Post-processing

Tools

There are two workflows for post-processing Hermes-3 results. The legacy way is to use the boutdata package, which can be used to extract the raw variables from the dump files individually, which then have to be unnormalised to be converted into SI units.

The recommended way is to use xHermes, which is built upon the Xarray BOUT++ post-processing tool xBOUT. The main advantage of xHermes is that it contains several routines for pre-processing the data, including automatic unnormalisation and geometry calaculations. The disadvantage is that it may be slower than boutdata when running in parallel due to the netCDF I/O overhead. This can be mitigated by squashing the dump files (see section Squashing output). Efforts to improve the performance are ongoing.

Please refer to the xHermes readme and examples for details.

Available diagnostic variables

It can be problematic to record all of the diagnostic variables in the documentation as the code is still in active development. Thankfully, all of the diagnostics are saved with helpful metadata containing the name, units, normalisation, description and the origin of the variable from within the code.

This is available in xHermes. You can access it by the following example:

ds["Nd"].attrs()

The attributes are:

time_dimension

This indicates that the variable is time evolving. If you remove this line, it will be saved only at the first RHS evaluation.

units

A string showing the units for post-processing. xHermes picks this up.

conversion

A float representing the normalisation factor. xHermes picks this up to do automatic conversion to SI units.

standard_name, long_name

We aren’t consistent on what should be in each, but they are meant to describe the variables in post-processing.

species, source

The relevant species and component that the diagnostic is coming from

Alternatively, the same attributes can be seen in the source code.

Reaction diagnostics convention

There are five categories of diagnostics. K is a simple reaction rate (always positive). S is a source of density and is positive if the ion density is increasing. E is a source of energy due to energy transfer (e.g. charge exchange) and is positive if the ion energy is increasing. F is a momentum transfer rate and is currently negative if the ion energy is increasing. R is a loss of energy from the system, e.g. due to radiation. It is always negative.

Variable prefix	Units	Description
K	\(s^{-1}\)	Reaction rate
S	\(m^{-3}s^{-1}\)	Density transfer source
E	\(Wm^{-3}\)	Energy transfer source
F	\(kgm^{-2}s^{-2}\)	Momentum transfer rate
R	\(Wm^{-3}\)	System loss source

Charge exchange can be slightly complicated:

For two species a and b, the channel Fab_cx is a source of momentum for species a due to charge exchange with species b. There are corresponding sinks for the products of the charge exchange reaction which are not saved.

For example,reaction d + t+ -> d+ + t will save the following forces (momentum sources): - Fdt+_cx is a source of momentum for deuterium atoms d and sink of momentum for deuterium ions d+. - Ft+d_cx is a source of momentum for tritium ions t+ and sink of momentum for tritium atoms t.

The reason for this convention is the existence of the inverse reactions: t + d+ -> t+ + d outputs diagnostics Ftd+_cx and Fd+t_cx.

Here are the definitions of some common channels:

Short name	Description
iz	Ionisation
ex	Excitation (ionisation) radiation
rec	Recombination
cx	Charge exchange

Flow diagnostics convention

Hermes-3 saves a number of different flow rates at a cell boundary. The boundary is located at either the “xlow” or “ylow” side (see Cell face notation). Positive values correspond to flow into the cell.

There are several types of flow diagnostics at the moment:

Variable prefix	Units	Description
pf	\(s^{-1}\)	Particle flow
ef	\(W\)	Energy flow
mf	\(N\)	Momentum flow

There are numerous variants of the above throughout the code, which are described in their metadata. Note that the diagnostics have not yet been implemented for every term.