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Getting started

Instructions for creating a mesh from partially processed data.

See Input Creation Steps for details on the steps leading up to this point. (Section 1, steps 1 - 65)

These workflows make a few assumptions about the directory struture of ADHydro input files. Typically, a top level directory for each mesh/map is used to setup and run ADHydro. The following structure is partially established and will be used throughout this training:

map_dir/
|-- ASCII
|   |-- mesh.1.chan.ele
|   |-- mesh.1.chan.node
|   |-- mesh.1.chan.prune
|   |-- mesh.1.chan.z
|   |-- mesh.1.edge
|   |-- mesh.1.ele
|   |-- mesh.1.geolType
|   |-- mesh.1.landCover
|   |-- mesh.1.link
|   |-- mesh.1.neigh
|   |-- mesh.1.node
|   |-- mesh.1.poly
|   |-- mesh.1.soilType
|   |-- mesh.1.z
|   |-- mesh.node
|   `-- mesh.poly
|-- ArcGIS
|   |-- intersect_wtrbodies_final.dbf
|   |-- intersect_wtrbodies_final.prj
|   |-- intersect_wtrbodies_final.shp
|   |-- intersect_wtrbodies_final.shx
|   |-- mesh_catchments.dbf
|   |-- mesh_catchments.prj
|   |-- mesh_catchments.qpj
|   |-- mesh_catchments.shp
|   |-- mesh_catchments.shx
|   |-- mesh_streams.dbf
|   |-- mesh_streams.prj
|   |-- mesh_streams.shp
|   |-- mesh_streams.shx
|   |-- mesh_waterbodies.dbf
|   |-- mesh_waterbodies.prj
|   |-- mesh_waterbodies.shp
|   |-- mesh_waterbodies.shx
|   |-- wtrbodies_streams_intersect_final.dbf
|   |-- wtrbodies_streams_intersect_final.prj
|   |-- wtrbodies_streams_intersect_final.shp
|   `-- wtrbodies_streams_intersect_final.shx
|-- TauDEM
|   |-- projected
|   |   |-- projected.tif
|   |   `-- projected.tif.aux.xml
|   |-- projectednet.dbf
|   |-- projectednet.prj
|   |-- projectednet.shp
|   `-- projectednet.shx
|-- analysis
|   |-- outline.cpg
|   |-- outline.dbf
|   |-- outline.prj
|   |-- outline.shp
|   `-- outline.shx
|-- data
|   |-- geology
|   |-- nlcd_2016
|   `-- soil
|       |-- SSURGO
|       `-- STATSGO
|-- drain_down
|   |-- display.nc
|   |-- geometry.nc
|   |-- parameter.nc
|   |-- state.nc
|   `-- superfile.ini
|-- forcing
|   |-- forcing_2020-10-2_2020-10-2.nc
|-- mesh_massage
|   |-- display.nc
|   |-- geometry.nc
|   |-- parameter.nc
|   |-- state.nc
|   `-- superfile.ini
`-- simulation
    |-- display.nc
    |-- geometry.nc
    |-- parameter.nc
    |-- state.nc
    |-- state.nc.maxDepth.txt
    `-- superfile.ini

You will one at least two terminals to use throughout this training.

The TauDEM directory contains the TauDEM generated stream network from previous steps, and the ArcGIS directory contains topologically corrected mesh catchments, streams, and waterbodies. From these, the following steps will begin populating the ASCII directory.

For these steps, you will be running an interactive adhydro-tools container, and entering commands on the terminal within that container.

Make sure your current terminal is in the directory you extracted the training_data in.

ls should show training_data in the current directory.

Next we will start the tools container and mount in the data.

docker run -it -v `pwd`/training_data:/data adhydro-tools

-it starts an interactive terminal in the container.

-v tells docker to mount the given directory to /data inside the container. This command uses a sub-shell to get the working directory so docker gets an absolute path the training_data directory as docker doesn't always play nice with mounting relative paths.

The last argument is the container we are running, adhydro-tools. Your terminal line should look like this once the container is running:

(base) bash-4.4#

The following steps will be run in this interactive terminal.

  1. Use a python script to create input files for triangle from these previously created shapefiles.

    1. Run the script create_triangle_files.py.

    From the docker terminal:

    python /scripts/preprocessing/create_triangle_files.py /data

    Now /data/ASCII should have the following files. These are simply ascii formatted geometry descriptions of the mesh catchments, streams, and waterbodies. These are specifically formatted to be inputs to the triangle mesh creation program.

