== Overview ==
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[[NoteBox(note,This page is part of the **Chemistry Model** (CHEM) documentation. \\ It contains a description of CHEM including the topics aerosol compounds\, deposition and emission.\\ For an overview of all CHEM-related pages\, see the **[wiki:doc/tec/chem CHEM main page]**.)]]


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

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 ([wiki:doc/app/chemref 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 ([wiki:doc/app/chemref 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, areosol compounds can be considered either as passive compounds or the sectional aerosol module [wiki:salsa SALSA]   ([wiki:doc/app/chemref 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 [wiki:doc/app/chemref Zhang et al. (2001)] while gases are deposited using the DEPAC model following [wiki:doc/app/chemref 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].