| 7 | | |
| 8 | | 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. |
| 9 | | |
| 10 | | All parts of code that are related to chemistry start with `chem_`. |
| 11 | | 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`. |
| 12 | | |
| 13 | | 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. |
| 14 | | |
| 15 | | The chemical preprocessor is located in the subdirectory `UTIL/chemistry/gasphase_preproc`. |
| 16 | | |
| 17 | | Currently PALM-4U includes the following sample of chemistry mechanisms:\\ |
| 18 | | * cbm4: Carbon Bond Mechanism (Gery et al. (1989), 32 compounds, 81 reactions)\\ |
| 19 | | * smog: Photochemical smog mechanism (13 compounds, 12 reactions)\\ |
| 20 | | * simple: Simplified version of SMOG (9 compounds, 7 reactions)\\ |
| 21 | | * simplep: 'simple' plus one tracer named PM10 (10 compounds, 7 real reactions plus one dummy 'reaction')\\ |
| 22 | | * phstat: Photo-stationary state (3 compounds, 2 reactions)\\ |
| 23 | | * phstatp: Photo-stationary state plus one passive tracer named PM10 (4 compounds, 2 real reactions plus one dummy 'reaction')\\ |
| 24 | | |
| 25 | | Additional 'mechanisms' are available that describe the transport of one or two passive tracers, i.e. no chemical reactions are necessary:\\ |
| 26 | | * passive1: Passive tracers (1 compound, 0 reactions)\\ |
| 27 | | * passive: Passive tracers (2 compounds, 0 reactions)\\ |
| 28 | | This list will be extended further in the future. |
| 29 | | |
| 30 | | The standard mechanism which is in the SOURCE directory is 'phstatp'. |
| 31 | | |
| 32 | | 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. |
| 33 | | |
| 34 | | 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. |
| 35 | | |
| 36 | | 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`. |
| 37 | | |
| 38 | | 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`. |
| 39 | | |
| 40 | | 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. |
| 41 | | |
| 42 | | |
| 43 | | 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). |
| 44 | | |
| 45 | | A main factor influencing atmospheric chemistry are the emissions of reactive compounds. In PALM-4U emissions can be applied in three different ways:\\ |
| 46 | | * 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`.\\ |
| 47 | | * 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.\\ |
| 48 | | * PRE-PROCESSED: Preprocessed hourly (other temporal intervals will be possible in later versions) 3-d emission fields must be supplied by the user. |
| 49 | | |
| 50 | | 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. |
| 51 | | |
| 52 | | 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. |
| 53 | | |
| 54 | | Find a more detailed description of the PALM-4U emission input in the corresponding attached document [wiki:chempar#no1 here]. |
| 55 | | |
| 56 | | The chemistry model is automatically activated when a {{{chemistry_parameters}}} namelist is included in the parameter file ({{{<run_identifier>_p3d}}}). |
| 57 | | |
| 58 | | |
| 59 | | |
| 60 | | |
| 61 | | |
| 62 | | \\\\ |
| 548 | | |
| 549 | | |
| 550 | | \\ |
| 551 | | |
| 552 | | == [=#output Output steering in `runtime_parameters`] == |
| 553 | | |
| 554 | | 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`]. |
| 555 | | |
| 556 | | Names of chemistry variables must be preceded by {{{kc_'}}}. |
| 557 | | |
| 558 | | Example: |
| 559 | | {{{ |
| 560 | | data_output = 'w', 'w_av', |
| 561 | | 'q', 'q_av', |
| 562 | | 'kc_PM10', 'kc_NO2', 'kc_NO', 'kc_O3', 'kc_PM10_av', 'kc_NO2_av', |
| 563 | | }}} |
| 564 | | |
| 565 | | Possible output includes 2d cross section and/or 3d volume data (instantaneous and averaged) as well as instantaneous and averaged profiles. |
| 566 | | |
| 567 | | |
| 568 | | ''Note that time series output is not available yet!'' |
| 569 | | |
| 570 | | |
| 571 | | \\ |
| 572 | | |
| 573 | | == [=#init Initialisation steering in `initialization_parameters`] == |
| 574 | | |
| 575 | | 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. |
| 576 | | |
| 577 | | Example:\\ |
| 578 | | {{{initializing_actions = 'inifor set_constant_profiles', }}} |
| 579 | | |
| 580 | | \\ |
| 581 | | |
| 582 | | == [=#testsetups Example setups] == |
| 583 | | |
| 584 | | 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'. |
| 585 | | |
| 586 | | 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). |
| 587 | | |
| 588 | | 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: |
| 589 | | two passive compounds ('passive')\\ |
| 590 | | the 'smog' mechanism\\ |
| 591 | | |
| 592 | | 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}}}). |
| 593 | | |
| 594 | | 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. |
| 595 | | |
| 596 | | \\ |
| 597 | | |
| 598 | | == References == |
| 599 | | |
| 600 | | 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.\\ |
| 601 | | |
| 602 | | Gery, M. W., Whitten, G. Z., Killus, J. P., Dodge, M. C. (1989): A photochemical kinetics mechanism for urban and regional |
| 603 | | scale computer modeling, J. Geophys. Res., 94, 12925–12956, https://doi.org/10.1029/JD094iD10p12925.\\ |
| 604 | | |
| 605 | | 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.\\ |
| 606 | | |
| 607 | | 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.\\ |
| 608 | | |
| 609 | | 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.\\ |
| 610 | | |
| 611 | | 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.\\ |
| 612 | | |
| 613 | | 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.\\ |
| 614 | | |
| 615 | | 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. \\ |
