The Fertilizer
Emission Scenario Tool for CMAQ (FEST-C) (http://www.cmascenter.org/fest-c/)
is a Java-based interface system that is used to simulate daily fertilizer
application information using the Environmental Policy Integrated Climate
(EPIC) model (http://epicapex.tamu.edu/
epic/) and to extract the EPIC daily output that is a required input for
bidirectional NH3 modeling performed using the Community Multiscale Air
Quality (CMAQ) modeling
system (http://www.cmascenter.org/cmaq/).
The FEST-C interface system and spatial
data processing tools were developed by the University of North Carolina at
Chapel Hill (UNC)’s Institute for the Environment, while work on EPIC modeling
for the FEST-C system was conducted by Benson Consulting. All work was performed under contract to the
U.S. EPA Office of Research and Development.
The EPA EPIC
implementation requires no previous estimates of fertilizer application; it estimates
daily fertilizer applications based entirely on simulated plant demand in
response to local soil and weather conditions.
The FEST-C interface integrates CMAQ with EPIC through the current
release of the Spatial Allocator (SA) Raster Tools system (http://www.cmascenter .org/sa-tools/) that has been developed under the Community
Modeling and Analysis System (CMAS) Center.
Figure 1 displays the process diagram of FEST-C linked with the Weather
Research and Forecasting (WRF) and CMAQ modeling system. The Biogenic Emissions Landcover
Database version 4 (BELD4), which is generated using the newly released BELD4
tool in the SA Raster Tools system, is consistently used in the FEST-C system
as well as the WRF/CMAQ modeling system.
The WRF/CMAQ system provides daily weather inputs, optionally with
nitrogen (N) deposition, to the FEST-C system.
In return, FEST-C generates initial soil and pH conditions and daily N
information for specific crops assumed to reside in the agricultural land areas
of the CMAQ bidirectional NH3 modeling grids. The FEST-C system can be used in assessing
not only the impacts of agricultural fertilization and management practices on
air quality (NH3) and climate (N2O), but also the impacts
of meteorology/climate and air quality (N deposition) on crop yield, soil
erosion, and overall nitrogen-carbon-phosphorus biogeochemical status of the
agricultural ecosystem.
Figure
1. The FEST-C process diagram.
FEST-C is
designed to be used for CMAQ domains in North America, particularly for domains
covering the conterminous United States (U.S.) as well as the southern region
of Canada where detailed crop census data are available. The current version of the EPIC system for
CMAQ has complete modeling capabilities for grids located within the U.S. To
apply this system to other regions, users have to modify the databases
(particularly for soil) that were created within the FEST-C system and to
change the agricultural management file generation, as different regions will
likely have different agricultural management practices as well as different
soil data. For areas outside the U.S.,
the bidirectional CMAQ internally estimates these inputs for regions in Canada
and Mexico. The system works for domains
at different resolutions and in any of the four WRF projection coordinate
systems: longitude/latitude, Lambert Conformal Conic, Universal Polar
Stereographic, and Mercator.
The version 1.2
release of the FEST-C system, which includes Java interface programs, EPIC
FORTRAN codes, and SA Raster Tools C++ programs, was developed in Linux-based
operating systems. The FEST-C Java
interface is licensed under the Gnu Public License (GPL) version 3. The downloaded FEST-C system contains the
following two directories:
·
festc
– contains the Java-based interface.
·
epic – stores EPIC
model version 0509, which has been modified by the EPA to meet CMAQ input
requirements; and related utilities and data.
The EPIC model description can be obtained from Texas A&M
University (TAMU), College Station, TX (http://epicapex.tamu.edu/files/2013/02/epic0509usermanualupdated.pdf
). The documentation of the modified
EPIC modeling system for CMAQ is included in the release of the FEST-C
system. It provides detailed information
on how this particular application of EPIC was developed.
The FEST-C system
requires that the SA Raster Tools system be installed on the same system where
FEST-C resides. For visualization, users
can configure FEST-C to view netCDF files using the Visualization
Environment for Rich Data Interpretation (VERDI) or NCVIEW. Both the SA Raster Tools and the VERDI system
and their documentation can be obtained from the CMAS web site (http://www.cmascenter.org/).
Users need to untar the obtained FEST-C and SA packages in their
system. The programs under FEST-C do not
need any compiling, as the system comes with static compiled tools. The Raster Tools under SA, which are required
by FEST-C, are not statically pre-compiled with the package. Depending on the system configuration, users
may need to recompile the SA Raster tools if there is a library call error when
running the tools using FEST-C. Assuming
that the downloaded FEST-C system is installed under the ${FESTC_HOME} directory and the Spatial Allocator is installed under
the ${SA_HOME} directory, users
should perform the following steps:
1. Modify
${FESTC_HOME}/config.properties
to set:
·
work.dir – working
directory for scenarios.
·
epic.home – epic home
directory, which should be ${FESTC_HOME}/epic;
includes common data and executables for both EPIC and utilities.
·
sa.home – installed
Spatial Allocator directory, which should be ${SA_HOME}.
·
visual.program.home –
directory containing VERDI program.
·
queue.cmd – queue job submission command such as
qsub or bsub. Queue configuration (includes queue.name and queue.bigmem as well) for job submission has to be modified
based on the user’s Linux system. Comment
out (place # sign in the front) the three queue configurations if user’s systems
do not have batch job queuing systems.
·
queue.name – queue name.
·
queue.bigmem – big
memory setup to be used by the EPIC-to-CMAQ
tool.
·
debug – set to “true”
to print out debug message. It is
recommended that users not change this setting.
·
allow.diff.check – set
to “true” for checking consistent input in "Minimum Crop Acres" and
"Fertilizer Year" fields from different subinterfaces. It is recommended that users not change this
setting.
2. Make
a directory called “festc”
under the user’s home directory, which is assumed to be ${USER_HOME}, then copy ${FESTC_HOME}/config.properties to the ${USER_HOME}/festc directory. Change the work.dir
setting if needed.
3. Modify
${FESTC_HOME}/festc/festc file to set:
·
FESTC_HOME to ${FESTC_HOME}/festc.
·
-Xmx1024M to -Xmx2048M (optional) if users want
to use 2 GB of RAM to run the interface.
·
JAVA path (optional) if users do not want to use
the Standard Edition Runtime Environment (JRE) version 8 for Linux 32-bit and
64-bit systems that is included in the FEST-C release.
4. Modify
${FESTC_HOME}/festc_setup.csh
to:
·
Set the ${FESTC_HOME}
and ${SA_HOME} directories.
·
Source the file in the user’s .cshrc file.
5. Launch
FEST-C 1.2 interface by typing:
·
festc
in any directory with the x-window capability.
Troubleshooting for the SA Raster Tools:
The SA Raster
Tools have compiled tools which are stored under ${SA_HOME}/bin/64bits. Those
executable files may not work depending on the system configuration. If there is a library error in running the SA
Raster Tools within FEST-C, users should:
·
Recompile all libraries under ${SA_HOME}/src/libs
following instructions in the ${SA_HOME}/src/libs/README file.
·
Modiy ${SA_HOME}/src/raster/Makefile for correct paths.
·
Type “make clean” to clean previous compiled
programs.
·
Type “make” to compile the tools.
·
Type “make -B install” or “make install” to
install compiled tools.
The FEST-C
interface facilitates the creation of the spatial associations, input files,
soil initialization, and application processes required by EPIC. After preliminary site information and soils
are assigned to each grid cell, a 25-year “spin-up” simulation is required to
generate initial soil and annual nitrogen demand conditions that represent the
management system the user has defined.
These initial conditions are provided to the year-specific application
and management scheme. To launch the FEST-C interface system,
type:
·
festc or ${FESTC_HOME}/festc/festc
The FEST-C interface allows the
user to create, select, and manage different scenario management schemes under
the File menu for EPIC modeling and 13 subinterface
tools (see Figure 2).
Figure 2. The FEST-C interface system.
The system is described in detail
in the remaining sections of this document:
- Section
2: File Structures for EPIC Modeling
- Section
3: Scenario Management Selections under the File Menu
- Section 4: The Pre-EPIC File Generation
Tools
1. BELD4
Data Generation
2. Crop
Site Info Generation
3. WRF/CMAQ
to EPIC
- Section
5: EPIC Spin-up Run Tools:
1. EPIC
Site File Generation
2. Soil
Match for EPIC Spin-up
3. Management
File Generation for Spin-up
4. View/Edit
EPIC Inputs
5. EPIC
Runs for Spin-up
- Section
6: EPIC Application Run Tools
1. Management
File Generation for Application
2. EPIC
Runs for Application
- Section
7: Output Processing and Visualizing Tools:
1. EPIC
Yearly Extraction
2. EPIC
to CMAQ
3. Visualization
·
Section 8: Future Work
The EPIC model
and related utilities and data are stored under the ${FESTC_HOME}/epic directory, scenarios are saved under work.dir, which can be different from epic.dir . The file structure for EPIC modeling within
the FEST-C system is displayed in Figure 3.
Figure 3. File structure for
EPIC modeling (directory names in black and files in blue)
The epic directory contains four subdirectories: model, util, common_data, and doc;
scenarios is under work.dir, which is specified
in config file under home directory. These are
described below.
