Mdanse

Latest version: v2.0.0b2

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2.0.0

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* 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

2.0.0b1

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* 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

1.5.2

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* 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)

1.5.1

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* 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

1.5.0

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* 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)
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* 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

1.4.0

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* 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

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