Re-allow commands after an exception was caught inside a run.

new checksum for LATTE download

Fixed bugs to the tersoff gpu styles for OpenCL builds and some maintenance

Fixes #995: Added tail correction to fix gcmc

Doc Reorganization - Tools Section

after an exception "all bets are off",
i.e. the user should be allowed to do anything to recover.
through setting Update::whichflag to 0, the guard against running commands during a run is removed.

Fixed bugs with time_q and time_quat not calling start() and stop() when _charge and/or _rot in Atom are true for OpenCL builds

Renamed dev_acc  to dev_ilist for better description and updated the 3-body styles accordingly; also fixed bugs with accessing dev_packed from the three_end kernel of tersoff/mod and tersoff/zbl gpu styles for OpenCL builds

Discrete element models for the BODY package

OpenCL related fixes and improvements to the GPU package

Fixes a memory leak when using OpenCL

- document previously undocumented OpenCL tune settings
- implement OpenCL platform selection through prefixing the device type with the platform id separated by a colon
- allow passing custom tune parameters though postfixing the device type with the 13 tuneable parameters separated by commas
- remove an extra clear() that would delete device properties structs an cause LAMMPS to output garbage strings

USER-DPD: propagate a minor performance bugfix throughout the DPDE code

The GPU package uses OpenCL events for measuring time. These have to be
released to free up memory. I removed the clReleaseEvent() calls in the
clear() method because in some cases they don't exist yet and I couldn't
find a way to check for a valid event (clRetainEvent didn't work). This
at least fixes the massive leak during simulations.

See issue #1006

The fix_shardlow_kokkos.cpp code had already factored out a redundant
sqrt() calculation in the innermost loop of ssa_update_dpde().  This
changeset propagates an equivilent optimization to:
  fix_shardlow.cpp
  pair_dpd_fdt_energy.cpp
  pair_dpd_fdt_energy_kokkos.cpp
The alpha_ij variable was really just an [itype][jtype] lookup parameter,
replacing a sqrt() and two multiplies per interacting particle pair
by a cached memory read.  Even if there isn't much time savings, the
code is now consistent across the various versions.

+ added examples for special cases with disks and rods for 2d, and spheres and rods for 3d,
+ corrected the definition of the cutoff distance in pair style command

include support for 'extra/XXX/per/atom' info in restart files