·
model – used to store the EPIC0509 model. It includes one subdirectory:
-
current: contains two current EPIC models for spin-up and
application simulations. The models were
developed for CMAQ modeling based on the EPIC0509 version of the EPIC model, obtained
from the AgriLife Research, Blackland
Research & Extension Center (http://epicapex.tamu.edu/epic/)
at TAMU. The documentation on the
development of the EPIC modeling system for CMAQ is included under the ${FESTC_HOME}/epic/doc directory.
·
util – contains utility
programs developed by Benson Consulting to generate site, soil, and management
input files required by EPIC. It has three subdirectories:
-
siteCreate: contains two programs used by the EPIC Site File Generation tool. The programs will not only generate EPIC site
files but also link EPIC sites (grid cell centroids) to the BELD4 crop grid assignments
and the 8-digit hydrologic cataloging units (HUCs) that contain the grid cells
to be used in the soil matching program.
Based on BELD4, this program assigns only those crops to a grid cell
that BELD4 indicates are present at that location. This minimizes the number of crop-specific
simulations performed across large domains.
-
soilMatch: contains six soil matching programs
used by the Soil Match for EPIC Spinup tool.
Soils are selected on the basis of the U.S. Department of Agriculture
(USDA) Natural Resource Inventory (NRI) assignment of each crop in each 8-digit
HUC to its most common HUC-8 soil type.
-
manageCreate: contains programs to create EPIC management
files for spin-up and application simulations by the Management File Generation for Spinup and
Management File Generation for
Application tools.
-
misc: contains
utility programs for converting the generated BELD4 land use file in netCDF format to be in IO/API format for the CMAQ
bi-directional modeling, aggregating EPIC variables from yearly average
extraction output by regions (e.g. 8-digit hydrologic units, states, counties,
and the whole domain) and by crops (e.g. 42 crops), summarizing N fertilizer
application from extracted daily files for CMAQ, and generating files with
selected EPIC daily output variables for the 8-digit HUC areas. Users can read the README file in the
directory and modify the C shell scripts in the subdirectories to use the tools. The tools use R codes and users need R
libraries installed for running the utilities.
·
common_data – contains data sets needed for EPIC and utility
programs. Also provided under this
subdirectory is the file EPIC_42crop_names.txt, which contains the crop names
and numbers, used in the FEST-C system.
This directory has the following subdirectories:
-
BaumerSoils: contains the soil data sets (22,838 soils) built
with soil parameters from the Baumer database
developed by Dr. Otto Baumer of National Soil Survey
Laboratory (NSSL) at USDA. Dr. Baumer used the SOILS5 database and soil pedon data to develop the representative EPIC data sets. Benson Consulting used this information to
create a subset of soil parameters in 22,838 soil files to be used with EPIC. Detailed information on the data set creation
can be obtained from the documentation of the EPIC modeling system for
CMAQ.
-
EPIC_model: contains two 5-year average CMAQ N deposition
daily files and the following two directories, which have common data files
required by EPIC spin-up and application runs:
·
spinup – has common files used for EPIC spin-up
simulations. For all crops except potatoes, the spin-up is set to run for 25
years using the EPIC statistical weather generator (see the weather generator discussion
in the EPIC documentation from TAMU). We
(Benson Consulting, EPA, and UNC) have arbitrarily set the starting year as 1978
in EPICCONT.DAT. For potatoes, the spin-up
is set to run for 100 years from 1903 in EPICCONT_POTATOES.DAT.
·
app – contains
common files used for EPIC application simulations. In the FEST-C system, users input the year (1
year only) for the EPIC application simulation.
When a new scenario is created, EPICCONT.DAT from this directory is
copied to the scenarios/“scenario name”/share_data directory and the simulation period is
changed to 2 years starting from the year previous to the simulation year. Two years’ worth of weather data are needed
to support production of fall-sown crops.
At present, the same weather is used for both years. In the future, an option may be added to
support input of two unique weather time series.
-
gisFiles: includes U.S. counties, U.S. states plus
some boundary areas in Canada and Mexico, and U.S. 8-digit HUC shapefiles and
elevation and slope image files. The readme
file in the directory describes each file and associated attributes in detail.
-
statWeath: contains weather station climate
statistics files distributed with the standard EPIC package.
-
util: includes common files used by the utility programs. This directory has two subdirectories:
·
soilMatch – has input files used by the soil
matching program to create EPIC soil files for the EPIC Runs for Spinup tool.
·
manageCreate – contain files to be used in
generating EPIC spin-up and application management files. We developed management data with fertilizer
types applied in 2001 and 2006 for each of 10 production regions (Northeast,
Appalachia, Southeast, Lake States, Corn Belt, Delta States, Northern Plains,
Southern Plains, Mountain, and Pacific) (see the region map in Cooter et al. [2012],
which is listed in the “Online Resources” section of the FEST-C web site [(http://www.cmascenter.org/fest-c/]). Fertilizer types (but not amounts) applied are based on fertilizer sales of 62 major fertilizer types by
state. Users can obtain detailed
information from the documentation for the EPIC modeling system for CMAQ. It is recommended that 2001 be used for
applications prior to 2006, and that 2006 be used for applications from 2006
through 2010. In the future, a 2011
fertilizer type file will be created to coincide with the released 2011
National Land Cover Data (NLCD). Fertilizer types applied are used by the EPIC
management file generation for application, and they are stored under the
following two subdirectories:
-
2001:
for 2001 fertilizer year management file generation.
-
2006: for
2006 fertilizer year management file generation.
In
both cases, regional fertilizer data information is stored under the directory:
-
regionFert
·
scenarios – contains EPIC application scenarios and is
described separately below this bulleted list.
·
doc – contains
documents on the EPIC modeling system for CMAQ (EPA_EPIC_application_v1_10252013.pdf).
In general, users should not change
the data files described in the above directories. All files generated by users’ applications
are stored under the scenarios directory. When the user creates a scenario by selecting
“New Scenario” under the File menu,
the following items are created:
·
scenariosInfo – stores information for the created
scenario, which is assumed to be named by the user as “scenario name”. This
directory contains:
-
“scenario name”: an XML file that stores the scenario information.
-
logs: directory
containing the script file used to create (or copy or delete as well) the
scenario and execution log file.
·
“scenario name” – scenario directory that will contain
all generated files for this scenario.
Under each scenario directory, the
following directories are created for EPIC modeling:
·
share_data – contains all data sets generated for EPIC
modeling and to be used by all crops modeled.
After users generate EPIC site files and daily weather, it will contain
the following two subdirectories:
-
SIT:
contains EPIC site files.
-
dailyWETH: contains daily
weather and N files for EPIC modeling.
·
scripts – stores
script and log files created to run the tools within the FEST-C interface. All tools are executed through the Linux
queue system. Users should always check
the log file to make sure that the queue job completed correctly. Unwanted files under this directory should be
cleaned out periodically.
·
work_dir – contains some intermediate or temporary files
created by the FEST-C tools. Currently,
not many files are created under this directory.
·
21 crop dirs ( "HAY", "ALFALFA",
"OTHER_GRASS", "BARLEY", "EBEANS",
"CORNG", "CORNS", "COTTON", "OATS",
"PEANUTS", "POTATOES", "RICE", "RYE",
"SORGHUMG", "SORGHUMS", "SOYBEANS", "SWHEAT",
"WWHEAT", "OTHER_CROP", "CANOLA",
"BEANS") – the 21 crop directories are created by the EPIC Site File Generation tool. Under each crop directory there are many
files that are created for generating EPIC input files. The spinup and app
subdirectories described below are also created from management file generation
and EPIC runs for spin-up and application:
-
spinup: contains files created from the EPIC
management file generation and EPIC runs for spin-up tools. It contains the following three
subdirectories:
·
manage – contains
EPIC run files, EPIC site management files created by the Management File Generation for Spinup
tool, and tile drain soil list file. The management files and tile drain soil
list file are contained under the following subdirectories:
-
OPC: contains
the management schedule for each domain grid cell containing rain-fed and
irrigated crop. Variables (schedule) can
be interpreted using the documentation for the EPIC modeling system for CMAQ.
-
tileDrain: contains the SOILLIST.DAT which has
soil tile drain information for EPIC spinup runs.
·
rainf – contains files
for each domain grid cell containing the particular crop that were created by
the EPIC Runs for Spinup
tool from rain-fed crops. It contains
the following output directories (see the EPIC documentation from TAMU):
-
DFA:
daily fertilizer and other output.
-
NCM:
monthly fertilizer and other output.
-
NCS: monthly
soil output.
-
OUT: standard
EPIC output file that contains various budget tables and summaries of the
simulation which are useful for debugging.
-
SOL:
soil output files that are used as initial values for the application.
-
TNA:
annual fertilizer and other outputs.
-
TNS:
annual soil output.
·
irr – contains files for
each domain grid cell containing the particular crop that were created by the EPIC Runs for Spinup
tool from irrigated crops. It contains
the following output directories:
-
DFA:
daily fertilizer and other output.
-
NCM:
monthly fertilizer and other output.
-
NCS:
monthly soil output.
-
OUT:
standard EPIC output file that contains various budget tables and summaries of
the simulation that are useful for debugging.
-
SOL:
soil output files.
-
TNA:
annual fertilizer and other outputs that are useful
for debugging.
-
TNS:
annual soil output.
