Performing a chemistry simulation

Two test cases are provided in the KTEST directory distributed with MesoNH: the 009_ICARTT case is a real case using MOCAGE large fields, emissions and with gas phase chemistry; the 011_KW78CHEM case is an idealized case with cloud chemistry and using idealized vertical profiles to initialize the chemistry.

Idealized simulation

The simplest way to run a chemical simulation is to initialize the chemical fields using vertical profiles, this initialization is done at the MESONH step in the chemical input file (see Example of chemistry file. To activate the use of initial vertical profiles, the chemistry namelist in the EXSEG1.nam have to be:

                      LCH_INIT_FIELD  = T,

Real case simulation

In this case, the chemical fields need to be initialize with results from regional or global models such as MOCAGE or MOZART-4. These large scale fields are also used for boundary conditions. In addition, the emission of primary chemical species has to be activated (see below for details on how consider emissions) in the surface namelist NAM_CH_SURFn in the EXSEG1.nam:


Coupling MOZART-4 with Meso-NH for initial and boundary conditions

Create your own chemical scheme

The following procedure is valid for Meso-NH versions since MASDEV4_9_0

STEP 1: write your chemical scheme

in a specified format (*.chf) like this one: ReLACS-mix-reac.chf

Edit this chf file and make the necessary changes.

STEP 2: create the fortran source

with the awk program m10.awk

Usage: "m10.awk ReLACS-mix-reac.chf"

STEP 3: compile your chemical scheme

Change the name of the chemical scheme to BASIC.f90

Create your user library (see the A-INSTALL file) and compile.

Scripts to create emissions files in the right format for PREP PGD


The following scripts are designed to convert the original emission files taken from the GEIA/ECCAD international program ( to the latitude-longitude-value ascii format needed by the PREP_PGD .

Emissions files are downloaded from the ECCAD web site in the netcdf format.

The scripts emiss_conv_nc_to_asc.ncl converts netcdf format to lat-lon-val with final emissions in molec/cm2/s.

The script needs to be adapted to the user requirements:


When running the model, the routine build_emisstabn.F90 in SURFEX will automatically make the conversion of the above mentioned units to molec/m2/s according to the keyword provided in the chemistry file under the EMISUNIT keyword: MOL (if emissions are provided in microMol/m2/day), MIX (if emissions are provided in ppp m/s), CON (emissions are provided in molec/cm2/s).


emission fluxes in microMole/m2/day

emission fluxes in ppp m/s

emission fluxes in molec/cm2/s

Then the routine build_pronoslistn.F90 in SURFEX makes the correspondence between the emitted species and the MESONH chemical species using the aggregation factors, which are provided in the chemistry file under the AGREGATION keyword. See example in the chemistry file of the KTEST 009_ICARTT

Example of input file for chemistry: CCHEM INPUT FILE

To run the chemistry in Meso-NH, additional informations are needed such as Henry's law coefficients, molecular masses, etc. These informations need to be provided in the input chemistry file which name is specified in the namelist EXSEG1.nam:

                      CCHEM_INPUT_FILE  = "MNHC.input",

An example of such a file is given here MNHC.input which is compatible with the default chemical scheme provided with the Meso-NH package. This example is for the COPT case described in Leriche et al. (2013), for which, the chemistry is initialized with vertical profiles provided in the chemistry file.


Photolysis rates are computed based on the TUV program developped at NCAR (Source:

In order to run the TUV program (version 5.3.1) in Meso-NH, additional files are needed which can be downloaded here: tuv531.tar.gz

MEGAN : _upload_files

The data files to run Meso-NH with MEGAN Support are here : MEGAN_EF.tgz

Mesonh-54: MesonhTEAMFAQ/Chemistry (last edited 2018-07-03 15:38:08 by JuanEscobar)