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CHANGELOG
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version 2.0.0b1 - 2024-10-15
--------------------------
* ADDED van Hove functions (self function and distinct function)
* FIXED Eccentricity analysis to give correct results
* ADDED Infrared analysis (only for molecules at the moment)
* FIXED MolecularTrace analysis data axes to make data plottable
* CHANGED the plotting interface to allow overplotting curves
* ADDED instrument profiles for storing user parameters
* ADDED logging in the code and a logger tab in the GUI
* ADDED charge information to the stored trajectory data
* ADDED support for H5MD trajectories
version 2.0.0 - 2024-02-15
--------------------------
* CHANGED programming language to Python 3
* CHANGED GUI library to Qt
* REMOVED NetCDF4 support
* ADDED ASE trajectory converter for native ASE trajectories and other formats
* CHANGED the formula for the Position Autocorrelation Function
version 1.5.2
--------------
* CHANGED issue #191 Extended and improved the text output of Analysis
* FIXED issues #178 #182 minor GUI problems have been removed
* CHANGED issue #157 DISABLED 3D viewer on ARM (Apple Silicon) MacOS; this will only be fixed in MDANSE 2
* ADDED issue #167 CP2K Trajectory Converter with example files have been added to MDANSE
* CHANGED issue #165 The Trajectory Viewer functionality can now be opened without having to open the Molecular Viewer first
* FIXED issue #158 Molecular Viewer and Elevation, Iso-Surface, and Scalar-Field plotters no longer crash MDANSE on Ubuntu 22
* FIXED issue #152 MDANSE API documentation that comes with released installers now has class inheritance diagrams displayed properly
* FIXED issue #151 MDANSE should no longer interfere with system functionalities such as nano on Ubuntu 22
* FIXED issue #148 The python2 script that comes with MacOS installer can now be used to run scripts
* FIXED issue #147 MDANSE installed with the installer can now be started on MacOS 11 and MacOS 12. However, Molecular Viewer, Animation, and the Elevation, Iso-Surface, and Scalar-Field plotters continue to crash MDANSE, which will not be fixed until MDANSE 2.0.0
* CHANGED (internal) issue #136 MDANSE is now tested only on MacOS 11 and MacOS 12 (for MacOS)
version 1.5.1
--------------
* ADDED issue #129 Installers for Ubuntu 22.x are now automatically generated and available for download
* FIXED issue #131 Importing MDANSE and other installed packages no longer raises exceptions
* FIXED issue #126 The error messages are now helpful when incorrect input is provided in fields like DL_POLY's 'aliases' that take Python object-like input
* CHANGED issue #127 The minimum size of Quick View in 2D/3D Plotter is now much smaller, allowing for resizing downwards
version 1.5.0
--------------
* ADDED issue #93 HDF5 format can now be used as output format of analyses as well as input for plotters
* ADDED issue #75 Added a new Units Editor window for handling unit definitions and expanded the range of unit conversions in plotters. The internal unit handling has been also rewritten
* ADDED issue #71 Trajectory files generated by MDANSE now contain units
* ADDED (internal) issue #68 The data used by plotters is now abstracted, allowing for easier implementation of different data format inputs
* ADDED issue #62 A new MDANSE script, mdanse_job, has been added which can be used to directly open the GUI window for a job
* ADDED issue #58 2 new plotters for visualising trajectory variables (configuration, velocities, and gradients) have been added
* ADDED issue #49 The new MDANSE User Guide is now accessible from the Help menu
* ADDED issue #45 Data Info now also lists the variables present in the trajectory
* ADDED issue #43 Gromacs converter can now be used to also convert TRR files. This creates a trajectory with velocities and gradients if present
* ADDED issue #26 Added velocity interpolation to Current Correlation Function
* ADDED issue #25 The Pair Distribution Function analysis now also calculates Radial Distribution Function and Total Correlation Function
* FIXED issue #100 The Atoms List Selection now displays the correct number in the 'Number of atoms' field and prevents its change when opened from an analysis
* FIXED issue #98 Centre of masses option in the Eccentricity analysis now works correctly
* FIXED issue #95 MaterialsStudio converters (such as Forcite, Discover, DFTB) now create atom clusters correctly
* FIXED issue #69 Fixed the variables generated by the Rigid Body Trajectory job
* FIXED issue #48 The 'Toggle toolbar' button now works correctly on Windows
* FIXED issue #46 Trajectory files generated by MDANSE no longer include temperature and kinetic energy variables
* FIXED issue #31 Gromacs converter is now able to process files of any size
* FIXED issue #30 Scalar Field Plotter now works on Windows
* FIXED issue #29 Elements Database GUI now works properly
* FIXED issue #22 Normalisation now works correctly in Position Autocorrelation Function and General Autocorrelation Function
* FIXED issue #21 Opening an analysis that implements Atom Selection or Reference Basis no longer causes other analyses' GUI windows to crash when opened
* FIXED issue #17 MDANSE can now be opened on all recent versions of MacOS, including computers with the M1 chip
* FIXED issue #15 CASTEP converter now works on MD files with headers of any size
* CHANGED issue #42 The 'variable' box in 2D/3D Plotter is now larger and resizeable
* CHANGED issue #41 Improved the default names of output files of analyses and conversions. A number is also appended to prevent overwriting
* CHANGED (internal) issue #67 Where possible Scientific.IO.NetCDF has been replaced with netCDF4 package
* CHANGED issue #28 Simple Help is now formatted nicely
* CHANGED issue #24 Plotters no longer show variables which contain non-numeric values
* CHANGED (internal) issue #19 The CI/CD has been migrated to use GitHub Actions and GitHub-hosted runners
* CHANGED (internal) MDANSE is now maintained by the ISIS Neutron and Muon Source. Licensing and other documents now reflect this
version 1.5.0.ill (unreleased)
--------------
* ADDED issue #59 Added smart_association in LAMMPS converter. When two or more masses are matching in a LAMMPS trajectory, and smart_association is set to True, we select the nearest one.