-
app: contains
files created from the management file generation and EPIC runs for application
tools. It contains the following three
subdirectories:
·
manage – contains
EPIC run files, EPIC site management files created by the Management File Generation for Application tool, and tile drain
soil list file. Management files and the
tile drain soil list file are contained under the following subdirectories:
-
OPC:
contains the management schedule for each domain grid cell containing rain-fed
and irrigated crop. Variables (schedule)
can be interpreted using the documentation for the EPIC modeling system for
CMAQ.
-
tileDrain: contains the SOILLIST.DAT which has
soil tile drain information for EPIC application runs.
·
rainf – contains files
created by the EPIC Runs for Application
tool from rain-fed crops. It contains
the following output directories (see the EPIC documentation from TAMU):
-
DFA:
daily fertilizer and other output.
-
NCM:
monthly fertilizer and other output.
-
NCS:
monthly soil output.
-
OUT:
standard EPIC output file that contains various budget tables and summaries of
the simulation (useful for debugging).
-
SOL:
soil output files.
-
TNA: annual
fertilizer and other outputs.
-
TNS:
annual soil output.
·
irr – contains files
created by the EPIC Runs for Application
tool from rain-fed crops. It contains
the following output directories:
-
DFA:
daily fertilizer and other output.
-
NCM:
monthly fertilizer and other output.
-
NCS:
monthly soil output.
-
OUT: standard
EPIC output file that contains various budget tables and summaries of the
simulation (useful for debugging).
-
SOL: soil
output files.
-
TNA:
annual fertilizer and other output.
-
TNS: annual
soil output.
·
output4CMAQ
– stores EPIC output files and extracted netCDF files
for quality assurance (QA) and CMAQ bidirectional NH3 modeling. This directory contains the two following
subdirectories:
-
spinup: contains all files created from EPIC spin-up
simulations for CMAQ. It contains the
following three subdirectories:
·
5years
– contains extracted average EPIC output for each crop from the last five years
of the spin-up simulation. Files are
named as “BELD4 Crop Number”.dat (see Table 1 in Section 4.1 for crop numbers).
·
daily – stores daily EPIC output files for the EPIC spin-up simulation
of each crop. “BELD4 Crop Number”.NCS is for soil output and “BELD4 Crop Number”.NCD is for fertilizer and other daily output.
·
toCMAQ – contains created
netCDF files with EPIC spin-up output for selected
modeling grid cells with crop data. The netCDF output files are created using the FEST-C tools by
extracting data files stored under the 5years
or daily directories listed above.
-
app: stores files
created from EPIC application simulations for CMAQ. It contains the following three
subdirectories:
·
year – contains extracted average EPIC output for the EPIC
application year. Files are named as
“BELD4 Crop Number”.dat.
·
daily – stores
daily EPIC output files for the EPIC application simulation of each crop. “BELD4 Crop Number”.NCS
is for soil output and “BELD4 Crop Number”.NCD is for
fertilizer and other daily output.
·
toCMAQ – contains created
netCDF files with EPIC application simulation results
for selected modeling grid cells with crop data. The netCDF output
files are created using the FEST-C tools by extracting data files stored under
the year or daily directories listed above.
There are five scenario management
selections (as well as Exit) under the File menu at the upper left of the
FEST-C tool bar: Open Scenario, New Scenario, Copy Scenario, Save Scenario, and
Delete Scenario. Each of these is described below.
·
Open Scenario – to open an already-created
scenario. Users always need to either open or create (see next bullet) a
scenario to work on. Users can select
any one of the scenarios under the scenarios/scenariosInfo directory. After users open a scenario, information for
the scenario, such as the domain description, will be automatically filled in
by the FEST-C tool interface. Within the
FEST-C system, users have to work within a scenario to execute any of the tools
except the Visualization tool. Figure 4 shows the interface used to open the
test case created in the FEST-C system (The test_case
scenario is described at the beginning of Section 4).
·
New Scenario – to create a new scenario (versus
opening one that’s already been created). In creating a new scenario, the user
has to provide the following information for a CMAQ modeling domain and EPIC
simulation year (see Figure 5):
-
Rows, Columns: the number of rows and columns
for the domain.
-
XCellSize, YCellSize: x and y resolution for the grid cell.
-
XMin, YMin: x and y coordinates of the lower left corner
of the lower left grid cell. Users can
often find this information in the GRIDDESC file in the Meteorology-Chemistry
Interface Processor (MCIP) output.
Figure
4. Open Scenario selection window used to open the test_case scenario.
Figure
5. New Scenario selection window with input to
create the test_case scenario within FEST-C.
-
Proj4Projection: domain projection defined in
Proj4 format (see details at http://www.remotesensing.org/geotiff/proj_list/). The interface sets the Lambert Conformal
Conic projection, which is used by the CMAQ U.S. 12-km domain as the
default. Users can change it to any
projection supported for CMAQ modeling.
-
Grid Name: user-supplied name for the domain,
using no more than 16 alphanumeric characters and no spaces.
-
Simulation Year: year (YYYY) for the EPIC
simulation. FEST-C is designed to
simulate yearly fertilizer application information for CMAQ bidirectional NH3
modeling.
-
NLCD/MODIS Data Year: year (YYYY) for the
NLCD/MODIS land cover data used for the EPIC simulation. NLCD/MODIS land cover data are required in
the EPIC simulation within FEST-C for CMAQ bidirectional NH3
modeling. Currently, users can select
2001 or 2006 NLCD/MODIS data year. 2011
NLCD/MODIS data selection will be added to the system in the future.
-
Scenario Name: name for the scenario, using
alphanumeric characters and no spaces.
When a new scenario is
created, the following files and directories are created:
-
scenarios/scenariosInfo/“scenario name”: XML file to store the scenario
information.
-
scenarios/“scenario name”: directory
to store all generated information for this scenario. Some subdirectories are also generated under
this scenario directory (see Section 2 for file structures).
-
scenarios/“scenario
name”/share_data/EPICCONT.DAT: contains EPIC
constant parameters. The simulation period
is a two-year period starting with the year before the simulation year.
·
Copy Scenario – to copy an existing scenario
under the scenarios/scenariosInfo
directory to a new scenario with a defined simulation year, which can be the same
as or different from the existing scenario year (see Figure 6). Note that if the existing scenario contains
many crop simulations, this action can take a long time to complete in a background
queue job.
·
Save Scenario – to save a scenario after a user
has worked on it. Only the input
information for the scenario tool interfaces is saved. When the user performs the FEST-C tool
actions, generated files are always saved under different directories,
described in Section 2.
Figure 6. Copy
Scenario selection window.
·
Delete
Scenario – to delete a scenario. This
is also run as a background submission and can take some time. All directories
and subdirectories for that scenario are deleted completely.
·
Exit – to exit the FEST-C interface. You will be asked if you want to save the
scenario you were working on before exiting the tool.
The action performed by making a selection
under the File menu (e.g., copy, create, delete) is executed by a script file
through the queue job. The script and log files are stored under the scenarios/scenariosInfo/logs
directory. Users should check the log files under
the directory to make sure that the selected action completely correctly.
Before describing the various
FEST-C tools in Sections 4 through 7, we must first discuss the test_case scenario in the FEST-C system, because we use this
scenario to demonstrate the input and output components on the tool
interface. The test_case
scenario is a small 12-km domain with 25 rows and 25 columns in the CMAQ
standard projection. The domain is
located in the northwest corner of Iowa and crosses into Minnesota, South
Dakota, and Nebraska. Figure 7 illustrates
the domain grid cells with the identification numbers (GRIDID) used in the
FEST-C system; colors are used to indicate the crop percentage for each grid cell
as generated from 2006 NLCD data. All
625 (25´25)
12-km grid cells in this test domain have crop coverage, and most of them have
more than 75% crop coverage. The GRIDID
for a grid cell with row and column starting from 1 is defined as:
(1)
where columns is the number of columns for the
domain. Row and column start from 1 at
the lower left corner cell in the domain.
Users can compute the row and column for a grid cell with GRIDID as:
(2)
(3)
where floor is for rounding down the value and
remainder is for taking the remainder
from the division.
Figure 7. FEST-C
test_case scenario 12-km domain in the U.S. northern Central
Plains. Associated with each grid cell is an identification number (GRIDID)
and a color that indicates crop coverage percentage. The domain’s cells are numbered from 1 for
the lower left corner cell to 625 for the upper right corner cell.
In Section 4,
we discuss the first three tools in the FEST-C interface: the BELD4 Data Generation tool, the Crop Site Info Generation tool, and the WRF/CMAQ-to-EPIC tool. These are used to
prepare site crop and spatial data for EPIC input file generation and to
generate required daily weather data and optional nitrogen deposition data for
the EPIC simulation year. All three
tools were developed in the SA Raster Tools system.
EPIC modeling for a CMAQ domain requires BELD4 data, which are used for
selecting grid cells with crop coverage.
The BELD4 Data Generation tool
allows users to compute the BELD4 dataset for a selected scenario. For detailed information on it, users can consult
the SA Raster Tools documentation: http://www.cmascenter.org/sa-tools/documentation/4.0/html/Raster_Users_Guide_4_0.htm.
Figure 8 shows the interface used to
compute the BELD4 dataset for the test_case
scenario.
Figure
8. The BELD4
Data Generation tool interface for the test_case
scenario.
Before running this tool, users
need only to make sure that the following two entries are correct for their
scenarios:
·
NLCD/MODIS Data Year – the year defined when creating
the scenario; it can be either 2001 or 2006.
