Both GSFLOW and GRASS have advanced in version since the publication of GSFLOW-GRASS, and this code base has not been updated to keep pace. Note the very specific versions below.

Anyone who would like to bring GSFLOW-GRASS up-to-date: Please do use this as a starting point. We invite you to fork and update and contact us.

Python toolkit using GRASS GIS to generate inputs for the USGS hydrologic model "GSFLOW".

GSFLOW is the US Geological Survey's combined groundwater (MODFLOW) and surface water (PRMS) model. GSFLOW-GRASS builds a stream network and its "hydrologic response units" -- here, watershed sub-basins -- that combine to form a surface-water hydrologic network (PRMS). It then links these to a regular finite difference grid to compute groundwater flow using MODFLOW.

These instructions are meant to take a user familiar with computers but new to (or a beginner with) GSFLOW and GRASS GIS through the basics of how to get GSFLOW-GRASS to work. Please leave a message if you have trouble working with GSFLOW-GRASS; your comments could assist both you and the more general improvement of this documentation.

When you use GSFLOW-GRASS, please cite:

Ng, G.-H.C., Wickert, A.D., Somers, L.D., Saberi, L., Cronkite-Ratcliff, C., Niswonger, R.G., and McKenzie, J.M., 2018, GSFLOW-GRASS v1.0.0: GIS-enabled hydrologic modeling of coupled groundwater–surface-water systems: Geoscientific Model Development, doi:10.5194/gmd-11-4755-2018.

In addition, please contact us if you have questions or suggestions!

This manual is written in the style of a quick(-ish) start guide that allows users to get GSFLOW up and running for their target watershed using mostly default options in our toolkit and without modifying GRASS-GIS or Python scripts. Additional customization is possible by more advanced users by editing our GRASS GIS and input file building scripts to extend the set of GSFLOW parameters that may be set through GSFLOW-GRASS.

Required:

• GSFLOW 1.2
• GRASS GIS 7.6.1 (updated for compatibility on Earth Day, 22 April 2019)
• Python 2.7.X
• GSFLOW-GRASS Toolkit (this software)

Optional:

• ffmpeg (for making movies)

Download and install GSFLOW 1.2.0 or 1.2.2

Obtain the source code for GSFLOW 1.2.0 from: https://github.com/UMN-Hydro/GSFLOW-1.2.0, compile and install it. For windows, the pre-compiled executable file for GSFLOW 1.2.2 will be downloadable soon (if not already) from the USGS website: https://water.usgs.gov/ogw/gsflow/#downloads. Note that GSFLOW-GRASS is not fully compatible with GSFLOW 1.2.1.

GSFLOW-GRASS has been tested on Python 2.7, and should work (with a few possible changes) on future versions of Python 2.X. It has not been tested on Python 3.X.

In order to run properly, GSFLOW-GRASS requires the following Python modules (in addition to those that come with GRASS GIS v7.6, above.):

• numpy
• matplotlib
• pandas
• osgeo (also listed under gdal)

For users who are new to Python, follow these directions to install the Python interpreters onto your computer.

Use your package manager to download and install the required Python packages. For Debian/Ubuntu, it will be something like:

# Basic packages
sudo apt-get install \
python python-numpy python-scipy \
python-setuptools python-matplotlib \
python-gdal

# pip (recommended for automatic installs via setuptools)
sudo apt-get install python-pip

# iPython console (very useful, optional)
sudo apt-get install ipython

# Sypder IDE (popular interface, optional)
sudo apt-get install spyder

# OSGEO / GDAL
sudo apt-get install python-gdal

We recommend using Anaconda, which comes with most of the Python modules that one need for the execution of the GSFLOW-GRASS codes: it includes numpy (computations and matrices), matplotlib (plotting), and pandas (database management), but does not include osgeo (geospatial libraries, labeled ``gdal'').

Download Anaconda for Python 2.7+ from https://www.anaconda.com/download. When you install it, you are given the option to have it become your system-wide Python install in a set of two check boxes. We recommend that you do so (they may be by default not checked), but GSFLOW-GRASS will still run fine if they are not. These boxes make your whole system recognize Anaconda as your Python install, rather than limiting it to its enclosed environment.

