Chemistry model (CHEM)

Main page of the chemistry model under construction. Click here for first information about capabilities and model steering.

Chemistry model parameters

Overview

Since Version 5.0 a chemistry model is available in PALM which computes chemical conversion and tranport of reactive trace gases. In addition, this module permits also the simulation of passive compounds in the gas phase and particulate matter. This documentation contains several sections:

INPUT

List of all namelist parameters that can be used to steer the MAS

The chemistry model is automatically activated when a chemistry_parameters namelist is included in the parameter file (<run_identifier>_p3d).

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Parameter list

NAMELIST group name: chemistry_parameters

Parameter Name	FORTRAN? Type?	Default Value	Explanation
bc_cs_b	C*20	'dirichlet'	Bottom boundary condition of the chemical species (cs) concentration. Allowed values are 'dirichlet' (cs(k=0) = const. = cs_surface + cs_surface_initial_change; When a constant surface concentration flux is used (surface_csflux) or emissions are applied (do_emis = .T.), bc_cs_b = 'neumann' must be used.
bc_cs_t	C*20	'initial_gradient'	Top boundary condition of the scalar concentration. Allowed are the values 'dirichlet' (cs(k=nz+1) does not change during the run), 'neumann' (cs(k=nz+1) = cs(k=nz)), and 'initial_gradient' . With the 'initial_gradient' boundary condition the value of the scalar concentration gradient at the top is calculated from the initial scalar concentration profile (see cs_surface, cs_vertical_gradient) by: bc_cs_t_val = (cs_init(k=nz) - ss_init(k=nz-1)) / dzu(nz). Using this value (assumed constant during the run) the concentration boundary values are calculated as cs(k=nz+1) = cs(k=nz) + bc_cs_t_val * dzu(nz+1) (up to k=nz the prognostic equation for the chemical species concentration is solved). When a constant cs flux is used at the top boundary (top_csflux), bc_cs_t = 'neumann' must be used, because otherwise the resolved scale may contribute to the top flux so that a constant value cannot be guaranteed.
call_chem_at_all_substeps	L	.FALSE.	Switch whether chemistry is called at each substep of the Runge-Kutta scheme or just at each full dynamical time step 'dt'. The latter will do since the chemistry solvers are using their own timestep steering.
chem_debug0	L	.FALSE.	Extra print output of chemistry variables.
chem_gasphase_on	L	.TRUE.	Switch for switching off the chemical reactions but still doing the transport for all chemical compounds. Useful for test purposes.
chem_mechanism	C*30	'phstatp'	Parameter for check of chemistry mechanism: The Setting in the namelist must match with the mechanism in the code, i.e. in chem_gasphase_mod.f90. chem_mechanism = 'phstatp' matches with the chemistry mechanism in chem_gasphase_mod.f90 that comes with PALM-4U when it is downloaded.
cs_heights	R(99,100)	9999999.9	Height levels above ground (in m) to go with cs_profile in order to define initial profiles of chemical species. The first index refers to the chemical compound, the second to height level. Example: cs_heights(1,:) = 0.0, 5.0, 15.0, 25.0, 35.0, 45.0, 55.0, 65.0, 75.0, 85.0, 95.0, (heights for profile of first chemical species) cs_heights(2,:) = 0.0, 5.0, 15.0, 25.0, 35.0, 45.0, 55.0, 65.0, 75.0, 85.0, 95.0, (heights for profile of second chemical species)
cs_name	C*11(99)	'novalue'	Names of chemical species where surface concentrations or concentration profiles (cs_profile) are prescribed. Example: cs_name = 'O3', 'NO', 'NO2', 'CO', 'RCHO', 'PM10', 'PM25', It is not necessary to specify cs_name (and cs_surface and cs_profile/cs_heights-pairs) for all compounds of the chosen chemical mechanism. Names of compounds which do not occur mechanism are ignored.
cs_profile	R(99,100)	9999999.9	Concentration values of chemical species (gases in ppm, particulate matter in kg m-3) at cs_heights. Example: cs_profile(1,:) = 0.020, 0.023, 0.026, 0.029, 0.032, 0.035, 0.038, 0.041, 0.044, 0.047, 0.050, (Values for initial profile of first species) cs_profile(2,:) = 0.080, 0.073, 0.064, 0.057, 0.050, 0.043, 0.036, 0.029, 0.022, 0.015, 0.007, (Values for initial profile of second species) The individual chemical species are identified using cs_name. These initial profiles become only effective when 'set_constant_profiles' is set for initializing_actions. 'set_constant_profiles' can be combined with 'inifor' if the file from inifor contails only meteorological variables and constant profiles are only set for chemistry.
cs_surface	R	0.0	Concentration value for chemical species at the surface (gases in ppm, particulate matter in kg m-3).
daytype_mdh	C*80		Type of weekday required for the MDH (MonthDayHour) case of the DEFAULT mode of the emissions module. Possible values are: workday, weekend, holiday
decycle_chem_lr	L	.FALSE.	Cyclic boundary conditions for chemistry may result in accumluation of chemical compounds. If decycle_chem_lr is set to true, initial concentration values are fixed at the left or right inflow boundary.
decycle_chem_ns	L	.FALSE.	Cyclic boundary conditions for chemistry may result in accumluation of chemical compounds. If decycle_chem_ns is set to true, initial concentration values are fixed at the southern or northern inflow boundary.
