v1.3.2

WARNING: the PyPI wheels for this release are built against "old" Numpy and will not work with Numpy 2.0. Source builds against the new Numpy ABI are expected to work.

• Requirements

  • packaging library added to dependencies.

• Bug fixes

  • Fixed an error loading QpointPhononModes from JSON when there is a
    single q-point in the data

• Improvements

  • When loading .castep_bin files, explicitly check the CASTEP
    version number and give a useful error message if this is < 17.1.
    (These files are missing information about the unit cell origins,
    and would previously cause an error with an unhelpful message.)

• Maintenance

  • Compatibility fix for spglib 2.4 update: a new sanity-check in
    spglib raises TypeError when using empty unit cell and this needs
    handling when looking for high-symmetry labels

  • Compatibility fix for Numpy 2.0 update: avoid some
    broadcasting issues with array shape returned by np.unique

  • Update reference to scipy.integrate.simpson (scipy.integrate.simps
    is deprecated)

  • Filter out spglib deprecation warnings caused by SeeK-path.

v1.3.1

• Maintenance

  • Updated versioneer for compatibility with Python 3.12
  • In tests, avoid checking an attribute of 3D plots which is unreliable in
    recent matplotlib versions
  • Update readthedocs configuration to fix documentation builds

v1.3.0

• Requirements

  • Python 3.7 is no longer supported

  • Minimum version of scipy increased from 1.1 to 1.10

    • This requires numpy >= 1.19.5

  • Minimum version of matplotlib increased from 2.2.2 to 3.2.0

  • Minimum version of pint increased from 0.10.1 to 0.19

  • Minimum version of h5py increaased form 2.8 to 2.10

• Improvements

  • Added variable-width broadening for 1-D and 2-D spectra. An
    arbitrary Callable can be provided relating the axis position to
    Gaussian or Lorentzian width parameter. euphonic-dos and
    euphonic-powder-map CLI tools accept polynomial coefficients
    as input. The broadening is implemented with the fast approximate
    interpolation method already available for adaptive broadening of
    DOS.

  • Added features to Spectrum classes

    • Added copy() methods returning an independent duplicate of data

    • Added __mul__ and __imul__ methods to Spectrum
      classes. This allows results to be conveniently scaled with
      infix notation * or *=

  • Added --scale parameter to euphonic-dos,
    euphonic-intensity-map, euphonic-powder-map to allow
    arbitrary scaling of results from command-line. (e.g. for
    comparison with experiment, or changing DOS normalisation from 1
    to 3N.)

• Bug Fixes:

  • Changed the masking logic for kinematic constraints: instead of
    requiring energy bin to entirely fall within accessible range at
    Q-bin mid-point, unmask bins if any part of energy range is
    accessible at this Q value. This gives much more intuitive
    behaviour, especially for narrow angle ranges.

v1.2.1

• Improvements

  • Added "prefer_non_loto" option to Castep .phonon file
    importers. When this is enabled, a block of q-points are
    encountered with splitting directions, and one q-point does not
    have a splitting direction, the data at this "exact" q-point is
    preferred and the other weights in the group are set to zero.

    This provides the intended behaviour of the Abins Castep parser
    and should give a reasonable result for Gamma-point only Castep
    calculations.

    The option is disabled by default, so existing scripts will not be
    affected.

• Bug Fixes:

  • Allow color to be passed as an extra kwarg to plot_1d and
    plot_1d_to_axis. Previously this caused a TypeError.
  • Fix bug where Py_None was not incremented before returning from
    calculate_phonons() in the C-extension causing a deallocation crash
  • Support phonopy.yaml files from Phonopy versions >= 1.18, which
    have moved the data relating to dipole-dipole
    corrections. (i.e. Born effective charges, static dielectric
    tensor and a related unit conversion factor.)

• Maintenance:

  • A deprecation in Numpy 1.25, which indirectly caused a test failure, has been addressed.

v1.2.0

• Improvements:

  • Euphonic now tests on Python 3.11
  • Euphonic now provides PyPI wheels for Python 3.11

• New features:

  • You can now perform linear interpolation of phonon frequencies and
    eigenvectors with the Brille <https://brille.github.io/stable/index.html>_
    library using the new
    euphonic.brille.BrilleInterpolator object. This should provide
    performance improvements for large unit cells which require the
    dipole correction.
  • There is a new command-line tool euphonic-brille-convergence to
    assist with choosing the BrilleInterpolator.from_force_constants
    arguments to achieve the desired accuracy.
  • Brille interpolation can be accessed from the euphonic-powder-map tool
    using the new --use-brille, --brille-grid-type, --brille-npts
    and --brille-npts-density arguments.

v1.1.0

• New features:

  • There is a new function ForceConstants.from_total_fc_with_dipole to allow
    reading force constants from other programs which contain long-ranged
    dipole-dipole interactions.

• Bug fixes:

  • Avoid occasional segmentation faults when using OpenBLAS, workaround for
    #191 <https://github.com/pace-neutrons/Euphonic/issues/191>_
  • Correctly read force constants from Phonopy with dipole-dipole
    interactions, see #239 <https://github.com/pace-neutrons/Euphonic/issues/239>_.

v1.0.0

• Changes:

  • Support for Python 3.6 has been dropped. This has also resulted in
    changes to the following dependencies:

    • numpy requirement increased from 1.12.1 to 1.14.5
    • scipy requirement increased from 1.0.0 to 1.1.0
    • pint requirement increased from 0.9 to 0.10.1
    • matplotlib requirement increased from 2.0.0 to 2.2.2
    • h5py requirement increased from 2.7.0 to 2.8.0

  • The following deprecated features have been removed:

    • The return_mode_widths argument in ForceConstants.calculate_qpoint_phonon_modes
      and ForceConstants.calculate_qpoint_frequencies has been removed
    • The eta_scale argument in calculate_qpoint_phonon_modes/frequencies
      has been removed
    • The alias command-line tool argument --weights has been removed
    • The alias arguments x_label, y_label, y_min and y_max to
      plot_1d/2d have been removed
    • The modes_from_file and force_constants_from_file functions from
      euphonic.cli.utils have been removed
    • Calling broaden on a Spectrum with uneven bin widths without
      specifying the method='convolve' argument will now raise a ValueError

  • DOS and PDOS calculated by the calculate_dos and
    calculate_dos_map methods of QpointPhononModes and
    QpointFrequencies, and QpointPhononModes.calculate_pdos are
    now calculated per atom rather than per unit cell (integrated area
    is 3 rather than 3*N_atom). This is to keep consistency with
    the structure factors calculated by
    QpointPhononModes.calculate_structure_factor which are calculated
    per atom.

  • The option average_repeat_points when importing q-point modes or
    frequencies from a CASTEP .phonon file with
    QpointFrequencies/QpointPhononModes.from_castep is now True
    by default. To recover previous behaviour set this to False.

v0.6.5

• New Features:

  • Kinematic constraints have been implemented for 2-D S(q,w)-like data.

    • A function euphonic.spectra.apply_kinematic_constraints(Spectrum2d, **kwargs) -> Spectrum2D
      is implemented which masks out inaccessible data, replacing it with NaN.
    • Both direct-geometry and indirect-geometry are supported, by
      using the appropriate argument to set incident or final neutron energy.
    • This function is exposed to the euphonic-powder-map tool, so these
      plots can be produced directly from the CLI.
    • Some parameters from real-world instruments are collected in the
      documentation for convenience.

  • There is a new function euphonic.util.convert_fc_phases, which converts
    a force constants matrix which uses the atom coordinates in the phase
    during interpolation (Phonopy-like), to one which uses the cell origin
    coordinates (Euphonic, CASTEP-like).

  • When importing q-point modes or frequencies from a CASTEP .phonon
    file, a new option (average_repeat_points=True) allows
    repeated entries (with the same q-point index) to be identified
    and their weights divided down by the number of entries. This
    option should give better statistics for sampling meshes that
    include the Gamma-point with LO-TO splitting.

• Improvements:

  • Documentation on the shape and format of the force constants, and how to
    read them from other programs has been improved.

  • The euphonic.util.get_qpoint_labels function, which is called when
    importing band-structure data to identify and label significant points,
    primarily identifies these points by searching for turning-points
    in the band path. The function will now also pick up any q-point
    that appears twice in succession. This is a common convention in
    band-structure calculations and helps with edge-cases such as when
    the path passes through a high-symmetry point without changing
    direction. This may pick up some previously-missing points in
    band-structure plots generated with euphonic-dispersion and
    euphonic-intensity-map

• Bug fixes:

  • Allow read of phonopy.yaml quantities in 'au' (bohr) units.
    Previously this was interpreted as an astronomical unit by Pint.

v0.6.4

• Improvements:

  • The euphonic-dos, euphonic-dispersion and
    euphonic-intensity-map command-line tools can now read
    files that don't contain eigenvectors, if eigenvectors are
    not required for the chosen options.

  • A new --save-json option is available for command-line tools
    which produce plots, this will output the produced spectrum to
    a Euphonic .json file.

  • There is now the option to use a fast, approximate variable-width broadening method when
    adaptively broadening dos:

    • Added new adaptive_method and adaptive_error arguments for calculate_dos
      which specify which adaptive broadening method to use (reference or fast) and an
      acceptable error level when using the fast method.
    • Fast adaptive broadening can be used in the euphonic-dos tool with the
      --adaptive-method and --adaptive-error arguments.

• Changes:

  • euphonic.cli.force_constants_from_file and modes_from_file
    have been deprecated in favour of euphonic.cli.load_data_from_file.
  • Using Spectrum1D/1DCollection/2D.broaden on an axis with unequal
    bin widths is now deprecated, as broadening is performed via convolution,
    which is incorrect in this case. In the future, this will raise a
    ValueError. To broaden anyway, method='convolve' can be supplied,
    which will just emit a warning.

v0.6.3

• New Features:

  • New Spectrum1D.to_text_file and Spectrum1DCollection.to_text_file
    methods to write to column text files

  • An expanded and consistent set of styling options is made
    available for command-line tools that produce plots.

  • Consistent styling and advanced changes can be made using
    Matplotlib stylesheet files, either as a CLI argument or
    using matplotlib.style.context() in a Python script.

• Improvements:

  • Internally, plot theming has been adjusted to rely on Matplotlib
    style contexts. This means user changes and style context are more
    likely to be respected.
  • Additional aliases for plot arguments in the command-line tools have
    been added, for example either --x-label or --xlabel can be used.

• Changes:

  • x_label, y_label, y_min and y_max in euphonic.plot
    functions have been deprecated in favour of xlabel, ylabel,
    ymin and ymax respectively, to match the Matplotlib arguments
    they refer to, and to match other arguments like vmin, vmax.