- Update to ase 3.22.1
  * Fixed compatibility of Brillouin zone plotting with matplotlib 3.5+.

• Files Changed
• Browse Source

- Update to ase 3.22.0
  * Calculators:
    - ase.calculators.qmmm.ForceQMMM was updated
    - use Abinit together with SocketIOCalculator. Requires Abinit 9.4+.
    - pass a function to SocketIOCalculator
    - Added PySocketIOClient
    - OpenKIM calculator updated to support kimpy 2.0.0.
    - DFTB+ calculator now reads dipole moments.
  * Algorithms:
    - Dedicated class ase.vibrations.VibrationsData
    - Major refactoring of ase.vibrations.Vibrations
    - phonons.get_dos() now returns a DOS object
    - ase.vibrations.Vibrations and ase.phonons.Phonons now use a
      simplified caching system. This breaks old cached calculations;
      see python3 -m ase.vibrations.pickle2json --help.
    - Added ase.md.contour_exploration.ContourExploration
    - ase.neb.NEB has been overhauled and given support for preconditioning
    - 3D Brillouin zone plots are now guaranteed isometric with Matplotlib 3.3+.
  * I/O:
    - Gaussian input file parsing has been greatly improved
    - Reading of “chemical json” file types with name *.cml is enabled.
    - LAMMPS dump: Reading of elements column added, with priority over types if given
    - For format readers a path 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.
    - Features that used pickle now either use JSON, no longer support saving, or require a manual port.
    - 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
  * 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.
    - Fix issue where occupancies in atoms.info would subtly change type when saved to JSON and reloaded.
- Update to ase 3.21.1
  * Some bug fixes
- Update to ase 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 radiuns.
    - 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.
    - get_velocities() will now return an array of zeros consistently with get_momenta() if not set. It previously returned None, which was an oversight.
    - 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.
    - 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.
- Update to ase 3.20.0
  * General changes:
    - get_calculator() and set_calculator() are deprecated. Use atoms.calc instead.
    - del atoms.calc is deprecated. Use atoms.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:
    - 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.
- Update to ase 3.19.2
  * Update png writer to be compatible with matplotlib 3.3.0.
- Update to ase 3.19.1
  * Update png writer to be compatible with matplotlib 3.2.
- Update to ase 3.19.0
  * General changes:
    - ase.build.bulk() now supports elements with tetragonal and 
      rhombohedral attices.
    - The rank and size constants from the ase.parallel module 
      have been deprecated. Use world.rank and world.size instead
      (and from ase.parallel import world).
    - atoms.set_masses('most_common') now sets the masses of each
      element according to most common isotope as stored in 
      ase.data.atomic_masses_common.
    - ase.utils.parsemath added to utils. This module parses simple
      mathematical expressions and returns their numerical value.
    - Plotting functions (such as band structure, EOS, …) no longer
      show the figure by default.
    - Atoms constructor now accepts velocities as keyword.
    - Documentation: New set of introductory ASE tutorials.
    - More detailed output of ase info --formats.
    - For completeness, ase.lattice now also supports the 1D Bravais lattice.
  * Algorithms:
    - Added DiffusionCoefficient so one can calculate atom/molecule
      mobility from trajectory as a function of time.
    - Added general linear parametric constraints based on the work 
      in: https://arxiv.org/abs/1908.01610, and allows for the positions
      and cell of a structure to be optimized in a reduced parameter space.
    - Added ase.build.graphene() for building graphene monolayers.
    - Added ase.md.switch_langevin module for thermodynamic
      integration via MD simulations.
    - Implemented “dynamic” or “ideal gas” contribution from atomic
      momenta to stress tensor Use <ase.Atoms.get_stress>(), e.g.,
      atoms.get_stress(include_ideal_gas=True).
  * Calculators:
    - Added Q-Chem calculator.
    - Added Psi4 calculator.
    - Added DemonNano calculator.
    - Added OpenKIM calculator, a special calculator for OpenKim models.
    - Gulp calculator now provides stress tensor.
    - The NWChem calculator has been completely rewritten, and now 
      supports DFT, SCF (Hartree Fock), MP2, CCSD, and TCE calculations 
      with gaussian-type orbitals. The calculator also now supports
      plane-wave calculations, including band structure calculations
      through ASE’s BandStructure utilities. To facilitate these changes,
      the format of the calculator keywords has been changed.
      Please read the updated NWChem calculator documentation for more details.
    - Siesta calculator refactored. The Siesta calculator now supports 
      the band structure machinery. There is only a single Siesta calculator
      now covering all versions of Siesta, consistently with other ASE calculators.
    - Added mixing module for the linear combination of arbitrary calculators.
    - New ase.calculators.idealgas.IdealGas calculator for non-interacting atoms
      The calculator does nothing. This can be useful for testing.
    - EMT calculator now support atom-specific energies as per atoms.get_energies().
  * I/O:
    - Read and write support for RMCProfile (rmc6f) file format.
    - Write support for Materials Studio xtd files.
    - More efficient storage of the “data” part of rows in the ase.db database.
      NumPy arrays are now stored in binary format instead of as text thereby
      using approximately a factor of two less space when storing numbers of np.float64.
    - The pov module can now render high-order bonds.
    - Atoms now provides the general-purpose JSON mechanism from ase.io.jsonio.
    - Added ase.data.pubchem module to search for structures in the PubChem database.
  * GUI:
    - It is now possible to copy and paste atoms: The “add atoms” function (Ctrl+A)
      will suggest the atoms in the current selection by default.
- Update to ase 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:
    - This makes it easier to execute custom code during runs. The conv variable
      indicates whether the current iteration meets the convergence criterion,
      although this behaviour may change in future versions.
    - The genetic algorithm module ase.ga now has operators for crystal
      structure prediction. See GA crystal structure prediction.
    - The genetic algorithm module ase.ga now has operators for crystal
      structure prediction. See GA crystal structure prediction.
    - New ase.geometry.dimensionality.analyze_dimensionality() function.
      See: Dimensionality analysis.
    - New ase.utils.deltacodesdft.delta() function: Calculates the difference
      between two DFT equation-of-states. See the new Calculating Delta-values tutorial.
    - Holonomic FixLinearTriatomic for QM/MM calculations.
  * I/O:
    - Database supports user defined tables
    - Preliminary Formula type added. Collects all formula manipulation functionality in one place.
    - Support for reading and writing DL_POLY format.
    - Support for reading CP2K DCD format.
    - Support for EON .con files with multiple images.
    - Support for writing Materials Studio xtd format.
    - Improved JSON support. Command line tool tools like ase band-structure and
      ase reciprocal now work with JSON representations of band structures and paths.
    - Support reading CIF files through the Pycodcif library. This can be useful for
      CIF features that are not supported by the internal CIF parser.
    - MySQL and MariaDB are supported as database backend
    - Support for writing isosurface information to POV format with ase.io.pov.add_isosurface_to_pov()
  * GUI:
    - Quickinfo dialog automatically updates when switching image.
    - Display information about custom arrays on Atoms objects; allow colouring by custom arrays.
    - Improved color scales.
- Update to ase 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 calculator for OpenMX.
    - Updated the Castep calculator
    - Espresso and dftb now support the BandStructure machinery
  * 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.
    - 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:
    - ase.db.core.Database.write() method now takes a id that allows you to overwrite an existing row.
    - ase.db.core.Database.update() can now update the Atoms and the data parts of a row.
    - ase.db.core.Database.update() method will no longer accept a list of row ID’s as the first argument.
    - 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.
- Update to ase 3.16.2
  * Fix unit tests failing due to flask module
  * Fix two less commonly reported issues with trajectory files:
    1) writing trajectories on bigendian architectures
    2) opening a trajectory in append mode and then writing images
       with different headers
  * 3.16.1 -> 3.16.2: Remove build files
- Update to ase 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” function now accepts identifiers for molecules in the G2 dataset.
  * Interface for the CRYSTAL <ase.calculators.crystal code has been added.
  * The ase.dft.bandgap.bandgap() function used with direct=True will now also consider spin-flip transitions. To get the spin-preserving direct gap (the old behavior), use:
  * Bug fixed in the ase.phonons.Phonons.symmetrize() method when using an even number of repeats.
- Remove compiled optimized files
- Combined python2/3 version
- Update to ase 3.15.0
- initial commit 

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- Update to ase 3.21.1
  * Some bug fixes

• Files Changed
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- Update to ase 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 radiuns.
    - 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.
    - get_velocities() will now return an array of zeros consistently with get_momenta() if not set. It previously returned None, which was an oversight.
    - 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.
    - 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.

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- Update to ase 3.20.0
  * General changes:
    - get_calculator() and set_calculator() are deprecated. Use atoms.calc instead.
    - del atoms.calc is deprecated. Use atoms.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:
    - 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.
- Update to ase 3.19.2
  * Update png writer to be compatible with matplotlib 3.3.0.

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- Update to ase 3.19.1
  * Update png writer to be compatible with matplotlib 3.2.

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- Update to ase 3.19.0
  * General changes:
    - ase.build.bulk() now supports elements with tetragonal and 
      rhombohedral attices.
    - The rank and size constants from the ase.parallel module 
      have been deprecated. Use world.rank and world.size instead
      (and from ase.parallel import world).
    - atoms.set_masses('most_common') now sets the masses of each
      element according to most common isotope as stored in 
      ase.data.atomic_masses_common.
    - ase.utils.parsemath added to utils. This module parses simple
      mathematical expressions and returns their numerical value.
    - Plotting functions (such as band structure, EOS, …) no longer
      show the figure by default.
    - Atoms constructor now accepts velocities as keyword.
    - Documentation: New set of introductory ASE tutorials.
    - More detailed output of ase info --formats.
    - For completeness, ase.lattice now also supports the 1D Bravais lattice.
  * Algorithms:
    - Added DiffusionCoefficient so one can calculate atom/molecule
      mobility from trajectory as a function of time.
    - Added general linear parametric constraints based on the work 
      in: https://arxiv.org/abs/1908.01610, and allows for the positions
      and cell of a structure to be optimized in a reduced parameter space.
    - Added ase.build.graphene() for building graphene monolayers.
    - Added ase.md.switch_langevin module for thermodynamic
      integration via MD simulations.
    - Implemented “dynamic” or “ideal gas” contribution from atomic
      momenta to stress tensor Use <ase.Atoms.get_stress>(), e.g.,
      atoms.get_stress(include_ideal_gas=True).
  * Calculators:
    - Added Q-Chem calculator.
    - Added Psi4 calculator.
    - Added DemonNano calculator.
    - Added OpenKIM calculator, a special calculator for OpenKim models.
    - Gulp calculator now provides stress tensor.
    - The NWChem calculator has been completely rewritten, and now 
      supports DFT, SCF (Hartree Fock), MP2, CCSD, and TCE calculations 
      with gaussian-type orbitals. The calculator also now supports
      plane-wave calculations, including band structure calculations
      through ASE’s BandStructure utilities. To facilitate these changes,
      the format of the calculator keywords has been changed.
      Please read the updated NWChem calculator documentation for more details.
    - Siesta calculator refactored. The Siesta calculator now supports 
      the band structure machinery. There is only a single Siesta calculator
      now covering all versions of Siesta, consistently with other ASE calculators.
    - Added mixing module for the linear combination of arbitrary calculators.
    - New ase.calculators.idealgas.IdealGas calculator for non-interacting atoms
      The calculator does nothing. This can be useful for testing.
    - EMT calculator now support atom-specific energies as per atoms.get_energies().
  * I/O:
    - Read and write support for RMCProfile (rmc6f) file format.
    - Write support for Materials Studio xtd files.
    - More efficient storage of the “data” part of rows in the ase.db database.
      NumPy arrays are now stored in binary format instead of as text thereby
      using approximately a factor of two less space when storing numbers of np.float64.
    - The pov module can now render high-order bonds.
    - Atoms now provides the general-purpose JSON mechanism from ase.io.jsonio.
    - Added ase.data.pubchem module to search for structures in the PubChem database.
  * GUI:
    - It is now possible to copy and paste atoms: The “add atoms” function (Ctrl+A)
      will suggest the atoms in the current selection by default.

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- Update to ase 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:
    - This makes it easier to execute custom code during runs. The conv variable
      indicates whether the current iteration meets the convergence criterion,
      although this behaviour may change in future versions.
    - The genetic algorithm module ase.ga now has operators for crystal
      structure prediction. See GA crystal structure prediction.
    - The genetic algorithm module ase.ga now has operators for crystal
      structure prediction. See GA crystal structure prediction.
    - New ase.geometry.dimensionality.analyze_dimensionality() function.
      See: Dimensionality analysis.
    - New ase.utils.deltacodesdft.delta() function: Calculates the difference
      between two DFT equation-of-states. See the new Calculating Delta-values tutorial.
    - Holonomic FixLinearTriatomic for QM/MM calculations.
  * I/O:
    - Database supports user defined tables
    - Preliminary Formula type added. Collects all formula manipulation functionality in one place.
    - Support for reading and writing DL_POLY format.
    - Support for reading CP2K DCD format.
    - Support for EON .con files with multiple images.
    - Support for writing Materials Studio xtd format.
    - Improved JSON support. Command line tool tools like ase band-structure and
      ase reciprocal now work with JSON representations of band structures and paths.
    - Support reading CIF files through the Pycodcif library. This can be useful for
      CIF features that are not supported by the internal CIF parser.
    - MySQL and MariaDB are supported as database backend
    - Support for writing isosurface information to POV format with ase.io.pov.add_isosurface_to_pov()
  * GUI:
    - Quickinfo dialog automatically updates when switching image.
    - Display information about custom arrays on Atoms objects; allow colouring by custom arrays.
    - Improved color scales.

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- Update to ase 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 calculator for OpenMX.
    - Updated the Castep calculator
    - Espresso and dftb now support the BandStructure machinery
  * 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.
    - 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:
    - ase.db.core.Database.write() method now takes a id that allows you to overwrite an existing row.
    - ase.db.core.Database.update() can now update the Atoms and the data parts of a row.
    - ase.db.core.Database.update() method will no longer accept a list of row ID’s as the first argument.
    - 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.

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- Update to ase 3.16.2

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- Update to ase 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” function now accepts identifiers for molecules in the G2 dataset.
  * Interface for the CRYSTAL <ase.calculators.crystal code has been added.
  * The ase.dft.bandgap.bandgap() function used with direct=True will now also consider spin-flip transitions. To get the spin-preserving direct gap (the old behavior), use:
  * Bug fixed in the ase.phonons.Phonons.symmetrize() method when using an even number of repeats.

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- Remove compiled optimized files
- Combined python2/3 version
- Update to ase 3.15.0
- initial commit 

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