This is the nMOLDYN version history file.

3.0.9 (January 2011):
=====================

Bug fixes:
----------
    - some GUI dependancy in the core code removed
    - small bug introduced in the version 3.0.8 in the MaterialsStudio converter
    - TrajectoryConversionDialog.py: typo that makes VASP converter crash    
    - GlobalMotionFilterTrajectory: the initial configuration changed at each step
    - bug fix for running analyses in cluster mode
    - bug fix in CDOS tests: wrong calculation for the energy fhwm corresponding to the 
      old fft window length parameter
    - bug in Master.py: taskName was not initialized for the Parallel classes.
    - bugs in all scattering related analysis due to the adding of conversion factor.
        
News:
-----
    - made "MacPortable" (thanks to Konrad Hinsen for the port file)
    - (re)introduced the possibility to perform a selection based on a function
    - added a LAMMPS file converter
    - added HBondSurvivalAnalysis analysis
    - (Re)introduced the possibility to select different units (time, distance, frequency, q).
    - new qvector generator (the anisotropic case is treated in reciprocal space)
    - introduced a GlobalVariables modules to store a few global variables

Updates:
--------
    - nMOLDYN compatible with Scientific >= 2.8.0
    - some internal changes (directories renamed/moved, files renamed/moved ...)
    - harmonized the output of some of the scattering related properties (DISF, DCSF, EISF, DISFGA)
    - recomputed the fwhm_e for a correct comparison with nMOLDYN2.2.5
    - some preferences variables removed
    - no need to declare a path for acrobat reader on MacOS
    - all the class are made python3 compatible (minimal inheritance from object)
    - improved the Error handler. More information about the error that occured.
    - simplified the PREFERENCES (not use singleton class anymore)
    - added a PREFERENCE to select which DB to use (MMTK or nMOLDYN)
    - GlobalMotionFilteredTrajectory: added the "target" parameter used to store in output a selection different from the one used to perform the global motion filtering
    - the nMOLDYN analysis input script used for a parallel cluster run can be launched with the taskname as argument
    - Materials Studio converters: the atoms are stored by block molecules with ascending xtd index order.
    - cythonized the pyx files and the setup.py
    - modified the setup script to suit for a Windows-64 bit build.
    - moved out the test trajectories from the nMOLDYN/Tests directory to the nMOLDYN/Trajectories directory
    - suppressed (thanks Konrad) all the global variables --> no need for Config.py file anymore
    
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3.0.8 (August 2010):
====================

Bug fixes:
----------
    - bug when setting the universe hierarchy for objects of MMTK Atom class: only the first 
      atom name was retained preventing from selecting the other ones from the selection dialog.
    - added events grabber for the parent dialog when closing the PyroServerDialog dialog.
    - added events grabber for the parent dialog when closing the SelectionDialog dialog.
    - Added an error message when the documentation in PDF format could not be opened.
    - nMOLDYN/Core/Monitoring.py: bug when setting the number of free procs on windows for a non 
      admin user.
    - bug in the VASP converter when mapping the coordinates to the atomic contents
    - bug in coordination number analysis when selecting a specific subset of atoms
    
News:
-----
    - added a CASTEP to MMTK NetCDF trajectory converter.
    - added the cartesian position autocorrelation function (by Konrad Hinsen))
      
Updates:
--------
    - Changed the format for the file storing the datas exported from a plot: the 3 first lines 
      start now with a '#' and there is no blank line between those 3 lines and the data block.
    - some small modifications in the README file about a known bug when using Pyro server
      on a windows machine    
    - some code cleaning in nMOLDYN/Core/IO.py    
    - the trajectory converters dialog were redesigned by adding a generic class in top of 
      them.
    - some changes in the repository structure
    
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3.0.7 (June 2010):
======

Bug fixes:
----------
    - all setup.cfg files are excluded from the MANIFEST when building a sdist distribution
    - bug when exporting a plot to an ASCII file, the axis name were the ones of the last plot
    - some bug fix in the Materials Studio converters
    - the atom selection mechanism from a file was buggy when the full path contained some spaces
    
News:
-----
    - new converter from a PDB frame to a MMTK NetCDF single frame trajectory.
    - new analysis: density profile used for reflectometry studies
    - better guess of the atom type in the DL_POLY converter: based on the compulsory atomic 
      mass stored in the FIELD file

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3.0.6:
======

Bug fixes:
----------
    - the 'name' attribute of the object was not considered when assigning the nMOLDYN name to an object.
    - bug fix in readXTDFile method of Discover/Forcite converter.
    - GlobalMotionFilteredTrajectory: the principal axis transformation setup for the first frame was actually not performed. 


News:
-----
    - nMOLDYN/Chemistry/Chemistry.py: added a look-up table from atomic mass (with one decimal) to atomic symbol
    - nMOLDYN/Core/IO.py: improvements in DL_POLY converter when guessing atom symbol from FIELD topology file.


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3.0.5:
======
    
Bug fixes:
----------
    - The acroread_path configuration variable at start up was not set correctly on Windows
    - Wrong formula implemented in PairDistributionFunction
    - Smoothed Static Coherent Structur Factor analysis could not be launched
    - Launching nMOLDYN on command-line using a script with -i options did not work properly
    - When setting up the logfile, it was always put in the default location whatever the preferences values.
    - When performing an analysis benchmark, when several test sets was run on a row, displaying the contents of a successful of
      failed test of one of the test set always displayed the one of the last set.
    - The group selection dialog was buggy
    - The Reorientational Correlation Function was not properly normalized
    - The Forcite trajectory converter did not work from the GUI
    - The Discover trajectory converter did not work for system with no PBC
    - Compatibility between 32/64 bit version (hopefully ...)

