``chop.x`` - Extract a subset of ``kaiju`` results ================================================== Introduction ------------ ``chop.x`` is a compiled tool that extracts a 3D portion of the domain from ``kaiju`` output on either the MAGE grid or interpolated onto a Cartesian or a spherical grid. ``chop.x`` also performs additional calculations such as field line tracing. Output is to an HDF5 file that can be visualized and analyzed similarly to ``kaiju`` output files. Before you start ---------------- In order to use ``chop.x``, you need the following: * A set of output files from a ``kaiju`` magnetosphere run. * An XML file describing the magnetosphere results and the settings for ``chop.x``. ``kaiju`` magnetosphere result files ------------------------------------ Any set of ``kaiju`` magnetosphere results can be used. This documentation assumes you used the MPI version the the ``kaiju`` software, e.g. ``gamera_mpi.x``. This should generate a number of HDF5 files which contain the model results from each MPI rank. Assume all result files are in the current directory. The XML file for ``chop.x`` --------------------------- The XML file read by ``chop.x`` should look something like this (file ``chop.xml``): .. code-block:: xml The elements and attributes of the XML file are described below. .. note:: Standard XML is *case-sensitive*. However, the XML parser used by the Fortran code in ``kaiju`` is *case-insensitive*. Therefore, all of the XML tags and attributes described below can be written with any combintion of upper and lower case. * ```` (required): Specifies XML version. * ```` (required): Outer element for all ``kaiju`` elements. * ```` (required): Inner element for Chimp-specific elements. * ```` (optional): Specify identifying information for the ``kaiju`` results to use, * ``runid`` (optional, default ``"Sim"``): String specifying the runid for the ``kaiju`` results to use as the basis for the extraction. * ``