    • mesh.1.link
    • mesh.node
    • mesh.poly

    Verify with ls /data/ASCII

  2. Now you will run triangle to generate the mesh in the ASCII directory:

    cd /data/ASCII

    triangle -pqAjenV mesh.poly

    or with docker from a non-interactive session:

    docker run -v `pwd`/data:/data adhydro_tools cd /data/ASCII && triangle -pqAjenV mesh.poly

    1. There may be lots of warnings about duplicate vertex and endpoints of segment are coincident. These can be ignored. If your dataset is big it can take triangle a long time just to print these out. If you want, you can edit the triangle source code to comment out these print statements and recompile.
    2. If there are overlaps and gaps in the mesh created by a topology failure described in step 70 then triangle might crash or go into an infinite loop generating tiny triangles in those problem areas. The only way I found to get around this is to run triangle in the debugger, break in to find what x, y coordinates it is getting hung up on and then find that location in ArcGIS and fix the gap or overlap by hand.

  3. You can analyze the mesh with the program adhydro_mesh_check. It will report problems with small triangles and triangles that have no catchment label.

    In another terminal/window run the following command to use the adhydro utility

    cd <project dir>

    docker run -v `pwd`/training_data:/data adhydro -c "adhydro_mesh_check /data/ASCII/"

    1. Triangles with no catchment label shouldn't occur. They can occur if a catchment polygon is bisected by streams, but because of the split polygons step there shouldn't be any of those situations. If there are triangles with no catchment label you will need to investigate why.
    2. Small triangles usually result from sharp angles in the catchment polygons. This can be fixed by hand in ArcGIS. See Input Creation Steps for details. For this example, we won't worry about these.

  4. Now you will use a python script to extract the z coordinate from the DEM for each point in the mesh. Switch back to the terminal running the adhydro-tools container. In this container we will run the following command.

    python /scripts/preprocessing/create_z_file.py /data

    This uses the .node file in the ASCII directory and the original non-pit-filled DEM in the TauDEM directory for input. It creates a .z file in the ASCII directory.

    ls /data/ASCII to verify the .z file was created.

  5. Run the program adhydro_channel_preprocessing. This will create three files: a .chan.ele file that contains the channel elements, a .chan.node file that contains the x,y coordinates of the channel nodes, and a .chan.prune file that contains pruned reach codes each paired with an unpruned reach code that the pruned reach code flows downstream into. The .chan.node file is in the same format as a triangle .node file so you can use the same script to generate the z coordinates files later.

    Switch to the other terminal, or in a new terminal/window run the following docker command to execute the adhydro channel preprocessing utility.

    docker run -v `pwd`/training_data:/data adhydro -c "adhydro_channel_preprocessing /data"

    1. We found that the values in the shapefiles for link type were not consistent across data sources. In Wyoming the values were words: "Ice Mass", "LakePond", "SwampMarsh", etc. In Colorado the values were numbers: "378" for Ice Mass, "390" for LakePond, "466" for SwampMarsh, etc. It seems likely that any time you process a mesh in a new political unit you will need to figure out what they use for link type and update the code of adhydro_channel_preprocessing. You will get an error message if the shapefiles use a link type string that is unrecognized.

    Now we will create the channel .z files from the .chan.node file and the original non-pit-filled DEM. The create_z_file.py script has a flag for processing channels.

    Back in the adhydro-tools container terminal, run the same script as before with the channel flag -c

    python /scripts/preprocessing/create_z_file.py -c /data

    This generates the .chan.z file in the ASCII directory.

    ls /data/ASCII

Parameter Data

This section is covered in detail in See Input Creation Steps, section IV: Process parameter data

In this section you will assign parameters like soil and vegetation type to mesh elements.

Download data

  1. Before creating the parameter files for a given mesh you need to download several kinds of publicly available source data. The downloaded source data can be used for processing just one mesh and then thrown away, or you can save it to use for multiple meshes. If you want to use it for multiple meshes you need to make sure that you download data that covers the complete area of all of the meshes you will use it for.

    1. Create a data directory for your project, <project path>/data, and create the following subdirectories: FIXME

      1. <project path>/data/soil
      2. <project path>/data/soil/SSURGO
      3. <project path>/data/soil/STATSGO
      4. <project path>/data/geology
      5. <project path>/data/nlcd_2016 -- FIXME in general

  2. You will now download SSURGO and STATSGO data by lat/long bounding rectangle.

    1. First we will generate a bounding box for the mesh using an adhydro script. This will be used in the next step. In the adhydro-tools container, run the following command

    mkdir /data/analysis

    python /scripts/gis/mesh_outline.py -o /data/analysis -b 1000 /data/ArcGIS/mesh_catchments.shp

    This same script can be used to simply report the extents of the mesh by using the -x flag.

