Outputs

This section describes how outputs are handled by GEOS

The outputs are defined in a <Outputs> XML block.

There are three available formats to output the results of a simulation: SILO, VTK, and Time History output into simple dataset HDF5 files which are consumable by post-processing scripts..

Defining an output

SILO Output

The SILO output is defined through the <Silo> XML node (subnode of <Outputs> XML block) as shown here:

<Outputs>
  <Silo name="siloOutput"/>
</Outputs>

The parameter options are listed in the following table:

XML Element: Silo

Name	Type	Default	Description
childDirectory	string		Child directory path
fieldNames	groupNameRef_array	{}	Names of the fields to output. If this attribute is specified, GEOSX outputs all (and only) the fields specified by the user, regardless of their plotLevel
logLevel	integer	0	Sets the level of information to write in the standard output (the console typically). Level 0 outputs no specific information for this solver. Higher levels require more outputs. 1 - Output timing information
name	groupName	required	A name is required for any non-unique nodes
onlyPlotSpecifiedFieldNames	integer	0	If this flag is equal to 1, then we only plot the fields listed in fieldNames. Otherwise, we plot all the fields with the required plotLevel, plus the fields listed in fieldNames
parallelThreads	integer	1	Number of plot files.
plotFileRoot	string	plot	(no description available)
plotLevel	integer	1	(no description available)
writeCellElementMesh	integer	1	(no description available)
writeEdgeMesh	integer	0	(no description available)
writeFEMFaces	integer	0	(no description available)
writeFaceElementMesh	integer	1	(no description available)

VTK Output

The VTK output is defined through the <VTK> XML node (subnode of <Outputs> XML block) as shown here:

<Outputs>
  <VTK name="vtkOutput"/>
</Outputs>

The parameter options are listed in the following table:

XML Element: VTK

Name	Type	Default	Description
childDirectory	string		Child directory path
fieldNames	groupNameRef_array	{}	Names of the fields to output. If this attribute is specified, GEOS outputs all the fields specified by the user, regardless of their plotLevel
format	geos_vtk_VTKOutputMode	binary	Output data format. Valid options: binary, ascii
levelNames	string_array	{}	Names of mesh levels to output.
logLevel	integer	0	Log level
name	groupName	required	A name is required for any non-unique nodes
numberOfTargetProcesses	integer	1	Number of output aggregate files to be written.
onlyPlotSpecifiedFieldNames	integer	0	If this flag is equal to 1, then we only plot the fields listed in fieldNames. Otherwise, we plot all the fields with the required plotLevel, plus the fields listed in fieldNames
outputRegionType	geos_vtk_VTKRegionTypes	all	Output region types. Valid options: cell, well, surface, particle, all
parallelThreads	integer	1	Number of plot files.
plotFileRoot	string	VTK	Name of the root file for this output.
plotLevel	integer	1	Level detail plot. Only fields with lower of equal plot level will be output.
writeFEMFaces	integer	0	(no description available)
writeFaceElementsAs3D	integer	0	Should the face elements be written as 3d volumes or not.
writeGhostCells	integer	0	Should the vtk files contain the ghost cells or not.

TimeHistory Output

The TimeHistory output is defined through the <TimeHistory> XML node (subnode of <Outputs> XML block) as shown here:

<Outputs>
  <TimeHistory name="timeHistoryOutput" sources="{/Tasks/collectionTask}" filename="timeHistory" />
</Outputs>

The parameter options are listed in the following table:

XML Element: TimeHistory

Name	Type	Default	Description
childDirectory	string		Child directory path
filename	string	TimeHistory	The filename to which to write time history output.
format	string	hdf	The output file format for time history output.
logLevel	integer	0	Log level
name	groupName	required	A name is required for any non-unique nodes
parallelThreads	integer	1	Number of plot files.
sources	groupNameRef_array	required	A list of collectors from which to collect and output time history information.

In order to properly collect and output time history information the following steps must be accomplished:

1. Specify one or more collection tasks using the Tasks Manager.

2. Specify a TimeHistory Output using the collection task(s) as source(s).

3. Specify an event in the Event Management to trigger the collection task(s).

4. Specify an event in the Event Management to trigger the output.

Note: Currently if the collection and output events are triggered at the same simulation time, the one specified first will also trigger first. Thus in order to output time history for the current time in this case, always specify the time history collection events prior to the time history output events.

