Fixed a bunch of cppcheck warnings.
Fixed a widespread typo in the license
Deleting unused variables
A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
Fixes to mdParser to handle vector assignments, fixes for VelocityVerletIntegrator deleting rnemd_ when it doesn't exist yet.
added a minimizer parsing block
Reorganized source directories, added RNEMD and flucQ blocks for options parsing.
updated copyright notices
fixing the build system
Creating busticated version of OpenMD
Adding property set to svn entries
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
Changes required for Inversions and Base Atom types. This will break OOPSE badly for a few days or so...
Checking in changes for Hefland moment calculations
Massive changes preparing for release of OOPSE-4: The main difference is that the new MD file format (.md, .dump, .eor) now contains meta-data information along with the configuration information.
Adding single precision capabilities to c++ side
Many performance improvements
Added check to make sure md file exists.
Throw exception if the file can not be opened for preprocessing
autoconf modernization and cruft removal
replace grammar for numerical parsing
fix a nasty negative integer parsing problem by refining the grammar
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser