FlexAOD

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.

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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
OPSSa	85	SSa AOD
OPSSc	86	SSc 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:

rundir=${HOME}/geos-chem/GEOS-Chem.${ver}.stdrun/runs/${met}.${res}/output/${lab}

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:

tracerinfo.dat.${tlab}
diaginfo.dat.${tlab}

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

input.dat

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

pointout.dat

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:

./flexaod.sh

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

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

References

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