fixing some bugs, adding Shake
added a minimizer parsing block
new goodness
Reorganized source directories, added RNEMD and flucQ blocks for options parsing.
Fixed compilation issues
Individual ForceField classes have been removed (they were essentially all duplicates anyway). ForceField has moved to brains, and since only one force field is in play at any time, the ForceFieldFactory and Register methods have been removed.
Adding fluctuating charges, still a work in progress
Updating the build
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.
Use the static version of the qhull library.
Fixing some bugs in the CMakeLists file
Added files for fcc and pentagonal nanorod builders. Updated runMe in samples/builders to include nanorod builders.
Simplifying build process
tweaking build process
Updating build process, copyright, and publications.
Doing some work to simplify cmake build process
Some fixes for CMake and single precision builds
Replacing most of the C-code with C++ code, and migrating the config.h file into the PROJECT_BINARY_DIR so that we can have multiple builds on the same architecture.
added an INSTALL file, using svn2cl to get the ChangeLog target
Added "doc" build target.
fixing install permissions
fixing the build system
changing build process
fixed cmake build system for single and parallel targets
Cmake fixes and updates.
More fixes for cmake.
Somewhat working cmake build system now. Does not yet build a parallel target. Builds all non-mpi programs.
Adding stuff for cmake
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