# 13 PEcAn Models

This section will contain information about all models and output variables that are supported by PEcAn.

Model Name Available in the VM Prescribed Inputs Input Functions/Values Restart Function
BioCro Yes Yes Yes No
CLM No No No No
DALEC Yes Yes Yes No
ED2 Yes Yes Yes Yes
FATES No Yes No
GDAY No No No No
LPJ-GUESS No Yes No No
MAESPA Yes Yes No No
PRELES Yes Yes Partially No
SiPNET Yes Yes Yes Yes

Available in the VM - Denotes if a model is publicly available with PEcAn.

Prescribed Inputs - Denotes whether or not PEcAn can prescribe inputs.

Input Functions/Values - Denotes whether or not PEcAn has functions to fully produce a model’s Input values.

Restart Function - Denotes status of model data assimilation capabilities.

Output Variables

PEcAn converts all model outputs to a single Output Standards. This standard evolved out of MsTMIP project, which is itself based on NACP, LBA, and other model-intercomparison projects. This standard was expanded for the PalEON MIP and the needs of the PEcAn modeling community to support variables not in these standards.

Model developers: do not add variables to your PEcAn output without first adding them to the PEcAn standard table! Also, do not create new variables equivalent to existing variables but just with different names or units.

### 13.0.1 BioCro

Model Information
Source Code https://github.com/ebimodeling/biocro
Authors Fernando E. Miguez, Deepak Jaiswal, Justin McGrath, David LeBauer, Scott Rohde, Dan Wang
PEcAn Integration David LeBauer, Dan Wang

### 13.0.2 Introduction

BioCro is a model that estimates photosynthesis at the leaf, canopy, and ecosystem levels and determines plant biomass allocation and crop yields, using underlying physiological and ecological processes to do so.

### 13.0.3 PEcAn configuration file additions

The following sections of the PEcAn XML are relevant to the BioCro model:

• model
• revision – Model version number
• run
• site/id – ID associated with desired site from BETYdb site entry
• inputs
• met/output – Set as BIOCRO
• met/path – Path to file containing meteorological data

### 13.0.4 Model specific input files

List of inputs required by model, such as met, etc.

### 13.0.5 Model configuration files

Genus-specific parameter files are secretly required. These are stored in the PEcAn.BIOCRO package and looked up under the hood.

#### 13.0.9.6 Installation notes

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

#### 13.0.9.9 TACC lonestar

module load hdf5
curl -o ED.r82.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/ED.r82.tgz
tar zxf ED.r82.tgz
rm ED.r82.tgz
cd ED.r82/ED/build/bin
curl -o include.mk.lonestar http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.lonestar
make OPT=lonestar

#### 13.0.9.10 TACC stampede

module load hdf5
curl -o ED.r82.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/ED.r82.tgz
tar zxf ED.r82.tgz
rm ED.r82.tgz
cd ED.r82/ED/build/bin
curl -o include.mk.stampede http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.stampede
make OPT=stampede

### 13.0.10 GDAY

Model Information
Source Code
Authors
PEcAn Integration

Introduction

Should list the model specific additions to the PEcAn file here

Model specific input files

List of inputs required by model, such as met, etc.

Model configuration files

MODEL is configured using 3 files which are placed in the run folder, as well as a symbolic link to the met file.

• file1 : template for this file is located at models/MODEL/inst/file1 and is not modified.
• file2 : template for this file is located at models/MODEL/inst/file2 and is not modified.
• file3 : template for this file is in models/MODEL/inst/file3 or it is specified in the <model> section as <template>. The values in this template are replaced by those computed in the earlier stages of PEcAN.

Installation notes

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

VM

Model Information
Source Code
Authors
PEcAn Integration

Introduction

Should list the model specific additions to the PEcAn file here

Model specific input files

List of inputs required by model, such as met, etc.

Model configuration files

MODEL is configured using 3 files which are placed in the run folder, as well as a symbolic link to the met file.

• file1 : template for this file is located at models/MODEL/inst/file1 and is not modified.
• file2 : template for this file is located at models/MODEL/inst/file2 and is not modified.
• file3 : template for this file is in models/MODEL/inst/file3 or it is specified in the <model> section as <template>. The values in this template are replaced by those computed in the earlier stages of PEcAN.

Installation notes

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

VM

### 13.0.12 LPJ-GUESS

Model Information
Source Code
Authors
PEcAn Integration

Introduction

Should list the model specific additions to the PEcAn file here

Model specific input files

List of inputs required by model, such as met, etc.

