3D-CMCC-FEM (Coupled Model Carbon Cycle) BioGeoChemical and Biophysical Forest Ecosystem Model User's Guide (v.5.x.x)

Abstract

Abstract
This is the 3D-CMCC-FEM (Three Dimensional - Coupled Model Carbon Cycle - Forest Ecosystem Model) user guide for the version 5.5-ISIMIP and 5.6. The 3D-CMCC-FEM is a biochemical, biophysical process-based model and is basically a research tool which is freely available only for non-commercial use. This user guide describes the essential steps for input data creation, model parameterization and for running the model code on different IDEs but even on R environment using different wrappers for pre- and post-processing for3D-CMCC-FEM (both versions: Light Use Efficiency and the fully BioGeoChemical version). We have developed the 3D-CMCC-FEM code relying solely on open source components, in order to facilitate its use and further development by others. The 3D-CMCC-FEM code is released under the GNU General Public Licence v3.0 (GPL).

Full text

website: www.forest-modelling-lab.com
Forest Modelling Laboratory – National Research Council of Italy
Institute for Agriculture and Forestry Systems in the Mediterranean (CNR–ISAFOM)
Via Madonna Alta 128 - 06128, Perugia (PG), Italy
3D-CMCC-FEM
(Coupled Model Carbon Cycle)
BioGeoChemical and Biophysical
Forest Ecosystem Model
User’s Guide (v.5.x.x)
(updated June 2023)

3D-CMCC-FEM User’s Guide
Page 2
Lab. contacts
(forest.modelling.lab@isafom.cnr.it, 3d.cmcc.fem@gmail.com)
Alessio Collalti (Lab. Head)
alessio.collalti@cnr.it
Institute for Agriculture and Forestry Systems in the Mediterranean of the National Research Council of Italy (CNR- ISAFOM)
Via della Madonna Alta, 128 - 06128 Perugia (PG) Italy
Daniela Dalmonech
daniela.dalmonech@cnr.it
Institute for Agriculture and Forestry Systems in the Mediterranean of the National Research Council of Italy (CNR- ISAFOM)
Via della Madonna Alta, 128 - 06128 Perugia (PG) Italy
Gina Marano
gina.marano@esys.ethz.ch
ETH Zürich, Department of Environmental System Sciences, Chair of Forest Ecology
Universitätstrasse 16, 8057 Zurich, Switzerland
Elia Vangi
elia.vangi@isafom.cnr.it
Institute for Agriculture and Forestry Systems in the Mediterranean of the National Research Council of Italy (CNR- ISAFOM)
Via della Madonna Alta, 128 - 06128 Perugia (PG) Italy
Paulina Puchi
paulina.ouchi@isafom.cnr.it
Institute for Agriculture and Forestry Systems in the Mediterranean of the National Research Council of Italy (CNR- ISAFOM)
Via della Madonna Alta, 128 - 06128 Perugia (PG) Italy
Maria Rosaria Orrico
mariarosaria.orrico@isafom.cnr.it
Institute for Agriculture and Forestry Systems in the Mediterranean of the National Research Council of Italy (CNR- ISAFOM)
Via Cavour 17-87036, Rende (CS) Italy

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Index
1.
Code availability......................................................................................................................................... 4
2.
Model description ..................................................................................................................................... 5
3.
Referencing the model .............................................................................................................................. 5
4.
Run the model ........................................................................................................................................... 7
4.1 Model inputs ...................................................................................................................................... 7
Stand initialization file ............................................................................................................................... 8
Soil initialization file ................................................................................................................................... 9
Topography initialization file ................................................................................................................... 10
Meteorological data file .......................................................................................................................... 11
CO2 atmospheric concentration file ........................................................................................................ 12
Species-Parameterization file .................................................................................................................. 13
Settings file .............................................................................................................................................. 17
4.2 Model outputs ................................................................................................................................. 20
Annual Outputs ........................................................................................................................................ 20
Monthly Outputs ..................................................................................................................................... 23
Daily Outputs ........................................................................................................................................... 24
5.
Management ........................................................................................................................................... 27
6.
3D-CMCC-FEM Usage .............................................................................................................................. 28
7.
How to run and develop the 3D-CMCC-FEM ........................................................................................... 31
7.1 Code characteristics ......................................................................................................................... 31
7.2 Eclipse usage instruction (for developers) ...................................................................................... 31
How to increase Eclipse available heap size (optional) ........................................................................... 32
How to work on Eclipse for bash scripts (optional) ................................................................................. 32
7.3 Bash launch (for UNIX users) ........................................................................................................... 32
8.
Questions or comments .......................................................................................................................... 33

3D-CMCC-FEM User’s Guide
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1.
Code availability
The 3D-CMCC-FEM (“Three Dimensional - Coupled Model Carbon Cycle - Forest Ecosystem Model”) is a
computer model and is primarily a research tool, and many versions have been developed for specific
purposes. The National Research Council of Italy and University of Tuscia maintain benchmark code
versions for public release and update these benchmark versions periodically as new knowledge is gained
on the research front. The code and executables accompanying this file represent the most recent
benchmark version. The 3D-CMCC-FEM code (any version) is copyrighted.
The 3D-CMCC-FEM is freely available only for non-commercial use. We have developed the 3D-CMCC-
FEM code relying solely on open source components, in order to facilitate its use and further
development by others. The 3D-CMCC-FEM is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. The 3D-CMCC-FEM code is released under the GNU General Public Licence (GPL) at:
https://github.com/Forest-Modelling-Lab/3D-CMCC-FEM. See the GNU General Public License for more
details. You should have received a copy of the GNU General Public License along with this program. If
not, see http://www.gnu.org/licenses/gpl.html.
The model has been developed and is maintained by the Forest Modelling Laboratory at the National
Research Council of Italy, Institute for Agricultural and Forestry Systems in the Mediterranean (CNR-
ISAFOM), Perugia. All source code and documents are subject to copyright © by the CNR. In case you have
copied and/or modified the 3D-CMCC-FEM code overall, even in small parts of it, you may not publish
data from it using the name 3D-CMCC-FEM or any 3D-CMCC-FEM variants unless you have either
coordinated your usage and their changes with the developers listed below, or publish enough details
about your changes so that they could be replicated.
The 3D-CMCC-FEM has been developed by: Alessio Collalti, Daniela Dalmonech and Gina Marano who are
part of (or associated to) the Forest Ecology Laboratory at the National Research Council of Italy (CNR),
Institute for Agricultural and Forestry Systems in the Mediterranean (ISAFOM), Via della Madonna Alta,
128, 06128 - Perugia (PG), Italy. CNR accepts no responsibility for the use of the 3D-CMCC-FEM in the
form supplied or as subsequently modified by third parties. CNR disclaims liability for all losses, damages
and costs incurred by any person as a result of relying on this software. Use of this software assumes
agreement to this condition of use. Removal of this statement violates the spirit in which 3D-CMCC-FEM
was released by CNR. The 3D-CMCC-FEM (both versions: Light Use Efficiency and the fully
BioGeoChemical version). Versions 5.5.x code is open. You can get a free copy of the code online from:
(GitHub Repository) https://github.com/Forest-Modelling-Lab/3D-CMCC-FEM.

3D-CMCC-FEM User’s Guide
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2.
Model description
The 3D-CMCC-FEM is biogeochemical, biophysical forest model that simulates the dynamics occurring in
homogeneous and heterogeneous forests with different plant species, for different age, diameter and
height classes. The model can reproduce forests from simple up to forests with a complex canopy
structure (i.e. constituted by cohorts competing for light and water resources). The 3D-CMCC-FEM
simulates carbon fluxes, in terms of gross and net primary productivity (GPP and NPP, respectively),
partitioning and allocation in the main plant compartments (stem, branch, leaf, fruit, fine and coarse root,
non-structural carbon) and water fluxes in terms of leaf and canopy transpiration, canopy and soil
evaporation and the overall forest water balance. In the recent versions, nitrogen fluxes and allocation, in
the same carbon pools, are also reproduced. The 3D-CMCC-FEM also takes into account management
practices, as thinning and harvest, to predict their effects on forest growth and carbon sequestration. The
3D-CMCC-FEM is written in C-programming language and divided into several subroutines. To run the
model, some input data are required. The meteorological forcing variables, on a daily time step, are
represented by average, minimum and maximum air temperature, shortwave solar radiation,
precipitation, vapor pressure deficit (or relative humidity). The model also needs some basic information
about soil, such as soil depth and texture (clay, silt and sand fractions), as well as the forest stand
information referred to plant species, ages, diameters, heights and stand density. An additional input is
represented by species-specific eco-physiological data for the model parameterization. Copyright © 2023,
Forest Modelling Laboratory – 3D-CMCC-FEM. All rights reserved.
3.
Referencing the model
If you use 3D-CMCC-FEM in your research, based on the version used, please include the following
acknowledgments in the relevant manuscript:
“3D-CMCC-FEM, Version 5.x.x was provided by Alessio Collalti and Daniela Dalmonech, or others, from
Forest Modelling Lab. | National Research Council of Italy, Institute for Agricultural and Forestry Systems in
the Mediterranean (CNR–ISAFOM);
Please also reference the following citation(s) as the most recent and complete description of the current
model versions:
v.4.0 (not more in use)
- “Sviluppo di un modello dinamico ecologico-forestale per foreste a struttura complessa”. A. Collalti, 2011.
University of Tuscia, Ph.D. Thesis, Ph.D. Advisor: Riccardo Valentini.
http://dspace.unitus.it/bitstream/2067/2398/1/acollalti_tesid.pdf, (in Italian)
- "A process-based model to simulate growth and dynamics in forests with complex structure: evaluation and
use of 3D-CMCC Forest Ecosystem Model in a deciduous forest in Central Italy". A. Collalti, L. Perugini, T. Chiti,
A. Nolè, G. Matteucci, R. Valentini. Ecological Modelling 2014.
https://doi.org/10.1016/j.ecolmodel.2013.09.016.
v.5.1.1 (not more in use)
- "Validation of 3D-CMCC Forest Ecosystem Model (v.5.1) against eddy covariance data for 10 European forest
sites". A. Collalti, S. Marconi, A. Ibrom, C. Trotta, A. Anav, E. D’Andrea, G. Matteucci, L. Montagnani, B. Gielen,
I. Mammarella, T. Grünwald, A. Knohl, F. Berninger, Y. Zhao, R. Valentini and M. Santini, Geoscientific Model

3D-CMCC-FEM User’s Guide
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Development, 2016. https://doi.org/10.5194/gmd-9-479-2016.
v.PSM (not more in use)
- “Assessing NEE and Carbon Dynamics among 5 European Forest types: Development and Validation of a new
Phenology and Soil Carbon routines within the process oriented 3D-CMCC-Forest-Ecosystem Model”, S.
Marconi, Jan 2013, University of Tuscia, M.Sc. Thesis, M.Sc. Advisors: R. Valentini, T. Chiti, A. Collalti.
- “The Role of Respiration in Estimation of Net Carbon Cycle: Coupling Soil Carbon Dynamics and Canopy
Turnover in a Novel Version of 3D-CMCC Forest Ecosystem Model”. S. Marconi, T. Chiti, A. Nolè, R. Valentini
and A. Collalti. Forests 2017. https://doi.org/10.3390/f8060220.
v.5.3.3-ISIMIP
- “Thinning can reduce losses in carbon use efficiency and carbon stocks in managed forests under warmer
climate”. Collalti A., Trotta C., Keenan T.F., Ibrom A., Lamberty B.B., Gröte R., Vicca S., Reyer C.P.O.,
Migliavacca M., Veroustraete F., Anav A., Campioli M., Scoccimarro E., Šigut L., Grieco E., Cescatti A., and
Matteucci G., Journal of Advances in Modelling Earth System 2018. https://doi.org/10.1029/2018MS001275.
- “Climate change mitigation by forests: a case study on the role of management on carbon dynamics of a pine
forest in South Italy”. Pellicone G., August 2018, University of Tuscia, Ph.D. Thesis, Ph.D. Advisors: G.
Scarascia-Mugnozza, G. Matteucci, A. Collalti.
v.5.3
- “The sensitivity of the forest carbon budget shifts across processes along with stand development and
climate change”. Collalti A., Thornton P.E., Cescatti A., Rita A., Borghetti M., Nolè A., Trotta C., Ciais
P., Matteucci G. Ecological Applications 2018.
https://doi.org/10.1002/eap.1837.
v.5.5 (and v.5.5–ISIMIP)
- “Plant respiration: Controlled by photosynthesis or biomass?” Collalti A., Tjoelker M.G., Hoch G., Mäkelä A.,
Guidolotti G., Heskel M., Petit G., Ryan M.G., Battipaglia G., Matteucci G., Prentice I.C. Global Change Biology
2020, https://doi.org/10.1111/gcb.14857
- “Simulating the effects of thinning and species mixing on stands of oak (Quercus petrea (Matt.) Liebl.
/ Quercus robur L.) and pine (Pinus sylvestris L.) across Europe”, Engel M., VVospernik S., Toigo M., Morin X.,
Tomao A., Trotta C., Steckel M., Barbati A., Nothdurft A. Pretzsch H., del Rio M., Skrzyszewski J., Ponette Q.,
Lof M., Jansons A., Brazaitis G., Ecological Modelling, 2021,
https://doi.org/10.1016/j.ecolmodel.2020.109406
- “Accuracy, realism and general applicability of European forest models” Mahnken, M., Cailleret M., Collalti A.,
Trotta C., Biondo C., D’Andrea E., Dalmonech D., Marano G., Mäkelä A., ..., Reyer C.P.O., Global Change
Biology, 2022, https://doi.org/10.1111/gcb.16384
- “Feasibility of enhancing carbon sequestration and stock capacity in temperate and boreal European forests
via changes to forest management”, Dalmonech D., Marano G., Amthor J., Cescatti A., Lindner M., Trotta C.,
Collalti A., Agricultural and Forest Meteorology, 2022 https://doi.org/10.1016/j.agrformet.2022.109203
v.5.6
- “Simulating diverse forest management in a changing climate on a Pinus nigra subsp. Laricio plantation in
Southern Italy”, Testolin R., Dalmonech D., Marano G., D’Andrea E., Matteucci G., Noce S., Collalti A., Science
of the Total Environment, 2023 https://doi.org/10.1016/j.scitotenv.2022.159361
If you have made any significant modifications to the code, please mention them in your manuscript.

3D-CMCC-FEM User’s Guide
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This User’s Guide is the only documentation released with 3D-CMCC-FEM.
The code itself contains extensive internal documentation, and users with specific questions about the
algorithms used to estimate particular processes should read the comments in the appropriate source code
files.
The file treemodel.c contains references to all the core science routines and is a good starting point for
this kind of inquiry. The files matrix.c defines the data structures that are used to pass information
between the process modules and includes both a short text description and the units for each internal
variable.
Shall you have questions about the code, appropriate model applications, possible programming errors,
etc., please read this entire guide first, and then feel free to contact us.
4.
Run the model
4.1 Model inputs
The 3D-CMCC-FEM model uses at least seven input files which are mandatory when not expressly defined
as optional. These files must be necessarily provided to run the model:
• “setting” file;
• “stand” file;
• “species” file;
• “meteo” file;
• “soil” file;
• “topo” file;
• “CO2” file;
• “Ndep” file (optional);
A brief description of all files is given first, followed by detailed discussions of each file.
Be sure to set the right arguments passed to the project and go into bin directory:
o cd bin
Run executable (e.g. in Bash Shell) with default parameters:
./3D-CMCC-Forest-Model -i input -o output -p parameterization -d
sitename_stand.txt -m sitename_meteo_firstyear.txt -s sitename_soil.txt -t
sitename_topo.txt -c sitename_settings.txt -k CO2_hist.txt > log.txt

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Stand initialization file
Figure 1 | Example of stand file
The first required input file is called the "sitename_stand.txt". It provides information about the stand
conditions.
Example for a cell resolution of 100 x 100 meters cell X = 0, Y = 0:
Year,x,y,Age,Species,Management,N,Stool,AvDBH,Height,Wf,Wrc,Wrf,Ws,Wbb,Wres,Lai
1944,0,0,23,Fagussylvatica,T,1767,0,3.619168081,6.666049802,0,0,0,0,0,0,0
1945,0,0,24,Fagussylvatica,T,1525,0,4.041901639,7.031160656,0,0,0,0,0,0,0
1946,0,0,25,Fagussylvatica,T,1525,0,4.459383607,7.391298361,0,0,0,0,0,0,0
1947,0,0,26,Fagussylvatica,T,1525,0,4.817278689,7.747770492,0,0,0,0,0,0,0
1948,0,0,27,Fagussylvatica,T,1326,0,5.128280543,8.105067873,0,0,0,0,0,0,0
1949,0,0,28,Fagussylvatica,T,1326,0,5.535475113,8.460180995,0,0,0,0,0,0,0
1950,0,0,29,Fagussylvatica,T,1326,0,5.961357466,8.814479638,0,0,0,0,0,0,0
…
The text file must be created following this logic architecture
- for each tree height class define the number of age classes and their values
-- for each height->dbh class
--- for each height->dbh->age class
---- for each height->dbh->age->species class define its state variables:
Comments are allowed in the parameter file. Comments can appear almost anywhere, must begin with two
forward slash characters '//', at the end of the line. Example parameter files are provided. Parameter
definition and its value must be separated by one-tab character.
IMPORTANT: Values are referred to the SIZECELL dimensions specified in the setting.txt file (e.g. if SIZECELL
= 100 meters variable values refer to tC ha-1).
NOTE: for easiest simulations you can also use the “average tree” concept which simplify (a lot) simulations
and analyses (see above).
Year
Reference year for stand data

