trunk/AUTHORS
|
added
|
trunk/ChangeLog
|
added
|
trunk/LICENSE
|
added
|
trunk/Makefile
|
added
|
trunk/README
|
added
|
trunk/ac-tools/
|
added
|
trunk/ac-tools/Make.conf.in
|
added
|
trunk/ac-tools/aclocal.m4
|
added
|
trunk/ac-tools/config.guess
|
added
|
trunk/ac-tools/config.sub
|
added
|
trunk/ac-tools/configure.in
|
added
|
trunk/ac-tools/fortran90.m4
|
added
|
trunk/ac-tools/install-sh
|
added
|
trunk/ac-tools/shtool
|
added
|
trunk/configure
|
added
|
trunk/doc/
|
added
|
trunk/doc/OOPSE.pdf
|
added
|
trunk/forceFields/
|
added
|
trunk/forceFields/Ag.VC.funcfl
|
added
|
trunk/forceFields/Ag.u3.funcfl
|
added
|
trunk/forceFields/Ag.u6.funcfl
|
added
|
trunk/forceFields/Al.VC.funcfl
|
added
|
trunk/forceFields/Au.VC.funcfl
|
added
|
trunk/forceFields/Au.u3.funcfl
|
added
|
trunk/forceFields/Au.u6.funcfl
|
added
|
trunk/forceFields/Cu.VC.funcfl
|
added
|
trunk/forceFields/Cu.u3.funcfl
|
added
|
trunk/forceFields/Cu.u6.funcfl
|
added
|
trunk/forceFields/DUFF.frc
|
added
|
trunk/forceFields/DipoleTest.frc
|
added
|
trunk/forceFields/EAM.VC.frc
|
added
|
trunk/forceFields/EAM.frc
|
added
|
trunk/forceFields/EAM.u3.frc
|
added
|
trunk/forceFields/EAM.u6.frc
|
added
|
trunk/forceFields/LJFF.frc
|
added
|
trunk/forceFields/Makefile.in
|
added
|
trunk/forceFields/Ni.VC.funcfl
|
added
|
trunk/forceFields/Ni.u3.funcfl
|
added
|
trunk/forceFields/Ni.u6.funcfl
|
added
|
trunk/forceFields/Pd.VC.funcfl
|
added
|
trunk/forceFields/Pd.u3.funcfl
|
added
|
trunk/forceFields/Pd.u6.funcfl
|
added
|
trunk/forceFields/Pt.VC.funcfl
|
added
|
trunk/forceFields/Pt.u3.funcfl
|
added
|
trunk/forceFields/Pt.u6.funcfl
|
added
|
trunk/forceFields/WATER.frc
|
added
|
trunk/make/
|
added
|
trunk/make/Makefile
|
added
|
trunk/make/_files/
|
added
|
trunk/make/_files/style.css
|
added
|
trunk/samples/
|
added
|
trunk/samples/Makefile.in
|
added
|
trunk/samples/alkane/
|
added
|
trunk/samples/alkane/Makefile.in
|
added
|
trunk/samples/alkane/alkanes.md
|
added
|
trunk/samples/alkane/butane.in
|
added
|
trunk/samples/alkane/butane.md
|
added
|
trunk/samples/argon/
|
added
|
trunk/samples/argon/500.in
|
added
|
trunk/samples/argon/500.md
|
added
|
trunk/samples/argon/Makefile.in
|
added
|
trunk/samples/argon/ar864.in
|
added
|
trunk/samples/argon/ar864.md
|
added
|
trunk/samples/argon/argonNVT.in
|
added
|
trunk/samples/argon/argonNVT.md
|
added
|
trunk/samples/argon/lj.md
|
added
|
trunk/samples/lipid/
|
added
|
trunk/samples/lipid/5x5.in
|
added
|
trunk/samples/lipid/5x5.md
|
added
|
trunk/samples/lipid/Makefile.in
|
added
|
trunk/samples/lipid/lipid.md
|
added
|
trunk/samples/lipid/water.md
|
added
|
trunk/samples/metals/
|
added
|
trunk/samples/metals/Au-Core-Ag-Shell_Nanoparticle.in
|
added
|
trunk/samples/metals/Au-Core-Ag-Shell_Nanoparticle.md
|
added
|
trunk/samples/metals/Au_bulk.in
|
added
|
trunk/samples/metals/Au_bulk_FBD.md
|
added
|
trunk/samples/metals/Au_bulk_voter.md
|
added
|
trunk/samples/metals/Au_nanoparticle.in
|
added
|
trunk/samples/metals/Au_nanoparticle.md
|
added
|
trunk/samples/metals/Makefile.in
|
added
|
trunk/samples/metals/metals.md
|
added
