mirror of
https://github.com/JHUAPL/kaiju.git
synced 2026-01-09 18:57:53 -05:00
262 lines
9.2 KiB
ReStructuredText
262 lines
9.2 KiB
ReStructuredText
Executable to perform field line tracing through GAMERA output data (trace.x)
|
|
=============================================================================
|
|
|
|
Introduction
|
|
------------
|
|
|
|
This executable takes output from an MHD simulation and extracts magnetic
|
|
field lines. Seed points are set uniformly in the in the equator (Z=0), within
|
|
a region selected by the user. See below for more details.
|
|
|
|
Example XML file
|
|
|
|
.. code-block:: xml
|
|
|
|
<?xml version="1.0" ?>
|
|
<KAIJU>
|
|
<Chimp>
|
|
<sim runid="IonFL"/>
|
|
<time T0="36000.0" dt="5.0" tFin="43200.0"/>
|
|
<fields doMHD="T" ebfile="msphere" grType="LFM" isMPI="T"/>
|
|
<parallel Ri="6" Rj="12" Rk="1"/>
|
|
<domain dtype="LFMCYL"/>
|
|
<units uid="EARTH"/>
|
|
<interp wgt="TSC"/>
|
|
<tracer epsds="0.05"/>
|
|
<points Nx1="1" Nx2="72" Nx3="16" grType="SPHERICAL"/>
|
|
<radius min="2.05" max="2.05"/>
|
|
<phi min="180.0" max="360.0"/>
|
|
<theta min="5.0" max="45.0"/>
|
|
</Chimp>
|
|
</KAIJU>
|
|
|
|
Parameter Descriptions
|
|
----------------------
|
|
|
|
``<sim>`` (optional): Specify identifying information for this computation.
|
|
|
|
``runid`` (optional, default ``"Sim"``): String specifying an identifier for
|
|
this run of ``psd.x``. A best practice is to use the ``runid`` in the name of
|
|
the XML file.
|
|
|
|
``<time>`` (optional): Specify time range and interval for calculation.
|
|
|
|
``T0`` (optional, default ``"0.0"``): Start time (simulated seconds) relative
|
|
to start of simulation results used as input.
|
|
|
|
``dt`` (optional, default ``"1.0"``): Time interval and output cadence
|
|
(simulated seconds) for calculation.
|
|
|
|
``tFin`` (optional, default ``"60.0"``): Stop time (simulated seconds)
|
|
relative to start of simulation results used as input.
|
|
|
|
``<fields>`` (required): Describes the input data from a MAGE model run.
|
|
|
|
``ebfile`` (optional, default ``"ebdata.h5"``): Path to HDF5 file containing
|
|
the electric and magnetic fields computed by a MAGE model run.
|
|
|
|
``grType`` (optional, default ``"EGG"``): String specifying grid type used by
|
|
the MAGE output file. Valid values are ``"EGG"``, ``"LFM"``, ``"SPH"``. If the
|
|
string is not one of the supported grid types, the default value (``"EGG"``)
|
|
is used, and a warning message is printed.
|
|
|
|
``doEBFix`` (optional, default ``"false"``): Set to ``"true"`` to "clean" the
|
|
electric field E so that the dot product of the electric and magnetic fields
|
|
is 0. See ``ebinterp.F90``.
|
|
|
|
``doMHD`` (optional, default ``"false"``): Set to ``"true"`` to pass the full
|
|
set of magnetohydrodynamic variables to CHIMP, rather than just electric and
|
|
magnetic fields. Includes velocity vector, density and pressure in the output
|
|
file. See ``ebtypes.F90``.
|
|
|
|
``isMPI`` (optional, default ``"false"``): Set to ``"true"`` is the MAGE
|
|
results file was generated with an MPI version of the model. See
|
|
``eblCstd.F90``.
|
|
|
|
``<domain>`` (optional): Options for the problem domain
|
|
|
|
``dtype`` (optional, default ``"SPH"``): Domain over which to perform CHIMP
|
|
calculations, separate from grid, enables the user to perform calculation on
|
|
a subset of the grid to reduce computation where it is not needed - See
|
|
``gridloc.F90``. Valid values are ``"SPH"``, ``"LFM"``, ``"LFMCYL"``,
|
|
``"MAGE"``, ``"EGG"``, ``"ELL"``.