Model configuration files

MODEL is configured using 3 files which are placed in the run folder, as well as a symbolic link to the met file.

• file1 : template for this file is located at models/MODEL/inst/file1 and is not modified.
• file2 : template for this file is located at models/MODEL/inst/file2 and is not modified.
• file3 : template for this file is in models/MODEL/inst/file3 or it is specified in the <model> section as <template>. The values in this template are replaced by those computed in the earlier stages of PEcAN.

Installation notes

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

VM

### 13.0.13 MAESPA

Model Information
Authors Belinda Medlyn and Remko Duursma
PEcAn Integration Tony Gardella, Martim DeKauwe, Remki Duursma

Introduction

Model specific input files

Model configuration files

MODEL is configured using 3 files which are placed in the run folder, as well as a symbolic link to the met file.

• file1 : template for this file is located at models/MODEL/inst/file1 and is not modified.
• file2 : template for this file is located at models/MODEL/inst/file2 and is not modified.
• file3 : template for this file is in models/MODEL/inst/file3 or it is specified in the <model> section as <template>. The values in this template are replaced by those computed in the earlier stages of PEcAN.

Installation notes

Installing the MAESPA model requires cloning the MAESPA Bitbucket Repository, executing the makefile, and ensuring that the Maeswarp R package is correctly installed.

To clone and compile the model, execute this code at the command line

git clone https://bitbucket.org/remkoduursma/maespa.git

cd maespa

make clean

make

maespa.out is your executable. Example input files can be found in the inputfiles directory. Executing measpa.out from within one of the example directories will produce output.

MAESPA developers have also developed a wrapper package called Maeswrap. The usual R package installation method install.packages may present issues with downloading an unpacking a dependency package called rgl. Here are a couple of solutions:

Solution 1

From the Command Line

sudo apt-get install r-cran-rgl

then from within R

install.packages("Maeswrap")

Solution 2

From the Command line

sudo apt-get install libglu1-mesa-dev

then from within R

install.packages("Maeswrap")



This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

VM

### 13.0.14 PRELES

Model Information
Source Code
Authors
PEcAn Integration

Introduction

Should list the model specific additions to the PEcAn file here

Model specific input files

List of inputs required by model, such as met, etc.

Model configuration files

MODEL is configured using 3 files which are placed in the run folder, as well as a symbolic link to the met file.

• file1 : template for this file is located at models/MODEL/inst/file1 and is not modified.
• file2 : template for this file is located at models/MODEL/inst/file2 and is not modified.
• file3 : template for this file is in models/MODEL/inst/file3 or it is specified in the <model> section as <template>. The values in this template are replaced by those computed in the earlier stages of PEcAN.

Installation notes

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

VM

### 13.0.15 SiPNET

Model Information
Source Code
Authors
PEcAn Integration Michael Dietze, Rob Kooper

Introduction

Should list the model specific additions to the PEcAn file here

Model specific input files

List of inputs required by model, such as met, etc.

Model configuration files

SIPNET is configured using 3 files which are placed in the run folder, as well as a symbolic link to the met file.

• sipnet.in : template for this file is located at models/sipnet/inst/sipnet.in and is not modified.
• sipnet.param-spatial : template for this file is located at models/sipnet/inst/template.param-spatial and is not modified.
• sipnet.param : template for this file is in models/sipnet/inst/template.param or it is specified in the <model> section as <default.param>. The values in this template are replaced by those computed in the earlier stages of PEcAN.

Installation notes

This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.

SIPNET version unk:

if [ ! -e ${HOME}/sipnet_unk ]; then cd curl -o sipnet_unk.tar.gz http://isda.ncsa.illinois.edu/~kooper/PEcAn/models/sipnet_unk.tar.gz tar zxf sipnet_unk.tar.gz rm sipnet_unk.tar.gz fi cd${HOME}/sipnet_unk/
make clean
make
sudo cp sipnet /usr/local/bin/sipnet.runk
make clean

SIPNET version 136:

if [ ! -e ${HOME}/sipnet_r136 ]; then cd curl -o sipnet_r136.tar.gz http://isda.ncsa.illinois.edu/~kooper/EBI/sipnet_r136.tar.gz tar zxf sipnet_r136.tar.gz rm sipnet_r136.tar.gz sed -i 's#$(LD) $(LIBLINKS) $$.*$$#$(LD) \1 $(LIBLINKS)#'${HOME}/sipnet_r136/Makefile
fi
cd \${HOME}/sipnet_r136/
make clean
make
sudo cp sipnet /usr/local/bin/sipnet.r136
make clean

VM