Changes between Version 1 and Version 2 of doc/tec/chem

Timestamp:

Jan 28, 2019 1:21:00 PM (6 years ago)

Author:

westbrink

Comment:

--

doc/tec/chem

@@ -2 +2 @@
 
 Main page of the chemistry model under construction. Click [wiki:doc/app/chempar here] for first information about capabilities and model steering.
+
+
+= Chemistry model parameters =
+[[TracNav(doc/app/partoc|nocollapse)]]
+
+== 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. 
+
+All parts of code that are related to chemistry start with `chem_`.
+The main routines and the driver of the chemistry module is included in [[source:palm/trunk/SOURCE/chemistry_model_mod.f90|chemistry_model_mod.f90]], subroutines are in `chem_gasphase_mod.f90`, `chem_photolysis_mod.f90`, and `chem_emissions.f90`.
+
+The module `chem_gasphase_mod.f90`, where the gas phase chemistry rate equations are solved within PALM-4U depends on the chosen chemical mechanism. `chem_gasphase_mod.f90` is generated by a preprocessor that is based on the Kinetic Pre-Processor KPP (Damian et al. (2002), Sandu et al. (2006)), Release 2.2.3 from November 2012 (http://people.cs.vt.edu/asandu/Software/Kpp/, kpp-2.2.3.tar.gz) and an adapted version of the KPP postprocessor KP4 (Jöckel et al (2010)). This adapted Version of KP4 which converts the KPP-generated code to a PALM-4U module is named kpp4palm.
+
+The chemical preprocessor is located in the subdirectory `UTIL/chemistry/gasphase_preproc`.
+
+Currently PALM-4U includes the following sample of chemistry mechanisms:\\
+  * cbm4: Carbon Bond Mechanism (Gery et al. (1989), 32 compounds, 81 reactions)\\
+  * smog: Photochemical smog mechanism (13 compounds, 12 reactions)\\
+  * simple: Simplified version of SMOG (9 compounds, 7 reactions)\\
+  * simplep: 'simple' plus one tracer named PM10 (10 compounds, 7 real reactions plus one dummy 'reaction')\\
+  * phstat: Photo-stationary state (3 compounds, 2 reactions)\\
+  * phstatp: Photo-stationary state plus one passive tracer named PM10 (4 compounds, 2 real reactions plus one dummy 'reaction')\\
+
+Additional 'mechanisms' are available that describe the transport of one or two passive tracers, i.e. no chemical reactions are necessary:\\
+  * passive1: Passive tracers (1 compound, 0 reactions)\\
+  * passive: Passive tracers (2 compounds, 0 reactions)\\
+This list will be extended further in the future. 
+
+The standard mechanism which is in the SOURCE directory is 'phstatp'.
+
+In order to select and apply a certain mechanism from this sample, please copy the respective ready-to-use `chem_gasephase_mod.f90` from `UTIL/chemistry/gasphase_preproc/mechanisms/def_MECH` (where `MECH` stands for any of the available mechanisms) into the USER_CODE directory of the respective simulation Setup, i.e. .../JOBS/<run_identifier>/USER_CODE/chem_gasphase_mod.f90.
+
+Alternatively, the chemistry preprocessor can be executed also for the available machanism in order to create `chem_gasphase_mod.f90` (although for the available mechanisms this is not necessary because the `chem_gasphase_mod.f90` files are already existing) instead of copying `chem_gasphase_mod.f90`: Enter the directory `UTIL/chemistry/gasphase_preproc` and apply the run script, i.e. {{{run_kpp4palm.ksh -m MECH}}}, where `MECH` stands for any of the mechanisms listed above. The resulting `chem_gasphase_mod.f90` will be copied by the script directly into the SOURCE directory. 
+
+In order to find out which reactions and compounds are included in the different mechanisms, please have a look into the files MECH.eqn and MECH.spc in `UTIL/chemistry/gasphase_preproc/mechanisms/def_MECH`.
+
+How to implement a new chemical mechanism or add further passive tracers see the [wiki:chempar#no1 Readme-File]. If more than two passive tracers or different names of the passive tracers are desired, a new 'mechanism' must be created as described in the Readme file. The Readme file is also available in the PALM-4U subdirectory `UTIL/chemistry/gasphase_preproc`. 
+
+Currently, areosol compounds can be considered either as passive compounds or the sectional aerosol module [wiki:salsa SALSA]   (Kokkola et al. (2008)) can be used to simulate the aerosol particle concentrations, and size distributions. 
+
+
+Deposition processes are also taken into account in the chemistry model. The deposition of particles is derived following Zhang et al. (2001) while gases are deposited using the DEPAC model following van Zanten et al. (2010).
+
+A main factor influencing atmospheric chemistry are the emissions of reactive compounds. In PALM-4U emissions can be applied in three different ways:\\
+  * PARAMETERIZED: Traffic emissions are parameterized depending on the the values of street_type in the static file. Emission values for each street type and chemical compound must be supplied in the namelist as described below. No other emissions are considered. street_type can be obtained from `OpenStreetMap`.\\
+  * DEFAULT: Gridded yearly emissions must be supplied by the user as specified in the PIDS document (see sample emissions file). Typical temporal variations are apllied by PALM4U.\\
+  * PRE-PROCESSED: Preprocessed hourly (other temporal intervals will be possible in later versions) 3-d emission fields must be supplied by the user.
+
+Importantly, for the DEFAULT and the PRE-PROCESSED mode of the emissions, the exact date of the start of the simulation must be indicated through the namelist parameter date_init of the date_and_time_mod module.    
+
+IMPORTANT: In the PRE-PROCESSED mode the initial date of the simulation has to coincide with the first day for which emission values are available.
+
+Find a more detailed description of the PALM-4U emission input in the corresponding attached document [wiki:chempar#no1 here].
+
+The chemistry model is automatically activated when a {{{chemistry_parameters}}} namelist is included in the parameter file ({{{<run_identifier>_p3d}}}). 
+
+
+
+
+
+\\\\
+== Parameter list ==
+'''NAMELIST group name: [=#chempar {{{chemistry_parameters}}}''']
+
+||='''Parameter Name'''  =||='''[[../fortrantypes|FORTRAN]]\\[[../fortrantypes|Type]]'''  =||='''Default\\Value'''  =||='''Explanation'''  =||
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#bc_cs_b '''bc_cs_b''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+C*20
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+'dirichlet'
+}}}
+{{{#!td
+Bottom boundary condition of the chemical species (`cs`) concentration.
+
+Allowed values are  'dirichlet'  (cs(k=0) = const. = [#cs_surface cs_surface] + cs_surface_initial_change; When a constant surface concentration flux is used ([#surface_csflux surface_csflux]) or emissions are applied ([#do_emis do_emis] = .T.), '''bc_cs_b''' =  'neumann'  must be used. 
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#bc_cs_t '''bc_cs_t''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+C*20
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+'initial_gradient'
+}}}
+{{{#!td
+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_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.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#call_chem_at_all_substeps '''call_chem_at_all_substeps''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+L
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+.FALSE.
+}}}
+{{{#!td
+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.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#chem_debug0 '''chem_debug0 ''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+L
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+.FALSE.
+}}}
+{{{#!td
+Extra print output of chemistry variables. 
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#chem_gasphase_on '''chem_gasphase_on''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+L
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+.TRUE.
+}}}
+{{{#!td
+Switch for switching off the chemical reactions but still doing the transport for all chemical compounds. Useful for test purposes.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#chem_mechanism '''chem_mechanism''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+C*30
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+'phstatp'
+}}}
+{{{#!td
+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.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#cs_heights '''cs_heights''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+R(99,100)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+9999999.9
+}}}
+{{{#!td
+Height levels above ground (in m) to go with [#cs_profile 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)\\
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#cs_name '''cs_name''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+C*11(99)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+'novalue'
+}}}
+{{{#!td
+Names of chemical species where surface concentrations or concentration profiles ([#cs_profile 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 cs_surface] and [#cs_profile cs_profile]/[#cs_heights cs_heights]-pairs) for all compounds of the chosen chemical mechanism.
+Names of compounds which do not occur mechanism are ignored.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#cs_profile '''cs_profile''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+R(99,100)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+9999999.9
+}}}
+{{{#!td
+Concentration values of chemical species (gases in ppm, particulate matter in kg m^-3^) at [#cs_heights 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 cs_name]. These initial profiles become only effective when {{{'set_constant_profiles'}}} is set for [#init 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.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#cs_surface '''cs_surface''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+R
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+0.0
+}}}
+{{{#!td
+Concentration value for chemical species at the surface (gases in ppm, particulate matter in kg m^-3^).
+
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#daytype_mdh '''daytype_mdh''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+C*80
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+}}}
+{{{#!td
+Type of weekday required for the MDH (!MonthDayHour) case of the DEFAULT mode of the emissions module.
+Possible values are: workday, weekend, holiday
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#decycle_chem_lr '''decycle_chem_lr''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+L
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+.FALSE.
+}}}
+{{{#!td
+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.
+
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#decycle_chem_ns '''decycle_chem_ns''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+L
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+.FALSE.
+}}}
+{{{#!td
+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.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#decycle_method '''decycle_method''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+C*20(4)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+'dirichlet'
+}}}
+{{{#!td
+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
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#do_depo '''do_depo''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+L
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+.FALSE.
+}}}
+{{{#!td
+Switches the deposition calculation for particles and gases ON (.TRUE.) or OFF (.FALSE.)
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#do_emis '''do_emis''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+L
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+.FALSE.
+}}}
+{{{#!td
+Switches the chem_emission module ON (.TRUE.) or OFF (.FALSE.)
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#emiss_factor_main '''emiss_factor_main''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+R(99)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+-9999.0
+}}}
+{{{#!td
+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 surface_csflux_name].
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#emiss_factor_side '''emiss_factor_side''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+R(99)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+-9999.0
+}}}
+{{{#!td
+Constant emission scaling factor for SIDE (secondary) street types, used in the PARAMETERIZED [#mode_emis 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 surface_csflux_name].
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#icntrl '''icntrl''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+I(20)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+0
+}}}
+{{{#!td
+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/
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#main_street_id '''main_street_id''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+I(99)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+0
+}}}
+{{{#!td
+Index for identifying MAIN streets following street type classes from `OpenStreetMap`.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#max_street_id '''max_street_id''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+I(99)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+0
+}}}
+{{{#!td
+Maximum index value for identifying ALL (MAIN and SIDE) streets following street type classes from `OpenStreetMap`.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#mode_emis '''mode_emis''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+C*80
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+'PARAMETERIZED'
+}}}
+{{{#!td
+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 [wiki:iofiles/pids#static_input _static] input file (e.g from `OpenStreetMap`).
+At the moment the values have to be in capital letters.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#my_steps '''my_steps''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+I(50)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+0
+}}}
+{{{#!td
+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. 
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#nest_chemistry '''nest_chemistry''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+L
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+.TRUE.
+}}}
+{{{#!td
+Flag for nesting mode of chemical species, independent on parent or not.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#photolysis_scheme '''photolysis_scheme''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+C*10
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+'simple'
+}}}
+{{{#!td
+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 [#../radpar simple clear sky] radiation scheme must be active.
+
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#rcntrl '''rcntrl''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+R(20)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+0.0 and see below
+}}}
+{{{#!td
+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.
+
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#side_street_id '''side_street_id''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+I(99)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+0
+}}}
+{{{#!td
+Index for identifying SIDE streets following street type classes from 'OpenStreetMap'.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#surface_csflux '''surface_csflux''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+R(99)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+0.0
+}}}
+{{{#!td
+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/m^2^*s,
