v0.6.2

• Improvements:

  • Wheels are now provided with PyPI releases
  • Type hinting is now handled more consistently across different Euphonic
    classes and functions

• Bug Fixes:

  • Will no longer raise a KeyError reading from phonopy.yaml if
    physical_unit key is not present, instead will assume default units
  • Can now read Phonopy BORN files where the (optional) NAC conversion
    factor is not present

v0.6.1

• Bug fixes:

  • The scaling of S(Q,w) as produced by StructureFactor.calculate_sqw_map
    was incorrect, and did not correctly scale with energy bin size (given its
    units are now length**2/energy). This has been fixed, and S(Q,w) scale
    has changed by a factor of (hartee to energy bin unit conversion)/(energy
    bin width magnitude). e.g. if using an energy bin width of 0.1 meV, the new
    S(Q,w) will be scaled by 2.72e4/0.1 = 2.72e5. The original structure factors
    can now be correctly recovered by multiplying S(Q,w) by the energy bin width.

v0.6.0

• Euphonic can now calculate neutron-weighted partial density of states, and
  has new Spectra features to handle PDOS data:

  • Added QpointPhononModes.calculate_pdos method
  • Added QpointFrequencies.calculate_dos_map method
  • New Spectrum1D.__add__ method, which adds 2 spectra together
  • New Spectrum1DCollection.__add__ method, which concatenates 2 collections
  • Enabled indexing of Spectrum1DCollection by a sequence
  • Added Spectrum1DCollection.group_by method, which allows grouping and
    summing spectra by metadata keys e.g. group_by('species')
  • Added Spectrum1DCollection.select method, which allows selection
    of spectra by metadata keys e.g. select(species='Si')
  • Added Spectrum1DCollection.sum method, which sums all spectra in a
    collection
  • Added -w={'coherent-dos','incoherent-dos','coherent-plus-incoherent-dos'}
    neutron-weighted PDOS options to euphonic-dos and euphonic-powder-map
  • Added --pdos options for plotting specific species PDOS to
    euphonic-dos and euphonic-powder-map
  • Deprecated --weights command-line argument in favour of --weighting
    for consistency with calculate_pdos

• Improvements:

  • LICENSE and CITATION.cff <https://citation-file-format.github.io/>_
    files are now included in Euphonic's installation
  • Add ability to interactively change the colormap intensity limits
    in euphonic-powder-map
  • euphonic-optimise-dipole-parameter can now read from Phonopy sources
  • euphonic-optimise-dipole-parameter can now also be used for non-polar
    materials to get general per-qpoint timings
  • Dimensioned Euphonic properties (e.g. frequencies, cell_vectors)
    now have setters so can be set, previously this would raise an
    AttributeError

• Changes:

  • The units of density of states as produced by calculate_dos have
    changed from dimensionless to 1/energy
  • The scaling of density of states has also changed. Previously the
    integration would sum to 1 (if the x_data were converted to Hartree
    units), now the integration will sum to 3N in the same units as x_data
  • StructureFactor.structure_factors have been changed to be in absolute
    units per atom (rather than per unit cell) so will have changed by a
    factor of 1/2*n_atoms, this formulation change has been reflected in the
    calculate_structure_factor docstring
  • The default unit of StructureFactor.structure_factors has been changed
    from angstrom**2 to millibarn
  • The unit of S(Q,w) as produced by StructureFactor.calculate_sqw_map
    has changed dimension from length**2 to length**2/energy. Also,
    as its unit is derived from the input StructureFactor object, its
    default units are now millibarn/meV
  • The eta_scale argument in calculate_qpoint_phonon_modes has been
    deprecated, dipole_parameter should be used instead.
  • This means the euphonic-optimise-eta script has been renamed to
    euphonic-optimise-dipole-parameter.

v0.5.2

• Improvements:

  • Added broaden method to Spectrum1DCollection

• Changes:

  • The return_mode_widths argument in calculate_qpoint_phonon_modes
    has been deprecated in favour of return_mode_gradients. The mode
    widths can still be obtained from the mode gradients with
    util.mode_gradients_to_widths

• Bug fixes:

  • Fixed memory leak when using the C extension and making multiple calls to
    calculate_qpoint_phonon_modes/frequencies
  • Fixed bug which resulted in incorrect energy bins being generated
    in euphonic-powder-map if units other than meV are used and
    --e-max and --e-min aren't specified
  • Use correct number of energy bins in euphonic-intensity-map,
    euphonic-powder-map and euphonic-dos. Previously only
    ebins - 1 bins were generated

v0.3.3

• Bug fixes:

  • Fixed memory leak when using the C extension and making multiple calls to
    calculate_qpoint_phonon_modes

v0.5.1

• New Features:

