Fixed a DumpWriter parallel bug.

Compilation and portability fixes

Fixed a bunch of cppcheck warnings.

Fixed a minor visitor bug

Chasing down bugs in the TIP4P_FQ model.

CLearing out some memory leaks

Fixes for Qhull static build strangeness

Added an ellipsoidal shaped lattice

Adding nanoparticle generators, fixing a Qhull static link bug

Added a new icosahedralBuilder for single-component Mackay Icosahedron nanoparticles.

Some bugfixes for cell-linked-list-style neighbor lists when the simulation
doesn't use periodic boundary conditions.   Cleaning up some of the Hull
stuff while we're in there.

Bug fixes to get new parallel decomposition methods working without periodic boundary conditions.  
Updated volume in stats file correctly.
LangevinHull fixes for low viscosity values.

First pass at angular momentum aware version of VSS-RNEMD.

Updated the integrator conserved quantity so that it doesn't trail the other properties

Fixed a widespread typo in the license 

Merging changes from trunk branch into development.

Fixed a bug in RigidBody, added a check for fixed vs. fluctuating charge

Only compute field for sites not excluded from the pairwise electrostatic contribution.
Also, now compute the mean field felt by the sites in a rigid body, and report that as
the rigid body's field.

Merging trunk changes back to development branch

Unified the computation of storageLayout into SimCreator, but that
value is stored in SimInfo.  We used to compute storageLayout values
in two places - now only one.

More careful with casts, fixed windows compilation issues

Windows compilation fixes

Fixed some cruft

Cleaning more cruft and unused variables.

Fixed some picky warnings from the new Intel compiler.

Performance boosts, cleaning up debugging cruft

New electrostatic bug fixes.

Forgot to merge some important accumulator changes

A bug fix in the electric field for the new electrostatic code.  Also comment fixes for Doxygen 

Adding stat2thcond back

Merging some of the trunk changes back to the development branch,
cleaning up a datastorage bug

Added 6, 8, 10 and 12 length alkane chains to thiols

Adding an electric field and the architecture for external perturbations.   Fixing a bug in MultipoleAtomTypesSectionParser.

Adding a sample of the shear and scale for argon.

Fixes to mdParser to handle vector assignments, fixes for VelocityVerletIntegrator deleting rnemd_ when it doesn't exist yet.

Cleaning up RNEMD log, adding XY area to Snapshot

Added the same fix for parallel runs

Adding some RNEMD interface samples

Fixed a bug in the FluctuatingChargeLangevin propagator, updated some samples.

Added Fluctuating Charge Langevin propagator, and made it the default
fixed some errors on the one-center slater coulomb integrals, and some
parameters in PhysicalConstants.

Refactored Snapshot and Stats to use the Accumulator classes.  Collected
a number of methods into Thermo that belonged there.

Calculates the tetrahedrality parameter as a function of zbins. Abandon all hope ye who enter here.

Some bugfixes (CholeskyDecomposition), more work on fluctuating charges,
migrating stats stuff into frameData

Fixed a strange bug where setting tempSet to false would still require a targetTemp

bugfixes for self interactions (particularly in parallel)

Removed a line in Integrator.cpp where the forceMan_ was being initialized too early. Additionally, added a dummy value for rCut_ in ForceManager.cpp::setupCutoffs. JRM

Added SiteData parsing and writing.

Fixing some bugs in optimization, fixing status functions so that they
dump correctly (although some things are deferred until the Stats is
accumulator-based).

fixing some bugs, adding Shake

added a minimizer parsing block

Fixes for minimization

Adding eigen Cmake stuff

Adding the Flucq constraints and objective function for minimization

added a forceman to the flucq propagator

Fixed fluctuating charge forces

Fixed the Slater overlap integral code, added dVdFq to the self interaction.

Make fluctuating charges also charges.

Fixed compilation issues

resolved

Forgot to delete the individual FF classes.

DarkSide isn't needed

Merging Shenyu's RNEMD changes from openmd-1 into the development branch.

Fixed a few bugs in that last commit

Adding fluctuating charges, still a work in progress

Adding the propagators for FlucQ

Added ability to read / write dump files with fluctuating charges and
electric fields.

Bugfixes (mostly related to particlePot and storageLayout).

Added an adapter layer between the AtomType and the rest of the code to 
handle the bolt-on capabilities of new types. 

