diff --git a/Dockerfile.tchem b/Dockerfile.tchem index b34de0eb8..0bb7453d5 100644 --- a/Dockerfile.tchem +++ b/Dockerfile.tchem @@ -28,6 +28,7 @@ RUN apt-get update \ RUN git clone https://github.com/PCLAeroParams/TChem-atm.git /tchem_dir/ WORKDIR /tchem_dir/ +RUN git checkout -b add_aerosol_driver origin/add_aerosol_driver RUN git submodule update --init --recursive RUN cmake -S /tchem_dir/external/Tines/ext/kokkos -B /build/kokkos_build \ diff --git a/src/run_part.F90 b/src/run_part.F90 index 2c380e713..d36376406 100644 --- a/src/run_part.F90 +++ b/src/run_part.F90 @@ -593,18 +593,12 @@ subroutine spec_file_read_run_part(file, run_part_opt, aero_data, & call spec_file_read_gas_state(sub_file, gas_data, gas_state_init) call spec_file_close(sub_file) - if (.not. run_part_opt%do_camp_chem) 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) - ! FIXME: Temporary to run PartMC. Replace with initialization from TChem - else if (run_part_opt%do_tchem) then + if (.not. (run_part_opt%do_camp_chem .or. 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 + else if (run_part_opt%do_camp_chem) then #ifdef PMC_USE_CAMP call aero_data_initialize(aero_data, camp_core) call aero_state_initialize(aero_state, aero_data, camp_core) diff --git a/src/tchem_interface.F90 b/src/tchem_interface.F90 index 136f75856..945f375d3 100644 --- a/src/tchem_interface.F90 +++ b/src/tchem_interface.F90 @@ -35,6 +35,29 @@ function TChem_getNumberOfSpecies() bind(c, name="TChem_getNumberOfSpecies") use iso_c_binding integer(kind=c_int) :: TChem_getNumberOfSpecies end function + function TChem_getNumberOfAeroSpecies() bind(c, & + name="TChem_getNumberOfAeroSpecies") + use iso_c_binding + integer(kind=c_int) :: TChem_getNumberOfAeroSpecies + end function + function TChem_getAerosolSpeciesDensity(i_spec) bind(c, & + name="TChem_getAerosolSpeciesDensity") + use iso_c_binding + integer(kind=c_int) :: i_spec + real(kind=c_double) :: TChem_getAerosolSpeciesDensity + end function + function TChem_getAerosolSpeciesMW(i_spec) bind(c, & + name="TChem_getAerosolSpeciesMW") + use iso_c_binding + integer(kind=c_int) :: i_spec + real(kind=c_double) :: TChem_getAerosolSpeciesMW + end function + function TChem_getAerosolSpeciesKappa(i_spec) bind(c, & + name="TChem_getAerosolSpeciesKappa") + use iso_c_binding + integer(kind=c_int) :: i_spec + real(kind=c_double) :: TChem_getAerosolSpeciesKappa + end function function TChem_getLengthOfStateVector() bind(c, & name="TChem_getLengthOfStateVector") use iso_c_binding @@ -52,6 +75,17 @@ subroutine TChem_setStateVector(array, i_batch) bind(c, & real(kind=c_double) :: array(*) integer(c_int), value :: i_batch end subroutine + function TChem_getNumberConcentrationVectorSize() bind(c, & + name="TChem_getNumberConcentrationVectorSize") + use iso_c_binding + integer(kind=c_int) :: TChem_getNumberConcentrationVectorSize + end function + subroutine TChem_setNumberConcentrationVector(array, i_batch) bind(c, & + name="TChem_setNumberConcentrationVector") + 