Release notes
Git master branch
Added
ase.calculators.fd.FiniteDifferenceCalculator
(MR: !3509)Improved
find_optimal_cell_shape()
to be rotationally invariant (MR: !3404)Added
ase.md.bussi.Bussi
(MR: !3350)
Version 3.23.0
31 May 2024: 3.23.0
Add
FixSubsetCom
to fix the center of mass of the specified subset of atoms (MR: !3193).Add the
indices
option toase.Atoms.get_center_of_mass()
to compute the center of mass of the specified subset of atoms (MR: !3193).All saddle-point search and minimum-energy path methods have been moved into a new
ase.mep
module. You should start importing from this location; e.g.,from ase.mep import NEB, DyNEB
(MR: !2974).Fix
ase.constraints.FixCom.adjust_momenta()
to have no center-of-mass momentum (MR: !2947)ase.build.surface.graphene()
now takes athickness
argument (MR: !2963)ase.build.bulk()
now assigns initial magnetic moments to BCC Fe, Co, and Ni.ase.build.make_supercell()
can now control how to order the atoms in the supercell via the optionorder
(MR: !2800)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.The
Cell
object now hasnormal()
andnormals()
which calculate normal vectors to one or all pairs of cell vectors. Also addedarea()
andareas()
, which return the area spanned by one or all pairs of cell vectors.New
a2b
andperiodic
formats forFormula
objects. Seease.formula.Formula.format()
. Theabc
format has been renamed toab2
.IO formats can now be implemented in separate packages and registered in ase with the entry point
ase.ioformats
in the external package configuration. This entry point only accepts objects of the typeExternalIOFormat
.ase.phonons.Displacement
now has acomm
keyword argument to better support parallelization.Fix
ase.build.rotate.minimize_rotation_and_translation()
for systems with periodic boundary conditions.Fix
ase.io.db.row.AtomsRow.charge()
, which was looking forinital_charges
instead ofinitial_charges
.Fixed definition of the Lennard-Jones potential in
ase.utils.ff
(MR: !2842)The
x3d
viewer has improved aesthetics (MR: !2831)Added a function,
ase.dft.kpoints.mindistance2monkhorstpack()
, to construct a Monkhorst-Pack grid (MR: !2811)Fixed turbomole calculator parsing issues when \(=\) are present in data groups (MR: !2808)
Fixed round-trip dict (de)serialization with
FixedMode
constraint (MR: !2801)Show total number of rows in ASE database (MR: !2797)
Fix units of magnetic moments in ASE database (MR: !2793)
General improvements to POVRay colors (MR: !2775, MR: !2767)
Remove deprecated CLI functions, such as the old
ase-gui
command (MR: !2770)Fix calculation of stresses in
ase.stress.full_3x3_to_voigt_6_stress()
(MR: !2765)Add polarization parser for FHI-AIMS calculator (MR: !2763)
Fix bug in
ase.atoms.Atoms.get_center_of_mass()
(MR: !2712)Fix multiprocessing bug with
ase.neb.NEB
(MR: !2695)NEB calculations now call
get_forces()
instead ofget_potential_energy()
followed byget_forces()
to prevent duplicate work (MR: !2678)Improve performance of
ase.build.supercells.make_supercell()
for large supercells (MR: !2639)Fix conservation of momentum in
ase.md.langevin.Langevin
(MR: !2632)Fix bug in
ase.vibrations.Vibrations
causing property calculations to always use the default method (MR: !3012)Replaced
ase.phasediagram.Pourbaix
class (to be deprecated) with thease.pourbaix
module. The latter includes a \(~ase.pourbaix.Pourbaix\) class able to plot a complete diagram given a set of references. The decomposition energy is now shown on a colormap and the phase boundaries are determined with a plane intersection method. (MR: !3280)
