Changelog

Unreleased

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 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

v0.5.1

• 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 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 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

  • Change broadening implementation from scipy.signal.fftconvolve to use scipy.ndimage functions for better handling of bright Bragg peaks, see #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-<TAB>”.

  • 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)

  • 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)

  • 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)

  • Fix interpolation for materials with non-symmetric supcercell matrices, see #81

  • Fix interpolation for force constants read from Phonopy for materials that have a primitive matrix and more than 1 species, see #77

v0.3.0

• Breaking Changes:

  • There has been a major refactor, for see the v0.3.0 docs for how to use, or here for refactor details

  • Python 2 is no longer supported. Supported Python versions are 3.6, 3.7 and 3.8

• New Features:

  • Euphonic can now read Phonopy input! See the docs for details.

• Improvements:

  • Added fall_back_on_python boolean keyword argument to ForceConstants.calculate_qpoint_phonon_modes to control whether the Python implementation is used as a fallback to the C extension or not, see #35

  • Added --python-only option to setup.py to enable install without the C extension

• Bug fixes:

  • On reading CASTEP phonon file header information, switch from a fixed number of lines skipped to a search for a specific line, fixing issue #23

  • Fix NaN frequencies/eigenvectors for consecutive gamma points, see #25

  • Fix issue saving plots to file with dispersion.py, see #27

  • Fix incorrect frequencies at gamma point when using dipole correction in C, #45

v0.2.2

• Bug fixes:

  • Add MANIFEST.in for PyPI distribution

v0.2.1

• Bug fixes:

  • Cannot easily upload C header files to PyPI without an accompanying source file, so refactor C files to avoid this

v0.2.0

• There are several breaking changes:

  • Changes to the object instantiation API. The former interface InterpolationData(seedname) has been changed to InterpolationData.from_castep(seedname) in anticipation of more codes being added which require more varied arguments.

  • Changes to the Debye-Waller calculation API when calculating the structure factor. The previous dw_arg kwarg accepted either a seedname or length 3 list describing a grid. The new kwarg is now dw_data and accepts a PhononData or InterpolationData object with the frequencies calculated on a grid. This is to make it clearer to the user exactly what arguments are being used when calculating phonons on the grid.

  • Changes to parallel functionality. The previous parallel implementation based on Python’s multiprocessing has been removed and replaced by a C/OpenMP version. This has both better performance and is more robust. As a result the n_procs kwarg to calculate_fine_phonons has been replaced by use_c and n_threads kwargs.

• Improvements:

  • The parallel implementation based on Python’s multiprocessing has been removed and now uses C/OpenMP which both has better performance and is more robust

  • Documentation has been moved to readthedocs and is more detailed

  • Clearer interface for calculating the Debye-Waller factor

  • Better error handling (e.g. empty InterpolationData objects, Matplotlib is not installed…)

• Bug fixes:

  • Fix gwidth for DOS not being converted to correct units

  • Fix qwidth for S(Q,w) broadening being incorrectly calculated