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 @@ -59,6 +93,13 @@ integer(kind=c_size_t) function TChem_getSpeciesName(index, result, & character(kind=c_char), intent(out) :: result(*) integer(kind=c_size_t), intent(in), value :: buffer_size end function + integer(kind=c_size_t) function TChem_getAerosolSpeciesName(index, result, & + buffer_size) bind(C, name="TChem_getAerosolSpeciesName") + 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 @@ -115,8 +156,7 @@ subroutine pmc_tchem_initialize(gas_config_filename, aero_config_filename, & !> Number of cells to solve. integer, intent(in) :: n_grid_cells - integer(kind=c_int) :: nSpec, nAeroSpec - integer :: n_species + integer(kind=c_int) :: n_aero_spec, n_gas_spec integer :: i real(kind=c_double), dimension(:), allocatable :: array character(:), allocatable :: val @@ -127,33 +167,38 @@ subroutine pmc_tchem_initialize(gas_config_filename, aero_config_filename, & n_grid_cells) ! Get size that gas_data should be - nSpec = TChem_getNumberOfSpecies() - call ensure_string_array_size(gas_data%name, nSpec) + n_gas_spec = TChem_getNumberOfSpecies() + call ensure_string_array_size(gas_data%name, n_gas_spec) ! Populate gas_data with gas species from TChem - do i = 1,nSpec - val = TChem_species_name(i-1) + do i = 1,n_gas_spec + val = TChem_species_name(i-1, .true.) 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))) + allocate(gas_data%mosaic_index(n_gas_spec)) 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 + n_aero_spec = TChem_getNumberOfAeroSpecies() + call ensure_string_array_size(aero_data%name, n_aero_spec) + call ensure_integer_array_size(aero_data%mosaic_index, n_aero_spec) + call ensure_real_array_size(aero_data%wavelengths, n_swbands) + call ensure_real_array_size(aero_data%density, n_aero_spec) + call ensure_integer_array_size(aero_data%num_ions, n_aero_spec) + call ensure_real_array_size(aero_data%molec_weight, n_aero_spec) + call ensure_real_array_size(aero_data%kappa, n_aero_spec) + do i = 1,n_aero_spec + val = TChem_species_name(i-1, .false.) + aero_data%name(i) = trim(val) + aero_data%density(i) = TChem_getAerosolSpeciesDensity(i-1) + aero_data%molec_weight(i) = TChem_getAerosolSpeciesMW(i-1) + aero_data%kappa(i) = TChem_getAerosolSpeciesKappa(i-1) + end do end subroutine pmc_tchem_initialize @@ -184,22 +229,28 @@ subroutine tchem_to_partmc(aero_data, aero_state, gas_data, gas_state, & type(env_state_t), intent(in) :: env_state integer(c_int) :: nSpec, stateVecDim - integer :: i_part + integer :: i_part, i_spec real(kind=c_double), dimension(:), allocatable :: stateVector + integer :: n_gas_spec, n_aero_spec + + n_gas_spec = gas_data_n_spec(gas_data) + n_aero_spec = aero_data_n_spec(aero_data) ! 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 + gas_state%mix_rat = stateVector(4:n_gas_spec+3) * 1000.d0 - ! Map aerosols do i_part = 1,aero_state_n_part(aero_state) - + do i_spec = 1,n_aero_spec + aero_state%apa%particle(i_part)%vol(i_spec) = stateVector( & + n_gas_spec + 3 + i_spec + (i_part -1) * n_aero_spec) & + / aero_data%density(i_spec) + end do end do end subroutine tchem_to_partmc @@ -221,33 +272,58 @@ subroutine tchem_from_partmc(aero_data, aero_state, gas_data, gas_state, & !