CHANGELOG.md

Changelog of postpic

current master

Highlights

• Add support to read the Smilei PIC (https://smileipic.github.io/Smilei/) data format in both cartesian and azimuthal geometry. Postpic uses a build in azimuthal mode expansion very similar to the one used for fbpic.
• To read smilei data, postpic only relies on the hdf5 package and not smilei's happi module for data access. Paricle ID's (ParticleTracking as described by smilei) can be read directly from the hdf5. Happi requires to sort the IDs and write a new hdf5, which can be twice as big as the original dumps. Using postpic's access this step will be skipped and thus access is much faster (but by default with unordered particle IDs as in any other code).

Incompatible adjustments to previous version

• scipy.integrate.simps has been removed in scipy 1.14. Postpic uses scipy.integrate.simpson which has been introduced in scipy 1.6.0 (Dec 31st 2020).

Other improvements and new features

• Compatibility with numpy 2.0 and the sanitizer checks of numexpr 2.8.6. (#281 -- a304e73)

v0.5

2022-10-22

This is the last version with python 2 support. Changes in setuptools (see for example python PEP 517 and PEP 660 ) require changes in the setup. Backward compatibility will therefore be dropped. Current tests already do not inlcude python2 anymore.

Highlights

• Parallelized implementation of Field.map_coordinates
• Added support for reading files written by the fbpic v0.13.0 code ( https://github.com/fbpic ). The fields can be accessed by Er and Etheta, which have been introduced to the fbpic data reader. Particles are saved in Cartesian coordinates, hence the interface does not change there.
• Reimplementation of Field.fft, see below.

Incompatible adjustments to previous version

• Reimplementation of Field.fft. This changes the phases of Fourier transforms in a way to make it more consistent. However, if your code depends on the phases, Field.fft() now has a parameter old_behaviour that can be used to switch back to the old behaviour.
• Indexing a field by a number (integer or float) will now remove the according axis altogether, instead of leaving behind a length-1 axis. A new class KeepDim was introduced through which the old behaviour can still be used. Behaviour of PostPic before this change:

field.shape == (x,y,z)
field[:, 0.0, :].shape == (x,1,z)

Using the new class KeepDim, it is possible to retain that behaviour in the new version:

field.shape == (x,y,z)
field[:, 0.0, :].shape == (x, z)
field[:, KeepDim(0.0), :].shape == (x,1,z)

Other improvements and new features

• New convenience method Field.copy

v0.4

2019-01-14

Highlights

• Improved interoperability with numpy:
  • Field now understands most of numpy's broadcasting
  • Field can be used as an argument to numpy's ufuncs.
• Import and export routines for Field incuding vtk, compatible with paraview.
• Coordinate mapping and transform for Field.
• Brand new Multispecies.__call__ interface: This takes an expression, which is evaluated by numexr, increasing the speed of per-particle scalar computations strongly. It's also really user-friendly.

Incompatible adjustments to previous version

• postpic.Field method exporttocsv is removed. Use export instead.
• postpic.Field method transform is renamed to map_coordinates, matching the underlying scipy-function.
• postpic.Field method mean has now an interface matching ndarray.mean. This means that, if the axis argument is not given, it averages across all axes instead the last axis.
• postpic.Field.map_coordinates applies now the Jacobian determinant of the transformation, in order to preserve the definite integral. In your code you will need to turn calls to Field.transform into calls to Field.map_coordinates and set the keyword argument preserve_integral=False to get the old behaviour.
• postpic.MultiSpecies.createField has now keyword arguments (bins, shape), which replace the corresponding entries from the optargsh dictionary. The use of theoptargsh keyword argument has been deprecated.
• The functions MultiSpecies.compress, MultiSpecies.filter, MultiSpecies.uncompress and ParticleHistory.skip return a new object now. Before this release, they modified the current object. Assuming ms is a MultiSpecies object, the corresponding adjustemens read:
  old: ms.filter('gamma > 2')
  new: ms = ms.filter('gamma > 2')
• plotter_matplotlib has a new default symmetric colormap

Other improvements and new features

• Overload of the ~ (invert) operator on postpic.MultiSpecies. If ms is a MultiSpecies object with filtered particles (created by the use of compress or filter), then ~ms inverts the selection of particles.
• postpic.Field has methods .loadfrom and .saveto. These can be used to save a Field to a .npz file for later use. Use .loadfrom to load a Field object from such a file. All attributes of the Field are restored.
• postpic.Field has methods .export and .import. These are used to export fields to and import fields from foreign file formats such as .csv, .vtk, .png, .tif, .jpg. It is not guaranteed to get all attributes back after .exporting and than .importing a Field. Some formats are not available for both methods.
• postpic has a new function time_profile_at_plane that 'measures' the temporal profile of a pulse while passing through a plane
• postpic has a new function unstagger_fields that will take a set of staggered fields and returns the fields after removing the stagger
• postpic has a new function export_vector_vtk that takes up to three fields and exports them as a vector field in the .vtk format
• postpic has a new function export_scalars_vtk that takes up to four fields and exports them as multiple scalar fields on the same grid in the .vtk format
• postpic.Field works now with all numpy ufuncs, also with ufunc.reduce, ufunc.outer, ufunc.accumulate and ufunc.at
• postpic.Field now supports broadcasting like numpy arrays, for binary operators as well as binary ufunc operations
• postpic.Field has methods .swapaxes, .transpose and properties .T and ndim compatible to numpy.ndarray
• postpic.Field has methods all, any, max, min, prod, sum, ptp, std, var, mean, clip compatible to numpy.ndarray
• postpic.Field has a new method map_axis_grid for transforming the coordinates only along one axis which is simpler than map_coordinates, but also takes care of the Jacobian
• postpic.Field has a new method autocutout used to slice away close-to-zero regions from the borders
• postpic.Field has a new method fft_autopad used to pad a small number of grid points to each axis such that the dimensions of the Field are favourable to FFTW
• postpic.Field has a new method adjust_stagger_to to adjust the grid origin to match the grid origin of another field
• postpic.Field has a new method phase to get the unwrapped phase of the field
• postpic.Field has a new method derivative to calculate the derivative of a field
• postpic.Field has new methods flip and rot90 similar to np.flip() and np.rot90()
• postpic.Field.topolar has new defaults for extent and shape
• postpic.Field.integrate now uses the simpson method by default
• postpic.Field.integrate now has a new 'fast' method that uses numexpr, suitable for large datasets
• New module postpic.experimental to contain experimental algorithms for your reference. These algorithms are not meant to be useable as-is, but may serve as recipes to write your own algorithms.
• k-space reconstruction from EPOCH dumps has greatly improved accuracy due to a new algorithm correctly incorporating the frequency response of the implicit linear interpolation performed by EPOCH's half-steps
• plotter_matplotlib.plotField allows to override aspect option to imshow

v0.3.1

2017-10-03

Only internal changes. Versioning is handled by versioneer.

v0.3

2017-09-28

Many improvements in terms of speed and features. Unfortunately some changes are not backwards-compatible to v0.2.3, so you may have to adapt your code to the new interface. For details, see the corresponding section below.

Highlights

• kspace reconstruction and propagation of EM waves.
• postpic.Field properly handles operator overloading and slicing. Slicing can be index based (integers) or referring the actual physical extent on the axis of a Field object (using floats).
• Expression based interface to particle properties (see below)

Incompatible adjustments to previous version

• New dependency: Postpic requires the numexpr package to be installed now.
• Expression based interface of for particles: If ms is a postpic.MultiSpecies object, then the call ms.X() has been deprecated. Use ms('x') instead. This new particle interface can handle expressions that the numexpr package understands. Also ms('sqrt(x**2 + gamma - id)') is valid. This interface is easier to use, has better functionality and is faster due to numexpr. The list of known per particle scalars and their definitions is available at postpic.particle_scalars. In addition all constants of scipy.constants.* can be used. In case you find particle scalar that you use regularly which is not in the list, please open an issue and let us know!
• The postpic.Field class now behaves more like an numpy.ndarray which means that almost all functions return a new field object instead of modifying the current. This change affects the following functions: half_resolution, autoreduce, cutout, mean.

Other improvements and new features

• postpic.helper.kspace can reconstruct the correct k-space from three EM fields provided to distinguish between forward and backward propagating waves (thanks to @Ablinne)
• postpic.helper.kspace_propagate will turn the phases in k-space to propagate the EM-wave.
• List of new functions in postpic from postpic.helper (thanks to @Ablinne): kspace_epoch_like, kspace, kspace_propagate.
• Field.fft function for fft optimized with pyfftw (thanks to @Ablinne).
• Field.__getitem__ to slice a Field object. If integers are provided, it will interpret them as gridpoints. If float are provided they are interpreted as the physical region of the data and slice along the corresponding axis positions (thanks to @Ablinne).
• Field class has been massively impoved (thanks to @Ablinne): The operator overloading is now properly implemented and thanks to __array__ method, it can be interpreted by numpy as an ndarray whenever necessary.
• List of new functions of the Field class (thanks to @Ablinne): meshgrid, conj, replace_data, pad, transform, squeeze, integrate, fft, shift_grid_by, __getitem__, __setitem__, evaluate.
• List of new properties of the Field class (thanks to @Ablinne): matrix, real, imag, angle.
• Many performance optimizations using pyfftw library (optional) or numexpr (now required by postpic) or by avoiding in memory data copying.
• Lots of fixes

v0.2.3

2017-02-17

This release brings some bugfixes and various new features.

Bugfixes

• Particle property Bz.
• plotting of contourlevels.

Improvements and new features

• openPMD support (thanks to @ax3l).
• ParticleHistory class to collect particle information over the entire simulation.
• added particle properties v{x,y,z} and beta{x,y,z}.
• Lots of performance improvemts: particle data will be much less copied in memory now.

v0.2.2 and earlier

There hasnt been any changelog. Dont use those versions anymore.