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You need to set the following environment variables to the appropriate locations:

OIFS_ICMCL_DIR  DIR  –  This points to a directory containing initial conditions for the first day of all months of the year 2010. The ICMCL files contain boundary conditions (e.g. SSTs) for the entire month. 
OIFS_INIDATA_DIR_TM5  –  Points to a directory containing TM5 'tm5' chemistry scheme initial conditions (with or without aerosol) for 2010-01-01 and boundary conditions (emission fluxes and deposition velocities) for 2010-01-01 to 2010-01-02.
OIFS_INIDATA_DIR_CBA  –  As above but for Bascoe/TM5 chemistry'bascoetm5' chemistry. 

The prep-ic-icmcl-compo.sh script requires external software: the CDO command line operators to manipulate and analyse climate and NWP model data which are available here: https://code.mpimet.mpg.de/projects/cdo/. 

You need to edit variables inside the file config.h to correspond with the chosen settings for your experiment before running the script to generate the initial data. The settings are described in the following section.

Running the prep script will take a few minutes and result in new data written to folder chem_ic.

Forecast without restarts – example settings

Select one of the following four configurations for your experiment.

Using TM5 chemistry without aerosol

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PLATFORM='ecmwf-atos'
RUNDIR=${SCRATCH}/43r3/experiments\${EXPID}\/runs  # where your experiment will run
AC_IC_DIR=${SCRATCH}/43r3/experiments\${EXPID}/chem_ic  # where your chemical initial conditions will be created
run_end_date="2010-01-03"

rst_freq='3 day'  # run for 3 days without restarts (no multi-leg exp)
USE_RESTART=false   # Do not write restart files (no multi-leg exp)
LCHEM=true
CHEM_SCHEME="tm5"
CHEM_VER="ver15"
OIFS_INIDATA_DIR=path$path_to_directory_T255L91-tm5-none
AC_IC_ONCE=${OIFS_INIDATA_DIR}/ICMUAoiac.ac_rst'
MET_IC_DIR='${OIFS_ICMCL_DIR}/aabg/2010010100'

LAERO=false
LAERCHEM=false
LCHEM_AEROI=false
LINJ_CHEM=false
LINJ_AER=false
LAEROSFC=false

LWAM=true" config.h
LRLXG=false" config.h
LAC4IC=true" config.h

Then run the prep script for initial conditions

./prep-ic-icmcl-compo.sh 2010-01-01 2010-01-03

Using TM5 chemistry with AER aerosol

We will run a 2 day forecast starting from 2010-01-01 with TM5 chemistry and the AER bulk aerosol scheme.

Use the following settings in config.h

PLATFORM='ecmwf-atos'
RUNDIR=${SCRATCH}/43r3/experiments\${EXPID}\/runs  # where your experiment will run
AC_IC_DIR=${SCRATCH}/43r3/experiments\${EXPID}/chem_ic  # where your chemical initial conditions will be created
run_end_date="2010-01-03"

rst_freq='3 day'  # run for 3 days without restarts (no multi-leg exp)
USE_RESTART=false   # Do not write restart files (no multi-leg exp)
LCHEM=true
CHEM_SCHEME="tm5"
CHEM_VER="ver15"
OIFS_INIDATA_DIR=$path_to_directory_T255L91-tm5-aer
AC_IC_ONCE=${OIFS_INIDATA_DIR}/ICMUAoiac.ac_rst'
MET_IC_DIR='${OIFS_ICMCL_DIR}/aabg/2010010100'

LWAM=true" config.h
LRLXG=false" config.h
LAC4IC=true" config.h

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