LANDIS II Biomass Succession V1.2 Pn ET V3.0 User Guide

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PnET-Succession v3.0
Extension User Guide
Eric J. Gustafson
US Forest Service
Northern Research Station
Brian R. Miranda
US Forest Service
Northern Research Station
Arjan M.G. de Bruijn
Purdue University

Last Revised: January 11, 2018

PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

Table of Contents
1

INTRODUCTION ...................................................................................................................................... 6
1.1 Major modifications made to PnET algorithms ....................................................................................... 6
1.2 Advantages and disadvantages of PnET-Succession compared to Biomass Succession ......................... 7
1.3 What’s new in version 3.0 ....................................................................................................................... 8
1.4 References ............................................................................................................................................... 9
1.5 Acknowledgments ................................................................................................................................. 10
1.6 Release History ...................................................................................................................................... 10
1.6.1
Major Releases ............................................................................................................................. 10
1.6.2
Minor Releases ............................................................................................................................. 12

PNET-SUCCESSION .............................................................................................................................. 14
2.1 Initializing Biomass ............................................................................................................................... 14
2.2 LAI Shade Calculation .......................................................................................................................... 15
2.3 Cohort Reproduction and Establishment ............................................................................................... 15
2.4 Cohort Competition ............................................................................................................................... 15
2.4.1
Light ............................................................................................................................................. 16
2.4.2
Water ............................................................................................................................................ 17
2.4.3
Other factors ................................................................................................................................ 22
2.5 Cohort Growth and Ageing ................................................................................................................... 23
2.6 Cohort Senescence and Mortality .......................................................................................................... 23
2.7 Dead Biomass Decay ............................................................................................................................. 23
2.8 References ............................................................................................................................................. 23

INPUT FILE - PNET-SUCCESSION..................................................................................................... 25
3.1
3.2
3.3
3.4
3.5
3.6
3.7
3.8
3.9
3.10
3.11

Example PnET-Succession input file .................................................................................................... 25
LandisData ............................................................................................................................................. 25
Timestep ................................................................................................................................................ 25
StartYear ................................................................................................................................................ 25
SeedingAlgorithm.................................................................................................................................. 26
PNEToutputsites .................................................................................................................................... 26
InitialCommunities ................................................................................................................................ 26
InitialCommunitiesMap ......................................................................................................................... 26
PnETGenericParameters ........................................................................................................................ 26
PnETSpeciesParameters ................................................................................................................... 27
EcoregionParameters ........................................................................................................................ 27

INPUT FILE – INITIAL COMMUNITY CLASSES ............................................................................ 28
4.1 Example File .......................................................................................................................................... 28
4.2 LandisData ............................................................................................................................................. 29
4.3 Initial Community Class Definitions ..................................................................................................... 29
4.3.1
MapCode ...................................................................................................................................... 29
4.3.2
Species Present ............................................................................................................................ 29
4.3.3
Grouping Species Ages into Cohorts ........................................................................................... 29

INPUT FILE – INITIAL COMMUNITY MAP .................................................................................... 30

INPUT FILE – CLIMATE ...................................................................................................................... 30

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension
6.1.1
Example File #1 ........................................................................................................................... 30
6.1.2
Example File #2 ........................................................................................................................... 31
6.2 Header Information................................................................................................................................ 31
6.3 Observations .......................................................................................................................................... 31
6.3.1
Year .............................................................................................................................................. 31
6.3.2
Month ........................................................................................................................................... 31
6.3.3
TMax ............................................................................................................................................ 31
6.3.4
TMin ............................................................................................................................................. 32
6.3.5
PAR .............................................................................................................................................. 32
6.3.6
Prec .............................................................................................................................................. 32
6.3.7
CO2 .............................................................................................................................................. 32
6.3.8
O3 (Optional) ............................................................................................................................... 32
7

INPUT FILE – GENERIC PNET SPECIES PARAMETERS ............................................................. 33
7.1
7.2
7.3
7.4
7.5
7.6
7.7
7.8
7.9
7.10
7.11
7.12
7.13
7.14
7.15
7.16
7.17
7.18
7.19

Example file: ......................................................................................................................................... 33
LandisData ............................................................................................................................................. 33
PnETGenericParameters ........................................................................................................................ 33
MaxCanopyLayers................................................................................................................................. 34
MaxDevLyrAv ...................................................................................................................................... 34
IMAX .................................................................................................................................................... 34
DVPD1, DVPD2 ................................................................................................................................... 34
BFolResp ............................................................................................................................................... 34
MaintResp.............................................................................................................................................. 34
TORoot/TOWood ............................................................................................................................. 35
Q10 ................................................................................................................................................... 35
FolLignin .......................................................................................................................................... 35
KWdLit ............................................................................................................................................. 35
InitialNSC ......................................................................................................................................... 35
CFracBiomass ................................................................................................................................... 35
PrecipEvents ..................................................................................................................................... 35
PreventEstablishment........................................................................................................................ 35
Wythers ............................................................................................................................................. 36
DTEMP ............................................................................................................................................. 36

INPUT FILE – PNET SPECIES PARAMETERS ................................................................................ 37
8.1
8.2
8.3
8.4
8.5
8.6
8.7
8.8
8.9
8.10
8.11
8.12
8.13
8.14

Example file: ......................................................................................................................................... 37
LandisData ............................................................................................................................................. 37
PnETSpeciesParameters (species name) ............................................................................................... 37
FolN ....................................................................................................................................................... 37
SLWmax ................................................................................................................................................ 37
SLWDel ................................................................................................................................................. 38
Tofol ...................................................................................................................................................... 38
AmaxA .................................................................................................................................................. 38
AmaxB ................................................................................................................................................... 38
HalfSat .............................................................................................................................................. 38
H2, H3, H4 ........................................................................................................................................ 38
PsnAgeRed ....................................................................................................................................... 38
PsnTMin ........................................................................................................................................... 39
PsnTOpt ............................................................................................................................................ 39

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension
8.15
8.16
8.17
8.18
8.19
8.20
8.21
8.22
8.23
8.24
8.25
9

INPUT FILE - ECOREGION PARAMETERS .................................................................................... 42
9.1
9.2
9.3
9.4
9.5
9.6
9.7
9.8
9.9
9.10
9.11

Example file: ..................................................................................................................................... 44
LandisData ........................................................................................................................................ 44
Timestep ........................................................................................................................................... 44
Species .............................................................................................................................................. 44
Map Name Template ........................................................................................................................ 44

INPUT FILE – PNETOUTPUTSITES ................................................................................................... 47
11.1
11.2
11.3

Example file: ......................................................................................................................................... 42
LandisData ............................................................................................................................................. 42
EcoregionParameters (ecoregion name) ................................................................................................ 42
SoilType ................................................................................................................................................ 42
Latitude .................................................................................................................................................. 42
RootingDepth ........................................................................................................................................ 43
PrecLossFrac ......................................................................................................................................... 43
LeakageFrac .......................................................................................................................................... 43
PrecIntConst .......................................................................................................................................... 43
SnowSublimFrac ............................................................................................................................... 43
ClimateFileName .............................................................................................................................. 43

INPUT FILE - OUTPUT-PNET ............................................................................................................. 44
10.1
10.2
10.3
10.4
10.5

k ........................................................................................................................................................ 39
DNSC ................................................................................................................................................ 39
FracBelowG ...................................................................................................................................... 39
EstMoist ............................................................................................................................................ 39
EstRad ............................................................................................................................................... 40
FracFol .............................................................................................................................................. 40
FrActWd ........................................................................................................................................... 40
CO2HalfSatEff.................................................................................................................................. 40
O3StomataSens (Optional) ............................................................................................................... 40
O3GrowthSens (Optional) ................................................................................................................ 40
FolNInt, FolNSlope (Optional) ......................................................................................................... 41

Example file: ..................................................................................................................................... 47
LandisData ........................................................................................................................................ 47
PnEToutputsites ................................................................................................................................ 47

OUTPUT FILE - SITEDATA TABLE (OPTIONAL PNETOUTPUTSITES OUTPUT) ................. 48
12.1
12.2
12.3
12.4
12.5
12.6
12.7
12.8
12.9
12.10
12.11

Time .................................................................................................................................................. 48
Ecoregion .......................................................................................................................................... 48
SoilType ............................................................................................................................................ 48
NrOfCohorts ..................................................................................................................................... 48
MaxLayerStdev................................................................................................................................. 48
Layers ............................................................................................................................................... 48
PAR0 ................................................................................................................................................ 48
Tday(C) ............................................................................................................................................. 48
Precip(mm_mo) ................................................................................................................................ 49
CO2(ppm) ......................................................................................................................................... 49
O3(cum_ppb_h) ................................................................................................................................ 49

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension
12.12
12.13
12.14
12.15
12.16
12.17
12.18
12.19
12.20
12.21
12.22
12.23
12.24
12.25
12.26
12.27
12.28
12.29
12.30
12.31
12.32
12.33
12.34
12.35
12.36
13

RunOff(mm_mo) .............................................................................................................................. 49
Leakage(mm) .................................................................................................................................... 49
PET(mm) .......................................................................................................................................... 49
Evaporation(mm) .............................................................................................................................. 49
Transpiration(mm) ............................................................................................................................ 49
Interception(mm) .............................................................................................................................. 49
SurfaceRunOff(mm_mo) .................................................................................................................. 49
Water(mm) ........................................................................................................................................ 50
PressureHead(m) ............................................................................................................................... 50
SnowPack (mm) ................................................................................................................................ 50
LAI(m2) ............................................................................................................................................ 50
VPD(kPa).......................................................................................................................................... 50
GrossPsn(gC/mo) .............................................................................................................................. 50
NetPsn(gC/mo) ................................................................................................................................. 50
MaintenanceRespiration(gC/mo) ...................................................................................................... 50
Wood(gDW) ..................................................................................................................................... 50
Root(gDW) ....................................................................................................................................... 50
Fol(gDW) .......................................................................................................................................... 50
NSC(gC) ........................................................................................................................................... 51
HeteroResp(gC_mo) ......................................................................................................................... 51
Litter(gDW/m2) ................................................................................................................................. 51
CWD(gDW/m2) ................................................................................................................................ 51
WoodySenescence (gDW/m2)........................................................................................................... 51
FoliageSenescence (gDW/m2) .......................................................................................................... 51
SubcanopyPAR ................................................................................................................................. 51

OUTPUT FILE - COHORTDATA TABLE (OPTIONAL PNETOUTPUTSITES OUTPUT) ......... 52
13.1
13.2
13.3
13.4
13.5
13.6
13.7
13.8
13.9
13.10
13.11
13.12
13.13
13.14
13.15
13.16
13.17
13.18
13.19
13.20
13.21
13.22

Time(yr) ............................................................................................................................................ 52
Age(yr) .............................................................................................................................................. 52
TopLayer(-)....................................................................................................................................... 52
LAI(m2) ............................................................................................................................................ 52
GrossPsn(gC/m2/mo)........................................................................................................................ 52
FolResp(gC/m2/mo) ......................................................................................................................... 52
MaintResp(gC/m2/mo) ..................................................................................................................... 52
NetPsn(gC/m2/mo) ........................................................................................................................... 52
Transpiration(mm/mo) ...................................................................................................................... 53
WUE(g/mm) ..................................................................................................................................... 53
Fol(gDW/m2) .................................................................................................................................... 53
Root(gDW/m2) .................................................................................................................................. 53
Wood(gDW/m2) ................................................................................................................................ 53
NSC(gC/m2) ...................................................................................................................................... 53
NSCfrac(-) ........................................................................................................................................ 53
fWater(-) ........................................................................................................................................... 53
fRad(-)............................................................................................................................................... 53
fOzone(-)........................................................................................................................................... 53
DelAmax(-) ....................................................................................................................................... 53
fTemp_psn(-) .................................................................................................................................... 54
fTemp_resp(-) ................................................................................................................................... 54
fAge(-) .............................................................................................................................................. 54

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension
13.23
13.24
13.25
13.26
13.27
14

OUTPUT FILE – ESTABLISHMENT TABLE (OPTIONAL PNETOUTPUTSITES OUTPUT) .. 55
14.1
14.2
14.3
14.4
14.5
14.6

LeafOn(-) .......................................................................................................................................... 54
FActiveBiomass(gDW_gDW) .......................................................................................................... 54
AdjFolN(gN_gC) .............................................................................................................................. 54
CiModifier(-) .................................................................................................................................... 54
AdjHalfSat ........................................................................................................................................ 54

Year .................................................................................................................................................. 55
Species .............................................................................................................................................. 55
Pest.................................................................................................................................................... 55
fWater ............................................................................................................................................... 55
fRad .................................................................................................................................................. 55
Est ..................................................................................................................................................... 55

APPENDIX. CALIBRATION TIPS. ..................................................................................................... 56

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

1 Introduction
This document describes the PnET-Succession extension for the LANDIS-II
model. For information about the model and its core concepts including
succession, see the LANDIS-II Conceptual Model Description.
The PnET-Succession extension is based on the Biomass Succession
extension of Sheller and Mladenoff (2004), embedding elements of the PnETII ecophysiology model of Aber et al (1995) to simulate growth as a
competition for available light and water, replacing the existing competition
for “growing space” algorithms. PnET (Photosynthesis and
EvapoTranspiration) is a simple, lumped parameter model of carbon and
water balances of forests (Aber and Federer 1992), built on two principal
relationships: 1) maximum photo-synthetic rate is a function of foliar nitrogen
concentration, and 2) stomatal conductance is a function of realized
photosynthetic rate.