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X,Y
Cell position
Age
Age of tree(s) (in years)
Species
Name of species (as exactly as the name of species file)
Management
Tree habitus (T = timber; C = Coppice)
N
Number of trees (for that class if more than one class) per cell
*Stool
Number of stool per cell
AvDBH
Average diameter at breast height (for that class if more than one class) (in cm)
Height
Tree height (for that class if more than one class) (in m)
*Wf
Foliage biomass (for that class if more than one class) (in tDM ha–1)
*Wrc
Coarse root biomass (for that class if more than one class) (in tDM ha–1)
*Ws
Stem biomass (for that class if more than one class) (in tDM ha–1)
*Wbb
Branch and Bark biomass (for that class if more than one class) (in tDM ha–1)
*Wres
Reserve (for that class if more than one class) (in tC ha–1)
*LAI
Leaf Area Index (for that class if more than one class) (in m2 m–2)
*Parameters not mandatory, mostly used from developers or in specific model versions under development
Soil initialization file
Figure 2| Example of soil characteristic file
The fourth required input file is "sitename_soil.txt". It contains information about soil and fertility of the
test site.
Comments are allowed in the parameter file. Comments can appear almost anywhere, must begin with two
forward slash characters '//', at the end of the line.
It contains the following parameters:
X,Y,LANDUSE,LAT,LON,CLAY_PERC,SILT_PERC,SAND_PERC,SOIL_DEPTH,FR,FN0,FNN,M,LITTER
C, LITTERN,SOILC,SOILN,DEADWOODC
0,0,F,49.3,18.32,20.63,20.63,58.74,80,0.65,0.5,0.5,0.2,-9999,-9999,-9999,-9999,-
9999

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X,Y
Cell position
LANDUSE
See LANDUSE section
LAT
Latitude (in °)
LONG
Longitude (in °)
CLAY_PERC
Soil clay (in %)
SILT_PERC
Soil silt (in %)
SAND_PERC
Soil sand (in %)
SOIL_DEPTH
Soil depth (in cm)
FR
Fertility rating (dim) (only LUE version)
FN0
Value of fertility modifier when FR=0 (dim)
M0
Value of ‘m’ when FR=0 (dim)
*LITTERC
Litter carbon (in tC ha–1) (Optional)
*LITTERN
Litter nitrogen (in tN ha–1) (Optional)
*SOILC
Soil carbon (in tC ha–1) (Optional)
*SOILN
Soil nitrogen (in tN ha–1) (Optional)
*DEADWOODC
Dead wood carbon (in tC ha–1) (Optional)
*Parameters not mandatory, mostly used from developers or in specific model versions under development
Topography initialization file
Figure 3| Example of topography file
The fifth required input file is "sitename_topo.txt". It contains information about topography of the test
site.
Comments are allowed in the parameter file. Comments can appear almost anywhere, must begin with two
forward slash characters '//', at the end of the line.
It contains the following parameters:
X,Y,40

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X,Y
Cell position
ELEV
Elevation (in m)
Meteorological data file
Figure 4| Example of meteorological forcing file
The second required input file is the meteorological data file, which is named using the start year of
simulation (e.g. "sitename_meteo.txt"), containing the daily meteorological data.
Years of simulation depends on the number years included in the met file.
Some met data are mandatory: temperature, precipitation, vapor pressure deficit (or relative humidity) and
short-wave solar radiation, whereas others are optional.
If the model runs in "spatial version" daily or monthly LAI values are mandatory otherwise they are not
considered in processes. Each variable must be separated by one-tab character. Model considers leap
years, so 29th of February has to be included.
Example for year 2007-2xxx in daily version:
Year Month n_days Rg_f Ta_f Tmax Tmin VPD_f Ts_f Precip SW LAI ET WS_f
2007
1
1
6.1
-9999*
10.4
5.8
0.2
6.3
0.2
0.27
-9999*
-9999*
125.3
2007
1
2
6.2
-9999*
9.9
3.1
0.3
3.3
0
0.39
-9999*
-9999*
126.6
2007
1
3
5.8
-9999*
10
1.9
0.1
0.5
0
0.2
-9999*
-9999*
124.4
...
*NO DATA = -9999
It contains the following variables:

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Rg_f
Mean daily global radiation (MJ m-2 day-1)
Ta_f
Daily Average temperature (°C)
Tmax
Daily Maximum temperature (°C)
Tmin
Daily Minimum temperature (°C)
VPD_f or RH_f
Daily Vapour Pressure Deficit (mbar-hPa) or Relative Humidity (%)
Ts_f
Daily Soil temperature (°C)
Precip
Cumulated daily precipitation (mm day-1)
*SWC
Soil Water Content (mm m-2)
*LAI
Leaf Area Index (m2 m-2) (Only in spatial version)
*ET
Evapotranspiration (mm m-2 day-1)
*WS_f
Windspeed (m sec-1)
*Parameters not mandatory, mostly used from developers or in specific model versions under development
NOTE: missing data (-9999) in mandatory variables may lead the model to interrupt execution.
CO2 atmospheric concentration file
Figure 5| Example of atmospheric CO2 concentration forcing file

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Species-Parameterization file
Figure 6|Example of species–specific parameterization file
The parameterization file is the species eco-physiological constants file, named with specie to simulate
(e.g."Fagussylvatica.txt").
Comments are allowed in the parameter file. Comments can appear almost anywhere, must begin with two
forward slash characters '//', at the end of the line.
Example parameter files are provided. Parameter definition and its value must be separated by one-tab
character.
It contains the following species-specific parameters:
LIGHT_TOL
Light Tolerance:
4 = very shade intolerant (canopy coverage = 90%),
3 = shade intolerant (canopy coverage 100%),
2 = shade tolerant (canopy coverage = 110%),
1 = very shade tolerant (canopy coverage = 120%)
PHENOLOGY
0.1 = deciduous broadleaf,
0.2 = deciduous needle leaf,
1.1 = broad leaf evergreen,
1.2 = needle leaf evergreen
ALPHA
Canopy quantum efficiency (molC molPAR-1)
EPSILONgCMJ
Light Use Efficiency (gC MJ-1) (used if ALPHA is not available)
K
Extinction coefficient for absorption of PAR by canopy
ALBEDO
Canopy albedo

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INT_COEFF
Precipitation interception coefficient
SLA_AVG0
Average Specific Leaf Area m2 KgC-1 for sunlit/shaded leaves (juvenile)
SLA_AVG1
Average Specific Leaf Area m2 KgC-1 for sunlit/shaded leaves (mature)
TSLA
Age at which SLA_AVG = (SLA_AVG1 + SLA_AVG0 )/2
SLA_RATIO
(DIM) ratio of shaded to sunlit projected SLA
LAI_RATIO
(DIM) all-sided to projected leaf area ratio
FRACBB0
Branch and Bark fraction at age 0 (m2 Kg-1)
FRACBB1
Branch and Bark fraction for mature stands (m2 Kg-1)
TBB
Age at which fracBB = (FRACBB0 + FRACBB1)/2
RHO0
Minimum Basic Density for young Trees (tDM m-3)
RHO1
Maximum Basic Density for mature Trees (tDM m-3)
TRHO
Age at which rho = (RHOMIN + RHOMAX)/2
FORM_FACTOR
Stem form factor (adim)
COEFFCOND
Define stomatal response to VPD in m sec-1
BLCOND
Canopy Boundary Layer conductance m sec-1
MAXCOND
Maximum Leaf Conductance in m sec-1
CUTCOND
Cuticular conductance in m sec-1
MAXAGE
Maximum tree age (years)
RAGE
Relative Age to give fAGE = 0.5
NAGE
Power of relative Age in function for Age
GROWTHTMIN
Minimum temperature for growth °C
GROWTHTMAX
Maximum temperature for growth °C
GROWTHTOPT
Optimum temperature for growth °C
GROWTHSTART
Thermic sum value for starting growth in °C
MINDAYLENGTH
Minimum day length for phenology (days)
SWPOPEN
Soil water potential open (MPa)
SWPCLOSE
Soil water potential close (MPa)
OMEGA_CTEM
Allocation parameter control the sensitivity of allocation to changes in water and light
availability
S0CTEM
Parameter controlling allocation to stem
R0CTEM
Parameter controlling allocation to root
F0CTEM
Parameter controlling allocation to foliage

