
.. _releasenotes:

=============
Release notes
=============

Git master branch
=================

:git:`master <>`.

* No changes yet


Version 3.19.0
==============

16 December 2019: :git:`3.19.0 <../3.19.0>`

General changes:

* :func:`ase.build.bulk` now supports elements with tetrahedral and
  rhombohedral attices.

* The ``rank`` and ``size`` constants from the :mod:`ase.parallel` module have
  been deprecated.  Use ``world.rank`` and ``world.size`` instead
  (and ``from ase.parallel import world``).

* ``atoms.set_masses('most_common')`` now sets the masses of each
  element according to most common isotope as stored in
  ``ase.data.atomic_masses_common``.

* :mod:`ase.utils.parsemath` added to utils. This module parses simple
  mathematical expressions and returns their numerical value.

* Plotting functions (such as band structure, EOS, ...)
  no longer show the figure by default.

* :class:`~ase.Atoms` constructor now accepts ``velocities`` as keyword.

* Documentation: New set of :ref:`introductory ASE tutorials <gettingstarted>`.

* More detailed output of ``ase info --formats``.

* For completeness, :mod:`ase.lattice` now also supports the 1D
  Bravais lattice.

Algorithms:

* Added :class:`~ase.md.analysis.DiffusionCoefficient` so one can
  calculate atom/molecule mobility from trajectory as a function of
  time.

* Added general linear parametric constraints :class:`ase.constraints.FixParametricRelations`,
  :class:`ase.constraints.FixScaledParametricRelations`, and
  :class:`ase.constraints.FixCartesianParametricRelations` to
  :mod:`ase.constraints`. These constraints are based off the work
  in: https://arxiv.org/abs/1908.01610, and allows for the positions and cell of a
  structure to be optimized in a reduced parameter space.

* Added :func:`ase.build.graphene` for building graphene monolayers.

* Added :mod:`ase.md.switch_langevin` module for thermodynamic
  integration via MD simulations.

* Implemented "dynamic" or "ideal gas" contribution from atomic
  momenta to stress tensor Use :meth:`<ase.Atoms.get_stress>`, e.g.,
  ``atoms.get_stress(include_ideal_gas=True)``.

Calculators:

* Added :mod:`Q-Chem <ase.calculators.qchem>` calculator.

* Added :class:`~ase.calculators.psi4.Psi4` calculator.

* Added :class:`~ase.calculators.demonnano.DemonNano` calculator.

* Added :mod:`OpenKIM <ase.calculators.kim>` calculator,
  a special calculator for `OpenKim <https://openkim.org/>`_ models.

* Gulp calculator now provides stress tensor.

* The :mod:`NWChem <ase.calculators.nwchem>` calculator has been completely rewritten, and now supports
  `DFT <https://github.com/nwchemgit/nwchem/wiki/Density-Functional-Theory-for-Molecules>`_,
  `SCF (Hartree Fock) <https://github.com/nwchemgit/nwchem/wiki/Hartree-Fock-Theory-for-Molecules>`_,
  `MP2 <https://github.com/nwchemgit/nwchem/wiki/MP2>`_,
  `CCSD <https://github.com/nwchemgit/nwchem/wiki/CCSD>`_,
  and `TCE <https://github.com/nwchemgit/nwchem/wiki/TCE>`_ calculations with gaussian-type orbitals.
  The calculator also now supports
  `plane-wave calculations <https://github.com/nwchemgit/nwchem/wiki/Plane-Wave-Density-Functional-Theory>`_,
  including band structure calculations through ASE's :class:`~ase.dft.band_structure.BandStructure` utilities.
  To facilitate these changes, the format of the calculator keywords has been changed. Please read the updated
  :mod:`NWChem <ase.calculators.nwchem>` calculator documentation for more details.

* :class:`~ase.calculators.siesta.siesta.Siesta` calculator refactored.
  The Siesta calculator now supports the band structure machinery.
  There is only a single Siesta calculator now covering all versions of Siesta,
  consistently with other ASE calculators.

* Added :mod:`~ase.calculators.mixing` module for the linear
  combination of arbitrary :mod:`~ase.calculators`.

* New :class:`ase.calculators.idealgas.IdealGas` calculator for
  non-interacting atoms.  The calculator does nothing.  This can be
  useful for testing.

* :class:`~ase.calculators.emt.EMT` calculator now support
  atom-specific energies as per ``atoms.get_energies()``.

I/O:

* Read and write support for RMCProfile (rmc6f) file format.

* Write support for Materials Studio xtd files.

* More efficient storage of the "data" part of rows in the :mod:`ase.db`
  database.  NumPy arrays are now stored in binary format instead of as text
  thereby using approximately a factor of two less space when storing numbers
  of ``np.float64``.

* The :mod:`~ase.io.pov` module can now render high-order bonds.

* :class:`~ase.Atoms` now provides the general-purpose JSON mechanism
  from :mod:`ase.io.jsonio`.

* Added :mod:`ase.data.pubchem` module to search for structures
  in the `PubChem <https://pubchem.ncbi.nlm.nih.gov/>`_ database.

GUI:

* It is now possible to copy and paste atoms: The "add atoms" function
  (Ctrl+A) will suggest the atoms in the current selection by default.

Version 3.18.2
==============

15 December 2019: :git:`3.18.2 <../3.18.2>`

* Fix an issue with the binary package (wheel) of 3.18.1.
  No bugfixes as such.

Version 3.18.1
==============

20 September 2019: :git:`3.18.1 <../3.18.1>`

* Multiple bugfixes.  Most importantly, deprecate ``atoms.cell.pbc``
  in order to avoid complexities from dealing with two
  ways of manipulating this piece of information.
  Use ``atoms.pbc`` instead; this works the same as always.
  Also, the :class:`~ase.cell.Cell` object now exposes almost the entire
  ``ndarray`` interface.  For a list of smaller bugfixes, see the git log.

Version 3.18.0
==============

19 July 2019: :git:`3.18.0 <../3.18.0>`

General changes:

* ASE no longer supports Python2.

* ``atoms.cell`` is now a :class:`~ase.cell.Cell` object.
  This object resembles a 3x3 array and also provides shortcuts to many common
  operations.

* Preliminary :class:`~ase.formula.Formula` type added.  Collects all
  formula manipulation functionality in one place.

* :class:`~ase.symbols.Symbols` objects, like ``atoms.symbols``, now have a
  :attr:`~ase.symbols.Symbols.formula` attribute.

* Added classes to represent primitive Bravais lattices and data
  relating to Brillouin zones to :mod:`ase.lattice`.  Includes 2D
  lattices.

* New :class:`~ase.dft.kpoints.BandPath` class to represent a band path
  specification like ``'GXL'`` along with actual k-point coordinates.
  :class:`~ase.dft.band_structure.BandStructure` objects now have a band
  path.

* :func:`ase.dft.kpoints.bandpath` now returns a
  :class:`~ase.dft.kpoints.BandPath` object.  Generation
  of band paths now works for (almost) any cell.

* Use ``atoms.cell.bandpath()`` as a shortcut to generate band paths.

* New holonomic :class:`constraint <ase.constraints.FixLinearTriatomic>`
  for trilinear molecules.

* Added ``ase info --calculators`` option which shows a list of
  calculators and whether they appear to be installed.

* Added :func:`ase.build.surfaces_with_termination.surfaces_with_termination`,
  a tool to build surfaces with a particular termination.

* Use the shortcut ``with ase.utils.workdir('mydir', mkdir=True):
  <code>`` to temporarily change directories.

* The ``ase test`` command now properly autocompletes test names and
  calculator names.

* Added keyword, ``atoms.wrap(pretty_translation=True)``, to minimize
  the scaled positions of the atoms.

Calculators:

* Added interface to :mod:`ACE-Molecule <ase.calculators.acemolecule>`.

* NWChem calculator now supports TDDFT runs.

* Multiple improvements to the ONETEP Calculator. Input files can now be
  written that specify LDOS, bsunfolding and many other functionalities.

* Calculation of stress tensor implemented for
  :class:`~ase.calculators.emt.EMT` potential.

* The :class:`~ase.calculators.octopus.Octopus` calculator now
  provides the stress tensor.

* Reworked :class:`~ase.calculators.lammpsrun.LAMMPS` calculator.  The
  calculator should now behave more consistently with other ASE
  calculators.

* Gromacs calculator updated to work with newer Gromacs.

* Fleur calculator updated to work with newer Fleur.

* Added :class:`~ase.calculators.ACN`, a QM/MM forcefield for acetonitrile.

* Improved eigenvalue parsing with Siesta calculator.

Algorithms:

* Determine Bravais lattice for any 2D or 3D cell using
  ``atoms.cell.get_bravais_lattice()``.

* Added function to Minkowski reduce a cell.

* Improved stability of Niggli reduction algorithm.

* Supercell generation using ``ase.build.make_supercell()`` now uses
  a constructive algorithm instead of cutting which was prone to tolerance
  errors.

* Setting an MD velocity distribution now preserves the temperature
  by default.

* :class:`Analysis tool <ase.geometry.analysis.Analysis>` for extracting
  bond lengths and angles from atoms.

* Dynamics and structure optimizers can now run as an iterator using the
  new ``irun()`` mechanism::

    for conv in opt.irun(fmax=0.05):
        print('hello')

  This makes it easier to execute custom code during runs.  The ``conv``
  variable indicates whether the current iteration meets the convergence
  criterion, although this behaviour may change in future versions.

* The genetic algorithm module :mod:`ase.ga` now has operators for crystal
  structure prediction. See :ref:`ga_bulk_tutorial`.

* The genetic algorithm module :mod:`ase.ga` now has operators for crystal
  structure prediction. See :ref:`ga_bulk_tutorial`.

* New :func:`ase.geometry.dimensionality.analyze_dimensionality` function.
  See: :ref:`dimtutorial`.