    /scripts/gis/mesh_outline.py -x /data/ArcGIS/mesh_catchments.shp

    1. Go to the USDA Web Soil Survey

    2. On the left, under Area of Interest, click "Import AOI"

    3. Click "Create AOI from Shapefile". Upload the outline.shp outline.shx, outline.prj files from training_data/analysis. Click "Set AOI"

    4. Once the AOI loads, click the "Download Soils Data" tab on top of the map.

    5. You should be on a "Your AIO (SSURGO)" section.

      1. Click "Create Download Link" near the bottom right of the section. Once it completes loading, the panel now has a "Download Link". Click it to download the SSURGO data, then move the downloaded zip file to training_data/data/soils/SSURGO/

    6. Click the "U.S. General Soil Map (STATSGO2)" section. Find the state/states that your area of interest is in, in this case MD, and download the zip/s. Move the STATSGO downloaded data to training_data/data/soils/STATSGO

  3. Now you will extract the archives and merge the spatial data needed for building ADHydro inputs. Run the script prepare_soil_data.py with the following command in the adhydro-tools container terminal.

    python /scripts/preprocessing/prepare_soil_data.py -x /data/data/soil/

    Next is a quick workaround that is needed to get the processing script later to work correctly. The AOI download packages the zip structure differently than the soil survey area, so we need to key the area of interested as if it were a soil survey area.

    mv /data/data/soil/SSURGO/wss_aoi_<tab> mv /data/data/soil/SSURGO/MD005 FIXME required??? When typing the above command, use tab complete to help

  4. Download the latest National Land Cover Database (NLCD) from http://www.mrlc.gov/. We can use the mesh extents discovered previously to download only a subset of the NLCD. The following url is constructed from these extents, rounded up slightly ensure we have proper coverage accross projections. You can use the controls in the data download box to adjust the extent for other meshes.

    https://www.mrlc.gov/viewer/?downloadBbox=39.28,39.35,-76.80,-76.71

    1. Follow the above link, in the Data Download box, select "Land Cover" and "2016 Land Cover ONLY".

    2. Enter your e-mail in the e-mail box, you should receive a download link momentarily if the extent isn't too large. Alternatively, you CAN download the conus dataset and use it. The follow steps apply to either case.

    3. Move the downloaded data to training_data/data/nlcd_2016 (and extract if using the subset)

    4. Create a virtual raster layer. From the adhydro-tools container terminal, run the following

      cd /data/data/nlcd_2016
gdalbuildvrt nlcd.vrt NLCD_2016_Land_Cover_L48_*.tiff
cd /data

  5. Download Geologic Units from http://mrdata.usgs.gov/geology/state/. Use the Conterminous US state geology https://mrdata.usgs.gov/geology/state/geol_poly.zip.

  6. Extract this dataset to training_data/data/geology

  7. You are now finished downloading the source data that you will need. The steps after this need to be done for each mesh even if you had the downloaded source data saved from a previous mesh.

Process Data

  1. Run parameter_preprocessing.py In the adhydro-tools container terminal run the following command. A quick note on the -m flag. This is the central meridian of the sinusoidal projection used for ADHydro meshes. This meridian is selected in the early steps of the mesh creation. It can be found in the ArcGIS .prj files if needed. For the Dead Run mesh, the value is -76

    python /scripts/preprocessing/parameter_preprocessing.py /data -m -76

    NOTE: For large meshes, this can take a while, about 8 hours for the Upper Colorado Basin -- 9,186,658 elements -- running on a 16 core machine with 126 GB memory. It used approximately 80 GB of memory at peak.

    This script will create a lot of intermediate files. The file names begin with "element_". For example, "element_cokey_data.parquet.0-X", "element_coord_data.parquet.0-X". These files can be used to recover from a crash by restarting partway through the run using the saved intermediate values. However, this isn't well documented. This functionality is really only useful on really large meshes that take a very long time to process. So you can delete these files if you want.

    The three files that you need that are created by this processing are "mesh.1.geolType", "mesh.1.landCover", and "mesh.1.soilType".

    Verify these files exist:

    ls /data/ASCII | grep mesh

Precondition the mesh with ADHydro

  1. At this point, you should have files ready to use as ASCII input files to the ADHydro simulation code. The following files will be read in by ADHydro. These are also listed in the example superfile.

    1. mesh.1.node
    2. mesh.1.z
    3. mesh.1.ele
    4. mesh.1.neigh
    5. mesh.1.landCover
    6. mesh.1.soilType
    7. mesh.1.geolType
    8. mesh.1.edge
    9. mesh.1.chan.node
    10. mesh.1.chan.z
    11. mesh.1.chan.ele
    12. mesh.1.chan.prune

  2. Read ASCII files with mesh massage

    In the training_data archive is an example superfile. On your machine in a terminal not running the adhydro-tools container, create a directory for this step. cd <project_path>/training_data/

    mkdir mesh_massage

    Copy the ADhydro example superfile to this directory. You can rename it to simply superfile.ini if you prefer.

    cp example_superfile.ini mesh_massage/superfile.ini

    This file will confiure the adhydro code. Open it in your favorite editor, and start with line 13, it should look like

    evapoTranspirationInitDirectoryPath = /adhydro/HRLDAS-v3.6/Run

    Uncomment line 33 initializeFromASCIIFiles and set it to true.

