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FlexAOD (Flexible Aerosol Optical Depth) is a post-processing tool of GEOS-Chem, aimed at extending the model on-line capabilities concerning calculations of Aerosol optical properties.


User's Guide

Download code & data

Source code, input & test data are at this link: http://pumpkin.aquila.infn.it/flexaod/download

From a Linux/Unix terminal, you may follow this procedure:

mkdir -p geos-chem/flexaod
cd geos-chem/flexaod
wget http://pumpkin.aquila.infn.it/flexaod/download/flexaod_v1.0.tgz
tar zxvf flexaod_v1.0.tgz

This will create the subdirectory "flexaod_v1.0", here is a quick look at the content:

Filename/Dirname Description
flexaod.sh Launch script
input.dat Configuration file
pointout.dat Point output configuration file (the actual name is set with point_file variable)
random_pointout.sh Random pointout.dat generator
loop.sh Loop script for automatic launch at several wavelengths and/or date intervals
loop_wave_rtm.sh Loop script for automatic launch and post-processing of libRadtran output at several wavelengths
src/ Fortran source code
src/Makefile.hdr.* Makefile headers for Fortran compiler configuration
data/ Optical input data (i.e. all but GEOS-Chem timeseries)
data/gads/optdat GADS/OPAC input database (Hess et al., 1998)
data/lsmask Land/sea mask calculated from gridded national IDs (CIESIN and CIAT, 2005), only needed if point_watonly=T
data/size_dist Parameters of size distributions and hygroscopic growth factors
data/water Water spectral refractive index (Segelstein, 1981)

Set up GEOS-Chem timeseries & data dir

FlexAOD needs GEOS-Chem timeseries in input (instantaneous (ND49) or satellite (ND51)). There is a minimum set of tracers to be saved in output timeseries:

Aerosol concentrations Tracer # Description
SO4 27 Sulfate
NH4 31 Ammonium
NIT 32 Nitrate
BCPI 34 Black carbon hydrophillic
OCPI 35 Primary organic carbon hydrophillic
BCPO 36 Black carbon hydrophobic
OCPO 37 Primary organic carbon hydrophobic
SOA1-4 45-48 Secondary organic aerosols classes 1-4
DST1-4 49-52 Mineral dust aerosols (size bins 1-4)
SSa 53 Sea salt aerosols accumulation mode
SSc 54 Sea salt aerosols coarse mode
Meteo fields Tracer # Description
AIRD 78 Air density (molecules/cm^3)
BOXH 93 Box Height (m)
RELH 94 Relative Humidity (%)
Optional (for comparison with on-line AOD) Tracer # Description
OPSO4 82 Sulfate aerosols AOD
OPBC 83 Black carbon AOD
OPOC 84 Organic carbon AOD
OPD 87 Total dust AOD

By default, FlexAOD will look for GEOS-Chem output into a subdirectory defined at line 168 of flexaod.sh:


where $ver, $met, $res, and $lab are all defined in input.dat. A GEOS-Chem user is familiar with the first three variables, the latter is introduced for further organization of the run directory, but its use is optional. Tailor the naming conventions of the run directory to your needs.

In addition to time series, FlexAOD expects to find under rundir:


where $tlab is an additional "time label" also defined in input.dat.

Sample GEOS-Chem timeseries output and info files are provided for testing. Go under your "rundir" and download data:

wget -r -nd -np -R*html* http://pumpkin.aquila.infn.it/flexaod/download/testdata


Here is a description of the FlexAOD configuration file input.dat:

