Git master branch¶
ase.build.bulk()now assigns initial magnetic moments to BCC Fe, Co, and Ni.
mask()returns the mask of nonzero cell vectors, an array of three booleans.
reciprocal()now guarantees that cell vectors which are zero correspond to reciprocal cell vectors that are also zero. Previously the reciprocal cell vectors could have small nonzero values due to floating point tolerance.
Cellobject now has
normals()which calculate normal vectors to one or all pairs of cell vectors. Also added
areas(), which return the area spanned by one or all pairs of cell vectors.
ase.calculators.kim.kimmodel.KIMModelCalculatorupdated to allow users to change the parameters of OpenKIM portable models at run time (see https://openkim.org/doc/repository/kim-content/ for an explanation of types of OpenKIM models).
24 June 2021: 3.22.0
ase.calculators.qmmm.ForceQMMMwas updated to enable correct handling of various periodic boundary conditions. Functions to import and export files with QM/MM mapping were also added.
It is now possible to use
SocketIOCalculator. Requires Abinit 9.4+.
PySocketIOClient, a helper class for using the socket I/O calculator with Python clients.
OpenKIM calculator updated to support kimpy 2.0.0.
DFTB+ calculator now reads dipole moments.
ase.vibrations.VibrationsDatato improve the representation of vibrational modes and associated data.
Major refactoring of
ase.vibrations.Vibrations. The calculated vibrational data can now be exported as a
phonons.get_dos()now returns a DOS object based on the new framework in
ase.phonons.Phononsnow use a simplified caching system where forces for each displacement are saved in JSON files inside a subdirectory. This breaks old cached calculations. Old vibrations calculations can be ported using a migration tool; see
python3 -m ase.vibrations.pickle2json --help.
ase.md.contour_exploration.ContourExploration. It evolves systems at fixed potential energy. This is useful for tracing potential energy contour lines or rapidly exploring the potential energy surface of a system and can be tuned to preferentially sample highly curved regions of the potential energy surface.
ase.neb.NEBhas been overhauled and given support for preconditioning via a new \(precon\) argument to its constructor, and two newly supported methods, \(spline\) for spline-interpolated tangets and \(string\) for the string method, both of which support preconditioning. The default behaviour should be unchanged.
Interpolating NEB images on constrained atoms will now raise an error if the interpolated positions would become different depending on whether the constraints were applied. Pass
ase.neb.interpolate()to choose a specific behaviour and silence the error.
3D Brillouin zone plots are now guaranteed isometric with Matplotlib 3.3+.
Gaussian input file parsing has been greatly improved. The parser now extracts all variables from the input file.
Reading of “chemical json” file types with name
LAMMPS dump: Reading of elements column added, with priority over types if given. All four of the position specifier columns read correctly now.
Format readers that would by default read or write specific files into current working directory no longer do so. A path, whether absolute or relative, is now mandatory for all I/O functions.
The Siesta .XV format is now a recognized I/O format,
Parsing an OUTCAR file will now produce an Atoms object with periodic boundary conditions.
For security, ASE no longer uses pickle for any kind of file I/O. This is because a maliciously crafted pickle file can execute arbitrary code.
Features that used pickle now either use JSON, no longer support saving, or require a manual port of older pickle files using a migration tool. If you have many old calculations and rely on your own old (trusted) pickle files which cannot be loaded now, consider writing and contributing a migration tool for those files.
The old PickleTrajectory format can still be loaded by manually overriding the security check.
Pickle is still used for communication between processes started by ASE (such as plotting tools in the GUI), which is not a security problem since an attacker cannot tamper with the data unless the system is already compromised.
Added Finnish translation.
Fix deadlock with DFTD3 calculator in MPI calculations.
Fix parsing of Quantum Espresso outputs with more than 1000 atoms.
Write netcdf trajectories compatible with Amber 20.
Fix bug where constraints could be applied inconsistently in MD simulations.
Allow disabling thermostat and barostat in NPT molecular dynamics.
Fix problem with whitespace in CIF parser.
Fix a problem where constraints would be applied inconsistently in MD simulations. As the interactions between MD and constraints are not trivial, users should in general verify carefully that simulations behave physically correctly.
Fix issue where occupancies in
atoms.infowould subtly change type when saved to JSON and reloaded.
24 January 2021: 3.21.1
Fix incorrect positions written to CIF files with mixed boundary conditions.
Writing a CIF with only 1 or 2 lattice vectors will now raise an error since CIF cannot represent those systems.
The name of the Vasp calculator is now
Fix attribute error in
18 January 2021: 3.21.0
center()now centers around 0 along directions which do not have a cell vector. Previously this operation had no effect in those directions.
Deprecated the following methods on
Atomsas they can be replaced by
atoms.number_of_lattice_vectors. Instead use
Removed deprecated code on
Atomsfor handling angles in radians.
get_velocities()will now return zeros rather than
Nonewhen there are no velocities, consistently with other optionals such as momenta.
For security reasons, pickle will no longer be used for persistent file storage in the future. Pickle has so far been replaced with JSON in
ase.dft.stm.STM. All remaining use of pickle for persistent storage will be likewise replaced in next release. Users are advised as always not to open pickle-files from untrusted sources.
ase.utils.opencew()to be replaced by
ase.utils.xwopen()which is a contextmanager and ensures that the file is closed correctly.
Clusters created by
ase.clusterwill no longer have cell vectors and will be centered around (0, 0, 0). Previously they had a “tight” cell and coordinates centered with zero vacuum.
Refactored external viewers in
ase.visualize.view. Viewers will now clean up their temporary files correctly on non-UNIX platforms.
Band structure module moved to
New objects for working with DOS and collections of DOS in
ase.spectrum. To begin with, this will mostly be relevant for format readers that want to retrieve such objects from calculations.
ase execsub-command for the ase command line interface.
Changed units for molecular dynamics modules. They now accept the temperature in Kelvin as a keyword-only argument
temperature_Kand Berendsen NPT accepts the pressure in eV/Å³ as a keyword-only argument
pressure_au. The previous arguments are still available and still take temperature and pressure in whatever unit the module used to accept, but now issue a warning.
Made Andersen thermostat available for molecular dynamics simulation.
The linear interpolation (
ase.neb.interpolate()) between images now supports cell-interpolation and the use of scaled positions.
SingleCalculatorNEBis deprecated. Use
ase.constraints.FixInternalsby possibility to fix linear combinations of bond lengths.
ase.build.connectedwhich finds groups of connected atoms inside an
Optimizers and molecular dynamics objects, which may open trajectories or logfiles, can now be used as context managers. Doing so ensures correct closing of the files that they open.
Faster codepath for minimum-image convention (MIC) distance calculations with “well-behaved” unit cells. This improves the speed of neighbour lists and certain constraints.
Cleanup and deprecations of certain methods on
ignore_bad_restart_fileargument supported by many calculators has been deprecated. The user should choose this kind of behaviour explicitly.
Cleaned up and fixed multiple issues with
Make-shift cleanup and fixes for
ase.calculators.abinit.Abinitupdated to work with Abinit 9.
Improved cleanup of old socket files under some types of failure with
Vaspnow uses the newer implementation formerly known as Vasp2.
Added smooth cutoff option to
ase.calculators.lj.LennardJones. This makes the forces continuous as atoms move past the cutoff radius.
LennardJonesis now much more efficient.
Many calculators would change the working directory in order to facilitate work with files. However doing so breaks threading. This has been fixed for most calculators (abinit, lammpsrun, )
ase.io.pov.write_pov()no longer includes an option to run povray on top of the written output. Instead it returns a renderer which can be used like this:
png_path = write_pov('myfile.pov').render()
Refactored CIF reader and writer, adding more extensive testing and fixing multiple bugs.
CIF writer now uses up-to-date variable definitions from the CIF standard instead of deprecated ones. Also, it no longer writes columns of dummy data that doesn’t depend on the atoms.
ase.io.cif.CIFBlockfor direct access to data inside a CIF, and
ase.io.cif.parse_cif()to iterate over such blocks from a CIF.
Fixed many cases of careless I/O handling where format readers or writers would open files without necessarily closing them.