  • New Crystal.get_symmetry_equivalent_atoms method which uses spglib
    to get the symmetry operations and equivalent atoms under each operation

• Improvements:

  • Added symmetrise argument to QpointPhononModes.calculate_debye_waller
    which will symmetrise it under the crystal symmetry operations. This
    means that there will no longer be a discrepancy between DebyeWaller
    calculated on a symmetry-reduced or full Monkhorst-Pack grid. By default,
    symmetrise=True
  • Added frequencies_min argument to calculate_debye_waller to
    exclude very small frequencies. This will also exclude negative
    frequencies. This improves on the previous behaviour which only excluded
    gamma-point acoustic modes, so would miss small/negative frequencies
    elsewhere
  • Loading the LAPACK libraries for the C extension now uses the
    interface <https://docs.scipy.org/doc/scipy/reference/linalg.cython_lapack.html_
    provided by scipy for cython instead of loading directly from a DLL.
    The new method means we don't have to guess the DLL filename anymore!

• Changes:

  • New dependency on spglib>=1.9.4
  • Fixed formula in calculate_debye_waller docstring to match actual
    implementation: moved 1/2 factor and added explicit q-point weights

v0.5.0

• New Features:

  • New command-line tool euphonic-powder-map allows generation
    and plotting of powder-averaged S(|q|,w) and DOS maps.
  • New QpointFrequencies object which allows storage of frequencies
    without eigenvectors, meaning that memory usage can be reduced if
    eigenvectors are not required.
  • StructureFactor now has a weights attribute and can be used
    to calculate DOS with calculate_dos and get dispersion with
    get_dispersion
  • Spectrum1D, Spectrum1DCollection and Spectrum2D objects
    have a new metadata attribute, see their docstrings for details
  • Euphonic can now read DOS/PDOS from CASTEP .phonon_dos files with
    Spectrum1D.from_castep_phonon_dos and
    Spectrum1DCollection.from_castep_phonon_dos
  • Adaptive broadening is now available for DOS, which can obtain a
    more representative DOS than standard fixed-width broadening. See
    the docs <https://euphonic.readthedocs.io/en/latest/dos.html#adaptive-broadening>_
    for details
  • Adaptive broadening can be used in the euphonic-dos tool with the
    --adaptive argument

• Improvements:

  • Improved default behaviour for C extension use and number of threads:

    • By default the C extension will be used if it is installed
    • By default the number of threads will be set by
      multiprocessing.cpu_count()
    • The environment variable EUPHONIC_NUM_THREADS can be used to set
      a specific number of threads, which takes priority over
      multiprocessing.cpu_count()
    • fall_back_on_python argument has been removed and superseded by the
      default use_c=None behaviour
    • threadpoolctl.threadpool_limits is used to limit the number of threads
      used by numerical libraries in Euphonic C function calls, resulting in
      better overall performance

  • Command-line interfaces have been refactored, giving a more
    uniform set of options and clearer sections of related arguments
    on the interactive help pages.

    • It is now possible where appropriate to specify Monkhorst-Pack
      sampling with a single-parameter --q-spacing as an
      alternative to setting Monkhorst-Pack divisions. This approach
      will account for the size and shape of reciprocal-lattice cells.

  • Build process tweaks

    • On Linux, the build process will now respect a user-defined
      C-compiler variable CC.

    • On Mac OSX, the build process will now respect a user-defined
      C-compiler variable CC. Homebrew library paths will only be
      set if CC is empty and the brew command is available.

    These tweaks are intended to facilitate Conda packaging.

• Breaking changes:

  • The --q-distance argument to euphonic-intensity-map has
    been renamed to --q-spacing for consistency with other tools.

  • Debye-Waller calculation in euphonic-intensity-map is now
    enabled by setting --temperature, which no longer has a
    default value.

  • Default Monkhorst-Pack meshes (i.e. [6, 6, 6] in euphonic-dos
    and [20, 20, 20] in sample_sphere_structure_factor()) have
    been replaced by default grid-spacing values.

  • The scaling of density of states has changed, due to a change
    in implementation

v0.4.0

• There have been some major changes and improvements to spectra, plotting
  and command line tools, including:

  • New command line tool euphonic-intensity-map for plotting weighted
    2D Spectra e.g. Coherent neutron S(Q,w)
  • Existing command line tools euphonic-dispersion and euphonic-dos
    have been updated to also read force constants and Phonopy files.
    Arguments are also more consistent across tools so some may have changed,
    check the command line tool help for details.
  • New Spectrum1DCollection object for containing 1D spectra with a
    shared x-axis (e.g. phonon dispersion modes)
  • New plot_1d_to_axis and plot_2d_to_axis functions to allow
    plotting on specific axes
  • get_bin_centres and get_bin_edges utility functions on spectra
  • The ratio argument to plot_2d has been removed, it should no longer
    be required due to better management of relative axis sizes.
  • The btol argument to plot_1d has been removed, it is recommended
    to use Spectrum1D.split() or Spectrum1DCollection.split() instead.
  • The plot_dispersion function has been removed. It is now recommended
    to plot dispersion using plot_1d(QpointPhononModes.get_dispersion()).
    See docs for details.