1.1 Major modifications made to PnET algorithms
Several modifications were made to PnET algorithms to make them tractable
at landscape scales, primarily by broadening the scale of integration
operations. (1) The PnET timestep was broadened from daily to monthly. (2)
The number of sub-layers within a canopy layer was 50 in PnET, but is here
set by the user (IMAX) to increase computational efficiency, where each sublayer represents an even proportion of the total LAI within the layer. A
greater number of subcanopy layers tighten the feedback between
photosynthesis and water stress, but significantly increases computation time.
(3) PnET adds foliage to successively deeper subcanopy layers until there is
insufficient light to support photosynthesis. PnET-Succession allocates
foliage in proportion to the active wood (xylem) that supports it. (4) Cohort
biomass is used as a surrogate for tree height to simulate canopy layers, which
are added when the variation in biomass among cohorts exceeds a userdefined amount. (5) Photosynthates are allocated to four pools (foliage, root,
wood and non-structural carbon (reserves, NSC)). Net photosynthesis is
initially allocated to the NSC pool, and then foliage allocation occurs,
followed by allocation to root and wood pools such that the above- and
below-ground biomass ratio is preserved. Maintenance respiration is then
deducted from the NSC pool. Details of model structure and modifications
can be found in De Bruijn et al (2014).

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

1.2 Advantages and disadvantages of PnET-Succession
compared to Biomass Succession
The goal for PnET-Succession was to make the simulation of growth and
competition more mechanistic and more explicitly linked to fundamental
drivers that are changing, such as climate and atmospheric composition (e.g.,
CO2 and ozone). It is believed that this more mechanistic approach will be
more robust for making projections under climate and other global changes
(Gustafson 2103).

Advantages of PnET-Succession compared to Biomass Succession
1) PnET-Succession replaces the input parameters ANPPmax and Bmax of
LANDIS-II Biomass Succession with mechanistic and dynamic calculations
of growth and senescence that depend on monthly climatic conditions and
competition for resources. Establishment and growth are now emergent
properties of the model and are explicitly linked to changing fundamental
drivers such as climate and CO2 concentrations.
2) Dynamic calculations of LAI and photosynthesis allow cohorts to die prior
to senescence, based on physiological constraints (too few carbon reserves).
This can typically occur when carbon reserves production is insufficient to
support growth due to shading, water competition, drought, diseases or pests.
This allows more realistic simulation of cohort death in the course of stand
development (i.e., mortality is highest in the younger cohorts), and a more
realistic accounting of biomass accumulation. An added benefit is that the
number of cohorts to be simulated is reduced.
3) PnET-Succession allows a more explicit simulation of species’ survival
strategies, by implementing a dynamic competition for light and water. For
example, one can parameterize species or species-group combinations of
respiration losses and water use efficiency to implement competition
advantages or disadvantages for particular species in sites that are dry or
shaded due to competing vegetation.

Disadvantages of PnET-Succession compared to Biomass Succession
1) PnET-Succession requires more parameters, which adds to uncertainty and
increases the parameter burden when using the model. However, uncertainty
may be no higher than when making ad hoc assumptions for other succession
extensions about how novel conditions will affect modeled processes.
2) Runtimes tend to be somewhat longer, but only slightly longer because
many cohorts senesce prior to reaching longevity age, greatly reducing the
number of cohorts that must be simulated. In both Biomass Succession and

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

PnET-Succession, simulation of dispersal is sometimes more time consuming
than the forest growth part.

1.3 What’s new in version 3.0
Latitude is now an ecoregion parameter, allowing for large study areas with
spatially dispersed ecoregions.
PnET-Succession v2.0 (and earlier) used equations from early versions of
PnET-II to compute the CO2 enrichment effect (DelAmax). The most recent
version of PnET-II uses an equation from Franks et al. (2013), which
moderates the CO2 effect, especially at high CO2 concentrations. We now use
a modified version of the Franks equation that uses internal leaf CO2
concentrations rather than external leaf CO2 concentrations (Gustafson et al in
prep).
Now compute a variable (CiModifier) to compute reduce conductance as a
function of water stress (fWater), ozone dose and species ozone tolerance.
This is used to reflect stomatal closure caused by water stress, which is
modified by sluggishness induced by elevated ozone, modeling its interaction
with conductance of CO2 and water. Absorption of CO2 and O3 and
transpiration of water are all reduced by CiModifier.
Modified the canopy layering algorithm so that all cohort canopy sublayers
are assigned to only one main canopy layer (i.e., a cohort cannot span
multiple main canopy layers).
Provide a parameter (CO2HalfSatEff) to optionally make HalfSat dynamic as
a function of CO2 concentration. Set this to zero to turn off effect.
Provide parameters (FolNInt, FolNSlope) to optionally make FolN dynamic
as a function of light (fRad), allowing photosynthetic capability (Amax) to
vary vertically through the canopy (by canopy sublayer) and in response to
cohort release or overtopping. Set these to 1.0 and 0.0 to turn off effect.
Added optional output variables to the PnETOutputSites file with speciesspecific amounts of dead wood (WoodySenescence) and foliage
(FoliageSenescence) added to the respective dead biomass pools.
Dropped the WUEConst species parameter. Water use efficiency is now
calculated directly from CO2 uptake (JCO2) and transpiration (JH2O).
Added the ability to optionally include ozone effects on photosynthesis.
These functions are activated only when the climate input file contains a field
with monthly cumulative ozone concentrations.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

Added the O3GrowthSens parameter to scale the computation of the speciesspecific ozone effect that reflects the damaging effects of ozone on
photosynthetic tissue. This is used to specify species sensitivity to ozone
damage of tissues, and is only needed when ozone data are provided in the
climate file.
Added the O3StomataSens parameter to reflect species differences in stomatal
sluggishness when exposed to ozone. This categorical class impacts how
CiModifier is calculated, and is only needed when ozone data are provided in
the climate file.
Litter decomposition is now computed once per year, including during initial
spin-up.
The Excel worksheet [PnET-Succession function worksheet.xlsx] that is also
available from (http://www.landis-ii.org/extensions/pnet-succession) is now
copied to the ‘docs’ folder along with the User Guide during installation.

1.4 References
Aber, J.D., Federer C.A. 1992. A generalized, lumped parameter model
of photosynthesis, evapotranspiration and net primary production in
temperate and boreal forest ecosystems. Oecologia 92: 463-474.
Aber, J.D., Ollinger, S.V., Federer, A., Reich, P.B., Goulden, M.L.,
Kicklighter D.W., Melillo J.M., Lathrop R.G. 1995. Predicting the
effects of climate change on water yield and forest production in the
northeastern United States. Climate Research 5:207-222.
De Bruijn AMG., Gustafson E.J, Sturtevant B., Foster J., Miranda B.,
Lichti N., Jacobs D.F. 2014. Toward more robust projections of
forest landscape dynamics under novel environmental conditions:
embedding PnET within LANDIS-II. Ecological Modelling 287:44–
57.
Franks, P. J., Adams, M. A., Amthor, J. S., Barbour, M. M., Berry, J. A.,
Ellsworth, D. S., Farquhar, G. D., Ghannoum, O., Lloyd, J.,
McDowell, N., Norby, R. J., Tissue, D. T. and von Caemmerer, S.
2013. Sensitivity of plants to changing atmospheric CO2
concentration: from the geological past to the next century. New
Phytologist 197:1077–1094. doi:10.1111/nph.12104.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

Gustafson, E.J. 2013. When relationships estimated in the past cannot be
used to predict the future: using mechanistic models to predict
landscape ecological dynamics in a changing world. Landscape
Ecology 28:1429-1437.
Scheller, R.M., Mladenoff, D.J. 2004. A forest growth and biomass
module for a landscape simulation model, LANDIS: Design,
validation, and application. Ecological Modelling 180(1):211-229.
Wythers K.R., Reich P.B., Bradford J.B. 2013. Incorporating
temperature-sensitive Q10 and foliar respiration acclimation
algorithms modifies modeled ecosystem responses to global change.
Journal of Geophysical Research: BioGeosciences 118:1–14.

1.5 Acknowledgments
Funding for the development of the PnET-Succession extension was
provided by a grant from the USDA/NASA NIFA/AFRI program to
Purdue University. Valuable scientific contributions to the development of
the extension were made by Arjan De Bruijn, Eric J. Gustafson, Brian R.
Sturtevant and Mark Kubiske. Critical assistance in the development of the
ozone capability was provided by Scott Ollinger and Zaixing Zhou
(University of New Hampshire) and Elena Paoletti and Yasutomo Hoshika
(Institute of Sustainable Plant Protection, National Research Council of
Italy).
Funding for the development of LANDIS-II was provided by the Northern
Research Station (Rhinelander, Wisconsin) of the U.S. Forest Service.
Valuable contributions to the development of LANDIS-II were made by
Robert M. Scheller, Brian R. Sturtevant, Eric J. Gustafson, and David J.
Mladenoff.

1.6 Release History
1.6.1 Major Releases
1.6.1.1 Version 2.0

New generic parameter: PrecipEvents. Divides incoming monthly
precipitation into discrete events within the month (n=PrecipEvents) and
applies each portion randomly during the sequence of processing canopy
sublayers. This prevents large cohorts from consuming a disproportionate
share of the available water in a given month.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

New generic parameter: Wythers. Option to apply the foliar respiration
correction as proposed by Wythers et al (2013).
New generic parameter: DTEMP. Option to apply the temperature reduction
factor (DTEMP) of PnET-II rather than the original PnET-Succession v1.2
temperature reduction factor. The v1.2 temperature reduction factor does not
explicitly penalize photosynthesis at temperatures above PsnTOpt.
New ecoregion parameter: SnowSublimFrac. Snowpack is reduced by this
amount prior to snowmelt, representing sublimation and meltwater runoff that
does not enter the soil.
New output options for woody senescence and foliage senescence by species.
Bug fixes:
•

A bug in the calculation of transpiration was fixed.

•

A bug that caused the decomposition of dead pools to not be simulated
during spin-up in prior versions was fixed.

•

A bug in the calculation of runoff was fixed.

•

Biomass values provided to disturbance extensions in prior versions
were the sum of above- and below-ground woody biomass, but no
foliar biomass. Version 2.0 includes aboveground and foliar biomass
to be consistent with other Biomass Succession extensions and is
therefore more compatible with biomass disturbance extensions.
Specific biomass pools can be now output as maps and total pool sizes
using the Output-PnET extension (Section 10).

•

Defoliation (by an external disturbance extension) is now applied
during June (previously it was January when deciduous species had no
foliage).

•

A bug in the processing of cohorts killed by disturbance was fixed.
The bug prevented disturbances from recording the cohorts being
removed.

•

A bug in the calculation of snow melt was fixed. The bug caused all
snow pack to melt at the same time. The rate of snowmelt was
changed to 2.74 mm/°C/day (see 2.4.2.1).

•

When snowpack is present, surface PAR is set to 0 which eliminates
soil water evaporation under snow (though sublimation of snow
occurs instead)

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

An Excel worksheet [PnET-Succession function worksheet.xlsx] is available
from (http://www.landis-ii.org/extensions/pnet-succession) that can be used to
better understand how selected input parameters affect state variable
computations.
1.6.1.2 Version 1.0

Original released version
1.6.2 Minor Releases
1.6.2.1 Version 2.1.1 (October 2017)

This release incorporates a change to the Biomass Cohort Library to
maintain compatibility with other extensions that use the same library (all
extensions that use cohorts with biomass attributes). The edit to the
Biomass Cohort Library enabled the proper tracking of dead biomass
(additions to the dead pools) when partial cohort removals occurred.
This version also adds compatibility with the Metadata Library that supports
output visualization using the VizTool.
1.6.2.2 Version 2.1 (May 2017)

An important bug related to dispersal was fixed in this version. Previously,
the age of the youngest cohort of a species was used to determine if a mature
cohort was present on a site for seeding purposes. The test should use the age
of the oldest cohort of a species to check for maturity and determine sources
of seed for dispersal. This error has been corrected.
Rename [SurfaceRunoff] to [PrecLoss] in the Site Output file to distinguish
between water lost due to soil saturation (SurfaceRunOff) and water lost due
to other factors (PrecLoss; e.g., slope, impervious surface). Add tracking of
PrecLoss variable.
Rename [Layer] to [TopLayer] in the Cohort Output file to denote that the
value reported is the highest layer in which the cohort appears. The top
canopy layer has the highest layer value.
The allocation of precipitation events to subcanopy layers has been adjusted
so that the precip events are randomly assigned to layers, but not constrained
to a single event per layer. This can result in multiple precip events occurring
(with their associated runoff, interception, leakage, etc.) for a given layer,
especially when the number of precipitation events is greater than the number

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

of subcanopy layers on a site. This resolves a discontinuity in the water cycle
when the number of cohorts was low relative to the number of precip events.
Bug Fixes:
•

Fixed the DiscreteUniformRandom function to be inclusive of the
maximum value. Previous implementation may have been slightly
biased in the shuffling of subcanopy layers.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

2 PnET-Succession
The PnET-Succession Extension generally follows the methods of the
Biomass Succession Extension: Age cohorts reproduce, grow (add biomass),
age, and die. The PnET-Succession Extension replaces the simple growth and
competition algorithms from the Biomass Succession Extension with the
photosynthesis and respiration equations from PnET-II to simulate growth of
specific cohort biomass components (root, foliage, wood, non-structural
carbon) as a competition for water and light.
PnET-Succession simulates the competition of cohorts for water and light as a
function of photosynthetic processes. Competition for water is simulated on
each site (grid cell) through a dynamic soil water balance that receives
precipitation and loses water as runoff, interception, percolation out of the
rooting zone and consumption by cohorts through transpiration. Competition
for light is modeled by tracking solar radiation through canopy layers (related
to cohort age) according to a standard Lambert-Beer formula. PnETSuccession requires average monthly temperature, precipitation,
photosynthetically active radiation and atmospheric CO2 concentration as
inputs.
Because monthly climate data are provided as an input to the extension,
species establishment probability is also calculated at each time step as a
function of the climate conditions during the time step.
The PnET-Succession Extension also changes the calculation of shade. LAI
is estimated for multiple canopy layers, and available light is computed for
each layer, including the sub-canopy (i.e., ground).
The PnET-Succession Extension tracks biomass in four live pools (foliage,
roots, wood and non-structural (C reserves)) and two dead pools (woody and
leaf litter). For disturbance extensions that request “biomass” from the
succession extension, PnET-Succession passes the sum of wood+foliage.

