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GEM Challenge

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Giovanni Lapenta edited this page Mar 12, 2021 · 16 revisions

We advise the first time users, after successfully completing installation and compilation, to try out the GEM challenge. We provide a modified version with double periodic boundary conditions in 2D so as to avoid boundary details and do a cleaner reference run.

Please complete the following steps:

  • Clone the Coils repository of iPic3D

  • Go to the subdirectory inputfiles and download the input file DH.inp

  • The example is set to use 8 cores and save the data in a directory called data. You need to make sure to have the directory existing before launching the code.

  • As the code runs it saves the data every 100 cycles (you can change this frequency in the input file). You can already monitor the output as it is created. Do not open a file while it is being created by the code.

  • You can check the file ConservedQuantities.txt in the directory data where some key integral quantities are saved (e.g. energy, momentum, charge)

  • Check then the output fields. These are saved in a file called DoubleHarris-Field_######.h5 (where ###### is the cycle saved). You can open this hdf5 file with any software you like (e.g. HDFview, https://www.hdfgroup.org/downloads/hdfview/).

  • To visualise the output you can use any software capable of reading hdf5 (e.g Matlab, python, paraview, YT). We provide an example python script called Cutay.py (in the directory postprocessing_tools/python) as an example to follow.

  • Here are two examples of the output at cycle 4000 when reconnection is well underway. The vertical component of the magnetic field By (Plot of By) forms two strong bipolar structures at the two sides of the reconnection sites. The out of plane magnetic field Bz (Plot of Bz) forms the famous quadrupolar magnetic field signature of the Hall effect, the main discovery coming out of the GEM challenge. Superimposed reported are the contour lines of the out of plane component of the vector potential indicating the formation of magnetic islands. The results are reproduced for qualitative comparison.

  • For quantitative comparison the conserved quantities at cycle 2000 are: 2000 0.000347283019918558 0.0107119806762357 5.39248647163386e-09 0.000267823377678753 7.94542497533339e-05

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