Calculators:
Remove
ase.calculators.vasp.vasp_auxiliary.xdat2traj
. Usease.io
instead (MR: !2948)Created new module
ase.calculators.harmonic
with thease.calculators.harmonic.HarmonicCalculator
for calculations with a Hessian-based harmonic force field. Can be used to compute Anharmonic Corrections to the Harmonic Approximation.Created new
ase.calculators.plumed.Plumed
that is an interface between ASE and Plumed for carrying out enhanced sampling methods and MD postprocessing.ase.calculators.kim.kimmodel.KIMModelCalculator
updated 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).ase.calculators.mopac.MOPAC
updated to support MOPAC version 22, which was released under GPL in May 2022. When using this MOPAC version or newer, the output “final heat of formation” will be interpreted as potential/free energy for ASE purposes.Fix ordering of kpoint and spin indices in
ase.calulators.abc.GetOutputsMixin.get_eigenvalues()
ase.calculators.vasp.Vasp
now supports theefermi
andnelmgw
.The
ase.calculators.orca.ORCA
calculator has been refactored to be based onase.calculators.GenericFileIOCalculator
.The
ase.calculators.abinit.AbinitProfile
now correctly executes in the user-specified directory.Fix reading of eigenvalues in
ase.calculators.dftb
(MR: !2819)Added an
energies
property to thelammpslib
calculator (MR: !2799)ase.calculator.lammpslib.is_upper_triangular()
is deprecated. Use the method outlined in this StackOverflow post (MR: !3102)ase.calculator.lammpslib.convert_cell()
is deprecated. Please usease.calculators.lammps.coordinatetransform.calc_rotated_cell()
instead. (MR: !3102)Fix
lsubsrot
typo in VASP calculator tolsubrot
(MR: !2762)Fix atomic polarizability for boron in
ase.calculators.bond_polarizability.LippincottStuttman
(MR: !2759)dielectric_tensor
andborn_effective_charges
parsing have been added to the aims and VASP calculators (MR: !2750)Update MOPAC calculator to support v22 (MR: !2745)
Fix ordering of forces in
lammpsrun
calculator when used with MPI (MR: !2737)FLEUR calculator has been removed in favor of external package (MR: !2736)
Compatability fixes for newer versions of Octopus (MR: !2734)
Fixed conversion of force units between LAMMPS and ASE (MR: !2720)
ORCA calculator now returns the correct energy in internal geometry optimizations (MR: !2699)
Support for 24Mar2022 version of LAMMPS in
lammpsrun
calculator (MR: !2693)DFTB+ calculator now supports the use of an xTB Hamiltonian (MR: !2682)
Fix WIEN2K writer when
rmt
is notNone
(MR: !2677)CP2K calculator support for libcx inputs (MR: !2676)
Fix bug in
ase run --equation-of-state
(MR: !2675)Support PBCs in Plumed calculator (MR: !2671)
Support z-matrix format for
FixCartesian`
constraints in Siesta (MR: !2669)Support spin-orbit coupling and non-colinear calculations in Siesta (MR: !2665, MR: !2665)
Support
k_grid_density
keyword in FHI-AIMS calculator (MR: !2662)Fix storing of
special_params
in VASP calculator (MR: !2661)Fix VASP OUTCAR parsing for systems with over 10 unique elements (MR: !2658)
Cache all available properties in the mixing calculators (MR: !2646)
Refactoring and bug fixes for
ase.calculators.dftd3.DFTD3
(MR: !2615)Added
ase.calculators.vasp.Vasp.read_vib_modes()
andase.calculators.vasp.Vasp.get_vibrations()
to read VASP-calculated vibrational modes (MR: !2605)
ase.calculators.nwchem.NWChem
now supports making initial guesses for wavefunctions using smaller basis sets and faster theoriesase.calculators.nwchem.NWChem
added support for direct and RI-MP2 computations.