* New :func:`ase.utils.deltacodesdft.delta` function:  Calculates the
  difference between two DFT equation-of-states.  See the new :ref:`dcdft tut`
  tutorial.

* Holonomic :class:`~ase.constraints.FixLinearTriatomic` for QM/MM
  calculations.

* The :class:`~ase.neighborlist.NeighborList` now uses kdtree from Scipy
  for improved performance.  It also uses Minkowsky reduction
  to improve performance for unusually shaped cells.

I/O:

* Database supports user defined tables

* Preliminary :class:`~ase.formula.Formula` type added.  Collects all
  formula manipulation functionality in one place.

* Support for reading and writing DL_POLY format.

* Support for reading CP2K DCD format.

* Support for EON .con files with multiple images.

* Support for writing Materials Studio xtd format.

* Improved JSON support.  :ref:`cli` tools like :program:`ase
  band-structure` and :program:`ase reciprocal` now work with
  JSON representations of band structures and paths.

* Support reading CIF files through the
  `Pycodcif <http://wiki.crystallography.net/cod-tools/CIF-parser/>`_
  library.  This can be useful for CIF features that are not supported
  by the internal CIF parser.

* :ref:`MySQL and MariaDB <MySQL_server>` are supported as database backend

* Support for writing isosurface information to POV format
  with :func:`ase.io.pov.add_isosurface_to_pov`

GUI:

 * Quickinfo dialog automatically updates when switching image.

 * Display information about custom arrays on Atoms objects; allow colouring
   by custom arrays.

 * Improved color scales.

Version 3.17.0
==============

12 November 2018: :git:`3.17.0 <../3.17.0>`

General changes:

* ``atoms.symbols`` is now an array-like object which works
  like a view of ``atoms.numbers``, but based on chemical symbols.
  This enables convenient shortcuts such as
  ``mask = atoms.symbols == 'Au'`` or
  ``atoms.symbols[4:8] = 'Mo'``.

* Test suite now runs in parallel.

* New :class:`~ase.dft.pdos.DOS` object for representing and plotting
  densities of states.

* Neighbor lists can now :meth:`get connectivity matrices
  <ase.neighborlist.NeighborList.get_connectivity_matrix>`.

* :ref:`ase convert <cli>` now provides options to execute custom code
  on each processed image.

* :class:`~ase.phonons.Phonons` class now uses
  the :class:`~ase.dft.pdos.DOS` and
  :class:`~ase.dft.band_structure.BandStructure` machinery.

* Positions and velocities can now be initialized from phononic
  force constant matrix; see
  :func:`~ase.md.velocitydistribution.PhononHarmonics`.

Algorithms:

* New Gaussian Process (GP) regression optimizer
  (:class:`~ase.optimize.GPMin`).  Check out this `performance test
  <https://wiki.fysik.dtu.dk/gpaw/devel/ase_optimize/ase_optimize.html>`_.

* New filter for lattice optimization,
  :class:`~ase.constraints.ExpCellFilter`, based on an exponential
  reformulation of the degrees of freedom pertaining to the cell.
  This is probably significantly faster than
  :class:`~ase.constraints.UnitCellFilter`.

* :class:`~ase.constraints.UnitCellFilter` now supports scalar pressure and
  hydrostatic strain.

* Compare if two bulk structure are symmetrically equivalent with
  :class:`~ase.utils.structure_comparator.SymmetryEquivalenceCheck`.

* :class:`~ase.neb.NEB` now supports a boolean keyword,
  ``dynamic_relaxation``, which will freeze or unfreeze images
  according to the size of the spring forces so as to save
  force evaluations.  Only implemented for serial NEB calculations.

* Writing a trajectory file from a parallelized :class:`~ase.neb.NEB`
  calculation is now much simpler.  Works the same way as for the serial
  case.

* New :class:`~ase.constraints.FixCom` constraint for fixing
  center of mass.

Calculators:

* Added :class:`ase.calculators.qmmm.ForceQMMM` force-based QM/MM calculator.

* Socked-based interface to certain calculators through the
  :mod:`~ase.calculators.socketio` module:
  Added support for
  communicating coordinates, forces and other quantities over
  sockets using the i-PI protocol.  This removes the overhead for
  starting and stopping calculators for each geometry step.
  The calculators which best support this feature are Espresso,
  Siesta, and Aims.

* Added calculator for :mod:`OpenMX <ase.calculators.openmx>`.

* Updated the :class:`~ase.calculators.castep.Castep` calculator as well as
  the related I/O methods in order to be more forgiving and less reliant on
  the presence of a CASTEP binary. The ``castep_keywords.py`` file has been
  replaced by a JSON file, and if its generation fails CASTEP files can still
  be read and written if higher tolerance levels are set for the functions that
  manipulate them.

* :class:`~ase.calculators.espresso.Espresso`
  and :mod:`~ase.calculators.dftb` now support the
  :class:`~ase.dft.band_structure.BandStructure` machinery
  including improved handling of kpoints, ``get_eigenvalues()``,
  and friends.

