Release notes

Git master branch

master.

  • No changes yet

Version 3.19.0

16 December 2019: 3.19.0

General changes:

  • ase.build.bulk() now supports elements with tetrahedral and rhombohedral attices.
  • The rank and size constants from the 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.
  • 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.
  • Atoms constructor now accepts velocities as keyword.
  • Documentation: New set of introductory ASE tutorials.
  • More detailed output of ase info --formats.
  • For completeness, ase.lattice now also supports the 1D Bravais lattice.

Algorithms:

  • Added DiffusionCoefficient so one can calculate atom/molecule mobility from trajectory as a function of time.
  • Added general linear parametric constraints ase.constraints.FixParametricRelations, ase.constraints.FixScaledParametricRelations, and ase.constraints.FixCartesianParametricRelations to 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 ase.build.graphene() for building graphene monolayers.
  • Added ase.md.switch_langevin module for thermodynamic integration via MD simulations.
  • Implemented “dynamic” or “ideal gas” contribution from atomic momenta to stress tensor Use <ase.Atoms.get_stress>(), e.g., atoms.get_stress(include_ideal_gas=True).

Calculators:

  • Added Q-Chem calculator.
  • Added Psi4 calculator.
  • Added DemonNano calculator.
  • Added OpenKIM calculator, a special calculator for OpenKim models.
  • Gulp calculator now provides stress tensor.
  • The NWChem calculator has been completely rewritten, and now supports DFT, SCF (Hartree Fock), MP2, CCSD, and TCE calculations with gaussian-type orbitals. The calculator also now supports plane-wave calculations, including band structure calculations through ASE’s BandStructure utilities. To facilitate these changes, the format of the calculator keywords has been changed. Please read the updated NWChem calculator documentation for more details.
  • 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 mixing module for the linear combination of arbitrary calculators.
  • New ase.calculators.idealgas.IdealGas calculator for non-interacting atoms. The calculator does nothing. This can be useful for testing.
  • 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 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 pov module can now render high-order bonds.
  • Atoms now provides the general-purpose JSON mechanism from ase.io.jsonio.
  • Added ase.data.pubchem module to search for structures in the PubChem 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: 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: 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 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: 3.18.0

General changes:

  • ASE no longer supports Python2.
  • atoms.cell is now a Cell object. This object resembles a 3x3 array and also provides shortcuts to many common operations.
  • Preliminary Formula type added. Collects all formula manipulation functionality in one place.
  • Symbols objects, like atoms.symbols, now have a formula attribute.
  • Added classes to represent primitive Bravais lattices and data relating to Brillouin zones to ase.lattice. Includes 2D lattices.
  • New BandPath class to represent a band path specification like 'GXL' along with actual k-point coordinates. BandStructure objects now have a band path.
  • ase.dft.kpoints.bandpath() now returns a 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 constraint for trilinear molecules.
  • Added ase info --calculators option which shows a list of calculators and whether they appear to be installed.
  • Added 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 ACE-Molecule.
  • 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 EMT potential.
  • The Octopus calculator now provides the stress tensor.
  • Reworked 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 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.

  • Analysis tool 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 ase.ga now has operators for crystal structure prediction. See GA crystal structure prediction.

  • The genetic algorithm module ase.ga now has operators for crystal structure prediction. See GA crystal structure prediction.

  • New ase.geometry.dimensionality.analyze_dimensionality() function. See: Dimensionality analysis.

  • New ase.utils.deltacodesdft.delta() function: Calculates the difference between two DFT equation-of-states. See the new Calculating Delta-values tutorial.

  • Holonomic FixLinearTriatomic for QM/MM calculations.

  • The 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 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. Command line tool tools like ase band-structure and ase reciprocal now work with JSON representations of band structures and paths.
  • Support reading CIF files through the Pycodcif library. This can be useful for CIF features that are not supported by the internal CIF parser.
  • MySQL and MariaDB are supported as database backend
  • Support for writing isosurface information to POV format with 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: 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 DOS object for representing and plotting densities of states.
  • Neighbor lists can now get connectivity matrices.
  • ase convert now provides options to execute custom code on each processed image.
  • Phonons class now uses the DOS and BandStructure machinery.
  • Positions and velocities can now be initialized from phononic force constant matrix; see PhononHarmonics().

Algorithms:

  • New Gaussian Process (GP) regression optimizer (GPMin). Check out this performance test.
  • New filter for lattice optimization, ExpCellFilter, based on an exponential reformulation of the degrees of freedom pertaining to the cell. This is probably significantly faster than UnitCellFilter.
  • UnitCellFilter now supports scalar pressure and hydrostatic strain.
  • Compare if two bulk structure are symmetrically equivalent with SymmetryEquivalenceCheck.
  • 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 NEB calculation is now much simpler. Works the same way as for the serial case.
  • New FixCom constraint for fixing center of mass.

Calculators:

  • Added ase.calculators.qmmm.ForceQMMM force-based QM/MM calculator.
  • Socked-based interface to certain calculators through the 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 OpenMX.
  • Updated the 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.
  • Espresso and dftb now support the 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 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 ase.db.core.Database.write() method now takes a id that allows you to overwrite an existing row.

  • The ase.db.core.Database.update() can now update the Atoms and the data parts of a row.

  • The 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 ase db 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 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: 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: 3.16.0

  • New linear-scaling neighbor list available as a function 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 STM simulations.

  • New method, get_angles(), for calculating multiple angles.

  • New ase reciprocal command for showing the 1. Brilluin zone, k-points and special points.

  • New ase convert command for converting between file formats.

  • Improved XRD/SAXS module: 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 CRYSTAL <ase.calculators.crystal code has been added.

  • The 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 ase.phonons.Phonons.symmetrize() method when using an even number of repeats.

Version 3.15.0

28 September 2017: 3.15.0

Version 3.14.1

28 June 2017: 3.14.1.

Version 3.14.0

20 June 2017: 3.14.0.

  • Python 2.6 no longer supported.

  • The command-line tools ase-??? have been replaced by a single ase command with sub-commands (see Command line tool). For help, type:

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

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

  • All methods of the Atoms object that deal with angles now have new API’s that use degrees instead of radians as the unit of angle (get_angle(), set_angle(), get_dihedral(), set_dihedral(), rotate_dihedral(), rotate(), 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 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 ase.db can now contain more than one ASE database.

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

  • 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 ase.data.isotopes.download_isotope_data() function for getting individual isotope masses from NIST.

  • New ase.eos.calculate_eos() helper function added.

  • Added DeltaCodesDFT data: ase.collections.dcdft.

  • ase.gui can now load and display any sequence of 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 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 DMol3.

  • Added calculator interface for GULP.

  • Added file formats .car, .incoor, and .arc, related to DMol3.

  • New function for interpolating from Monkhors-Pack sampled values in the BZ to arbitrary points in the BZ: ase.dft.kpoints.monkhorst_pack_interpolate().

  • New band-structure command for the ase Command line tool.

  • Two new functions for producing chemical formulas: ase.utils.formula_hill() and ase.utils.formula_metal().

  • The ase.dft.bandgap.get_band_gap() function is now deprecated. Use the new one called ase.dft.bandgap.bandgap() (it’s more flexible and returns also band indices).

  • New Viewer for Jupyter notebooks.

Version 3.13.0

7 February 2017: 3.13.0.

  • The default unit-cell when you create an 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 ase.Atoms.number_of_lattice_vectors attribute equal to, big surprise, the number of non-zero lattice vectors.
  • The 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 ase.geometry.complete_cell() that will complete a unit cell.
  • graphene_nanoribbon() no longer adds 2.5 Å of vacuum by default.
  • All functions that create molecules, chains or surfaces (see the 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 center() method.
  • Many of the surface generating functions 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 ase.geometry.is_orthorhombic() and ase.geometry.orthorhombic() functions added.
  • ase.gui now works on Python 3.
  • NEB-tools class has been renamed to NEBTools.
  • Optimizers now try force-consistent energies if possible (instead of energies extrapolated to 0.0 K).

Version 3.12.0

24 October 2016: 3.12.0.

Version 3.11.0

10 May 2016: 3.11.0.

  • Special \(\mathbf{k}\)-points from the [Setyawan-Curtarolo] paper was added: ase.dft.kpoints.special_points.
  • New ase.collections module added. Currently contains the G2 database of molecules and the S22 set of weakly interacting dimers and complexes.
  • Moved modules:
  • The InfraRed that used to be in the ase.infrared or ase.vibrations.infrared modules is now called Infrared and should be imported from the 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 Atoms objects are now in the new ase.build module. The remaining functions have been moved to the new ase.geometry module.
  • The ase.lattice.bulk() function has been moved to ase.build.bulk().
  • Two new functions: cell_to_cellpar() and cellpar_to_cell().
  • We can now read() and write() magres files.
  • NEB improvement: calculations for molecules can now be told to minimize ratation and translation along the path.

Version 3.10.0

17 Mar 2016: 3.10.0.

Version 3.9.1

21 July 2015: 3.9.1.

  • Added function for finding maximally-reduced Niggli unit cell: ase.build.niggli_reduce().
  • Octopus interface added (experimental).

Version 3.9.0

28 May 2015: 3.9.0.

Version 3.8.0

22 October 2013: 3.8.0.

  • ASE’s gui renamed from ag to ase-gui.
  • New STM module.
  • Python 2.6 is now a requirement.
  • The old ase.build.bulk function is now deprecated. Use the new one instead (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: 3.7.0.

Version 3.6.0

24 Feb 2012: 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: Command line tool 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 Atoms and Atom
    • ase.calculators is now empty

Version 3.5.1

24 May 2011: 3.5.1.

  • Problem with parallel vibration calculations fixed.

Version 3.5.0

13 April 2011: 3.5.0.

  • Improved EMT potential: uses a NeighborList object and is now ASAP compatible.
  • ase.optimize.BFGSLineSearch> is now the default (QuasiNewton==BFGSLineSearch).
  • There is a new interface to the LAMMPS molecular dynamics code.
  • New ase.phonons module.
  • Van der Waals corrections for DFT, see GPAW usage.
  • New 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 ~/.ase/gui.py.
  • Database library 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.

Version 3.4.1

11 August 2010: 3.4.1.