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2003-09-10 16:28 mmeineke |
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2004-07-16 11:31 gezelter |
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* src/oose.cpp: New web address |
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2004-07-16 11:29 gezelter |
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* libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizer.cpp, |
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libmdtools/OOPSEMinimizer.hpp, libmdtools/SimSetup.cpp, |
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src/oopse.cpp: Minor changes |
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2004-07-15 14:43 chrisfen |
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* samples/water/: spce/water.mdl, ssde/water.mdl, tip4p/water.mdl: |
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Expanded the water.mdl file |
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2004-07-15 14:37 chrisfen |
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* forceFields/WATER.frc: Added the SPC water model |
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2004-07-15 14:29 chrisfen |
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* samples/water/tip4p/tp4.bass: quick change in tp4.bass |
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2004-07-15 14:28 chrisfen |
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* samples/water/tip4p/: TP4init.in, tp4.bass, water.mdl: Added |
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TIP4P water sample |
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2004-07-14 17:25 chrisfen |
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* samples/water/spce/: SPCEinit.in, spce.bass, water.mdl: Added |
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SPCE water sample |
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2004-07-14 15:58 chrisfen |
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* samples/water/ssde/: 256init.in, ssde.bass, water.mdl: Good ssde |
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simulation sample added |
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2004-07-14 15:11 gezelter |
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* configure, libmdtools/ConstraintIterator.hpp, |
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libmdtools/Integrator.hpp: Fixes for MacOS X with xlc++ and xlf |
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2004-07-12 13:08 chuckv |
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* ac-tools/fortran90.m4: [no log message] |
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2004-07-02 16:41 gezelter |
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* libmdtools/calc_shapes.F90: Added a bunch of stuff |
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2004-06-29 17:52 tim |
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* libmdtools/Mat3x3d.cpp: fixed a bug in Mat3x3d.cpp |
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2004-06-29 16:15 gezelter |
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* libmdtools/calc_shapes.F90: added SHAPE force routine |
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2004-06-21 13:52 tim |
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* ChangeLog, libmdtools/CallbackFunctor.hpp, |
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libmdtools/ConstraintAlgorithm.cpp, |
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libmdtools/ConstraintElement.hpp, libmdtools/Integrator.cpp, |
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libmdtools/Rattle.cpp, libmdtools/RigidBody.cpp, |
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libmdtools/RigidBody.hpp, libmdtools/Roll.cpp, libmdtools/Roll.hpp, |
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samples/alkane/alkanes.mdl: roll in progress |
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2004-06-11 14:46 gezelter |
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* libmdtools/notifyCutoffs.F90: nicer error message formatting |
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2004-06-11 14:24 gezelter |
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* libmdtools/: Make.dep, Makefile.in: Fixed dependency bug (we |
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hope) |
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2004-06-11 12:16 tim |
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* ChangeLog, libBASS/MoleculeStamp.cpp, |
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libmdtools/ConstraintAlgorithm.cpp, |
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libmdtools/ConstraintAlgorithm.hpp, |
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libmdtools/ConstraintElement.cpp, libmdtools/DumpReader.cpp, |
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libmdtools/Euler3.cpp, libmdtools/Euler3.hpp, |
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libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
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libmdtools/Integrator.hpp, libmdtools/Make.dep, |
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libmdtools/Mat3x3d.cpp, libmdtools/Mat3x3d.hpp, libmdtools/NPT.cpp, |
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libmdtools/NVT.cpp, libmdtools/Rattle.hpp, libmdtools/Roll.cpp, |
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libmdtools/Roll.hpp: roll in progress |
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2004-06-11 11:46 gezelter |
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* samples/metals/Au.bass: Sample now does variant |
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2004-06-11 11:46 gezelter |
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* libmdtools/EAM_FF.cpp: General fixes for formatting |
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2004-06-11 11:45 gezelter |
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* forceFields/: Ag.VC.funcfl, Al.VC.funcfl, Au.VC.funcfl, |
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Cu.VC.funcfl, Ni.VC.funcfl, Pd.VC.funcfl, Pt.VC.funcfl: Converted |
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D's to E's in the funcfl files so that C can read them. |
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2004-06-11 11:35 gezelter |
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* forceFields/: Ag.VC.funcfl, Ag.Voter.eam, Ag.u3.eam, |
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Ag.u3.funcfl, Ag.u6.eam, Ag.u6.funcfl, Al.VC.funcfl, Al.Voter.eam, |
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Au.VC.funcfl, Au.Voter.eam, Au.u3.eam, Au.u3.funcfl, Au.u6.eam, |
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Au.u6.funcfl, Cu.VC.funcfl, Cu.Voter.eam, Cu.u3.eam, Cu.u3.funcfl, |
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Cu.u6.eam, Cu.u6.funcfl, EAM.VC.frc, EAM.Voter.frc, EAM.frc, |
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EAM.u3.frc, EAM.u6.frc, Ni.VC.funcfl, Ni.Voter.eam, Ni.u3.eam, |
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Ni.u3.funcfl, Ni.u6.eam, Ni.u6.funcfl, Pd.VC.funcfl, Pd.Voter.eam, |
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Pd.u3.eam, Pd.u3.funcfl, Pd.u6.eam, Pd.u6.funcfl, Pt.VC.funcfl, |
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Pt.u3.eam, Pt.u3.funcfl, Pt.u6.eam, Pt.u6.funcfl: changing file |
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extensions to be more in line with what's actually in the file |
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2004-06-11 10:31 gezelter |
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* forceFields/: Ag.Voter.eam, Ag.u3.eam, Ag.u6.eam, Al.Voter.eam, |
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Au.Voter.eam, Au.u3.eam, Au.u6.eam, Cu.Voter.eam, Cu.u3.eam, |
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Cu.u6.eam, EAM.frc, EAM.u6.frc, Ni.Voter.eam, Ni.u3.eam, Ni.u6.eam, |
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Pd.Voter.eam, Pd.u3.eam, Pd.u6.eam, Pt.u3.eam, Pt.u6.eam, |
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ag.u3.eam, au.u3.eam, cu.u3.eam, ni.u3.eam, pd.u3.eam, pt.u3.eam: |
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Added a bunch of files for EAM variants |
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2004-06-11 09:14 gezelter |
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* samples/metals/Au.bass: Modified EAM to use forceFieldVariant, |
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show sample in Au.bass |
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2004-06-11 09:14 gezelter |
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* libmdtools/: EAM_FF.cpp, ForceFields.hpp, SimSetup.cpp, |
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SimSetup.hpp: Modified EAM to use forceFieldVariant |
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2004-06-11 09:13 gezelter |
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* libBASS/: Globals.cpp, Globals.hpp: Added forceFieldVariant |
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global |
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2004-06-10 17:15 gezelter |
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* forceFields/: EAM.Voter.frc, EAM.frc, EAM.u3.frc, EAM_FF.frc, |
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ag.u3.eam, agu3.eam, au.u3.eam, auu3.eam, backup.DUFF.frc, |
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cu.u3.eam, cuu3.eam, ni.u3.eam, niu3.eam, pd.u3.eam, pdu3.eam, |
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pt.u3.eam, ptu3.eam: reorg of EAM force fields to have variants |
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2004-06-10 12:09 chrisfen |
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* libmdtools/ForceFields.cpp: Fixed a thermodynamic integration |
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issue. Force and torque scaling loops over atoms, not stuntdoubles |
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2004-06-10 10:00 gezelter |
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* libBASS/: MakeStamps.cpp, MoleculeStamp.cpp: Removed debugging |
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printf statements |
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2004-06-10 09:59 gezelter |