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FRUIT_PERC
%age of NPP to fruit
*CONES_LIFE_SPAN
Life span for cones (years)
FINE_ROOT_LEAF
Allocation new fine root C:new leaf (ratio)
STEM_LEAF
Allocation new stem C:new leaf (ratio)
COARSE_ROOT_STEM
Allocation new coarse root C:new stem (ratio)
LIVE_TOTAL_WOOD
Allocation new live wood C:new total wood C (ratio)
N_RUBISCO
Fraction of leaf N in Rubisco (ratio)
CN_LEAVES
CN of leaves (kgC kgN-1)
CN_FALLING_LEAVES
CN of leaf litter (kgC kgN-1)
CN_FINE_ROOTS
CN of fine roots (kgC kgN-1)
CN_LIVEWOODS
CN of live woods (kgC kgN-1)
CN_DEADWOOD
CN of dead woods (kgC kgN-1)
*LEAF_LITT_LAB_FRAC
leaf litter labile fraction (dimension lees)
*LEAF_LITT_CEL_FRAC
leaf litter cellulose fraction (dimension lees)
*LEAF_LITT_LIGN_FRAC
leaf litter lignin fraction (dimension lees)
*FROOT_LITT_LAB_FRAC
fine root litter labile fraction (dimension lees)
*FROOT_LITT_CEL_FRAC
fine root litter cellulose fraction (dimension lees)
*FROOT_LITT_LIGN_FRAC
fine root litter lignin fraction (dimension lees)
*DEADWOOD_CEL_FRAC
dead wood litter cellulose fraction (dimension lees)
*DEADWOOD_LIGN_FRAC
dead wood litter lignin fraction (dimension lees)
BUD_BURST
Days of bud burst at the beginning of growing season (only for deciduous) (days)
LEAF_FALL_FRAC_GROWING
Proportions of the growing season of leaf fall
LEAF_FINEROOT_TURNOVER
Average yearly leaves and fine root turnover rate
LIVEWOOD_TURNOVER
Annual yearly live wood turnover rate
SAPWOOD_TURNOVER
Annual yearly sapwood turnover rate
DBHDCMAX
Maximum dbh crown diameter relationship when minimum density
DBHDCMIN
Minimum dbh crown diameter relationship when maximum density
SAP_A
a coefficient for sapwood
SAP_B
b coefficient for sapwood
SAP_LEAF
Sapwood/max leaf area ratio in pipe model (m2 m-2)
SAP_WRES
Sapwood-Reserve biomass ratio used if no Wres data are available

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STEMCONST_P
Constant in the stem mass vs. diameter relationship
STEMPOWER_P
Power in the stem mass vs. diameter relationship
CRA
Chapman-Richards a parameter (maximum height, meter)
CRB
Chapman-Richards b parameter
CRC
Chapman-Richards c parameter
*HDMAX_A
A parameter for Height (m) to Base diameter (m) ratio MAX
*HDMAX_B
B parameter for Height (m) to Base diameter (m) ratio MAX
*HDMIN_A
A parameter for Height (m) to Base diameter (m) ratio MIN
*HDMIN_B
B parameter for Height (m) to Base diameter (m) ratio MIN
*CROWN_FORM_FACTOR
Crown form factor (0 = cylinder, 1 = cone, 2 = sphere, 3 = ellipsoid)
*CROWN_A
Crown a parameter
*CROWN_B
Crown b parameter
*MAXSEED
Maximum seeds number (see TREEMIG)
*MASTSEED
Masting year (see TREEMIG)
*WEIGHTSEED
Single fruit weight in g
*SEXAGE
Age for sexual maturity
*GERMCAPACITY
Germinability rate (%)
ROTATION
Rotation for final harvest (based on tree age)
THINNING
Thinning regime (based on year simulation)
THINNING_REGIME
Thinning regime (0 = above, 1 = below)
THINNING_INTENSITY
Thinning intensity (% of Basal Area N-tree to remove–1)
*Parameters not mandatory, mostly used from developers or in specific model versions under development

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Settings file
Figure 7 | Examples of settings file
It contains the following setting parameters:
SITENAME
Name of site
VERSION
Must be 'f' for FEM version or 'b', for BGC version for FOREST LANDUSE
SPATIAL
Must be 's' or 'u', spatial or un-spatial
TIME
Must be 'm' or 'd', monthly or daily
SPINUP
Must be 'on' or 'off'
SPINUP_YEARS
Number of years for spin-up (under development)
SCREEN_OUTPUT
Must be ‘on' or 'off'
DEBUG_OUTPUT
Must be 'on' or 'off'
DAILY_OUTPUT
Must be 'on' or 'off'
MONTHLY_OUTPUT
Must be 'on' or 'off'
ANNUAL_OUTPUT
Must be 'on' or 'off'
SOIL_OUTPUT
Must be 'on' or 'off'
NETCDF_OUTPUT
Must be ‘off’

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YEAR_START
Starting year simulation
YEAR_END
Ending year simulation
YEAR_RESTART
Year to restart. Must be ‘off’
PSN_mod
Must be '0' (FvCB version) or '1' (LUE version) for photosynthesis approach
CO2_trans
Must be 'on' or 'off'
YEAR_START_CO2_FIXED
-9999 . When Co2_trans = var, year at which fix [CO2]
*Ndep_fixed
Must be 'on' or 'off' (under development)
Photo_accl
Photosynthesis temperature acclimation Must be 'on' or 'off'
Resp_accl
Q10 temperature acclimation. Must be 'on' or 'off'
*regeneration
Must be 'on' or 'off'
management
Must be 'on', 'off', or ‘var’ (see below for differences)
YEAR_START_MANAGEMENT
First year of management
Progn_Aut_Resp
Prognostic autotrophic respiration. Must be 'on' or 'off', if off Y values are used
SIZECELL
Its value must be within 10 and 100 (is meter: 10 = 10x10 = 100m2)
Y
Assimilate use efficiency-Respiration rate-NPP/GPP
CO2CONC
CO2 concentration refers to 2000
CO2_INCR
1% increment in [CO2]
INIT_FRAC_MAXASW
0.1 Minimum fraction of Available Soil Water (ASW) based on maxASW (wilting point)
TREE_LAYER_LIMIT
Define differences among tree heights in meters classes to define a new layer
*SOIL_LAYER
Define soil layer(s ) to consider
THINNING_REGIME
Thinning regime (Above or Below)
REPLANTED_SPECIES
Species name of replanted trees (mandatory)
*REPLANTED_MANAGEMENT
(T) management of replanted trees (should be only T) (mandatory)
REPLANTED_TREE
Number of replanted trees (mandatory)
REPLANTED_AGE
(yr) age of replanted trees (mandatory)
REPLANTED_AVDBH
(cm) average dbh of replanted trees (mandatory)
*REPLANTED_LAI
(m2m-2) LAI for replanted trees (mandatory for evergreen useless for deciduous)
REPLANTED_HEIGHT
(m) height of replanted trees (mandatory)
*REPLANTED_WS
(tDM ha-1) stem biomass of replanted trees (optional)

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*REPLANTED_WCR
(tDM ha-1) coarse root biomass of replanted trees (optional)
*REPLANTED_WFR
(tDM ha-1) fine root biomass of replanted trees (optional)
*REPLANTED_WL
(tDM ha-1) leaf biomass of replanted trees (optional for evergreen if LAI!= 0,
otherwise useless)
*REPLANTED_WBB
(tDM ha-1) branch biomass of replanted trees (optional)
*REGENERATION_SPECIES
NOT USED it comes from species that produces seeds
*REGENERATION_MANAGEMENT
(T) management of replanted trees (should be only T) (mandatory)
*REGENERATION_N_TREE
number of replanted trees (mandatory) (NOT USED)
*REGENERATION_AGE
(yr) age of regeneration trees (mandatory) (SHOULD BE ALWAYS 1)
*REGENERATION_AVDBH
(cm) average dbh of regeneration trees (mandatory)
*REGENERATION_LAI
(m2m-2) LAI for regeneration trees (mandatory for evergreen, useless for deciduous)
*REGENERATION_HEIGHT
(m) height of replanted trees (mandatory)
*REGENERATION_WS
(tDM ha-1) stem biomass of regeneration trees (optional)
*REGENERATION_WCR
(tDM ha-1) coarse root biomass of regeneration trees (optional)
*REGENERATION_WFR
(tDM ha-1) fine root biomass of regeneration trees (optional)
*REGENERATION_WL
(tDM ha-1) leaf biomass of regeneration trees (optional for evergreen if LAI!= 0,
otherwise useless)
*REGENERATION_WBB
(tDM ha-1) branch biomass of regeneration trees (optional)
*PRUNING
Must be 'on' or 'off'
*IRRIGATION
Must be 'on' or 'off'
*Parameters not mandatory, mostly used from developers or in specific model versions under development