Algorithms:
Fix bugs in
PrimitiveNeighborList
when used withbothways=True
and eitherself_interaction=True
orsorted=True
(MR: !3239)Change
ase.optimize.optimize.Dynamics.irun()
so that it yields its convergence status after logging and dumping for the corresponding step (issue: #1339; MR: !3072)ExpCellFilter
is deprecated. UseFrechetCellFilter
instead. (MR: !2981)Fix inconsistency of
mask
inFixCartesian
between the argument and the attribute. (MR: !3195)
Optimizers:
Add
ase.optimize.climbfixinternals.BFGSClimbFixInternals
class for transition state search and optimization along internal reaction coordinates (MR: !2299)ase.optimize.optimize.Optimizers.irun()
andase.optimize.optimize.Optimizers.run()
now respectsteps=0
(issue: #1183; issue: #1258; MR: !2922).Added the
.trajectory
attribute toase.optimize.optimize.Dynamics
(MR: !2901).Fixed a bug when
ase.optimize.precon.precon.PreconImages
is initialized with a list ofprecon
objects (MR: !2875)ase.optimize.mdmin.MDMin
now takes in amaxstep
parameter that directly restricts how much atoms can move in a single optimization step (MR: !3065).Removed
Berny
optimizer (MR: !3151)
Thermochemistry:
All thermochemistry modules now sort the vibrational energies before cutting them down to the physically appropriate amount.
I/O:
Add support for reading Mulliken, Löwdin, or Hirshfeld atomic charges in
ase.io.gaussian.read_gaussian_out()
(MR: !3332)Add support for reading POSCAR files with negative and multiple scaling factors in
ase.io.vasp.read_vasp()
(MR: !3029)Fix parsing of dipole moment in
ase.io.nwchem
from output files with trailing spaces (MR: !3018)Fix to read and write a compressed trajectory file like
xxx.traj.gz
(MR: !2997)Fix
index
ofase.io.vasp.read_vasp_xdatcar()
to be consistent withase.io.read()
(MR: !2993)Change
write_lammps_data
not to reshape the cell by default (MR: !2986)Fix
ase.io.lammpsdata.write_lammps_data()
to tilt the cell correctly (MR: !2986)GaussView-formatted
.mol
files can now be read (MR: !2956)Reading of “chemical json” file types is assigned to names
*.cjson
as used in avogadro2Fixes
IndexError
whenlammps_data_to_ase_atoms()
is run on a system with 1 atom.Added several missing
__init__
parameters toself
inase.io.trajectory.TrajectoryReader
andase.io.trajectory.TrajectoryWriter
.Add an option to
ase.io.lammpsdata.write_lamps_data()
to print the atomic masses.Add support for reading CUBE files with “negative” number of atoms, as is common in Gaussian.
Fix parsing of periodic boundary conditions for
extxyz
format.Increase compatibility of CIF parser
Extended XYZ writer now works with
GenericFileIOCalculator
Add numerical stress skips for SCF re-initialization in
ase.io.aims.AimsOutCalcChunk
.Deprecated calling
ase.io.aims.write_aims()
withvelocities
. Usewrite_velocities
instead (MR: !2910).Fix
ValueError
that was raised when using quaternions withase.io.lammpsrun.lammps_data_to_ase_atoms()
.ase.io.castep.CASTEP
now suports reading.castep
force blocksase.io.castep.CASTEP
no longer reads symmetry operations.Added
ase.io.abinit.read_abinit_gsr()
to read a netcdf file (MR: !2855)SDF reader can now read file with >100 atoms (MR: !2845)
ase.io.v_sim.read_v_sim()
now properly accounts for periodic boundary conditions (MR: !2835)Bug fix in the
ase.io.aims
parser for reading the eigenvalues (MR: !2825)Recognize
.castep
files from Materials Studio (MR: !2822)Enable reading of GPAW stresses from gpaw-out file (MR: !2798)
Add support for reading a VASP VTST CENTCAR file (MR: !2751)
Fix I/O for FHI-aims when the minimal basis set is used (MR: !2738)
Fix XYZ read/write round-trip when initial and final charges are set (MR: !2692)
CASTEP I/O can now read/write custom masses (MR: !2686)
Default dmol3 extension for arc files is now .arc (MR: !2686)
Add PBC support for
ase.io.cube
(MR: !2679)Fix
sort_by_id=True
setting inase.io.lammpsdata.read_lammps_data()
(MR: !2660)More robust GPAW log file reading (MR: !2609)
Fix for PDB file I/O involving trajectories (MR: !2598)
Improved XCrysden file I/O (MR: !2594)
Fix JSON encoder for Atoms objects with
FixAtoms
constraints (MR: !2592)Removed
ase.io.gaussian_reader
(MR: !2329)
Version 3.22.1
1 December 2021: 3.22.1
Fixed compatibility of Brillouin zone plotting with matplotlib 3.5+.