Additional modules, such as OSGEO/GDAL may be installed with either "conda" (the Anaconda package manager) or "pip" (the Python package manager). For the sake of an example, with numpy (already installed), you may type one of the following:

# Anaconda
conda install numpy
# Pip
pip install numpy

We recommend that if you use Anaconda, that you use the conda comands to maintain a consistent Python environment.

If you have installed Anaconda without ticking the system-wide install check box, you need to use "conda" through the Anaconda Prompt rather than the standard terminal: After installing Anaconda, go to the Windows start menu, and search programs and files for "Anaconda Prompt". If you have installed Ananconda system-wide, you may do this through either the Ananconda prompt or the standard DOS prompt (command line / terminal). Installing osgeo/gdal downgrades a few packages (e.g., HDF libraries), and requries that you reinstall numpy:

# In the Anaconda Prompt
# Or in either this or the DOS prompt if you have installed
# Anaconda system-wide
conda install gdal
conda upgrade numpy

You may receive a message saying that you don't have the necessary permissions. If this happens, on-screen directions will tell you how to proceed. Follow them, and then enter the above commands.

Anaconda also comes with the Spyder development environment, which is a helpful graphical interface that can be used to individually run or edit the Python codes.

Download and install GRASS GIS 7.6

(GSFLOW-GRASS may work on the development version of GRASS GIS, v7.7 at the time of writing, but this is untested.)

("Precompiled binary " = the normal kind of software that you download and just works)

Go to https://grass.osgeo.org/download/software/ and download GRASS GIS 7.6 (new stable version) for your appropriate OS.

For Mac, follow the instructions to install the "framework packages" after following the links from the main download page. Note that the most recent stable version of GRASS GIS for Mac is 7.4. This is outdated, but should still be compatible with the modern GSFLOW-GRASS. Please contact the GSFLOW-GRASS developers with specific errors if this does not work!

For Ubuntu:

sudo apt-get install grass

• Instructions to build from source:
  • https://grasswiki.osgeo.org/wiki/Compile_and_Install
  • https://grasswiki.osgeo.org/wiki/Compile_and_Install_Ubuntu

Note that it can still help to obtain the dependencies via the package manager by installing the older version of GRASS:

sudo apt-get install grass

If you choose to compile GRASS GIS from source, we have used these configuration flags many times on Ubuntu Linux (configure_ubuntu.sh):

CFLAGS="-O2 -Wall" LDFLAGS="-s" ./configure \
--enable-largefile=yes \
--with-nls \
--with-cxx \
--with-readline \
--with-pthread \
--with-proj-share=/usr/share/proj \
--with-geos=/usr/bin/geos-config \
--with-wxwidgets \
--with-cairo \
--with-opengl-libs=/usr/include/GL \
--with-freetype=yes --with-freetype-includes="/usr/include/freetype2/" \
--with-postgres=yes --with-postgres-includes="/usr/include/postgresql" \
--with-sqlite=yes \
--with-mysql=yes --with-mysql-includes="/usr/include/mysql" \
--with-odbc=no \
--with-netcdf=/usr/bin/nc-config

(Optional)

In order to make movies, you need an active copy of ffmpeg on your computer. For Linux, this is simple:

sudo apt-get install ffmpeg

For Windows or Mac, download via https://www.ffmpeg.org/download.html. You can select the correct version for your operating system under “More downloading options” and “Get the packages” and follow the links therein. Ffmpeg is installed by adding the executable file to your system's or user path variable. Windows installation instructions can be found here https://www.wikihow.com/Install-FFmpeg-on-Windows.

You can alternatively install all above mentioned packages and libraries by creating a docker image.

Take a shell and cd to folder GSFLOW-GRASS/gsflow_grass_docker:

cd GSFLOW-GRASS/gsflow_grass_docker

This folder includes a docker-compose.yml file and the folder gsflow_grass with the required Dockerfile and additional scripts called by the Dockerfile.

Run docker-compose build in order to create the image:

docker-compose build

Then run docker-compose up in order to run the image:

docker-compose up

Once running the image, you will get the following message:

You need to run grass from a shell created by a docker exec invocation

Take a shell in the image as following:

First run docker ps in order to see the CONTAINER ID locally obtained:

docker ps

Then, copy this id in the following command:

docker exec -it CONTAINER ID bash

This will give you a shell where you can type grass in order to start the software.