I/O:

* CIF reader now parses fractional occupancies if present.
  The GUI visualizes fractional occupancies in the style of Pacman.

* Support for downloading calculations from the Nomad archive.
  Use ``ase nomad-get nmd://<uri> ...`` to download one or more URIs
  as JSON files.  Use the :mod:`ase.nomad` module to download
  and work with Nomad entries programmatically.  ``nomad-json``
  is now a recognized IO format.

* Sequences of atoms objects can now be saved as animations using
  the mechanisms offered by matplotlib.  ``gif`` and ``mp4`` are now
  recognized output formats.

Database:

* The :meth:`ase.db.core.Database.write` method now takes a ``id`` that
  allows you to overwrite an existing row.

* The :meth:`ase.db.core.Database.update` can now update the Atoms and the data
  parts of a row.

* The :meth:`ase.db.core.Database.update` method will no longer accept a list of
  row ID's as the first argument.  Replace this::

      db.update(ids, ...)

  with::

      with db:
          for id in ids:
              db.update(id, ...)

* New ``--show-keys`` and ``--show-values=...`` options for the
  :ref:`ase db <cli>` command line interface.

* Optimized performance of ase db, with enhanced speed of
  queries on key value pairs for large SQLite (.db) database files.
  Also, The ase db server (PostgreSQL) backend now uses
  native ARRAY and JSONB data types for storing NumPy arrays and
  dictionaries instead of the BYTEA datatype. Note that backwards
  compatibility is lost for the postgreSQL backend, and that
  postgres version 9.4+ is required.

GUI:

* Added callback method :meth:`ase.gui.gui.GUI.repeat_poll` to the GUI.
  Useful for programmatically updating the GUI.

* Improved error handling and communication with subprocesses (for plots)
  in GUI.

* Added Basque translation.

* Added French translation.

Version 3.16.2
==============

4 June 2018: :git:`3.16.2 <../3.16.2>`

* Fix test failure for newer versions of flask due to error within the test itself.  Fix trajectory format on bigendian architectures.  Fix issue with trajectory files opened in append mode where header would not be written correctly for images with different length, atomic species, boundary conditions, or constraints.


Version 3.16.0
==============

21 March 2018: :git:`3.16.0 <../3.16.0>`

* New linear-scaling neighbor list
  available as a function :meth:`~ase.neighborlist.neighbor_list`.

* Castep calculator: option for automatic detection of pseudopotential files from a given directory (castep_pp_path); support for GBRV pseudopotential library; updated outfile parsing to comply with CASTEP 18.1.

* New LAMMPS calculator LAMMPSlib utilizing the Python bindings provided by LAMMPS instead of file I/O. Very basic calculator but can serve as base class for more sophisticated ones.

* Support for µSTEM xtl data format.

* New scanning tunnelling spectroscopy (STS) mode for
  :class:`~ase.dft.stm.STM` simulations.

* New method, :meth:`~ase.Atoms.get_angles`, for calculating multiple angles.

* New ``ase reciprocal`` :ref:`command <cli>` for showing the
  1. Brilluin zone, **k**-points and special points.

* New ``ase convert`` :ref:`command <cli>` for converting between file formats.

* Improved XRD/SAXS module:  :mod:`ase.utils.xrdebye`.

* New cell editor for the GUI.

* Improved "quick info" dialog in the GUI.  The dialog now lists results
  cached by the calculator.

* The "add atoms" dialog now offers a load file dialog as was the case before the tkinter port.  It also provides a chooser for the G2 dataset.

* Interface for the :mod:`CRYSTAL <ase.calculators.crystal` code has been
  added.

* The :func:`ase.dft.bandgap.bandgap` function used with ``direct=True``
  will now also consider spin-flip transitions.  To get the spin-preserving
  direct gap (the old behavior), use::

      min(bandgap(..., spin=s, direct=True) for s in [0, 1])

* Bug fixed in the :meth:`ase.phonons.Phonons.symmetrize` method when using an
  even number of repeats.


Version 3.15.0
==============

28 September 2017: :git:`3.15.0 <../3.15.0>`

* If you are running your Python script in :mod:`parallel <ase.parallel>`
  then by default, :func:`ase.io.read` and :func:`ase.io.iread` will read on
  the master and broadcast to slaves, and :func:`ase.io.write` will only
  write from master.  Use the new keyword ``parallel=False`` to read/write
  from the individual slaves.

* New ``ase find`` :ref:`command <cli>` for finding atoms in files.

* Added :class:`Espresso <ase.calculators.espresso.Espresso>` calculator for
  Quantum ESPRESSO in module :mod:`ase.calculators.espresso`.

* The :func:`ase.dft.kpoints.get_special_points` function has a new call
  signature:  Before it was ``get_special_points(lattice, cell)``, now it is
  ``get_special_points(cell, lattice=None)``.  The old way still works, but
  you will get a warning.