|
trunk/samples/minimizer/
|
added
|
trunk/samples/minimizer/Makefile.in
|
added
|
trunk/samples/minimizer/WATER.frc
|
added
|
trunk/samples/minimizer/ssdEM.in
|
added
|
trunk/samples/minimizer/ssdEM.md
|
added
|
trunk/samples/minimizer/tip4p_two.in
|
added
|
trunk/samples/minimizer/tip4p_two.md
|
added
|
trunk/samples/minimizer/water.md
|
added
|
trunk/samples/water/
|
added
|
trunk/samples/water/Makefile.in
|
added
|
trunk/samples/water/dimer/
|
added
|
trunk/samples/water/dimer/Makefile.in
|
added
|
trunk/samples/water/dimer/two.in
|
added
|
trunk/samples/water/dimer/two.md
|
added
|
trunk/samples/water/dimer/water.md
|
added
|
trunk/samples/water/spce/
|
added
|
trunk/samples/water/spce/Makefile.in
|
added
|
trunk/samples/water/spce/spce.in
|
added
|
trunk/samples/water/spce/spce.md
|
added
|
trunk/samples/water/spce/water.md
|
added
|
trunk/samples/water/ssd/
|
added
|
trunk/samples/water/ssd/Makefile.in
|
added
|
trunk/samples/water/ssd/ssd.in
|
added
|
trunk/samples/water/ssd/ssd.md
|
added
|
trunk/samples/water/ssd/water.md
|
added
|
trunk/samples/water/ssde/
|
added
|
trunk/samples/water/ssde/Makefile.in
|
added
|
trunk/samples/water/ssde/ssde.in
|
added
|
trunk/samples/water/ssde/ssde.md
|
added
|
trunk/samples/water/ssde/water.md
|
added
|
trunk/samples/water/tip3p_ice/
|
added
|
trunk/samples/water/tip3p_ice/Makefile.in
|
added
|
trunk/samples/water/tip3p_ice/tp3.in
|
added
|
trunk/samples/water/tip3p_ice/tp3.md
|
added
|
trunk/samples/water/tip3p_ice/water.md
|
added
|
trunk/samples/water/tip4p/
|
added
|
trunk/samples/water/tip4p/Makefile.in
|
added
|
trunk/samples/water/tip4p/tp4.in
|
added
|
trunk/samples/water/tip4p/tp4.md
|
added
|
trunk/samples/water/tip4p/water.md
|
added
|
trunk/samples/zcons/
|
added
|
trunk/samples/zcons/Makefile.in
|
added
|
trunk/samples/zcons/water.md
|
added
|
trunk/samples/zcons/zconsFixed.in
|
added
|
trunk/samples/zcons/zconsFixed.md
|
added
|
trunk/samples/zcons/zconsMoving.in
|
added
|
trunk/samples/zcons/zconsMoving.md
|
added
|
trunk/scripts/
|
added
|
trunk/scripts/cleanSrc
|
added
|
trunk/scripts/cvs2cl.pl
|
added
|
trunk/scripts/makers
|
added
|
trunk/scripts/sfmakedepend
|
added
|
trunk/src/
|
added
|
trunk/src/Makefile
|
added
|
trunk/src/UseTheForce/
|
added
|
trunk/src/UseTheForce/DUFF.cpp
|
added
|
trunk/src/UseTheForce/DarkSide/
|
added
|
trunk/src/UseTheForce/DarkSide/Makefile
|
added
|
trunk/src/UseTheForce/DarkSide/atype_module.F90
|
added
|
trunk/src/UseTheForce/DarkSide/calc_LJ_FF.F90
|
added
|
trunk/src/UseTheForce/DarkSide/calc_charge_charge.F90
|
added
|
trunk/src/UseTheForce/DarkSide/calc_dipole_dipole.F90
|
added
|
trunk/src/UseTheForce/DarkSide/calc_eam.F90
|
added
|
trunk/src/UseTheForce/DarkSide/calc_gb.F90
|
added
|
trunk/src/UseTheForce/DarkSide/calc_reaction_field.F90
|
added
|
trunk/src/UseTheForce/DarkSide/calc_sticky_pair.F90
|
added
|
trunk/src/UseTheForce/DarkSide/force_globals.F90
|
added
|
trunk/src/UseTheForce/DarkSide/neighborLists.F90
|
added
|
trunk/src/UseTheForce/DarkSide/notifyCutoffs.F90
|
added
|
trunk/src/UseTheForce/DarkSide/switch_module.F90
|
added
