ERF currently generates plotfile in the native AMReX format.

There are several visualization tools that can be used for AMReX plotfiles, specifically ParaView, VisIt and yt.


The open source visualization package ParaView v5.10 and later can be used to view ERF plotfiles with and without terrain. You can download the paraview executable at

To open a plotfile

  1. Run ParaView v5.10, then select “File” \(\rightarrow\) “Open”.

  2. Navigate to your run directory, and select either a single plotfile or a set of plotfiles. Open multiple plotfile at once by selecting plt.. Paraview will load the plotfiles as a time series. ParaView will ask you about the file type – choose “AMReX/BoxLib Grid Reader”.

  3. If you have run the ERF executable with terrain, then the mapped grid information will be stored as nodal data. Choose the “point data” called “nu”, then click on “Warp by Vector” which can be found via Filters–>Alphabetical. This wil then plot data onto the mapped grid locations.

  4. Under the “Cell Arrays” field, select a variable (e.g., “x_velocity”) and click “Apply”. Note that the default number of refinement levels loaded and vizualized is 1. Change to the required number of AMR level before clicking “Apply”.

  5. For “Representation” select “Surface”.

  6. For “Coloring” select the variable you chose above.

  7. To add planes, near the top left you will see a cube icon with a green plane slicing through it. If you hover your mouse over it, it will say “Slice”. Click that button.

  8. You can play with the Plane Parameters to define a plane of data to view, as shown in 4.


4 : Plotfile image generated with ParaView


AMReX data can also be visualized by VisIt, an open source visualization and analysis software. To follow along with this example, first build and run the first heat equation tutorial code.

Next, download VisIt from and install. To open a single plotfile, run VisIt, then select “File” \(\rightarrow\) “Open file …”, then select the Header file associated the the plotfile of interest (e.g., plt00000/Header). Assuming you ran the simulation in 2D, here are instructions for making a simple plot:

  • To view the data, select “Add” \(\rightarrow\) “Pseudocolor” \(\rightarrow\) “phi”, and then select “Draw”.

  • To view the grid structure (not particularly interesting yet, but when we add AMR it will be), select “Add” \(\rightarrow\) “Subset” \(\rightarrow\) “levels”. Then double-click the text “Subset - levels”, enable the “Wireframe” option, select “Apply”, select “Dismiss”, and then select “Draw”.

  • To save the image, select “File” \(\rightarrow\) “Set save options”, then customize the image format to your liking, then click “Save”.

Your image should look similar to the left side of 2.

2 : 2D (left) and 3D (right) images generated using VisIt.



In 3D, you must apply the “Operators” \(\rightarrow\) “Slicing” \(\rightarrow\) “ThreeSlice”, with the “ThreeSlice operator attribute” set to x=0.25, y=0.25, and z=0.25. You can left-click and drag over the image to rotate the image to generate something similar to right side of 2.

To make a movie, you must first create a text file named movie.visit with a list of the Header files for the individual frames. This can most easily be done using the command:

~/amrex/Tutorials/Basic/HeatEquation_EX1_C> ls -1 plt*/Header | tee movie.visit

The next step is to run VisIt, select “File” \(\rightarrow\) “Open file…”, then select movie.visit. Create an image to your liking and press the “play” button on the VCR-like control panel to preview all the frames. To save the movie, choose “File” \(\rightarrow\) “Save movie …”, and follow the on-screen instructions.


The Visit reader determines “Cycle” from the name of the plotfile (directory), specifically from the integer that follows the string “plt” in the plotfile name.

So … if you call it plt00100 or myplt00100 or this_is_my_plt00100 then it will correctly recognize and print Cycle: 100.

If you call it plt00100_old it will also correctly recognize and print Cycle: 100

But, if you do not have “plt” followed immediately by the number, e.g. you name it pltx00100, then VisIt will not be able to correctly recognize and print the value for “Cycle”. (It will still read and display the data itself.)


yt, an open source Python package available at, can be used for analyzing and visualizing mesh and particle data generated by AMReX codes. Some of the AMReX developers are also yt project members. Below we describe how to use on both a local workstation, as well as at the NERSC HPC facility for high-throughput visualization of large data sets.

Note - AMReX datasets require yt version 3.4 or greater.

Using on a local workstation

Running yt on a local system generally provides good interactivity, but limited performance. Consequently, this configuration is best when doing exploratory visualization (e.g., experimenting with camera angles, lighting, and color schemes) of small data sets.

