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Author: cli2
Date: Mon Sep 7 16:31:51 2009 UTC (14 years, 8 months ago)
Log Message: 
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

Changed paths

Path Details
Directorytrunk/OOPSE-4/src/applications/oopse/oopse.cpp modified , text changed
Directorytrunk/OOPSE-4/src/applications/utilities/principalAxisCalculator modified , text changed
Directorytrunk/OOPSE-4/src/integrators/Integrator.hpp modified , text changed
Directorytrunk/OOPSE-4/src/integrators/VelocityVerletIntegrator.cpp modified , text changed
Directorytrunk/OOPSE-4/src/integrators/VelocityVerletIntegrator.hpp modified , text changed
Directorytrunk/OOPSE-4/src/io/DumpReader.hpp modified , text changed
Directorytrunk/OOPSE-4/src/io/Globals.cpp modified , text changed
Directorytrunk/OOPSE-4/src/io/Globals.hpp modified , text changed
Directorytrunk/OOPSE-4/src/io/Makefile modified , text changed
Directorytrunk/OOPSE-4/src/io/RestReader.cpp modified , text changed
Directorytrunk/OOPSE-4/src/io/RestReader.hpp modified , text changed
Directorytrunk/OOPSE-4/src/io/RestWriter.cpp modified , text changed
Directorytrunk/OOPSE-4/src/io/RestWriter.hpp modified , text changed
Directorytrunk/OOPSE-4/src/math/DynamicRectMatrix.hpp modified , text changed
Directorytrunk/OOPSE-4/src/math/Quaternion.hpp modified , text changed
Directorytrunk/OOPSE-4/src/math/SVD.hpp modified , text changed
Directorytrunk/OOPSE-4/src/math/SquareMatrix3.hpp modified , text changed
Directorytrunk/OOPSE-4/src/mdParser/MDLexer.cpp modified , text changed
Directorytrunk/OOPSE-4/src/mdParser/MDLexer.hpp modified , text changed
Directorytrunk/OOPSE-4/src/mdParser/MDParser.cpp modified , text changed
Directorytrunk/OOPSE-4/src/mdParser/MDParser.g modified , text changed
Directorytrunk/OOPSE-4/src/mdParser/MDParser.hpp modified , text changed
Directorytrunk/OOPSE-4/src/mdParser/MDTokenTypes.hpp modified , text changed
Directorytrunk/OOPSE-4/src/mdParser/MDTreeParser.cpp modified , text changed
Directorytrunk/OOPSE-4/src/mdParser/MDTreeParser.g modified , text changed
Directorytrunk/OOPSE-4/src/mdParser/MDTreeParser.hpp modified , text changed
Directorytrunk/OOPSE-4/src/mdParser/MDTreeParserTokenTypes.hpp modified , text changed
Directorytrunk/OOPSE-4/src/primitives/DirectionalAtom.cpp modified , text changed
Directorytrunk/OOPSE-4/src/primitives/Molecule.cpp modified , text changed
Directorytrunk/OOPSE-4/src/primitives/Molecule.hpp modified , text changed
Directorytrunk/OOPSE-4/src/primitives/RigidBody.cpp modified , text changed
Directorytrunk/OOPSE-4/src/primitives/StuntDouble.hpp modified , text changed
Directorytrunk/OOPSE-4/src/restraints/Makefile modified , text changed
Directorytrunk/OOPSE-4/src/restraints/MolecularRestraint.cpp added
Directorytrunk/OOPSE-4/src/restraints/MolecularRestraint.hpp added
Directorytrunk/OOPSE-4/src/restraints/ObjectRestraint.cpp added
Directorytrunk/OOPSE-4/src/restraints/ObjectRestraint.hpp added
Directorytrunk/OOPSE-4/src/restraints/RestraintForceManager.cpp added
Directorytrunk/OOPSE-4/src/restraints/RestraintForceManager.hpp added
Directorytrunk/OOPSE-4/src/restraints/Restraints.cpp deleted
Directorytrunk/OOPSE-4/src/restraints/Restraints.hpp deleted
Directorytrunk/OOPSE-4/src/restraints/ThermoIntegrationForceManager.cpp modified , text changed
Directorytrunk/OOPSE-4/src/restraints/ThermoIntegrationForceManager.hpp modified , text changed
Directorytrunk/OOPSE-4/src/selection/SelectionEvaluator.cpp modified , text changed
Directorytrunk/OOPSE-4/src/selection/SelectionToken.hpp modified , text changed
Directorytrunk/OOPSE-4/src/selection/TokenMap.cpp modified , text changed
Directorytrunk/OOPSE-4/src/types/Makefile modified , text changed
Directorytrunk/OOPSE-4/src/types/RestraintStamp.cpp added
Directorytrunk/OOPSE-4/src/types/RestraintStamp.hpp added
Directorytrunk/OOPSE-4/src/types/ZconsStamp.cpp modified , text changed