|
trunk/src/UseTheForce/EAM_FF.cpp
|
added
|
trunk/src/UseTheForce/ForceFields.cpp
|
added
|
trunk/src/UseTheForce/ForceFields.hpp
|
added
|
trunk/src/UseTheForce/LJFF.cpp
|
added
|
trunk/src/UseTheForce/Makefile
|
added
|
trunk/src/UseTheForce/WATER.cpp
|
added
|
trunk/src/UseTheForce/do_Forces.F90
|
added
|
trunk/src/UseTheForce/fForceField.h
|
added
|
trunk/src/UseTheForce/fSwitchingFunction.h
|
added
|
trunk/src/UseTheForce/fortranWrapDefines.hpp
|
added
|
trunk/src/UseTheForce/fortranWrappers.cpp
|
added
|
trunk/src/UseTheForce/fortranWrappers.hpp
|
added
|
trunk/src/UseTheForce/mpiComponentPlan.h
|
added
|
trunk/src/UseTheForce/mpiForceField.c
|
added
|
trunk/src/UseTheForce/mpiForceField.h
|
added
|
trunk/src/UseTheForce/mpiSimulation_module.F90
|
added
|
trunk/src/UseTheForce/wrappers.F90
|
added
|
trunk/src/applications/
|
added
|
trunk/src/applications/BaseLattice.cpp
|
added
|
trunk/src/applications/BaseLattice.hpp
|
added
|
trunk/src/applications/Dump2XYZ.cpp
|
added
|
trunk/src/applications/Dump2XYZ.ggo
|
added
|
trunk/src/applications/Dump2XYZCmd.c
|
added
|
trunk/src/applications/Dump2XYZCmd.h
|
added
|
trunk/src/applications/Lattice.cpp
|
added
|
trunk/src/applications/Lattice.hpp
|
added
|
trunk/src/applications/LatticeCreator.cpp
|
added
|
trunk/src/applications/LatticeCreator.hpp
|
added
|
trunk/src/applications/LatticeFactory.cpp
|
added
|
trunk/src/applications/LatticeFactory.hpp
|
added
|
trunk/src/applications/Makedepend
|
added
|
trunk/src/applications/Makefile
|
added
|
trunk/src/applications/MoLocator.cpp
|
added
|
trunk/src/applications/MoLocator.hpp
|
added
|
trunk/src/applications/Vector3d.hpp
|
added
|
trunk/src/applications/cmdline.c
|
added
|
trunk/src/applications/cmdline.h
|
added
|
trunk/src/applications/getopt.c
|
added
|
trunk/src/applications/getopt1.c
|
added
|
trunk/src/applications/gnugetopt.h
|
added
|
trunk/src/applications/nanoBuilder.cpp
|
added
|
trunk/src/applications/nanoBuilder.hpp
|
added
|
trunk/src/applications/oopse.cpp
|
added
|
trunk/src/applications/quickLate.c
|
added
|
trunk/src/applications/simpleBuilder.cpp
|
added
|
trunk/src/applications/simpleBuilder.ggo
|
added
|
trunk/src/applications/simpleBuilderCmd.c
|
added
|
trunk/src/applications/simpleBuilderCmd.h
|
added
|
trunk/src/brains/
|
added
|
trunk/src/brains/Exclude.cpp
|
added
|
trunk/src/brains/Exclude.hpp
|
added
|
trunk/src/brains/ForceFields.cpp
|
added
|
trunk/src/brains/Makedepend
|
added
|
trunk/src/brains/Makefile
|
added
|
trunk/src/brains/SimInfo.cpp
|
added
|
trunk/src/brains/SimInfo.hpp
|
added
|
trunk/src/brains/SimSetup.cpp
|
added
|
trunk/src/brains/SimSetup.hpp
|
added
|
trunk/src/brains/SimState.cpp
|
added
|
trunk/src/brains/SimState.hpp
|
added
|
trunk/src/brains/SkipList.cpp
|
added
|
trunk/src/brains/SkipList.hpp
|
added
|
trunk/src/brains/Thermo.cpp
|
added
|
trunk/src/brains/Thermo.hpp
|
added
|
trunk/src/brains/fSimulation.h
|
added
|
trunk/src/brains/mpiSimulation.cpp
|
added
|
trunk/src/brains/mpiSimulation.hpp
|
added
|
trunk/src/brains/simulation_module.F90
|
added
|
trunk/src/config.h.in
|
added
|
