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Several fixes and enhancements for AMBER NetCDF trajectories

Lars Pastewka requested to merge pastewka/ase:18_NetCDF_Fix2 into master
  • Fixed a bug related to reordering the atom order when an atom index is present in NetCDF; only affects trajectories written with LAMMPS netcdf/mpiio dump style.
  • Fixed #150 (closed) NetCDF file format is now autodetected and can be read with the ase.io.read function.
  • Reduce memory footprint when reading large files.
  • Removed code for scipy.io.netcdf.netcdf_file ; was commented out before

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