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2005-04-15 17:03 gezelter |
2 |
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|
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* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
4 |
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UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, |
5 |
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UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
6 |
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UseTheForce/ForceFieldCreator.hpp, |
7 |
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UseTheForce/ForceFieldFactory.cpp, |
8 |
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UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
9 |
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UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, |
10 |
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UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, |
11 |
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UseTheForce/notifyCutoffs.F90, |
12 |
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UseTheForce/notifyCutoffs_interface.F90, |
13 |
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UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
14 |
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UseTheForce/DarkSide/atype.F90, |
15 |
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UseTheForce/DarkSide/atype_interface.F90, |
16 |
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UseTheForce/DarkSide/eam.F90, |
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UseTheForce/DarkSide/eam_interface.F90, |
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UseTheForce/DarkSide/eam_interface.h, |
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UseTheForce/DarkSide/electrostatic.F90, |
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UseTheForce/DarkSide/electrostatic_interface.F90, |
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UseTheForce/DarkSide/electrostatic_interface.h, |
22 |
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UseTheForce/DarkSide/force_globals.F90, |
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UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
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UseTheForce/DarkSide/lj_interface.F90, |
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UseTheForce/DarkSide/lj_interface.h, |
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UseTheForce/DarkSide/neighborLists.F90, |
27 |
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UseTheForce/DarkSide/reactionField.F90, |
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UseTheForce/DarkSide/shapes.F90, |
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UseTheForce/DarkSide/shapes_interface.F90, |
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UseTheForce/DarkSide/shapes_interface.h, |
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UseTheForce/DarkSide/simParallel.F90, |
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UseTheForce/DarkSide/simParallel_interface.F90, |
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UseTheForce/DarkSide/simParallel_interface.h, |
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UseTheForce/DarkSide/simulation.F90, |
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UseTheForce/DarkSide/simulation_interface.F90, |
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UseTheForce/DarkSide/simulation_interface.h, |
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UseTheForce/DarkSide/sticky.F90, |
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UseTheForce/DarkSide/sticky_interface.F90, |
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UseTheForce/DarkSide/sticky_interface.h, |
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UseTheForce/DarkSide/switcheroo.F90, |
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applications/dump2Xyz/Dump2XYZ.cpp, |
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applications/dump2Xyz/Dump2XYZCmd.c, |
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applications/dump2Xyz/Dump2XYZCmd.h, |
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applications/dynamicProps/CrossTimeCorrFunc.cpp, |
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applications/dynamicProps/CrossTimeCorrFunc.hpp, |
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applications/dynamicProps/DipoleCorrFunc.cpp, |
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applications/dynamicProps/DipoleCorrFunc.hpp, |
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applications/dynamicProps/DynamicProps.cpp, |
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applications/dynamicProps/DynamicPropsCmd.c, |
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applications/dynamicProps/DynamicPropsCmd.h, |
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applications/dynamicProps/FrameTimeCorrFunc.hpp, |
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applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
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applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
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applications/dynamicProps/RCorrFunc.cpp, |
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applications/dynamicProps/RCorrFunc.hpp, |
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applications/dynamicProps/TimeCorrFunc.cpp, |
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applications/dynamicProps/TimeCorrFunc.hpp, |
58 |
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applications/dynamicProps/VCorrFunc.cpp, |
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applications/dynamicProps/VCorrFunc.hpp, |
60 |
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applications/nanoRodBuilder/GeometryBuilder.cpp, |
61 |
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applications/nanoRodBuilder/GeometryBuilder.hpp, |
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applications/nanoRodBuilder/nanorodBuilder.cpp, |
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applications/nanoRodBuilder/nanorodBuilderCmd.c, |
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applications/nanoRodBuilder/nanorodBuilderCmd.h, |
65 |
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applications/oopse/oopse.cpp, |
66 |
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applications/simpleBuilder/simpleBuilder.cpp, |
67 |
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applications/simpleBuilder/simpleBuilderCmd.c, |
68 |
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applications/simpleBuilder/simpleBuilderCmd.h, |
69 |
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applications/staticProps/GofAngle2.cpp, |
70 |
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applications/staticProps/GofAngle2.hpp, |
71 |
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applications/staticProps/GofR.cpp, |
72 |
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applications/staticProps/GofR.hpp, |
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applications/staticProps/GofRAngle.cpp, |
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applications/staticProps/GofRAngle.hpp, |
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applications/staticProps/GofXyz.cpp, |
76 |
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applications/staticProps/GofXyz.hpp, |
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applications/staticProps/RadialDistrFunc.cpp, |
78 |
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applications/staticProps/RadialDistrFunc.hpp, |
79 |
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applications/staticProps/StaticProps.cpp, |
80 |
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applications/staticProps/StaticPropsCmd.c, |
81 |
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applications/staticProps/StaticPropsCmd.h, |
82 |
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brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
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brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
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brains/Exclude.hpp, brains/ForceManager.cpp, |
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brains/ForceManager.hpp, brains/MoleculeCreator.cpp, |
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brains/MoleculeCreator.hpp, brains/Register.cpp, |
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brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
88 |
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brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
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brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, |
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brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, |
91 |
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brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
92 |
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brains/fSimulation.h, constraints/ConstraintElem.hpp, |
93 |
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constraints/ConstraintPair.hpp, constraints/Rattle.cpp, |
94 |
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constraints/Rattle.hpp, constraints/ZconsStruct.hpp, |
95 |
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constraints/ZconstraintForceManager.cpp, |
96 |
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constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
97 |
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integrators/DLM.hpp, integrators/Integrator.cpp, |
98 |
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integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
99 |
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integrators/IntegratorFactory.cpp, |
100 |
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integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
101 |
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integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
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integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
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integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
104 |
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integrators/NVT.cpp, integrators/NVT.hpp, |
105 |
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integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
106 |
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integrators/Velocitizer.hpp, |
107 |
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integrators/VelocityVerletIntegrator.cpp, |
108 |
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integrators/VelocityVerletIntegrator.hpp, |
109 |
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io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
110 |
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io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
111 |
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io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
112 |
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io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
113 |
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io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
114 |
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io/ChargeAtomTypesSectionParser.hpp, |
115 |
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io/DirectionalAtomTypesSectionParser.cpp, |
116 |
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io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
117 |
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io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
118 |
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io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
119 |
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io/Globals.cpp, io/Globals.hpp, |
120 |
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io/LennardJonesAtomTypesSectionParser.cpp, |
121 |
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io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
122 |
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io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, |
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io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, |
124 |
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io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, |
125 |
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io/SectionParser.cpp, io/SectionParser.hpp, |
126 |
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io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
127 |
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io/StatWriter.cpp, io/StatWriter.hpp, |
128 |