Triggering the outputs

The outputs can be triggered using the Event Management. It is recommended to use a <PeriodicEvent> to output results with a defined frequency:

<PeriodicEvent name="outputs"
               timeFrequency="5000.0"
               targetExactTimestep="1"
               target="/Outputs/siloOutput" />

The keyword target has to match with the name of the <Silo>, <VTK>, or <TimeHistory> node.

Visualisation of the outputs

We suggest the use of VisIT, Paraview, and MatPlotLib to visualize the outputs.

Visualizing Silo outputs with VisIT

If the <Silo> XML node was defined, GEOS writes the results in a folder called siloFiles.

In VisIT :

1. File > Open file…

2. On the right panel, browse to the siloFiles folder.

3. On the left panel, select the file(s) you want to visualize. Usually, one file is written according the frequency defined in the timeFrequency keyword of the Event that has triggered the output.

4. To load fields, use the “Add” button and browse to the fields you want to plot.

5. To plot fields, use the “Draw” button.

Please consult the VisIT documentation for further explanations on its usage.

Visualizing VTK outputs with VisIT

If the <VTK> XML node was defined, GEOS writes the results in a folder named after the plotFileRoot attribute (default = vtkOutputs). For problems with multiple active regions (e.g. Hydraulic Fracturing), additional work may be required to ensure that vtk files can be read by VisIt. Options include:

1. Using a VisIt macro / python script to convert default multi-region vtk files (see GEOS/src/coreComponents/python/visitMacros/visitVTKConversion.py).

2. Using the outputRegionType attribute to output separate sets of files per region. For example:

<Problem>
  <Events>
    <!-- Use nested events to trigger both vtk outputs -->
    <PeriodicEvent
      name="outputs"
      timeFrequency="2.0"
      targetExactTimestep="0">
      <PeriodicEvent
        name="outputs_cell"
        target="/Outputs/vtkOutput_cell"/>
      <PeriodicEvent
        name="outputs_surface"
        target="/Outputs/vtkOutput_surface"/>
    </PeriodicEvent>
  </Events>

  <Outputs>
    <VTK
      name="vtkOutput_cell"
      outputRegionType="cell"
      plotFileRoot="vtk_cell"/>

    <VTK
      name="vtkOutput_surface"
      outputRegionType="surface"
      plotFileRoot="vtk_surface"/>
  </Outputs>
</Problem>

In VisIt, the prepared files can be visualized as follows:

1. Click the Open icon (or select File/Open from the top menu).

2. Enter the vtk output folder in the left-hand panel (these will be separate if you use option 2 above).

3. Select the desired *.vtm group in the right-hand panel (by double-clicking or selecting OK).

4. (Repeat for any additional datasets/regions.)

5. In the main window, select the desired dataset from the Active Sources dropdown menu.

6. Click on the Add icon, and select a parameter to visualize from the mesh, psuedocolor, or vector plot options

7. At some point you may be prompted to create a Database Correlation. If you select Yes, then VisIt will create a new time slider, which can be used to change the time state while keeping the various aspects of the simulation synchronized.

8. Finally, click the Draw button and use the time slider to visualize the output.

Please consult the VisIT documentation for further explanations on its usage.

Visualizing VTK outputs with Paraview

If the <VTK> XML node was defined, GEOS writes a folder and a .pvd file named after the string defined in name keyword.

The .pvd file contains references to the .pvtu files. One .pvtu file is output according the frequency defined in the timeFrequency keyword of the Event that has triggered the output.

One .pvtu contains references to .vtu files. There is as much .vtu file as there were MPI processes used for the computation.

All these files can be opened with paraview. To have the whole results for every output time steps, you can open the .pvd file.

Visualizing TimeHistory outputs with MatPlotLib

If the <TimeHistory> XML node was defined, GEOS writes a file named after the string defined in the filename keyword and formatted as specified by the string defined in the format keyword (only HDF5 is currently supported).

The TimeHistory file contains the collected time history information from each specified time history collector. This information includes datasets for the time itself, any metadata sets describing index association with specified collection sets, and the time history information itself.

It is recommended to use MatPlotLib and format-specific accessors (like H5PY for HDF5) to access and easily plot the time history datat.