Fixed a long-standing bug in how storageLayout was being set to the maximum
possible value.

Started to add infrastructure for Polarizable and fluc-Q calculations.

Adding some new atom types, fixing a convex hull bug, removing silly stuff 
from Snapshot

fixed an initialization bug in Dump2XYZ

qhull modifications for compilation 

Un-did some changes that weren't ready to be committed.

Adding a vector parsing option to the parameter Manager.

tweaking build process

Doing some work to simplify cmake build process

Fixed a number of force files to use new Gay Berne format

Fixes for compilation under LLVM compiler
Bug-fix for switching function in Gay-Berne

Fixed bug with rigidbodies not updating velocities for heat flux calculation.

Debugging heat flux calculation for rigid bodies.

Bug fixes for v_j not being set correctly and accumulation error.

Added revision to svn for Gianluca.

Batch of sample files for testing different configurations of Gay-Berne atoms. Included is a force file and test atom build for running the '.md' files.

Fixed two bugs in new Gay-Berne module.  Torque 2 had a sign error, and there
was a subtle mixing bug for dissimilar particles in different orderings.

Update for energy units conversion.

Adding experimental branch for calculation of the heatflux based on old version of OpenMD.
This will need to be ported to the development branch later.

updated copyright notices

Added a waterReplacer script.  A bit rough around the edges, but seems
to do the right thing for a slab of ice.

Minor modifications to set environment variable.

Adding validation python code.

First few fixes for explicit interactions.

fixed a compile bug for PGI

added an INSTALL file, using svn2cl to get the ChangeLog target

fixing install permissions

cleaning up build cruft

update for cmake build and install

removing build cruft

removing old build cruft

removing cruft from build system

fixing a link order problem

cleaning up the development branch a bit, removing cruft, etc.

Updated antlr, fixed a clang compilation bug, removed a warning message

cleaning up the configure script

Merging changes from old branch into development branch

Splitting out ifstrstream into a header and an implementation.  This
means that much of the code that depends on it can be compiled only
once and the parallel I/O is concentrated into a few files.  To do
this, a number of files that relied on basic_ifstrstream to load the
mpi header had to be modified to manage their own headers.

Adding RepulsivePower interaction to development branch.

Build fixes for qhull 2011, fixes for compilation with PGI.

Fixing cutoff groups

Fixed a parallel bug in computing exclude lists.
Added file versioning information in MD files.
Still tracking down cutoff group bugs.

First OpenMP version.

Fortran begone!

Completing the Fortran removal project.  Fixes for compilation with
clang / llvm, debugging, removing code that we'd never used.

Updated ordered neighbor list generation.

Adding initial OpenMP support using new neighbor lists.

test

Efficiency fix

Fixing some parallel bugs

Fixes

bug fixes.

Well, the potential energy values are still garbage, but the LJ sample
runs.

Forgot Grid3d

bug fixes

more parallel fixes

Added Atypes to new C++ force decomposition.

A few more fixes for the missing routines

Fixed some busted stuff in buildNeighborList

For efficiency, pointers instead of objects will be passed during main
force loop. 

Fortran removal

more fortran removal

more minor changes to help build

still busted, but much progress

working on communicators

Starting a Parallel architecture

forgot one method

Well, it compiles and builds, but still has a bus error at runtime.

One more fortran file that we don't need:

Moved switching functions and force options over to the C++ side, and
removed them from Fortran.

Doesn't build yet, but getting much closer...

Less busted than it was on last check-in, but still won't completely
build.

Changes to remove more of the low level stuff from the fortran side.

Starting migration of Morse to C++

Fixed case typos in cmake.

Somewhat working cmake build system now. Does not yet build a parallel target. Builds all non-mpi programs.

Fixing headers. They are now .hpp files.

Adding exception and reporting mechanism from ProtoMol to OpenMD.

Adding some error reporting and debuging code to OpenMD. This code is borrowed from ProtoMol.

Converting Sticky over to C++

Added GB module to the C++ side, got rid of it on the fortran side.

fixed phi mixing

Added EAM.  Still segfaults but compiles.

fixed some destructor bugs dealing with the TypeContainers

fixing c/fortran bugs

Added nonbonded directory.  Compiles, links, runs, but gives incorrect
answer.

attempts at c++->fortran linkage.  Still busticated.

well, it compiles, but still segfaults

Creating busticated version of OpenMD