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4.2 Model outputs
For each simulation the 3D-CMCC-FEM creates ex–novo or rewrites into the output folder a file named
"output.txt".
In this folder 4 other subfolders based on time-scale and settings choices should created. These files
contain every result for debug (if necessary) daily, monthly and annual time-step simulations. It is also
useful to check which model functions have been used. These results can be obtained at stand level or for
each type of class level (layer, dbh, age or species class) on Unix like platforms, if you need to extrapolate a
variable it is advised to use the "grep" tool.
E.g. open a terminal into the output folder and for the variable NPP type:
"cat output.txt | grep 'Stand NPP' " if you want to see grep output into terminal;
"cat output.txt | grep 'Stand NPP' > NPP.txt" if you want to redirect grep output into an NPP
file inside the output folder
IMPORTANT: be sure to use the correct declaration of the output as grep parameter.
The Model provides outputs both at class level that at cell level (by summing up or averaging across the
classes).
Annual Outputs
At class level:
YEAR Year of simulation
LAYER Layer of tree class
HEIGHT Average height of a species (m)
DBH Average diameter at breast height of a species (cm)
AGE Age of trees (years)
SPECIES Tree Species
MANAGEMENT T = Timber
GPP Yearly Gross Primary Production (gC m-2 year-1)
GPP_SUN:GPP Yearly Gross Primary Production for sun leaves (gC m-2 year-1)
GPP_SHADE:GPP Yearly Gross Primary Production for shaded leaves (gC m-2 year-1)
v_SUN:A_SUN Carboxylation rate/Final assimilation rate ratio for sun leaves
Aj_SUN:A_SUN RuBP regeneration/Final assimilation rate ratio for sun leaves
Av_SHADE:A_SHADE Carboxylation rate/Final assimilation rate ratio for shaded leaves
Aj_SHADE:A_SHADE RuBP regeneration/Final assimilation rate ratio for shaded leaves
Av_TOT:A_TOT Carboxylation rate/Final assimilation rate ratio
Aj_TOT:A_TOT RuBP regeneration/Final assimilation rate ratio
GR Growth respiration (gC m-2 year-1)
MR Maintenance Respiration (gC m-2 year-1)
RA Autotrophic respiration (gC m-2 year-1)
NPP Net Primary Production (gC m-2 year-1)
BP Yearly Biomass Production (gC m-2 year-1)
reser_as_diff -
ResAlloc Annual reserve allocated (tNSC cell-1 year-1)
ResDeple Annual reserve depleted (tNSC cell-1 year-1)
ResUsage Annual reserve used (tNSC cell-1 year-1)

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BP/NPP Biomass productivity vs. Net Primary Production
ResAlloc/NP Annual reserve allocated vs. Net Primary Production
ResAlloc/BP Annual reserve allocated vs. Biomass productivity
ResDeple/NPP Annual reserve depleted vs. Net Primary Production
ResDeple/BP Annual reserve depleted vs. Biomass productivity
ResUsage/NPP Annual reserve used vs. Net Primary Production
ResUsage/BP Annual reserve used vs. Biomass productivity
CUE Annual Carbon Use Efficiency (gC NPP gC GPP-1)
BPE Biomass Production Efficiency (gC BP gC GPP-1)
diffCUE-BPE CUE - BPE
Y(PERC) RA/GPP * 100
PeakLAI Peak LAI (maximum attainable LAI) (m2m-2)
MaxLAI Maximum of LAI (maximum reached LAI) (m2m-2)
SLA Specific Leaf Area (m2Kg-1)
SAPWOOD_AREA Tree sapwood area (cm2)
CC-Proj Projected Canopy Cover (frac)
DBHDC DBH/Crown diameter relationship
CROWN_DIAMETER Crown Projected Diameter (m)
CROWN_HEIGHT Crown Height (m)
CROWN_AREA_PROJ Crown Projected Area (at zenith angle) (m2)
APAR Absorbed Photosynthetically Active Radiation (molPARm-2year-1)
LIVETREE Number of live trees (ntree cell-1)
DEADTREE Number of dead trees (ntree cell-1)
THINNEDTREE Number of thinned trees (ntree cell-1)
VEG_D Annual number of vegetative days (days year-1)
FIRST_VEG_DAY First annual day of vegetative period (DIM)
CTRANSP Canopy Transpiration (mm m-2year-1)
CINT Canopy Interception (mm m-2year-1)
CLE Canopy Latent Heat (W m-2year-1)
WUE Annual Water Use Efficiency (DIM)
MIN_RESERVE_C Current Minimum reserve carbon pool (tC cell-1)
RESERVE_C Current Reserve carbon pool (tC cell-1)
STEM_C Current Stem carbon pool (tC cell-1)
STEMSAP_C Current Stem sapwood carbon pool (tC cell-1)
STEMHEART_C Current Stem heartwood carbon pool (tC cell-1)
STEMSAP_PERC Stem Sapwood vs. Total Stem (%age)
STEMLIVE_C Current Stem live wood carbon pool (tC cell-1)
STEMDEAD_C Current Stem dead wood carbon pool (tC cell-1)
STEMLIVE_PERC Live stem vs. Total stem (%age)
MAX_LEAF_C Maximum Current Leaf carbon pool (tC cell -1year-1)
MAX_FROOT_C Maximum Current Fine Root carbon pool (tC cell -1year-1)
CROOT_C Current Coarse Root carbon pool (tC cell-1)
CROOTLIVE_C Current Coarse root live wood carbon pool (tC cell-1)
CROOTDEAD_C Current Coarse root dead wood carbon pool (tC cell-1)
CROOTLIVE_PERC Live Coarse Root vs. Total stem (%age)
BRANCH_C Current Branch carbon pool (tC cell-1)
BRANCHLIVE_C Current Branch live wood carbon pool (tC cell-1)
BRANCHDEAD_C Current Branch dead wood carbon pool (tC cell-1)
BRANCHLIVE_PERC Live Branch vs. Total stem (%age)

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FRUIT_C Current Fruit carbon pool (tC cell-1)
MAX_FRUIT_C Annual Fruit carbon pool (tC cell-1year-1)
RESERVE_N Current Reserve nitrogen pool (tC cell-1)
STEM_N Current Stem nitrogen pool (tC cell-1)
STEMLIVE_N Current Live Stem nitrogen pool (tN cell-1)
STEMDEAD_N Current Dead Stem nitrogen pool (tN cell-1)
CROOT_N Current Coarse Root nitrogen pool (tN cell-1)
CROOTLIVE_N Current Coarse root live wood nitrogen pool (tN cell-1)
CROOTDEAD_N Current Coarse root dead wood nitrogen pool (tN cell-1)
BRANCH_N Current Branch nitrogen pool (tN cell-1)
BRANCHLIVE_N Current Branch live wood nitrogen pool (tN cell-1)
BRANCHDEAD_N Current Branch dead wood nitrogen pool (tN cell-1)
FRUIT_N Current Fruit nitrogen pool (tN cell-1)
STANDING_WOOD Standing wood carbon (tC cell-1)
DELTA_WOOD Annual wood increment (tC cell-1year-1)
CUM_DELTA_WOOD Cumulated annual wood increment (tC cell-1year1)
BASAL_AREA Individual basal area (m2ha-1)
TREE_CAI Single Tree Current Annual Volume Increment (m3tree-1year1)
TREE_MAI Single Tree Mean Annual Volume Increment (m3tree-1year1)
CAI Current Annual Volume Increment (m3class-1year-1)
MAI Mean Annual Volume Increment (m3class-1year-1)
VOLUME Stem volume (m3class-1)
TREE_VOLUME Single tree volume (m3tree-1)
DELTA_TREE_VOL (perc) Tree volume increment (%)
DELTA_AGB Aboveground biomass increment (tC cell-1year-1)
DELTA_BGB Belowground biomass increment (tC cell-1year-1)
AGB Aboveground Biomass pool (tC cell-1)
BGB Belowground Biomass pool (tC cell-1)
BGB.AGB BGB/AGB
DELTA_TREE_AGB Aboveground biomass increment (tC cell-1year-1)
DELTA_TREE_BGB Belowground biomass increment (tC cell-1year-1)
C_HWP Annual harvested woody products removed from (tC cell-1year-1)
VOLUME_HWP Annual volume harvested woody products removed (m3cell- 1year-1)
STEM_RA Stem autotrophic respiration (gC m-2year-1)
LEAF_RA Leaf autotrophic respiration (gC m-2year-1)
FROOT_RA Fine root autotrophic respiration (gC m-2year-1)
CROOT_RA Coarse root autotrophic respiration (gC m-2year-1)
BRANCH_RA Branch autotrophic respiration (gC m-2year-1)
*variables may change across the different model versions
At cell level:
gpp Gross Primary Production (gC m-2year-1)
npp Net Primary Production (gC m-2year-1)
ar Autotrophic respiration (gC m-2year-1)
hr Heterotrophic Respiration (gC m-2year-1)
rsoil Soil respiration flux (gC m-2year-1)
rsoilCO2 Soil respiration flux (gC m-2year-1)
reco Annual ecosystem respiration (gC m-2year-1)

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nee Annual net ecosystem exchange (gC m-2year-1)
nep Annual net ecosystem production (gC m-2year-1)
et Annual evapotranspiration (mm m-2year-1)
le Latent heat flux (W m-2year-1)
soil.evapo Annual soil evaporation (mm m-2year-1)
asw Current available soil water (mm volume-1)
iWue Annual intrinsic Water Use Efficiency (DIM)
vol Current volume (m-3cell)
cum_vol Cumulated volume (m-3cell)
run_off Current amount of water outflow (runoff) (mm m-2year-1)
litrC Litter carbon (gC m-2)
litr1C Litter labile carbon (gC m-2)
litr2C Litter unshielded carbon (gC m-2)
litr3C Litter shielded carbon (gC m-2)
litr4C Litter lignin carbon (gC m-2)
cwd_C Cwd carbon (gC m-2)
cwd_2C Cwd unshielded (gC m-2)
cwd_3C Cwd shielded (gC m-2)
cwd_4C Cwd lignin (gC m-2)
soilC Soil carbon (gC m-2)
soil1C Microbial recycling pool carbon (fast) (gC m-2)
soil2C Microbial recycling pool carbon (medium) (gC m-2)
soil3C Microbial recycling pool carbon (slow) (gC m-2)
soil4C Recalcitrant SOM carbon (humus, slowest) (gC m-2)
litterN Litter nitrogen (gN m-2)
litter1N Litter labile nitrogen (gN m-2)
litter2N Litter unshielded cellulose nitrogen (gN m-2)
litter3N Litter shielded cellulose nitrogen (gN m-2)
litter4N Litter lignin nitrogen (gN m-2)
cwd_N Cwd nitrogen (gN m-2)
cwd_2N Cwd unshielded nitrogen (gN m-2)
cwd_3N Cwd shielded nitrogen (gN m-2)
cwd_4N Cwd lignin nitrogen (gN m-2)
soilN Soil nitrogen (gN m-2)
soil1N Microbial recycling pool nitrogen (fast) (gN m-2)
soil2N Microbial recycling pool nitrogen (medium) (gN m-2)
soil3N Microbial recycling pool nitrogen (slow) (gN m-2)
soil4N Recalcitrant SOM nitrogen (humus, slowest) (gN m-2)
solar_rad Incoming short-wave radiation (MJ m-2year-1)
*variables may change across the different model versions
Monthly Outputs
At class level:
YEAR Year of simulation
MONTH Month of simulation
LAYER Layer of tree class
HEIGHT Average height of a species (m)
DBH Average diameter at breast height of a species (cm)
AGE Age of trees (years)

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SPECIES Tree species
MANAGEMENT T = Timber
GPP Gross Primary Production (gC m-2 month-1)
NET_ASS Monthly net assimilation (gC m-2 month-1)
RA Autotrophic Respiration (gC m-2 month-1)
NPP Net Primary Production (gC m-2 month-1)
CUE Monthly Carbon Use Efficiency (0→1) (gCNPP gCGPP–1)
CTRANSP Canopy Transpiration (mm m-2month-1)
CET Canopy Evapotranspiration (mm m-2month-1)
CLE Canopy Latent Heat (W m-2month-1)
CC Canopy Cover
DBHDC DBH/Crown diameter relationship
HD_EFF Effective Height/Diameter ratio (DIM)
HDMAX Height (m) to Base diameter (m) ratio MAX (DIM)
HDMIN Height (m) to Base diameter (m) ratio MIN (DIM)
N_TREE Number of trees (n tree cell-1)
WUE Monthly Water Use Efficiency (DIM)
Wres Reserve carbon pool (tC cell-1)
WS Stem carbon pool (tC cell-1)
WSL Stem live wood pool (tC cell-1)
WSD Stem dead wood (tC cell-1)
PWL Maximum leaf wood (tC cell-1)
PWFR Maximum fine root wood (tC cell-1)
WCR Coarse root biomass (tC cell-1)
WCRL Coarse root live wood biomass (tC cell-1)
WCRD Coarse root deadwood biomass (tC cell-1)
WBB Branch biomass (tC cell-1)
WBBL Branch live wood biomass (tC cell-1)
WBBD Branch dead wood biomass (tC cell-1)
*variables may change across the different model versions
At cell level:
gpp Gross Primary Production (gC m-2month-1)
npp Net Primary Production (gC m-2month-1)
ar Autotrophic respiration (gC m-2month-1)
et Monthly evapotranspiration (gC m-2month-1)
le Latent heat flux (W m-2)
asw Available soil water (mm volume–1)
iWue Intrinsic Water Use Efficiency
*variables may change across the different model versions
Daily Outputs
At class level:
YEAR Year of simulation
MONTH Month of simulation
DAY Day of simulation
LAYER Layer of forest structure
HEIGHT Average height of a specie (m)

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DBH Average diameter at breast height of a specie (cm)
AGE Age of trees (years)
SPECIES Tree species
MANAGEMENT T = Timber
GPP Gross Primary Production (gC m-2day-1)
Av_TOT Carboxylation rate for limited assimilation (µmol m-2s-1)
Aj_TOT RuBP regeneration limited assimilation (µmol m-2s-1)
A_TOT Final assimilation rate (µmol m-2s-1)
RG Growth respiration (gC m-2day-1)
RM Maintenance Respiration (gC m-2day-1)
RA Autotrophic respiration (gC m-2day-1)
NPP Net Primary Production (gC m-2day-1)
BP Daily biomass production (gC m-2day-1)
CUE Daily carbon Use Efficiency (gCNPP gCGPP–1)
BPE Daily biomass production efficiency (gC m-2day-1)
LAI_PROJ LAI for Projected Area overed (at zenith angle) (m2 m-2)
PEAK-LAI_PROJ Peak Projected LAI (maximum attainable LAI) (m2 m-2)
LAI_EXP LAI for Exposed Area covered (m2 m-2)
D-CC_P Projected Canopy Cover (frac)
DBHDC DBH/Crown diameter relationship
CROWN_AREA_PROJ Crown Projected Area (at zenith angle) (m2)
PAR Photosynthetically Active Radiation (molPAR m-2day–1)
APAR Absorbed Photosynthetically Active Radiation (molPAR m2day-1)
fAPAR Fraction of Absorbed Photosynthetically Active Radiation (unitless)
NTREE Number of trees
VEG_D Day of vegetative period for class (Days/Year)
INT Canopy Interception (mm m-2day-1)
WAT Canopy Water stored (mm m-2)
EVA Canopy Evaporation (mm m-2day-1)
TRA Canopy Transpiration (mm m-2day-1)
ET Canopy Evapotranspiration (mm m-2day-1)
LE Canopy Latent Heat (W m-2)
WUE Water Use Efficiency (DIM)
RESERVE_C Current Reserve carbon pool (tC cell-1)
STEM_C Current Stem carbon pool (tC cell-1)
STEMSAP_C Current Stem sapwood carbon pool (tC cell-1)
STEMLIVE_C Current Stem live wood carbon pool (tC cell-1)
STEMDEAD_C Current Stem dead wood carbon pool (tC cell-1)
LEAF_C Current Leaf carbon pool (tC cell-1)
FROOT_C Current Fine root carbon pool (tC cell-1)
CROOT_C Current Coarse root carbon pool (tC cell-1)
CROOTSAP_C Current Coarse root sapwood carbon pool (tC cell-1)
CROOTLIVE_C Current Coarse root live wood carbon pool (tC cell-1)
CROOTDEAD_C Current Coarse root dead wood carbon pool (tC cell-1)
BRANCH_C Current Branch carbon pool (tC cell-1)
BRANCHSAP_C Current Branch sapwood carbon pool (tC cell-1)
BRANCHLIVE_C Current Branch live wood carbon pool (tC cell-1)
BRANCHDEAD_C Current Branch dead wood carbon pool (tC cell-1)
FRUIT_C Current Fruit carbon pool ((tC cell-1)
DELTARESERVE_C Daily allocation to reserve (tC cell-1day-1)