decycle_method	C*20(4)	'dirichlet'	Decycling method at horizontal boundaries (1=left, 2=right, 3=south, 4=north) 'dirichlet' = initial size distribution and chemical composition set for the ghost points and first three grid points 'neumann' = zero gradient
do_depo	L	.FALSE.	Switches the deposition calculation for particles and gases ON (.TRUE.) or OFF (.FALSE.)
do_emis	L	.FALSE.	Switches the chem_emission module ON (.TRUE.) or OFF (.FALSE.)
emiss_factor_main	R(99)	-9999.0	Constant emission scaling factor for MAIN street types, used in the PARAMETERIZED mode of chem_emission module. The number and the order of the values has to correspond to the names of the emission species provided for surface_csflux_name.
emiss_factor_side	R(99)	-9999.0	Constant emission scaling factor for SIDE (secondary) street types, used in the PARAMETERIZED mode of chem_emission module. The number and the order of the values has to correspond to the names of the emission species provided for surface_csflux_name.
icntrl	I(20)	0	Selection and steering of the chemistry solver. In order to offer more control over the integrator, the KPP-generated Integrator subroutine (e.g. SUBROUTINE rosenbrock in chem_gasphase_mod.f90) provides the optional input parameters ICNTRL_U and RCNTRL_U. Each of them is an array of 20 elements that allow the fine-tuning of the integrator, e.g. by setting a particular Integrator method, tolerances, minimum and maximum step sizes, etc. Note: For input parameters equal to zero the default values of the corresponding variables are used. ICNTRL(1) = 1: F = F(y) Independent of T (AUTONOMOUS), = 0: F = F(t,y) Depends on T (NON-AUTONOMOUS) ICNTRL(2) = 0: abstol, reltol are N-dimensional vectors, = 1: Abstol, Reltol are scalars ICNTRL(3) -> selection of a particular Rosenbrock method 0 : Rodas3 (Default from KPP) 1 : Ros2 (Simplest Rosenbrock solver, will also do) 2 : Ros3 3 : Ros4 4 : Rodas3 5 : Rodas4 ICNTRL(4) -> maximum number of integration steps; For ICNTRL(4) =0) the default value of 100000 is used Example: icntrl(3) = 1, ! ros2 (a bit less time consuming than the Rodas3 solver recommended by KPP) icntrl(4) = 500, ! berlin setup max. number of chem-substeps See ​http://people.cs.vt.edu/asandu/Software/Kpp/
main_street_id	I(99)	0	Index for identifying MAIN streets following street type classes from OpenStreetMap.
max_street_id	I(99)	0	Maximum index value for identifying ALL (MAIN and SIDE) streets following street type classes from OpenStreetMap.
mode_emis	C*80	'PARAMETERIZED'	Mode of chemistry emissions. Possible values are: 'DEFAULT' Input of yearly gridded emissions and MDH courses. 'PRE-PROCESSED' Input of fully preprocessed emissions at fixed time intervals (currently only hourly intervals) 'PARAMETERIZED' Parameterized traffic emissions based on street types supplied additionally in the _static? input file (e.g from OpenStreetMap). At the moment the values have to be in capital letters.
my_steps	I(50)	0	List of fixed timesteps: my_step(1) = 0.0 automatic stepping Is ignored in scalar mode. Only relvant for vector mode, i.e. the vectorized Rosenbrock solvers.
nest_chemistry	L	.TRUE.	Flag for nesting mode of chemical species, independent on parent or not.
photolysis_scheme	C*10	'simple'	Currently two somple photolysis Options are available: 'constant' and 'simple' 'constant' uses photolysis frequencies at a zenith angle of 45 degrees. 'simple' describes parameterized time-dependent photolysis frequencies as supplied with MCM (​http://mcm.leeds.ac.uk/MCM, Saunders et al. (2003)). As the solar zenith angle must be available for this scheme, at least the simple clear sky radiation scheme must be active.
rcntrl	R(20)	0.0 and see below	Steering of the chemistry solver. RCNTRL(1) -> Hmin, lower bound for the integration step size. It is strongly recommended to keep Hmin = ZERO RCNTRL(2) -> Hmax, upper bound for the integration step size RCNTRL(3) -> Hstart, starting value for the integration step size RCNTRL(4) -> Facmin (lower bound on step decrease factor, default=0.2) RCNTRL(5) -> Facmax (upper bound on step increase factor, default=6) RCNTRL(6) -> Facrej (step decrease factor after multiple rejections) RCNTRL(7) -> Facsafe (by which the new step is slightly smaller than the predicted value, default=0.9) See ​http://people.cs.vt.edu/asandu/Software/Kpp/ Example: rcntrl(3) = 0.1, ! hstart in sec. Setting of hstart can result in savoings of computstinal time of 30% and more.
side_street_id	I(99)	0	Index for identifying SIDE streets following street type classes from 'OpenStreetMap?'.
surface_csflux	R(99)	0.0	Values of surface fluxes of chemistry emissions to be used in the PARAMETERIZED mode. The number and the order of the values has to correspond to the names of the emission species provided to surface_csflux_name. Units of the input values differ between gases and PMs. In the first case, emissions must be provided in micromole/m2*s, while for PMs, input emission values have to be in kg/m2*s.
surface_csflux_name	C*11(99)	'novalue'	Names of chemical species which are emitted. Required only for mode_emis = 'PARAMETERIZED'. Example: surface_csflux_name = 'NO', 'NO2', 'CO', 'RCHO', 'PM10', 'PM25', It is not necessary to specify surface_csflux_name for all compounds of the chosen chemical mechanism. Names of compounds which do not occur in the mechanism are ignored.
time_fac_type	C*80	MDH	Type of time treatment for DEFAULT mode of the chem_emission module. Possible values are: HOUR or MDH