To use yt on an AMReX plot file, first start a Jupyter notebook or an IPython kernel, and import the yt module:

In [1]: import yt

In [2]: print(yt.__version__)

Next, load a plot file; in this example we use a plot file from the Nyx cosmology application:

In [3]: ds = yt.load("plt00401")
yt : [INFO     ] 2017-05-23 10:03:56,182 Parameters: current_time              = 0.00605694344696544
yt : [INFO     ] 2017-05-23 10:03:56,182 Parameters: domain_dimensions         = [128 128 128]
yt : [INFO     ] 2017-05-23 10:03:56,182 Parameters: domain_left_edge          = [ 0.  0.  0.]
yt : [INFO     ] 2017-05-23 10:03:56,183 Parameters: domain_right_edge         = [ 14.24501  14.24501  14.24501]

In [4]: ds.field_list
[('DM', 'particle_mass'),
 ('DM', 'particle_position_x'),
 ('DM', 'particle_position_y'),
 ('DM', 'particle_position_z'),
 ('DM', 'particle_velocity_x'),
 ('DM', 'particle_velocity_y'),
 ('DM', 'particle_velocity_z'),
 ('all', 'particle_mass'),
 ('all', 'particle_position_x'),
 ('all', 'particle_position_y'),
 ('all', 'particle_position_z'),
 ('all', 'particle_velocity_x'),
 ('all', 'particle_velocity_y'),
 ('all', 'particle_velocity_z'),
 ('boxlib', 'density'),
 ('boxlib', 'particle_mass_density')]

From here one can make slice plots, 3-D volume renderings, etc. An example of the slice plot feature is shown below:

In [9]: slc = yt.SlicePlot(ds, "z", "density")
yt : [INFO     ] 2017-05-23 10:08:25,358 xlim = 0.000000 14.245010
yt : [INFO     ] 2017-05-23 10:08:25,358 ylim = 0.000000 14.245010
yt : [INFO     ] 2017-05-23 10:08:25,359 xlim = 0.000000 14.245010
yt : [INFO     ] 2017-05-23 10:08:25,359 ylim = 0.000000 14.245010

In [10]:

In [11]:
yt : [INFO     ] 2017-05-23 10:08:34,021 Saving plot plt00401_Slice_z_density.png
Out[11]: ['plt00401_Slice_z_density.png']

The resulting image is 5. One can also make volume renderings with ; an example is show below:


5 : Slice plot of \(128^3\) Nyx simulation using yt.

In [12]: sc = yt.create_scene(ds, field="density", lens_type="perspective")

In [13]: source = sc[0]

In [14]: source.tfh.set_bounds((1e8, 1e15))

In [15]: source.tfh.set_log(True)

In [16]: source.tfh.grey_opacity = True

In [17]:
<Scene Object>:
    source_00: <Volume Source>:YTRegion (plt00401): , center=[  1.09888770e+25   1.09888770e+25   1.09888770e+25] cm, left_edge=[ 0.  0.  0.] cm, right_edge=[  2.19777540e+25   2.19777540e+25   2.19777540e+25] cm transfer_function:None
    <Camera Object>:
    position:[ 14.24501  14.24501  14.24501] code_length
    focus:[ 7.122505  7.122505  7.122505] code_length
    north_vector:[ 0.81649658 -0.40824829 -0.40824829]
    width:[ 21.367515  21.367515  21.367515] code_length
    resolution:(512, 512)
Lens: <Lens Object>:
    viewpoint:[ 0.95423473  0.95423473  0.95423473] code_length

In [19]:
yt : [INFO     ] 2017-05-23 10:15:07,825 Rendering scene (Can take a while).
yt : [INFO     ] 2017-05-23 10:15:07,825 Creating volume
yt : [INFO     ] 2017-05-23 10:15:07,996 Creating transfer function
yt : [INFO     ] 2017-05-23 10:15:07,997 Calculating data bounds. This may take a while.
Set the TransferFunctionHelper.bounds to avoid this.
yt : [INFO     ] 2017-05-23 10:15:16,471 Saving render plt00401_Render_density.png

The output of this is 6.


6 Volume rendering of \(128^3\) Nyx simulation using yt. This corresponds to the same plot file used to generate the slice plot in 5.