Processed 2001 and 2006 crop tables from the U.S. and Canada are stored
under the ${SA_HOME}/data directory
for this tool. The 42 rain-fed and
irrigated crops generated from the BELD4 tool and modeled in the FEST-C system
are displayed in Table 1. In addition to
crop numbers used in BELD4 (new version of BELD), the table also lists BELD3
(older version) numbers, because we started building the FEST-C system using
the BELD3 data. Crop numbers used in
EPIC modeling often follow the BELD3 crop numbers (from 22 to 63), but the
output files from EPIC modeling for use in CMAQ use the BELD4 crop numbers
(from 1 to 42). If a new crop is to be
modeled in the FEST-C system, new crop tables under the SA data directory have to be generated and the BELD4 tool has to be
modified as well.
Table 1. The 42 rain-fed and irrigated crops modeled in the
FEST-C system.
|
BELD4
|
BELD3
|
Crop
Name
|
BELD4
|
BELD3
|
Crop
Name
|
BELD4
|
BELD3
|
Crop
Name
|
|
1
|
22
|
Hay
|
15
|
36
|
Cotton
|
29
|
50
|
SorghumSilage
|
|
2
|
23
|
Hay_ir
|
16
|
37
|
Cotton_ir
|
30
|
51
|
SorghumSilage_ir
|
|
3
|
24
|
Alfalfa
|
17
|
38
|
Oats
|
31
|
52
|
Soybeans
|
|
4
|
25
|
Alfalfa_ir
|
18
|
39
|
Oats_ir
|
32
|
53
|
Soybeans_ir
|
|
5
|
26
|
Other_Grass
|
19
|
40
|
Peanuts
|
33
|
54
|
Wheat_Spring
|
|
6
|
27
|
Other_Grass_ir
|
20
|
41
|
Peanuts_ir
|
34
|
55
|
Wheat_Spring_ir
|
|
7
|
28
|
Barley
|
21
|
42
|
Potatoes
|
35
|
56
|
Wheat_Winter
|
|
8
|
29
|
Barley_ir
|
22
|
43
|
Potatoes_ir
|
36
|
57
|
Wheat_Winter_ir
|
|
9
|
30
|
BeansEdible
|
23
|
44
|
Rice
|
37
|
58
|
Other_Crop
|
|
10
|
31
|
BeansEdible_ir
|
24
|
45
|
Rice_ir
|
38
|
59
|
Other_Crop_ir
|
|
11
|
32
|
CornGrain
|
25
|
46
|
Rye
|
39
|
60
|
Canola
|
|
12
|
33
|
CornGrain_ir
|
26
|
47
|
Rye_ir
|
40
|
61
|
Canola_ir
|
|
13
|
34
|
CornSilage
|
27
|
48
|
SorghumGrain
|
41
|
62
|
Beans
|
|
14
|
35
|
CornSilage_ir
|
28
|
49
|
SorghumGrain_ir
|
42
|
63
|
Beans_ir
|
·
NLCD/MODIS List File – set to the fixed-format
text file that contains downloaded NLCD land use, imperviousness, and canopy
data files and downloaded tiled MODIS land cover (MCD12Q1) data sets. The interface sets the file ${SA_HOME}/data/ nlcd_modis_files_{NLCD/MODIS Data
Year}.txt as the default file. Users
need to download NLCD and MODIS land cover data sets and modify the text file
accordingly using the paths and names for the downloaded data sets. The text file has to have the same fixed
titles and format as in the default file.
${SA_HOME}/data/ sat/README contains instructions on downloading the
data sets. If users want to generate a 2001
BELD4 data set, 2001 NLCD and MODIS land cover data sets have to be downloaded
from the NLCD web site (http://imsdemo.cr.usgs.gov/webappcontent/mrlc/nlcdrlc.php)
and MODIS land products web site (https://lpdaac.usgs.gov/products/modis_products_
table/mcd12q1 ), and the nlcd_modis_files_2001.txt list file has to be modified
following the format in this sample file.
When the Run button on the BELD4 Data Generation tool interface is
clicked, a csh script file is generated under the scenarios/”scenario name”/scripts directory. This
file is submitted to the system as a queue job after the user clicks OK, and a
log file for the job execution will be generated after the queue job is finished. Users
should always check for error messages in the log file, based on the
information provided in the Message Box (shown in Figure 8).
The outputs produced by the tool
are the following two files, which are stored under the scenarios/”scenario name”/share_data directory:
·
beld4_{Gird Name}_{NLCD/MODIS Data Year}.nc (beld4_TESTGRIDS_2006.nc for the test_case
scenario) – a netCDF file containing gridded percentage
data for imperviousness, canopy, 194 tree species, 40 NLCD/MODIS land cover
classes, and 42 BELD4 crops. This domain-
and resolution-specific data file is a required input to the Crop Site Info Generation tool discussed
in the next section. For the CMAQ
bi-directional NH3 modeling, the BELD4 output file has to be
converted into an IOAPI file by using the run_Beld_nc2ioapi.csh
script file under {FESTC_HOME}/epic/util/misc.
·
beld4_{Grid Name}_{ NLCD/MODIS Data Year}.txt
(beld4_TESTGRIDS_2006.txt for the test_case scenario)
– a text table containing gridded percentage data for imperviousness, canopy,
and 40 NLCD/MODIS land cover classes for a specific domain and grid resolution.
The Crop Site Info Generation tool is used
to compute EPIC site (grid cells) and crop information for EPIC modeling. The tool processes spatial boundary
shapefiles and elevation and slope image data to generate site information
data needed in EPIC modeling. Figure 9
displays the tool interface used to compute the crop site information for the test_case scenario.
The tool uses the spatial data sets stored under ${FESTC_HOME}/epic/common_data/gisFiles and input files from the ${SA_HOME}/data directory. Before
running this tool, users need only to choose the following two entries for this
tool:
Figure 9. The Crop Site Info Generation
tool interface used for the test_case scenario.
·
BELD4 netCDF File – this
is often the BELD4 netCDF file generated using the
previous tool. The file name should be of
the form beld4_{Gird Name}_{NLCD/MODIS Data Year}.nc (beld4_TESTGRIDS_2006.nc for the test_case
scenario). If this file does not exist,
the interface will indicate this after Run is clicked. If this is the case, users need to either run
the previous tool to generate this data set or input anywhere within the
computer system a BELD4 netCDF file that is based on
the same domain as the domain of the scenarios with which the users are
working.
·
Minimum Crop Acres – this is the minimum crop
area for at least one of the 42 possible crops in a grid cell if the grid cell
is to be selected for EPIC simulation.
The default is set to 40 acres, which is what we have used for CMAQ 12-km
grid modeling; this is intended to represent the smallest commercially viable
farm size. For finer grid resolutions or
for domains in which smaller commercial enterprises make up a significant
fraction of farms (e.g., orchards, some vegetable and specialty crops), users
may need to reduce this minimum to adequately characterize the distribution of
agricultural lands. Doing so may
increase the number of simulated grid cells (sites), which can also increase
run time.
After Run has
been clicked and the queue job has completed, users should check the log file
under their scenario’s scripts directory
to see whether any errors occurred during execution.
The tool
generates the following two text output files stored under scenarios/”scenario name”/share_data:
·
EPICSites_Info.csv – contains the GRIDID,
XLONG, YLAT, ELEVATION, SLOPE_P, HUC8, REG10, STFIPS, CNTYFIPS, GRASS, CROPS,
CROP_P, COUNTRY, and COUNTRY-PROVINCE items used for creating EPIC site files.
·
EPICSites_Crop.csv – contains the GRIDID,
acreages of 42 possible crops within each grid cell, COUNTRY, and HUC8 items
used in EPIC site and soil file generation.
The WRF/CMAQ-to-EPIC tool is used to generate
EPIC daily weather data and, if the option is selected, N deposition input
files to be used in EPIC application simulations. The tool reads EPIC grid cell information
stored in the EPICSites_Info.csv file generated using the previous tool. It extracts EPIC daily weather input data
from WRF simulation output. There are
three options currently available for the inclusion of daily atmospheric data:
(1) no N deposition, (2) the original EPIC default (assumes a
constant N concentration of 0.8 ppm in precipitation and no dry deposition),
and (3) CMAQ hourly output files (DRYDEP, WETDEP1) from a previous CMAQ
run (unidirectional or bidirectional). In
the vicinity of areas receiving significant atmospheric dry deposition, such as
areas immediately surrounding large animal feeding operations, this information
can impact EPIC biogeochemistry and subsequent estimates of plant N application
needs. If speciated
N deposition is available, oxidized wet and dry deposition are assumed to enter
the EPIC soil nitrate pool, and reduced wet and dry deposition is assumed to
enter the EPIC soil ammonium pool. If
CMAQ hourly output files are used, the MCIP and CMAQ domains must be the same
as the domain defined in the EPIC scenario.
Figure 10 shows this tool interface as used for the test_case
scenario.
Figure
10. The WRF/CMAQ-to-EPIC
tool interface used for the test_case scenario.
Before running this tool, users
have to provide input for the following three items in the interface:
·
MCIP Data Directory – this directory contains
processed WRF files output by MCIP for the EPIC simulation year. This tool requires only MCIP METCRO2D output
files. METCRO2D output files have to have
names of the format METCRO2D*{DATE} in which * can be any nondigit
characters and {DATE} can be in one of four date formats: YYYYMMDD, YYMMDD,
YYYYDDD, or YYDDD (e.g., METCRO2D_051226 )
·
Deposition Selection – used to select one of the
following three options:
-
CMAQ deposition directory: select this option to
use CMAQ deposition output files. If
this is selected, users have to set the CMAQ deposition file directory in the next
field on the interface.