2.1 Initializing Biomass
At the beginning of a scenario, the initial communities begin with appropriate
living and dead biomass values estimated for each site. However, the user
does not supply the initial biomass estimates. Rather, the PnET-Succession
extension uses its growth algorithms to iterate the number of time steps equal
to the maximum cohort age for each site. Beginning at time (t - oldest cohort
age), cohorts are added at each time step corresponding to the time when the
existing cohorts were established. Thus, each cohort undergoes growth and
mortality for the number of years equal to its current age, and its initial
biomass value reflects competition among cohorts. Note: this is a

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

computationally intensive process that may require significant time for
complex initial landscapes. Additionally, climate data are required back to t oldest cohort age. To facilitate climatic input in years where weather records
do not exist, it is possible to supply mean monthly climate data for a range of
years (see section 6.1.2)
This biomass initialization does not account for disturbances that would likely
happen prior to initialization and therefore tends to overestimate initial live
biomass and underestimate initial dead biomass. Furthermore, some cohorts
may not survive spin-up.

2.2 LAI Shade Calculation
Site shade is calculated based on LAI in canopy layers (see section 2.4.1).

2.3 Cohort Reproduction and Establishment
Cohort establishment is the result of two distinct processes: 1) production and
dispersal of seeds and 2) seed germination and successful recruitment of a
viable new cohort.
Seed is produced by every cohort that is at least the age of sexual maturity.
Seed dispersal is modeled as a spatial process according to the dispersal
method selected by the user, as in the Biomass Succession extension.
When seeds disperse to a cell, establishment (recruitment) first requires
sufficient light (amount dependent on species shade tolerance) and is then
stochastic based on a probability of establishment that is calculated as a
function of soil moisture and sub-canopy radiation during the time step.
Establishment is only attempted during optimal months, computed from the
climate file as the first three physiologically active months in the year and one
month after the maximum precipitation. Initial biomass is computed for a 1year old cohort.
Note: this initial cohort will be grouped (‘binned’) appropriately into a larger
cohort (e.g., age 1 – 10) at the next succession time step.

2.4 Cohort Competition
Biomass growth is driven by photosynthesis, which depends on light, soil
moisture and foliage biomass. Multiplicative reduction factors are applied to
gross photosynthesis to account for water stress, suboptimal radiation, vapor
pressure deficit, and temperature. A similar growth enhancement factor
(DelAmax) is applied for CO2 concentrations above 350 ppm.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

2.4.1 Light
The reduction of radiation intensity through the canopy is estimated using an
exponential decrease function (i.e., Beer-Lambert law), where incoming
radiation drives photosynthetic activity (Aber and Federer, 1992). A
laboratory-derived relationship between foliar nitrogen concentration and
assimilation rates under optimal growth conditions is used to estimate
potential gross photosynthesis.
PnET-Succession assumes that LAI and biomass are spatially homogeneous
on a site (i.e., cell). PnET-Succession defines canopy layers according to
biomass, with high biomass cohorts achieving dominance with regard to
access to light. Because senescing cohorts are more likely to lose biomass
due to death of suppressed individuals or branches breaking off rather than
due to the top breaking (i.e. they lose biomass without losing height),
maximum lifetime biomass of a tree-species cohort is used as a proxy for tree
height. Note that changes have been made to the model described paper in
Ecological Modeling (De Bruijn et al 2014). We no longer set (arbitrary) age
limits on the development of canopy layers. Rather, each cohort is divided
into a number IMAX (=5 by default, set in the GenericParameters file) of
canopy sublayers of equal biomass (Figure 1, left). The cohort sublayers are
overlaid and the model iteratively clusters sublayers into canopy layers until
the deviation of the newly formed canopy boundaries (i.e. LyrMax -LyrAv)
decreases below a user defined parameter MaxDevLyrAv (Figure 1, right).
This process produces boundaries of canopy layers such that the variation of
subcanopy boundaries within the canopy layers is minimized and the variance
of subcanopy boundary between canopy layers is maximized. MaxDevLyrAv
is calibrated by the user to produce the maximum number of canopy layers
expected in the system, or to control how long it takes for multiple canopy
layers to form. The maximum number of canopy layers can further be limited
with the generic MaxCanopyLayers parameter (section 7.4). Subcanopy
layers within a canopy layer have equal access to the light reaching the
canopy layer, and the light passing through a canopy layer is a function of the
LAI and extinction coefficient of the cohorts making up the canopy layer.
Light stress for a cohort is calculated by: fRad = Radiation /
(Radiation+HalfSat).

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

LyrMax
Canopy layer=1

Relative foliage mass of cohort

Subcanopy boundary
LyrAv

Canopy layer=0

Figure 1. Canopy layer assignment. Each tree represents the foliage of a
species-cohort on a site, and the solid horizontal lines are subcanopy
boundaries (IMAX=5). Dotted lines are computed canopy layers that
minimize the variance of foliage biomass within canopy layers and maximize
the variance between canopy layers. All cohort subcanopy layers are
assigned to the single canopy layer in which most of the cohort’s subcanopy
layers occur. Note that the diagram shows canopy shape only to enhance
interpretation; in the model, subcanopy layers represent cohort foliage across
the site, not tree crowns, and they all have equal biomass.

2.4.2 Water
Soil water is calculated in a bulk-hydrology model that updates soil water
depending on precipitation, evaporation, soil drainage and consumption by
the trees (Figure 2).
2.4.2.1 Water In

Sources of bulk soil water (soil_water in mm) are precipitation (P in
mm/month) and melting water (snow_melt in mm/mo). Incoming
precipitation is intercepted by existing foliage at a rate controlled by a user
parameter (PrecipIntConst), which defines the proportion of precipitation
intercepted for each unit of leaf area (LAI).

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼 = 𝑃𝑃 × 𝑒𝑒 (−𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃∗𝐿𝐿𝐿𝐿𝐿𝐿)

Intercepted precipitation is assumed to evaporate from the leaf surface and
does not enter the soil. Sites with no live cohorts have no precipitation
interception. When average temperature is below freezing, precipitation
(snow) is not subject to interception and is allocated to snow_pack (mm),
where it remains until air temperature induces melting. Sublimation of snow
is modeled as a direct reduction of snow pack prior to melting at a rate set by
the ecoregion parameter SnowSublimFrac (default is 0.15 [Hood et al. 1999]).
At above-freezing temperatures, snow melts at a rate of 2.74 mm/°C/day
(USDA NRCS 2004). Snow melt is not subject to interception by foliage.
The combination of non-intercepted precipitation and snow melt define the
potential incoming water. The incoming precipitation is divided into discrete
precipitation events, with the number of events within a month set by the
PrecipEvents ecoregion parameter. Precipitation from individual events is
randomly assigned to individual subcanopy layers, with some layers
potentially receiving multiple events and others receiving none. This random
assignment ensures that all layers have equal priority to the incoming water.
The incoming water is subject to surface runoff, which is controlled by a userdefined ecoregion parameter (PrecipLossFrac), which is intended to increase
with slope or other factors (e.g., rocky soil) that would increase surface runoff
even when the soil is not saturated. Incoming precipitation and snowmelt are
reduced in proportion to PrecipLossFrac, with the runoff not entering the soil.
The actual water infiltrating the soil is:
𝑊𝑊𝑊𝑊𝑊𝑊𝑊𝑊𝑊𝑊𝑊𝑊𝑊𝑊 = (1 − 𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑎𝑎𝑎𝑎) ×

2.4.2.2 Water Out

[𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠_𝑚𝑚𝑚𝑚𝑚𝑚𝑚𝑚 + 𝑃𝑃 − 𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼)]
𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃𝑃

Water that infiltrates the soil is subject to both fast and slow “leakage”.
Infiltration is limited by the soil saturation parameter (θS), and any water in
excess of saturation is subject to immediate runoff. Fast leakage is correlated
to the soil hydraulic conductivity (Ksat) and occurs before plants have a
chance to utilize water. The ecoregion parameter LeakageFrac defines the
proportion of water above field capacity (-3.37 m pressure head) that
immediately drains through the water profile. A parameter value of 1.0
implies immediate draining to field capacity, which will likely be appropriate
for most real applications. Values of less than 1 for LeakageFrac could be
appropriate to represent soil conditions that prevent leakage through the
bottom of the soil profile (e.g., bedrock, clay layer, permafrost). Slow
leakage occurs after plant use (transpiration) and evaporation, and keeps the

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

water level at or below field capacity (-3.37 m pressure head) at the end of
each monthly time step.
After fast leakage loss has been subtracted, the soil water is subject to further
depletion by transpiration and/or evaporation. Transpiration is calculated as
the result of plant growth (see section 2.5). The rate of evaporation is a
function of surface radiation (under the canopy), temperature and the soil
texture class. Potential evaporation is calculated as a simplified PenmannMonteith calculation according to Priestley and Taylor (1972) as discussed in
Brutsaert (1982, p. 217). This method was successfully applied in the
PROGRASS model (Calanca et al. 2009).
Actual evaporation is calculated as:
AET = Max(c x PET – Transpiration, 0),
where c is a proportion that decreases linearly from 1.0 when water content is
75% of field capacity, to c = 0 when pressure head is 153 m (i.e., the physical
wilting point (Fig 3) (Robock et al. 1995)). AET is limited to the water above
the wilting point, so that evaporation ceases when the soil water falls to the
wilting point. Transpiration is subtracted from evaporation to reflect
decreasing evaporation when the vegetation increases. De facto evaporation
is 0.0 when LAI > 3.0. Also, surface radiation is automatically 0 when snow
cover is present, which results in no evaporation under snow pack.
Transpiration is assumed to use water that otherwise would be subject to
evaporation. Therefore, when transpiration exceeds evaporation, no
additional water is lost to evaporation.
When some snow melts prior to soil thaw, it runs off and should not become
soil water. The best way to account for this is to add the proportion of the
snowpack lost to runoff to the SnowSublimFrac parameter (section 9.10).

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

Figure 2. Soil water processes in PnET-Succession
2.4.2.3 Water Stress

Water stress in the model depends on the water pressure in the soil according
to Feddes et al. (1978). Water pressure in the soil (water retention curves)
depends on soil water content and the soil type according to Saxton and
Rawls (2006), who provide equations to estimate water retention curves for
soils based on soil texture characteristics (i.e., % sand, % silt, % clay, %
organic matter, % gravel, salinity).
Default values for the required parameters (from Saxton and Rawls 2004) are
provided with PnET-Succession for 12 different soil types (Figure 3, left
panel), but users are able to modify existing soil type parameters or provide
custom soil types with parameters. A BEDR (stone) soil type is also included
to represent soils with no water holding ability. The user implements a soil
type as an ecoregion-specific parameter in the ecoregion parameter table
using a corresponding abbreviation for the soil type.
Water stress for a species-cohort is calculated from soil water pressure using
four species-specific water pressure thresholds (Figure 3, right panel) labeled

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

H1-H4 in Feddes et al. (1978). Note that PnET-Succession uses the absolute
value of pressure head. Parameter H1 (the pressure head below which
photosynthesis cannot occur (waterlogging)) is hardcoded in PnETSuccession (H1 = 0 meter pressure). Often, little is known about H2
(cessation of waterlogging stress), so it is recommended to use the generic
value H2=0.0 unless you are explicitly modeling waterlogging effects. H3
(onset of stress caused by too little water) can be set to reflect the drought
sensitivity of a species, and should fall somewhere between H2 and H4. Most
literature sources use a generic H4 (cessation of photosynthesis because of
inadequate water) of -153 m pressure head (wilting point).

Figure 3. Default pressure head curves (left) and examples of inverse water
stress (fWater, right). fWater is calculated by linear interpolation between
parameters H1-H4. H1=0 is hardcoded and cannot be changed by the user.
In this example all species have H1 and H2 = 0, with varied values for H3 (75
– 100) and H4 (120 – 150).
Starting with v3.0, water stress (fWater) is used as a reduction factor for the
absorption of CO2 and O3 and the transpiration of water vapor, in addition to
its role as a direct growth reduction factor. The internal variable CiModifier
is an index of stomatal openness, which is equal to fWater when ozone is not
simulated (see 2.4.3.2 for how ozone affects CiModifier). CiModifier acts as
a linear reduction factor in the calculation of the conductance of gases
between the atmosphere and the leaves.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

2.4.3 Other factors
2.4.3.1 Temperature

Vapor pressure deficit is calculated from the temperature fluctuations during
the day, and accounts for the effect of elevated atmospheric CO2. CO2 affects
growth in two ways; 1) it increases water use efficiency and 2) it increases the
reference rate of photosynthesis (Amax). The temperature reduction factor
increases from 0 at PsnTMin, to 1 at PsnTOpt. Supra-optimal temperatures
do not reduce the temperature reduction factor (unless DTEMP=true; see
Section 7.19), but net photosynthesis is reduced by VPD effects on
conductance and elevated water stress through increased evaporation and
transpiration. Foliar respiration is calculated as a user-defined fraction of
maximum gross photosynthesis, modified by a temperature reduction factor
using a Q-10 relationship. When Wythers=true, foliar respiration is modified
to account for acclimation to temperature (see Section 7.18).
2.4.3.2 Ozone

Ozone can dramatically reduce photosynthesis rates by damaging
photosynthetic tissues and inhibiting stomatal function. The model will
simulate these effects when it is optionally supplied with monthly cumulative
growing seasons ozone dose in the climate file. For applications where ozone
is not of interest, simply do not supply ozone inputs and no ozone calculations
will be made.
The stomatal sluggishness effects of ozone are simulated by altering
(increasing) CiModifier (see 2.4.2.3 for water stress influence on CiModifier)
to reflect the limited ability of stomata to completely close. Changes to
CiModifier (an index of stomatal openness) ripple through the model, altering
the CO2 fertilization effect (DelAmax), water use efficiency and water stress
(through transpiration). Species-specific sensitivity to ozone-induced
stomatal sluggishness is controlled by the specification of each species as
Sensitive, Intermediate or Tolerant (O3StomataSens).
Ozone damage to tissues is simulated using an ozone growth reduction factor
(fO3) that reduces Amax to reflect decreased photosynthetic capacity.
Species-specific sensitivity to ozone-induced growth reduction is controlled
by a scaling parameter (O3GrwothSens) that scales the ozone effect to be
higher or lower than the average effect.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

2.5 Cohort Growth and Ageing
The model computes net photosynthesis, and gross photosynthesis is
estimated by adding foliar respiration to net photosynthesis. Gross
photosynthesis is used to compute transpiration. Net photosynthesis
production is allocated to maintenance respiration and then to the root,
foliage, wood and non-structural biomass pools, according to fixed allocation
ratios. A proportion of foliage and wood biomass is also moved to the dead
pools to simulate leaf-fall and stem (self-thinning)/branch/root death. Cohort
ageing is simply the addition of the time step to each existing cohort age.

