Dynaphopy

Fix bug in MEM function that may produce a memory leak. (function returns NaN array)
Added support for multiple fitting functions (easily extensible): Lorentzian, Assimetric Lorentzian and Dumped harmonic oscillator functions available.
Added support for calculating FFT/correlation in GPU using CUDA c extension.
Added fitting to normal distribution in the atomic displacements analysis
Minor changes to the API
Other minor corrections and fixes

Fix error in determining the supercell size when generating harmonic trajectory from eigenvectors (--generate_trajectory)
Added support to read atomic velocities from LAMMPS output files instead of positions. This requires to change custom dump command in lammps input file from "x y z" to "vx vy vz". File type is detected automatically.
Other minor details.

Added new feature to use memory mapped on disk for most heavy arrays. RAM memory consumption decreases considerably but calculation is slower.
Added new feature to calculate the full power spectrum projected into one atom (no eigenvector necessary). Also works for DOS and thermal properties calculation.
Changed trapezoidal integration (using numpy) to Simpson integration (using scipy) along all the code.
Many bugs fixed including:
- Force constants are no longer necessary to compute full power spectrum
- Wrong results when also request "wave vector projected power spectrum" and "peak analysis" together in the same run.

Thermal properties included in interactive interface.
Partial DoS/power spectrum calculations.
Thermal properties can be calculated using partial DoS.
Power spectrum now is normalized by Boltzmann distribution instead of Bose-Einstein.
Added option to force DoS be normalized to one in the calculation of thermal properties.
General improvements and minor fixes.
Thermal properties directly calculated by phonopy are not displayed by default.

Fixed energy correction in Internal energy and free energy
Added option (MD_commensurate) to use commensurate points MD supercell instead of phonopy cell
(only phonon dispersion relations and thermal properties)
Improved commensurate point check
Minor fixes and improvements

Calculation of thermal properties from quasiparticles and MD
Generate a harmonic displacements for testing
Added function to generate MD input for VASP and LAMMPS from POSCAR cell
Fix the error in phonon occupancy calculation
Now fit temperature is calculated from phonon occupancy (using Bose-Einstein distribution instead of Maxwell Boltzmann)
Other minor improvements