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* libBASS/: MakeStamps.cpp, MoleculeStamp.cpp, make_nodes.c: Fixed |
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indexing bug in stamps |
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2004-06-09 11:59 tim |
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* ChangeLog, libmdtools/Roll.cpp: Roll in progress |
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2004-06-09 11:16 tim |
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* libmdtools/: ConstraintAlgorithm.hpp, ConstraintElement.hpp, |
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Euler3.cpp, Euler3.hpp, Integrator.hpp, Make.dep, Makefile.in, |
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Mat3x3d.cpp, Mat3x3d.hpp, Quaternion.cpp, Quaternion.hpp, |
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Rattle.cpp, Rattle.hpp, RigidBody.cpp, RigidBody.hpp, Roll.cpp, |
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Roll.hpp, Shake.cpp, Shake.hpp, Vector3d.cpp, Vector3d.hpp: 1. |
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adding some useful math classes(Mat3x3d, Vector3d, Quaternion, |
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Euler3) these classes use anonymous union and struct to support |
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double[3], double[3][3] and double[4] 2. adding roll constraint |
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algorithm |
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2004-06-08 11:49 gezelter |
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* libmdtools/: NPT.cpp, NPTf.cpp, StuntDouble.cpp, Thermo.cpp: |
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Fixed a bug in NPTf (vScale was declared in the cpp file in |
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addition to the declaration in Integrator.hpp file) |
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2004-06-07 09:26 gezelter |
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* libBASS/Globals.cpp, libmdtools/AtomVisitor.cpp, |
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libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.hpp, |
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libmdtools/ConstraintIterator.hpp, |
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libmdtools/ConstraintManager.hpp, libmdtools/ConstraintPair.hpp, |
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libmdtools/DirectionalAtom.cpp, libmdtools/DumpReader.cpp, |
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libmdtools/DumpWriter.cpp, libmdtools/MatVec3.c, |
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libmdtools/MatVec3.h, libmdtools/StreamTokenizer.hpp, |
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libmdtools/ZConsReader.cpp: Fixes from gcc -Wall |
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2004-06-07 09:09 chrisfen |
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* libmdtools/Thermo.cpp: Dan cleaned up the pressure calculation a |
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bit... Got rid of some unnecessary lines of code in Thermo.cpp |
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2004-06-04 16:00 gezelter |
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* libmdtools/: ConstraintIterator.hpp, OOPSEMinimizer.cpp, |
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StuntDouble.cpp: small bugfixes |
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2004-06-04 15:29 tim |
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* libmdtools/Integrator.hpp: [no log message] |
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2004-06-04 14:30 tim |
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* ChangeLog, libmdtools/CallbackFunctor.cpp, |
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libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.cpp, |
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libmdtools/ConstraintAlgorithm.hpp, libmdtools/Integrator.hpp, |
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libmdtools/OOPSEMinimizer.cpp, libmdtools/Rattle.hpp, |
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libmdtools/Shake.hpp, libmdtools/ShakeMin.cpp, |
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libmdtools/ShakeMin.hpp: constraint algorithm for minimization is |
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working |
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2004-06-04 11:23 gezelter |
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* forceFields/charmm27.vdw: Moved to SHAPES |
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2004-06-04 11:23 gezelter |
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* forceFields/: LJ.vdw, amber99.vdw, gaff.vdw, oplsaal.vdw: [no log |
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message] |
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2004-06-04 09:59 gezelter |
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* libmdtools/: notifyCutoffs.F90, status_module.F90, wrappers.F90: |
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More work on Fortran side of error handler |
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2004-06-04 09:59 gezelter |
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* configure, ac-tools/aclocal.m4: fixed a typo in autoconf script |
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2004-06-04 09:35 gezelter |
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* libmdtools/: Makefile.in, fInfo.c, status_module.F90: Unifying |
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the error handlers |
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2004-06-04 09:17 gezelter |
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* libBASS/: MemberStamp.cpp, MemberStamp.hpp: Not used anymore |
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2004-06-04 09:11 gezelter |
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* libBASS/: config.h.in, fError.c: forgot to add these |
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2004-06-03 22:15 tim |
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* ChangeLog, libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
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libmdtools/CallbackFunctor.cpp, libmdtools/ConstraintAlgorithm.cpp, |
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libmdtools/ConstraintManager.cpp, libmdtools/GenericData.cpp, |
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libmdtools/GenericData.hpp, libmdtools/Integrator.cpp, |
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libmdtools/Integrator.hpp, libmdtools/Make.dep, |
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libmdtools/Makefile.in, libmdtools/Molecule.cpp, |
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libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NVT.cpp, |
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libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, |
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libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
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libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
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libmdtools/SimSetup.cpp, libmdtools/StuntDouble.cpp, |
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libmdtools/StuntDouble.hpp, utils/Vector3.hpp: new rattle algorithm |
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is working |
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2004-06-03 21:38 gezelter |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
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libBASS/Makefile.in, libBASS/mpiBASS.h, libBASS/simError.c, |
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libBASS/simError.h, libmdtools/Makefile.in, libmdtools/config.h.in, |
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libmdtools/notifyCutoffs.F90, src/Makefile.in: Config changes for |
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fortran access to SimError |
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2004-06-03 16:51 tim |
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* libmdtools/: CallbackFunctor.cpp, CallbackFunctor.hpp, |
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ConstraintAlgorithm.cpp, ConstraintAlgorithm.hpp, |
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ConstraintElement.cpp, ConstraintElement.hpp, |
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ConstraintIterator.hpp, ConstraintManager.cpp, |
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ConstraintManager.hpp, ConstraintPair.hpp, Rattle.cpp, Rattle.hpp, |
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Shake.cpp, Shake.hpp, ShakeMin.cpp, ShakeMin.hpp, TypeInfo.hpp: new |
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implementation of constraint |
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2004-06-03 16:06 tim |
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* libmdtools/DumpWriter.cpp: fixed a bug which only writes out the |
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first atom of a molecule |
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2004-06-03 15:02 gezelter |
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* libmdtools/SimSetup.cpp: Fixed groupOffset bug |
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2004-06-03 15:02 gezelter |
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* ac-tools/: aclocal.m4, configure.in: Working on MPI scripting for |
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autoconf |
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2004-06-02 13:28 gezelter |
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* samples/argon/Makefile: Shouldn't have been in CVS |
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2004-06-02 13:28 gezelter |
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* samples/argon/Makefile: Why is this in CVS? |
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2004-06-02 13:27 gezelter |
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* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Make.dep, |
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Makefile.in, WATER.cpp: formatting error messages, dependency fixes |
