GMS:MODFLOW with HDF5: Difference between revisions
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U2DREL and U2DINT were modified so that if the key word HDF5 was encountered when attempting to read an array then an external procedure is called to read in the data. We have added support for the following: | U2DREL and U2DINT were modified so that if the key word HDF5 was encountered when attempting to read an array then an external procedure is called to read in the data. We have added support for the following: | ||
:{| class='wikitable' | :{| class='wikitable' | ||
|+ <small>Explanation of variables</small> | |+ <small>Explanation of variables</small> | ||
Revision as of 21:18, 15 May 2012
| MODFLOW | |
|---|---|
| Pre-processing | |
| MODFLOW Commands | |
| Building a MODFLOW Model | |
| Map to MODFLOW | |
| Calibration | |
| Packages Supported in GMS | |
| Saving a MODFLOW Simulation | |
| Importing MODFLOW Files | |
| Unsupported MODFLOW Features | |
| Run MODFLOW | |
| Post-processing | |
| MODFLOW Display Options | |
| MODFLOW Post-Processing Viewing Options | |
| Reading a MODFLOW Simulation | |
| Tutorials | |
| Packages | |
| Flow: | BCF6, HUF, LPF, UPW |
| Solvers: | SMS |
| Other: | UZF1 |
The versions of MODFLOW 2000, MODFLOW 2005[1], and SEAWAT[1] that ship with the GMS software have been modified to be able to read input data stored in HDF5 files. GMS saves some MODFLOW data to an HDF5 file that is saved with the other MODFLOW files. Some MODFLOW files will have references to the HDF5 file. For more information about HDF5, click here[1].
Contents
Advantages to HDF5
The HDF5 file format is a cross platform binary format for storing scientific data. One advantage of using HDF5 is that the data is stored in binary format so the disk reads and writes are much faster than with ASCII files (although not nearly as elegant to read). You can view the data stored in an HDF5 file by using HDFView (or some other available viewer).
Another advantage of using the HDF5 libary with MODFLOW package data and array data is that HDF5 will compress the data. For example, if you have a transient simulation using the river package the typical line in a river package file would look like this:
[K] [I] [J] [STAGE] [CONDUCTANCE] [ELEVATION]
1 3 4 10.2 5.8 9.5
Then during the next stress period typically the stage would change. The line in the file would look like this:
1 3 4 10.8 5.8 9.5
So we repeated all of the data except that 10.2 changed to 10.8. With compression those repeated values do not take up much space on disk so that the resulting file is smaller.
In one example a river file that was 437 MB was saved to HDF5 format with a compression level of 1; the resulting file was 14 MB. In another example an HDF5 file that contained drain and general head data was 8 MB while the drain file was 253 MB and the general head 141 MB. Not only do the files compress extremely well but the read/write times for the HDF5 file are much faster than the ASCII files.
Changes to MODFLOW 2000 & 2005[1] code
The following subroutines in ult6.f were modified: U2DREL, U2DINT, and ULSTRD. The stream package reading routines were also modified in the str6.f file.
ult.f modifications
U2DREL and U2DINT were modified so that if the key word HDF5 was encountered when attempting to read an array then an external procedure is called to read in the data. We have added support for the following:
Explanation of variables HDF5 a card to indicate that this is read from an HDF5 file CNSTNT the multiplier for the array IPRN print flag for the output control for MODFLOW "FNAME" the HDF5 file where the array is stored "pathInFile" path to the data set in the HDF5 file nDim number of dimensions that the data set has (this is 1, 2, 3) start1 the index (NOTE: these are 0 based not 1) for the starting point to read the data set in the first dimension nToRead1 the number of values to read in the first dimension start2 the index for the starting point to read the data set in the second dimension nToRead2 the number of values to read in the second dimension start3 the index for the starting point to read the data set in the third dimension nToRead3 the number of values to read in the third dimension
- example: "HDF5 1.0 0 "input.h5" "Recharge/07. Property" 3 0 1 0 132 0 1"
- This type of formatting will work for any HDF5 data set that has 3 dimensions or less and the data set can be a 4 byte float or an 8 byte double. The other available format that can be used with the HDF5 key word for the array reading utilities is the following:
- HDF5 CONSTANT CNSTNT
- example: HDF5 CONSTANT 3.0
- This type of formating will assign a constant value to the array. This type of formatting may seem unnecessary. However, the constant identifier can be useful when using parameters to define arrays. Parameters will be explained in another section.
ULSTRD was also modified to read data from an HDF file. This format is specific to the types of HDF5 files that GMS creates.
- GMS_HDF5_01 "FNAME" "pathInFile" SP
Explanation of variables GMS_HDF5_01 a card to indicate that this is read from an HDF5 file "FNAME" the HDF5 file where the array is stored "pathInFile" path to the group in the HDF5 file where all of the data for the boundary condition is stored SP stress period number
- Here is an example of a regular modflow drain file and a drain file with the HDF5 modifications.