Version 3.22.0
24 June 2021: 3.22.0
Calculators:
ase.calculators.qmmm.ForceQMMM
was 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
Abinit
together withSocketIOCalculator
. Requires Abinit 9.4+.It is now possible to pass a function to
SocketIOCalculator
to customize startup of a socket client. This decouples socket I/O calculators fromFileIOCalculator
.Added
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.
Algorithms:
Dedicated class
ase.vibrations.VibrationsData
to improve the representation of vibrational modes and associated data.Major refactoring of
ase.vibrations.Vibrations
. The calculated vibrational data can now be exported as aVibrationsData
object.phonons.get_dos()
now returns a DOS object based on the new framework inase.spectrum
.ase.vibrations.Vibrations
andase.phonons.Phonons
now 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; seepython3 -m ase.vibrations.pickle2json --help
.Added
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.NEB
has 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
apply_constraint=True
orFalse
toase.neb.NEB.interpolate()
orase.neb.interpolate()
to choose a specific behaviour and silence the error.3D Brillouin zone plots are now guaranteed isometric with Matplotlib 3.3+.
I/O:
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
*.cml
is enabled.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,
siesta-xv
.Parsing an OUTCAR file will now produce an Atoms object with periodic boundary conditions.
Breaking changes:
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.
GUI:
Added Finnish translation.
Bug fixes:
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.info
would subtly change type when saved to JSON and reloaded.
Web-page:
There used to be two versions of the ASE web-page which was quite confusing. The https://wiki.fysik.dtu.dk/ase/dev/ web-page has now been dropped. There is now only https://wiki.fysik.dtu.dk/ase/ and it documents the use of the in development version of ASE.
Version 3.21.1
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
'vasp'
as intended.Fix attribute error in
write_jmol()
.
Version 3.21.0
18 January 2021: 3.21.0
General changes:
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
Atoms
as they can be replaced by~ase.cell.Cell
:atoms.get_cell_lengths_and_angles()
,atoms.get_reciprocal_cell()
,atoms.number_of_lattice_vectors
. Instead useatoms.cell.cellpar()
,atoms.cell.reciprocal()
, andatoms.cell.rank
, respectively.Removed deprecated code on
Atoms
for handling angles in radians.get_velocities()
will now return zeros rather thanNone
when 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.io.bundletrajectory.BundleTrajectory
andase.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 byase.utils.xwopen()
which is a contextmanager and ensures that the file is closed correctly.Clusters created by
ase.cluster
will 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
ase.spectrum.band_structure
.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.
Command-line interface:
Added
ase exec
sub-command for the ase command line interface.
Algorithms:
Removed
ase.build.voids
(MR: !2078)Removed unused code in
ase.transport.tools
(MR: !2077)Removed
ase.visualize.primiplotter
andase.visualize.fieldplotter
(MR: !2060)Changed units for molecular dynamics modules. They now accept the temperature in Kelvin as a keyword-only argument
temperature_K
and Berendsen NPT accepts the pressure in eV/ų as a keyword-only argumentpressure_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.
Refactored
ase.neb.NEB
.The linear interpolation (
ase.neb.interpolate()
) between images now supports cell-interpolation and the use of scaled positions.SingleCalculatorNEB
is deprecated. Usease.neb.NEB(allow_shared_calculator=True)
instead.Extended constraint
ase.constraints.FixInternals
by possibility to fix linear combinations of bond lengths.FixInternals
constraints now support constraining linear combinations of angles or dihedrals. It is also possible to slice atoms objects withFixInternals
constraints on them.Added
ase.build.connected
which finds groups of connected atoms inside anAtoms
object.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
Phonons
.