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2004-06-02 13:27 gezelter |
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* libBASS/simError.h: starting fortran-usable version of simError |
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2004-06-02 09:56 chrisfen |
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* samples/argon/Makefile: Probably shouldn't be in CVS |
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2004-06-02 09:56 chrisfen |
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* libmdtools/: Integrator.cpp, NVT.cpp, ReadWrite.hpp, |
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Restraints.cpp, SimInfo.cpp, StatWriter.cpp: Formatting Changes, |
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removed writeRaw |
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2004-06-02 09:56 chrisfen |
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* libBASS/simError.c: Formatting Changes |
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2004-06-02 09:21 gezelter |
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* libBASS/simError.c, libBASS/simError.h, libmdtools/SimInfo.cpp: |
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severity levels in simError |
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2004-06-01 16:45 gezelter |
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* libmdtools/: Exclude.cpp, SimInfo.cpp, calc_LJ_FF.F90, |
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do_Forces.F90, mpiSimulation.cpp, neighborLists.F90, |
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simulation_module.F90: Bug fix (fixes of skipList and neighbor list |
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under MPI) |
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2004-06-01 16:44 gezelter |
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* libBASS/MoleculeStamp.cpp: Bug fix (memory leak) |
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2004-06-01 13:43 gezelter |
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* samples/argon/argon.bass: Testing |
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2004-06-01 13:42 gezelter |
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* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
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SimSetup.hpp, do_Forces.F90, fortranWrapDefines.hpp, |
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mpiSimulation.cpp, mpiSimulation_module.F90, simulation_module.F90: |
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Cutoff Groups for MPI |
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2004-06-01 13:07 chrisfen |
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* libmdtools/: ForceFields.cpp, StatWriter.cpp: Fixed bug in |
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useLiquidThermInt routine in ForceFields.cpp |
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2004-06-01 12:15 chrisfen |
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* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
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SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Implemented a separate |
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solid and liquid thermodynamic integration routines |
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2004-06-01 10:57 tim |
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|
371 |
> |
* libmdtools/: CutoffGroup.hpp, SimSetup.cpp: cutoff group in |
372 |
> |
progress |
373 |
> |
|
374 |
> |
2004-06-01 09:27 chrisfen |
375 |
> |
|
376 |
> |
* libBASS/: Globals.cpp, Globals.hpp: Added useLiquidThermInt |
377 |
> |
keyword and changed useThermInt to useSolidThermInt |
378 |
> |
|
379 |
> |
2004-06-01 09:21 chrisfen |
380 |
> |
|
381 |
> |
* libBASS/: Globals.cpp, Globals.hpp: Paving the way for separate |
382 |
> |
solid and liquid thermodynamic integration routines |
383 |
> |
|
384 |
> |
2004-05-28 10:21 gezelter |
385 |
> |
|
386 |
> |
* libmdtools/do_Forces.F90: bugfix starting |
387 |
> |
|
388 |
> |
2004-05-27 15:06 chrisfen |
389 |
> |
|
390 |
> |
* libmdtools/: Integrator.cpp, StatWriter.cpp: Fixed a bug in |
391 |
> |
Integrator.cpp where it called writeRaw() when useThermInt = |
392 |
> |
false... |
393 |
> |
|
394 |
> |
2004-05-27 14:51 tim |
395 |
> |
|
396 |
> |
* ChangeLog, libmdtools/do_Forces.F90, |
397 |
> |
libmdtools/simulation_module.F90: Bug fix for SkipList |
398 |
> |
|
399 |
> |
2004-05-27 14:26 gezelter |
400 |
> |
|
401 |
> |
* libmdtools/SimSetup.cpp: bugfix in simsetup? |
402 |
> |
|
403 |
> |
2004-05-27 13:59 gezelter |
404 |
> |
|
405 |
> |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, |
406 |
> |
InitializeFromFile.cpp, SimInfo.cpp, SimSetup.cpp, SimSetup.hpp, |
407 |
> |
ZConsWriter.cpp, ZConstraint.cpp, fortranWrapDefines.hpp, |
408 |
> |
mdProfile.cpp, mpiSimulation.cpp, mpiSimulation.hpp, |
409 |
> |
mpiSimulation_module.F90, randomSPRNG.cpp, simulation_module.F90: |
410 |
> |
Cutoff group changes under MPI |
411 |
> |
|
412 |
> |
2004-05-27 11:20 gezelter |
413 |
> |
|
414 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: Fixes for |
415 |
> |
xlc++ |
416 |
> |
|
417 |
> |
2004-05-27 10:31 tim |
418 |
> |
|
419 |
> |
* libmdtools/SimInfo.cpp: groupList new bases on global index of |
420 |
> |
atoms |
421 |
> |
|
422 |
> |
2004-05-27 10:21 gezelter |
423 |
> |
|
424 |
> |
* src/: oopse.cpp, oose.cpp: Modified the nifty banner |
425 |
> |
|
426 |
> |
2004-05-27 10:21 gezelter |
427 |
> |
|
428 |
> |
* libmdtools/: Make.dep, do_Forces.F90, simulation_module.F90: |
429 |
> |
Fixed off-by-one error in groupStartRow and groupStartCol |
430 |
> |
|
431 |
> |
2004-05-26 19:48 tim |
432 |
> |
|
433 |
> |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/DumpWriter.cpp, |
434 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
435 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
436 |
> |
libmdtools/ZConsWriter.cpp, libmdtools/calc_LJ_FF.F90, |
437 |
> |
libmdtools/calc_charge_charge.F90, |
438 |
> |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, |
439 |
> |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
440 |
> |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
441 |
> |
libmdtools/force_globals.F90, libmdtools/mdProfile.cpp, |
442 |
> |
libmdtools/mpiComponentPlan.h, libmdtools/mpiSimulation.cpp, |
443 |
> |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
444 |
> |
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
445 |
> |
libmdtools/simulation_module.F90: in the progress of fixing MPI |
446 |
> |
version of cutoff group |
447 |
> |
|
448 |
> |
2004-05-26 11:41 gezelter |
449 |
> |
|
450 |
> |
* libmdtools/do_Forces.F90: Compacted all of the 8 copies of the |
451 |
> |
force loop into one. |
452 |
> |
|
453 |
> |
2004-05-24 17:24 gezelter |
454 |
> |
|
455 |
> |
* libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes |
456 |
> |
|
457 |
> |
2004-05-24 16:23 chrisfen |
458 |
> |
|
459 |
> |
* libmdtools/Restraints.cpp: Removed unnecessary variables and |
460 |
> |
changed error messages in Restraints.cpp |
461 |
> |
|
462 |
> |
2004-05-24 16:03 gezelter |
463 |
> |
|
464 |
> |
* libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90, |
465 |
> |
calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
466 |
> |
calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes |
467 |
> |
for stress / pressure tensor by cutoff group |
468 |
> |
|
469 |
> |
2004-05-22 15:55 chrisfen |
470 |
> |
|
471 |
> |
* libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp... |
472 |
> |
Too many arguements in a function call. |
473 |
> |
|
474 |
> |
2004-05-22 13:17 chrisfen |
475 |
> |
|
476 |
> |
* libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword |
477 |
> |
useThermInt. |
478 |
> |
|
479 |
> |
2004-05-22 13:16 chrisfen |
480 |
> |
|
481 |
> |
* libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
482 |
> |
ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp, |
483 |
> |
Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp, |
484 |
> |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp, |
485 |
> |
StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration |
486 |
> |
code. |
487 |
> |
|
488 |
> |
2004-05-21 10:58 gezelter |
489 |
> |
|
490 |
> |
* libmdtools/: do_Forces.F90, simulation_module.F90: Major changes |
491 |
> |
to skipThisPair for efficiency |
492 |
> |
|
493 |
> |
2004-05-21 09:22 gezelter |
494 |
> |
|
495 |
> |
* configure, ac-tools/configure.in, forceFields/LJ.vdw, |
496 |
> |
forceFields/amber99.vdw, forceFields/charmm27.vdw, |
497 |
> |
forceFields/gaff.vdw, forceFields/oplsaal.vdw, |
498 |
> |
samples/argon/Makefile: Changes for SHAPES potential |
499 |
> |
|
500 |
> |
2004-05-20 15:27 chrisfen |
501 |
> |
|
502 |
> |
* libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit |
503 |
> |
included the bass keywords |
504 |
> |
|
505 |
> |
2004-05-20 15:24 chrisfen |
506 |
> |
|
507 |
> |
* libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp, |
508 |
> |
Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp, |
509 |
> |
Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several |
510 |
> |
additions... Restraints.cpp and .hpp were included for restraining |
511 |
> |
particles in thermodynamic integration. By including these, |
512 |
> |
changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, |
513 |
> |
StatWriter, and possibly some other files. Two bass keywords were |
514 |
> |
also added for performing thermodynamic integration: a lambda value |
515 |
> |
one and a k power one. |
516 |
> |
|
517 |
> |
2004-05-13 16:08 gezelter |
518 |
> |
|
519 |
> |
* libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list |
520 |
> |
|
521 |
> |
2004-05-12 17:01 tim |
522 |
> |
|
523 |
> |
* samples/: argon/Makefile, argon/argonEM.bass, |
524 |
> |
argon/init_argon.eor, minimizer/water/Makefile, |
525 |
> |
minimizer/water/Makefile.in, minimizer/water/WATER.frc, |
526 |
> |
minimizer/water/init_ssd.eor, minimizer/water/ssdEM.bass, |
527 |
> |
minimizer/water/tip4p_two.bass, minimizer/water/tip4p_two.init, |
528 |
> |
minimizer/water/water.mdl: add minimizer sample |
529 |
> |
|
530 |
> |
2004-05-12 16:54 gezelter |
531 |
> |
|
532 |
> |
* libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X |
533 |
> |
compilation |
534 |
> |
|
535 |
> |
2004-05-12 15:54 gezelter |
536 |
> |
|
537 |
> |
* libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes |
538 |
> |
for compilation under Mac OS X with IBM's xl compilers |
539 |
> |
|
540 |
> |
2004-05-12 15:14 gezelter |
541 |
> |
|
542 |
> |
* src/: oopse.cpp, oose.cpp: Added a nifty neato banner |
543 |
> |
|
544 |
> |
2004-05-12 15:14 gezelter |
545 |
> |
|
546 |
> |
* libmdtools/LJFF.cpp: Removed an extraneous write |
547 |
> |
|
548 |
> |
2004-05-12 15:13 gezelter |
549 |
> |
|
550 |
> |
* libBASS/simError.h: Starting to change the error model |
551 |
> |
|
552 |
> |
2004-05-12 14:45 gezelter |
553 |
> |
|
554 |
> |
* utils/Dump2XYZ.cpp: const char* fix |
555 |
> |
|
556 |
> |
2004-05-12 14:44 gezelter |
557 |
> |
|
558 |
> |
* libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
559 |
> |
src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous |
560 |
> |
write statements |
561 |
> |
|
562 |
> |
2004-05-12 11:38 tim |
563 |
> |
|
564 |
> |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
565 |
> |
ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
566 |
> |
SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and |
567 |
> |
massratio from simState, creat cutoff group forevery atom which |
568 |
> |
does not belong to cutoff group defined at mdl file |
569 |
> |
|
570 |
> |
2004-05-12 10:58 gezelter |
571 |
> |
|
572 |
> |
* libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in |
573 |
> |
CutoffGroup |
574 |
> |
|
575 |
> |
2004-05-12 10:35 gezelter |
576 |
> |
|
577 |
> |
* samples/water/water.mdl: Added the cutoff Groups to the default |
578 |
> |
water.mdl file |
579 |
> |
|
580 |
> |
2004-05-12 10:02 tim |
581 |
> |
|
582 |
> |
* ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp: |
583 |
> |
fixed a bug in CutoffGroup::getCOM() |
584 |
> |
|
585 |
> |
2004-05-12 09:29 gezelter |
586 |
> |
|
587 |
> |
* libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
588 |
> |
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
589 |
> |
samples/water/ssd.bass: bug fixes for cutoffGroups |
590 |
> |
|
591 |
> |
2004-05-11 17:28 tim |
592 |
> |
|
593 |
> |
* utils/Vector3.hpp: adding generic Vector3 class |
594 |
> |
|
595 |
> |
2004-05-11 16:44 tim |
596 |
> |
|
597 |
> |
* libmdtools/Integrator.hpp: adding instantiation of |
598 |
> |
Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8 |
599 |
> |
|
600 |
> |
2004-05-11 16:31 gezelter |
601 |
> |
|
602 |
> |
* libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90, |
603 |
> |
calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90, |
604 |
> |
calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90: |
605 |
> |
Fortran-side changes for group-based cutoffs |
606 |
> |
|
607 |
> |
2004-05-11 16:20 tim |
608 |
> |
|
609 |
> |
* libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp |
610 |
> |
|
611 |
> |
2004-05-11 16:14 tim |
612 |
> |
|
613 |
> |
* libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp, |
614 |
> |
SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix |
615 |
> |
anoter one in CutoffGroup which causes seg fault |
616 |
> |
|
617 |
> |
2004-05-11 15:33 tim |
618 |
> |
|
619 |
> |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
620 |
> |
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
621 |
> |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup |
622 |
> |
into OOPSE |
623 |
> |
|
624 |
> |
2004-05-11 15:07 gezelter |
625 |
> |
|
626 |
> |
* libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup |
627 |
> |
|
628 |
> |
2004-05-11 11:00 gezelter |
629 |
> |
|
630 |
> |
* libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
631 |
> |
fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to |
632 |
> |
use the simplified cutoff stuff in the BASS library |
633 |
> |
|
634 |
> |
2004-05-10 23:21 gezelter |
635 |
> |
|
636 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, |
637 |
> |
CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, |
638 |
> |
Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
639 |
> |
MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c, |
640 |
> |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
641 |
> |
parse_tree.c: BASS changes for adding CutoffGroups to molecules. |
642 |
> |
Also restructured the plethora of cutoff radii into one |
643 |
> |
cutoffRadius and one switchingRadius. Also removed the |
644 |
> |
useMolecularCutoffs keyword |
645 |
> |
|
646 |
> |
2004-05-10 15:28 tim |
647 |
> |
|
648 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize |
649 |
> |
DumpWriter |
650 |
> |
|
651 |
> |
2004-05-07 16:36 gezelter |
652 |
> |
|
653 |
> |
* libmdtools/: fSwitchingFunction.h, switch_module.F90: New module |
654 |
> |
for fortran group-based switching function |
655 |
> |
|
656 |
> |
2004-05-07 16:35 gezelter |
657 |
> |
|
658 |
> |
* libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, |
659 |
> |
Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, |
660 |
> |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
661 |
> |
calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, |
662 |
> |
force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, |
663 |
> |
mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, |
664 |
> |
simulation_module.F90: Many changes to get group-based cutoffs to |
665 |
> |
work |
666 |
> |
|
667 |
> |
2004-05-01 13:52 tim |
668 |
> |
|
669 |
> |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
670 |
> |
libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, |
671 |
> |
libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, |
672 |
> |
libmdtools/do_Forces.F90, libmdtools/fSimulation.h, |
673 |
> |
libmdtools/fortranWrapDefines.hpp, |
674 |
> |
libmdtools/simulation_module.F90: C++ pass groupList to fortran |
675 |
> |
|
676 |
> |
2004-04-29 11:03 tim |
677 |
> |
|
678 |
> |
* ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in |
679 |
> |
calc_charge_charge when using molecular cutoff |
680 |
> |
|
681 |
> |
2004-04-28 21:11 tim |
682 |
> |
|
683 |
> |
* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
684 |
> |
unmatched c/fortran interface |
685 |
> |
|
686 |
> |
2004-04-28 18:09 tim |
687 |
> |
|
688 |
> |
* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
689 |
> |
keep the previous position of cantilever in SMD |
690 |
> |
|
691 |
> |
2004-04-28 17:34 tim |
692 |
> |
|
693 |
> |
* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
694 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
695 |
> |
in Molecule.cpp which initialize massRatio before creat the array. |
696 |
> |
fix two bugs in ZconsVisitor |
697 |
> |
|
698 |
> |
2004-04-28 17:06 gezelter |
699 |
> |
|
700 |
> |
* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
701 |
> |
Adding molecular cutoffs |
702 |
> |
|
703 |
> |
2004-04-28 16:39 gezelter |
704 |
> |
|
705 |
> |
* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
706 |
> |
fSimulation.h, force_globals.F90, simulation_module.F90: work on |
707 |
> |
molecular cutoffs |
708 |
> |
|
709 |
> |
2004-04-28 16:39 gezelter |
710 |
> |
|
711 |
> |
* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
712 |
> |
Globals |
713 |
> |
|
714 |
> |
2004-04-27 11:26 tim |
715 |
> |
|
716 |
> |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
717 |
> |
ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
718 |
> |
fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
719 |
> |
molecule and massRation into atom class |
720 |
> |
|
721 |
> |
2004-04-26 16:16 mmeineke |
722 |
> |
|
723 |
> |
* libBASS/Globals.cpp: modified the defaults for the system init |
724 |
> |
time and system init state. |
725 |
> |
|
726 |
> |
2004-04-26 09:29 gezelter |
727 |
> |
|
728 |
> |
* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
729 |
> |
calc_charge_charge.F90 |
730 |
> |
|
731 |
> |
2004-04-23 23:31 tim |
732 |
> |
|
733 |
> |
* ChangeLog, libmdtools/AtomVisitor.cpp, |
734 |
> |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
735 |
> |
reaction field correction to charge-charge interaction |
736 |
> |
|
737 |
> |
2004-04-22 16:33 tim |
738 |
> |
|
739 |
> |
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
740 |
> |
Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
741 |
> |
calculation of pressure tensor |
742 |
> |
|
743 |
> |
2004-04-22 09:55 tim |
744 |
> |
|
745 |
> |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
746 |
> |
another bug in InitFromFile. MPI verion of OOPSE is working again |
747 |
> |
|
748 |
> |
2004-04-21 22:29 tim |
749 |
> |
|
750 |
> |
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
751 |
> |
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
752 |
> |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
753 |
> |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
754 |
> |
DumpWriter |
755 |
> |
|
756 |
> |
2004-04-21 00:32 tim |
757 |
> |
|
758 |
> |
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
759 |
> |
libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
760 |
> |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
761 |
> |
useless files |
762 |
> |
|
763 |
> |
2004-04-20 11:56 tim |
764 |
> |
|
765 |
> |
* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
766 |
> |
SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
767 |
> |
velocitize at thermo |
768 |
> |
|
769 |
> |
2004-04-20 00:39 tim |
770 |
> |
|
771 |
> |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
772 |
> |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
773 |
> |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
774 |
> |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
775 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
776 |
> |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
777 |
> |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
778 |
> |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
779 |
> |
|
780 |
> |
2004-04-19 17:13 gezelter |
781 |
> |
|
782 |
> |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
783 |
> |
Thermo.cpp: Fixed a charge bug |
784 |
> |
|
785 |
> |
2004-04-19 15:54 tim |
786 |
> |
|
787 |
> |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
788 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
789 |
> |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
790 |
> |
a bug in CompositeVisitor which cause the double counting problem |
791 |
> |
|
792 |
> |
2004-04-19 12:44 tim |
793 |
> |
|
794 |
