-10 + B: 0.0 + C: -0.0 + products: + FMCL: 0.85 + HCL: 0.15 + HO2: 1.0 + ISPD: 1.0 + XO2: 1.0 + reactants: + CL: 1.0 + ISOP: 1.0 + rxn_id: CL15 + type: ARRHENIUS +- coefficients: + A: 8.2e-11 + B: 0.0 + C: -34.0 + products: + CO: 1.0 + HCL: 1.0 + HO2: 1.0 + reactants: + CL: 1.0 + FORM: 1.0 + rxn_id: CL16 + type: ARRHENIUS +- coefficients: + A: 7.9e-11 + B: 0.0 + C: -0.0 + products: + C2O3: 1.0 + HCL: 1.0 + reactants: + ALD2: 1.0 + CL: 1.0 + rxn_id: CL17 + type: ARRHENIUS +- coefficients: + A: 1.3e-10 + B: 0.0 + C: -0.0 + products: + CXO3: 1.0 + HCL: 1.0 + reactants: + ALDX: 1.0 + CL: 1.0 + rxn_id: CL18 + type: ARRHENIUS +- coefficients: + A: 5.5e-11 + B: 0.0 + C: -0.0 + products: + FORM: 1.0 + HCL: 1.0 + HO2: 1.0 + reactants: + CL: 1.0 + MEOH: 1.0 + rxn_id: CL19 + type: ARRHENIUS +- coefficients: + A: 8.2e-11 + B: 0.0 + C: 45.0 + products: + ALD2: 1.0 + HCL: 1.0 + HO2: 1.0 + reactants: + CL: 1.0 + ETOH: 1.0 + rxn_id: CL20 + type: ARRHENIUS +- coefficients: + A: 6.58e-13 + B: 1.16 + C: 58.0 + products: + CL: 1.0 + reactants: + HCL: 1.0 + OH: 1.0 + rxn_id: CL21 + type: ARRHENIUS +- coefficients: + A: 2.7e-12 + B: 0.0 + C: 360.0 + products: + NO: 1.0 + reactants: + NO: 1.0 + TOLRO2: 1.0 + rxn_id: SA01 + type: ARRHENIUS +- coefficients: + A: 1.9e-13 + B: 0.0 + C: 1300.0 + products: + HO2: 1.0 + reactants: + HO2: 1.0 + TOLRO2: 1.0 + rxn_id: SA02 + type: ARRHENIUS +- coefficients: + A: 2.7e-12 + B: 0.0 + C: 360.0 + products: + NO: 1.0 + reactants: + NO: 1.0 + XYLRO2: 1.0 + rxn_id: SA03 + type: ARRHENIUS +- coefficients: + A: 1.9e-13 + B: 0.0 + C: 1300.0 + products: + HO2: 1.0 + reactants: + HO2: 1.0 + XYLRO2: 1.0 + rxn_id: SA04 + type: ARRHENIUS +- coefficients: + A: 2.47e-12 + B: 0.0 + C: -206.0 + products: + BENZRO2: 0.764 + OH: 1.0 + reactants: + BENZENE: 1.0 + OH: 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/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.dat b/test/tchem/gas_emit.dat new file mode 100644 index 000000000..28b9485ed --- /dev/null +++ b/test/tchem/gas_emit.dat @@ -0,0 +1,6 @@ +# time (s) +# rate (s^{-1}) +# emissions (mol m^{-2} s^{-1}) +time 0 +rate 1 +CO 1e-8 diff --git a/test/tchem/gas_init.dat b/test/tchem/gas_init.dat new file mode 100644 index 000000000..333b64aca --- /dev/null +++ b/test/tchem/gas_init.dat @@ -0,0 +1,2 @@ +# species init mixing ratio (ppb) +CO 50.0 diff --git a/test/tchem/height.dat b/test/tchem/height.dat new file mode 100644 index 000000000..d4927c431 --- /dev/null +++ b/test/tchem/height.dat @@ -0,0 +1,4 @@ +# time (s) +# height (m) +time 0 +height 1000 diff --git a/test/tchem/pressure.dat b/test/tchem/pressure.dat new file mode 100644 index 000000000..07215617a --- /dev/null +++ b/test/tchem/pressure.dat @@ -0,0 +1,4 @@ +# time (s) +# pressure (Pa) +time 0 +pressure 1e5 diff --git a/test/tchem/run_part.spec b/test/tchem/run_part.spec new file mode 100644 index 000000000..e3494dbd7 --- /dev/null +++ b/test/tchem/run_part.spec @@ -0,0 +1,48 @@ +run_type particle # particle-resolved run +output_prefix out/tchem # prefix of output files +n_repeat 1 # number of Monte Carlo repeats +n_part 10000 # 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 86400 # total simulation time (s) +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_tchem yes +tchem_config chem.yaml + +gas_init gas_init.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.dat # temperature profile file +pressure_profile pressure.dat # pressure profile file +height_profile height.dat # height profile file +gas_emissions gas_emit.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 0.999 # 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/temp.dat b/test/tchem/temp.dat new file mode 100644 index 000000000..491945f6e --- /dev/null +++ b/test/tchem/temp.dat @@ -0,0 +1,4 @@ +# time (s) +# temp (K) +time 0 +temp 288 diff --git a/test/tchem/test_tchem_1.sh b/test/tchem/test_tchem_1.sh new file mode 100755 index 000000000..25e7edcaa --- /dev/null +++ b/test/tchem/test_tchem_1.sh @@ -0,0 +1,12 @@ +#!/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.spec