|
|
|
|
``rClosed`` (optional, default set by choice of ``units/uid``): Radial value
|
|
for field line endpoint to reach to be considered closed - See
|
|
``chmpunits.F90``.
|
|
|
|
``rmax`` (optional, default computed): Maximum radius of Domain region - See
|
|
``gridloc.F90``.
|
|
|
|
``rmin`` (optional, default computed): Minimum radius of Domain region - See
|
|
``gridloc.F90``.
|
|
|
|
``xSun`` (optional,default 20.0): if dType is "LFM" or "MAGE", the Domain
|
|
region includes all i-shells which have distances along the Earth-Sun line is
|
|
less than this value (in Re)
|
|
|
|
``xTail`` (optional,default -100.0): if dType is "LFM" or "MAGE", the Domain
|
|
region includes cells in the magnetotail up until this value (in Re)
|
|
|
|
``yzMax`` (optional,default 40.0): if dType is "LFM" or "MAGE", the Domain
|
|
region includes cells with Y and Z coordinates between +/- yzMax (in Re)
|
|
|
|
``<output>`` (optional): Options related to driver output
|
|
|
|
``timer`` (optional, default ``"false"``): Set to ``"true"`` to turn time
|
|
flags on See ``starter.F90``.
|
|
|
|
``tsOut`` (optional, default ``"10"``): Cadence to output diagnostics to
|
|
run-log file See ``starter.F90``.
|
|
|
|
``<parallel>`` (optional): Options if ebfile was generated using an MPI
|
|
version of the code (read if fields/doMPI is set to ``"true"``, file name in
|
|
form of ebfile_Ri_Rj_Rk_i_j_k.gam.h5)
|
|
|
|
``Ri`` (optional, default ``"1"``): Number of ranks used in decomposition of
|
|
``"i"`` dimension See iotable.F90.
|
|
|
|
``Rj`` (optional, default ``"1"``): Number of ranks used in decomposition of
|
|
``"j"`` dimension See iotable.F90.
|
|
|
|
``Rk`` (optional, default ``"1"``): Number of ranks used in decomposition of
|
|
``"k"`` dimension See iotable.F90.
|
|
|
|
``doOldNaming`` (optional, default ``"false"``): Allow for backward
|
|
compatibility for MHD files generated with the now deprecated naming
|
|
convention See ``chmpdefs.F90``.
|
|
|
|
``<units>`` (optional): Name of units system used in the model run.
|
|
|
|
``uID`` (optional, default ``"Earth"``): See chmpunits.F90. Valid values are
|
|
``"EARTH"``, ``"EARTHCODE"``, ``"JUPITER"``, ``"JUPITERCODE"``, ``"SATURN"``,
|
|
``"SATURNCODE"``, ``"HELIO"``, ``"LFM"``, ``"LFMJUPITER"``.
|
|
|
|
``<interp>`` (optional): Options related to interpolation
|
|
|
|
``wgt`` (optional, default ``"TSC"``): Sets 1D interpolation type. Valid
|
|
values are ``"TSC"`` (1D triangular shaped cloud), ``"LIN"`` (linear),
|
|
``"QUAD"`` (parabolic). See ``starter.F90``.
|
|
|
|
Parameters specific to field line tracing
|
|
|
|
``<tracer>`` (optional): Options related to field line tracing performed by
|
|
CHIMP
|
|
|
|
``epsds`` (optional, default ``"1.0e-2"``): Tolerance for field line tracing
|
|
computations See chmpdefs.F90.
|
|
|
|
``<points>`` (optional): Options related to initialization for field line seed
|
|
points. All points are set uniformly between min/max bounds. 2D grids are
|
|
seeded in the magnetic equator (Z=0).
|
|
|
|
``grType`` (optional, default ``"RP"``): Sets seed point grid type. Valid
|
|
values are ``"RP"`` (2D polar grid), ``"XY"`` (2D cartesian grid), ``"RTP"``
|
|
or ``"SPHERICAL"`` (3D spherical grid). See ``tracex.F90``.
|
|
|
|
``Nx1`` (optional, default ``"100"``): Number of cells in X or R depending on
|
|
grid specified.
|
|
|
|
``Nx2`` (optional, default ``"100"``): Number of cells in Y or Phi depending
|
|
on grid specified.
