JohnKendrick/PDielec: PDielec - ATR support

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 . Version v5.0 sees the removal of the command line interface. All calculations are now performed by PDGui. Calculation of ATR spectra has now been incorporated into the package. Version v4.0 Sees the release of a version of PDielec with a graphical user interface. PDGui allows access to nearly all of the functionality of PDielec. In addition there is a visualiser which allows the normal modes to be shown using an arrow to describe the atomic displacements, or as an animation. There is also the ability to break down each phonon mode into inter and intra-molecular contributions. Included in this release is a Windows compatible installation executable, which installs a version of PDielec/PDGui onto a Windows machine. A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed. v3.0.1 Has updates to the PReader helper program. PReader now has an interface which is consistent with PDielec. PReader reads output files from the supported QM/MM packages and summarises the output in a format which can be read easily into a spreadsheet. v3.1.0 now runs in parallel on multicore machines. Changes to the examples and the example testing routines mean that the tests are less sensitive to change in the machine/BLAS libraries. Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP