== Overview ==
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[[NoteBox(note,This page is part of the ** Chemistry Model** (CHEM) documentation. \\ It contains a listing of the chemistry mechanisms included in PALM. \\ For an overview of all CHEM-related pages\, see the **[wiki:doc/tec/chem CHEM main page]**.)]]

== Chemistry mechanism ==
Currently PALM-4U includes the following sample of chemistry mechanisms:\\
  * cbm4: Carbon Bond Mechanism ([wiki:doc/app/chemref 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 [https://palm.muk.uni-hannover.de/trac/attachment/wiki/doc/tec/chem/Readme_KPP4PALM.pdf 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`.