2.6 Cohort Senescence and Mortality
Senescence is implemented as a reduction of gross photosynthetic rate with
age such that respiration eventually exceeds production and cohorts die. A
cohort dies when non-structural carbon decreases to <1% of the combined
structural biomass pools. The PsnAgeRed parameter controls the shape of the
function used to calculate the age-related reduction factor, which reaches zero
at the longevity specified in the LANDIS-II species parameter file.

2.7 Dead Biomass Decay
When a cohort dies and is removed (e.g., harvest or insect mortality), its
biomass is added to one or both of the dead biomass pools: woody and leaf.
Decomposition rate of woody litter depends on a decay rate that is weighted
by additions of woody material and user-supplied species specific decay rates
(KWdLit). Decomposition rate of non-woody litter depends on a weighted
decay rate according to additions of foliage and their associated
decomposition rates that depend on species specific foliage lignin
concentrations (FolLignin) and ecosystem determined AET according to
Meentemeyer (1978). Disturbances can alter the dead biomass pools. They
can add dead biomass (e.g., wind) and/or remove dead biomass (e.g., fire may
add some woody dead biomass and remove all leaf dead biomass).

2.8 References
Brutsaert, W. 1982. Evaporation into the Atmosphere: Theory, History and
Applications. Springer, NY.
De Bruijn A., Gustafson E.J., Sturtevant B.R., Foster J.R., Miranda B.R.,
Lichti N.I., Jacobs D.F. 2014. Toward more robust projections of forest
landscape dynamics under novel environmental conditions: embedding
PnET within LANDIS-II. Ecological Modelling 287:44–57.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

Feddes, R.A., P.J. Kowalik, and H. Zaradny. 1978. Simulation of Field Water
Use and Crop Yield. John Wiley & Sons, New York, NY.
Hood, E., M. Williams, D. Cline. 1999. Sublimation from a seasonal
snowpack at a continental, mid-latitude alpine site. Hydrol. Process.
13:1781-1797.
Lazzarotto, P., P. Calanca, J. Fuhrer. 2009. Dynamics of grass–clover
mixtures—An analysis of the response to management with the
PROductive GRASsland Simulator (PROGRASS). Ecological
Modelling 220:703–724.
Meentemeyer, V. 1978. Macroclimate and lignin control of litter
decomposition rates. Ecology 59:465-472.
Priestley C.H.B. and R.J. Taylor. 1972. On the assessment of surface heat
flux and evaporation using large-scale parameters. Monthly Weather
Review 100(2):81-92
Robock, A., Vinnikov, K. Y., Schlosser, C. A., Speranskaya, N. A., & Xue,
Y. (1995). Use of midlatitude soil moisture and meteorological
observations to validate soil moisture simulations with biosphere and
bucket models. Journal of Climate, 8(1), 15-35.
Saxton, K. E. and W. J. Rawls. 2004. Soil water characteristic equations.xls.
Online database (http://hrsl.arsusda.gov/SPAW/SPAWDownload.html)
Saxton, K. E., W. J Rawls, J. S. Romberger and R. I. Papendick. 1986.
Estimating generalized soil water characteristics from texture. Soil Sci.
Soc. Amer. J. 50(4):1031-1036.
USDA Natural Resources Conservation Service (NRCS). 2004. National
Engineering Handbook Part 630 (Hydrology), Chapter 11 (Snowmelt).
Accessed online at:
http://www.wcc.nrcs.usda.gov/ftpref/wntsc/H&H/NEHhydrology/ch11.p
df
Wythers, K.R., P.B. Reich, J.B. Bradford. 2013. Incorporating temperaturesensitive Q10 and foliar respiration acclimation algorithms modifies
modeled ecosystem responses to global change. Journal of Geophysical
Research: BioGeosciences 118:1-14.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

3 Input File - PnET-Succession
The input parameters for this extension are specified in two primary input
files: the PnET-Succession input file and the PnET Species Parameters input
file. The general species parameter input file used by all versions of LANDIS
is also required, and is described in Chapter 6 of the LANDIS-II Model User
Guide. The input files must comply with the general format requirements
described in section 3.1 Text Input Files in the LANDIS-II Model User Guide.

3.1 Example PnET-Succession input file
LandisData

"PnET-Succession"

PnET-Succession
Value
>>----------------------------Timestep 10
StartYear
1961
SeedingAlgorithm WardSeedDispersal
Latitude
45
MaxDevLyrAv 6000
PNEToutputsites

PnETOutput.txt

InitialCommunities Oconto_initial-communities.txt
InitialCommunitiesMap
Oconto _initial-communities.img
PnETGenericParameters
PnETGenericParameters.txt
PnETSpeciesParameters
PnET_Oconto_species.txt
EcoregionParameters Oconto _EcoregionParameters.txt

3.2 LandisData
This parameter’s value must be "PnET-Succession".

3.3 Timestep
This parameter is the time step of the extension. A value <5 is recommended.
Random shuffling of cohort foliage into sub-canopy layers for access to light
is done at each time step, so a poor random assignment in a long time step
may kill cohorts that would survive with a shorter time step. Longer time
steps do not markedly speed up simulations or reduce output because the
internal time step of PnET-Succession is monthly, but they do reduce the
frequency of outputs. Value: integer >0. Units: years.

3.4 StartYear
This parameter indicates the climate year in which simulation begins.
Climate file observations prior to this date are used for spin-up (as necessary)

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

and observations from this date forward are used for simulations. The climate
file may contain more years than will actually be used by the model. Value:
integer > 0. Units: years.

3.5 SeedingAlgorithm
This parameter is the seed dispersal algorithm to be used. Valid values are
"WardSeedDispersal", "NoDispersal" or "UniversalDispersal". The
algorithms are described in section 4.5.1 Seeding of the LANDIS-II
Conceptual Model Description.

3.6 PNEToutputsites
Optional: Invoke the output extension PnETOutputsites and specify its input
file (see section 10).

3.7 InitialCommunities
This parameter gives the name of the initial communities text file. This file
assigns species and cohorts to each value found in the initial communities
map (see section 4).

3.8 InitialCommunitiesMap
This parameter gives the file name of the initial communities map. This map
contains a unique integer value for each combination of species and cohorts
found on the landscape. Each cell value for an active site on the landscape must
be one of the map codes listed in the initial communities input file (see section
5).

3.9 PnETGenericParameters
This optional parameter gives the name of a PnET Generic Parameter text
file. Any parameter that is not species-specific, or is typically specified in the
PnETSpeciesParameter file (Chapter 8), but is identical for all species can be
supplied either in the default generic parameter file installed in C:\Program
Files\LANDISII\v6\bin\extensions\Defaults\GenericPnETSpeciesParameters.txt with the
rest of the model, or in a custom generic parameter file specified here. Any
parameters not specified in the PnETSpeciesParameter file will be read from
the custom generic file, and if not found there, will be read from the default
generic file. Thus, values found in the PnETSpeciesParameter file will
always take precedence over the default generic file, but cannot be duplicated
in the PnETGerneicParameters file. The format of the PnET Generic
Parameter text file is described in section 7.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

3.10 PnETSpeciesParameters
This parameter gives the name of the PnET Species Parameter text file. The
format of this file is described in section 8.

3.11 EcoregionParameters
This parameter gives the name of the PnET Ecoregions Parameter text file,
which is described in section 9.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

4 Input File – Initial community classes
This file contains the definitions of the initial community classes. Each active
site on the landscape is assigned to an initial community class. The class
specifies the tree species that are present along with the particular age cohorts
that are present for each species. Avoiding a proliferation of similar-aged cohorts
of the same species on a site will speed run times with little effect on simulation
results because those cohorts would be competing with each other.

4.1 Example File
LandisData "Initial Communities"
>>Old jackpine oak
MapCode 7
acerrubr 30
pinubank 90
pinuresi 110 140
querelli 40 240
>> young jackpine oak
MapCode 0
pinubank 50
querelli 10 70
>> young aspen
MapCode 2
poputrem 10
>> old maple hardwoods
MapCode 55
abiebals 10 60 120
acerrubr 90 120
acersacc 20 50 150 200
betualle 40 140 200
fraxamer 10 100 180
piceglau 180
querrubr 100 160 180
thujocci 200 260
tiliamer 20 80 150
tsugcana 30 80 120 220 320 340
>> old pine
MapCode 6
abiebals
piceglau
pinuresi
pinustro

- spruce - fir
10 50 80
100 180 220
140 180
200 280 350

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

4.2 LandisData
This parameter’s value must be "Initial Communities".

4.3 Initial Community Class Definitions
Each class has an associated map code and a list of species present at sites in
the class.

4.3.1 MapCode
This parameter is the code used for the class in the input map (see chapter 5).
Value: 0 ≤ integer ≤ 65,535. Each class map code must be unique. Map
codes can appear in any order, and need not be consecutive.
4.3.2 Species Present
A list of species present at the class’ sites comes after the map code. Each
species is listed on a separate data line.
species age age age ...
The species name comes first, followed by one or more ages. The name and
ages are separated by whitespace. An age is an integer and must be between 1
and the species’ Longevity parameter. The ages can appear in any order.
acersacc 10 5 21 60 100
The list may be empty, which will result in the sites in the class being
initialized with no species cohorts.

4.3.3 Grouping Species Ages into Cohorts
The list of ages for each species is grouped into cohorts based on the
succession extension’s timestep. This timestep determines the size of each
cohort. For example, if the timestep is 20, then the cohorts are ages 1 to 20, 21
to 40, 41 to 60, etc.
Suppose an initial community class has this species in its list:
acersacc 10 25 30 40 183 200
If the succession timestep is 10, then the cohorts for this species initially at
each site in this class will be:
acersacc 10 20 30 40 190 200

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

5 Input File – Initial community map
This is a GIS file of the initial community classes. Each active site on the
landscape is assigned to a MapCode that links to the initial community class
defined in the Initial Community Class Definitions. The file can be in any valid
LANDIS-II map format.

6 Input File – Climate
This file contains weather records of monthly parameter values.
6.1.1 Example File #1
Year

Month

Tmax

Tmin

Prec

PAR

CO2

1700-1979 1

1.57

-7.86

96.59

493.10

335

1700-1979 2

3.46

-6.94

87.36

671.21

335

1700-1979 3

8.54

-3.16

110.79

852.52

335

1700-1979 4

15.50

2.34

110.38

925.71

335

1700-1979 5

20.37

7.69

133.10

873.77

335

1700-1979 6

24.39

12.38

123.72

872.04

335

1700-1979 7

26.28

14.81

135.81

847.05

335

1700-1979 8

25.64

14.00

109.89

842.81

335

1700-1979 9

22.07

10.13

100.57

760.33

335

1700-1979 10

16.06

4.03

89.03

624.86

335

1700-1979 11

9.83

-0.88

101.25

463.20

335

1700-1979 12

3.77

-5.33

100.48

411.67

335

1980

1.57

-7.21

53.32

496.07

338

1980

-0.37

-9.99

47.78

697.67

338

1980

6.85

-4.81

133.22

857.97

338

1980

14.52

2.06

139.30

907.75

338

1980

21.07

7.89

122.41

927.89

338

1980

23.51

9.96

137.54

925.58

338

1980

26.88

15.04

154.32

818.81

338

1980

26.42

15.58

169.70

799.45

338

1980

23.97

11.23

65.91

797.72

338

1980

14.23

2.19

76.10

634.71

338

1980

7.82

-2.33

93.34

445.37

338

1980

3.12

-6.90

47.77

468.97

338

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

6.1.2 Example File #2
Year Month

Tmax

Tmin

1995

-4.22

-13.70

1995

-4.21

1995

PAR

Prec

CO2

262.4

9.9

367

0.0

-14.7

487.9

367

0.0

5.08

-6.67

1012.02

35.9

367

0.0

7.58

-3.68

741.21

49.3

367

0.0

1995

18.37

5.12

1021.65

103.4

367.7

2769

1995

27.26

12.67

1292.2

21.5

362.8

3279

1995

26.37

14.15

1287.3

137.2

367.9

3589

1995

25.87

15.41

1118.77

145.8

372.5

5686

1995

19.55

6.24

770.17

65.6

364.9

7723

1995

12.10

2.72

531.73

138

368

8167

1995

-1.58

-10.74

299.5

51.6

368

0.0

1995

-5.45

-15.41

233.53

34.5

368

0.0

6.2 Header Information
The first line of the file must contain the following text:
Year

Month

TMax

TMin

PAR

Prec

CO2

6.3 Observations
Subsequent lines of the file contain monthly values for the 7 variables.
Observations must appear in chronological order.
6.3.1 Year
The year of the weather observation. Alternatively, a range of years may
appear, delineated by a hyphen (see example 6.1.2). Value: 4-digit integer
>0.
6.3.2 Month
The month of the weather observation. Value: 1< integer <12.
6.3.3 TMax
The maximum temperature observed in the month. Value: decimal. Units:
degrees C.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