-
Default: this option assumes that the N mixing
ratio is 0.8 ppm for wet oxidized N deposition.
The tool computes wet oxidized N deposition based only on rainfall, and
other N deposition variables are assumed to be zero.
-
Zero: this option assumes that there is no
atmospheric N.
·
CMAQ Deposition Directory – used to set the
directory containing the CMAQ dry and wet deposition output files for the simulation
year if “CMAQ deposition directory” was chosen in the previous field. The dry and wet deposition file names must
contain the string “DRYDEP” or “WETDEP”.
In addition, the deposition file names must end with “*{DATE}” in the
format that is described for the MCIP files above (e.g., an MCIP file can be named
as METCRO2D_20030416 and the deposition files can be named CCTM_M2f_v14soa_v3.4beta3_2003.DRYDEP.20030416
and CCTM_M2f_v14soa_v3.4beta3_2003.WETDEP1.20030416)
After Run has
been clicked and the queue job has finished, users should check the log file
under their scenario’s scripts directory
to see whether any errors occurred during execution. The tool generates the following three output
files stored under scenarios/”scenario
name”/share_data:
·
dailyWETH/“GRIDID”.dly – daily weather and N files for each selected grid cell
for EPIC modeling. “GRIDID” is the
identification number for a selected grid cell (see Figure 7). Each daily file contains 14 formatted data items
(listed in Table 2) to be used in the EPIC runs for the simulation year (same
as the weather year). This daily weather
file is duplicated for the year before the simulation year because we run the
EPIC model for a two-year period using daily time steps.
·
EPICW2YR.2YR – daily weather file list to be
used in EPIC application modeling. It is
defined in ${FESTC_HOME}/epic/common_data/EPIC_model/app/EPICFILE.DAT.
·
site_weather_dep_${YEAR}0101_to_${YEAR}1231.nc – a single netCDF
file with daily time steps for the simulation year. It contains extracted daily weather and N
deposition data for the EPIC grid cells in the EPICSites_Info.csv file. Users can use the Visualization tool (discussed in Section 7) to display the values
of a selected variable spatially.
Table
2. EPIC daily weather and nitrogen deposition
variables.
|
Index
|
Variable
|
Index
|
Variable
|
|
1
|
Year
|
8
|
Daily Average Relative Humidity
|
|
2
|
Month
|
9
|
Daily Average 10-m Wind Speed (m s-1)
|
|
3
|
Day
|
10
|
Daily Total Wet Oxidized N (g/ha)
|
|
4
|
Daily Total Radiation (MJ m2)
|
11
|
Daily Total Wet Reduced N (g/ha)
|
|
5
|
Daily Maximum 2-m Temperature (C)
|
12
|
Daily Total Dry Oxidized N (g/ha)
|
|
6
|
Daily minimum 2-m temperature (C)
|
13
|
Daily Total Dry Reduced N (g/ha)
|
|
7
|
Daily Total Precipitation (mm)
|
14
|
Daily Total Wet Organic N (g/ha)
|
Users must run EPIC spin-up
simulations to generate soil files and initial annual plant N demand data,
which are used in EPIC application-year simulations. Described in this section are the five EPIC
spin-up run tools: EPIC Site File
Generation, Soil Match for EPIC Spinup, Management
File Generation for Spinup, View/Edit EPIC Inputs, and View/Edit
EPIC Inputs. Users can use these tools sequentially to generate files
needed for EPIC spin-up simulations. (Note:
Although there are 42 rain-fed and irrigated crops in the FEST-C system, the
current system is not yet set to model the DRY BEANS (BEANS) crop; users should
therefore not select BEANS in running the FEST-C tools.) Users can obtain detailed information on
building the EPIC databases using developed programs from the documentation for
the EPIC modeling system for CMAQ, and on the file formats and parameter
descriptions from the EPIC model documentation from TAMU (http://epicapex.tamu.edu/files/
2013/02/epic0509usermanualupdated.pdf).
The EPIC Site File Generation tool uses the
FORTRAN programs stored under ${FESTC_HOME}/epic/util/siteCreate. This tool generates EPIC site files for the
selected grid cells with the minimum crop acreage limit criterion. It also creates 21 crop directories with a
crop site list file that is to be used in the other tools. Figure 11 displays the tool interface for the
test_case scenario.
As explained in Section 4.2, users can change the Minimum Crop Acres if the
40-acre limit is too large for their modeling domain’s grid cells.
Figure 11. The EPIC Site File Generation
interface for the test_case scenario.
After the queue job run has finished,
users should check the log file under their scenario’s scripts directory to see whether any errors occurred during
execution. The tool generates the
following files and directories:
·
“scenario name”/share_data/SIT/“GRIDID”0.SIT
– EPIC site files to be used for all EPIC crop modeling. A description of the file format can be
obtained from the EPIC model documentation.
·
“scenario name”/share_data/SITELIST.DAT
– EPIC site list file for all crops to be used in EPIC modeling.
·
“scenario name”/“crop name”/“crop name”-LIST.DAT – EPIC
site list for the particular crop, to be used in the Soil Match for EPIC Spinup tool discussed
in the following section. If there are
no grid cells that contain that crop, this file will be empty.
The Soil Match for EPIC Spinup
tool selects a soil for each crop within a grid cell and creates the EPIC soil
file. The EPIC soil datasets are built
to represent the sample point soils selected for USDA NRI data points at the
HUC-8 spatial scale. This tool links built EPIC soil datasets contained in the BaumerSoils subdirectory
to the soil series from the USDA NRI for the crop and grid cell. It uses the FORTRAN programs stored under ${FESTC_HOME}/epic/util
/soilMatch with the common data files stored
under ${FESTC_HOME}/epic/common_data/ util/soilMatch and the generated soil list data under each
crop directory. Figure 12 shows the tool
interface used to match soils for all crops except BEANS (as explained at the
beginning of Section 5) for the current version of FEST-C. After selecting the crops, users click the
Run button to run the tool in the queue.
After the job has finished, users should check the queue job and log
file in the “scenario name”/scripts directory,
based on the information provided in the Message Box (shown in Figure 12).
The tool generates many output
files under each crop directory, but most of them are intermediate files. The final data file created for the EPIC
spin-up simulation is “scenario name”/
“crop name”/SOILLIST.DAT, which contains the matched BaumerSoils soil file with other
parameters for each grid cell under each crop directory.
Figure 12. The Soil Match for EPIC Spinup
tool interface used for the test_case scenario.
Users can select single or multiple crops (except BEANS, for the current FEST-C
version).
The Management File Generation for Spinup tool interface is used to create the EPIC management
for each crop within a grid cell. The EPICRUN file that has the linkages for
the grid cell, statistical weather and wind files, soil files, and management
files is also created for the rain-fed and irrigated forms of the crop. This tool uses the FORTRAN programs ManGenSU.exe
and soildrain.exe stored under ${FESTC_HOME}/epic/util/manageCreate with the
common data files stored under ${FESTC_HOME}/epic/common_data/util/manageCreate and many other data files generated under each
crop directory. Figure 13 shows the tool
interface used to generate management files for the test_case
scenario.
Figure 13. The Management
File Generation for Spinup tool used for the test_case scenario.
Users need to make sure that the
following two fields are selected correctly:
·
Fertilizer Year – select either 2001 or 2006 for
choosing the correct common data sets stored under ${FESTC_HOME}/epic/common_data/util/manageCreate.
·
Selected Crops – select one crop or multiple
crops (except BEANS).
After the user clicks the Run
button and then “OK”, a queue job to generate management files for each
selected crop is submitted. After the
job has finished, users should check the queue job and log file in the “scenario name”/scripts directory, based
on the information provided in the Message Box (shown in Figure 13).
There are many output files
generated under each crop, but many of these are used just for verification.
The tool generates the following files to be used for the EPIC spin-up
simulations under the directory “scenario
name”/“crop name”/spinup/manage for each crop:
·
EPICRUNFILERAIN.DAT – EPIC run file for rain-fed
spin-up simulation of this crop.
·
EPICRUNFILEIRR.DAT – EPIC run file for irrigated
spin-up simulation of this crop.
·
GRIDS_OPC.DAT – the list of management file
names to be used in EPIC modeling.
·
OPC/“GRIDID”0“BELD3
Crop Number”.OPC – grid cell EPIC management files
under the OPC directory. Table 1 in Section 4.1 lists the crop numbers
in the BELD data.
·
tileDrain/SOILLIST.DAT – soil list file which contains tile drain
information for EPIC simulations and is used when “tileDrain”
is selected when running EPIC spinup simulations.
The View/Edit EPIC Inputs interface allows
users to view or edit five main EPIC simulation files (listed in Figure 14). Users generally do not need to edit these files,
but viewing them can be helpful for debugging. The user has to select a crop
first and then select the EPIC simulation type.
The simulation type can be SPINUP if the Management File Generation for Spinup
tool (previous section) has been executed for the selected crop; or the user
can select the simulation type APP after the Management File Generation for Application tool (discussed in
Section 6.1) has been executed for the crop. Figure 14 shows the View/Edit EPIC Inputs tool interface for
the test_case scenario.