Vasp output formats return atoms with fully periodic boundary conditions as appropriate.
Vasp POSCAR/CONTCAR writer will now use the Vasp5 format by default.
Test suite now prints a descriptive header with dependency versions including a list of installed/enabled calculators.
All tests with random numbers now use a specific seed so as to run reproducibly.
CI now supports integration testing with many additional calculators. The full list of external calculators that can be integration-tested via CI is: Abinit, Asap, CP2K, DFTB, DFTD3, Elk, Espresso, Exciting, GPAW, Gromacs, Lammpslib, Lammpsrun, NWChem, Octopus, OpenMX, Siesta.
11 August 2020: 3.20.1
Minor fix related to package version requirements on pypi.
11 August 2020: 3.19.3
Minor fix related to package version requirements on pypi.
8 August 2020: 3.20.0
del atoms.calcis deprecated. Use
atoms.calc = Noneinstead.
atoms.cell.pbchas been removed.
More utility methods for
Many tests have been improved and simplified, making use of pytest for parametrization and test fixtures.
The continuous integration tests on Gitlab now use custom dockers. The docker files can be found at https://gitlab.com/ase/ase-dockers.
Some calculators can now be tested via Gitlab’s CI.
Code coverage statistics are now available on https://ase.gitlab.io/ase. They currently exclude calculators and IO formats.
Our CI now uses mypy for static analysis of the code.
Functions for attaching structures in
Standardize optimizers maximum step variable name to maxstep and default value to 0.2 for all optimizers.
Pybernygeometry optimizer. This optimizer can be very efficient for molecules, but is currently unreliable and therefore should be considered experimental.
Removed interface to FindSym due to lack of users and maintainers. If you need this, please find it in git history, make it work, and write tests.
The tangent estimates used to make the nudged elastic band (NEB) plots are slightly improved to use center, rather than forward differences. This does not affect how NEBs are run; only how they are displayed.
ase.neb.NEBToolsnow allows the simultaneous plotting of all bands from a trajectory of a nudged elastic band calculation (or similar); this funciton is also available at the command line as
ase nebplot neb.traj.
The image-dependent pair-potential (IDPP) interpolation scheme for connecting states—i.e., in a saddle-point search—has been moved into the method
ase.neb.idpp_interpolate(). This method is a more feature-rich version than that accessible via
Reduced code duplication in the
ase.gamodule by incorporating the ‘bulk’ GA functionality into the corresponding ‘standard’ modules. Using the now deprecated ‘bulk’ GA modules (i.e.
ase.ga.bulk_utilities) raises a warning with pointers to the corresponding ‘standard’ modules.
Extended the genetic algorithm to cases where 1 or 2 cell vectors are part of the global optimization problem, which can be useful in searching for nanowire and thin film structures.
Added a new tutorial on molecular crystal structure prediction using a genetic algorithm, see Genetic algorithm search for molecular crystal structures.
Allow setting the initial hessian in \(optimize.BFGS\) via the keyword \(alpha\) or explicitly via \(opt.H0 = ...\) after instantiation.
dimensionalitysub-command for the ase command line interface.
Added a diff CLI for displaying and comparing the positions, forces, and energies of atoms objects. The classes and functions used in the CLI are also available in
ase db db1.db <selection> --insert-into db2.dbcommand now respects
Read and write support for qball sys file format.
Added write support for the Vasp 5 XDATCAR file format.
Added Z-matrix parser for use in input/output file readers.
Added support for writing prismatic and computem xyz file. Required arguments to write mustem xtl file have been updated to be consistent with prismatic and computem xyz file export.
Removed ETSF format reader since it depends on ScientificPython which requires Python 2.7.
Removed Dacapo-NetCDF reader which has not worked since ancient times.
Use Ctrl+C, Ctrl+X, and Ctrl+V to copy/cut/paste atoms using the operating system’s clipboard. The copies use the JSON format.
Removed old GUI modules which were never fully ported to Tkinter. If you miss them, please find them in git history and rehabilitate them.
Added Russian translation.