Parameter Description Examples/Possible values
ver GEOS-Chem version v8-02-02
met GEOS-Chem met-fields version geos5
res GEOS-Chem horizontal resolution 2x25
compiler Fortran compiler option IFORT (used to link to corresponding src/Makefile.hdr.<compiler>)
lab GEOS-Chem simulation label CTRL (optional, see Set up GEOS-Chem timeseries & data_dir)
tlab GEOS-Chem time label 200701 (mandatory, see Set up GEOS-Chem timeseries & data_dir)
typ GEOS-Chem timeseries type inst (ND49) or
sat (ND51)
dini Initial date of FlexAOD run 20070101 (YYYYMMDD)
dend Final date of FlexAOD run 20070131 (YYYYMMDD)
wl Wavelegth (nm) 443 (range limited by optical input)
optsrc Optical properties option OPAC (OPAC/GADS, only option currently)
distsrc Size distribution option STD (associates to data/size_dist/dist_<distsrc>.dat)
hgfsrc Hygroscopic growth option OPAC (from OPAC/GADS) or
CHIN (from Chin et al, 2002)
watsrc Water refractive index option SEGEL (Segelstein, 1981, only option currently)
fullmie Mie calculations option F (create Mie look-up table) or
T (Mie calculation for every grid-cell, NOT YET IMPLEMENTED, VERY CPU INTENSIVE!)
aodlab FlexAOD output label CTRL
gridout Switch for full 3-D output T or F
point_prof Switch for point profile output T or F
point_rtm Switch for point RTM output (libRadtran) T or F
point_file Point output list filename `pwd`/pointout.dat
point_watonly Point output only over water pixels T or F


The pointout.dat contains the list of points (time and place) for FlexAOD point output. The actual name of the file may vary and is set with variable point_file in input.dat.

The format (free ASCII format) of the file is the following:

column 1: point number
column 2: time (YYYYMMDDHH)
column 3: latitude (degrees north)
column 4: longitude (degrees east)

Here is an example:

#   N     Date/hour     Lat      Lon
#       (YYYYMMDDHH)  (deg N)  (deg E)
1        2006010109    42.0      13.0
2        2006010110    42.0     -33.0

All the lines beginning with "#" will be removed by FlexAOD.

The utility random_pointout.sh generates a random list of points, between user defined dates and coordinates, that may be used for testing or random data model extraction.

Program Launch

Once you set up input.dat and, optionally, pointout.dat, launch FlexAOD from a shell:


or, if you want a background job and log file (bash syntax):

./flexaod.sh &> log &
tail -f log


  1. Center for International Earth Science Information Network (CIESIN), Columbia University; and Centro Internacional de Agricultura Tropical (CIAT) (2005), Gridded Population of the World Version 3 (GPWv3): National Identifier Grid. Palisades, NY: Socioeconomic Data and Applications Center (SEDAC), Columbia University. http://sedac.ciesin.columbia.edu/gpw/
  2. Chin M, Ginoux P, Kinne S, Torres O, Holben BN, Duncan BN, Martin RV, Logan JA, Higurashi A, Nakajima T (2002), Tropospheric aerosol optical thickness from the GOCART model and comparisons with satellite and Sun photometer measurements, J. Atmos. Sci., 59(3), 461-483. (Table 3 of the paper)
  3. Hess, M., P. Koepke, and I. Schult (1998), Optical Properties of Aerosols and clouds: The software package OPAC, Bull. Am. Met. Soc., 79, 831-844. http://www.lrz.de/~uh234an/www/radaer/opac.html
  4. Mishchenko, M. I., J. M. Dlugach, E. G. Yanovitskij, and N. T. Zakharova, (1999), Bidirectional reflectance of flat, optically thick particulate laters: an efficient radiative transfer solution and applications to snow and soil surfaces, J. Quant. Spectrosc. Radiat. Transfer, Vol. 63, 409-432.
  5. Mishchenko, M. I., L. D. Travis, and A. A. Lacis (2002), Scattering, Absorption, and Emission of Light by Small Particles, Cambridge University Press, Cambridge. http://www.giss.nasa.gov/staff/mmishchenko/brf/
  6. Segelstein, D. (1981), The Complex Refractive Index of Water, M.S. Thesis, University of Missouri, Kansas City. http://www.philiplaven.com/p20.html