    Next set the ASCIIInputDirectoryPath to the directory where the mesh files were created in the previous steps, i.e

    ASCIIInputDirectoryPath = /data/ASCII

    Comment out line 54, adhydroInputDirectoryPath since we are initializing from ASCII first.

    Set the output directory on line 70 to the mesh_massage path, i.e.

    adhydroOutputDirectoryPath = /data/mesh_massage

    On line 79, set the map projection information. Uncomment centralMeridianDegrees and set it accordingly.

    centralMeridianDegrees = -76.0

    Then uncomment the falseEasting and falseNorthing lines, but you shouldn't need to change these values.

    The mesh_massage doesn't actually do any simulation, but ADHydro requires a referenceDate and currentTime to be set regardless, so uncomment the referenceDateJulian variable on line 89 and the currentTime on line 99.

    Finally, uncomment line 139, doMeshMassage and set it to true

    Now run adhydro using this superfile. From the <project path> in the terminal (using the same one as before, simple cd ..)

    docker run --cap-add=SYS_PTrace -v `pwd`/training_data:/data adhydro -c "adhydro superfile.ini"

  3. Create forcing data. For this training, we will use National Water Model analysis and assimilation forcings pulled from Google Cloud Platform. This is provided in the training material under forcing/data.

    Use the adhydro-tools container terminal to run the following command. It will resample the gridded forcings and create a single time varying forcing netCDF file that ADHydro can read during simulations. First, change to the forcing data directory.

    cd /data/forcing

    then

    python /scripts/forcing/nwm/nwm_2.0_to_adhydro.py -s 2019-07-01:00 -e 2019-12-31:23 -m -76 -c 2 /data /data/forcing/data/

  4. Do drain-down run. You can set up the data directory and edit the superfile form the host machine terminal.

    In the <project path>/training_data directory:

    Create a directory called drain_down and copy the mesh_massage superfile to this directory.

    cp mesh_massage/superfile.ini drain_down/

    Now we need to turn off the ASCII initialization and use the mesh_massage generated netCDF files. Open the drain_down/superfile.ini file in your favorite editor.

    Edit line 33, comment the line out with a ; or set the value to false.

    Uncomment line 54 and set it to the mesh_massage directory.

    adhydroInputDirectoryPath = /data/mesh_massage

    Uncomment line line 58 and set its value to the forcing file created.

    adhydroInputForcingFilePath = /data/forcing/forcing_2020-10-2_2020-10-2.nc FIXME filename

    Set the output directory on line 70 to the drain_down path, i.e.

    adhydroOutputDirectoryPath = /data/drain_down

    Since we are actually going to prepare a simulation, we need to set the reference time accordingly. This should be the julian date of the first available forcing time.

    One way to find this is to use ncdump and copy the first output of the variable JULTIME.

    ncdump -v JULTIME forcing_2020-10-2_2020-10-2.nc | grep JULTIME

    Set line 89 referenceDateJulian to this value. Alternatively, comment out line 89 and set each subsequent date value.

    Leave currentTime on line 99 to indicate starting at the beginning of the forcing record.

    Set the drain_down duration, about 2 weeks should be sufficient. Uncomment line 102 and set the simulationDuration to 2 weeks, in seconds:

    simulationDuration = 1209600.00

    Finally, comment out line 139, doMeshMassage or set it to false, and then uncomment drainDownMode on line 133 and set it to true.

    Save this file and then execute adhydro.

    docker run --cap-add=SYS_PTrace -v `pwd`/training_data:/data adhydro -c "mpirun -n 8 adhydro /data/drain_down/superfile.ini"

  5. Run simulation Again, on the host machine terminal, make a simulation directory and copy the drain_down superfile to this directory.

    cp drain_down/superfile.ini simulation/

    Edit the superfile to configure the simulation.

    Edit the input directory path on line 54 to point to the drain_down location.

    adhydroInputDirectoryPath = /data/drain_down

    Set the output directory on line 70 to the simulation directory.

    adhydroOutputDirectoryPath = /data/simulation

    Uncomment and set the simulation duration on line 102 based on the amount of time, in seconds, you want to simulate (relative to the reference date). You can run longer than forcing is available, in which case the last known values of forcing are used for the rest of the simulation. In general, though, set this duration for the duration of available forcing. To run 1 day:

    For one day:

    simulationDuration = 86400.0

    For 180 days:

    simulationDuration = 15552000.0

    Set the outputPeriod on line 106 to an approriate interval, in seconds.

    For hourly output:

    outputPeriod = 3600.0

    Disable the drainDownMode on line 133 by commenting or setting to false.

    Run the simulation:

    adhydro simulation/superfile.ini