> |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
795 |
> |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
796 |
> |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
797 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
798 |
> |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
799 |
> |
Dump2XYZ is almost working except atoms in rigidbody are double |
800 |
> |
counted |
801 |
> |
|
802 |
> |
2004-04-18 22:52 tim |
803 |
> |
|
804 |
> |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
805 |
> |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
806 |
> |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
807 |
> |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
808 |
> |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
809 |
> |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
810 |
> |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
811 |
> |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
812 |
> |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
813 |
> |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
814 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
815 |
> |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
816 |
> |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
817 |
> |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
818 |
> |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
819 |
> |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
820 |
> |
implement of quickLate using visitor and composite pattern |
821 |
> |
|
822 |
> |
2004-04-15 17:15 tim |
823 |
> |
|
824 |
> |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
825 |
> |
exclude list |
826 |
> |
|
827 |
> |
2004-04-15 11:18 tim |
828 |
> |
|
829 |
> |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
830 |
> |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
831 |
> |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
832 |
> |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
833 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
834 |
> |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
835 |
> |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
836 |
> |
whole bunch of bugs :-) |
837 |
> |
|
838 |
> |
2004-04-14 12:20 chrisfen |
839 |
> |
|
840 |
> |
* forceFields/WATER.frc: Added the WATER.frc force field |
841 |
> |
|
842 |
> |
2004-04-14 11:32 gezelter |
843 |
> |
|
844 |
> |
* libmdtools/Molecule.cpp: fixed for get_potential |
845 |
> |
|
846 |
> |
2004-04-14 10:37 tim |
847 |
> |
|
848 |
> |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
849 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
850 |
> |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
851 |
> |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
852 |
> |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
853 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
854 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
855 |
> |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
856 |
> |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
857 |
> |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
858 |
> |
Change DumpWriter and InitFromFile |
859 |
> |
|
860 |
> |
2004-04-13 11:26 gezelter |
861 |
> |
|
862 |
> |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
863 |
> |
molecules can keep track of their own IntegrableObjects (and |
864 |
> |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
865 |
> |
RigidBodies (which was done incorrectly before). |
866 |
> |
|
867 |
> |
2004-04-13 11:25 gezelter |
868 |
> |
|
869 |
> |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
870 |
> |
(will back out momentarily) |
871 |
> |
|
872 |
> |
2004-04-13 10:10 gezelter |
873 |
> |
|
874 |
> |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
875 |
> |
Those were old. |
876 |
> |
|
877 |
> |
2004-04-13 10:09 gezelter |
878 |
> |
|
879 |
> |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
880 |
> |
to add IntegrableObjects |
881 |
> |
|
882 |
> |
2004-04-12 16:02 gezelter |
883 |
> |
|
884 |
> |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
885 |
> |
|
886 |
> |
2004-04-12 15:32 gezelter |
887 |
> |
|
888 |
> |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
889 |
> |
test run |
890 |
> |
|
891 |
> |
2004-04-12 15:32 gezelter |
892 |
> |
|
893 |
> |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
894 |
> |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
895 |
> |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
896 |
> |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
897 |
> |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
898 |
> |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
899 |
> |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
900 |
> |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
901 |
> |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
902 |
> |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
903 |
> |
(Somewhat extensive) |
904 |
> |
|
905 |
> |
2004-04-12 15:31 gezelter |
906 |
> |
|
907 |
> |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
908 |
> |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
909 |
> |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
910 |
> |
Changes for RigidBody dynamics |
911 |
> |
|
912 |
> |
2004-03-17 09:22 tim |
913 |
> |
|
914 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
915 |
> |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
916 |
> |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
917 |
> |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
918 |
> |
does not sound a good choice, next commit will seperate SMD and |
919 |
> |
ZConstraint |
920 |
> |
|
921 |
> |
2004-03-16 14:22 tim |
922 |
> |
|
923 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
924 |
> |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
925 |
> |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
926 |
> |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
927 |
> |
now can support sequential moving. Refactorying is needed to |
928 |
> |
support SMD in ZConstraint |
929 |
> |
|
930 |
> |
2004-03-02 15:32 tim |
931 |
> |
|
932 |
> |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
933 |
> |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
934 |
> |
support large file |
935 |
> |
|
936 |
> |
2004-03-01 16:17 tim |
937 |
> |
|
938 |
> |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
939 |
> |
|
940 |
> |
2004-03-01 15:01 tim |
941 |
> |
|
942 |
> |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
943 |
> |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
944 |
> |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
945 |
> |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
946 |
> |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
947 |
> |
program which can be used to replace atom type for zconstraint into |
948 |
> |
OOPSE |
949 |
> |
|
950 |
> |
2004-02-24 11:36 tim |
951 |
> |
|
952 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
953 |
> |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
954 |
> |
message] |
955 |
> |
|
956 |
> |
2004-02-24 10:49 tim |
957 |
> |
|
958 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
959 |
> |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
960 |
> |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
961 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
962 |
> |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
963 |
> |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
964 |
> |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
965 |
> |
|
966 |
> |
2004-02-24 10:44 tim |
967 |
> |
|
968 |
> |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
969 |
> |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
970 |
> |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
971 |
> |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
972 |
> |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
973 |
> |
compose to implement Minimizer both versions are working |
974 |
> |
|
975 |
> |
2004-02-17 14:23 tim |
976 |
> |
|
977 |
> |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
978 |
> |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
979 |
> |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
980 |
> |
libmdtools/MinimizerParameterSet.hpp, |
981 |
> |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
982 |
> |
to remove the constraint force along bond direction |
983 |
> |
|
984 |
> |
2004-02-10 16:33 tim |
985 |
> |
|
986 |
> |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
987 |
> |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
988 |
> |
single version of energy minimization is working. |
989 |
> |
|
990 |
> |
2004-02-09 15:38 mmeineke |
991 |
> |
|
992 |
> |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
993 |
> |
the massive memory overusage by OOPSE |
994 |
> |
|
995 |
> |
2004-02-09 09:48 chrisfen |
996 |
> |
|
997 |
> |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
998 |
> |
hardwired LJ_rcut |
999 |
> |
|
1000 |
> |
2004-02-06 19:14 tim |
1001 |
> |
|
1002 |
> |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
1003 |
> |
message] |
1004 |
> |
|
1005 |
> |
2004-02-06 16:37 tim |
1006 |
> |
|
1007 |
> |
* ChangeLog, libBASS/Globals.cpp, |
1008 |
> |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
1009 |
> |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
1010 |
> |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
1011 |
> |
energy minimization for argon is working, need to add constraint |
1012 |
> |
|
1013 |
> |
2004-02-06 14:05 tim |
1014 |
> |
|
1015 |
> |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
1016 |
> |
one more file into Makefile.in |
1017 |
> |
|
1018 |
> |
2004-02-06 13:58 tim |
1019 |
> |
|
1020 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
1021 |
> |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
1022 |
> |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
1023 |
> |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
1024 |
> |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
1025 |
> |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
1026 |
> |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
1027 |
> |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
1028 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1029 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
1030 |