Multiple improvements and bugfixes to OpenMX calculator; OpenMX calculator now supports OpenMX 3.9.
Removed interface to Dacapo due to lack of users and maintainers.
Gaussiancalculator. The new calculator should be completely backwards compatible with the previous one, while having a more flexible design and supporting more keyword arguments.
GaussianIRCclasses for performing geometry optimization and IRC calculations with the Gaussian calculator. These classes are the canonical way to use Gaussian’s built-in geometry optimization routines.
ase.calculators.espresso.Espressoso that specifying a Γ-point calculation with
kpts=(1, 1, 1)does not enable the optimized codepath (which halves memory and cpu). Use
kpts=Noneto enable the optimized codepath.
Added the properties
energiesto the Lennard-Jones potential
ase.calculators.lj.LennardJones. Functionality for other properties should be unchanged. Testing and documentation have also been expanded.
22 July 2020: 3.19.2
Compatibility fixes related to matplotlib: Update png writer to be compatible with matplotlib 3.3.0. Update incompatible calls to
4 April 2020: 3.19.1
Update png writer to be compatible with matplotlib 3.2.
16 December 2019: 3.19.0
ase.build.bulk()now supports elements with tetragonal and rhombohedral lattices.
sizeconstants from the
ase.parallelmodule have been deprecated. Use
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.utils.parsemathadded 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.
Atomsconstructor now accepts
Documentation: New set of introductory ASE tutorials.
More detailed output of
ase info --formats.
ase.latticenow also supports the 1D Bravais lattice.
DiffusionCoefficientso one can calculate atom/molecule mobility from trajectory as a function of time.
Added general linear parametric constraints
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.
ase.build.graphene()for building graphene monolayers.
ase.md.switch_langevinmodule for thermodynamic integration via MD simulations.
Implemented “dynamic” or “ideal gas” contribution from atomic momenta to stress tensor Use
Gulp calculator now provides stress tensor.
NWChemcalculator 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
BandStructureutilities. To facilitate these changes, the format of the calculator keywords has been changed. Please read the updated
NWChemcalculator documentation for more details.
Siestacalculator 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.
ase.calculators.idealgas.IdealGascalculator for non-interacting atoms. The calculator does nothing. This can be useful for testing.
EMTcalculator now support atom-specific energies as per
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.dbdatabase. 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
povmodule can now render high-order bonds.
Atomsnow provides the general-purpose JSON mechanism from
ase.data.pubchemmodule to search for structures in the PubChem database.
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.
15 December 2019: 3.18.2
Fix an issue with the binary package (wheel) of 3.18.1. No bugfixes as such.
20 September 2019: 3.18.1
Multiple bugfixes. Most importantly, deprecate
atoms.cell.pbcin order to avoid complexities from dealing with two ways of manipulating this piece of information. Use
atoms.pbcinstead; this works the same as always. Also, the
Cellobject now exposes almost the entire
ndarrayinterface. For a list of smaller bugfixes, see the git log.
19 July 2019: 3.18.0
ASE no longer supports Python2.
atoms.cellis now a
Cellobject. This object resembles a 3x3 array and also provides shortcuts to many common operations.
Formulatype added. Collects all formula manipulation functionality in one place.
atoms.symbols, now have a
Added classes to represent primitive Bravais lattices and data relating to Brillouin zones to
ase.lattice. Includes 2D lattices.
BandPathclass to represent a band path specification like
'GXL'along with actual k-point coordinates.
BandStructureobjects now have a band path.
atoms.cell.bandpath()as a shortcut to generate band paths.
constraintfor trilinear molecules.
ase info --calculatorsoption which shows a list of calculators and whether they appear to be installed.
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.
ase testcommand now properly autocompletes test names and calculator names.
atoms.wrap(pretty_translation=True), to minimize the scaled positions of the atoms.
Added interface to
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
Octopuscalculator now provides the stress tensor.
LAMMPScalculator. 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.
ACN, a QM/MM forcefield for acetonitrile.
Improved eigenvalue parsing with Siesta calculator.
Determine Bravais lattice for any 2D or 3D cell using
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 toolfor extracting bond lengths and angles from atoms.
