1.17.15

fix qha_extract to work with the latest version of phonopy

Updated to phonopy 2.x

Moved to phonopy 2.x API.
Dropped support for phonopy 1.x
Python 2.7.x still works but not tested anymore.
Fixed issue when reading LAMMPS trajectory file with triclinic unit cell.
Other minor improvements.

dynaphopy

First release

1.15.3

Merge branch 'development'

yaml and autobands

Force constants and force sets now are python classes
Added store phonon quasiparticle properties in yaml formatted file
Add support for seekpath to generate automatically the k-path if no path is specified
Other minor bug and fixes

Improved ADP and equilibrium atomic position calculations

Improved ADP calculation. Now ADP are calculated respect to the equilibrium positions in the MD.
The average positions are calculate taking in account the translation crystal symmetry.
Changed the normalization of the total power of the power spectra. Now the total power corresponds to the vibrational kinetic energy.

Minor changes in the API.
Minor changes in the DynaPhoPy script (user interface):
load_velocity -> load_data
save_velocity -> save_data

Other minor changes

CUDA, multiple fitting functions and bug fixes

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

Reading atomic velocity from LAMMPS files

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.

Memory mapping on disk

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.

Partial DoS / Thermal properties changes

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.