6.3.4 TMin
The minimum temperature observed in the month. Value: decimal. Units:
degrees C.
6.3.5 PAR
Mean monthly value of Photosynthetically Active Radiation during
daylight hours. Value: decimal > 0.0. Units: User choice. Typically
µmol/m2/sec or W/m2. The units for the half-saturation constant
(SpeciesParameter file) must be the same as PAR. THE MODEL WILL
NOT CHECK TO ENSURE THAT THE UNITS ARE THE SAME.
This is a user responsibility.
6.3.6 Prec
The sum of precipitation observed in the month. Value: decimal >0.
Units: mm.
6.3.7 CO2
Mean montly atmospheric CO2 concentration. Value: decimal >0. Units:
ppm.
6.3.8 O3 (Optional)
Cumulative atmospheric ozone (O3) dose over 40 ppb (CumD40) for the
growing season. Computed by subtracting 40 from each hourly O3 value
and summing non-negative values for all hours between 0800 and 1900
hours in the month. Each monthly total is added to the previous monthly
total to give the cumulative growing season hourly dose through the
current month. Value: decimal >0. Units: ppb-h.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

7 Input File – Generic PnET Species Parameters
This file contains PnET parameters that are not species-specific or are
identical for all species. Only parameters that are not described in Chapter
8 are described here. Parameters may appear in any order. NOTE: Any of
these parameters may instead be set in the
PnETGenericDefaultParameters.txt file in the Defaults folder found where
PnET-Succession is installed (usually in C:\Program Files\....\extensions\).
Parameters set here will over-ride settings in the
PnETGenericDefaultParameters file. Also, most (but not all) of these
parameters may instead appear in the PnETSpeciesParameter file (Section
8), but may not appear in both files.

7.1 Example file:
LandisData PnETGenericParameters
PnETGenericParameters Value
>>-----------------------------------MaxCanopyLayers
2
MaxDevLyrAv
6000
IMAX
10
PreventEstablishment
true
DVPD1
0.05
DVPD2
2
BFolResp
0.1
MaintResp
0.002
TOroot
0.02
TOwood
0.01
Q10
2FolLignin
KWdLit
0.01
InitialNSC
7
CFracBiomass
0.45
PrecipEvents
11
Wythers
true
DTEMP
true

7.2 LandisData
This parameter’s value must be "PnETGenericParameters".

7.3 PnETGenericParameters
This keyword must be followed by "Value".

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0.2

PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

7.4 MaxCanopyLayers
Optional parameter that caps the number of canopy layers that can be
implemented. Typically, forest canopy layers will not exceed 5 and
applying many canopy layers slows the model dramatically. The number of
canopy layers should primarily be regulated through MaxDevLyrAv, but
when MaxDevLyrAv is given low values, the result would otherwise be an
extreme number of canopy layers. MaxCanopyLayers has a default value
of 5.

7.5 MaxDevLyrAv
This optional parameter is used to lump species-age cohorts into canopy
layers, and specifies the maximum variation of cohort biomass that can occur
within a canopy layer. It is given a default value of a maximum float, which
results in a single canopy layer regardless of biomass distribution amongst
subcanopy layers (see section 2.4.1).

7.6 IMAX
Optional: Each cohort is subdivided into a number of layers (IMAX) for
integration. In PnET (Aber and Federer, 1992), the number of subcanopy
layers was fixed at 50. Reducing IMAX saves computation time, with
robust results when IMAX > ~5 (De Bruijn et al. 2014). When omitted,
the model uses the default IMAX=10.

7.7 DVPD1, DVPD2
Coefficients for converting vapor pressure deficit (VPD) to DVPD
according to DVPD = 1 -DVPD1 * vpd^DVPD2 (photosynthesis reduction
factor due to vapor pressure). Value: decimal. Units: kPa-1.

7.8 BFolResp
Base Foliar Respiration Fraction - Foliar respiration as a fraction of
maximum photosynthetic rate. Value: 0.0< decimal <1.0. Units:
proportion.

7.9 MaintResp
Loss of NSC due to maintenance respiration. This rate is modified by
temperature using a Q10 relationship, and is applied to the biomass pool
monthly. Value: 0.0< decimal <1.0. Units: proportion of NSC lost per
month.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

7.10 TORoot/TOWood
Turnover of Root/Wood - Fraction of root/wood biomass lost per year to
damage, breakage or death. Value: 0.0< decimal <1.0. Units: proportion
per year.

7.11 Q10
Respiration Q10 value for foliar respiration, a measure of the rate of change
of respiration when temperature is increased by 10 °C. Value: 0.0<
decimal <10.0. Units: none.

7.12 FolLignin
Mass fraction of lignin in foliage tissue. Value: 0.0< decimal<0.8. Units:
gr/gr.

7.13 KWdLit
Annual decomposition rate (decay constant, k) of woody litter. Value:
0.0< decimal<0.4. Units: proportion per year.

7.14 InitialNSC
Amount of NSC assigned to newly established cohorts. Value: integer>0.
Units: g.

7.15 CFracBiomass
Carbon fraction of biomass by weight. Value: 0.0< decimal <1.0. Units:
proportion.

7.16 PrecipEvents
Monthly total precipitation is evenly divided among this number of events
to allow cohorts more opportunities to compete stochastically for incoming
water. Lower values tend to reduce the competitiveness of species with
lower H3/H4 values. Default=11. Value: decimal >1.0. Units: count.

7.17 PreventEstablishment
Boolean variable turning establishment on or off. Value= “true” or “false”.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

7.18 Wythers
Boolean variable turning the Wythers correction on or off. The Wythers
correction accounts for acclimation of foliar respiration to elevated
temperatures (Wythers et al 2013). Value: true/false.

7.19 DTEMP
Boolean variable turning the PnET-II DTEMP temperature reduction factor
(Aber and Federer 1992) on or off. A value of “true” uses the DTEMP
function, which reduces NetPsn symmetrically from 1.0 at PsnTOpt to 0.0 at
both PsnTMin and PsnTMax. PsnTMax is computed as
PsnTOpt+(PsnTopt-PsnTMin). A value of “false” will use the original
PnET-Succession (v1.0) function that behaves the same as DTEMP at
temperatures below PsnTOpt, but does not reduce NetPsn at temperatures
above PsnTOpt, relying solely on VPD-driven reductions to drop NetPsn to
zero at about 40 oC. DTEMP produces somewhat more of a NetPsn penalty
above PsnTOpt for species with PsnTOpt <~24 oC. The difference between
the functions is small for species with PsnTOpt >24 oC. Value: true/false.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

8 Input File – PnET Species Parameters
These parameter values typically vary by species. If they do not, they may
more conveniently be placed in the PnETGenericParameters file (Section 7).
All parameters for a species appear on a single line. Parameters may appear
in any order.

8.1 Example file:
LandisData PnETSpeciesParameters
PnETSpeciesParameters
FolN SLWmax
SLWDel
TOfol AmaxA AmaxB
HalfSat
H3
H4
PsnAgeRed
PsnTMin
PsnTOpt
k
DNSC FracBelowG EstMoist
EstRad
FracFol
FrActWd
CO2HalfSatEff O3StomataSens
O3GrowthSens
FolNInt
FolNSlope
abiebal
1.5
19
0.5
Sensitive

160
0.05
2.0

0
0.25
0.8

0.25
10
0.4

5.3
3

21.5 150
150
275
0.053 0.00002 -1.0

acerrub
2.5
26
0.58
Sensitive

65
0.05
2.0

0.2
0.33
0.5

1
5
1.0

-46
5

71.9 200
150
500
0.028 0.00004 -0.0

acersac
23
0.0

50
0.05
0.4

0.2
0.33

1
10

-46
1

71.9
0.02

5
2
Tolerant

2.4
0.58
0.8

100
150
275
0.00002 -0.0

8.2 LandisData
This parameter’s value must be "PnETSpeciesParameters".

8.3 PnETSpeciesParameters (species name)
The species name as it appears in the species parameter input file (see
Chapter 6 of the LANDIS-II Model User Guide).

8.4 FolN
Foliar nitrogen content (%). Value: 00.

8.10 HalfSat
Half saturation light level for photosynthesis. Lower values reflect more
shade tolerance. Value: integer >0. Units: User choice. Typically
µmol/m2/sec or W/m2. The units of PAR in the climate input file must be
the same as HalfSat. THE MODEL WILL NOT CHECK TO ENSURE
THAT THE UNITS ARE THE SAME. This is a user responsibility.
Note: HalfSat is the only parameter that determines shade tolerance in PnETSuccession; the ShadeTolerance parameter required in the LANDIS-II
species file is ignored by PnET-Succession.

8.11 H2, H3, H4
Water stress parameters according to Feddes et al. (1978). See Section
2.4.2.3. H1 is hardcoded at 0 meter pressure head. H2, H3 and H4 should be
successively larger positive values. Note that this is the absolute value of
values usually reported in the literature. Units: m pressure head.

8.12 PsnAgeRed
Reduction factor reducing leaf photosynthesis rate as cohorts age, with
fAge=1.0 at age 1 and fAge =0.0 at the longevity specified in the LANDIS-II
species parameter file. Longevity should be specified as longevity under

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

optimal conditions because the various reduction factors will combine to
almost always result in cohort death prior to the specified longevity age. A
value <1.0 results in a rapid initial decline in max photosynthesis with age, a
value of 1.0 results in a linear decline and a value >1.0 results in slow initial
decline, according to y=(age/longevity)^PsnAgeDecline. Cohorts die when
NSC is <1% of the value of the other biomass pools combined at the end of a
calendar year. Value: 0.0< decimal 0.0. Units: °C.

8.14 PsnTOpt
Optimal temperature for photosynthesis. Value: decimal >0.0. Units: °C.

8.15 k
Canopy light attenuation constant (light extinction coefficient). Value: 0.0<
decimal <1.0. Units: none.

8.16 DNSC
Proportion of NSC relative to total active biomass that will be maintained as
long as net photosynthesis exceeds maintenance respiration. Value: 0.0<
decimal <1.0. Units: proportion of active biomass.

8.17 FracBelowG
Fraction of non-foliar biomass that is belowground (root pool). Allocations
vary at each time step to maintain this fraction. Value: 0.0< decimal <1.0.
Units: proportion.

8.18 EstMoist
Tuning parameter to control the sensitivity of establishment (Pest) to soil
moisture. Calculated using fWater^EstMoist where fWater = the growth
response to sub, or supra optimal water content according to Section 2.4.2.3
and Figure 3 (right pane). High values make establishment more sensitive to
moisture stress. A value of 1.0 results in a linear relationship between
moisture stress and Pest, and little additional effect occurs with values over
50. Value: 0.0< decimal. Units: unitless.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

8.19 EstRad
Tuning parameter to control the sensitivity of establishment (Pest) to light
level (radiation). Calculated using (sub-canopy
radiation/(2*HalfSat))^EstRad. High values make establishment more
sensitive to radiation stress. A value of 1.0 results in a linear relationship
between light availability and Pest, and little additional effect occurs with
values over 50. Value: 0.0< decimal. Units: unitless.

8.20 FracFol
Fraction of the amount of active woody biomass (above and belowground)
that is allocated to foliage per year. The active fraction of wood is calculated
by the model using FracActWd. Value: 0.0< decimal<1.0. Units: proportion
per year.

8.21 FrActWd
Shape parameter of negative exponential function that calculates the amount
of woody biomass that has active xylem capable of supporting foliage. All
wood is active when the parameter =0.0, and increasing values decrease the
fraction of active wood as biomass increases according to: active_wood = e^
–(FrActWd * biomass). Value: 0.0< decimal<0.4. Units: unitless.

8.22 CO2HalfSatEff
Slope coefficient used to reduce HalfSat (increase shade tolerance) as CO2
concentration increases. Value: decimal<0.0. Units: unitless. Default=0.0.
Set to zero to turn off effect. See PnET-Succession function worksheet.xlsx
to see how the parameter affects HalfSat.

8.23 O3StomataSens (Optional)
Categorical parameter indicating the species’ susceptibility of the stomata to
ozone-induced sluggishness. Values: one of – Sensitive, Intermediate,
Tolerant.

8.24 O3GrowthSens (Optional)
Scaling parameter controlling the species’ susceptibility to ozone-induced
tissue damage. Zero indicates no sensitivity to ozone, 2.0 indicates twice as
much sensitivity as 1.0, 3.0 indicates three times as much sensitivity as 1.0.
Value: 0.00. Units: mm.

9.7 PrecLossFrac
Precipitation Loss Fraction. Proportion of precipitation that does not enter
the soil (e.g., runoff not due to soil saturation). Value: 0.0< decimal <1.0.
Units: proportion.

9.8 LeakageFrac
Leakage Fraction. Proportion of soil water above field capacity that is
subject to “fast leakage” (see Figure 2). Fast leakage is the drainage of
infiltrated water that leaks out of the rooting zone soil more quickly than
plants can access the water. Therefore, water lost to fast leakage is not
available for transpiration. A value of 1.0 for LeakageFrac will cap plant
available water at field capacity. Value: 0.0< decimal <1.0. Units:
proportion.

9.9 PrecIntConst
This represents the rate of precipitation interception for each unit of leaf
area index, which is lost to evaporation, and therefore does not enter the
soil. See the interception equation in section 2.4.2.1. Value: decimal ≥0.0.
Units: unitless.