Dynamics and structure optimizers can now run as an iterator using the new
for conv in opt.irun(fmax=0.05): print('hello')
This makes it easier to execute custom code during runs. The
convvariable indicates whether the current iteration meets the convergence criterion, although this behaviour may change in future versions.
The genetic algorithm module
ase.ganow has operators for crystal structure prediction. See Genetic algorithm search for bulk crystal structures.
ase.geometry.dimensionality.analyze_dimensionality()function. See: Dimensionality analysis.
FixLinearTriatomicfor QM/MM calculations.
NeighborListnow uses kdtree from Scipy for improved performance. It also uses Minkowsky reduction to improve performance for unusually shaped cells.
Database supports user defined tables
Formulatype 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
Quickinfo dialog automatically updates when switching image.
Display information about custom arrays on Atoms objects; allow colouring by custom arrays.
Improved color scales.
12 November 2018: 3.17.0
atoms.symbolsis 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.
DOSobject 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.
Phononsclass now uses the
Positions and velocities can now be initialized from phononic force constant matrix; see
UnitCellFilternow supports scalar pressure and hydrostatic strain.
Compare if two bulk structure are symmetrically equivalent with
NEBnow 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
NEBcalculation is now much simpler. Works the same way as for the serial case.
FixComconstraint for fixing center of mass.
ase.calculators.qmmm.ForceQMMMforce-based QM/MM calculator.
Socked-based interface to certain calculators through the
socketiomodule: 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
Castepcalculator 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.pyfile 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.
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.nomadmodule to download and work with Nomad entries programmatically.
nomad-jsonis now a recognized IO format.
Sequences of atoms objects can now be saved as animations using the mechanisms offered by matplotlib.
mp4are now recognized output formats.
ase.db.core.Database.write()method now takes a
idthat allows you to overwrite an existing row.
ase.db.core.Database.update()can now update the Atoms and the data parts of a row.
ase.db.core.Database.update()method will no longer accept a list of row ID’s as the first argument. Replace this:
with db: for id in ids: db.update(id, ...)
--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.
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.
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.
21 March 2018: 3.16.0
New linear-scaling neighbor list available as a function
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
get_angles(), for calculating multiple angles.
ase reciprocalcommand for showing the 1. Brilluin zone, k-points and special points.
ase convertcommand for converting between file formats.
Improved XRD/SAXS module:
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.crystalcode has been added.
ase.dft.bandgap.bandgap()function used with
direct=Truewill 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.
28 September 2017: 3.15.0
If you are running your Python script in
parallelthen by default,
ase.io.iread()will read on the master and broadcast to slaves, and
ase.io.write()will only write from master. Use the new keyword
parallel=Falseto read/write from the individual slaves.
ase findcommand for finding atoms in files.
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.
ase.dft.dos.DOSobject 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
ase.io.read()can now read QBox output files.
New Surface adsorption study using the ASE database tutorial.
ase.gui: Improved atom colouring options; support the Render Scene (povray) and Ctrl+R rotation features again; updated German and Chinese translations.
28 June 2017: 3.14.1.
direct=Truewould return band indices that were off by one. Fixed now.
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 3.0to get the old behavior.
All methods of the
Atomsobject that deal with angles now have new API’s that use degrees instead of radians as the unit of angle (
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:
>>> 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)
>>> 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 PostgreSQL backend for
ase.dbcan 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:
ase.data.atomic_masseshas 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])
ase.data.isotopes.download_isotope_data()function for getting individual isotope masses from NIST.
ase.eos.calculate_eos()helper function added.
Added DeltaCodesDFT data:
Trajectory files can now store any sequence of
Atomsobjects. 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:
New band-structure command for the ase Command line tool.
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).
7 February 2017: 3.13.0.
The default unit-cell when you create an
Atomsobject has been changed from
ase.Atoms.number_of_lattice_vectorsattribute equal to, big surprise, the number of non-zero lattice vectors.
ase.Atoms.get_cell()method has a new keyword argument
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.buildmodule) 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
vacuumkeyword that all of the 0-d, 1-d and 2-d functions have or, equivalently, call the
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.
ase.guinow works on Python 3.