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DELTA_STEM_C Daily allocation to stem (tC cell-1day-1)
DELTA_LEAF_C Daily allocation to leaf (tC cell-1day-1)
DELTA_FROOT_C Daily allocation to fine root (tC cell-1day-1)
DELTA_CROOT_C Daily allocation to coarse root (tC cell-1day-1)
DELTA_BRANCH_C Daily allocation to branch (tC cell-1day-1)
DELTA_FRUIT_C Daily allocation to fruit (tC cell-1day-1)
RESERVE_N Current reserve nitrogen pool (tN cell-1)
STEM_N Current stem nitrogen pool (tN cell-1)
STEMLIVE_N Current Live Stem nitrogen pool (tN cell-1)
STEMDEAD_N Current Dead Stem nitrogen pool (tN cell-1)
LEAF_N Current leaf nitrogen pool (tN cell-1)
FROOT_N Current Fine Root nitrogen pool (tN cell-1)
CROOT_N Current Coarse Root nitrogen pool (tN cell-1)
CROOTLIVE_N Current Coarse root live wood nitrogen pool (tN cell-1)
CROOTDEAD_N Current Coarse root dead wood nitrogen pool (tN cell-1)
BRANCH_N Current Branch nitrogen pool (tN cell-1)
BRANCHLIVE_N Current Branch live wood nitrogen pool (tN cell-1)
BRANCHDEAD_N Current Branch dead wood nitrogen pool (tN cell-1)
FRUIT_N Current Fruit nitrogen pool (tN cell-1)
DELTARESERVE_N Daily allocation to reserve (tN cell-1day-1)
DELTA_STEM_N Daily allocation to stem (tN cell-1day-1)
DELTA_LEAF_N Daily allocation to leaf ((tN cell-1day-1)
DELTA_FROOT_N Daily allocation to fine root (tN cell-1day-1)
DELTA_CROOT_N Daily allocation to coarse root (tN cell-1day-1)
DELTA_BRANCH_N Daily allocation to branch (tN cell-1day-1)
DELTA_FRUIT_N Daily allocation to fruit (tN cell-1day-1)
STEM_AR Stem autotrophic respiration (gC m-2day-1)
LEAL_AR Leaves autotrophic respiration (gC m-2day-1)
FROOT_AR Fine Roots autotrophic respiration (gC m-2day-1)
CROOT_AR Coarse Roots autotrophic respiration (gC m-2day-1)
BRANCH_AR Branch autotrophic respiration (gC m-2day-1)
F_CO2 CO2 fertilization effect (DIM) (as choiced in script)
F_CO2_VER CO2 fertilization effect (DIM) (Veroustraete’s version)
F_CO2_FRA CO2 fertilization effect (DIM) (Franks et al.’s version)
FCO2_TR CO2 fertilization effect (DIM) (for stomatal conductance)
FLIGHT Light modifier
FAGE Age modifier (0→1)
FT Air temperature modifier (0→1)
FVPD VPD modifier (0→1)
FN Soil nutrient modifier (0→1)
FSW Soil water modifier (0→1)
LITR_C Current Litter Carbon Pool (tC cell-1)
CWD_C Coarse Woody Debris Carbon (tC cell-1)
*variables may change across the different model versions
At cell level:
gpp Gross Primary Production (gC m-2day-1)
npp Net Primary Productivity (gC m-2day-1)
ar Autotrophic respiration (gC m-2day-1)
hr Heterotrophic respiration (gC m-2day-1)

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rsoil Soil respiration flux (gC m-2year-1)
reco Daily ecosystem respiration (gC m-2day-1)
nee Daily net ecosystem exchange (gC m-2day-1)
nep Daily net ecosystem production (gC m-2day-1)
et Daily evapotranspiration (mm m-2day-1)
le Daily latent heat flux (W m-2)
soil_evapo Daily soil evaporation (mm m-2day-1)
snow_pack Current Amount of Snow (Kg m-2)
asw Current available soil water (mm volume–1)
moist_ratio Soil moisture ratio (DIM)
iWue Daily intrinsic Water Use Efficiency (DIM)
litrC Litter carbon (gC m-2)
litr1C Litter labile carbon (gC m-2)
litr2C Litter unshielded carbon (gC m-2)
litr3C Litter shielded carbon (gC m-2)
litr4C Litter lignin carbon (gC m-2)
cwd_C Cwd carbon (gC m-2)
cwd_2C Cwd unshielded (gC m-2)
cwd_3C Cwd shielded (gC m-2)
cwd_4C Cwd lignin (gC m-2)
soilC Soil carbon (gC m-2)
soil1C Microbial recycling pool carbon (fast) (gC m-2)
soil2C Microbial recycling pool carbon (medium) (gC m-2)
soil3C Microbial recycling pool carbon (slow) (gC m-2)
soil4C Recalcitrant SOM carbon (humus, slowest) (gC m-2)
litterN Litter Nitrogen (gN m-2)
litter1N Litter labile Nitrogen (gN m-2)
litter2N Litter unshielded cellulose Nitrogen (gN m-2)
litter3N Litter shielded cellulose Nitrogen (gN m-2)
litter4N Litter lignin Nitrogen (gN m-2)
cwd_N Cwd Nitrogen (gN m-2)
cwd_2N Cwd unshielded Nitrogen (gN m-2)
cwd_3N Cwd shielded Nitrogen (gN m-2)
cwd_4N Cwd lignin Nitrogen (gN m-2)
soilN Soil Nitrogen (gN m-2)
soil1N Microbial recycling pool Nitrogen (fast) (gN m-2)
soil2N Microbial recycling pool Nitrogen (medium) (gN m-2)
soil3N Microbial recycling pool Nitrogen (slow) (gN m-2)
soil4N Recalcitrant SOM Nitrogen (humus, slowest) (gN m-2)
tsoil Soil Temperature (°C)
daylenght Day length
*variables may change across the different model versions
5.
Management
The model simulates several management practices on high stands, while coppice management is still
under development. Three different management practices can be simulated by 3D-CMCC-FEM. For each
treatment the user can specify intensity, interval and rotation age.
There are three main settings for management:
• "man on": the model will simulate the management as set in the species.txt file (e.g.

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Fagus_sylvatica.txt), for example the thinning.
• "man var": the model simulates the observed management (the thinning as observed in the
changes of stand density in the stand file “input.txt”) and then simulates the thinning interval and
final harvesting at the years taken from an external table (NAMESITE_management.txt) but with
the intensity as in the species.txt file (e.g. Fagus_sylvatica.txt). Note, in this case mortality is not
simulated at all.
• "man off": no management will be applied.
6.
3D-CMCC-FEM Usage
3D-CMCC-FEM is a command line program, and its behaviour is controlled by several command line
options:
*-i input path
i.e.: -i c:\input\directory\
*-o output path
i.e.: -o c:\output\directory\
*-p parameterization directory
i.e.: -i c:\parameterization\directory\
-d dataset filename stored into input directory
i.e.: -d input.txt
-m met filename list stored into input directory
i.e.: -m meteo.txt or meteo.nc
-s soil filename stored into input directory
i.e.: -s soil.txt or soil.nc
-t topo filename stored into input directory
i.e.: -t topo.txt or topo.nc
-c settings filename stored into input directory
i.e.: -c settings.txt
-k CO2 atmospheric concentration file
i.e.: -k co2_conc.txt
-n ndep file
i.e.: -n ndep.txt
-r output vars list
i.e.: -r output_vars.lst
-u benchmark path
(for model developers)
-h
print this help
*Parameters NOT mandatory, mostly used from developers or in specific model versions under development
More specifically:
-i
This is not a mandatory parameter. if not used, input files will be searched where
program is.
-o
This is not a mandatory parameter. If not used, output files will be created where program is.
-p
This is not a mandatory parameter. If not used, parameterization file will be searched where
program is.

