Release notes

Git master branch

master.

  • 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” function now accepts identifiers for molecules in 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, direst=True) for s in [0, 1])
    

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 have been replaced by a single ase command with sub-commands (see Command line tool).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 [Setyawana-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: Ticket #80.

Version 3.5.0

13 April 2011: 3.5.0.

  • Improved EMT potential: uses a NeighborList object and is now ASAP compatible.
  • 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.