patch for allowing prd command to work with sorted atoms

doc/src/Manual.txt

examples/prd/README

examples/prd/log.15Feb16.prd.g++.4

examples/prd/log.29Sep16.prd.g++.4

examples/prd/log.29Sep16.prd.g++.8

examples/prd/screen.29Sep16.prd.g++.4.0

examples/prd/screen.29Sep16.prd.g++.4.1

examples/prd/screen.29Sep16.prd.g++.4.2

examples/prd/screen.29Sep16.prd.g++.4.3

examples/prd/screen.29Sep16.prd.g++.8.0

examples/prd/screen.29Sep16.prd.g++.8.1

examples/prd/screen.29Sep16.prd.g++.8.2

examples/prd/screen.29Sep16.prd.g++.8.3

src/REPLICA/fix_neb.cpp

src/REPLICA/prd.cpp

src/REPLICA/prd.h

src/REPLICA/tad.cpp

src/version.h