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io/StickyAtomTypesSectionParser.cpp, |
129 |
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io/StickyAtomTypesSectionParser.hpp, |
130 |
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io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
131 |
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io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
132 |
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io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, |
133 |
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io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, |
134 |
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io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, |
135 |
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io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, |
136 |
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lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, |
137 |
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lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
138 |
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lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, |
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lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, |
140 |
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math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
141 |
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math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
142 |
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math/ParallelRandNumGen.hpp, math/Polynomial.hpp, |
143 |
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math/Quaternion.hpp, math/RandNumGen.hpp, |
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math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
145 |
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math/RectMatrix.hpp, math/SeqRandNumGen.cpp, |
146 |
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math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, |
147 |
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math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, |
148 |
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minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, |
149 |
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minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, |
150 |
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minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
151 |
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minimizers/MinimizerFactory.hpp, |
152 |
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minimizers/MinimizerParameterSet.cpp, |
153 |
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minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
154 |
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minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
155 |
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minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
156 |
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primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
157 |
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primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
158 |
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primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
159 |
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primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
160 |
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primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, |
161 |
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primitives/Molecule.cpp, primitives/Molecule.hpp, |
162 |
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primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
163 |
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primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
164 |
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primitives/Torsion.cpp, primitives/Torsion.hpp, |
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primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
166 |
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profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
167 |
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profiling/timing.F90, restraints/Restraints.cpp, |
168 |
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restraints/Restraints.hpp, |
169 |
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restraints/ThermoIntegrationForceManager.cpp, |
170 |
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restraints/ThermoIntegrationForceManager.hpp, |
171 |
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selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
172 |
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selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
173 |
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selection/NameFinder.cpp, selection/NameFinder.hpp, |
174 |
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selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, |
175 |
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selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
176 |
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selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
177 |
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selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, |
178 |
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selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, |
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types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
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types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
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types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
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types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
183 |
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types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
184 |
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types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
185 |
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types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
186 |
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types/DirectionalAtomType.hpp, types/FixedBondType.hpp, |
187 |
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types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, |
188 |
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types/MakeStamps.cpp, types/MakeStamps.hpp, |
189 |
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types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
190 |
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types/MorseBondType.hpp, types/OplsTorsionType.hpp, |
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types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
192 |
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types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, |
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types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, |
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types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
195 |
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types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
196 |
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types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
197 |
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types/TorsionType.hpp, types/UreyBradleyBendType.hpp, |
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types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, |
199 |
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utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
200 |
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utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
201 |
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utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, |
202 |
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utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, |
203 |
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utils/PropertyMap.cpp, utils/PropertyMap.hpp, |
204 |
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utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
205 |
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utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
206 |
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utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
207 |
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utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, |
208 |
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utils/any.hpp, utils/definitions.F90, utils/fError.c, |
209 |
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utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, |
210 |
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utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, |
211 |
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utils/residentMem.h, utils/simError.c, utils/simError.h, |
212 |
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utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, |
213 |
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visitors/AtomData.hpp, visitors/AtomVisitor.cpp, |
214 |
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visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, |
215 |
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visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, |
216 |
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visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
217 |
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visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, |
218 |
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visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, |
219 |
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visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has |
220 |
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been drafted to perform our indentation services |
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|
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2005-04-15 17:03 gezelter |
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|
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* configure, ac-tools/configure.in: Jedi mind-trick warning |
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messages have been added to make users ignore CGAL. |
226 |
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|
227 |
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2005-04-15 13:41 tim |
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|
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* make/Makefile.in: fix make install |
230 |
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|
231 |
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2005-04-15 13:41 tim |
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|
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* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: |
234 |
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add Makefile of samples |
235 |
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|
236 |
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2005-04-15 13:33 tim |
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|
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* samples/: lipid/Makefile, water/dimer/Makefile, |
239 |
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water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not |
240 |
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installed correctly |
241 |
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|
242 |
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2005-04-14 16:41 gezelter |
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|
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* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
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make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, |
246 |
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scripts/filepp, scripts/filepp.in: configure now searches for perl |
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to use with filepp |
248 |
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|
249 |
|
2005-04-14 16:20 gezelter |
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|
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* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |