Release notes

Git master branch

master.

  • Add FixSubsetCom to fix the center of mass of the specified subset of atoms (MR: !3193).

  • Add the indices option to ase.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 a thickness 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 option order (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 has normal() and normals() which calculate normal vectors to one or all pairs of cell vectors. Also added area() and areas(), which return the area spanned by one or all pairs of cell vectors.

  • New a2b and periodic formats for Formula objects. See ase.formula.Formula.format(). The abc format has been renamed to ab2.

  • 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 type ExternalIOFormat.

  • ase.phonons.Displacement now has a comm 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 for inital_charges instead of initial_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 of get_potential_energy() followed by get_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)

Calculators:

  • Accelerate EMT using NumPy more (MR: !3241)

  • Remove ase.calculators.vasp.vasp_auxiliary.xdat2traj. Use ase.io instead (MR: !2948)

  • Created new module ase.calculators.harmonic with the ase.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 the efermi and nelmgw.

  • The ase.calculators.orca.ORCA calculator has been refactored to be based on ase.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 the lammpslib 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 use ase.calculators.lammps.coordinatetransform.calc_rotated_cell() instead. (MR: !3102)

  • Fix lsubsrot typo in VASP calculator to lsubrot (MR: !2762)

  • Fix atomic polarizability for boron in ase.calculators.bond_polarizability.LippincottStuttman (MR: !2759)

  • dielectric_tensor and born_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 not None (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() and ase.calculators.vasp.Vasp.get_vibrations() to read VASP-calculated vibrational modes (MR: !2605)

Algorithms:

  • Fix bugs in PrimitiveNeighborList when used with bothways=True and either self_interaction=True or sorted=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. Use FrechetCellFilter instead. (MR: !2981)

  • Fix inconsistency of mask in FixCartesian 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() and ase.optimize.optimize.Optimizers.run() now respect steps=0 (issue: #1183; issue: #1258; MR: !2922).

  • Added the .trajectory attribute to ase.optimize.optimize.Dynamics (MR: !2901).

  • Fixed a bug when ase.optimize.precon.precon.PreconImages is initialized with a list of precon objects (MR: !2875)

  • ase.optimize.mdmin.MDMin now takes in a maxstep 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 of ase.io.vasp.read_vasp_xdatcar() to be consistent with ase.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 avogadro2

  • Fixes IndexError when lammps_data_to_ase_atoms() is run on a system with 1 atom.

  • Added several missing __init__ parameters to self in ase.io.trajectory.TrajectoryReader and ase.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() with velocities. Use write_velocities instead (MR: !2910).

  • Fix ValueError that was raised when using quaternions with ase.io.lammpsrun.lammps_data_to_ase_atoms().

  • ase.io.castep.CASTEP now suports reading .castep force blocks

  • ase.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 in ase.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)

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 with SocketIOCalculator. 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 from FileIOCalculator.

  • 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 a VibrationsData object.

  • phonons.get_dos() now returns a DOS object based on the new framework in ase.spectrum.

  • ase.vibrations.Vibrations and ase.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; see python3 -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 or False to ase.neb.NEB.interpolate() or ase.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:

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 use atoms.cell.cellpar(), atoms.cell.reciprocal(), and atoms.cell.rank, respectively.

  • Removed deprecated code on Atoms for handling angles in radians.

  • get_velocities() will now return zeros rather than None 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 and 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.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:

  • 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 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.

  • 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. Use ase.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 with FixInternals constraints on them.

  • Added ase.build.connected which finds groups of connected atoms inside an Atoms 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:

  • 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 as Vasp2. 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:

  • Reads Wannier90 .wout files. See ase.io.wannier90.read_wout() and ase.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, 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.

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 with maxmove; please use maxstep (MR: !1725).

Version 3.20.0

8 August 2020: 3.20.0

General changes:

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:

  • 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.

  • 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 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 ase.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 and 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.

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.

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.

  • 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 and GaussianIRC 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 of ase.calculators.espresso.Espresso so that specifying a Γ-point calculation with kpts=(1, 1, 1) does not enable the optimized codepath (which halves memory and cpu). Use kpts=None to enable the optimized codepath.

  • Added the properties stresses and energies to the Lennard-Jones potential ase.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 in label 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 and size constants from the ase.parallel module have been deprecated. Use world.rank and world.size instead (and from ase.parallel import world).

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

  • ase.utils.parsemath added to utils. This module parses simple mathematical expressions and returns their numerical value.

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

  • Atoms constructor now accepts velocities as keyword.

  • Documentation: New set of introductory ASE tutorials.

  • More detailed output of ase info --formats.

  • For completeness, ase.lattice now also supports the 1D Bravais lattice.

Algorithms:

  • Added DiffusionCoefficient so one can calculate atom/molecule mobility from trajectory as a function of time.

  • Added general linear parametric constraints ase.constraints.FixParametricRelations, ase.constraints.FixScaledParametricRelations, and ase.constraints.FixCartesianParametricRelations to ase.constraints. These constraints are based off the work in: 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’s BandStructure utilities. To facilitate these changes, the format of the calculator keywords has been changed. Please read the updated NWChem calculator documentation for more details.

  • Siesta calculator refactored. The Siesta calculator now supports the band structure machinery. There is only a single Siesta calculator now covering all versions of Siesta, consistently with other ASE calculators.

  • Added mixing module for the linear combination of arbitrary calculators.

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

  • EMT calculator now support atom-specific energies as per atoms.get_energies().

I/O:

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

  • Write support for Materials Studio xtd files.

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

  • The pov module can now render high-order bonds.

  • Atoms now provides the general-purpose JSON mechanism from ase.io.jsonio.

  • Added ase.data.pubchem module to search for structures in the PubChem database.

GUI:

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

Version 3.18.2

15 December 2019: 3.18.2

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

  • 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. Use atoms.pbc instead; this works the same as always. Also, the Cell object now exposes almost the entire ndarray interface. For a list of smaller bugfixes, see the git log.

  • 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 a Cell object. This object resembles a 3x3 array and also provides shortcuts to many common operations.

  • Preliminary Formula type added. Collects all formula manipulation functionality in one place.

  • Symbols objects, like atoms.symbols, now have a formula attribute.

  • Added classes to represent primitive Bravais lattices and data relating to Brillouin zones to ase.lattice. Includes 2D lattices.

  • New BandPath class to represent a band path specification like 'GXL' along with actual k-point coordinates. BandStructure objects now have a band path.

  • ase.dft.kpoints.bandpath() now returns a BandPath object. Generation of band paths now works for (almost) any cell.

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

  • New holonomic constraint for trilinear molecules.

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

  • Added ase.build.surfaces_with_termination.surfaces_with_termination(), a tool to build surfaces with a particular termination.

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

  • The ase test command now properly autocompletes test names and calculator names.

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

Calculators:

  • Added interface to ACE-Molecule.

  • NWChem calculator now supports TDDFT runs.

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

  • Calculation of stress tensor implemented for EMT potential.

  • The Octopus calculator now provides the stress tensor.

  • Reworked LAMMPS calculator. The calculator should now behave more consistently with other ASE calculators.

  • Gromacs calculator updated to work with newer Gromacs.

  • Fleur calculator updated to work with newer Fleur.

  • Added ACN, a QM/MM forcefield for acetonitrile.

  • Improved eigenvalue parsing with Siesta calculator.

Algorithms:

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

  • Added function to Minkowski reduce a cell.

  • Improved stability of Niggli reduction algorithm.

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

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

  • Analysis tool for extracting bond lengths and angles from atoms.

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

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

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

  • The genetic algorithm module ase.ga now has operators for crystal structure prediction. See 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 of atoms.numbers, but based on chemical symbols. This enables convenient shortcuts such as mask = atoms.symbols == 'Au' or atoms.symbols[4:8] = 'Mo'.

  • Test suite now runs in parallel.

  • New DOS object for representing and plotting densities of states.

  • Neighbor lists can now get connectivity matrices.

  • ase convert now provides options to execute custom code on each processed image.

  • Phonons class now uses the DOS and BandStructure machinery.

  • Positions and velocities can now be initialized from phononic force constant matrix; see PhononHarmonics().

Algorithms:

  • New Gaussian Process (GP) regression optimizer (GPMin). Check out this performance test.

  • New filter for lattice optimization, ExpCellFilter, based on an exponential reformulation of the degrees of freedom pertaining to the cell. This is probably significantly faster than UnitCellFilter.

  • UnitCellFilter now supports scalar pressure and hydrostatic strain.

  • Compare if two bulk structure are symmetrically equivalent with SymmetryEquivalenceCheck.

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

  • Writing a trajectory file from a parallelized NEB calculation is now much simpler. Works the same way as for the serial case.

  • New FixCom constraint for fixing center of mass.

Calculators:

  • Added ase.calculators.qmmm.ForceQMMM force-based QM/MM calculator.

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

  • Added calculator for OpenMX.

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

  • Espresso and dftb now support the BandStructure machinery including improved handling of kpoints, get_eigenvalues(), and friends.

I/O:

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

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

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

Database:

  • The ase.db.core.Database.write() method now takes a id that allows you to overwrite an existing row.

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

  • The ase.db.core.Database.update() method will no longer accept a list of row ID’s as the first argument. Replace this:

    db.update(ids, ...)

    with:

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

  • New --show-keys and --show-values=... options for the ase db command line interface.

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

GUI:

  • Added callback method ase.gui.gui.GUI.repeat_poll() to the GUI. Useful for programmatically updating the GUI.

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

  • Added Basque translation.

  • Added French translation.

Version 3.16.2

4 June 2018: 3.16.2

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

Version 3.16.0

21 March 2018: 3.16.0

  • New linear-scaling neighbor list available as a function neighbor_list().

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

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

  • Support for µSTEM xtl data format.

  • New scanning tunnelling spectroscopy (STS) mode for STM simulations.

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

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

  • New ase convert command for converting between file formats.

  • Improved XRD/SAXS module: ase.utils.xrdebye.

  • New cell editor for the GUI.

  • Improved “quick info” dialog in the GUI. The dialog now lists results cached by the calculator.

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

  • Interface for the CRYSTAL <ase.calculators.crystal code has been added.

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

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

  • Bug fixed in the ase.phonons.Phonons.symmetrize() method when using an even number of repeats.

Version 3.15.0

28 September 2017: 3.15.0

Version 3.14.1

28 June 2017: 3.14.1.

Version 3.14.0

20 June 2017: 3.14.0.

  • Python 2.6 no longer supported.

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

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

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

  • All methods of the Atoms object that deal with angles now have new API’s that use degrees instead of radians as the unit of angle (get_angle(), set_angle(), get_dihedral(), set_dihedral(), rotate_dihedral(), rotate(), euler_rotate()).

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

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

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

    Old API:

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

    New API:

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

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

  • The PostgreSQL backend for ase.db can now contain more than one ASE database.

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

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

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

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

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

  • Added DeltaCodesDFT data: ase.collections.dcdft.

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

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

  • Added calculator interface for DMol3.

  • Added calculator interface for GULP.

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

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

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

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

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

  • New Viewer for Jupyter notebooks.

Version 3.13.0

7 February 2017: 3.13.0.

  • The default unit-cell when you create an Atoms object has been changed from [[1,0,0],[0,1,0],[0,0,1]] to [[0,0,0],[0,0,0],[0,0,0]].

  • New ase.Atoms.number_of_lattice_vectors attribute equal to, big surprise, the number of non-zero lattice vectors.

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

  • graphene_nanoribbon() no longer adds 2.5 Å of vacuum by default.

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

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

  • New ase.geometry.is_orthorhombic() and ase.geometry.orthorhombic() functions added.

  • ase.gui now works on Python 3.

  • NEB-tools class has been renamed to NEBTools.

  • Optimizers now try force-consistent energies if possible (instead of energies extrapolated to 0.0 K).

Version 3.12.0

24 October 2016: 3.12.0.

Version 3.11.0

10 May 2016: 3.11.0.

  • Special \(\mathbf{k}\)-points from the [Setyawan-Curtarolo] paper was added: ase.dft.kpoints.special_points.

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

  • Moved modules:

  • The InfraRed that used to be in the ase.infrared or ase.vibrations.infrared modules is now called Infrared and should be imported from the ase.vibrations module.

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

  • The ase.lattice.bulk() function has been moved to ase.build.bulk().

  • Two new functions: cell_to_cellpar() and cellpar_to_cell().

  • We can now read() and write() magres files.

  • NEB improvement: calculations for molecules can now be told to minimize ratation and translation along the path.

Version 3.10.0

17 Mar 2016: 3.10.0.

Version 3.9.1

21 July 2015: 3.9.1.

  • Added function for finding maximally reduced Niggli unit cell: ase.build.niggli_reduce().

  • Octopus interface added (experimental).

Version 3.9.0

28 May 2015: 3.9.0.

Version 3.8.0

22 October 2013: 3.8.0.

  • ASE’s gui renamed from ag to ase-gui.

  • New STM module.

  • Python 2.6 is now a requirement.

  • The old ase.build.bulk function is now deprecated. Use the new one instead (ase.lattice.bulk()).

  • We’re now using BuildBot for continuous integration: https://ase-buildbot.fysik.dtu.dk/waterfall

  • New interface to the JDFTx code.

Version 3.7.0

13 May 2013: 3.7.0.

Version 3.6.0

24 Feb 2012: 3.6.0.

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

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

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

    • ase now contains only Atoms and Atom

    • ase.calculators is now empty

Version 3.5.1

24 May 2011: 3.5.1.

  • Problem with parallel vibration calculations fixed.

Version 3.5.0

13 April 2011: 3.5.0.

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

  • ase.optimize.BFGSLineSearch> is now the default (QuasiNewton==BFGSLineSearch).

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

  • New ase.phonons module.

  • Van der Waals corrections for DFT, see GPAW usage.

  • New BundleTrajectory added.

  • Updated GUI:

    • 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.