> Environment state. type(env_state_t), intent(in) :: env_state - real(kind=dp), allocatable :: stateVector(:) - integer :: stateVecDim + real(kind=dp), allocatable :: stateVector(:), number_concentration(:) + integer :: stateVecDim, tchem_n_part, i_spec integer :: i_part integer :: i_water + integer :: n_gas_spec, n_aero_spec + + n_gas_spec = gas_data_n_spec(gas_data) + n_aero_spec = aero_data_n_spec(aero_data) + ! Get size of stateVector stateVecDim = TChem_getLengthOfStateVector() allocate(stateVector(stateVecDim)) + + ! Get size of number concentration + tchem_n_part = TChem_getNumberConcentrationVectorSize() + allocate(number_concentration(tchem_n_part)) + ! 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 + stateVector(4:n_gas_spec + 3) = gas_state%mix_rat / 1000.d0 - ! TODO: Map aerosols do i_part = 1,aero_state_n_part(aero_state) + do i_spec = 1,n_aero_spec + stateVector(n_gas_spec + 3 + i_spec + (i_part - 1) * n_aero_spec) = & + aero_particle_species_mass(aero_state%apa%particle(i_part), & + i_spec, aero_data) + end do + number_concentration(i_part) = aero_state_particle_num_conc( & + aero_state, aero_state%apa%particle(i_part), aero_data) + end do + ! FIXME: What do we have to do here for this to work well? + do i_part = aero_state_n_part(aero_state)+1,tchem_n_part + do i_spec = 1,n_aero_spec + stateVector(n_gas_spec + 3 + i_spec + (i_part-1) * n_aero_spec) = & +1d-10 + end do + number_concentration(i_part) = 0.0d0 end do call TChem_setStateVector(stateVector, 0) + call TChem_setNumberConcentrationVector(number_concentration, 0) + end subroutine tchem_from_partmc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! @@ -286,19 +362,26 @@ end subroutine TChem_initialize !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !> Get species name from TChem for a given index. - function TChem_species_name(i_spec) result(species_name) + function TChem_species_name(i_spec, is_gas) result(species_name) use iso_c_binding - ! Species name. + !> Index of species. + integer(kind=c_int), intent(in) :: i_spec + !> Logical for if the species is a gas + logical :: is_gas + !> 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) + if (is_gas) then + N = TChem_getSpeciesName(i_spec, cbuf, N) + else + N = TChem_getAerosolSpeciesName(i_spec, cbuf, N) + end if allocate(character(N) :: species_name) species_name = cbuf(:N) diff --git a/test/tchem/aero_init_comp.dat b/test/tchem/aero_init_comp.dat index ef33bcba8..89ed752c6 100644 --- a/test/tchem/aero_init_comp.dat +++ b/test/tchem/aero_init_comp.dat @@ -1,2 +1,2 @@ # mass fractions -SI 1 +POA 1 diff --git a/test/tchem/config_aero_cb05cl_ae5_with_SIMPOL.yaml b/test/tchem/config_aero_cb05cl_ae5_with_SIMPOL.yaml new file mode 100644 index 000000000..81f9c3612 --- /dev/null +++ b/test/tchem/config_aero_cb05cl_ae5_with_SIMPOL.yaml @@ -0,0 +1,147 @@ +NCAR-version: +- absolute integration tolerance: 0.001 + description: gas-phase product from isoprene oxidation by OH + molecular weight [kg mol-1]: 0.08806 + diffusion coeff [m2 s-1]: 9.5e-06 + name: ISOP-P1 + notes: + - using diffusion coefficient from dry deposition + - see notes on ISOP-P1_aero species + type: CHEM_SPEC +- absolute integration tolerance: 0.001 + description: gas-phase product from isoprene oxidation by O3 + molecular weight [kg mol-1]: 0.09003 + name: ISOP-P2 + diffusion coeff [m2 s-1]: 9.5e-06 + notes: + - using diffusion coefficient from dry deposition + - see notes on ISOP-P2_aero species + type: CHEM_SPEC +- absolute integration tolerance: 0.001 + description: gas-phase product from monoterpene oxidation by OH + molecular weight [kg mol-1]: 0.17025 + diffusion coeff [m2 s-1]: 9.5e-06 + name: TERP-P1 + notes: + - using diffusion coefficient from dry deposition + - see notes on TERP-P1_aero species + type: CHEM_SPEC +- absolute integration tolerance: 0.001 + description: gas-phase product from monoterpene oxidation by O3 + molecular weight [kg mol-1]: 0.202162 + diffusion coeff [m2 s-1]: 9.5e-06 + name: TERP-P2 + diffusion coeff [m2 s-1]: 9.5e-06 + notes: + - using diffusion coefficient from dry deposition + - see notes on TERP-P2_aero species + type: CHEM_SPEC +- absolute integration tolerance: 1.0e-05 + density [kg m-3]: 1800.0 + description: lumped hydrophobic particulate matter + kappa: 0.0 + molecular weight [kg mol-1]: 0.41475 + name: POA + note: Using C30H54 for molecular weight. TODO find best surrogate + num_ions: 0 + phase: AEROSOL + type: CHEM_SPEC +- absolute integration tolerance: 1.0e-05 + density [kg m-3]: 1800.0 + description: First isoprene SOA species in 2-product scheme + kappa: 0.1 + molecular weight [kg mol-1]: 0.08806 + name: ISOP-P1_aero + diffusion coeff [m2 s-1]: 9.5e-06 + note: + - Using ketopropanoic acid for molecular weight. TODO find best surrogate + - TODO update SIMPOL parameters based on MW of new surrogate + num_ions: 0 + phase: AEROSOL + type: CHEM_SPEC +- absolute integration tolerance: 1.0e-05 + density [kg m-3]: 1800.0 + description: Second isoprene SOA species in 2-product scheme + kappa: 0.1 + molecular weight [kg mol-1]: 0.09003 + name: ISOP-P2_aero + diffusion coeff [m2 s-1]: 9.5e-06 + note: + - Using oxalic acid for molecular weight. TODO find best surrogate + - TODO update SIMPOL parameters based on MW of new surrogate + num_ions: 0 + phase: AEROSOL + type: CHEM_SPEC +- absolute integration tolerance: 1.0e-05 + density [kg m-3]: 1800.0 + description: First monoterpene SOA species in 2-product scheme + kappa: 0.1 + diffusion coeff [m2 s-1]: 9.5e-06 + molecular weight [kg mol-1]: 0.17025 + name: TERP-P1_aero + note: + - Using 2-hydroxy-3-isopropyl-6-methyl-cyclohexanone for molecular weight + - TODO find best surrogate + - TODO update SIMPOL parameters based on MW of new surrogate + num_ions: 0 + phase: AEROSOL + type: CHEM_SPEC +- absolute integration tolerance: 1.0e-05 + density [kg m-3]: 1800.0 + description: Second monoterpene SOA species in 2-product scheme + diffusion coeff [m2 s-1]: 9.5e-06 + kappa: 0.1 + molecular weight [kg mol-1]: 0.202162 + name: TERP-P2_aero + note: + - Using 2-methyl-5-carboxy-2,4-hexodienoic acid. TODO find best surrogate + - TODO update SIMPOL parameters based on MW of new surrogate + num_ions: 0 + phase: AEROSOL + type: CHEM_SPEC +- maximum computational particles: 20 + name: my aero rep 2 + type: AERO_REP_SINGLE_PARTICLE +- name: MONARCH mod37 + reactions: + - B: [3810.0, -21.3, 0.0, 0.0] + aerosol phase: organic_matter + aerosol-phase species: ISOP-P1_aero + gas-phase species: ISOP-P1 + type: SIMPOL_PHASE_TRANSFER + - B: + - 3810.0 + - -20.9 + - 0.0 + - 0.0 + aerosol phase: organic_matter + aerosol-phase species: ISOP-P2_aero + gas-phase species: ISOP-P2 + type: SIMPOL_PHASE_TRANSFER + - B: + - 2190.0 + - -17.5 + - 0.0 + - 0.0 + aerosol phase: organic_matter + aerosol-phase species: TERP-P1_aero + gas-phase species: TERP-P1 + type: SIMPOL_PHASE_TRANSFER + - B: + - 2190.0 + - -15.3 + - 0.0 + - 0.0 + aerosol phase: organic_matter + aerosol-phase species: TERP-P2_aero + gas-phase species: TERP-P2 + type: SIMPOL_PHASE_TRANSFER + type: MECHANISM +notes: +- 2-product SOA scheme from MONARCH model. Based on Tsigaridis and Kanakidou (2007). +- Details in Spada et al. (2013) in prep for Geosci. Model Dev. +- Gas-phase rate constants taken from CB05 reactions with same reactants +- TODO the CB05 reactions should be updated/removed to avoid competition with SOA + scheme +- Clausius clapyron parameters (C* and -dH/R) converted to SIMPOL.1 paramaters + diff --git a/test/tchem/config_gas_cb05cl_ae5_with_SIMPOL.yaml b/test/tchem/config_gas_cb05cl_ae5_with_SIMPOL.yaml new file mode 100644 index 000000000..5e356522b --- /dev/null +++ b/test/tchem/config_gas_cb05cl_ae5_with_SIMPOL.yaml @@ -0,0 +1,2882 @@ +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: third body + name: M +- description: molecular oxygen + name: O2 +- description: N2 + name: N2 +- description: methane + name: CH4 +- description: molecular hydrogen + name: H2 +- description: water vapor + name: H2O +species: +- description: gas-phase product from isoprene oxidation by OH + name: ISOP-P1 +- description: gas-phase product from isoprene oxidation by O3 + name: ISOP-P2 +- description: gas-phase product from monoterpene oxidation by OH + name: TERP-P1 +- description: gas-phase product from monoterpene oxidation by O3 + name: TERP-P2 +- 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: +- type: ARRHENIUS + reactants: + OH: 1 + ISOP: 1 + products: + ISOP-P1: 0.192 + coefficients: + A: 2.54e-11 + C: 407.6 +- type: ARRHENIUS + reactants: + O3: 1 + ISOP: 1 + products: + ISOP-P2: 0.215 + coefficients: + A: 7.86e-15 + C: -1912.0 +- type: ARRHENIUS + reactants: + OH: 1 + TERP: 1 + products: + TERP-P1: 0.0288 + coefficients: + A: 1.5e-11 + C: 449.0 +- type: ARRHENIUS + reactants: + O3: 1 + TERP: 1 + products: + TERP-P2: 0.232 + coefficients: + A: 1.2e-15 + C: -821.0 +- 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: 1 + type: ARRHENIUS + coefficients: + A: 1e-20 + B: 0.0 + C: -0.0 +- MUSICA_name: R28 + reactants: + NO2: 1 + OH: 1 + products: + HNO3: 1 + type: TROE + coefficients: + k0_A: 2e-30 + k0_B: -3.0 + k0_C: -0.0 + kinf_A: 2.5e-11 + kinf_B: 0.0 + kinf_C: -0.0 + Fc: 0.6 + N: 1.0 +- MUSICA_name: R30 + reactants: + HO2: 1 + NO: 1 + products: + OH: 1 + NO2: 1 + type: ARRHENIUS + coefficients: + A: 3.5e-12 + B: 0.0 + C: 250.0 +- MUSICA_name: R31 + reactants: + HO2: 1 + NO2: 1 + products: + PNA: 1 + type: TROE + coefficients: + 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 + Fc: 0.6 + N: 1.0 +- MUSICA_name: R32 + reactants: + PNA: 1 + products: + HO2: 1 + NO2: 1 + type: TROE + coefficients: + 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 + Fc: 0.6 + N: 1.0 +- MUSICA_name: R33 + reactants: + OH: 1 + PNA: 1 + products: + NO2: 1 + type: ARRHENIUS + coefficients: + A: 1.3e-12 + B: 0.0 + C: 380.0 +- MUSICA_name: R34 + reactants: + HO2: 2 + products: + H2O2: 1 + DUMMY: 1 + type: CMAQ_H2O2 + coefficients: + k1_A: 2.3e-13 + k1_C: 600.0 + k2_A: 1.7e-33 + k2_C: 1000.0 +- MUSICA_name: R35 + reactants: + HO2: 2 + H2O: 1 + products: + H2O2: 1 + type: CMAQ_H2O2 + coefficients: + k1_A: 3.22e-34 + k1_C: 2800.0 + k2_A: 2.38e-54 + k2_C: 3200.0 +- MUSICA_name: R36 + reactants: + H2O2: 1 + products: + OH: 2.0 + type: ARRHENIUS + coefficients: + A: 0.0001 + note: PHOTOLYSIS (A := photolysis rate) +- MUSICA_name: R37 + reactants: + OH: 1 + H2O2: 1 + products: + HO2: 1 + type: ARRHENIUS + coefficients: + A: 2.9e-12 + B: 0.0 + C: -160.0 +- MUSICA_name: R38 + reactants: + O1D: 1 + H2: 1 + products: + OH: 1 + HO2: 1 + type: ARRHENIUS + coefficients: + A: 1.1e-10 + B: 0.0 + C: -0.0 +- MUSICA_name: R39 + reactants: + OH: 1 + H2: 1 + products: + HO2: 1 + type: ARRHENIUS + coefficients: + A: 5.5e-12 + B: 0.0 + C: -2000.0 +- MUSICA_name: R40 + reactants: + OH: 1 + O: 1 + products: + HO2: 1 + type: ARRHENIUS + coefficients: + A: 2.2e-11 + B: 0.0 + C: 120.0 +- MUSICA_name: R41 + reactants: + OH: 2 + products: + O: 1 + type: ARRHENIUS + coefficients: + A: 4.2e-12 + B: 0.0 + C: -240.0 +- MUSICA_name: R42 + reactants: + OH: 2 + products: + H2O2: 1 + type: TROE + coefficients: + k0_A: 6.9e-31 + k0_B: -1.0 + k0_C: -0.0 + kinf_A: 2.6e-11 + kinf_B: 0.0 + kinf_C: -0.0 + Fc: 0.6 + N: 1.0 +- MUSICA_name: R43 + reactants: + OH: 1 + HO2: 1 + products: + DUMMY: 1 + type: ARRHENIUS + coefficients: + A: 4.8e-11 + B: 0.0 + C: 250.0 +- MUSICA_name: R44 + reactants: + HO2: 1 + O: 1 + products: + OH: 1 + type: ARRHENIUS + coefficients: + A: 3e-11 + B: 0.0 + C: 200.0 +- MUSICA_name: R45 + reactants: + H2O2: 1 + O: 1 + products: + OH: 1 + HO2: 1 + type: ARRHENIUS + coefficients: + A: 1.4e-12 + B: 0.0 + C: -2000.0 +- MUSICA_name: R46 + reactants: + NO3: 1 + O: 1 + products: + NO2: 1 + type: ARRHENIUS + coefficients: + A: 1e-11 + B: 0.0 + C: -0.0 +- MUSICA_name: R47 + reactants: + NO3: 1 + OH: 1 + products: + HO2: 1 + NO2: 1 + type: ARRHENIUS + coefficients: + A: 2.2e-11 + B: 0.0 + C: -0.0 +- MUSICA_name: R48 + reactants: + NO3: 1 + HO2: 1 + products: + HNO3: 1 + type: ARRHENIUS + coefficients: + A: 3.5e-12 + B: 0.0 + C: -0.0 +- MUSICA_name: R49 + reactants: + NO3: 1 + O3: 1 + products: + NO2: 1 + type: ARRHENIUS + coefficients: + A: 1e-17 + B: 0.0 + C: -0.0 +- MUSICA_name: R50 + reactants: + NO3: 2 + products: + NO2: 2.0 + type: ARRHENIUS + coefficients: + A: 8.5e-13 + B: 0.0 + C: -2450.0 +- MUSICA_name: R51 + reactants: + PNA: 1 + products: + HO2: 0.61 + NO2: 0.61 + OH: 0.39 + NO3: 0.39 + type: ARRHENIUS + coefficients: + A: 0.0001 + note: PHOTOLYSIS (A := photolysis rate) +- MUSICA_name: R52 + reactants: + HNO3: 1 + products: + OH: 1 + NO2: 1 + type: ARRHENIUS + coefficients: + A: 0.0001 + note: PHOTOLYSIS (A := photolysis rate) +- MUSICA_name: R53 + reactants: + N2O5: 1 + products: + NO2: 1 + NO3: 1 + type: ARRHENIUS + coefficients: + A: 0.0001 + note: PHOTOLYSIS (A := photolysis rate) +- MUSICA_name: R54 + reactants: + XO2: 1 + NO: 1 + products: + NO2: 1 + type: ARRHENIUS + coefficients: + A: 2.6e-12 + B: 0.0 + C: 365.0 +- MUSICA_name: R55 + reactants: + XO2N: 1 + NO: 1 + products: + NTR: 1 + type: ARRHENIUS + coefficients: + A: 2.6e-12 + B: 0.0 + C: 365.0 +- MUSICA_name: R56 + reactants: + XO2: 1 + HO2: 1 + products: + ROOH: 1 + type: ARRHENIUS + coefficients: + A: 7.5e-13 + B: 0.0 + C: 700.0 +- MUSICA_name: R57 + reactants: + XO2N: 1 + HO2: 1 + products: + ROOH: 1 + type: ARRHENIUS + coefficients: + A: 7.5e-13 + B: 0.0 + C: 700.0 +- MUSICA_name: R58 + reactants: + XO2: 2 + products: + DUMMY: 1 + type: ARRHENIUS + coefficients: + A: 6.8e-14 + B: 0.0 + C: -0.0 +- MUSICA_name: R59 + reactants: + XO2N: 2 + products: + DUMMY: 1 + type: ARRHENIUS + coefficients: + A: 6.8e-14 + B: 0.0 + C: -0.0 +- MUSICA_name: R60 + reactants: + XO2: 1 + XO2N: 1 + products: + DUMMY: 1 + type: ARRHENIUS + coefficients: + A: 6.8e-14 + B: 0.0 + C: -0.0 +- MUSICA_name: R61 + reactants: + NTR: 1 + OH: 1 + products: + HNO3: 1 + HO2: 1 + FORM: 0.33 + ALD2: 0.33 + ALDX: 0.33 + PAR: -0.66 + type: ARRHENIUS + coefficients: + A: 5.9e-13 + B: 0.0 + C: -360.0 +- MUSICA_name: R62 + reactants: + NTR: 1 + products: + NO2: 1 + HO2: 1 + FORM: 0.33 + ALD2: 0.33 + ALDX: 0.33 + PAR: -0.66 + type: ARRHENIUS + coefficients: + A: 0.0001 + note: PHOTOLYSIS (A := photolysis rate) +- MUSICA_name: R63 + reactants: + ROOH: 1 + OH: 1 + products: + XO2: 1 + ALD2: 0.5 + ALDX: 0.5 + type: ARRHENIUS + coefficients: + A: 3.01e-12 + B: 0.0 + C: 190.0 +- MUSICA_name: R64 + reactants: + ROOH: 1 + products: + OH: 1 + HO2: 1 + ALD2: 0.5 + ALDX: 0.5 + type: ARRHENIUS + coefficients: + A: 0.0001 + note: PHOTOLYSIS (A := photolysis rate) +- MUSICA_name: R65 + reactants: + OH: 1 + CO: 1 + products: + HO2: 1 + type: CMAQ_H2O2 + coefficients: + k1_A: 1.44e-13 + k1_C: 0.0 + k2_A: 3.43e-33 + k2_C: 0.0 +- MUSICA_name: R66 + reactants: + OH: 