> |
some lines into global.cpp to make it work with energy minimization |
1031 |
> |
|
1032 |
> |
2004-02-04 17:26 tim |
1033 |
> |
|
1034 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
1035 |
> |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
1036 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
1037 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
1038 |
> |
Single version of conjugate gradient with golden search linesearch |
1039 |
> |
pass a couple of functions test. Brent's algorithm is still broken |
1040 |
> |
|
1041 |
> |
2004-02-03 17:54 tim |
1042 |
> |
|
1043 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
1044 |
> |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
1045 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
1046 |
> |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
1047 |
> |
|
1048 |
> |
2004-02-03 15:47 tim |
1049 |
> |
|
1050 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
1051 |
> |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
1052 |
> |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
1053 |
> |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
1054 |
> |
SteepestDescent.hpp: [no log message] |
1055 |
> |
|
1056 |
> |
2004-02-03 15:43 tim |
1057 |
> |
|
1058 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
1059 |
> |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
1060 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
1061 |
> |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
1062 |
> |
constraint class |
1063 |
> |
|
1064 |
> |
2004-02-03 12:10 tim |
1065 |
> |
|
1066 |
> |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
1067 |
> |
|
1068 |
> |
2004-02-03 10:21 tim |
1069 |
> |
|
1070 |
> |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
1071 |
> |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
1072 |
> |
|
1073 |
> |
2004-02-02 15:29 tim |
1074 |
> |
|
1075 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
1076 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
1077 |
> |
Adding GoldenSection and Brent LineSearch Method |
1078 |
> |
|
1079 |
> |
2004-01-30 16:47 tim |
1080 |
> |
|
1081 |
> |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
1082 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
1083 |
> |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
1084 |
> |
MinimizerBase instead of a functor to do line seach |
1085 |
> |
|
1086 |
> |
2004-01-30 10:00 chrisfen |
1087 |
> |
|
1088 |
> |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
1089 |
> |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
1090 |
> |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
1091 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
1092 |
> |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
1093 |
> |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
1094 |
> |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
1095 |
> |
has a working WATER.cpp forcefield and parser. This involved |
1096 |
> |
changes to WATER.cpp and ForceFields amoung other files. One |
1097 |
> |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
1098 |
> |
This will be removed on the next commit... |
1099 |
> |
|
1100 |
> |
2004-01-29 18:00 gezelter |
1101 |
> |
|
1102 |
> |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
1103 |
> |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
1104 |
> |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
1105 |
> |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
1106 |
> |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
1107 |
> |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
1108 |
> |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
1109 |
> |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
1110 |
> |
member list fixes for rigid bodies |
1111 |
> |
|
1112 |
> |
2004-01-29 16:44 tim |
1113 |
> |
|
1114 |
> |
* libmdtools/MinimizerParameterSet.hpp: Adding |
1115 |
> |
MinimizerParameterSet class. |
1116 |
> |
|
1117 |
> |
2004-01-28 17:44 tim |
1118 |
> |
|
1119 |
> |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
1120 |
> |
NLModel0 and NLModel1 |
1121 |
> |
|
1122 |
> |
2004-01-28 15:40 tim |
1123 |
> |
|
1124 |
> |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
1125 |
> |
of NLModel |
1126 |
> |
|
1127 |
> |
2004-01-27 15:34 gezelter |
1128 |
> |
|
1129 |
> |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
1130 |
> |
water.mdl file, updated ssd.bass to use new SSD name |
1131 |
> |
|
1132 |
> |
2004-01-27 15:34 gezelter |
1133 |
> |
|
1134 |
> |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
1135 |
> |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
1136 |
> |
stuff |
1137 |
> |
|
1138 |
> |
2004-01-27 14:39 gezelter |
1139 |
> |
|
1140 |
> |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
1141 |
> |
|
1142 |
> |
2004-01-27 14:39 gezelter |
1143 |
> |
|
1144 |
> |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
1145 |
> |
|
1146 |
> |
2004-01-27 14:38 gezelter |
1147 |
> |
|
1148 |
> |
* samples/argon/argon.bass: Longer run time to test argon |
1149 |
> |
|
1150 |
> |
2004-01-27 14:38 gezelter |
1151 |
> |
|
1152 |
> |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
1153 |
> |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
1154 |
> |
morning |
1155 |
> |
|
1156 |
> |
2004-01-27 14:37 gezelter |
1157 |
> |
|
1158 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
1159 |
> |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
1160 |
> |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
1161 |
> |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
1162 |
> |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
1163 |
> |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
1164 |
> |
do new rigidBody scheme |
1165 |
|
|
1166 |
< |
* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more |
4 |
< |
work on getting gofR working. |
1166 |
> |
2004-01-27 14:15 tim |
1167 |
|
|
1168 |
< |
2003-09-09 16:50 mmeineke |
1168 |
> |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
1169 |
> |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
1170 |
> |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
1171 |
> |
constraint for Nonlinear Optimization Model |
1172 |
|
|
1173 |
< |
* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the |
9 |
< |
beginings of the GofR pair correlation. |
10 |
< |
|
11 |
< |
added identification of identI in matchI. |
1173 |
> |
2004-01-26 17:01 gezelter |
1174 |
|
|
1175 |
+ |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
1176 |
+ |
Euler angles for orientation instead of unit vectors required |
1177 |
+ |
changes in MoLocator |
1178 |
+ |
|
1179 |
+ |
2004-01-26 16:53 gezelter |
1180 |
+ |
|
1181 |
+ |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
1182 |
+ |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
1183 |
+ |
water/water.mdl: Changed orientation lines from unit vectors to |
1184 |
+ |
euler angles |
1185 |
+ |
|
1186 |
+ |
2004-01-26 16:52 gezelter |
1187 |
+ |
|
1188 |
+ |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
1189 |
+ |
|
1190 |
+ |
2004-01-26 16:45 gezelter |
1191 |
+ |
|
1192 |
+ |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
1193 |
+ |
use Euler angles in the following order: phi, theta, psi Removed |
1194 |
+ |
the ability to set orientation using a unit vector |
1195 |
+ |
|
1196 |
+ |
2004-01-26 16:26 gezelter |
1197 |
+ |
|
1198 |
+ |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
1199 |
+ |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
1200 |
+ |
Euler angles in the following order: phi, theta, psi Removed the |
1201 |
+ |
ability to set orientation using a unit vector |
1202 |
+ |
|
1203 |
+ |
2004-01-26 13:52 gezelter |
1204 |
+ |
|
1205 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
1206 |
+ |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
1207 |
+ |
|
1208 |
+ |
2004-01-22 12:34 chrisfen |
1209 |
+ |
|
1210 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
1211 |
+ |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
1212 |
+ |
Corrected spelling in several directories, and stated WATER.cpp |
1213 |
+ |
|
1214 |
+ |
2004-01-21 17:16 tim |
1215 |
+ |
|
1216 |
+ |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
1217 |
+ |
NLOPModel.hpp: constraint class in energy minimization |
1218 |
+ |
|
1219 |
+ |
2004-01-20 15:34 tim |
1220 |
+ |
|
1221 |
+ |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
1222 |
+ |
|
1223 |
+ |
2004-01-20 15:32 tim |
1224 |
+ |
|
1225 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
1226 |
+ |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
1227 |
+ |
|
1228 |
+ |
2004-01-19 16:17 gezelter |
1229 |
+ |
|
1230 |
+ |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
1231 |
+ |
more user-friendly |
1232 |
+ |
|
1233 |
+ |
2004-01-19 13:51 chrisfen |
1234 |
+ |
|
1235 |
+ |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
1236 |
+ |
|
1237 |
+ |
2004-01-19 13:36 tim |
1238 |
+ |
|
1239 |
+ |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
1240 |
+ |
time, status time, thermal time and reset time are not divisible by |
1241 |
+ |
dt |
1242 |
+ |
|
1243 |
+ |
2004-01-19 11:10 gezelter |
1244 |
+ |
|
1245 |
+ |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
1246 |
+ |
won't complain |
1247 |
+ |
|
1248 |
+ |
2004-01-19 11:10 gezelter |
1249 |
+ |
|
1250 |
+ |
* samples/lipid/5x5.bass: Fixed old bass file |
1251 |
+ |
|
1252 |
+ |
2004-01-19 11:09 gezelter |
1253 |
+ |
|
1254 |
+ |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
1255 |
+ |
required a change in how the MoleculeStamps are used by divideLabor |
1256 |
+ |
in mpiSimulation.cpp |
1257 |
+ |
|
1258 |
+ |
2004-01-19 11:08 gezelter |
1259 |
+ |
|
1260 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
1261 |
+ |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
1262 |
+ |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
1263 |
+ |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
1264 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
1265 |
+ |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
1266 |
+ |
|
1267 |
+ |
2004-01-16 16:55 tim |
1268 |
+ |
|
1269 |
+ |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
1270 |
+ |
eor file |
1271 |
+ |
|
1272 |
+ |
2004-01-16 16:51 mmeineke |
1273 |
+ |
|
1274 |
+ |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
1275 |
+ |
write eor files |
1276 |
+ |
|
1277 |
+ |
2004-01-16 10:01 mmeineke |
1278 |
+ |
|
1279 |
+ |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
1280 |
+ |
initialization of the AtomStruct |
1281 |
+ |
|
1282 |
+ |
2004-01-15 16:57 chuckv |
1283 |
+ |
|
1284 |
+ |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
1285 |
+ |
|
1286 |
+ |
2004-01-15 10:51 gezelter |
1287 |
+ |
|
1288 |
+ |
* ac-tools/aclocal.m4: Changes for altivec |
1289 |
+ |
|
1290 |
+ |
2004-01-15 09:22 gezelter |
1291 |
+ |
|
1292 |
+ |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
1293 |
+ |
|
1294 |
+ |
2004-01-14 23:33 gezelter |
1295 |
+ |
|
1296 |
+ |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
1297 |
+ |
|
1298 |
+ |
2004-01-14 20:14 gezelter |
1299 |
+ |
|
1300 |
+ |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
1301 |
+ |
notifyCutoffs.F90: More work for adding charges |
1302 |
+ |
|
1303 |
+ |
2004-01-14 17:41 gezelter |
1304 |
+ |
|
1305 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1306 |
+ |
src/Makefile.in: autoconf fixes |
1307 |
+ |
|
1308 |
+ |
2004-01-14 11:28 mmeineke |
1309 |
+ |
|
1310 |
+ |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
1311 |
+ |
|
1312 |
+ |
2004-01-14 10:48 gezelter |
1313 |
+ |
|
1314 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1315 |
+ |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
1316 |
+ |
changes for icc8 |
1317 |
+ |
|
1318 |
+ |
2004-01-13 18:01 gezelter |
1319 |
+ |
|
1320 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
1321 |
+ |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
1322 |
+ |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
1323 |
+ |
Changes for adding direct charge-charge interactions (with |
1324 |
+ |
switching function) |
1325 |
+ |
|
1326 |
+ |
2004-01-13 17:34 gezelter |
1327 |
+ |
|
1328 |
+ |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
1329 |
+ |
oopseMPI_module.F90: Some changes for new MPI organization and |
1330 |
+ |
direct charge-charge interactions |
1331 |
+ |
|
1332 |
+ |
2004-01-13 17:11 tim |
1333 |
+ |
|
1334 |
+ |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
1335 |
+ |
|
1336 |
+ |
2004-01-13 16:22 tim |
1337 |
+ |
|
1338 |
+ |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
1339 |
+ |
|
1340 |
+ |
2004-01-13 15:35 tim |
1341 |
+ |
|
1342 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
1343 |
+ |
eor file whenever it is used instead of rewinding it |
1344 |
+ |
|
1345 |
+ |
2004-01-13 15:04 tim |
1346 |
+ |
|
1347 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
1348 |
+ |
of writeFrame |
1349 |
+ |
|
1350 |
+ |
2004-01-13 10:46 tim |
1351 |
+ |
|
1352 |
+ |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
1353 |
+ |
Merge the code of writeFinal and writeDump; |
1354 |
+ |
Adding sortingIndex into DumpWriter; |
1355 |
+ |
Fix a bug of writing last frame twice in integrator |
1356 |
+ |
|
1357 |
+ |
2004-01-12 17:54 tim |
1358 |
+ |
|
1359 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
1360 |
+ |
a bug in copying string |
1361 |
+ |
|
1362 |
+ |
2004-01-12 15:37 tim |
1363 |
+ |
|
1364 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
1365 |
+ |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
1366 |
+ |
master nodes |
1367 |
+ |
|
1368 |
+ |
2004-01-10 04:46 tim |
1369 |
+ |
|
1370 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
1371 |
+ |
roll it back fix a bug of copying string to a pointer Still have |
1372 |
+ |
Seg fault, it looks like a random MPI seg fault in totalview |
1373 |
+ |
|
1374 |
+ |
2004-01-09 21:15 tim |
1375 |
+ |
|
1376 |
+ |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
1377 |
+ |
|
1378 |
+ |
2004-01-09 15:29 gezelter |
1379 |
+ |
|
1380 |
+ |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
1381 |
+ |
|
1382 |
+ |
2004-01-08 17:25 chuckv |
1383 |
+ |
|
1384 |
+ |
* libmdtools/DumpWriter.cpp: A work in progress... |
1385 |
+ |
|
1386 |
+ |
2004-01-08 13:59 gezelter |
1387 |
+ |
|
1388 |
+ |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
1389 |
+ |
case |
1390 |
+ |
|
1391 |
+ |
2004-01-08 13:13 mmeineke |
1392 |
+ |
|
1393 |
+ |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
1394 |
+ |
state bug. |
1395 |
+ |
|
1396 |
+ |
2004-01-08 13:05 gezelter |
1397 |
+ |
|
1398 |
+ |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
1399 |
+ |
|
1400 |
+ |
2004-01-08 12:57 mmeineke |
1401 |
+ |
|
1402 |
+ |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
1403 |
+ |
exstended state bug |
1404 |
+ |
|
1405 |
+ |
2004-01-08 12:40 gezelter |
1406 |
+ |
|
1407 |
+ |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
1408 |
+ |
|
1409 |
+ |
2004-01-08 10:44 mmeineke |
1410 |
+ |
|
1411 |
+ |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
1412 |
+ |
XS state info flag |
1413 |
+ |
|
1414 |
+ |
2004-01-07 14:26 tim |
1415 |
+ |
|
1416 |
+ |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
1417 |
+ |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
1418 |
+ |
sending message from master node to itself in DumpWriter.cpp and |
1419 |
+ |
InitializeFromFile.cpp |
1420 |
+ |
|
1421 |
+ |
2004-01-06 14:49 chuckv |
1422 |
+ |
|
1423 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
1424 |
+ |
performance fixes in the dipole dipole and reaction field code |
1425 |
+ |
|
1426 |
+ |
2004-01-06 13:54 chuckv |
1427 |
+ |
|
1428 |
+ |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
1429 |
+ |
little more sane |
1430 |
+ |
|
1431 |
+ |
2004-01-05 17:49 chuckv |
1432 |
+ |
|
1433 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
1434 |
+ |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
1435 |
+ |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
1436 |
+ |
performance by reducing spurious function calls |
1437 |
+ |
|
1438 |
+ |
2004-01-05 17:18 chuckv |
1439 |
+ |
|
1440 |
+ |
* libmdtools/do_Forces.F90: mangling forces even further |
1441 |
+ |
|
1442 |
+ |
2004-01-05 17:18 chuckv |
1443 |
+ |
|
1444 |
+ |
* configure, ac-tools/configure.in: mpich mucking |
1445 |
+ |
|
1446 |
+ |
2004-01-05 17:12 chuckv |
1447 |
+ |
|
1448 |
+ |
* libmdtools/do_Forces.F90: mangled do_forces... |
1449 |
+ |
|
1450 |
+ |
2004-01-05 16:00 chuckv |
1451 |
+ |
|
1452 |
+ |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
1453 |
+ |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
1454 |
+ |
lookup |
1455 |
+ |
|
1456 |
+ |
2003-12-29 14:56 chuckv |
1457 |
+ |
|
1458 |
+ |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
1459 |
+ |
third-party directory for code not written by us. Also added |
1460 |
+ |
Mersenne Twister random number generator code. This will eventually |
1461 |
+ |
replace sprng as the random number generator used by OOPSE. |
1462 |
+ |
|
1463 |
+ |
2003-12-22 16:26 chuckv |
1464 |
+ |
|
1465 |
+ |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
1466 |
+ |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
1467 |
+ |
Fixes to profile code. |
1468 |
+ |
|
1469 |
+ |
2003-12-19 15:36 mmeineke |
1470 |
+ |
|
1471 |
+ |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
1472 |
+ |
timing.F90, timing.f90: More profiling fixes. |
1473 |
+ |
|
1474 |
+ |
2003-12-19 15:19 chuckv |
1475 |
+ |
|
1476 |
+ |
* libmdtools/timing.f90: Another change for MPI in timing. |
1477 |
+ |
|
1478 |
+ |
2003-12-19 15:17 chuckv |
1479 |
+ |
|
1480 |
+ |
* libmdtools/timing.f90: Small update to timing in MPI |
1481 |
+ |
|
1482 |
+ |
2003-12-19 13:53 mmeineke |
1483 |
+ |
|
1484 |
+ |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
1485 |
+ |
profiling commands work now. Will start adding PROFILE ifdefs into |
1486 |
+ |
the code |
1487 |
+ |
|
1488 |
+ |
2003-12-19 12:25 mmeineke |
1489 |
+ |
|
1490 |
+ |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
1491 |
+ |
some profiling routines |
1492 |
+ |
|
1493 |
+ |
2003-12-19 10:12 mmeineke |
1494 |
+ |
|
1495 |
+ |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
1496 |
+ |
and GofRomega |
1497 |
+ |
|
1498 |
+ |
additional work on randomBilayer |
1499 |
+ |
|
1500 |
+ |
2003-12-19 10:12 mmeineke |
1501 |
+ |
|
1502 |
+ |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
1503 |
+ |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
1504 |
+ |
GofRomega |
1505 |
+ |
|
1506 |
+ |
2003-12-18 16:47 mmeineke |
1507 |
+ |
|
1508 |
+ |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
1509 |
+ |
some profile functionality |
1510 |
+ |
|
1511 |
+ |
2003-12-18 15:46 chuckv |
1512 |
+ |
|
1513 |
+ |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
1514 |
+ |
Added functions for simple profiling in fortran. |
1515 |
+ |
|
1516 |
+ |
2003-12-17 15:13 chuckv |
1517 |
+ |
|
1518 |
+ |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
1519 |
+ |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
1520 |
+ |
rho_col were scattered into the same array. Unfortunately, MPI |
1521 |
+ |
zeros the array between scatters so half of the sum was being lost. |
1522 |
+ |
Fixed by added a temp array for column scatter, then sum loop over |
1523 |
+ |
nlocal. |
1524 |
+ |
|
1525 |
+ |
2003-12-16 15:49 mmeineke |
1526 |
+ |
|
1527 |
+ |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
1528 |
+ |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
1529 |
+ |
gofRomega. both need to be debugged and tested. |
1530 |
+ |
|
1531 |
+ |
2003-12-12 10:42 gezelter |
1532 |
+ |
|
1533 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1534 |
+ |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
1535 |
+ |
gradients (to do minimizations) |
1536 |
+ |
|
1537 |
+ |
2003-12-12 10:33 mmeineke |
1538 |
+ |
|
1539 |
+ |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
1540 |
+ |
header |
1541 |
+ |
|
1542 |
+ |
2003-12-10 11:52 mmeineke |
1543 |
+ |
|
1544 |
+ |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
1545 |
+ |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
1546 |
+ |
randomBilayer to the build. Also move the random bilayer builder |
1547 |
+ |
from bilayerSys to randomBilayer |
1548 |
+ |
|
1549 |
+ |
2003-11-25 10:44 mmeineke |
1550 |
+ |
|
1551 |
+ |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
1552 |
+ |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
1553 |
+ |
TB3 in DUFF.frc |
1554 |
+ |
|
1555 |
+ |
2003-11-21 15:09 mmeineke |
1556 |
+ |
|
1557 |
+ |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
1558 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