* FIXED issue #58 Some LAMMPS files could not be converted with MDANSE
* FIXED issue #57 On macOS, MDANSE did not use the embedded python
* CHANGED LAMMPS converter accepts now "0" as the number of steps (=> automatic detection of the steps number)
* CHANGED Default mass tolerance in LAMMPS converter in now 10^-3 instead of 10^-5
* CHANGED (internal) netCDF version has been updated on macOS
version 1.4.0
--------------
* FIXED issue #56 Layout on Windows differed from macOS and Linux (we keep Windows Layout: "Data" on top, "Plugins" below)
* FIXED issue #55 Plotter (1D, 2D, Plotter, NetCDF Plotter) had several issues (see https://code.ill.fr/scientific-software/mdanse/issues/55)
* FIXED issue #54 Some Gromacs trajectories cannot be opened (due to the presence of "M" dummy atoms)
* FIXED issue #53 VASP NPT trajectories could not be opened
* FIXED issue #52 QVector circular lattice generator created an error
* FIXED issue #51 SFFSF job was accessible from MMTK trajectory and molecular viewer
* FIXED issue #50 Some results could be inconsistent when using multiple atom selections
* FIXED issue #49 Some LAMMPS files could not be converted
* FIXED issue #48 There was an error in NDTSF analysis
* FIXED issue #47 GUI converter did not close
* CHANGED (internal) Docker build has been changed
* CHANGED (internal) macOS build has been changed
version 1.3.1
--------------
* FIXED issue #46 There was an error message when closign converter plugins. The error is no more here but the converter still does not close.
version 1.3.0
--------------
* ADDED Neutron Dynamic Total Structure Factor analysis
* ADDED User can now launch a script with qvector parameters instead of saved qvector definition
* FIXED issue #45 MSD computing on non-orthorombic universe was wrong (fixed with new mmtk version) /!\ Modifies MSD, VACF and DoS, and maybe others... /!\ Units in MMTK have slightly changed
* FIXED issue #44 An error message appeared when display, close and reopen molecular viewer and animation plugins
* FIXED issue #43 The weights are no more normalized with absolute sum /!\ Modifies at least CCF, DCSF and SSF job behavior
* FIXED issue #42 Plotter units could be inconsistent
* FIXED issue #41 Instrument resolution window froze GUI on macOS
* FIXED issue #40 MDANSE could not be used on Ubuntu Bionic systems (due to vtk dependency name)
* FIXED issue #38 Interface was frozen when jobs were launched. A delay of 2s is added at the end of jobs before suppressing the status file
version 1.2.1
--------------
* FIXED issue #39 Time scale in Gromacs converter was incorrect
version 1.2.0
--------------
* ADDED issue #27 Better error handling when an error occurs when running an analysis from the GUI
* ADDED issue #10 Implemented Gromacs trajectory converter
* FIXED issue #36 Jobs could not be launched on Windows machines
* FIXED issue #35 Result of RBT was incorrect /!\ Modifies API (removes stepwise parameter) /!\ Modifies job behavior
* FIXED issue #32 Result of DCSF was incorrect (the QVectors changed over frames) /!\ Modifies job behavior
* FIXED issue #31 Result of RMSD was incorrect (the sqrt was not applied) /!\ Modifies job behavior
* FIXED issue #30 Normalization of VACF total value was incorrect /!\ Modifies job behavior
* FIXED issue #29 Some jobs (AC, CCF, DOS, DACF, DCSF, DISF, GACF, GDISF, MSD, PACF, RMSD, VACF) did not behave properly if first time of the MD is not zero /!\ Modifies jobs behaviors
* FIXED issue #28 The time step is now part of the settings for DCD based converters /!\ Modifies API (with default value) /!\ Modifies jobs CHARMM, NAMD and XPLOR behaviors
* FIXED issue #26 Data can be deleted from the GUI
* FIXED issue #25 The plotter is now compliant with all matplotlib versions (was crashing on ubuntu-xenial)
* FIXED issue #24 Q vectors in CCF Job were incorrect /!\ Modifies job behavior
* FIXED issue #21 "Save a template for new analysis" button produced an error
* FIXED issue #20 Opening the theoretical help on MacOS is now OK
* FIXED issue #18 The items of the checkable combobox are now checkable on Windows
* FIXED issue #16 The file filter combo box is now available from the input file dialog on MacOS
* CHANGED (internal) issue #34 source code is moved to Src/ instead of MDANSE/
* CHANGED (internal) MDANSE can now be built without documentation
* CHANGED (internal) issue #33 The macOS dmg is now ligher than before
* CHANGED (internal) MDANSE is now built with system python on macOS (2.7.10)
version 1.1.3
--------------
* FIXED issue #19 Users could not display user definitions
* FIXED issue #17 The plotter crashed when user was clicking on "plot in new window"
version 1.1.2
--------------
* ADDED issue #15 An automatic mode for data loading is added to compel with the fact that data filter does not appear in data loading popup on macOS
version 1.1.1
--------------
* FIXED issue #14 Package name was not valid for debian package in 1.1.0 version
* CHANGED Moving artifacts for more convenient user downloading
version 1.1.0
--------------
* ADDED issue #12 MDANSE has now three different development phases (beta, rc, release)
* ADDED issue #11 MDANSE is now compliant with 16.04 and 18.04 Ubuntu systems
* CHANGED Replacing all "output_file" occurences by "output_files" /!\ Modifies API /!\
* FIXED issue #13 The changelog was not updated in the windows installer
* FIXED issue #9 updated the macos build scripts in order to have an universal dmg
* FIXED issue #7 suppression of the appearance of an error dialog when closing widgets
* ADDED (internal) Reference data files integrated in functional tests
* CHANGED (internal) MDANSE is now build on new build servers (2018)
* CHANGED (internal) Complete refactoring of build scripts
version 1.0.11
-------------
* bug fix when converting MS trajectories due to a too small value for recursionlimit parameter
version 1.0.10
-------------
* bug fix due to missing import in ElementsDatabaseEditor
* bug fix when loading trajectory with missing unknown MMTK atoms
version 1.0.9
-------------
* use the short git commit id instead of long
version 1.0.8
-------------
* bug fix when getting git commit id in long format
version 1.0.7
-------------
* = 1.0.6.a
version 1.0.6.a
----------------
* bug fix when setting the commit id in __pkginfo__
version 1.0.6
----------------
* the bug report button opens now the default mail client for sending bug report
* the __pkginfo__ is now updated with the commit id when MDANSE is built
version 1.0.5
----------------
* bug fix on macos when closing the application from the Finder: the jobs manager thread was not properly closed
* the macos dmg file was corrupted due to the use of pkg_resources module for storing resources
version 1.0.4.rc4
----------------
* bug fix in coordination number analysis: some pairs were never taken into account
* bug fix when transmutating atoms from an atom selection different to 'all'
version 1.0.4.rc3
----------------
* bug fix in debian packager: add the python-setuptools dependency
* improved LAMMPS converter: the parsing of the config file is more tolerance in term of required keyword format
version 1.0.4.rc2
----------------
* added support for gitflow bugfix branch to gitlab config file
* the DL_POLY converter is now compliant with DL_POLY 4
* added the mass tolerance to LAMMP converter
* updated the LAMMP example trajectory with more accurate masses
version 1.0.4.rc1
----------------
* bug fix in IWidget: the label of the configurator was not taken into account
* bug fix path_to_module function: the list of directories has to be parsed backwards
* raise an error when none or more than atom matches the mass stored in the LAMMPS config file
* modified the label for r value
version 1.0.3.e:
----------------
* bug fix relative to REGISTRY update
version 1.0.3.d:
----------------
* redirected the sys.stdout and sys.stderr to the LOGGER
* implemented a write method so as ConsoleHandler behaves as a file-like object
* the job short name appears now explicitely in the saved job files
* small refactoring of MDANSE __init__
* small refactoring of ClassRegistry
* removed the explicit imports of the framework classes
* the plotter show the last loaded data now
* bug fix in rmsd job: the PBC were not applied to the calculation
* bug fix in AtomSelectionConfigurator::get_indexes
* bug fix when saving user definitions
* bug fix with the initial size of the user definitions plugins
* updated the job template writing
* small refactoring of the save job template command line option
* removed unused imports
* removed white spaces
version 1.0.3.c:
----------------
* bug fix with JobControllerPanel in case of crashing jobs
* regression fixed due to trials to get rid of relative imports MDANSE/Externals/pubsub package
version 1.0.3.a:
----------------
* updated `MDANSE/__pkginfo__.py` module