9.10 SnowSublimFrac
Fraction of the snowpack that sublimates. This fraction is removed just prior
to snowmelt. Recommended default is 0.15 (Hood et al 1999). Value: 0.0
0. Units:
years.

10.4 Species
This keyword lists the species for which data are to be output. Value: spacedelimited list of species names or the generic term All.

10.5 Map Name Template
Subsequent input lines list the variables to be output along with the output file
naming rules. List one variable per line. Each line begins with the variable to
be output, followed by a description of where the output files are placed and
their naming convention. The first portion lists the directory where the files
should be placed, relative the location of the scenario text file (e.g.,

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

output/agemaps/). The second portion includes one or two variables (depending
on the variable) for creating file names. {species} will be replaced with the
species name. {timestep} will be replaced with the output time step. Other
characters can be inserted as desired. An appropriate file extension (e.g., .img,
txt) should also be included for the type of output. For example:
Water output/SoilWater/water-{timestep}.img

Note: Most output maps are not compatible with the .gis map output type
because the values are not integers.
Here are the valid variable names and the required naming variables and file
type of the output files: All variables are optional.

Biomass, {species}, {timestep}. Map. Units: g/m2. Biomass is the sum
of wood and roots, but not foliage biomass.
AbovegroundBiomass, {timestep}. Map. Units: g/m2.
AbovegroundBiomass includes aboveground wood and foliage.
BelowgroundBiomass, {timestep}. Map. Units: g/m2.
BelowgroundBiomass includes roots only.
WoodySenescence, {species}, {timestep}. Map. Units: g/m2. Outputs
woody biomass of the species added to woody dead pool.
FoliageSenescence, {species}, {timestep}. Map. Units: g/m2. Outputs
foliage biomass of the species added to litter dead pool.
LeafAreaIndex, {species}, {timestep}. Map. Units: m2.
Establishment, {species}, {timestep}. Map. Units: # cohorts
EstablishmentProbability, {species}, {timestep}. Map. Units: probability.
MonthlyNetPsn, {species}, {timestep}. Map. Units: g/m2.
MonthlyFolResp, {species}, {timestep}. Map. Units: g/m2.
MonthlyGrossPsn, {species}, {timestep}. Map. Units: g/m2.
MonthlyMaintResp, {species}, {timestep}. Map. Units: g/m2.
Water, {timestep}. Map. Units: mm.
SubCanopyPAR, {timestep}. Map. Units: W/m2 or mmol/m2, depending
on input units.
CohortsPerSpecies, {timestep}. Map. Units: count.
AnnualPsn, {timestep}. Map. Units: g/m2.
WoodyDebris, {timestep}. Map. Units: g/m2.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

Litter, {timestep}. Map. Units: g/m2.
AgeDistribution, {timestep}. Map. Units: # cohorts
WoodSenescence, {species}, {timestep}. Map. Units: g/m2.
FoliageSenescence {species}, {timestep}. Map. Units: g/m2.
CohortBalance, {filename}. Tab-delimited text file containing landscape
total or average values of the following variables for each time step.
# of cohorts (landscape total)
Average Age of all cohorts on the landscape (years)
Average Biomass / site (g/m2)
Average LAI / site (m2)
Average Water / site (mm)
SubCanopy PAR / site (W/m2 or µmol/m2, depending on input
units)
Litter / site (gDW/m2)
WoodyDebris / site (gDW/m2)
AverageBelowGround / site (g/m2)
AverageFoliage / site (g/m2)
AverageNSC / site (gC/m2)
AverageAET / site (mm/yr)

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

11 Input File – PNEToutputsites
This file contains parameters for the site data output extension. This
extension outputs state variables each month for individual sites. This
extension is used primarily for debugging input parameters because it
slows model execution.

11.1 Example file:
LandisData

PNEToutputsites

>>PNEToutputsites MapCoordinatesX
MapCoordinatesY
MapCoordinatesMaxX
MapCoordinatesMaxY
>>----------------------------------------------------->>Site1
715,187.037 4,413,258.694
734284.375 4413934
PNEToutputsites
Row
Column
>>-----------------------------------------------------Site1 1
1
Site2 1
2

11.2 LandisData
This parameter’s value must be "PnEToutputsites".

11.3 PnEToutputsites
This keyword is followed by either map coordinate keywords or grid
coordinate keywords (row/column). Each site (cell) to be output is listed on
subsequent lines with a Site number and the appropriate coordinates (map
coordinates must be compatible with the input maps). See example above for
syntax.

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

12 Output file - SiteData Table (Optional
PNEToutputsites output)
This comma-delimited table contains site-level PnET state variable values
at the end of each month from the start of the spin-up period to the end of
the simulation. The sites reported are specified in the input file. Values
are for the entire cell and include the presence of all species and cohorts on
the cell. Units for each variable are given in the header. This output is
turned on in the PnET-Succession Input File by specifying the cell(s) to be
output.

12.1 Time
Simulation year.

12.2 Ecoregion
Ecoregion for the cell.

12.3 SoilType
Soil type assigned to the cell’s ecoregion.

12.4 NrOfCohorts
Number of cohorts (all species) occurring on the cell.

12.5 MaxLayerStdev
Maximum standard deviation of biomass of all cohorts present on the cell.
Used to calculate the number of canopy layers (section 2.4).

12.6 Layers
Number of canopy layers on the cell.

12.7 PAR0
Photosynthetically Active Radiation (light) above the upper canopy layer.
Same units as PAR in the input climate file.

12.8 Tday(C)
Mean air temperature (oC) in the daytime, derived from TMin and TMax
from the climate file.

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12.9 Precip(mm_mo)
The monthly precipitation (as read from the climate file, mm/mo).

12.10

CO2(ppm)

Monthly CO2 concentration (as read from the climate file, parts per
million)

12.11

O3(cum_ppb_h)
Monthly ozone dosage (as read from the climate file). Units should be
ppb-h (see 6.3.8).

12.12

RunOff(mm_mo)

Monthly runoff that occurs from precipitation when the soil is saturated
(mm/mo).

12.13

Leakage(mm)

Water lost out of the bottom of the rooting zone.

12.14

PET(mm)

Potential EvapoTranspiration. Potential evapotranspiration is computed as
the value under minimum advection according to Priestley and Taylor
(1972) as discussed in Brutsaert (1982, p. 217). Code from the
PROGRASS model (Lazzarotto et al. 2009).

12.15

Evaporation(mm)

Precipitation lost to evaporation from the soil surface as a function of the
LAI on the site.

12.16

Transpiration(mm)

Transpiration of all cohorts.

12.17

Interception(mm)

Precipitation intercepted by foliage and stems and not entering the soil.

12.18

SurfaceRunOff(mm_mo)

Monthly precipitation runoff that occurs due to surface conditions (e.g.,
slope, impervious surface) when the soil is not fully saturated saturated
(mm/mo).

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12.19

Water(mm)

Amount of soil water as calculated by the bulk hydrology model (mm).
Note that this gives the amount of water at the end of the month. To
compute the amount of water at the beginning of the month, sum water,
evaporation and transpiration.

12.20

PressureHead(m)

Pressure head (at the end of the month) as calculated by the bulk hydrology
model (m).

12.21

SnowPack (mm)

Water equivalent contained in the snowpack (mm).

12.22

LAI(m2)

Leaf Area Index (all species combined)

12.23

VPD(kPa)

Mean vapor pressure deficit for the month (kPa).

12.24

GrossPsn(gC/mo)

Gross photosynthesis of all species combined (gC/ m2/mo).

12.25

NetPsn(gC/mo)

Net photosynthesis of all species combined (gC/m2/mo).

12.26

MaintenanceRespiration(gC/mo)

Maintenance respiration of all species combined (gC/mo).

12.27

Wood(gDW)

Sum of aboveground woody biomass of all species (gDW).

12.28

Root(gDW)

Sum of root biomass of all species (gDW)

12.29

Fol(gDW)

Sum of foliage biomass of all species (gDW).

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12.30

NSC(gC)

Sum of NSC (Non-structural carbon) of all species (gC).

12.31

HeteroResp(gC_mo)
Heterotrophic respiration (decay of dead pools).

12.32

Litter(gDW/m2)

Biomass (all species) in the litter dead biomass pool (gDW/m2).

12.33

CWD(gDW/m2)

Biomass (all species) in the coarse woody debris dead biomass pool
(gDW/m2).

12.34

WoodySenescence (gDW/m2)
Total woody biomass added to the dead pool each month.

12.35

FoliageSenescence (gDW/m2)
Total litter biomass added to the dead pool each month.

12.36

SubcanopyPAR

Photosynthetically Active Radiation (light) below all canopy layers (i.e., at
ground level). Same units as PAR in the input climate file.

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13 Output file - CohortData Table (Optional
PNEToutputsites output)
This table contains monthly PnET cohort-level state variable values for the
sites specified in the input file. A file is created when a cohort is
established, and the records give month-end state variable values for the
cohort from establishment to death (or the end of the simulation). Files are
also produced for cohorts established during the spin-up period. Units for
each variable are given in the header. This output is turned on in the
PNEToutputsites input file by specifying the cell(s) to be output.

13.1 Time(yr)
Simulation year.

13.2 Age(yr)
Current age of the cohort (calendar years).

13.3 TopLayer(-)
The highest layer number to which the cohort is assigned, with 0 being the
lowest layer.

13.4 LAI(m2)
Leaf area index of the cohort.

13.5 GrossPsn(gC/m2/mo)
Cohort gross photosynthesis (gC/m2/mo).

13.6 FolResp(gC/m2/mo)
Cohort foliar respiration (gC/m2/mo).

13.7 MaintResp(gC/m2/mo)
Cohort maintenance respiration, including tissue repair and nutrient
transport (gC/m2/mo). This amount comes out of the NSC pool.

13.8 NetPsn(gC/m2/mo)
Cohort net photosynthesis (gC/m2/mo).

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13.9 Transpiration(mm/mo)
Cohort water actually lost to transpiration (mm/mo).

13.10

WUE(g/mm)

Cohort mean water use efficiency (gC/mm H2O).

13.11

Fol(gDW/m2)

Biomass of the cohort foliage pool (gDW/m2).

13.12

Root(gDW/m2)

Biomass of the cohort root pool (gDW/m2).

13.13

Wood(gDW/m2)

Biomass of the cohort wood pool (gDW/m2).

13.14

NSC(gC/m2)

Amount of carbon in the cohort non-structural carbon pool (gC/m2).

13.15

NSCfrac(-)

Fraction of carbon in the cohort non-structural carbon pool relative to
active biomass (NSC / (FActiveBiom * (wood + root+ foliage ). Cohorts
die when NSCfrac is <0.01 at the end of a calendar year.

13.16

fWater(-)

Reduction factor related to water availability.

13.17

fRad(-)

Reduction factor related to light availability at the top of the canopy layer
occupied by a cohort.

13.18

fOzone(-)
Reduction factor related to ozone effects.

13.19

DelAmax(-)

Enhancement factor related to CO2 effects on photosynthesis.

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13.20

fTemp_psn(-)

Reduction factor related to sub-optimal temperature for photosynthesis.

13.21

fTemp_resp(-)

Reduction factor related to temperature effects on maintenance respiration.

13.22

fAge(-)

Reduction factor for age-related declines in photosynthesis efficiency.

13.23

LeafOn(-)

Indicates growing season status. When TRUE, new foliage can be added
and old foliage has not yet been dropped.

13.24

FActiveBiomass(gDW_gDW)

Fraction of active biomass. Indicates the computed fraction of wood
biomass that is considered active and able to transport water to support
foliage.

13.25

AdjFolN(gN_gC)
Adjusted foliar nitrogen (gN/gC). When using the optional FolNInt
and FolNSlope parameters, the adjusted FolN can be different from
the species FolN value, depending on canopy position and the
resulting PAR. Averaged across the cohort’s subcanopy layers.

13.26

CiModifier(-)
Reduction factor for gas conductance due to stomatal closure caused
by water stress and modified by ozone. Value of 1.0 indicates no
reduction in conductance. Averaged across the cohort’s subcanopy
layers.

13.27

AdjHalfSat
Adjusted HalfSat. When using the optional CO2HalfSatEff, the
adjusted HalfSat can be different from the species HalfSat value,
depending on concentration of CO2. Averaged across the cohort’s
subcanopy layers. Units are typically µmol/m2/sec or W/m2 and will
be the same as the input units of PAR in the climate input file and the
species HalfSat value.

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14 Output file – Establishment Table (Optional
PNEToutputsites output)
This comma-delimited table reports site-level establishment information
for each species. The reported values reflect state variables in the model at
intervals of one PnET-Succession time step.

14.1 Year
Simulation year (timestep).

14.2 Species
Species.

14.3 Pest
Probability of establishment for the species during the given time step as a
function of the values of water and PAR. Pest =
fRad^EstRadSensitivity*fWater^EstMoistSensitivity.

14.4 fWater
Water availability reduction factor.

14.5 fRad
Light availability reduction factor.

14.6 Est
Indicates if an establishment of the species can occur in the time step.
Actual establishment additionally requires a source tree within seeding
distance.