trunk/src/constraints/
|
added
|
trunk/src/constraints/AbstractClasses.hpp
|
added
|
trunk/src/constraints/Makefile
|
added
|
trunk/src/constraints/ZConstraint.cpp
|
added
|
trunk/src/integrators/
|
added
|
trunk/src/integrators/AbstractClasses.hpp
|
added
|
trunk/src/integrators/AllIntegrator.hpp
|
added
|
trunk/src/integrators/Integrator.cpp
|
added
|
trunk/src/integrators/Integrator.hpp
|
added
|
trunk/src/integrators/Makefile
|
added
|
trunk/src/integrators/NPT.cpp
|
added
|
trunk/src/integrators/NPTf.cpp
|
added
|
trunk/src/integrators/NPTi.cpp
|
added
|
trunk/src/integrators/NPTxyz.cpp
|
added
|
trunk/src/integrators/NVT.cpp
|
added
|
trunk/src/io/
|
added
|
trunk/src/io/BASS_interface.cpp
|
added
|
trunk/src/io/BASS_interface.h
|
added
|
trunk/src/io/BASS_parse.c
|
added
|
trunk/src/io/BASS_parse.h
|
added
|
trunk/src/io/BASSlex.l
|
added
|
trunk/src/io/BASSyacc.y
|
added
|
trunk/src/io/DumpReader.cpp
|
added
|
trunk/src/io/DumpWriter.cpp
|
added
|
trunk/src/io/Globals.cpp
|
added
|
trunk/src/io/Globals.hpp
|
added
|
trunk/src/io/InitializeFromFile.cpp
|
added
|
trunk/src/io/LinkedAssign.cpp
|
added
|
trunk/src/io/LinkedAssign.hpp
|
added
|
trunk/src/io/LinkedCommand.cpp
|
added
|
trunk/src/io/LinkedCommand.hpp
|
added
|
trunk/src/io/Makefile
|
added
|
trunk/src/io/ReadWrite.hpp
|
added
|
trunk/src/io/StatWriter.cpp
|
added
|
trunk/src/io/ZConsReader.cpp
|
added
|
trunk/src/io/ZConsReader.hpp
|
added
|
trunk/src/io/ZConsWriter.cpp
|
added
|
trunk/src/io/ZConsWriter.hpp
|
added
|
trunk/src/io/interface.c
|
added
|
trunk/src/io/make_nodes.c
|
added
|
trunk/src/io/make_nodes.h
|
added
|
trunk/src/io/mpiBASS.c
|
added
|
trunk/src/io/mpiBASS.h
|
added
|
trunk/src/io/node_list.h
|
added
|
trunk/src/io/parse_interface.h
|
added
|
trunk/src/io/parse_me.h
|
added
|
trunk/src/io/parse_tree.c
|
added
|
trunk/src/io/parse_tree.h
|
added
|
trunk/src/math/
|
added
|
trunk/src/math/Euler3.cpp
|
added
|
trunk/src/math/Euler3.hpp
|
added
|
trunk/src/math/Makefile
|
added
|
trunk/src/math/MatVec3.c
|
added
|
trunk/src/math/MatVec3.h
|
added
|
trunk/src/math/mt19937ar.c
|
added
|
trunk/src/math/randomSPRNG.cpp
|
added
|
trunk/src/math/randomSPRNG.hpp
|
added
|
trunk/src/minimizers/
|
added
|
trunk/src/minimizers/CGFamilyMinimizer.cpp
|
added
|
trunk/src/minimizers/Makefile
|
added
|
trunk/src/minimizers/MinimizerParameterSet.hpp
|
added
|
trunk/src/minimizers/OOPSEMinimizer.cpp
|
added
|
trunk/src/minimizers/OOPSEMinimizer.hpp
|
added
|
trunk/src/minimizers/PRCG.cpp
|
added
|
trunk/src/minimizers/SDMinimizer.cpp
|
added
|
trunk/src/primitives/
|
added
|
trunk/src/primitives/AbstractClasses.hpp
|
added
|
trunk/src/primitives/Atom.cpp
|
added
|
trunk/src/primitives/Atom.hpp
|
added
|
trunk/src/primitives/Bend.cpp
|
added
|
trunk/src/primitives/BendExtensions.cpp
|
added
|
trunk/src/primitives/Bond.cpp
|
added
|
trunk/src/primitives/BondExtensions.cpp
|
added
|
trunk/src/primitives/CutoffGroup.hpp
|
added
|
trunk/src/primitives/DirectionalAtom.cpp
|
added
|
trunk/src/primitives/DirectionalAtom.hpp
|
added
|
trunk/src/primitives/GhostBend.cpp
|
added
|