Figure 14. The View/Edit
EPIC Inputs tool for the test_case scenario.
The EPIC Runs for Spinup
tool interface is used to run the EPIC model for spin-up (EPICsu.exe program),
which is stored under the
directory ${FESTC_HOME}/epic/model/current.
The tool uses input files stored primarily in the following directories:
·
${FESTC_HOME}/epic/common_data/EPIC_model/spinup – for the common model input files.
·
scenarios/“scenario
name”/share_data – for site files and list file.
·
${FESTC_HOME}/epic/common_data/statWeath – for
observed climate station statistical data (see http://epicapex.tamu.edu/epic/)
·
scenarios/“scenario
name”/“crop name”/spinup/manage – for the run
files, management files, and management list file.
·
scenarios/“scenario
name”/ “crop name” – for the soil list file.
Spin-up
simulations are performed primarily to generate EPIC soil files to be used as
initial conditions in the application run for the simulation year. As discussed in Section 2, the spin-up
simulation is run for 25 years starting from 1978 for all crops except
potatoes; for potatoes it is run for 100 years starting from 1903. Figure 15 displays the tool interface used
for the test_case scenario. Users can select one or more crops (except
BEANS) for the simulation. After
clicking the Run button, a script file is generated to run the rain-fed and
irrigated EPIC spin-up simulations for each crop. The user submits the script file to the queue
by clicking OK. After the job has
finished, users should check the queue job and log file in the “scenario name”/scripts directory,
based on the information provided in the Message Box (shown in Figure 15).
Figure 15. The EPIC Runs for Spinup
tool used for the test_case scenario.
Users need to make sure that the
following three fields are selected correctly:
·
CO2 Level (ppm) - input the correct
CO2 level for the simulation (e.g. 380). The input level overwrites the CO2
level defined in EPICCONT.DAT and site file.
·
Daily Average N Deposition – select N input to
be used in the simulation. Users can
select using the values defined in EPIC input files, daily average N input from
5-year CMAQ simulations from 2002 to 2006, or daily average N input from 5-year
CMAQ simulations from 2006 to 2010. The 5-year
CMAQ N daily input files are stored under ${FESTC_HOME}/epic/common_data/EPIC_model.
·
Run TileDrain – select
whether tile drain is applied for saturated soils. If YES is selected, SOILLIST file under scenarios/“scenario
name”/“crop name”/spinup/manage/tileDrain
will be used for all crops except hay (1, 2), alfalfa (3, 4), Other_Grass (5, 6) and rice (23, 24).
The tool generates many directories
and files for each crop. The original
EPIC output files are stored under the two following subdirectories in the “scenario name”/“crop name”/spinup directory:
·
rainf – contains output
from EPIC rain-fed spin-up simulations for this crop.
·
irr – contains output
from EPIC irrigated spin-up simulations for this crop.
In both cases,
soil files to be used in the EPIC application simulation are:
-
SOL/“GRIDID”0“BELD3
Crop Number”.SOL
The output data created for CMAQ
modeling are used primarily for QA purposes, and are stored under the following
two directories in the “scenario
name”/output4CMAQ/spinup directory:
·
5years
– contains average EPIC output data from the last five years of the spin-up
simulations for the crops.
·
daily – stores daily EPIC output data from EPIC spin-up runs
for the crops simulated.
After users
complete the EPIC simulations for spin-up, they can proceed to the EPIC
application run tools for the simulation year.
The spin-up simulations need to be run only once for a given domain and
grid resolution—in other words, the initial conditions can be re-used for
multiple application years. The first step in running an EPIC application is to
generate management files for the application year (as described in Section
6.1). The application management program
needs to be run only once for a given domain and grid resolution; it is not year-specific. The user can then run the EPIC model for the
application year (as described in
Section 6.2) if the daily weather and N deposition files for the scenario have already
been generated using the tool described in Section 4.3.
The Management File Generation for Application
tool interface is used to create (1) the EPIC management files for each crop to
be used in the EPIC application-year modeling; and (2) the EPICRUN file for the
rain-fed and irrigated simulations, which contains the linkages for the
statistical weather and wind files, the soil files, and the management files
for EPIC grid cells. The tool uses the
FORTRAN programs ManGenFERT.exe and soildrain.exe stored under the ${FESTC_HOME}/ epic/util/manageCreate directory with the common data files
stored under ${FESTC_HOME} /epic/common_data/util/manageCreate and many other data files generated under each
crop directory. Figure 16 shows the tool
interface used to generate management files for the test_case
scenario. The user needs to make sure
that the following two entries are selected correctly:
·
Fertilizer Year – select 2001 or 2006. The common management and fertilizer data
sets created under the ${FESTC_HOME}/epic/common_data/util/manageCreate will be used accordingly. This
management tool uses the created fertilizer data types for the 10 crop
production regions.
·
Selected Crops – select one or more crops
(except BEANS).
After clicking the Run button, a
script file is generated to compute the management files for the selected
crops. The user submits the script file
to the queue by clicking OK. After the
job has finished, users should check the queue job and log file in the “scenario name”/scripts directory, based
on the information provided in the Message Box (shown in Figure 16).
Figure 16. The Management File Generation for Application
tool interface used
for the test_case scenario.
The tool will generate many output
files under each crop, but many of these are used just for verification. The
tool generates the following files under the “scenario name”/“crop name”/app/manage directory:
·
EPICRUNFILERAINDW.DAT – EPIC run file for rain-fed
application simulation.
·
EPICRUNFILEIRRDW.DAT – EPIC run file for
irrigated application simulation.
·
GRIDS_OPC.DAT – the list of management file
names to be used in EPIC modeling.
·
OPC/“GRIDID”0“BELD3
Crop Number”.OPC – grid cell EPIC management files
under the OPC directory. Table 1 in Section 4.1 lists the crop numbers
in the BELD data.
·
tileDrain/SOILLIST.DAT – soil list file which contains tile drain
information for EPIC simulations and is used when “tileDrain”
is selected when running EPIC application simulations.
The EPIC Runs for Application tool interface
is used to run the EPIC model for the simulation year (EPICapp.exe program), which
is stored under the directory ${FESTC_HOME}/epic/
model/current. However, the user
must already have generated the site daily weather and N deposition files using
the WRF/CMAQ-to-EPIC tool interface (see
Section 4.3). The EPIC Runs for Application tool uses input files stored primarily in
the following directories:
·
${FESTC_HOME}/epic/common_data/EPIC_model/app –
for the common model input files.
·
scenarios/“scenario name”/share_data – for the EPICCONT.DAT file, site files, and
site list file, and daily weather and N deposition files and weather list
file.
·
${FESTC_HOME}/epic/common_data/statWeath – for observed climate station statistical
data.
·
scenarios/“scenario name”/
“crop name” /app/manage – for the run files, management files, and
management list file.
·
scenarios/“scenario
name”/ “crop name”/spinup/rainf/SOL
– for the soil files to be used in the rain-fed simulations.
·
scenarios/“scenario
name”/ “crop name”/spinup/irr/SOL
– for the soil files to be used in the irrigated simulations.
Figure 17 shows
the tool interface used for the test_case
scenario. The Simulation Year is defined
when the user creates the scenario.
Users can select one or multiple crops (except BEANS) for the
simulation. After clicking the Run
button, a script file is generated to run the rain-fed and irrigated EPIC
application simulations for each crop. The
EPIC application simulations will run for a two-year period (the previous year
and the simulation year) using the same daily weather and N deposition files
for the simulation year; the two-year period is needed in order to simulate a
full growing season for fall-sown crops. The user submits the script file to
the queue by clicking OK. After the job
has finished, users should check the queue job and log file in the “scenario name”/scripts directory, based
on the information provided in the Message Box (shown in Figure 17).
Figure 17. The EPIC Runs for Application tool interface
used for the test_case scenario.
Users need to make sure that the
following three fields are selected correctly:
·
CO2 Level (ppm) - input the correct
CO2 level for the simulation (e.g. 380). The input level overwrites the CO2
level defined in EPICCONT.DAT and site file.
·
Daily Average N Deposition – select N input to
be used in the simulation. Users can
select using the CMAQ N values in daily weather files, values defined in EPIC
input files, daily average N input from the 5-year CMAQ simulations from 2002
to 2006, or daily average N input from the 5-year CMAQ simulations from 2006 to
2010. The 5-year CMAQ N daily input
files are stored under ${FESTC_HOME}/epic/common_data/EPIC_model.
·
Run TileDrain – select
whether tile drain is applied for saturated soils. If YES is selected, SOILLIST file under scenarios/“scenario
name”/“crop name”/app/manage/tileDrain will be
used for all crops except hay (1, 2), alfalfa (3, 4), Other_Grass
(5, 6) and rice (23, 24).
The tool generates many directories
and files for each crop. The original
EPIC output files are stored under the following two subdirectories in the “scenario name”/“crop name”/app directory:
·
rainf – contains output
from EPIC rain-fed application simulations for this crop.
·
irr – contains output
from EPIC irrigated application simulations for this crop.
The output data created for CMAQ
modeling are stored under the following two subdirectories in the “scenario name”/output4CMAQ/app directory:
·
year – contains average EPIC output data for the simulation
year (one year) run for the crops simulated.
These data are used primarily for QA purposes.