+while for PMs, input emission values have to be in kg/m^2^*s.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#surface_csflux_name '''surface_csflux_name''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+C*11(99)
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+'novalue'
+
+}}}
+{{{#!td
+Names of chemical species which are emitted. Required only for  [#mode_emis 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.
+}}}
+|----------------
+{{{#!td style="vertical-align:top; width: 150px"
+[=#time_fac_type '''time_fac_type''']
+}}}
+{{{#!td style="vertical-align:top; width: 50px"
+C*80
+}}}
+{{{#!td style="vertical-align:top; width: 75px"
+MDH
+}}}
+{{{#!td
+Type of time treatment for DEFAULT mode of the chem_emission module.
+Possible values are: HOUR or MDH
+}}}
+
+|----------------
+
+
+\\
+
+== [=#output Output steering in `runtime_parameters`] ==
+
+Output of chemistry variables follows the usual output steering as described in [https://palm.muk.uni-hannover.de/trac/wiki/doc/app/d3par#output `Data Output`]. 
+
+Names of chemistry variables must be preceded by {{{kc_'}}}.
+
+Example:
+{{{
+    data_output = 'w',  'w_av',
+                  'q',  'q_av',
+                  'kc_PM10', 'kc_NO2', 'kc_NO', 'kc_O3', 'kc_PM10_av', 'kc_NO2_av',
+}}}
+
+Possible output includes 2d cross section and/or 3d volume data (instantaneous and averaged) as well as instantaneous and averaged profiles. 
+
+
+''Note that time series output is not available yet!''
+
+
+\\
+
+== [=#init Initialisation steering in `initialization_parameters`] ==
+
+If large-scale forcings from INIFOR are used only for meteorology, then user defined initial concentration and initial vertical [#cs_profiles profiles] can be activated by combining {{{set_constant_profiles}}} with {{{inifor}}} separated by a space only in the [wiki:inipar#initializing_actions initializing_parameters] namelist. 
+
+Example:\\
+ {{{initializing_actions = 'inifor set_constant_profiles', }}}
+
+\\
+
+== [=#testsetups Example setups] ==
+
+The PALM-4U subdirectory TESTS/cases contains some sample setups for different application types. An setup for a very small urban area with the 'phstatp' mechanism can be found in 'urban_environment' and 'urban_environment_restart'.
+
+An example setup with two passive tracers for the small test_urban model domain is attached to this page (Attachment test_urban_chem_passive.tar).  
+
+Further setups are attached for a 1km x 1km model domain with 10 m grid width, which is centered around the Ernst-Reuter-Platz in Berlin . For this domain, example input files are supplied for two chemistry settings:
+ two passive compounds ('passive')\\ 
+ the 'smog' mechanism\\
+
+Please note that PALM-4U comes by default with the code for the photostationay equilibrium between NO, NO2 and O3 plus one passive tracer, i.e. {{{chem_gashase_mod.f90}}} is prepared for 'phstatp'. In order to run PALM-4U e.g. with the 'smog' mechanism, copy the {{{chem_gashase_mod.f90}}}, which is supplied in {{{UTIL/chemistry/gasphase_preproc/mechanisms/def_smog}}} into {{{SOURCE}}} (or execute {{{run_kpp4palm.ksh -m smog}}}). 
+
+So far, all example setups are supplied for 'PARAMETERIZED' emissions. Example emissions files for 'PREPROCESSED' and 'DEFAULT' emissions will be supplied here at a later time. 
+
+\\
+
+== References ==
+
+Damian, V. et al (2002): The kinetic preprocessor KPP—A software environment for solving chemical kinetics, Computers & Chemical Engineering, 26, 1567-1579, https://doi.org/10.1016/S0098-1354(02)00128-X.\\
+
+Gery,  M.  W.,  Whitten,  G.  Z.,  Killus,  J.  P., Dodge,  M.  C. (1989): A  photochemical  kinetics  mechanism  for  urban  and  regional
+scale computer modeling, J. Geophys. Res., 94, 12925–12956, https://doi.org/10.1029/JD094iD10p12925.\\
+
+Jöckel, P. et al (2010): Development cycle 2 of the Modular Earth Submodel System (MESSy2) , Geoscientific Model Development, 3, 717-752, https://doi.org/10.5194/gmd-3-717-2010.\\
+
+Kokkola, H., Korhonen, H., Lehtinen, K. E. J., Makkonen, R., Asmi, A., Järvenoja, S., Anttila, T., Partanen, A.-I., Kulmala, M., Järvinen, H., Laaksonen, A., and Kerminen, V.-M. (2008): SALSA - a Sectional Aerosol module for Large Scale Applications, Atmospheric Chemistry and Physics, 8, 2469–2483, ​https://doi.org/10.5194/acp-8-2469-2008.\\
+
+Sandu, A. and Sander, R. E. (2006): Technical Note: Simulating chemical systems in Fortran90 and Matlab with the Kinetic !PreProcessor KPP-2.1, Atmospheric Chemistry and Physics, 6, 187-195, https://doi.org/10.5194/acp-6-187-2006.\\
+
+Saunders, S. M., Jenkin, M. E., Derwent, R. G., Pilling, M. J. (2003): Protocol for the development of the Master Chemical Mechanism, MCM v3 (Part A): tropospheric degradation of non-aromatic volatile organic compounds , Atmospheric Chemistry and Physics, 3, 161-180, https://doi.org/10.5194/acp-3-161-2003.\\
+
+Van Zanten, M. C. et al (2010): Description of the DEPAC module. Dry deposition modelling with DEPAC_GCN2010, RIVM report 680180001/2010, Bilthoven, The Netherlands, 74 pp.\\
+
+Zhang, L., Gong, S., Padro, J., and Barrie, L. (2001): A size-segregated particle dry deposition scheme for an atmospheric aerosol module, Atmospheric Environment, 35, 549–560, ​https://doi.org/10.1016/S1352-2310(00)00326-5. \\