Calculators:
Removed
ase.calculators.ase_qmmm_manyqm
(MR: !2092)The
ignore_bad_restart_file
argument supported by many calculators has been deprecated. The user should choose this kind of behaviour explicitly.Cleaned up and fixed multiple issues with
ELK
calculator.Make-shift cleanup and fixes for
Exciting
calculator.ase.calculators.abinit.Abinit
updated to work with Abinit 9.Improved cleanup of old socket files under some types of failure with
ase.calculators.socketio.SocketIOCalculator
.Vasp
now uses the newer implementation formerly known asVasp2
.Vasp2
is deprecated.Added smooth cutoff option to
ase.calculators.lj.LennardJones
. This makes the forces continuous as atoms move past the cutoff radius.LennardJones
is 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, )
I/O:
Removed
ase.io.iwm
(MR: !2064)Removed
ase.io.plt
(MR: !2057)Reads Wannier90
.wout
files. Seease.io.wannier90.read_wout()
andase.io.wannier90.read_wout_all()
.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.
Added
ase.io.cif.CIFBlock
for direct access to data inside a CIF, andase.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.
Development:
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.
Version 3.20.1
11 August 2020: 3.20.1
Minor fix related to package version requirements on pypi.
Version 3.19.3
11 August 2020: 3.19.3
Minor fix related to package version requirements on pypi.
Deprecated calling the
ase.optimize.fire.FIRE
constructor withmaxmove
; please usemaxstep
(MR: !1725).
Version 3.20.0
8 August 2020: 3.20.0
General changes:
Removed old
ase.data
modules (MR: !1720)get_calculator()
andset_calculator()
are deprecated. Useatoms.calc
instead.del atoms.calc
is deprecated. Useatoms.calc = None
instead.The deprecated
atoms.cell.pbc
has been removed.More utility methods for
atoms.symbols
:species()
,search()
,indices()
.
Development:
Test suite now uses pytest. This means it requires pytest and optionally pytest-xdist for parallelization. The
ase test
command works as before although its output will be different and improved.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.
Algorithms:
Removed
ase.build.adsorb
(MR: !1845)Removed unused code in
ase.utils.ff
(MR: !1844)Removed
ase.utils.extrapolate
(MR: !1808)Functions for attaching structures in
attach
introduced.Standardize optimizers maximum step variable name to maxstep and default value to 0.2 for all optimizers.
Added
Pyberny
geometry 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. (MR: !1692)
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.NEBTools
now 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 asase 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 viaase.neb.NEB.interpolate()
.Reduced code duplication in the
ase.ga
module by incorporating the ‘bulk’ GA functionality into the corresponding ‘standard’ modules. Using the now deprecated ‘bulk’ GA modules (i.e.ase.ga.bulk_startgenerator
,ase.ga.bulk_crossovers
,ase.ga.bulk_mutations
andase.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.
Command-line interface:
New
dimensionality
sub-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.cli.template
.
I/O:
The
ase db db1.db <selection> --insert-into db2.db
command now respects--limit
and--offset
.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. (MR: !1892)
GUI:
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.
Calculators:
Multiple improvements and bugfixes to OpenMX calculator; OpenMX calculator now supports OpenMX 3.9.
Added
ORCA
calculator.Added
GAMESS-US
calculator.Removed interface to Dacapo due to lack of users and maintainers. (MR: !1721, MR: !1604)
Completely refactored
Gaussian
calculator. The new calculator should be completely backwards compatible with the previous one, while having a more flexible design and supporting more keyword arguments.Added
GaussianOptimizer
andGaussianIRC
classes 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.Fixed
kpts
option ofase.calculators.espresso.Espresso
so that specifying a Γ-point calculation withkpts=(1, 1, 1)
does not enable the optimized codepath (which halves memory and cpu). Usekpts=None
to enable the optimized codepath.Added the properties
stresses
andenergies
to the Lennard-Jones potentialase.calculators.lj.LennardJones
. Functionality for other properties should be unchanged. Testing and documentation have also been expanded.