* The :class:`ase.dft.dos.DOS` object will now use linear tetrahedron
  interpolation of the band-structure if you set ``width=0.0``.  It's slow,
  but sometimes worth waiting for.  It uses the
  :func:`ase.dft.dos.linear_tetrahedron_integration` helper function.

* :func:`ase.io.read` can now read QBox output files.

* The :mod:`ase.calculators.qmmm` module can now also use
  :ref:`Turbomole <turbomole qmmm>` and :mod:`DFTB+ <ase.calculators.dftb>`
  as the QM part.

* New :ref:`db tutorial` tutorial.

* :mod:`ase.gui`:  Improved atom colouring options; support the Render Scene (povray) and Ctrl+R rotation features again; updated German and Chinese translations.

* Get the :class:`~ase.spacegroup.Spacegroup` object from an
  :class:`~ase.Atoms` object with the new :func:`ase.spacegroup.get_spacegroup`
  function.


Version 3.14.1
==============

28 June 2017: :git:`3.14.1 <../3.14.1>`.

* Calling the :func:`ase.dft.bandgap.bandgap` function with ``direct=True``
  would return band indices that were off by one.  Fixed now.


Version 3.14.0
==============

20 June 2017: :git:`3.14.0 <../3.14.0>`.

* Python 2.6 no longer supported.

* The command-line tools :program:`ase-???` have been replaced by a
  single :program:`ase` command with sub-commands (see :ref:`cli`).
  For help, type::

      $ ase --help
      $ ase sub-command --help

* The old :program:`ase-build` command which is now called
  :program:`ase build` will no longer add vacuum by default.  Use
  ``ase build -V 3.0`` to get the old behavior.

* All methods of the :class:`~ase.Atoms` object that deal with angles now
  have new API's that use degrees instead of radians as the unit of angle
  (:meth:`~ase.Atoms.get_angle`, :meth:`~ase.Atoms.set_angle`,
  :meth:`~ase.Atoms.get_dihedral`, :meth:`~ase.Atoms.set_dihedral`,
  :meth:`~ase.Atoms.rotate_dihedral`, :meth:`~ase.Atoms.rotate`,
  :meth:`~ase.Atoms.euler_rotate`).

  The old way of calling these methods works as always, but will give
  you a warning.  Example:

  >>> water.get_angle(0, 1, 2)  # new API
  104.52
  >>> water.get_angle([0, 1, 2])  # old API
  /home/jensj/ase/ase/atoms.py:1484: UserWarning: Please use new API (which will return the angle in degrees): atoms_obj.get_angle(a1,a2,a3)*pi/180 instead of atoms_obj.get_angle([a1,a2,a3])
  1.8242181341844732

  Here are the changes you need to make in order to get rid of warnings:

  Old API:

  >>> a1 = atoms.get_angle([0, 1, 2])
  >>> atoms.set_angle([0, 1, 2], pi / 2)
  >>> a2 = atoms.get_dihedral([0, 1, 2, 3])
  >>> atoms.set_dihedral([0, 1, 2, 3], pi / 6)
  >>> atoms.rotate_dihedral([0, 1, 2, 3], 10.5 * pi / 180)
  >>> atoms.rotate('z', pi / 4)
  >>> atoms.rotate_euler(phi=phi, theta=theta, psi=psi)

  New API:

  >>> a1 = atoms.get_angle(0, 1, 2) * pi / 180
  >>> atoms.set_angle(0, 1, 2, angle=90)
  >>> a2 = atoms.get_dihedral(0, 1, 2, 3) * pi / 180
  >>> atoms.set_dihedral(0, 1, 2, 3, angle=30)
  >>> atoms.rotate_dihedral(0, 1, 2, 3, angle=10.5)
  >>> atoms.rotate(45, 'z')
  >>> atoms.euler_rotate(phi=phi * 180 / pi,
  ...                    theta=theta * 180 / pi,
  ...                    psi=psi * 180 / pi)

* The web-interface to the :mod:`ase.db` module now uses Bootstrap and looks
  much nicer.  Querying the database is also much easier.  See
  https://cmrdb.fysik.dtu.dk for an example.

* The PostgreSQL backend for :mod:`ase.db` can now contain more than one ASE
  database.

* An ASE database can now have :ref:`metadata` describing the data.
  Metadata is a dict with any of the following keys: ``title``,
  ``key_descriptions``, ``default_columns``, ``special_keys`` and
  ``layout``.

* :data:`ase.data.atomic_masses` has been updated to IUPAC values from
  2016. Several elements will now have different weights which will affect
  dynamic calculations. The old values can be recovered like this:

  >>> from ase.data import atomic_masses_legacy
  >>> atoms.set_masses(atomic_masses_legacy[atoms.numbers])

* New :func:`ase.data.isotopes.download_isotope_data` function for getting
  individual isotope masses from NIST.

* New :func:`ase.eos.calculate_eos` helper function added.

* Added DeltaCodesDFT data: :data:`ase.collections.dcdft`.

* :mod:`ase.gui` can now load and display any sequence of :class:`~ase.Atoms`
  objects; it is no longer restricted to sequences with a constant number
  of atoms or same chemical composition.

