call w python

Newline fix

version the docs inside the bucket

John's fixes to documentation

Jason's fixes to documentation

Added discussion of loading CHARMM files

Edits to documentation based on Jason's comments

AMBER example script uses periodic box vectors from inpcrd

Prevent sphinx from adding an index to PDF file

Marked GBVIForce as deprecated and removed it from the manual

Deleted obsolete documentation files

Very minor fix in developer guide

First draft of landing page

Remove unused stuff

unused

push landing page to s3

clarify

reindent

Add favicon

Cosmetic changes, full width jumbotron, links to Benchmarks, better css theme

I misspelled 'success'

Fix favicon link

Add cdn for html5shiv

Fix heading sizes

Fix favicon again

Remove landing page

small typo in checkpointreporter.py true --> True
 Changes to be committed:
	modified:   checkpointreporter.py

there is a small typo in checkpointreporter.py in openmm. line 81 has:
self._own_handle = true
instead of True.

Improve warning messages coming from the CHARMM parsers.

Clean up some methods that serve no purpose in OpenMM.

Added scripts for generating force field XML files

Began implementing CustomManyParticleForce

Continuing to create reference implementation of CustomManyParticleForce

Finished reference implementation of CustomManyParticleForce

Fixed errors building Python wrapper for CustomManyParticleForce

Began working on CPU implementation of CustomManyParticleForce

Continuing to implement CPU version of CustomManyParticleForce

CPU version of CustomManyParticleForce is multithreaded

Began vectorizing CustomManyParticleForce

Finished CPU implementation of CustomManyParticleForce

Eliminated some unnecessary memory allocation in CpuCustomManyParticleForce

Beginning of CUDA implementation of CustomManyParticleForce

Continuing to work on CUDA implementation of CustomManyParticleForce

Implemented type filters for CUDA version of CustomManyParticleForce

Implemented exclusions for CUDA version of CustomManyParticleForce

Wrote code to build neighbor list for CUDA version of CustomManyParticleForce

CUDA version of CustomManyParticleForce uses neighbor list

Optimizations to CUDA version of CustomManyParticleForce

Fixed a bug in Python wrapper for CustomManyParticleForce

CustomManyParticleForce offers two different "permutation modes".  Implemented it for Reference and CPU platforms.

Minor optimization to CUDA version of CustomManyParticleForce

Implemented UniqueCentralParticle mode in CUDA version of CustomManyParticleForce

Bug fixes to CustomManyParticleForce

Bug fixes to CUDA version of CustomManyParticleForce

ForceField allows defining CustomManyParticleForces in XML files

Added documentation for CustomManyParticleForce

Created OpenCL version of CustomManyParticleForce (not yet fully debugged)

Fixed errors on Windows

Fixed a potential segfault

Bug fix

Bug fixes to OpenCL version of CustomManyParticleForce

Fixed errors compiling kernels in double precision mode

Made test cases more robust

Fixed error using type filters in UniqueCentralParticle mode

Added serialization support for CustomManyParticleForce

Added a missing return statement

Bug fix to addExtraParticles()

Fixed bug in CustomManyParticleForce that caused crash

Rewrote findBlocksWithInteractions() in a way that is both faster and simpler.

Ported the new version of findBlocksWithInteractions() to OpenCL (not yet debugged)

Bug fixes

Improved performance of building neighbor list on AMD GPUs

Fixed bug on Intel GPUs

Cleaned up obsolete code

Prevent nan in CPU platform when two excluded particles are exactly on top of each other

Fixed a compilation error in double precision mode

Switched to a slightly faster (and more accurate) approximation for erfc()

Reversed a change that didn't help

Updated code to obey BUILD_TESTING to allow for disabling of test compilation

Update AmoebaMultipoleForceImpl.cpp

@rmcgibbo and @mpharrigan convinced me I should have just fixed it myself.

Update AmoebaMultipoleForceImpl.h

typo fix

Update AmoebaMultipoleForce.cpp

typo fix

Update AmoebaMultipoleForce.h

typo fix

Update amoebaKernels.h

typo fix

Update AmoebaReferenceKernels.h

typo fix

AMOEBA uses fast approximation for erfc()

Fix issue where the last CMAP defined in a parameter file is not added to the
parameter set.

Fix comments.

Set cutoff correctly for CHARMM polarizable force field