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-d “stand”
This file will be searched in input path, if specified. It can be an ASCII or NETCDF file. You
can use '//' for comment it. ASCII file must have following header, separated by a comma:
Mandatory parameters: “Year, x, y, Age, Species, Management, N,
Stool, AvDBH, Height”
NOTE: Please see [SPECIES]* section and [MANAGEMENT]** section to check allowed
values. Same columns name applies to variables name in NETCDF version of file.
-m “meteo”
This file will be searched in input path, if specified. It can be an ASCII or NETCDF file. You can
specify a .lst ( list ) file if you have separated values.
List file must contain the name of NETCDF files to import, one row for variable e.g.:
6_WS_f_2000_2001_123_456.nc
6_TOT_PREC_2000_2001_123_456.nc
6_SWC_2000_2001_123_456.nc
6_TMAX_2M_2000_2001_123_456.nc
6_TMIN_2M_2000_2001_123_456.nc
6_TSOIL_2000_2001_123_456.nc
6_VPD_2000_2001_123_456.nc
6_ET_2000_2001_123_456.nc
6_LAI_2000_2001_123_456.nc
6_RADS_2000_2001_123_456.nc
ASCII file must have following header, separated by a tab (/t) :
Mandatory parameters: “Year, Month, n_days, Rg_f, Ta_f, Tmax,
Tmin, Rh_f, Ts_f, Precip, SWC, LAI, ET, WS_f”
Same columns name applies to variables name in NETCDF version of file.
-s “soil”
This file will be searched in input path, if specified.
It can be an ASCII or NETCDF file. ASCII file must have following header, separated by a
comma:
Mandatory parameters: “X, Y, LANDUSE, LAT, LON, CLAY_PERC,
SILT_PERC, SAND_PERC, SOIL_DEPTH, SOIL_DEPTH, FR, FN0, FNN,
M0, LITTERC, LITTERN, SOILC, SOILN, DEADWOODC”
Please see [LANDUSE] section to check allowed values. Same columns name applies to
variables name in NETCDF version of file.

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-t “topography”
This file will be searched in input path, if specified.
It can be an ASCII or NETCDF file.
ASCII file must have following header, separated by a comma
Mandatory parameters: “X, Y, ELEV”
Same columns name applies to variables name in NETCDF version of file.
-c “model setting”
This file will be searched in input path, if specified.
It must be an ASCII file. You can put comment using '//' token;
NOTE: the file must contain the rows described in the “Settings file” section.
-k “[CO2]”
This file will be searched in input path, if specified.
It must be an ASCII file and must have following header, separated by a tab (/t):
Mandatory parameters: “year (/t) CO2_ppm”
NOTE: mandatory parameter only if “CO2_trans” in settings file is set on 'on' or 'var'
-n “N deposition”
This file will be searched in input path, if specified.
It must be an ASCII file and must have following header, separated by a tab (/t):
Mandatory parameters: ““year (/t) ndep”
NOTE: mandatory parameter only if “Ndep_fixed” in settings file is set on 'off'
-r
this is not a mandatory parameter. Use it if you want export variables values inside a NETCDF
file.
You can specify more variables per row using a comma as delimiter. Each variable must
have "daily_", "monthly_" or "annual_" prefix. i.e.:
daily_gpp, annual_GPP, daily_ar, monthly_ar, annual_npp
In previous example, daily values for GPP and AR are exported. Monthly values for AR are
exported and annual values for GPP and NPP are exported. Files will be created in output
path if any or where program is.
[SPECIES]*
Following species can be used on relative column inside an ASCII dataset
(without indexes)
NOTE: Please note that you must use their indexes if you use a NETCDF file.
0,Fagussylvatica
1,Castaneasativa
2,Larixdecidua
3,Piceaabies
4,Pinussylvestris
5,Quercuscerris
6,Quercusilex

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7,Quercusrobur
8, quercus_deciduous
9,quercus_evergreen
[MANAGEMENT]**
Following type of management can be used on relative column inside as ASCII dataset
(without indexes).
NOTE: Please note that you must use their indexes if you use a NETCDF file.
T is for timber
C is for Coppice (under development)
0,T
1,C
[LANDUSE]***
Following type of landuse can be used on relative column inside as ASCII dataset
(without indexes).
Please note that you must use their indexes if you use a NETCDF file.
F is for Forest
Z is for Crop (currently not implemented)
0,F
1,Z
7.
How to run and develop the 3D-CMCC-FEM
7.1 Code characteristics
3D-CMCC-FEM was primarily developed on UNIX-Linux with Eclipse IDE Platforms and is compiled using
GNU GCC 4.7.2.
IMPORTANT: Be sure to execute 3D-CMCC-FEM on a Linux machine with architecture X86_64 (64 bit),
otherwise you firstly need to rebuild code to obtain the object files needed for runs.
7.2 Eclipse usage instruction (for developers)
To Run or to modify (develop the model we suggest using Eclipse CDT simply following these steps (be sure
if you choose to use Eclipse, to have installed Git and Egit and to have an internet connection):
1) Save the 3D-CMCC-FEM Model (https://github.com/Forest-Modelling-Lab/3D- CMCC-FEM) directory
in the path you are going to use as Eclipse Workspace;
2) to prevent error from NETCDF libraries, open terminal and type:
• $ sudo apt-get install netcdf-bin
• $ sudo apt-get install libnetcdf-dev
3) To make the model work under Eclipse CDT (any version) using Git follow these steps:
• download from terminal Git and build-essential
o $ sudo apt-get install build-essential
o $ sudo apt-get install git

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• download from Ubuntu software center jre 7-8 or jdk (if not installed)
o $ sudo apt-get install default-jdk
4) Download from Eclipse site the most recent version of Eclipse IDE for C/C++ Developers
(https://www.eclipse.org/downloads/packages/)
5) Open Eclipse and set your Workspace as the same path in which you've placed the Model's folder - to
do so click on File, then "switch Workspace" and click on "Other..."; here input your current path;
6) File -> Import -> Git -> Projects from Git -> Clone Url and in URL please paste the code version you
find over the GitHub https://github.com/Forest-Modelling-Lab/3D-CMCC-FEM
For NETCDF file you need to add libraries within eclipse through:
Project->Properties->C/C++ Build->Settings->Cross G++ Linker->Libraries-> in Libraries (-l) add "netcdf"->OK
How to increase Eclipse available heap size (optional)
Some JVMs put restrictions on the total amount of memory available on the heap. If you are getting
OutOfMemoryErrors while running Eclipse, the VM can be told to let the heap grow to a larger amount by
passing the -vmargs command to the Eclipse launcher
(http://wiki.eclipse.org/FAQ_How_do_I_increase_the_heap_size_available_to_Eclipse%3F).
Here follows a short how to:
1) Search for the location of your eclipse.ini file (usually usr/lib/eclipse);
2) Open eclipse.ini using gedit command from terminal as super user (sudo gedit eclipse.ini);
BE EXTREMELY CAREFUL TO FOLLOW ECLIPSE DEVELOPERS RULES
Each option and each argument to an option must be on its own line.
All lines after -vmargs are passed as arguments to the JVM, so all arguments and options for eclipse must
be specified before -vmargs (just like when you use arguments on the command- line).
Any use of -vmargs on the command-line replaces all -vmargs settings in the .ini file unless – launcher
.appendVmargs is specified either in the .ini file or on the command-line. (doc):
in line 12 change -Xms40m into -Xms512m (just replace 40 with 512 without changing the rest of the line).
in line 13 change -Xmx256m into -Xmx1024m (just replace 256 with 11024 without changing the rest of the
line)
save eclipse.ini and restart eclipse.
How to work on Eclipse for bash scripts (optional)
To work in Bash Shell scripts within the Eclipse IDE you need to install ShellED eclipse package through the
web.
7.3 Bash launch (for UNIX users)
If you are interested only in running the 3D-CMCC-FEM with no interest in developing the model code you
can either run the model code in the terminal (i.e. Bash) once check that you have the executable (in Debug
or Release folder) build for your OS (be careful that it fits with your architecture: i.e. 36 or 64 bit) through:
o ./3D_CMCC_Forest_Model …., …., ….

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Figure 8|Launching the model in Bash
8.
Questions or comments
Shall you have issues with the code or for any suggestions, please let us know. For any questions on how to
parameterize or run the code, please read this file first.
Contacts:
The laboratory forest.modelling.lab@gmail.com
The developers 3d_cmcc_fem@gmail.com
Alessio Collalti alessio.collalti@cnr.it
Daniela Dalmonech daniela.dalmonech@cnr.it
Elia Vangi elia.vangi@isafom.cnr.it
Paulina Puchi paulina.puchi@isafom.cnr.it
Gina Marano ginamarano.forest@gmail.com
Version updated: 1 July, 2023