* Trajectory files can now store any sequence of :class:`~ase.Atoms`
  objects.  Previously, atomic numbers, masses, and constraints were
  only saved for the first image, and had to apply for all subsequent ones.

* Added calculator interface for DMol\ :sup:`3`.

* Added calculator interface for GULP.

* Added file formats .car, .incoor, and .arc, related to DMol\ :sup:`3`.

* New function for interpolating from Monkhors-Pack sampled values in the BZ
  to arbitrary points in the BZ:
  :func:`ase.dft.kpoints.monkhorst_pack_interpolate`.

* New *band-structure* command for the :program:`ase` :ref:`cli`.

* Two new functions for producing chemical formulas:
  :func:`ase.utils.formula_hill` and :func:`ase.utils.formula_metal`.

* The :func:`ase.dft.bandgap.get_band_gap` function is now deprecated.  Use
  the new one called :func:`ase.dft.bandgap.bandgap` (it's more flexible and
  returns also band indices).

* New :mod:`Viewer for Jupyter notebooks <ase.visualize.nglview>`.


Version 3.13.0
==============

7 February 2017: :git:`3.13.0 <../3.13.0>`.

* The default unit-cell when you create an :class:`~ase.Atoms` object has
  been changed from ``[[1,0,0],[0,1,0],[0,0,1]]`` to
  ``[[0,0,0],[0,0,0],[0,0,0]]``.

* New :attr:`ase.Atoms.number_of_lattice_vectors` attribute equal to,
  big surprise, the number of non-zero lattice vectors.

* The :meth:`ase.Atoms.get_cell` method has a new keyword argument
  ``complete``.  Use ``atoms.get_cell(complete=True)`` to get a complete
  unit cell with missing lattice vectors added at right angles to the
  existing ones.  There is also a function :func:`ase.geometry.complete_cell`
  that will complete a unit cell.

* :func:`~ase.build.graphene_nanoribbon` no longer adds 2.5 Å of vacuum by
  default.

* All functions that create molecules, chains or surfaces
  (see the :mod:`ase.build` module) will no longer add "dummy" lattice
  vectors along the non-periodic directions.  As an example, the surface
  functions will generate unit cells of the type
  ``[[a1,a2,0],[b1,b2,0],[0,0,0]]``.  In order to define all three lattice
  vectors, use the ``vacuum`` keyword that all
  of the 0-d, 1-d and 2-d functions have or, equivalently, call the
  :meth:`~ase.Atoms.center` method.

* Many of the :ref:`surface generating functions <surfaces>` have changed
  their behavior when called with ``vacuum=None`` (the default).  Before, a
  vacuum layer equal to the interlayer spacing would be added on the upper
  surface of the slab. Now, the third axis perpendicular to the surface will be
  undefined (``[0, 0, 0]``).  Use ``vacuum=<half-the-interlater-distance>`` to
  get something similar to the old behavior.

* New :func:`ase.geometry.is_orthorhombic` and
  :func:`ase.geometry.orthorhombic` functions added.

* :mod:`ase.gui` now works on Python 3.

* NEB-tools class has been renamed to :class:`~ase.neb.NEBTools`.

* :mod:`Optimizers <ase.optimize>` now try force-consistent energies if
  possible (instead of energies extrapolated to 0.0 K).


Version 3.12.0
==============

24 October 2016: :git:`3.12.0 <../3.12.0>`.

* New :class:`ase.constraints.ExternalForce` constraint.

* Updated :mod:`ase.units` definition to CODATA 2014. Additionally, support
  for older versions of CODATA was added such that the respective units can
  be created by the user when needed (e.g. interfacing codes with different
  CODATA versions in use).

* New :mod:`ase.calculators.checkpoint` module.  Adds restart and rollback
  capabilities to ASE scripts.

* Two new flawors of :class:`~ase.neb.NEB` calculations have been added:
  ``method='eb'`` and ``method='improvedtangent'``.

* :func:`ase.io.write` can now write XSD files.

* Interfaces for deMon, Amber and ONETEP added.

* New :ref:`defects` tutorial and new super-cell functions:
  :func:`~ase.build.get_deviation_from_optimal_cell_shape`,
  :func:`~ase.build.find_optimal_cell_shape`,
  :func:`~ase.build.make_supercell`.

* New :class:`~ase.dft.band_structure.BandStructure` object.  Can identify
  special points and create nice plots.

* Calculators that inherit from :class:`ase.calculators.calculator.Calculator`
  will now have a :meth:`~ase.calculators.calculator.Calculator.band_structure`
  method that creates a :class:`~ase.dft.band_structure.BandStructure` object.

* Addition to :mod:`~ase.geometry` module:
  :func:`~ase.geometry.crystal_structure_from_cell`.

* New functions in :mod:`ase.dft.kpoints` module:
  :func:`~ase.dft.kpoints.parse_path_string`,
  :func:`~ase.dft.kpoints.labels_from_kpts` and
  :func:`~ase.dft.kpoints.bandpath`.