|
|
|
|
``Nx3`` (optional, default ``"1"``): Number of cells in Theta, set only if
|
|
grType is ``"RTP"`` or ``"SPHERICAL"``.
|
|
|
|
``x1Max`` (optional, default ``"10.0"``): Maximum value of the X dimension
|
|
used to initialize the seed points. Used if grType is ``"XY"``.
|
|
|
|
``x1Min`` (optional, default ``"-10.0"``): Minimum value of the X dimension
|
|
used to initialize the seed points. Used if grType is ``"XY"``.
|
|
|
|
``x2Max`` (optional, default ``"10.0"``): Maximum value of the Y dimension
|
|
used to initialize the seed points. Used if grType is ``"XY"``.
|
|
|
|
``x2Min`` (optional, default ``"-10.0"``): Minimum value of the Y dimension
|
|
used to initialize the seed points. Used if grType is ``"XY"``.
|
|
|
|
``<radius>`` (optional): Radial range for initialization of seed point
|
|
locations. Used if grType is ``"RP"``, ``"RTP"`` or ``"SPHERICAL"``.
|
|
|
|
``min`` (optional, default ``"5.0"``): Minimum seed points are initialized at.
|
|
|
|
``max`` (optional, default ``"25.0"``): Maximum radius seed points are
|
|
initialized at.
|
|
|
|
``<phi>`` (optional): Azimuthal angle range for initialization of seed point
|
|
locations. Used if grType is ``"RP"``, ``"RTP"`` or ``"SPHERICAL"``.
|
|
|
|
``min`` (optional, default ``"0.0"``): Minimum longitude (in degrees) seed
|
|
points are initialized at. A value of 0 corresponds to the +X direction.
|
|
|
|
``max`` (optional, default ``"360.0"``\): Maximum longitude (in degrees) seed
|
|
points are initialized at.
|
|
|
|
``<theta>`` (optional): Polar angle range for initialization of seed point
|
|
locations. Used if grType is ``"RTP"`` or ``"SPHERICAL"``.
|
|
|
|
``min`` (optional, default ``"0.0"``): Minimum longitude (in degrees) seed
|
|
points are initialized at. A value of 0 corresponds to the +X direction.
|
|
|
|
``max`` (optional, default ``"90.0"``): Maximum longitude (in degrees) seed
|
|
points are initialized at.
|
|
|
|
Run Script example
|
|
------------------
|
|
|
|
An example pbs script on ``cheyenne``, RunTrace.pbs to submit field line
|
|
tracing job:
|
|
|
|
.. code-block:: bash
|
|
|
|
#!/bin/bash
|
|
#PBS -A P28100045
|
|
#PBS -N traceFL
|
|
#PBS -j oe
|
|
#PBS -q regular
|
|
#PBS -l walltime=4:00:00
|
|
#PBS -l select=1:ncpus=72:ompthreads=72
|
|
export EXE=${slice}
|
|
export RUNID=${PBS_JOBNAME}
|
|
|
|
#Replace this with your module set
|
|
module purge
|
|
module restore kaiju
|
|
|
|
module list
|
|
hostname
|
|
date
|
|
export OMP_NUM_THREADS=72
|
|
export KMP_STACKSIZE=128M
|
|
echo "Running $EXE"
|
|
./trace.x ${RUNID}.xml > ${RUNID}.out
|
|
date
|
|
|
|
This job can be submitted with the command
|
|
|
|
.. code-block:: bash
|
|
|
|
qsub RunTrace.pbs
|
|
|
|
This will create an HDF5 file with a similar group structure for time slices
|
|
(Step#0,Step#1,xxx) but with each time slice also containing a group for each
|
|
field line seed, i.e.
|
|
|
|
Step#0
|
|
|
|
Line#0
|
|
|
|
Line#1
|
|
|
|
Step#1
|
|
|
|
Line#0
|
|
|
|
Line#1
|
|
|
|
In the above example, the field line seed points are set in a spherical
|
|
coordinate system with Nx1,Nx2,Nx3 points in r,phi,theta.
|
|
|
|
The script kaiju/scripts/genXLine.py can be run on the output HDF5 data to
|
|
create an XDMF file that can be read by VisIt or Paraview.
|