Grid generator for BOUT++
Project description
Documentation
Stable (release version): https://hypnotoad.readthedocs.io/en/stable/
Latest (master
branch): https://hypnotoad.readthedocs.io/en/latest/
Installation
From conda
hypnotoad
is available from the conda-forge
channel. Install with
$ conda install -c conda-forge hypnotoad
To use the GUI, one of PySide2 or PyQt5 is needed (PySide and PyQt4 may also work, but have not been tested). Install with
$ conda install -c conda-forge pyside2
or
$ conda install -c conda-forge pyqt
From PyPi
hypnotoad
can be installed using pip
by running
$ pip install --user hypnotoad
To use the GUI, one of PySide2 or PyQt5 is needed (PySide and PyQt4 may also work, but have not been tested). These can be fetched by choosing a variant. For PySide2 use
$ pip install --user hypnotoad[gui-pyside2]
or for PyQt5 use
$ pip install --user hypnotoad[gui-PyQt5]
git repo
If you need to modify the hypnotoad code, or get development versions, clone from github
$ git clone git@github.com:boutproject/hypnotoad.git
You can install from the git repo with pip
, this is useful to get the
executables added to your path. If you use conda
you may wish to first
install the dependencies using
$ conda install boututils matplotlib netcdf4 numpy optionsfactory pyqt pyyaml qt.py scipy
(replacing pyqt
with pyside2
if you prefer PySide2 to PyQt5) to ensure
they are not pip
-installed. Make sure to do an 'editable' install using
-e
or --editable
option like
$ cd hypnotoad
$ pip install --user -e .
(you may also need to pip
-install PySide2
or PyQt5
to use the GUI).
If installing in a conda environment you do not need the --user
argument.
This installs executables which use the code that's currently in the git repo,
so if you edit or update it you will see the updates. If you install with pip install .
(without the -e
) then pip
can get confused because it can't
tell which version number is newer, as the git repo versions have a version
number based on the git hash, not a simple x.y.z; then pip may for example not
uninstall hypnotoad correctly.
Usage
Note
A collection of tips about grid generation is kept on the wiki: https://github.com/boutproject/hypnotoad/wiki. Please add to it!
Options are read and set up in the Equilibrium (child-)class object, and passed from there to the Mesh (child-)class object.
User-settable options, with their current values, are printed when an Equilibrium object is created. Internal options should not need to be set by the user, but can be overridden with keyword arguments to the Equilibrium constructor.
Hypnotoad can be run either as an executable (hypnotoad-geqdsk
), which just
reads from an input file, using the gui (hypnotoad-gui
) or interactively
from a Python shell. To ensure reproducibility, it is suggested to create your
final grid non-interactively. The interactive mode is intended to make it
easier to prototype the grid and find a good set of input parameters. Once you
have found a configuration you are happy with, you can save the current input
parameters using the save dialog in the gui, or with
Equilibrium.saveOptions(filename='hypnotoad-options.yaml')
from the Python
shell; this may be especially useful if you have changed some options from the
Python shell with keyword-arguments.
Grid generation can take a while with the default options, which are set for high accuracy. When prototyping, it is suggested to temporarily use lower accuracy. The following may be a good starting point:
- finecontour_Nfine=100. This speeds up the creation of the internal, high-resolution, fixed-spacing representation of contours, and also calculations of distance along contours and some interpolation functions.
- gradPsiRtol=2.e-6 and gradPsiAtol=1.e-6. These control the maximum error on the integration along grad(psi) used to trace grid lines orthogonal to the flux surfaces. They do not usually make a huge difference, but affect the time spent in 'Following perpendicular'.
- If your wall is given by a large number of points (say more than 20) it might be worth creating a simpler one with fewer points for prototyping. This will speed up the 'finding wall intersections' stage. Note that the wall only matters where it intersects the grid.
- Decreasing the resolution of the grid will also help. The grid points will probably not be in exactly the same place, but the algorithms are intended to produce grid spacings that are inversely proportional to the total number of points, so the structure should be very similar.
Utilities
Hypnotoad provides several executables for working with equilibria and grid files:
hypnotoad-gui
is the main GUI interfacehypnotoad-geqdsk
is a command line interface for creating tokamak equilibria from geqdsk equilibrium fileshypnotoad-circular
is a command line interface for creating grid files for concentric, circular flux surfaceshypnotoad-torpex
is a command line interface for creating grid files for TORPEX X-point configurationshypnotoad-plot-equilibrium
is a command line tool for creating plots of the equilibrium (flux surfaces, wall and separatrix) from a geqdsk filehypnotoad-plot-grid-cells
creates a plot of the grid cells from a grid file generated by hypnotoadhypnotoad-recreate-inputs
extracts from a grid file copies of the input YAML file and geqdsk file that were used to create the grid file originally
For more information, pass the --help
flag to any of these commands.
Developing
Developer documentation is here.
Project details
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