3. ParaView for DORiE Results

ParaView is a powerful data analysis and visualization application. Its many features make for a rather overwhelming GUI. For analyzing the output of DORiE, we typically only need a small subset of the available tools. This is a quick introduction on how to use ParaView for first-time users.

3.1. Opening an Output File

DORiE prints the output of every time step into a separate .vtu file containing the grid information and the data on it. We typically do not want to open single output files but the time series .pvd files. This file references all output files and stores their respective simulation time stamp.

Note

In case of a parallel run, there is one .vtu output file for each processor per time stamp. Additionally, a single .pvtu file collects all .vtu files for displaying the complete data set. The .pvd file will then reference the .pvtu files, so opening it gives you the data just like for a sequential run.

If you have ParaView installed and associated with the appropriate file types, you can simply open the file with it by double-clicking the file in the folder overview. Alternatively, open ParaView, choose File > Open…, and select the file, or use the Open symbol (1).

The file will appear in the Pipeline Browser (2), where you can click on the eye symbol to enable or disable the display of any object in your currently selected View. You may then need to click Apply (3) in the Properties View right below to actually load the data.

ParaView screenshot on how to load data.

3.2. Working with the Direct Data Visualization

Inside the Render View, the content of your file is now displayed. The 2D or 3D render is interactive: You can drag the view around and rotate it. With the symbols in the second toolbar (1) you can reset the view direction along certain axes.

3.2.1. Choosing Datasets

Select the dataset you want to evaluate using the dropdown menu (2). If the dataset is non-scalar (like e.g., flux) you can choose to evaluate certain components or the magnitude of the quantity.

The visualization type can be chosen with the adjacent dropdown menu (2). Most appropriate for 2D and 3D datasets are Surface and Volume, respectively. You can additionally superimpose the grid structure onto the surface visualization by choosing Surface with Edges.

3.2.2. Color Maps

Use the Rescale buttons (3) to rescale the color map to the current data range, the data range across all time steps, the visible data range, and a custom range.

Select Edit Color Map (4) to open the Color Map Editor (5). Here, you can tick Use log scale when mapping […] to enable a logarithmic color map. Switch between many preset color maps by clicking on the Choose preset button (7), choosing a color map, and clicking Apply. The current color map can be inverted by clicking the Invert the transfer functions button (6).

ParaView screenshot on selecting datasets and color maps.

3.3. Animations

All data displayed typically relates to a single dataset describing a single moment in simulation time. Use the time controls (1) in the topmost toolbar to step through the time sequence and play an animation. By default, the animation mode is set to Snap To TimeSteps which displays every dataset for the same amount of time, independently from the respective time stamp.

To visualize the sequence of datasets on a time axis, open the Animation View (2) by selecting View > Animation View. For a real time sequence, choose RealTime from the Mode dropdown menu. This mode will display the datasets in the fraction of animation duration corresponding to their respective simulation time. You can enter the desired total animation duration in seconds in the Duration field (3).

ParaView screenshot with animation view opened.

3.4. Line Plots

The Plot Over Line filter evaluates the dataset across a line and displays the data in a line plot. Select the filter from the Filter menu or the button (1) in the third toolbar.

You can choose simple locations in the Properties window with the PlotOverLine pipeline selected in the Pipeline Browser. You can also set the endpoint coordinates explicitly here. Additionally, the line indicating the evaluation locations can be dragged around in the Render View.

Applying the Plot Over Line filter opens a new Line Chart View (2) where the data is displayed. The distance along the line is given on the x-axis and the respective dataset values are displayed on the y-axis.

With the Line Chart View of the line plot and the PlotOverLine pipeline both selected, you can choose the variables displayed in the line plot, and modify their colors and legend names (3).

ParaView screenshot displaying a Plot Over Line pipeline.

Tip

You can display multiple Plot Over Line pipelines inside a single Line Chart View by selecting the target view and enabling the desired pipelines with the eye symbol in the Pipeline Browser.

3.4.1. Exporting Line Plot Data

If you want to further analyze the data displayed by a Line Plot, you can export it into a CSV file. To do so, select the LineChartView displaying the desired data and then select File > Save Data…. Choose Comma or Tab Delimited Files in the Files of type dropdown menu, a destination file name, and a directory, and click OK. If desired, you can change the output floating point precision in the now opening Configure Writer window. Confirming with OK will write the file.

Tip

The resulting CSV file can be loaded into a numpy data array using the numpy.loadtxt function.

3.5. Visualizing Fluxes

A useful tool for visualizing fluxes in a transient situation is the Glyph filter. Apply it by first selecting the dataset in the Pipeline Browser and then choosing the filter from the Filter menu or the symbol (1) in the third toolbar. The glyphs will be superimposed onto the visualization in the Render View.

In the Properties window (2), select flux or flux_RTx (if enabled) as Orientation Array and Scale Array, and choose Scale by Magnitude as the Vector Scale Mode (3). Since the magnitues are quite low, you will likely see no glyphs at this time. Choose a Scale Factor in the order of 1E4 to get arrows with reasonable extensions (3).

Additionally, you can choose the flux magnitude or any other data for coloring the glyphs in the Coloring sub-menu in the Properties window (2). You can access the Color Map Editor for the glyphs like for any other dataset.

ParaView screenshot displaying the use of glyphs.