News:
-----
    - A new documentation is available
    - Parallelization is fully supported on Windows, Linux and hopefully Mac
    - The Radial Distribution analysis has been renamed PairDistributionFunction
    - Adding of DensityFunction calculation in PairDistributionFunction analysis
    - Removed the "Check job status" onglet. It was not useful anymore because it
      was redundant with the message displayed on the console and the logfile.
      Moreover, it was not user-friendly to have to open a new nMOLDYN instance
      to check for a running analysis o another instance ...
    - Reintroduced the xrange and yrange settings in the plotting interface
    - Some improvments in the Export plot functionnality
    - Updated and refreshed the API (still many things to do here)
    - Partial terms for msd, vacf and dos in cluded
    - Internal code reorganization: Chemistry and Mathematics modules created.
    - Back converter from NetCDF to VASP CONTCAR and XDATCAR
    - New Windows installer
    - nMOLDYN icon for windows version
    - New version checker available in command-line and from the GUI.
    - The CHANGELOG can be read from the GUI by settings in the preferences 
      the path to a text editor

To do:
------
    - New NetCDF plotter:
          * several plots displayable
          * do not use Tkagg anymore
          * superplot button within a 2D plot
          * Dialog with the variables name (+ None) and the settings
    - Correct the paths that are not properly set with os.normpath
    - Case of the paths defined in the preferences that does not exist
      (e.g. PREFERENCES.outputfilepath triggers a crash at the end of 
      the analysis if it does not exist)
    - Create Write_Output_File_Header


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3.0.4:
======

Bug fixes:
----------
    - Angular Correlation analysis
    - Angular VACF analysis
    - QHA analysis

News:
-----
    - Lighter version for executables automatic search at start up. Should be faster now.
    - New GUI for the effective mode viewer
    - Added the 'groupinglevel' keyword in group selection in order to focus selection at 
      different level in a molecule (e.g. for a protein: atom->chemical fragment->residue
      ->chain->protein)
    - DL_POLY trajectory conveerter: the keywords can now be in lower or upper case
    - Added spatial density analysis (currently very slow)
    - A version controller was implemented to check whether a nMOLDYN script is launched using
      a newer version of nMOLDYN. This may trigger some conflicts when parsing some parameters
      that have changed slightly.
    - Added stability tests for AVACF, ISFG, EISF and ARA analysis

To do:
------

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3.0.3:
======

Bug fixes:
----------
    - nMOLDYN could not be launched on machines where Tix was not installed.
      The few Tix-widgets used in nMOLDYN were replaced by 
      Tk equivalents:
          * Tix.Meter --> TK.Scale
          * Tix.NoteBook --> set of radiobuttons

News:
-----
    - The extension files for some analysis are now provided 
      in C. As a consequence, Pyrex does not necessary need to 
      be installed.

To do:
------

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3.0.2:
======

Bug fixes:
----------
    - The automatic search  for executables at start up did not work on Windows
    - The Help menu was not disabled when acroread path was not set

News:
-----

To do:
------

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3.0.1:
======

Bug fixes:
----------

News:
-----
    - Added the Angular Correlation analysis
    - The ncdump and ncgen executables (3.6.1) are now provided with the installation on Windows

To do:
------

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3.0.0:
======

Bug fixes:
----------

News:
-----
    - New analysis:
      * Root Mean Square Deviation
      * Radius Of Gyration
      * Global Motion Filtered Trajectory
      * Center Of Mass Trajectory
      * Quasi Harmonic Analysis
      * Static Coherent Structure Factor
      * Radial Distribution Function
      * Coordination Number
      * ScrewFit Analysis
      * NMR Order parameter
      * NMR Order Parameter using Contact Model

    - Others:
      * global reorganization of the code
      * brand new graphical user interface
      * new plotting engine
      * new trajectory converters
      * new netCDF and ASCII converters
      * preferences settings
      * embedded documentation (HTML and  PDF formats)
      * embedded API (HTML and PDF formats)
      * embedded analysis benchmark
      * online access to the mailing list
      * job status

To do:
------

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2.2.6:
======

Bug fixes:
----------

News:
-----
    - Calculation of Scattering Function can be made with isotropic, anisotropic 
      and explicit list of Q vectors (See Documentation for details).

    - Periodic Box dimensions (direct and reciprocal basis) are shown in "View" menu.

    - DL_POLY trajectories can be opened directly from "File" menu.

To do:
------

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2.2.4:
======

Bug fixes:
----------

News:
-----
    - Works under Windows using the standard Python for Windows (before it
      worked only under Cygwin)

To do:
------

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2.2.3:
======

Bug fixes:
----------

News:
-----
    - Compatibility with MMTK 2.5

To do:
------

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2.0.1:
======

Bug fixes:
----------

    - The time information (first step/last step/skip) set in the 
      graphical user interface was not taken into account in the
      calculations.

    - The graphical user interface (xMoldyn) did not work with
      Python versions before 2.0.

News:
-----
    - The scattering function plots (View-Display) show the
      quantity and unit on the x-axis (time/frequency/q-length).

To do:
------

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