This site contains a collection of Matlab
scripts for environmental, atmospheric chemistry, BVOC emission modeling and micrometeorological
(c) These scripts
calculate the source/sink distribution within a forest canopy from measured in-canopy concentration profiles based
on the Inverse Lagrangian Transport (ILT) concept published by Raupach, Agr. For. Met., 1989
. The ILT accounts for in-homogenous dispersion
within the canopy (simple K-theory
does not apply here) and splits the dispersion into a near (=non-diffusive) and far (=diffusive)
field term. The result is a dispersion matrix D, that relates the source / sink distribution to the concentration gradient C according
to: C = D x S. Technical note: In this script the number of source layers (sh) needs to be smaller than the number of concentration
layers (zc). If the number of source layers is too small (e.g. 1-3), the calculated flux might be underestimated. For a concentration
vector of size 10, I usually choose a source vector (sh) of size 4-7.
(d) Calculate approximate height of the planetary boundary layer (PBL) according to LCL (lifting condensation level
). The routine
calculates the LCL, which should coincide with the lowest level of a cumulus humilis cloud deck. During clear sky conditions this
should be close to the PBL height. Additional scripts to calculate CAPE, CINE and plot a skew-T diagram based on radiosonde data can
be downloaded here (metpack.zip
); these scripts were translated and partially adapted from a public fortran code.
(e) Simple random walk model (randomwalkx.m
) to illustrate the flux footprint concept. The model is mostly suitable for educational
purposes. Takes about 40 s to run on Windows XP (Intel Duo Core, 2GHz). More information on flux footprints can be found here
routine releases 1000 particles at four different locations (blue, red, yellow and green) along the x axis and lets them disperse
/ diffuse as they are transported by the horizontal wind. The script randomcount.m can be used to select an area on the plot and calculate
the relative distribution of blue, red, yellow and green particles.
(f) The script (horst.m) calculates a differential and cumulative flux footprint according to Horst and Weil, BLM, 1992
. The script
also calculates the differential footprint as a function of stability class expressed as Obhukov length scale (L)
. You can download
the package (horst.m; horst1.m; horst2.m; footp1.m) here
. To run start horst.m. All calculations are done by the main routine (horst1.m)
which uses the footprint function footp1.m.
Other useful routines (mostly 3rd party scripts found on the web - follow instructions and stipulations as outlined in each script)
(a) Positive Matrix Factorization tools
(e) Non-linear peak fitting script ipf.m
(a) Simple routine (isotopen.m
) that calculates isotopic distribution (run using isotopen.m).
(b) Calculate longitudinal and lateral diffusion in SIFDT instrument
(setup and run with runsifdt.m).
last updated 08/2014
Tom Karl tomkarl Thomas Karl
Instrumentation - Mass Spectrometry
Please acknowledge by citing Karl, T., A. Guenther, R. J. Yokelson, J. Greenberg, M. Potosnak, D. R. Blake, and P. Artaxo, 2007: The
tropical forest and fire emissions experiment: Emission, chemistry, and transport of biogenic volatile organic compounds in the lower
atmosphere over Amazonia, J. Geophys. Res., 112, D18302, doi:10.1029/2007JD008539
in any publication using these scripts.
Please acknowledge by citing Karl, T., Apel, E., Hodzic, A., Riemer, D.,
Blake, D., and C. Wiedinmyer, 2009: Emissions of volatile
compounds inferred from airborne flux measurements over a megacity.
Atmos. Chem. Phys., 9, 271-285 and Torrence, C. and Compo,
G. P.: A practical guide to wavelet analysis, B. Am. Meteorol. Soc., 79, 61-78, 1998
in any publication using these scripts.
Please acknowledge by citing Karl, T., Guenther, A., Turnipseed, A., Patton, E.G., and K. Jardine, 2008: Chemical sensing of plant
stress at the ecosystem scale, Biogeosciences, 5, 1287-1294
and Karl, T., Potosnak, M., Guenther, A., Clark, D., Walker, J., Herrick,
J.D. and C. Geron, 2004: Exchange Processes of Volatile Organic Compounds above a Tropical Rainforest - Implications for Modeling
Tropospheric Chemistry above Dense Vegetation, J. Geophys. Res., 109, D18306, 10.1029/2004JD004738 in any publication using these
Atmospheric Chemistry (in preparation 01/2012)
(a) Simple chemical boxmodel
(b) MOZART Chemistry Mechanism v4. Scripts can be used to run as diluting box model including emission, deposition and chemistry.
As a simple test, run using runmozartcarbon.m. The script will calculate the carbon balance and reactivity for isoprene as a function
of photochemical age. (mozart.zip
(c) Sequential reaction model: compare initial isoprene oxidation products in different mechanisms
Biosphere-Atmosphere Exchange / Micrometerology
(d) Sequential reaction model: new mechanism for inital oxidation of isoprene
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