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15 Appendix. Calibration tips.
Calibration tips
Eric Gustafson (egustafson@fs.fed.us)

January 3, 2018

General
One of the compelling features of PnET-Succession is that its parameters are mostly
empirically estimable values, and it autonomously produces very realistic growth responses
under a wide variety of abiotic conditions when its parameters are set correctly. The
developers of the PnET model claim (perhaps too optimistically) that PnET does not need
calibration, but there are some changes that have been made to PnET-Succession to make it
tractable at landscape scales that cause the model to require modest calibration. However, of
the dozens of parameters used by PnET-Succession, only a few typically need calibration,
and most applications can use default values for most parameters.
I calibrate each species separately, using a single cohort initialized on a single cell and grown
for about 150 years. I compare simulated biomass (wood) growth through time with
empirical biomass growth curves. Use the PNEToutputsites option to produce the cohort
growth output files needed for calibration.
To produce predictable competitive interactions that can be controlled by intuitive
modification of a small number of parameters for individual species, it is best to use common
parameter values across all species as much as possible. These can be conveniently
maintained (and modified as necessary) in the GenericPnETSpeciesParameters file. Other
parameters vary by life history trait or growth form, and each species having a particular trait
should have the same (or similar) parameter value to represent that trait. Examples of such
traits include shade tolerance (HalfSat), drought tolerance (H3 & H4), extinction coefficient
(k), relationship between foliar N and photosynthetic capacity (AmaxA and AmaxB), leaf
weight change by canopy position (SLWdel) and fraction of foliar biomass relative to active
wood biomass (FracFol). Parameters that the model is highly sensitive to (for which
common values should be used as much as possible) include: MaintResp, TOroot, TOwood,
BFolResp, FracBelowG, FracFol and FrActWd.
Calibration is ideally done by modifying only FolN (to control relative productivity), FracFol
(to control gross LAI and the initial growth part of the growth curve), SLWmax (to fine-tune
mature LAI and the ability to compete for light), and FrActWd (which controls the amount of
foliage in mature cohorts and the maximum height of the growth curve). FracFol and
FrActWd can have a profound effect on the competitive ability of cohorts, so to achieve
reasonable competitive interactions it is best to find a common value to use for both of these

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parameters for all species having a common growth form (deciduous v. conifer), modifying
them only for species that have exceptionally unusual growth curves. FracFol must generally
be much higher for conifers because their AmaxA and AmaxB terms produce much less
growth per unit of foliage. Find a value that generally works for all species of a growth form
and be hesitant to modify it for individual species unless there is a compelling biological or
empirical reason.
I set up a landscape with a single active cell, and initialize it with a single species at a time. I
calibrate species under good to ideal growing conditions, recognizing that their growth will
and should be less under poorer conditions and when competing. I calibrate on a soil with
relatively high water holding capacity (e.g., SALO) and a weather stream with average or
better precipitation for the regions where the species are typically found. I calibrate with
PsnTOpt of all species set to approximate the average growing season temperate (mean of
Tmax and Tmin) found in the weather stream, avoiding the hassle of creating a different
weather stream for each species. The key is to calibrate under nearly ideal conditions (i.e.,
growing season temperatures approximating PsnTOpt). Thus, regardless of what the actual
species PsnTOpt is, it will have been calibrated to grow its best when the actual temperature
it experiences is near its PsnTOpt. I use a constant climate for calibrating, to avoid
confounding the calibration by extreme events. Again, nearly ideal conditions are the goal.
Consequently, I am content if my calibrated curve produces growth somewhat better than the
average of my empirical growth data. Use CO2 (and O3 if applicable) values typical of those
experienced by the trees measured for your empirical biomass growth curves.
The calibration process is expedited by plotting simulated wood biomass against empirical
growth data in a spreadsheet. I create a separate spreadsheet tab for each species and also
plot foliage biomass and LAI. Other variables for which empirical data are available can
also be plotted against each other. Using a macro, I can quickly copy and paste data from the
cohort output file of PnET-Succession to iteratively achieve the desired behavior through
multiple model runs.
MaintResp is a critical parameter for PnET-Succession because it is the primary determinant
of cohort growth limitations and death, and growth is highly sensitive to variation in this
parameter. Unfortunately, this parameter is rarely known empirically, so it must be
calibrated. If MaintResp is too low, cohorts will never die from stress and growth will be
virtually unconstrained. If MaintResp is too high, growth will quickly level off because of
high maintenance costs and cohorts will be highly susceptible to stress. For most studies,
competitive outcomes should be a function of competition for light and water, not from a
difference in maintenance costs. Therefore, it is recommended to find a value for MaintResp
that works across life history traits and growth forms. This is fairly easily done. Choose
some representative species having generic growth parameters (including great longevity)
and simulate their growth curves, searching for a value of MaintResp that flattens (levels off)

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the growth curve after a few decades. Then gradually reduce MaintResp until the growth
curve takes the shape of that typically seen in the growth curves of your long-lived species.
Select a value of MaintResp that produces acceptable behavior for all life forms, etc., and use
it for all species. In summary, you are searching for a value that is as high as it can be
without creating a flattened growth curve.
Useful empirical data needed for calibration.
1. The range of FolN for each species across sites, age, canopy position. This is a great
starting point and helps put bounds on acceptable values, but it is important to recognize
that productivity is closely related to FolN in PnET, so it is more important that FolN
reflect relative productivity among species rather than matching empirical values closely.
That said, it is usually possible to select a value of FolN that is within the range of
empirically measured values. If you have empirical values of Amax, use your values of
AmaxA and AmaxB (or see Fig. 2 in Aber et al 1996) to estimate the FolN that produces
that Amax value. NOTE: if you plan to implement dynamic FolN (FolNInt and
FolNSlope set to values other than default), then be sure to set FolNInt and FolNSlope to
values you will use in your simulations.
2. Species SLWmax helps determine LAI. Thicker leaves (higher SLW) reduce LAI. LAI
determines the ability of a cohort to compete for light, so it is important to calibrate so
that LAI approximates empirical values. Again, it is more important to get LAI
approximately right than to keep SLWmax within the empirical range.
3. Growth curves by species. Growth and yield tables are useful for this purpose and
volume measures can be converted to biomass using specific gravity values for the
species (Miles and Smith 2009). Ensure that units are the same as output by PnETSuccession. Most growth and yield tables account for only the merchantable part of
trees, so consider them to be near the lower boundary of the woody biomass output of
PnET-Succession. The primary feature of the growth curve that you should calibrate to
is the maximum height of the curve. The rate of initial increase can be matched quite
readily using FracFol, but if you have different values of FracFol across species, the
lower valued species will compete poorly. So, avoid the temptation to match the initial
rate of increase and focus instead on the height of the curve. Make modest exceptions for
species that tend to outgrow their competitors when establishing on open sites (e.g.
pioneer species) and for species that have unusually slow growth compared to
competitors with similar life history traits (e.g., white cedar, hemlock). The shape of the
senescence decline can be controlled by PsnAgeRed, but again resist the temptation to
calibrate this individually for each species unless the species has well-known anomalous
senescence characteristics.
Calibration procedure

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1. First, set parameter values that are known from the literature (e.g., TOFol, FolN, SLW,
HalfSat, PsnTMin, PsnTOpt, k, etc.). When there is considerable range in empirical
values, begin with an intermediate value. HalfSat should be varied to reflect shade
tolerance, because the LANDIS-II shade tolerance parameter has no effect in PnETSuccession. Some PnET parameters (e.g., SLWDel, AmaxA, AmaxB, Q10, DVPD1,
DVPD2) are hard to estimate and most studies use generic values (e.g., Aber et al 1995,
Ollinger and Smith 2005). Decide whether you will use the Wythers=TRUE option; I
recommend using it. NOTE: if you use dynamic FolN, you should start with FolN values
near the bottom of their empirical range.
2. Use the GenericPnETSpeciesParameters file for all parameters that are never varied
among species. Set parameters that will be held constant for your particular experiment
or study (e.g., TOroot/wood, BaseFolResp, InitialNSC, etc.) Again, it is advisable to
hold as many parameters constant across species as possible to allow you less
confounded control of competitive interactions with the remaining parameters.
3. PsnTMin controls the length of the growing season. You should verify that the
appropriate months are active (LeafOn=TRUE). PsnTMin should vary coarsely
according to leaf-on and leaf senescence dates, and typically ranges from 0-3 oC for
temperate species. PsnTMin will also control how productive the species is at the
beginning and end of the growing season, and will produce a growth response to shifts in
temperature even when the number of growing season months is unchanged. Similarly,
in some years you may get some modeled photosynthesis activity in a month when the
species is not typically active, but this is not a problem as long as NetPsn is quite low in
those months.
4. In lieu of empirical values, PsnTOpt can be estimated using the average mid-summer
temperature at the center of the species’ range. Note that temperatures above PsnTOpt
will limit photosynthesis only through VPD effects. Use the DTEMP=true option to
impose a greater heat-related penalty on species with PsnTOpt <24 oC. Use the PnETSuccession function worksheet to explore how the DTEMP option affects photosynthesis.
5. Calibration tuning is best done by matching simulated wood biomass increase to
empirical biomass values for a species through time. If your empirical values represent
something less than whole tree aboveground biomass, your tuned values should be higher
than the empirical values. Your goal is not to match the empirical curve exactly, but to
approximate it. Simulate a monoculture and plot Wood and Root+Wood (whole tree)
biomass through time. There are some published estimates of whole tree biomass
through time by species groups to provide some indication of belowground biomass (e.g.,
Smith et al 2006). Comparison of empirical aboveground and whole tree biomass can
help you estimate the FracBelowG parameter. The calibration simulations should run for
at least as many years as your empirical data, and it may be informative to see how the
model extrapolates growth beyond your empirical data. When you find it difficult to
match an empirical growth curve without setting a parameter outside its empirical range
or to a very different value than similar species, modifying FracBelowG (or TOWood or

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TORoot) can produce a marked effect on the growth curve with a small change in value.
An increase in one pool will reduce the other pool. It would be beneficial to have some
justification for your selected value from empirical evidence.
6. Choose a single soil type for calibration of all species, preferably a soil type that is both
common and productive. Ultimately, growth is limited by water, so you want to calibrate
under somewhat ideal conditions to reflect realistic competition for water. I typically do
not choose the soil type with the greatest water holding capacity, but one that is above
average. Soil water is determined by inputs (precipitation) and outputs (PrecLossFrac,
percolation out of the rooting zone (controlled by SoilType) and transpiration). Tuning
of soil water is done primarily with PrecLossFrac, LeakageFrac and SoilType, which
assumes that transpiration is correct if the photosynthesis and growth behavior is correct.
PrecLossFrac typically represents water lost where slope is sufficient for water to run off
before it can enter the soil. You should calibrate for a slope condition that is flatter than
average in your study area.
7. Calibrate all species under optimal temperature and precipitation conditions, which will
result in growth reductions under other conditions. If you don’t uniformly calibrate
species under optimal conditions, then their competition will be unrealistic and
unpredictable during simulations. This is most easily done by using a fixed annual
weather stream (long-term monthly averages), calculating the mean growing season
temperature (mean of TMin and TMax though the growing season months), and setting
PsnTOpt of ALL species to the July value of TMax (for calibration ONLY). To ensure
comparability of tuned parameters, use a common PsnTMin also. Use typical monthly
precipitation values. When you finish calibration, remember to set PsnTOpt (and
PsnTMin) of each species back to its real value. During your simulation applications,
whenever a species receives a monthly temperature that is equal to its real PsnTOpt, it
will then perform as calibrated and growth will decline as temperatures depart from its
optimal temperature.
8. You will need starting parameter values. Here are some generic ones for temperate forest
species that are widely used in PnET-Succession simulations:
a. SLWDel: 0.0 for evergreen, 0.2 for deciduous
b. AmaxA: 5.3 for evergreen, -46 for deciduous
c. AmaxB: 21.5 for evergreen, 71.9 for deciduous
d. BFolResp: 0.1
e. k: 0.5 for evergreen, 0.58 for deciduous
f. DNSC: 0.05
g. Q10: 2
h. DVPD1: 0.05
i. DVPD2: 2
j. IMAX: 5-10 (there is a significant performance cost with values higher than these)
k. TOWood: 0.01
l. TORoot: 0.02

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Here are some other values I have used, but which you may need to modify for your
purposes:
a. HalfSat: 300 (µmol/s) for shade-intolerant, 100 for shade-tolerant; I use a gradient
across 5 classes.
b. H3/H4: 100/140 for drought intolerant, 118/153 for drought tolerant; I use a
gradient across 4 classes.
c. MaintResp: 0.002
d. PsnAgeRed: 5
e. FracBelowG: 0.33
f. FracFol: 0.10 for evergreen, 0.02 for deciduous
g. FracActWd: 0.00004
h. PrecipEvents: 9-11
i. EstMoist, EstRad: 2.8
9. Relative growth rate among species should be controlled with FolN. Conifers and
deciduous species must have FolN scaled separately because they use different values of
AmaxA and AmaxB. Unless specific, high quality estimates of AmaxA and AmaxB are
known, it is recommended to use the values commonly used in PnET publications (see
above). Published values of FolN are commonly available, but use these only as a
starting point. In PnET-Succession, FolN is the primary parameter that controls
relative growth rate (Amax) among species. Set FolN of your suite of species based on
what is known about relative growth rates among your species. Be aware that differences
in shade tolerance and drought tolerance will prevent FolN from scaling perfectly with
growth rate among all species. I have found that FolN should be increased ~0.1 for each
decrease in shade tolerance class (of 5 classes) to produce approximately the same
growth rate. However, you should be able to use a FolN value for each species that is
within the range of empirical values. If you find you must use a FolN value that is out of
range, modify other parameters to bring it within range, starting with FracFol,
FracActWd or FracBelowG. Don’t forget that you will have a different range of FolN
values for species with different AmaxA and AmaxB values. If you are using dynamic
FolN, check the AdjFolN values to see if they vary within empirical limits.
10. Foliage biomass is controlled by FracFol and FrActWd, and you will find that FracFol
also tightly controls the lag time of significant biomass increase (early years). Because
this lag time has a strong effect on competitive ability in PnET-Succession, it is
recommended that you attempt to use common (or very similar) values of FracFol and
FrActWd. It may be preferable to have similar lag times than to match empirical lag
times closely; this will produce better competitive interactions in the model. Super slowgrowing species (e.g., white cedar, black spruce) may be an exception. Often empirical
growth curves are measured in mixed forests, and shade-tolerant species (e.g., eastern
hemlock) will tend to have longer lag times than when grown in the open as in the
calibration simulations. You should monitor the shape of the foliage curve along with