• Other changes:

  • Some of Euphonic's dependency version requirements have been changed, but
    can now be relied on with more certainty due to better CI testing. This
    includes:

    • numpy requirement increased from 1.9.1 to 1.12.1
    • matplotlib requirement increased from 1.4.2 to 2.0.0
    • pint requirement decreased from 0.10.1 to 0.9
    • h5py requirement decreased from 2.9.0 to 2.7.0
    • pyyaml requirement decreased from 5.1.2 to 3.13

• Improvements:

  • yaml.CSafeLoader is now used instead of yaml.SafeLoader by
    default, so Phonopy .yaml files should load faster
  • Metadata __euphonic_version__ and __euphonic_class__ have been
    added to .json file output for better provenance

• Bug fixes:

  • Fix read of Phonopy 'full' force constants from phonopy.yaml and
    FORCE_CONSTANTS files
  • Fix structure factor calculation at gamma points with splitting, see
    #107 <https://github.com/pace-neutrons/Euphonic/issues/107>_
  • Change broadening implementation from scipy.signal.fftconvolve
    to use scipy.ndimage functions for better handling of bright
    Bragg peaks, see
    #108 <https://github.com/pace-neutrons/Euphonic/issues/108>_

v0.3.2

• New Features:

  • Added weights as an argument to
    ForceConstants.calculate_qpoint_phonon_modes, this will allow easier
    use of symmetry reduction for calculating density of states, for example.

  • Modules have been added to support spherical averaging from 3D
    q-points to mod(q)

    • euphonic.sampling provides pure functions for the generation of
      points on (2D) unit square and (3D) unit sphere surfaces.
    • A script is provided for visualisation of the different schemes
      implemented in euphonic.sampling. This is primarily intended for
      education and debugging.
    • euphonic.powder provides functions which, given force constants
      data, can use these sampling methods to obtain
      spherically-averaged phonon DOS and coherent structure factor
      data as 1D spectrum objects. (It is anticipated that this module
      will grow to include schemes beyond this average over a single
      sphere.)

  • Added Crystal.to_spglib_cell convenience function

• Changes:

  • The Scripts folder has been removed. Command-line tools are now
    located in the euphonic.cli module. The entry-points are managed
    in setup.py, and each tool has the prefix "euphonic-" to avoid
    namespace clashes with other tools on the user's
    computer. (e.g. euphonic-dos)
  • From an interactive shell with tab-completion, one can find all
    the euphonic tools by typing "euphonic-".
  • Changed arguments for util.get_qpoint_labels(Crystal, qpts)
    to util.get_qpoint_labels(qpts, cell=None) where
    cell = Crystal.to_spglib_cell()

• Bug fixes:

  • Correctly convert from Phonopy's q-point weight convention to Euphonic's
    when reading from mesh.yaml (see
    7509043 <https://github.com/pace-neutrons/Euphonic/commit/7509043>_)
  • Avoid IndexError in ForceConstants.calculate_qpoint_phonon_modes when
    there is only one q-point (which is gamma) and splitting=True

v0.3.1

• New Features:

  • A system has been added for reference data in JSON files. These
    are accessed via euphonic.utils.get_reference_data and some
    data has been added for coherent scattering lengths and cross-sections.
    This system has been made available to the
    calculate_structure_factor() method; it is no longer necessary to
    craft a data dict every time a program uses this function.

• Changes:

  • Fixed structure factor formula in docs (|F(Q, nu)| -> |F(Q, \\nu)|^2
    and e^(Q.r) -> e^(iQ.r))

• Bug fixes:

  • Fix 'born':null in ForceConstants .json files when Born is not
    present in the calculation (see
    c20679c <https://github.com/pace-neutrons/Euphonic/commit/c20679c>_)
  • Fix incorrect calculation of LO-TO splitting when reduce_qpts=True,
    as the 'reduced' q rather than the actual q was used as the q-direction
    (see 3958072 <https://github.com/pace-neutrons/Euphonic/commit/3958072>_)
  • Fix interpolation for materials with non-symmetric supcercell matrices,
    see #81 <https://github.com/pace-neutrons/Euphonic/issues/81>_
  • Fix interpolation for force constants read from Phonopy for materials that
    have a primitive matrix and more than 1 species, see
    #77 <https://github.com/pace-neutrons/Euphonic/issues/77>_