NEB-tools class has been renamed to
Optimizersnow try force-consistent energies if possible (instead of energies extrapolated to 0.0 K).
24 October 2016: 3.12.0.
ase.unitsdefinition 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).
ase.calculators.checkpointmodule. Adds restart and rollback capabilities to ASE scripts.
Two new flawors of
NEBcalculations have been added:
ase.io.write()can now write XSD files.
Interfaces for deMon, Amber and ONETEP added.
BandStructureobject. Can identify special points and create nice plots.
Helper function for generation of Monkhorst-Pack samplings and BZ-paths:
Useful class for testing band-structure stuff:
cellattribute of an
Atomsobject and the
cellkeyword for the
Atomsconstructor and the
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
Galician translation of ASE’s GUI.
Two new preconditioned structure optimizers available. See
Trajectory files now contain information about the calculator and also information from an optimizer that wrote the trajectory.
10 May 2016: 3.11.0.
ase.collectionsmodule added. Currently contains the G2 database of molecules and the S22 set of weakly interacting dimers and complexes.
ase.lattice.surface. The functions from these modules that will create and manipulate
Atomsobjects are now in the new
ase.buildmodule. The remaining functions have been moved to the new
ase.lattice.bulk()function has been moved to
NEBimprovement: calculations for molecules can now be told to minimize ratation and translation along the path.
17 Mar 2016: 3.10.0.
PickleTrajectory files can no longer be used. See Converting old PickleTrajectory files to new Trajectory files.
New iterator function
ase.io.iread()for iteratively reading Atoms objects from a file.
ase.io.read()function and command-line tools can now read
Source code moved to https://gitlab.com/ase/ase.
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.
ase.geometry.get_duplicate_atoms()function for finding and removing atoms on top of each other.
New: A replacement
Siestacalculator was implemented. It closely follows the
ase.calculators.calculator.FileIOCalculatorclass which should ease further development. Handling pseudopotentials, basis sets and ghost atoms have been made much more flexible in the new version.
21 July 2015: 3.9.1.
Added function for finding maximally reduced Niggli unit cell:
Octopus interface added (experimental).
28 May 2015: 3.9.0.
Genetic algorithm implemented;
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.
ase.lattice.bulkfunction can now build the Wurtzite structure.
ase.utils.timing.Timerwas moved from GPAW to ASE.
Bash completion can now be enabled.
Preliminary support for Python 3.
New improved method for initializing NEB calculations:
New pickle-free future-proof trajectory file format added: The TrajectoryReader and TrajectoryWriter objects.
We can now do Phase diagrams and Pourbaix diagrams.
ase.build.mx2()function for 1T and 2H metal dichalcogenides and friends.
22 October 2013: 3.8.0.
New STM module.
Python 2.6 is now a requirement.
ase.build.bulkfunction is now deprecated. Use the new one instead (
We’re now using BuildBot for continuous integration: https://ase-buildbot.fysik.dtu.dk/waterfall
New interface to the JDFTx code.
13 May 2013: 3.7.0.
ASE’s GUI can now be configured to be more friendly to visually impaired users: High contrast settings.
ase.neb.NEBobject now accepts a list of spring constants.
Important backwards incompatible change: The
ase.build.surface()function now returns a right-handed unit cell.
Mopac, NWChem and Gaussian interfaces and EAM potential added.
The Calculator interface proposal has been implemented and 6 ASE calculators are now based on the new base classes.
ASE now runs on Windows and Mac.
Constrained minima hopping (global optimization) added to ASE.
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 explicitly.
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:
24 May 2011: 3.5.1.
Problem with parallel vibration calculations fixed.
13 April 2011: 3.5.0.
ase.optimize.BFGSLineSearch>is now the default (
There is a new interface to the LAMMPS molecular dynamics code.
Van der Waals corrections for DFT, see GPAW usage.
Stability and usability improvements.
Povray render facility.
Updated expert user mode.
Enabled customization of colours and atomic radii.
Enabled user default settings via
Database libraryexpanded 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.
11 August 2010: 3.4.1.