Pdielec

Major changes to the testing system. Reliance on make has been removed.
A new command pdmake has been introduced.
pdmake tests
pdmake test-preader
pdmake test-p2cif
pdmake vibanalysis
Each directory in the Examples has a command.pdmake file which describes the test
A particular test can be started using;
pdmake command.pdmake
pdmake --view command.pdmake

Bug fix for changing directory when calling a script

Added a single crystal tab to show transmission and reflectance at a single crystal surface
The method used is that described by Passler et al
Rewrote the calculation of dielectric permittivity so that it would be much more general.
There is now a class which looks after dielectric permittivity information
The sign convention for the imaginary component of the permittivity has changed - e(real)-e(imag)j
Moved the CrystalPermittivity to the SettingsTab
Modified the scripting, scripts written before version 7 may not work.
Modified the way masses are handled, so if the gui modifies the masses they are written out to the script.
Changed the communication between tabs, it was completed before and it still is unfortunately
Stopped setting the requestRefresh variable directly - now use a subroutine to do it.
Added a lot of debugging information to the tabs so it is much clearer what the flow is through the code
Two new input file type has been added 'experimental' and 'pdgui'.
'experimental' allows an experimental dieletric to be specified this includes a lorentz type spectrum
'pdgui' allows a script to be read in and executed 'experimental' and 'pdgui'.
'experimental' allows an experimental dieletric to be specified this includes a lorentz type spectrum
'pdgui' allows a script to be read in and executed.
Scripts read in like this must have the 'program' and 'output file name' specified in the mainTab.settings dictionary.
The mainTab gui no longer needs to have specified the 'program' name (eg. castep, or vasp).
This is determined from the name of the file.
Added a new example of using the fitter and the fitting tab
Revised all the documentation
Added the Mie module from PyMieScatt as there were some issues about crossover
Major changes to the parallel methods used by the code. Now using 'partial' from functools
also removed sending the whole crystal_permittivity array at once.
also create the pool in the notebook and keep reusing it.
also switch back to multiprocessing
MKL threads are no longer changed by the code

Fixed a couple of problems when switching molecule using the GUI. The sigmas array and the mode fitting flags are now reset when a new molecule/crystal is read in.
Modified the ViewerTab to display super-cells
Added a new VibAnalysis module based on the work of filipe teixeira https://github.com/teixeirafilipe/vibAnalysis
Example output in Examples/Castep/AsparticAcid/phonon.nm (generated with 'vibanalysis phonon)
Examples/Vasp/Na2SO42/OUTCAR.nma (generated with 'vibanalysis OUTCAR)
Added sklearn to the list of required packages

Added an option in viewerTab to write the vibrating molecule as a cif file.
Modified the cif output format so it is more like that of Mercury
Introduced psutil.cpu_count as this will give the number of physical processors
Switched the multiprocessing module to the multiprocess module (pickling is better)
Overrode the mkl environment variable for the number of threads. PDgui now uses mkl threading, unless it is in multiprocessing mode.
Used dill for the pickling itself.
In preader added an option to pickle each of the readers that are created and store them in a file
Added a script, pickled_reader which can read the pickled file. The script is just an example of how the readers can be read in and the contents accessed.
Modified UnitCell.py to use print_info instead of printInfo
New set of pyhton packages are needed for the above;
dill,multiprocess,psutil
Added new test for p2cif
Removed redundant imports from all files

Modified p2cif so that it becomes a windows executable
Modified p2cif and preader to be more robust when reading phonopy output
Re-introduced fitting the frequency scaling in the fitter tab