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the biomass curve. If FrActWd is too high, foliage biomass will decline markedly with
age, which is not likely realistic. If it is too low, foliage biomass will increase
indefinitely, which is also not realistic. Experience shows that a value of 0.00004 will
produce a level or slightly declining foliar biomass after about 50 years.
11. Before adjusting the height of the biomass curve, verify that LAI is not way out of
bounds for the species. LAI is controlled by FracFol, FrActWd, SLWmax (and
SLWdel). FracFol directly controls the amount of foliar biomass, and LAI is calculated
by dividing foliage biomass by SLWmax. Note that FolN and SLWMax are generally
inversely correlated in the literature. SLWdel controls the reduction of SLW from top to
bottom in the canopy, and can have a large effect on LAI when there is a lot of foliage
biomass. To estimate whether SLW at the bottom of the canopy may be reasonable, use
SLWmin = SLWmax - SLWdel * foliage biomass. FrActWd controls the amount of
foliage biomass later in life, and has an important effect on maximum LAI achieved; use
this to control LAI if SLWmax values are well established empirically. In lieu of
empirical values, LAI should generally range between 2-4 for shade intolerant species
and 4-6 for shade tolerant species, with values over 7 not unreasonable for highly shade
tolerant species. LAI is fairly insensitive to changes in FolN, so fine tuning FolN will not
spoil your tuning of LAI.
12. The height of the biomass growth curve is primarily controlled by FolN, FracFol,
FrActWd, but is ultimately determined by water limitation. Remember that FracBelowG,
TORoot, TOWood also have an effect. H3/H4 has a slight effect by modifying water
stress and HalfSat can modify light stress. Also remember that MaintResp can cause the
curve to plateau regardless of other parameter settings. It is recommended to make major
adjustments to the height of the biomass curve with FracFol, FrActWd and then fine-tune
it using FolN and SLWmax (within empirical limits). Note that raising LAI using
SLWmax generally reduces the height of the growth curve slightly, presumably because
less light penetrates deeper into the canopy. When calibrating conifers, note that higher
values of TOfol depress the growth curve because more of the NetPsn is needed to build
leaves. Thus, higher FolN may be needed for species with shorter leaf longevity
compared to similar species with longer leaf longevity.
13. The timing of the peak of the biomass growth curve is primarily determined by species
longevity. To modify the timing of the onset of senescence, adjust PsnAgeRed. A value
of 5 seems to work well for most species.
14. You should be able to control most aspects of the shape of the biomass growth curve.
The initial increase is controlled with FracFol, the height by FolN and FrActWd, and the
decline by longevity and PsnAgeRed. Fine-tuning is done with FolN and SLW. FolN
has a predictable effect on the growth curve, but you may find SLW a bit more erratic
because it interacts with foliage biomass and leaf area to affect light competition within
the canopy. FolN tends to shift all parts of the growth curve up or down without
changing its shape. For species that accumulate markedly less biomass than most
species, reduce FracFol modestly and/or increase FrActWd to 0.00005 or 0.00006.

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15. NetPsn is primarily controlled by FracF and FracActWd, given FolN, SLW and
BaseFolResp. Transpiration is highly correlated with GrossPsn, scaled by WUE (which
is modified by CO2 and O3 through their effect on Ci. Recall that GrossPsn is calculated
by PnET-Succession using NetPsn and BaseFolResp, which is not intuitive.
16. DNSC is the target proportion of carbon reserves that is maintained, and it has little effect
on cohort competition unless it is set so low that the cohort has minimal reserves to
survive stress, or so high that the species can rarely be stressed enough to die. Set this in
the middle of the range of empirical measures of total % sugars and starch in active
tissues. In lieu of empirical values, use 0.05.
17. InitialNSC similarly has little effect on cohort competition unless values among species
vary by more than an order of magnitude.
18. Establishment probability is reduced in direct proportion to light and water
photosynthesis reduction factors for the species at the time of establishment when
EstMoistSens and EstRadSens = 1.0. On sites with no light or water stress, probability of
establishment would equal 1.0, which is unreasonably high, so it is calibrated to an
appropriate magnitude using EstMoistSens and EstRadSens. This cannot be done on a
single cell, and must be done on a landscape before you conduct landscape-scale
experiments. In lieu of concrete evidence that one factor is more important than the
other, keep the values the same. I tune such that the number of cohorts on the landscape
quickly finds an equilibrium under a scenario that mimics historical conditions. I used a
value of 2.8 of most species in western Maryland. Modify these values to weight the
influence of the light and water reduction factors on establishment if the conditions for
optimal establishment vary markedly from the conditions for optimal growth.
General notes. 1) Again, to ensure realistic competition, it is advisable to use common
parameter values across species, unless you have empirical data that are comparable and
reliable across species. If you are planning to experimentally vary some parameters, holding
the others constant will improve the signal from your experiment. Minimizing species
differences in parameters such as SLWDel, PsnAgeRed, k, MaintResp, DNSC, WUEc,
FracBelowG, FracFol and FracActWd will make competitive interactions more predictable.
Hold these as close to each other as possible, varying other parameters to calibrate as much
as possible within empirical limits. However, when you cannot calibrate adequately using
the common parameter values, do not hesitate to vary the one or two other parameters that
will produce good performance. It is very likely that such modifications reflect biological
reality. 2) Use the PnET-Succession function worksheet to help you understand how the
parameters determine the behavior of cohort state variables as a function of the abiotic
inputs, both intermediate variables and the ones that ultimately reflect competition and
growth (e.g., NetPsn, foliar and wood biomass, NSCfrac). It is available from the PnETSuccession page of the LANDIS-II website (http://www.landis-ii.org/extensions/pnetsuccession) and in the ‘docs’ folder where this User Guide was installed. 3) It is highly
recommended that you verify your calibrations by simulating several similar species together

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PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

to ensure that they in fact compete as expected. If not, often a slight tweak of one parameter
can bring them in line with expectation. The likely parameters to tweak are FolN (general
growth rate), H3/H4 (competition for water) and HalfSat (competition for light), or FracFol
(amount of foliage).
Here are some commonly used generic values, for your reference.
LandisData PnETGenericParameters
PnETGenericParameters
Value
BFolResp
0.1
TOroot
0.02
TOwood
0.01
MaxDevLyrAv
6000
MaxCanopyLayers 2
IMAX
5
DNSC
0.05 <>calibrated for Wythers=true
Species
FolN SLW
TO
max
Fol
>>Upper Midwest
abiebals
0.9 225
0.25 150
acerrubr
2.2 60
1
150
acersacc
2.1 47
1
100
betualle
2.2 50
1
150
betupapy
2.4 75
1
250

Half
Sat
105
111
105
105
100

Psn
TMin

H4
143
147
143
143
140

2
3
3
3
3

- 64 -

19
26
23
21
21

Psn
TOpt
0.1
0.02
0.02
0.02
0.022

Frac
Fol

FrAct
Wd

0.00004
0.00004
0.00004
0.00004
0.00004

0.023
0.081
0.075
0.045
0.045

KWd
Lit
0.2
0.11
0.11
0.2
0.2

Fol
Lignin

PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension
carycord
fagugran
fraxamer
fraxnigr
fraxpenn
larilari
piceglau
picemari
pinubank
pinuresi
pinustro
popubals
popugran
poputrem
prunsero
queralba
querelli
quermacr
querrubr
quervelu
thujocci
tiliamer
tsugcana

2.5
2.0
2.5
2.6
2.5
2.7
1.1
1.0
1.3
1.5
1.8
2.4
2.5
2.5
2.5
2.7
2.6
2.7
2.6
2.3
1.0
2.5
1.4

70
47
60
65
60
60
225
200
245
230
220
85
85
85
70
70
65
60
60
55
130
50
105

1
1
1
1
1
1
0.25
0.25
0.333
0.333
0.5
1
1
1
1
1
1
1
1
1
0.5
1
0.333

250
100
200
250
200
300
200
200
300
250
200
300
300
300
250
250
250
200
200
200
200
150
90

105
111
111
100
111
105
111
111
118
118
111
100
100
100
111
118
118
118
111
114
105
111
105

143
147
147
140
147
143
147
147
153
153
147
140
140
140
147
153
153
153
147
148
143
147
143

3
3
3
3
4
1
2
2
2
3
3
1
2
2
3
2
2
3
2
2
3
3
3

25
23
25
23
25
20
21
20
20
21
21
19
22
21
25
26
21
23
24
24
20
23
21

0.02
0.02
0.02
0.02
0.02
0.022
0.1
0.08
0.1
0.1
0.1
0.025
0.025
0.025
0.022
0.02
0.02
0.02
0.02
0.02
0.08
0.02
0.07

0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00006
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00006
0.00004
0.00004

0.05
0.047
0.075
0.045
0.05
0.028
0.025
0.025
0.025
0.023
0.125
0.046
0.046
0.043
0.075
0.063
0.05
0.05
0.075
0.075
0.026
0.075
0.028

0.2
0.2
0.12
0.2
0.2
0.2
0.2
0.2
0.2
0.2
0.25
0.2
0.2
0.2
0.18
0.17
0.2
0.2
0.17
0.2
0.2
0.12
0.2

>>Mid-Atlantic
castdent
2.6
caryglab
2.1
lirituli
2.8
magnacum 2.4
nysssylv
2.1
pinuechi
1.5
pinupung
1.2
pinurigi
1.4
pinuvirg
2.0
quercocc
2.8
querprin
2.6
robipseu
2.4
sassalbi
2.5
ulmuamer 2.5
juglnigr
2.8
betulent
2.4
caryovat
2.2
ostrvirg
1.9
platocci
2.6

50
60
85
55
50
235
200
235
240
75
65
85
65
55
70
75
60
50
55

1
1
1
1
1
0.333
0.333
0.333
0.5
1
1
1
1
1
1
1
1
1
1

150
200
300
200
100
300
300
300
300
300
250
300
300
200
250
250
150
100
200

114
111
100
100
105
118
118
118
118
114
118
105
105
105
105
105
111
111
105

148
147
140
140
143
153
153
153
153
148
153
143
143
143
143
143
147
147
143

2
3
3
2
3
3
3
3
3
2
2
3
2
3
3
3
3
3
3

24
27
25
24
27
25
21
21
21
24
24
25
26
27
27
23
25
26
27

0.02
0.02
0.025
0.025
0.02
0.1
0.08
0.1
0.1
0.022
0.02
0.025
0.02
0.02
0.02
0.022
0.02
0.02
0.02

0.00004
0.00004
0.00004
0.00005
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004
0.00004

0.043
0.166
0.107
0.075
0.126
0.125
0.125
0.063
0.125
0.05
0.17
0.015
0.075
0.075
0.075
0.18
0.166
0.075
0.075

0.09
0.17
0.16
0.11
0.12
0.25
0.25
0.25
0.25
0.17
0.26
0.26
0.12
0.12
0.12
0.15
0.17
0.17
0.11

>>Northeast
acerpens
piceabie
picerube
prunpens

45
220
200
85

1
0.25
0.25
1

100
200
150
250

111
111
111
111

147
147
147
147

2
2
2
2

20
20
20
20

0.02
0.1
0.1
0.03

0.00004
0.00004
0.00004
0.00004

0.075
0.125
0.125
0.075

0.25
0.25
0.25
0.186

1.9
1.2
0.9
2.6

- 65 -

PnET-Biomass Succession v3.0 – User GuideLANDIS-II Extension

References
Melillo, JM, Aber JD, Muratore JF. 1982. Nitrogen and Lignin Control of Hardwood Leaf
Litter Decomposition Dynamics. Ecology 63:621-626.
Aber, JD, Ollinger SV, Federer A, Reich PB, Goulden ML, Kicklighter DW, Melillo JM,
Lathrop RG Jr. 1995. Predicting the effects of climate change on water yield and forest
production in the northeastern United States. Climate Research 5:207-222.
Aber, JD, Reich, PB, Goulden, ML. 1996. Extrapolating leaf CO2 exchange to the canopy:
a generalized model of forest photosynthesis compared with measurements by eddy
correlation. Oecologia 106:257-265.
Ollinger SV, Smith M-L. 2005. Net primary production and canopy nitrogen in a temperate
forest landscape: an analysis using imaging spectroscopy, modeling and field data.
Ecosystems 8:760-778.
Mattson KG, Swank WT, Waide JB. 1987. Decomposition of woody debris in a
regenerating, clear-cut forest in the Southern Appalachians. Canadian Journal of Forest
Research 17:712-721.
Miles P, Smith WB. 2009. Research Note-NRS-38. Specific gravity and other properties of
wood and bark for 156 tree species found in North America. Res. Note NRS-38.
Newtown Square, PA: U.S. Department of Agriculture, Forest Service, Northern
Research Station. 35 p.
Smith, J.E., Heath, L.S., Skog, K.E., Birdsey, R.A. 2006. Methods for calculating forest
ecosystem and harvested carbon with standard estimates for forest types of the United
States. USDA Forest Service General Technical Report NE-343. Northeastern Research
Station, Newtown Square, PA, USA. 216 p.

- 66 -

Source Exif Data:

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Author                          : Eric Gustafson;Arjan De Bruijn
Comments                        : 
Company                         : University of Wisconsin-Madison
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Extension Name                  : Biomass Succession
Extension Version               : 1.2
Modify Date                     : 2018:01:11 10:07:29-06:00
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Title                           : LANDIS-II Biomass Succession v1.2
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Creator                         : Eric Gustafson;Arjan De Bruijn
Producer                        : Adobe PDF Library 15.0
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Extension 0020 Name             : Biomass Succession
Extension 0020 Version          : 1.2
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