Version 3.19.2
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
matplotlib.use()
.Deprecated calling
ase.calculators.vasp.vasp2.Vasp2
constructor with directory inlabel
parameter (MR: !1940)
Version 3.19.1
4 April 2020: 3.19.1
Update png writer to be compatible with matplotlib 3.2.
Version 3.19.0
16 December 2019: 3.19.0
General changes:
ase.build.bulk()
now supports elements with tetragonal and rhombohedral lattices.The
rank
andsize
constants from thease.parallel
module have been deprecated. Useworld.rank
andworld.size
instead (andfrom ase.parallel import world
).atoms.set_masses('most_common')
now sets the masses of each element according to most common isotope as stored inase.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 acceptsvelocities
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
, andase.constraints.FixCartesianParametricRelations
toase.constraints
. These constraints are based off the work in: arXiv: 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’sBandStructure
utilities. To facilitate these changes, the format of the calculator keywords has been changed. Please read the updatedNWChem
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 arbitrarycalculators
.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 peratoms.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 ofnp.float64
.The
pov
module can now render high-order bonds.Atoms
now provides the general-purpose JSON mechanism fromase.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.
Deprecated
ase.calculator.siesta.base_siesta
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. Useatoms.pbc
instead; this works the same as always. Also, theCell
object now exposes almost the entirendarray
interface. For a list of smaller bugfixes, see the git log.Deprecated
ase.Atoms.get_number_of_atoms
(MR: !1295)
Version 3.18.0
19 July 2019: 3.18.0
General changes:
ASE no longer supports Python2.
atoms.cell
is now aCell
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, likeatoms.symbols
, now have aformula
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 aBandPath
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 Genetic algorithm search for bulk crystal structures.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
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 ofatoms.numbers
, but based on chemical symbols. This enables convenient shortcuts such asmask = atoms.symbols == 'Au'
oratoms.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 theDOS
andBandStructure
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 thanUnitCellFilter
.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. Thecastep_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
anddftb
now support theBandStructure
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 thease.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
andmp4
are now recognized output formats.
Database:
The
ase.db.core.Database.write()
method now takes aid
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 withdirect=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
If you are running your Python script in
parallel
then by default,ase.io.read()
andase.io.iread()
will read on the master and broadcast to slaves, andase.io.write()
will only write from master. Use the new keywordparallel=False
to read/write from the individual slaves.New
ase find
command for finding atoms in files.Added
Espresso
calculator for Quantum ESPRESSO in modulease.calculators.espresso
.The
ase.dft.kpoints.get_special_points()
function has a new call signature: Before it wasget_special_points(lattice, cell)
, now it isget_special_points(cell, lattice=None)
. The old way still works, but you will get a warning.The
ase.dft.dos.DOS
object will now use linear tetrahedron interpolation of the band-structure if you setwidth=0.0
. It’s slow, but sometimes worth waiting for. It uses thease.dft.dos.linear_tetrahedron_integration()
helper function.ase.io.read()
can now read QBox output files.The
ase.calculators.qmmm
module can now also use Turbomole andDFTB+
as the QM part.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.Get the
Spacegroup
object from anAtoms
object with the newase.spacegroup.get_spacegroup()
function.
Version 3.14.1
28 June 2017: 3.14.1.
Calling the
ase.dft.bandgap.bandgap()
function withdirect=True
would return band indices that were off by one. Fixed now.
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
andlayout
.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 ofAtoms
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()
andase.utils.formula_metal()
.The
ase.dft.bandgap.get_band_gap()
function is now deprecated. Use the new one calledase.dft.bandgap.bandgap()
(it’s more flexible and returns also band indices).
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 argumentcomplete
. Useatoms.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 functionase.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 thevacuum
keyword that all of the 0-d, 1-d and 2-d functions have or, equivalently, call thecenter()
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]
). Usevacuum=<half-the-interlater-distance>
to get something similar to the old behavior.New
ase.geometry.is_orthorhombic()
andase.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.
New
ase.constraints.ExternalForce
constraint.Updated
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
ase.calculators.checkpoint
module. Adds restart and rollback capabilities to ASE scripts.Two new flawors of
NEB
calculations have been added:method='eb'
andmethod='improvedtangent'
.ase.io.write()
can now write XSD files.Interfaces for deMon, Amber and ONETEP added.
New Tools for defect calculations tutorial and new super-cell functions:
get_deviation_from_optimal_cell_shape()
,find_optimal_cell_shape()
,make_supercell()
.New
BandStructure
object. Can identify special points and create nice plots.Calculators that inherit from
ase.calculators.calculator.Calculator
will now have aband_structure()
method that creates aBandStructure
object.Addition to
geometry
module:crystal_structure_from_cell()
.New functions in
ase.dft.kpoints
module:parse_path_string()
,labels_from_kpts()
andbandpath()
.Helper function for generation of Monkhorst-Pack samplings and BZ-paths:
ase.calculators.calculator.kpts2ndarray()
.Useful class for testing band-structure stuff:
ase.calculators.test.FreeElectrons
.The
cell
attribute of anAtoms
object and thecell
keyword for theAtoms
constructor and theset_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 correspondingget_cell_lengths_and_angles()
method.Galician translation of ASE’s GUI.
Two new preconditioned structure optimizers available. See
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: 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:
ase.utils.eos
moved toase.eos
ase.calculators.neighborlist
moved toase.neighborlist
ase.lattice.spacegroup
moved toase.spacegroup
The
InfraRed
that used to be in thease.infrared
orase.vibrations.infrared
modules is now calledInfrared
and should be imported from thease.vibrations
module.Deprecated modules:
ase.structure
,ase.utils.geometry
,ase.utils.distance
,ase.lattice.surface
. The functions from these modules that will create and manipulateAtoms
objects are now in the newase.build
module. The remaining functions have been moved to the newase.geometry
module.The
ase.lattice.bulk()
function has been moved toase.build.bulk()
.Two new functions:
cell_to_cellpar()
andcellpar_to_cell()
.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.
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.The
ase.io.read()
function and command-line tools can now read.gz
and.bz2
compressed files.Two new decorators
parallel_function()
andparallel_generator()
added.Source code moved to https://gitlab.com/ase/ase.
Preliminary
ase.calculators.qmmm
module.Improved
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.
New
ase.dft.kpoints.get_special_points()
function.New
ase.geometry.get_duplicate_atoms()
function for finding and removing atoms on top of each other.New: A replacement
Siesta
calculator was implemented. It closely follows thease.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: 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.
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.The
ase.lattice.bulk
function can now build the Wurtzite structure.The
ase.utils.timing.Timer
was moved from GPAW to ASE.New
ase.db
module.New functions:
ase.build.fcc211()
andase.visualize.mlab.plot()
.New
Atoms
methods:ase.Atoms.get_distances()
andase.Atoms.get_all_distances()
.Bash completion can now be enabled.
Preliminary support for Python 3.
Wrapping: new
ase.Atoms.wrap()
method andase.geometry.wrap_positions()
function. Also addedwrap=True
keyword argument toase.Atoms.get_scaled_positions()
that can be used to turn off wrapping.New improved method for initializing NEB calculations:
ase.neb.NEB.interpolate()
.New pickle-free future-proof trajectory file format added: The TrajectoryReader and TrajectoryWriter objects.
We can now do Phase diagrams and Pourbaix diagrams.
New
ase.build.mx2()
function for 1T and 2H metal dichalcogenides and friends.New
ase.dft.bandgap.get_band_gap()
functionCP2K
interface.
Version 3.8.0
22 October 2013: 3.8.0.
ASE’s
gui
renamed fromag
toase-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.
ASE’s GUI can now be configured to be more friendly to visually impaired users: High contrast settings.
The
ase.neb.NEB
object 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.
New
set_initial_charges()
andget_initial_charges()
methods. Theget_charges()
method will now ask the calculator to calculate the atomic charges.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.
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 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:
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:
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.