* Helper function for generation of Monkhorst-Pack samplings and BZ-paths:
  :func:`ase.calculators.calculator.kpts2ndarray`.

* Useful class for testing band-structure stuff:
  :class:`ase.calculators.test.FreeElectrons`.

* The ``cell`` attribute of an :class:`~ase.Atoms` object and the ``cell``
  keyword for the :class:`~ase.Atoms` constructor and the
  :meth:`~ase.Atoms.set_cell` method now accepts unit cells given ase
  ``[a, b, c, alpha, beta, gamma]``, where the three angles are in degrees.
  There is also a corresponding :meth:`~ase.Atoms.get_cell_lengths_and_angles`
  method.

* Galician translation of ASE's GUI.

* Two new preconditioned structure optimizers available.  See
  :mod:`ase.optimize.precon`.

* Trajectory files now contain information about the calculator and also
  information from an optimizer that wrote the trajectory.


Version 3.11.0
==============

10 May 2016: :git:`3.11.0 <../3.11.0>`.

* Special `\mathbf{k}`-points from the [Setyawan-Curtarolo]_ paper was added:
  :data:`ase.dft.kpoints.special_points`.

* New :mod:`ase.collections` module added.  Currently contains the G2 database
  of molecules and the S22 set of weakly interacting dimers and complexes.

* Moved modules:

  * ``ase.utils.eos`` moved to :mod:`ase.eos`
  * ``ase.calculators.neighborlist`` moved to :mod:`ase.neighborlist`
  * ``ase.lattice.spacegroup`` moved to :mod:`ase.spacegroup`

* The ``InfraRed`` that used to be in the ``ase.infrared`` or
  ``ase.vibrations.infrared`` modules is now called
  :class:`~ase.vibrations.Infrared` and should be imported from the
  :mod:`ase.vibrations` module.

* Deprecated modules: ``ase.structure``, ``ase.utils.geometry``,
  ``ase.utils.distance``, ``ase.lattice.surface``.  The functions from these
  modules that will create and manipulate :class:`~ase.Atoms` objects are now
  in the new :mod:`ase.build` module.  The remaining functions have been moved
  to the new :mod:`ase.geometry` module.

* The ``ase.lattice.bulk()`` function has been moved to :func:`ase.build.bulk`.

* Two new functions: :func:`~ase.geometry.cell_to_cellpar` and
  :func:`~ase.geometry.cellpar_to_cell`.

* We can now :func:`~ase.io.read` and :func:`~ase.io.write` magres files.

* :class:`~ase.neb.NEB` improvement:  calculations for molecules can now be
  told to minimize ratation and translation along the path.


Version 3.10.0
==============

17 Mar 2016: :git:`3.10.0 <../3.10.0>`.

* :ref:`old trajectory` files can no longer be used.  See :ref:`convert`.

* New iterator function :func:`ase.io.iread` for iteratively reading Atoms
  objects from a file.

* The :func:`ase.io.read` function and command-line tools can now read ``.gz``
  and ``.bz2`` compressed files.

* Two new decorators :func:`~ase.parallel.parallel_function` and
  :func:`~ase.parallel.parallel_generator` added.

* Source code moved to https://gitlab.com/ase/ase.

* Preliminary :mod:`ase.calculators.qmmm` module.

* Improved :mod:`~ase.calculators.tip3p.TIP3P` potential.

* Velocity Verlet will now work correctly with constraints.

* ASE's GUI no longer needs a special GTK-backend for matplotlib to work.
  This will make installation of ASE much simpler.

* We can now :func:`~ase.io.read` and :func:`~ase.io.write` JSV files.

* New :func:`ase.dft.kpoints.get_special_points` function.

* New :func:`ase.geometry.get_duplicate_atoms` function for finding and
  removing atoms on top of each other.

* New: A replacement :mod:`Siesta <ase.calculators.siesta>` calculator was
  implemented. It closely follows the
  :class:`ase.calculators.calculator.FileIOCalculator` class which should
  ease further development. Handling pseudopotentials, basis sets and ghost
  atoms have been made much more flexible in the new version.


Version 3.9.1
=============

21 July 2015: :git:`3.9.1 <../3.9.1>`.

* Added function for finding maximally-reduced Niggli unit cell:
  :func:`ase.build.niggli_reduce`.

* Octopus interface added (experimental).


Version 3.9.0
=============

28 May 2015: :git:`3.9.0 <../3.9.0>`.

* Genetic algorithm implemented; :mod:`ase.ga`. This can be used
  for the optimization of: atomic cluster structure, materials
  properties by use of template structures. Extension to other projects
  related to atomic simulations should be straightforward.

* The ``ase.lattice.bulk`` function can now build the Wurtzite structure.

* The :class:`ase.utils.timing.Timer` was moved from GPAW to ASE.

* New :mod:`ase.db` module.

* New functions: :func:`ase.build.fcc211` and
  :func:`ase.visualize.mlab.plot`.

