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Update Python code to work with Python 3

* Update README.md and generate pipenv .env file

* Update README.md
Co-authored-by: James Vance <vance@uni-mainz.de>

* Update examples to work with recent update to Py3

* Updated examples to work with changes in the code base

* Updated other examples for integer division in python3
Co-authored-by: James Vance <vance@uni-mainz.de>

Update DumpXTC for latest GROMACS version

provide gromacs/fileio/xtcio.h file

Massive commit - migrate codebase to work with Py3
Co-authored-by: James Vance <vance@uni-mainz.de>

FIX: pdbreader according to pdb format, and updated pdb format reference

.travis.yml: clean up

.travis.yml: fix docker deploy

* ENH: HeSpaDDA updated the distribution of processors independent on the axis sequence X,Y,Z or Z,Y,X; among others

* ENH: HeSPaDDA update procs allocator axis independent

* ENH: HeSpaDDA updated/faster the distribution of processors

* ENH: HeSpaDDA updates tests

* ENH: HeSpaDDA updated tests and solved Int3D() or decomp.py

* ENH: HeSpaDDA updated copyright and uncommented variables in tuneSkin

* ENH: updated print statement when not using HeSpaDDA
Co-authored-by: Jakub Krajniak <563684+jkrajniak@users.noreply.github.com>
Co-authored-by: Christoph Junghans <junghans@votca.org>

cmake: improve MPI detection

* Update Dockerfile

* Speedup verlet lists with exclusion

* Turn off verlet list buffers in polymer_melt_tabulated since there are too few particles/cell

* Update Dockerfile
Co-authored-by: James Vance <vance@uni-mainz.de>

* Vectorized verlet list rebuild and force calculation

* Implemented rebuildPairs which must be called before running non-vectorized analysis

* Added some lines for documentation

* Added some lines for documentation

* Removed some restrict and auto keywords not compatible with gcc

* Added test for vectorization

* Added/fixed documentation

* Added cellAdjust signal

* Added sample script showing vectorized LJ simulation

* Reduced number of steps for vectorization test

* Fixed errors with restrict on clang

* Fixed errors with restrict on clang

* Reduce Travis CI log file size by switching off deprecated declaration warnings

* Reduce verlet_list_buffer test data

* Revert "Reduce Travis CI log file size by switching off deprecated declaration warnings"

This reverts commit 374b8244350b3cd63a22baf0979140674923e5d4.

* Use camel case for C++ methods

* Added labels for AOS and SOA, and simplified if block

* Added separate test for AOS and SOA

* Removed slower and obsolete parts of vectorized verlet list

* Simplified if block in addition of particles to neighborList

* Updated copyright year for vectorization source files

* Minor cleanup

* Reduce number of warnings emitted by gcc causing travis-ci log to exceed limit

* Updated copyright

* Reduce time to perform verlet_list_buffer test

* Updated copyright and license to files changed in PR 292

* Added onCellAdjust signal

* Added onCellAdjust signal to DomainDecompositionAdress

* Added timers to VerletList

* Implemented verlet list rebuilds with buffers

* Removed onCellAdjust signal

* Added some documentation to verlet list

* Use buffers in Verlet List by default

* Added test and performance comparison for verlet_list_buffer

* Consistent formatting and removed commented code

* Use buffers for Verlet list rebuild by default

* Removed need for 0 as first element of c_range

allow id>=0 for the first particle in chain analysis routines