GSFLOW-GRASS has four main directories:

• domain_builder holds GRASS GIS commands and associated code to turn a DEM into an input domain of Hydrologic Response Units (HRUs) and stream segments.
• input_file_builder holds code that turns the outputs from domain_builder and user-specified parameters in the settings file (see Step 1, below) into the set of input files that are required by GSFLOW
• Run holds the files to run GSFLOW using these inputs
• visualization holds scripts to build plots and movies based on the outputs from both GSFLOW and the GRASS GIS domain builder

In addition, the "figures" directory holds images used for this README.

Generating inputs to GSFLOW using Python and GRASS

The Settings file holds user-defined information that defines how GSFLOW is set up and will run.

Use settings_template.ini in the 'Run' folder as a template for creating your own Settings File, which can have any name. Boldface options are required, and those that are Boldface and italic font is used to represent one of a set of options that must be given, depending on the value of a particular switch variable that is set. Each *.ini file includes:

Land-cover classes are set as integer values as follows:

0. Bare soil
1. Grasses
2. Shrubs
3. Trees

Soil classes are set as integer values as well:

1. Sand
2. Loam
3. Clay

GSFLOW-GRASS will obtain land-cover and soil inputs based on the first of these that is possible:

1. Import the file given below; if this is empty
2. Use the provided cov_type and soil_type (below) for spatially uniform properties; failing this
3. Look for existing GRASS GIS rasters called "land_cover" and "soil"
4. If all of this is not possible, then default values will be chosen: (cov_type = 0, soil_type=2)

Please note that for the raster values, the current implementation is crude: each HRU will import the value at the centroid of the HRU, instead of picking the modal value. This will require a new GRASS GIS module and/or an update to v.rast.stats.

1. Launch GRASS GIS.

• If on Linux, you must start GRASS GIS from the command line to ensure that you have a window where you can type the GSFLOW-GRASS commands. If you used apt to install GRASS GIS, simply open a terminal window (CTRL+ALT+T) and type grass or grass76 (the compatible version at the time of writing).
• If on Windows, a command prompt should always appear when you start GRASS GIS.

2. Create a folder to hold your GRASS locations. This is typically called "grassdata" and placed in your home directory.
3. Click on "New", and follow the prompts.

• We recommend naming the "Project Location" the same as "proj_name".
• No "Location Title" is needed.
• We suggest that you "Read projection and datum terms from a georeferenced data file" to set the coordinate system. Each GRASS GIS location has only one coordinate system. Your DEM must be in a projected coordinate system: we do not test our codes using geographic (lat/lon) coordinate systems.

Important: Your DEM must be at least 2 full MODFLOW grid cells larger on each side than the catchment that you seek to model. This will ensure that (1) offmap flow is not a problem and (2) the constant-head MODFLOW boundary condition at the outlet may properly be built. As additional cells with offmap flow inputs will be removed from the DEM, it is often wise to pad the DEM even more than this.

If you "Read projection and datum terms from a georeferenced data file", GRASS GIS will ask you if you want to import that file to the workspace. There is no need to do so -- "build_domain_grass.py" will do this for you -- but you can if you want to be able to start GRASS GIS and look at it.

With your location selected, click "Start GRASS session".

If you need to choose your pour point manually, we recommend that either you (a) import the DEM and find it now using GRASS, or (b) use another program like QGIS to find this location. You should still keep the path of the DEM in DEM_file_path_to_import until you have finished the first run of the code. Keeping this in during later runs will not cause problems; it will just take extra time as the DEM is re-imported and re-corrected.

First time running GRASS GIS only, or after GRASS extension updates

Either using the terminal (highly recommended) or clicking on the "Console" tab in the GRASS GIS Layer Manager, run install all of the necessary extensions for GSFLOW-GRASS.

In the terminal, this may be done as follows:

On Linux, cd GSFLOW-GRASS/domain_builder and type:

sh install_extensions.sh

On Windows, likewise cd to GSFLOW-GRASS\domain_builder and type:

install_extensions

Perhaps more easily, on either operating system, just copy and paste the contents of install_extensions.sh into the terminal or GRASS GIS console. We have also pasted these here for convenience.

# From us
g.extension v.gsflow.export
g.extension v.gsflow.gravres
g.extension v.gsflow.grid
g.extension v.gsflow.hruparams
g.extension v.gsflow.reaches
g.extension v.gsflow.segments
g.extension r.gsflow.hydrodem
g.extension v.stream.inbasin
g.extension v.stream.network
g.extension r.cell.area

# From others
g.extension r.stream.basins
g.extension r.hydrodem

Either using the terminal (highly recommended, Linux) or clicking on the "Console" tab in the GRASS GIS Layer Manager (Linux or Windows), run buildDomainGRASS.py. For example, from within the "GSFLOW-GRASS" folder::

Linux

python domain_builder/buildDomainGRASS.py /PATH/TO/settings.ini

Windows

python domain_builder\buildDomainGRASS.py DRIVE_LETTER:\PATH\TO\settings.ini

Time will pass and a lot of text will go past on the screen. If it ends with "Done.", it has succeeded! This is regardless of warning/error messages about adding fields to shapefiles, skipping features without categories, or file extensions not being allowed by the GPKG specification. If it does not end with "Done.", please contact us!

Once this has finished check our "gsflow_simdir" for a "GIS" subfolder that contains the outputs of your work here. The files there will be automatically read in during Step 4.

Pat yourself on the back! The GRASS portion is complete.

The goGSFLOW File (goGSFLOW.sh on Linux and goGSFLOW.bat on Windows) in the Run folder, is for pre-processing and running GSFLOW.

At the top of the file, the user may customize:

• settings_file Full pathname for Settings File (customized in Step 1).
• toolkit_dir full pathname for location of GSFLOWGRASS_toolkit

Alternatively, for goGSFLOW.sh, the user may pass the settings_file as the first argument and (optionally) the toolkit_dir as the second argument.

The rest of the file will execute scripts to: (1) set up certain model inputs (climate forcing data and hydraulic conductivity) according to the Settings File, (2) create GSFLOW input files (GSFLOW control file, PRMS parameter file, and MODFLOW input files), and (3) run GSFLOW. In the default implementation, the user does not need to change the bottom part of the file with Python scripts. However, certain lines may be commented out or changed, as described in the following:

• createSpatialHydCond.py: If fl_create_hydcond=1 in Settings File, this script creates spatially distributed hydraulic conductivity values; see top of this script to select from options. This line may be changed to a different script name if the user writes their own script for creating spatially distributed hydraulic conductivity. If fl_create_hydcond=0, this line may be left in; nothing will be done in the script.
• printClimatehru.py If fl_print_climate_hru=1 in Settings File, this script creates climate_hru files with spatially uniform conditions, based on data from climate_data_file in the Settings File. This line may be changed to a different script name if the user writes their own script for creating spatially distributed climate inputs. If fl_print_climate=0, this line may be left in; nothing will be done in the script.
• printGSFLOWControlfile.py: This script creates GSFLOW control file. This line generally should be included, but it may be commented out if the user has already run the script previously and will be using the same file in its same location.
• printPRMSparamfile.py: This script creates the PRMS parameter file. This line generally should be included, but it may be commented out if the user has already run the script previously and will be using the same file in its same location.
• printMODFLOWInputs.py: This script creates all the MODFLOW input files. This line generally should be included, but it may be commented out if the user has already run the script previously and will be using the same files in their same location.
• runGSFLOW.py: This script executes the GSFLOW model. This line generally should be included, but it may be commented out if the user only wishes to create the input files without running the model.

Note that the above Python scripts can also be run independently using Python, outside of the goGSFLOW File; just be sure to include the Settings File name as an argument.