1 + CH4: 1 + products: + MEO2: 1 + type: ARRHENIUS + coefficients: + A: 2.45e-12 + B: 0.0 + C: -1775.0 +- MUSICA_name: R67 + reactants: + MEO2: 1 + NO: 1 + products: + FORM: 1 + HO2: 1 + NO2: 1 + type: ARRHENIUS + coefficients: + A: 2.8e-12 + B: 0.0 + C: 300.0 +- MUSICA_name: R68 + reactants: + MEO2: 1 + HO2: 1 + products: + MEPX: 1 + type: ARRHENIUS + coefficients: + A: 4.1e-13 + B: 0.0 + C: 750.0 +- MUSICA_name: R69 + reactants: + MEO2: 2 + products: + FORM: 1.37 + HO2: 0.74 + MEOH: 0.63 + type: ARRHENIUS + coefficients: + A: 9.5e-14 + B: 0.0 + C: 390.0 +- MUSICA_name: R70 + reactants: + MEPX: 1 + OH: 1 + products: + MEO2: 0.7 + XO2: 0.3 + HO2: 0.3 + type: ARRHENIUS + coefficients: + A: 3.8e-12 + B: 0.0 + C: 200.0 +- MUSICA_name: R71 + reactants: + 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+n_repeat 1 # number of Monte Carlo repeats +n_part 10 # 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_gas_cb05cl_ae5_with_SIMPOL.yaml +tchem_aero_config config_aero_cb05cl_ae5_with_SIMPOL.yaml +tchem_numerics_config solver_cb05cl_ae5_with_SIMPOL.yaml + +gas_init gas_init_cb05cl_ae5.dat # initial gas mixing ratios + +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/solver_cb05cl_ae5_with_SIMPOL.yaml b/test/tchem/solver_cb05cl_ae5_with_SIMPOL.yaml new file mode 100644 index 000000000..ea617709e --- /dev/null +++ b/test/tchem/solver_cb05cl_ae5_with_SIMPOL.yaml @@ -0,0 +1,9 @@ +solver_info: + atol_time: 1e-12 + rtol_time: 1e-3 + dtmin: 1e-20 + atol_newton: 1e-12 + rtol_newton: 1e-8 + max_newton_iterations: 20 + max_time_iterations: 200000 + jacobian_interval: 100 diff --git a/test/tchem/tchem_cb05cl_ae5_aero_time_saved.txt b/test/tchem/tchem_cb05cl_ae5_aero_time_saved.txt new file mode 100644 index 000000000..3250b331a --- /dev/null +++ b/test/tchem/tchem_cb05cl_ae5_aero_time_saved.txt @@ -0,0 +1,11 @@ +0.000000000000000000e+00 1.000000000000000000e+09 2.621796702599999904e-02 2.621796702599999904e-02 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 +6.000000000000000000e+01 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3.000000000000000000e+02 3.403125107369324165e-01 1.000000000000000000e+09 2.095000000000000000e+08 7.808000000000000000e+08 1.850000000000000000e+03 5.600000000000000000e+02 1.000000000000000000e+06 diff --git a/test/tchem/test_tchem_1.sh b/test/tchem/test_tchem_1.sh index ecdcb3c8c..a38af6f51 100755 --- a/test/tchem/test_tchem_1.sh +++ b/test/tchem/test_tchem_1.sh @@ -9,6 +9,6 @@ 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 +../../partmc run_part_cb05cl_ae5_with_SIMPOL.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/tchem/test_tchem_2.sh b/test/tchem/test_tchem_2.sh index 15c2dce2b..b6aaf2715 100755 --- a/test/tchem/test_tchem_2.sh +++ b/test/tchem/test_tchem_2.sh @@ -9,6 +9,5 @@ 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 +../../extract_aero_time out/tchem_cb05cl_ae5_0001 +../../numeric_diff --rel-tol 0.4 out/tchem_cb05cl_ae5_0001_aero_time.txt tchem_cb05cl_ae5_aero_time_saved.txt