* New :class:`~ase.Atoms` methods:
  :meth:`ase.Atoms.get_distances()` and
  :meth:`ase.Atoms.get_all_distances()`.

* :ref:`bash completion` can now be enabled.

* Preliminary support for Python 3.

* Wrapping: new :meth:`ase.Atoms.wrap` method and
  :func:`ase.geometry.wrap_positions` function.  Also
  added ``wrap=True`` keyword argument to
  :meth:`ase.Atoms.get_scaled_positions` that can be used to turn
  off wrapping.

* New improved method for initializing NEB calculations:
  :meth:`ase.neb.NEB.interpolate`.

* New pickle-free future-proof trajectory file format added:
  :ref:`new trajectory`.

* We can now do :ref:`phase diagrams`.

* New :func:`ase.build.mx2` function for 1T and 2H metal
  dichalcogenides and friends.

* New :func:`ase.dft.bandgap.get_band_gap` function

* :class:`~ase.calculators.cp2k.CP2K` interface.


Version 3.8.0
=============

22 October 2013: :git:`3.8.0 <../3.8.0>`.

* ASE's :mod:`gui <ase.gui>` renamed from ``ag`` to ``ase-gui``.
* New :ref:`STM <stm>` module.
* Python 2.6 is now a requirement.
* The old ``ase.build.bulk`` function is now deprecated.
  Use the new one instead (:func:`ase.lattice.bulk`).
* We're now using BuildBot for continuous integration:
  https://ase-buildbot.fysik.dtu.dk/waterfall
* New interface to the JDFTx code.


Version 3.7.0
=============

13 May 2013: :git:`3.7.0 <../3.7.0>`.

* ASE's GUI can now be configured to be more friendly to visually
  impaired users: :ref:`high contrast`.

* The :class:`ase.neb.NEB` object now accepts a list of spring constants.

* *Important backwards incompatible change*: The
  :func:`ase.build.surface` function now returns a
  right-handed unit cell.

* Mopac, NWChem and Gaussian interfaces and EAM potential added.

* New :meth:`~ase.Atoms.set_initial_charges` and
  :meth:`~ase.Atoms.get_initial_charges` methods.  The
  :meth:`~ase.Atoms.get_charges` method will now ask the
  calculator to calculate the atomic charges.

* The :ref:`aep1` has been implemented and 6 ASE calculators are now
  based on the new base classes.

* ASE now runs on Windows and Mac.

* :ref:`mhtutorial` added to ASE.


Version 3.6.0
=============

24 Feb 2012: :git:`3.6.0 <../3.6.0>`.

* ASE GUI translations added, available: da_DK, en_GB, es_ES.

* New function for making surfaces with arbitrary Miller indices with
  the smallest possible surface unit cell:
  ase.build.surface()

* New ase.lattice.bulk() function.  Will replace old
  ase.build.bulk() function.  The new one will produce a more
  natural hcp lattice and it will use experimental data for crystal
  structure and lattice constants if not provided explicitely.

* New values for ase.data.covalent_radii from Cordeo *et al.*.

* New command line tool: :ref:`cli` and tests based on it:
  abinit, elk, fleur, nwchem.

* New crystal builder for ase-gui

* Van der Waals radii in ase.data

* ASE's GUI (ase-gui) now supports velocities for both graphs and coloring

* Cleaned up some name-spaces:

  * ``ase`` now contains only :class:`~ase.Atoms` and
    :class:`~ase.atom.Atom`
  * ``ase.calculators`` is now empty


Version 3.5.1
=============

24 May 2011: :git:`3.5.1 <../3.5.1>`.

* Problem with parallel vibration calculations fixed.


Version 3.5.0
=============

13 April 2011: :git:`3.5.0 <../3.5.0>`.

* Improved EMT potential:  uses a
  :class:`~ase.neighborlist.NeighborList` object and is
  now ASAP_ compatible.

* :class:`ase.optimize.BFGSLineSearch>` is now the default
  (``QuasiNewton==BFGSLineSearch``).

* There is a new interface to the LAMMPS molecular dynamics code.

* New :mod:`ase.phonons` module.

* Van der Waals corrections for DFT, see GPAW_ usage.

* New :class:`~ase.io.bundletrajectory.BundleTrajectory` added.

* Updated GUI interface:

  * Stability and usability improvements.
  * Povray render facility.
  * Updated expert user mode.
  * Enabled customization of colours and atomic radii.
  * Enabled user default settings via :file:`~/.ase/gui.py`.

* :mod:`Database library <ase.data>` expanded to include:

  * The s22, s26 and s22x5 sets of van der Waals bonded dimers and
    complexes by the Hobza group.
  * The DBH24 set of gas-phase reaction barrier heights by the Truhlar
    group.

* Implementation of the Dimer method.


.. _ASAP: https://wiki.fysik.dtu.dk/asap
.. _GPAW: https://wiki.fysik.dtu.dk/gpaw/documentation/xc/vdwcorrection.html


Version 3.4.1
=============

11 August 2010: :git:`3.4.1 <../3.4.1>`.