·
daily – stores daily EPIC output data from EPIC application
runs for the crops simulated. These data
are used to extract the input for CMAQ bidirectional NH3 modeling.
EPIC is a
site-based model that generates output in formatted text files. In the domain-based EPIC modeling within
FEST-C, the crops in each grid cell are modeled individually. Thus, there are many text output files
generated for each crop in each grid cell selected for EPIC modeling. In this section we first describe the EPIC
Yearly Extraction tool and the EPIC-to-CMAQ tool. Developed in the SA Raster Tools system, these two tools extract
yearly or daily EPIC output variables into NetCDF-format
files for QA purposes and for CMAQ modeling.
We then discuss the Visualization
tool interface, which allows users to prepare spatial views of the EPIC output
variables in the created NetCDF files over their
modeling scenario domain.
The EPIC Yearly Extraction tool is used to
extract 31 crop-specific variables and 22 crop-area-weighted variables into two
NetCDF files from the yearly average EPIC output
files for all simulated crops within the grid cells that were selected. The output from this tool is used primarily for
QA purposes, to make sure that the EPIC simulation
results appear to be spatially reasonable over the domain area. Figure 18 shows the tool interface used for
the test_case scenario. The only item users need to select is Output
Type:
·
EPIC SPINUP – select this to extract yearly
average variables from the EPIC spin-up simulations. Yearly average variables
from the last five years of the simulations are from the output stored under
the “scenario name”/output4CMAQ/spinup/5years directory.
·
EPIC APP – select this to extract yearly average
variables from the EPIC simulations for the application year. The yearly average variables are from the
output stored under the “scenario
name”/output4CMAQ/app/year directory.
Figure 18. The EPIC Yearly Extraction tool interface used for the test_case scenario.
Table 3 lists all of the variables that
are in the two EPIC output files created by the tool: epic2cmaq_year.nc (crop-specific output) and
epic2cmaq_year_total.nc (crop-weighted output). These files are stored in one
of the following two directories:
·
scenarios/“scenario
name”/output4CMAQ/spinup/ toCMAQ – if the EPIC SPINUP
output type was selected.
·
scenarios/“scenario
name”/output4CMAQ/app/toCMAQ if the EPIC APP
output type was selected.
Users should check the log file
under their scenario’s scripts directory
to see whether any errors occurred when the tool was run.
If the user is visualizing the data
using the VERDI tool for visualization, there is no time dimension. Data layers are assigned to individual crops
(see Table 1 in Section 4.1 for the BELD crop numbers).
Table
3. EPIC yearly extraction output variables.
|
epic2cmaq_year.nc - crop specific
output
|
|
|
|
|
Index
|
Name
|
Variable
|
Index
|
Name
|
Variable
|
|
1
|
GMN
|
N Mineralized (kg/ha)
|
19
|
T_YLDG
|
T - Grain Yield (1000ton)
|
|
2
|
NMN
|
Humus Mineralization (kg/ha)
|
20
|
YLDF
|
Forage Yield (t/ha)
|
|
3
|
NFIX
|
N Fixation (kg/ha)
|
21
|
T_YLDF
|
T - Forage Yield (1000ton)
|
|
4
|
NITR
|
N - Nitrified NH3 (kg/ha)
|
22
|
YLN
|
N Used by Crop (kg/ha)
|
|
5
|
AVOL
|
N - Volatilization (kg/ha)
|
23
|
YLP
|
P Used by Crop (kg/ha)
|
|
6
|
DN
|
N-NO3 Denitrification (kg/ha)
|
24
|
FTN
|
N Applied (kg/ha)
|
|
7
|
YON
|
N Loss with Sediment (kg/ha)
|
25
|
FTP
|
P Applied (kg/ha)
|
|
8
|
QNO3
|
N Loss in Surface Runoff (kg/ha)
|
26
|
IRGA*
|
Irrigation Volume Applied (mm)
|
|
9
|
SSFN
|
N in Subsurface Flow (kg/ha)
|
27
|
WS
|
Water Stress Days (days)
|
|
10
|
PRKN
|
N Loss in Percolate (kg/ha)
|
28
|
NS
|
N Stress Days (days)
|
|
11
|
FNO
|
N - Organic Fertilizer (kg/ha)
|
29
|
IPLD
|
Planting Date (Julian Date)
|
|
12
|
FNO3
|
N - Nitrate Fertilize (kg/ha)
|
30
|
IGMD
|
Germination Date (Julian Date)
|
|
13
|
FNH3
|
N - Ammonia Fertilize (kg/ha)
|
31
|
IHVD
|
Harvest Date (Julian Date)
|
|
14
|
OCPD
|
Organic Carbon in Plow Layer (mt/ha)
|
32
|
YP
|
P Loss with Sediment (kg/ha)
|
|
15
|
TOC
|
Organic Carbon in Soil Profile (mt/ha)
|
33
|
QAP
|
Labile P Loss in Runoff (kg/ha)
|
|
16
|
TNO3
|
Total NO3 in Soil Profile (kg/ha)
|
34
|
YW
|
Wind Erosion (ton/ha)
|
|
17
|
DN2
|
N-N2O from NO3 Denitrification (kg/ha)
|
35
|
Q*
|
Runoff (mm)
|
|
18
|
YLDG
|
Grain Yield (t/ha)
|
|
|
|
|
|
|
|
|
|
|
|
epic2cmaq_year_total.nc - crop
weighted output
|
|
|
|
|
Index
|
Name
|
Variable
|
Index
|
Name
|
Variable
|
|
1
|
T_GMN
|
N Mineralized (mt - metric
ton)
|
14
|
T_OCPD
|
Organic Carbon in Plow Layer (1000mt)
|
|
2
|
T_NMN
|
Humus Mineralization (mt)
|
15
|
T_TOC
|
Organic Carbon in Soil Profile (1000mt)
|
|
3
|
T_NFIX
|
N Fixation (mt)
|
16
|
T_TNO3
|
Total NO3 in Soil Profile (mt)
|
|
4
|
T_NITR
|
N - Nitrified NH3 (mt)
|
17
|
T_DN2
|
N-N2O from NO3 Denitrification (mt)
|
|
5
|
T_AVOL
|
N - Volatilization (mt)
|
18
|
T_YLN
|
N Used by Crop (mt)
|
|
6
|
T_DN
|
N-NO3 Denitrification (mt)
|
19
|
T_YLP
|
P Used by Crop (mt)
|
|
7
|
T_YON
|
N Loss with Sediment (mt)
|
20
|
T_FTN
|
N Applied (mt)
|
|
8
|
T_QNO3
|
N Loss in Surface Runoff (mt)
|
21
|
T_FTP
|
P Applied (mt)
|
|
9
|
T_SSFN
|
N in Subsurface Flow (mt)
|
22
|
T_IRGA*
|
Irrigation Volume Applied (mm)
|
|
10
|
T_PRKN
|
N Loss in Percolate (mt)
|
23
|
T_YP
|
T - P Loss with Sediment (mt)
|
|
11
|
T_FNO
|
N - Organic Fertilizer (mt)
|
24
|
T_QAP
|
T - Labile P Loss in Runoff (mt)
|
|
12
|
T_FNO3
|
N - Nitrate Fertilizer (mt)
|
25
|
T_YW
|
T - Wind Erosion (1000ton)
|
|
13
|
T_FNH3
|
N - Ammonia Fertilizer (mt)
|
26
|
T_Q*
|
T - Runoff (mm)
|
*Water on agricultural
lands.
The EPIC-to-CMAQ
tool is used to extract 13 variables from EPIC soil output files and
59 variables from EPIC daily output files into NetCDF
files for all simulated crops within the grid cells that were selected. The output from this tool is used as input to
CMAQ bidirectional NH3 modeling over the domain area. Figure 19 shows the tool interface used for
the test_case scenario. The user needs to input only one item:
·
Output File Prefix – this is used as the file
prefix for all of the NetCDF output file names.
Figure 19. The
EPIC-to-CMAQ tool interface used for
the test_case scenario.
The following output files produced
by the tool are stored under the scenarios/“scenario
name”/output4CMAQ/app/toCMAQ directory:
·
“Output
File Prefix”_soil.nc – soil output file that contains 13 soil variables
extracted from the EPIC soil output files (“scenario
name”/output4CMAQ /app/daily/“BELD4 Crop Number”.NCS);
these variables are listed in Table 4.
Layer1 and Layer2 are for the soil depth from 0 to 1 cm and from 1 cm to
100 cm, respectively.
·
“Output
File Prefix”_timeYYYYMMDD.nc – daily NetCDF files for
the simulation year. A daily NetCDF file contains 59 variables extracted from the EPIC
daily output files (“scenario
name”/output4CMAQ /app/daily/“BELD4 Crop Number”.NCD”);
these variables are listed in Table 5.
Layer1, Layer2, and Layert are for the soil
depth from 0 to 1 cm, from 1 cm to 100 cm, and from 0 cm to the
full Baumer soil profile depth, which can be more than
1 m.
EPIC SPINUP –
select this to extract daily variables from the EPIC spin-up simulations. Daily
variables from the simulations are from the output stored under the “scenario name”/output4CMAQ/spinup/daily directory.
·
EPIC APP – select this to extract daily variables
from the EPIC simulations for the application year. The daily variables are from the output
stored under the “scenario
name”/output4CMAQ/app/daily directory.
Table
4. EPIC-to-CMAQ soil output variables.
|
Index
|
Name
|
Soil
Variable
|
Index
|
Name
|
Soil
Variable
|
|
1
|
L1_SoilNum
|
Soil Number (none)
|
8
|
L2_Bulk_D
|
Layer2 Bulk Density (t/m**3)
|
|
2
|
L1_Bulk_D
|
Layer1 Bulk Density (t/m**3)
|
9
|
L2_Wilt_P
|
Layer2 Wilting Point (m/m)
|
|
3
|
L1_Wilt_P
|
Layer1 Wilting Point(m/m)
|
10
|
L2_Field_C
|
Layer2 Field Capacity (m/m)
|
|
4
|
L1_Field_C
|
Layer1 Field Capacity (m/m)
|
11
|
L2_Porosity
|
Layer2 Porosity (%)
|
|
5
|
L1_Porosity
|
Layer1 Porosity (%)
|
12
|
L2_PH
|
Layer2 PH (none)
|
|
6
|
L1_PH
|
Layer1 PH (none)
|
13
|
L2_Cation
|
Layer2 Cation Ex (cmol/kg)
|
|
7
|
L1_Cation
|
Layer1 Cation Ex (cmol/kg )
|
|
|
|
Table
5. EPIC-to-CMAQ daily output variables.
|
Index
|
Name
|
Variable
|
Index
|
Name
|
Variable
|
|
1
|
QNO3
|
N Loss in Surface Runoff (kg/ha)
|
30
|
L2_ON
|
Layer2 Organic N (kg/ha)
|
|
2
|
SSFN
|
N in Subsurface Flow (kg/ha)
|
31
|
L2_P
|
Layer2 Mineral P (kg/ha)
|
|
3
|
PRKN
|
N Loss in Percolate (kg/ha)
|
32
|
L2_OP
|
Layer2 Organic P (kg/ha)
|
|
4
|
DN
|
N-NO3 Denitrification (kg/ha)
|
33
|
L2_C
|
Layer2 Carbon (kg/ha)
|
|
5
|
DN2*
|
N-N2O from NO3 Denitrification (kg/ha)
|
34
|
L2_NITR
|
Layer2 N - Nitrified NH3 (kg/ha)
|
|
6
|
AVOL*
|
N-NH3 Emission (kg/ha)
|
35
|
T1_DEP
|
Layert
Depth (m)
|
|
7
|
HMN
|
OC Change by Soil Respiration (kg/ha)
|
36
|
T1_BD
|
Layert Bulk
Density (t/m**3)
|
|
8
|
NFIX
|
N Fixation (kg/ha)
|
37
|
T1_NO3
|
Layert N -
Nitrate (kg/ha)
|
|
9
|
YP
|
P Loss with Sediment (kg/ha)
|
38
|
T1_NH3
|
Layert N -
Ammonia (kg/ha)
|
|
10
|
QAP
|
Labile P Loss in Runoff (kg/ha)
|
39
|
T1_ON
|
Layert
Organic N (kg/ha)
|
|
11
|
YON
|
N Loss with Sediment (kg/ha)
|
40
|
T1_P
|
Layert
Mineral P (kg/ha)
|
|
12
|
YW
|
Wind Erosion (ton/ha)
|
41
|
T1_OP
|
Layert
Organic P (kg/ha)
|
|
13
|
Q
|
Runoff (mm)
|
42
|
T1_C
|
Layert
Carbon (kg/ha)
|
|
14
|
HUSC
|
Heat Unit Schedule (none)
|
43
|
T1_NITR
|
Layert N -
Nitrified NH3 (kg/ha)
|
|
15
|
HU_BASE0
|
Base Heat Unit (none)
|
44
|
L1_ANO3
|
Layer1 N-NO3 AppRate (kg/ha)
|
|
16
|
HU_FRAC
|
Heat Unit fraction (none)
|
45
|
L1_ANH3
|
Layer1 N-NH3 AppRate (kg/ha)
|
|
17
|
L1_DEP
|
Layer1 Depth (m)
|
46
|
L1_AON
|
Layer1 ON AppRate (kg/ha)
|
|
18
|
L1_BD
|
Layer1 Bulk Density (t/m**3)
|
47
|
L1_AMP
|
Layer1 MP AppRate (kg/ha)
|
|
19
|
L1_NO3
|
Layer1 N - Nitrate (kg/ha)
|
48
|
L1_AOP
|
Layer1 OP AppRate (kg/ha)
|
|
20
|
L1_NH3
|
Layer1 N - Ammonia (kg/ha)
|
49
|
L2_ANO3
|
Layer2 N-NO3 AppRate
(kg/ha)
|
|
21
|
L1_ON
|
Layer1 Organic N (kg/ha)
|
50
|
L2_ANH3
|
Layer2 N-NH3 AppRate
(kg/ha)
|
|
22
|
L1_P
|
Layer1 Mineral P (kg/ha)
|
51
|
L2_AON
|
Layer2 ON AppRate (kg/ha)
|
|
23
|
L1_OP
|
Layer1 Organic P (kg/ha)
|
52
|
L2_AMP
|
Layer2 MP AppRate (kg/ha)
|
|
24
|
L1_C
|
Layer1 Carbon (kg/ha)
|
53
|
L2_AOP
|
Layer2 OP AppRate (kg/ha)
|
|
25
|
L1_NITR
|
Layer1 N - Nitrified NH3 (kg/ha)
|
54
|
UN1
|
N Uptake by Crop (kg/ha)
|
|
26
|
L2_DEP
|
Layer2 Depth (m)
|
55
|
HUI
|
Heat Unit Index (none)
|
|
27
|
L2_BD
|
Layer2 Bulk Density (t/m**3)
|
56
|
LAI
|
Leaf Area Index (none)
|
|
28
|
L2_NO3
|
Layer2 N - Nitrate (kg/ha)
|
57
|
CPHT
|
Crop Height (m)
|
|
29
|
L2_NH3
|
Layer2 N - Ammonia (kg/ha)
|
|
|
|
|
|
|
|
|
|
|
*DN2 is currently under revision, and AVOL is
an initial estimate that is revised within the bidirectional CMAQ.
When the user clicks the Run
button, a script file is generated under the scenario’s scripts directory. The
script file is submitted to the queue for execution after the user clicks OK. A CMAQ-ready file is generated for each day
and is viewable in VERDI. After the
queue job has completed, users should check the log file under the scripts directory to see whether any
errors occurred during execution.
The Visualization tool interface is used to
invoke the VERDI interface to view a selected NetCDF
data set. Figure 20 shows the appearance
of the tool interface before an input file has been selected. Users can select the data type on the left
side of the interface window and then by browse through the file systems to select
a NetCDF file created or used within the FEST-C
system (e.g., an EPIC output NetCDF file created by
the previous two tools, a BELD4 data set, MCIP and CMAQ data sets, a daily
weather and N deposition NetCDF output file). Clicking the Display button invokes the VERDI
interface to visualize the selected NetCDF file. Note: For this to work properly, the
user has to have set the VERDI system in the FEST-C configuration file config.properties (see Section 1.3). Information on how to use the VERDI system
can be obtained from the CMAS VERDI site: http://www.cmascenter.org/verdi/.
A newer version
of the EPIC model in modular format (EPIC v1102) is being adapted to the EPA
application format and will be added into the FEST-C system after thorough
testing and evaluation. This new version
of EPIC has an improved treatment of N modeling. In addition, we will continue to improve the
land use data using the released 2011 NLCD data. This will be accompanied by an updated
fertilizer type scenario, also keyed to 2011.
We are also exploring the possibility of moving to computing crop land
use data directly from USDA National Agricultural Statistics Service (NASS)
Cropland Data Layer (CDL) data. This
would provide higher-resolution information; however, these data do not include
some information that is critical for using EPIC (such as differentiation
between irrigated and rain-fed crops), so further exploration is needed.
Figure 20. The Visualization tool interface.
In the near-term,
we anticipate developing a long-term average daily wet and dry deposition data
layer that can be used in spin-up or application simulations. A notice will be posted on the CMAS web site
when that data layer is ready for release.
We are also helping
the EPA apply the FEST-C system to address multimedia (air, land, water)
questions related to biofuels production and climate change. We are exploring using FEST-C to study not
only the effects of agricultural practices (e.g., fertilizing and management practices)
on air quality (NH3), climate (N2O), and climate change,
but also the effects of meteorology and climate on agricultural productivity,
soil erosion, water quantity, and water quality.
The development of the FEST-C system
is being sponsored and directed by the U.S. EPA’s Atmospheric Modeling and
Analysis Division (AMAD) under two U.S. EPA contracts: EP‑W‑09‑023,
“Operation of the Center for Community Air Quality Modeling and Analysis (CMAS),”
and EP‑D-12-044, “Emissions, Air Quality, and Meteorological Modeling
Support (EMAQ).” We thank Dr. Ellen Cooter, the EPA Work Assignment Manager for
the work described in this document, for her leadership on this project. We also greatly appreciate the continuing and generous
intellectual support we have received from Dr. Jimmy R. Williams at Texas A&M AgriLife Research, Blackland Research & Extension Center (Temple, TX). We thank Joe Slater, Manager of Fertilizer/AG
Lime Control Services, University of Missouri Agricultural Experiment Station
at Columbia, MO, for his invaluable insights regarding fertilizer sales and
use. Finally, we thank Dr. Qun He for his design and support on the FEST-C interface
development.