For the default implementation, the user can proceed to Step 5. However, extra steps are needed if the user has specified any of the following:

• Settings File, fl_create_hydcond=1: Set options at the top of the Create_hydcond_array.py input-file-builder script for different spatial distribution configurations. Other steps may be needed if the user replaces this script with their own to create spatially distributed hydraulic conductivity fields.
• Settings File, fl_print_climate=1: Create the file specified in climate_data_file, which should have climate data time series from one weather station for daily minimum temperature, maximum temperature, and precipitation. See example problems for the file format (e.g., in Shullcas -> UserData -> ), which has the following format:
  • line 1: comment
  • line 2: tmax for daily maximum temperature, 1 for number of weather stations
  • line 3: tmin for daily minimum temperature, 1 for number of weather stations
  • line 4: precip for daily precipitation, 1 for number of weather stations
  • line 5: #################################### to indicate start of data
  • line 6: YYYY Month Day 0 0 0 (tmax value) (tmin value) (precip value), etc. for all dates in daily time series All temperature data in this file are assumed to be in [°C], and precipitation data in [mm/d] (these are eventually converted to [°C] and [in/d] for the PRMS model component). This file can be expanded to include relative humidity (in [%]) (used if Penman-Monteith option is selected for the potential ET module) and solar radiation (in [MJ/m²]) if available. Other steps may be needed if the user replaces this script with their own to create spatially distributed hydraulic conductivity fields.
• Settings File, fl_print_climate_hru=0: Make sure climate_hru_dir is directory with pre-existing climate_hru data files containing HRU-distributed climate inputs: tmin.day, tmax.day, precip.day, and empty.day. See GSFLOW manual or example files in example cases (e.g., in Shullcas -> inputs -> PRMS_GSFLOW) for format of climate_hru data files.

Changing other input parameters: See "Advanced Customization" below.

The pre-processing and GSFLOW model execution can be carried out by entering the Go-GSFLOW at the command line:

• Linux prompt: ./goGSFLOW.sh (user needs to press Enter at the end, to return to command prompt)
• Windows command prompt: goGSFLOW in the directory containing goGSFLOW.bat, or by double clicking on goGSFLOW.bat file in Windows explorer

Output files will be located in the gsflow_simdir (specified in Step 1 in the Settings File) -> outputs.

After running GSFLOW, the user should check the following:

• Model ran to completion: GSFLOW will print "Normal termination of simulation". For Windows, this will print to the screen. For Linux, this will appear at the end of out.txt created in the directory where go-GSFLOW.sh is executed (all output to screen is redirected to out.txt).
• Model converged: Check gsflow_simdir -> control -> gsflow.log. This will summarize convergence performance.
• Model ran with good water balance: Check gsflow_simdir -> outputs -> PRMS_GSFLOW -> gsflow.out. This will report instances when there are large water balance discrepancies (indicated with "WARNING...")
• MODFLOW component ran smoothly: Check gsflow_simdir -> outputs -> MODFLOW_NWT -> test.lst. This will include convergence and run details specific to MODFLOW, which are only summarized in gsflow.log.

Our toolkit includes Python scripts in GSFLOW-toolkit -> visualization for graphically depicting major GSFLOW inputs and outputs. Currently these scrips work only with GSFLOW 1.2.0. The USGS is updating their standards, and we will update our visualization methods only after they have settled on new (and possibly NetCDF-based) file-output formats, organization, and nomenclature. Most of of these scripts can be run using the following syntax

run <visualization_script>.py <Settings File full path> # in a Python shell
./<visualization_script>.py <Settings File full path> # in bash (Unix shell)
python <visualization_script>.py <Settings File full path> # bash or MS-DOS shell

However, plotMODFLOW.py is a bit more complicated because it has a parser that allows you to enter more options. Its help information follows:

usage: plotMODFLOW.py [-h] -i INFILE
                      [-p {topo,head,wtd,dhead,hydcond,hydcond_vertical,ss,sy}]
                      [-o OUTMOVIE]

Plot animated time-series of groundwater conditions from GSFLOW.

optional arguments:
  -h, --help            show this help message and exit
  -o OUTMOVIE, --outmovie OUTMOVIE
                        Output file (mp4) for movie, if desired (default:
                        None)

required arguments:
  -i INFILE, --infile INFILE
                        input <settings>.ini fiile for GSFLOW
  -p {topo,head,wtd,dhead,hydcond,hydcond_vertical,ss,sy}, --plot {topo,head,wtd,dhead,hydcond,hydcond_vertical,ss,sy}
                        Plot variable selector: topography (topo), head, water
                        table depth (wtd), change in head (dhead), hydraulic
                        conductivity (hydcond), vertical hydraulic
                        conductivity (hydcond_vert) specific storage (ss), or
                        specific yield (sy) (default: wtd)