trunk/src/primitives/Makefile
|
added
|
trunk/src/primitives/Molecule.cpp
|
added
|
trunk/src/primitives/Molecule.hpp
|
added
|
trunk/src/primitives/RigidBody.cpp
|
added
|
trunk/src/primitives/RigidBody.hpp
|
added
|
trunk/src/primitives/SRI.hpp
|
added
|
trunk/src/primitives/StuntDouble.cpp
|
added
|
trunk/src/primitives/StuntDouble.hpp
|
added
|
trunk/src/primitives/Torsion.cpp
|
added
|
trunk/src/primitives/TorsionExtensions.cpp
|
added
|
trunk/src/profiling/
|
added
|
trunk/src/profiling/Makefile
|
added
|
trunk/src/profiling/mdProfile.cpp
|
added
|
trunk/src/profiling/mdProfile.hpp
|
added
|
trunk/src/profiling/timing.F90
|
added
|
trunk/src/restraints/
|
added
|
trunk/src/restraints/Makefile
|
added
|
trunk/src/restraints/Restraints.cpp
|
added
|
trunk/src/restraints/Restraints.hpp
|
added
|
trunk/src/types/
|
added
|
trunk/src/types/AtomStamp.cpp
|
added
|
trunk/src/types/AtomStamp.hpp
|
added
|
trunk/src/types/BendStamp.cpp
|
added
|
trunk/src/types/BendStamp.hpp
|
added
|
trunk/src/types/BondStamp.cpp
|
added
|
trunk/src/types/BondStamp.hpp
|
added
|
trunk/src/types/Component.cpp
|
added
|
trunk/src/types/Component.hpp
|
added
|
trunk/src/types/CutoffGroupStamp.cpp
|
added
|
trunk/src/types/CutoffGroupStamp.hpp
|
added
|
trunk/src/types/MakeStamps.cpp
|
added
|
trunk/src/types/MakeStamps.hpp
|
added
|
trunk/src/types/Makefile
|
added
|
trunk/src/types/MoleculeStamp.cpp
|
added
|
trunk/src/types/MoleculeStamp.hpp
|
added
|
trunk/src/types/RigidBodyStamp.cpp
|
added
|
trunk/src/types/RigidBodyStamp.hpp
|
added
|
trunk/src/types/TorsionStamp.cpp
|
added
|
trunk/src/types/TorsionStamp.hpp
|
added
|
trunk/src/types/ZconStamp.cpp
|
added
|
trunk/src/types/ZconStamp.hpp
|
added
|
trunk/src/utils/
|
added
|
trunk/src/utils/GenericData.cpp
|
added
|
trunk/src/utils/GenericData.hpp
|
added
|
trunk/src/utils/Makefile
|
added
|
trunk/src/utils/StreamTokenizer.cpp
|
added
|
trunk/src/utils/StreamTokenizer.hpp
|
added
|
trunk/src/utils/StringUtils.c
|
added
|
trunk/src/utils/StringUtils.cpp
|
added
|
trunk/src/utils/StringUtils.h
|
added
|
trunk/src/utils/StringUtils.hpp
|
added
|
trunk/src/utils/TypeInfo.hpp
|
added
|
trunk/src/utils/Utility.cpp
|
added
|
trunk/src/utils/Utility.hpp
|
added
|
trunk/src/utils/definitions_module.F90
|
added
|
trunk/src/utils/fError.c
|
added
|
trunk/src/utils/oopseMPI_module.F90
|
added
|
trunk/src/utils/simError.c
|
added
|
trunk/src/utils/simError.h
|
added
|
trunk/src/utils/status_module.F90
|
added
|
trunk/src/utils/vector_class.F90
|
added
|
trunk/src/visitors/
|
added
|
trunk/src/visitors/AtomVisitor.cpp
|
added
|
trunk/src/visitors/AtomVisitor.hpp
|
added
|
trunk/src/visitors/BaseVisitor.hpp
|
added
|
trunk/src/visitors/CompositeVisitor.cpp
|
added
|
trunk/src/visitors/CompositeVisitor.hpp
|
added
|
trunk/src/visitors/Makefile
|
added
|
trunk/src/visitors/OtherVisitor.cpp
|
added
|
trunk/src/visitors/OtherVisitor.hpp
|
added
|
trunk/src/visitors/RigidBodyVisitor.cpp
|
added
|
trunk/src/visitors/RigidBodyVisitor.hpp
|
added
|
trunk/src/visitors/ZconsVisitor.cpp
|
added
|
trunk/src/visitors/ZconsVisitor.hpp
|
added
|