Comparison of MODFLOW Drain files Traditional Drain file Drain file with HDF5 3 40 AUX IFACE AUX CONDFACT AUX CELLGRP
3 0
1 3 2 19.0 10.0 6 1.0 -1
1 4 3 19.0 10.0 4 1.0 -1
1 5 4 19.0 10.0 5 1.0 -1
3 0
1 3 2 18.9 11.0 6 1.0 -1
1 4 3 18.9 11.0 4 1.0 -1
1 5 4 18.9 11.0 5 1.0 -1
3 0
1 3 2 19.0 10.0 6 1.0 -1
1 4 3 19.0 10.0 4 1.0 -1
1 5 4 19.0 10.0 5 1.0 -1
#GMS_HDF5_01
3 40 AUX IFACE AUX CONDFACT AUX CELLGRP
3 0 0
GMS_HDF5_01 "sg_t_pest_65.h5" "Drain" 1
3 0 0
GMS_HDF5_01 "sg_t_pest_65.h5" "Drain" 2
3 0 0
GMS_HDF5_01 "sg_t_pest_65.h5" "Drain" 3
str6.f modifications
Since the STR package does not use the ULSTRD utility the str6.f file had to be modified to read the same data that ULSTRD was modified to read: GMS_HDF5_01 "FNAME" "pathInFile" SP.
Parameters
MODFLOW 2000 introduced the concept of parameters as native input to MODFLOW. Starting with version 6.5, GMS no longer writes out native MODFLOW parameters (except when clusters are defined) and the use of the MODFLOW PES process is not available from within GMS. Even when native MODFLOW files are exported from GMS, native MODFLOW parameters are not used (except when clusters are defined) and instead the parameter starting values are written. However, GMS still supports PEST and users may create parameters in the GMS interface as they have been able to do previously. Parameters are created in GMS by assigning a "key" value (usually a negative number) to a MODFLOW input. When MODFLOW is running and calls our external routine to read in the HDF5 a check is made in the data that is read from the HDF5 file. If one of the parameter "key" values is found in the data then the parameter value is substituted into the array or list.
By adopting this approach it was much easier to support transient parameters and very large sets of pilot points.
Also, adopting this approach allows GMS users to use parameters with the BCF package. This feature is not available with the MODFLOW PES process.
Pilot Points
In previous versions of GMS, pilot points were supported by using the multiplier arrays in MODFLOW. Beginning with version 6.5 the pilot point interpolation takes place with in our external routine that is called by MODFLOW. For example, if MODFLOW calls our routine to read an HK array and that array has parameter key values that are associated with a parameter that is defined using pilot points then our routine will perform the pilot point interpolation and substitute the appropriate value. This includes any log interpolation that the user has specified.
Reading MODFLOW files which include HDF5 data
When GMS writes out the MODFLOW files for the list based packages, the first item written to the file is #GMS_HDF5_01. When GMS reads these MODFLOW files with this special comment, it does not read any more of the package file and the data from the *.h5 file will be used.
When GMS saves the RCH or EVT package with parameter that are defined with cluster (and instances). Then a different special comment is written to the top of the file: #GMS_PARAM_CLUSTERS. If GMS is reading a project file that includes a MODFLOW simulation then when this special comment is encountered GMS will not read any more of the package file. However, if a user is reading a MODFLOW model (not a project file) then the rest of this package file will be read and new data sets will be created on the 3D grid that are used to define the clusters used by the parameters.
Exporting Native MODFLOW Files
To export native MODFLOW ASCII files from GMS 6.5 (or later), use the following steps:
- Open a project in GMS (6.5 or later).
- In the 3D Grid Module, select MODFLOW|Export Native MF2K text....
- In the window that appears, double-click the Name file of the MODFLOW model that you want to convert to ASCII format.
- A DOS prompt will appear. Press the Enter key when the executable is finished.
- A folder called Out_Mf2k is created in the same folder as the name file you selected. Out_Mf2k contains all the MODFLOW input files in ASCII format.
If the DOS prompt does not appear after selecting the name file, then go to Edit|Preferences... and select Models. Verify that the Gms2Mf2k executable (the application that converts MODFLOW files from HDF5 to ASCII format) has the correct path next to it. If it doesn't, select Browse... and locate the executable. It will probably be located at c:\program files\gms 6.5\models\mf2k\Gms2Mf2k.exe.
Notes
| GMS – Groundwater Modeling System | ||
|---|---|---|
| Modules: | 2D Grid • 2D Mesh • 2D Scatter Point • 3D Grid • 3D Mesh • 3D Scatter Point • Boreholes • GIS • Map • Solid • TINs • UGrids |  |
| Models: | FEFLOW • FEMWATER • HydroGeoSphere • MODAEM • MODFLOW • MODPATH • mod-PATH3DU • MT3DMS • MT3D-USGS • PEST • PHT3D • RT3D • SEAM3D • SEAWAT • SEEP2D • T-PROGS • ZONEBUDGET | |
| Aquaveo | ||