For example, one could type within a Python shell:

run plotMODFLOW.py -i <Settings File full path> -p wtd -o TEST.mp4

By default, the visualization scripts will plot output files in directories specified by Settings File; this facilitates visualizing results directly after running GSFLOW with this toolkit. However, the user can over-ride these file locations in the section *** CHANGE FILE NAMES AS NEEDED in order to plot arbitrary output files (not based on Settings File). However, our visualization scripts assume certain output file formats and are not guaranteed to work with GSFLOW output files generated outside of this toolkit.

For other main plotting options, the user should use the section at the top of each visualization script indicated with *** SET THE FOLLOWING:.... Other more detailed customizations (e.g., figure formatting etc) can be manually made in the rest of the script.

The visualization scripts in the toolkit include the following:

• Visualization scripts for plotting GSFLOW inputs and outputs:
  • plotBasin.py: Creates figure showing HRU and stream discretization. User specifies HRU id's to be highlighted.
  • plotMODFLOW.py: Creates various figures showing spatially discretized MODFLOW inputs: active grid cells, top elevation of each layer, bottom elevation of each layer, and hydraulic conductivity for each layer. Also creates movies of spatially discretized hydraulic head (with options to show water table depth and change-in-head over print time steps) and unsaturated zone outputs (recharge from unsaturated to saturated zone).
  • plotHRUvars.py: Creates movie of HRU-discretized output variables.
  • plotSegmentDischarge.py: Creates movie of stream segment-discretized discharge values.
  • plotGSFLOWTimeSeries.py: Creates a time series figure with basin-total variables.

Our toolkit is set up to easily change hydraulic conductivity, climate, and infiltration inputs through the Settings File. To change other model input parameters (described in the GSFLOW manual), the user must locate those entries in the Python input-file-builder scripts and edit the values there. These scripts are in Toolkit_GSFLOW ->input_file_builder and include:

• printGSFLOWControlfile.py: Builds GSFLOW control file, which controls model options. See commented Section headings to make changes.
• printPRMSparamfile.py: Builds PRMS parameter file, which contains all (non-stream) surface properties in "Section 2: Parameters." While any of these may be customized, those of particular interest are commented with "# *** CHANGE FOR SPECIFIC SITE"
• printMODFLOWInputs.py: Includes functions to build the various MODFLOW input files. See individual functions to change input parameters for the different corresponding MODFLOW packages.
• Subdirectories of domain_builder hold the GRASS GIS commands. If the user needs to expand the set of variables exported under these commands, one should:
  1. Open the desired .py file and follow the pattern shown to edit its parser inputs/outputs (formatted comments near the top) and the Python code inside that first parses these comments and then runs GRASS GIS commands
  2. Ensure that you have a C compiler installed (gcc)
  3. Run make MODULE_TOPDIR=<PATH_TO_YOUR_GRASS_GIS_INSTALL> to compile the updated GRASS GIS commands. See and/or makeall.sh, in which this path is provided by the user, for a simple way to recompile many commands.

Our GRASS GIS commands are open-source and may be edited; we expect that the most likely reason for users to do so would be to add additional GSFLOW options to the attribute tables for the HRUs and MODFLOW cells.

To write the extensions, follow the advice given at the GRASS GIS wiki, https://grasswiki.osgeo.org/wiki/AddOns, and/or simply follow the pattern of the code in GSFLOW-GRASS/domain_builder.

Our extensions are stored at both our GitHub repository and in the official GRASS GIS add-ons subversion (svn) repository. The latter requires write access from the GRASS GIS team. If you lack this write access, we suggest that you make pull requests to our GitHub repository and work with us to test your changes, and then we will add them to the official svn repository, from which your changes will be compiled and made available via the g.extension command.

We would be happy to include your contributions in the main code base, and any changes to the GRASS GIS commands to the main GRASS GIS extensions (add-ons) repository: this will help future users!