1559 |
+ |
message in SimInfo. Added a more informative error message in |
1560 |
+ |
InitializeFromFile |
1561 |
+ |
|
1562 |
+ |
2003-11-21 15:07 mmeineke |
1563 |
+ |
|
1564 |
+ |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
1565 |
+ |
ing in the GofR,CosTheta |
1566 |
+ |
|
1567 |
+ |
2003-11-21 14:31 chrisfen |
1568 |
+ |
|
1569 |
+ |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
1570 |
+ |
a bug in SimInfo ordering of radii |
1571 |
+ |
|
1572 |
+ |
2003-11-11 12:20 mmeineke |
1573 |
+ |
|
1574 |
+ |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
1575 |
+ |
a min function. |
1576 |
+ |
|
1577 |
+ |
2003-11-10 16:50 mmeineke |
1578 |
+ |
|
1579 |
+ |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
1580 |
+ |
reordered the rcut/ecr/boxSize initialization |
1581 |
+ |
|
1582 |
+ |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
1583 |
+ |
now exit when it runs into rcut or ecr. |
1584 |
+ |
|
1585 |
+ |
2003-11-07 16:46 chuckv |
1586 |
+ |
|
1587 |
+ |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
1588 |
+ |
oopseMPI_module.F90: Added support for compiling fortran without |
1589 |
+ |
use of mpich modules. We use mpif.h instead.: |
1590 |
+ |
|
1591 |
+ |
2003-11-07 12:09 mmeineke |
1592 |
+ |
|
1593 |
+ |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
1594 |
+ |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
1595 |
+ |
the atom loop in the NPT family of integrators. |
1596 |
+ |
|
1597 |
+ |
2003-11-06 17:01 mmeineke |
1598 |
+ |
|
1599 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
1600 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
1601 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1602 |
+ |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
1603 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
1604 |
+ |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
1605 |
+ |
* useIntiTime => useInitialTime |
1606 |
+ |
|
1607 |
+ |
2003-11-06 14:24 mmeineke |
1608 |
+ |
|
1609 |
+ |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
1610 |
+ |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
1611 |
+ |
parse_tree.h: fixed the includes in the Make.dep |
1612 |
+ |
|
1613 |
+ |
2003-11-06 14:11 mmeineke |
1614 |
+ |
|
1615 |
+ |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
1616 |
+ |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
1617 |
+ |
new-templateless branch to the main trunk. |
1618 |
+ |
|
1619 |
+ |
bug Fixes include: * fixed the switching function from ortho to |
1620 |
+ |
non-ortho box. !!!!! THis was responsible for all of the |
1621 |
+ |
sudden deaths we saw. * some formating in the string when we |
1622 |
+ |
write out the extended system state. * added NPT.cpp to the |
1623 |
+ |
makefile.in |
1624 |
+ |
|
1625 |
+ |
2003-11-06 13:20 mmeineke |
1626 |
+ |
|
1627 |
+ |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
1628 |
+ |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
1629 |
+ |
bug. The box was not switching between orthorhombic and |
1630 |
+ |
non-orthorhombic wrapping correctly. we added a fabs() to |
1631 |
+ |
the check.which should fix it. |
1632 |
+ |
|
1633 |
+ |
2003-11-05 14:16 mmeineke |
1634 |
+ |
|
1635 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
1636 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
1637 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
1638 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
1639 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
1640 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
1641 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
1642 |
+ |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
1643 |
+ |
some work on trying to find the compression bug |
1644 |
+ |
|
1645 |
+ |
2003-11-03 17:07 mmeineke |
1646 |
+ |
|
1647 |
+ |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
1648 |
+ |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
1649 |
+ |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
1650 |
+ |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
1651 |
+ |
most of standard template library from OOPSE. |
1652 |
+ |
|
1653 |
+ |
2003-10-31 16:06 mmeineke |
1654 |
+ |
|
1655 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1656 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
1657 |
+ |
SimSetup.cpp: started work on template removal. |
1658 |
+ |
|
1659 |
+ |
2003-10-31 13:28 mmeineke |
1660 |
+ |
|
1661 |
+ |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
1662 |
+ |
added template stuff to the Maikefile template |
1663 |
+ |
|
1664 |
+ |
little changes to some printf format statements |
1665 |
+ |
|
1666 |
+ |
2003-10-31 13:28 mmeineke |
1667 |
+ |
|
1668 |
+ |
* libBASS/Makefile.in: added template stuff to the Maikefile |
1669 |
+ |
template |
1670 |
+ |
|
1671 |
+ |
2003-10-30 13:59 gezelter |
1672 |
+ |
|
1673 |
+ |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
1674 |
+ |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
1675 |
+ |
rList problems |
1676 |
+ |
|
1677 |
+ |
2003-10-30 09:11 gezelter |
1678 |
+ |
|
1679 |
+ |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
1680 |
+ |
queried before q0 was allocated. |
1681 |
+ |
|
1682 |
+ |
2003-10-29 15:41 mmeineke |
1683 |
+ |
|
1684 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
1685 |
+ |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
1686 |
+ |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
1687 |
+ |
in bass.l |
1688 |
+ |
|
1689 |
+ |
fixed a little bug in the first time step, regarding the setting of |
1690 |
+ |
ecr and est in fortran |
1691 |
+ |
|
1692 |
+ |
2003-10-29 15:40 mmeineke |
1693 |
+ |
|
1694 |
+ |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
1695 |
+ |
|
1696 |
+ |
2003-10-29 12:55 mmeineke |
1697 |
+ |
|
1698 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1699 |
+ |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
1700 |
+ |
rcut is setup, as well as additional debugging comments. |
1701 |
+ |
|
1702 |
+ |
2003-10-29 09:28 gezelter |
1703 |
+ |
|
1704 |
+ |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
1705 |
+ |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
1706 |
+ |
templates |
1707 |
+ |
|
1708 |
+ |
2003-10-28 22:16 gezelter |
1709 |
+ |
|
1710 |
+ |
* src/Makefile.in: Refixed broken makefile |
1711 |
+ |
|
1712 |
+ |
2003-10-28 22:06 gezelter |
1713 |
+ |
|
1714 |
+ |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
1715 |
+ |
fixes |
1716 |
+ |
|
1717 |
+ |
2003-10-28 19:19 tim |
1718 |
+ |
|
1719 |
+ |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
1720 |
+ |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
1721 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
1722 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
1723 |
+ |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
1724 |
+ |
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
1725 |
+ |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
1726 |
+ |
file. |
1727 |
+ |
|
1728 |
+ |
2003-10-28 17:25 mmeineke |
1729 |
+ |
|
1730 |
+ |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
1731 |
+ |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
1732 |
+ |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
1733 |
+ |
how c calls fortran. All function pointers and fortran calls are |
1734 |
+ |
rigidly typecast now. |
1735 |
+ |
|
1736 |
+ |
2003-10-28 15:42 gezelter |
1737 |
+ |
|
1738 |
+ |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
1739 |
+ |
Portability fixes |
1740 |
+ |
|
1741 |
+ |
2003-10-28 15:09 gezelter |
1742 |
+ |
|
1743 |
+ |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
1744 |
+ |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
1745 |
+ |
src/Makefile.in: Compatibility fixes |
1746 |
+ |
|
1747 |
+ |
2003-10-28 12:08 mmeineke |
1748 |
+ |
|
1749 |
+ |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
1750 |
+ |
started work on template removal |
1751 |
+ |
|
1752 |
+ |
2003-10-28 12:04 gezelter |
1753 |
+ |
|
1754 |
+ |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
1755 |
+ |
trying to understand extern "C" stuff for pointers |
1756 |
+ |
|
1757 |
+ |
2003-10-28 11:20 gezelter |
1758 |
+ |
|
1759 |
+ |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
1760 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
1761 |
+ |
|
1762 |
+ |
2003-10-28 11:03 gezelter |
1763 |
+ |
|
1764 |
+ |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
1765 |
+ |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
1766 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
1767 |
+ |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
1768 |
+ |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
1769 |
+ |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
1770 |
+ |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
1771 |
+ |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
1772 |
+ |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
1773 |
+ |
more portable c header stuff Also, mod file fixes and portability |
1774 |
+ |
changes Some fortran changes will need to be reversed. |
1775 |
+ |
|
1776 |
+ |
2003-10-28 11:03 gezelter |
1777 |
+ |
|
1778 |
+ |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
1779 |
+ |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
1780 |
+ |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
1781 |
+ |
portable c header stuff Also, mod file fixes and portability |
1782 |
+ |
changes |
1783 |
+ |
|
1784 |
+ |
2003-10-28 11:02 gezelter |
1785 |
+ |
|
1786 |
+ |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
1787 |
+ |
stuff |
1788 |
+ |
|
1789 |
+ |
2003-10-27 18:00 gezelter |
1790 |
+ |
|
1791 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1792 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, |
1793 |
+ |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
1794 |
+ |
|
1795 |
+ |
2003-10-27 17:08 mmeineke |
1796 |
+ |
|
1797 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1798 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
1799 |
+ |
added routines for the sysbuilder to work with simSetup |
1800 |
+ |
|
1801 |
+ |
remved the QuickBass routines, and had all parsing go through |
1802 |
+ |
SimSetup. LatticeBilayer is in complete working order now. |
1803 |
+ |
|
1804 |
+ |
2003-10-27 17:07 mmeineke |
1805 |
+ |
|
1806 |
+ |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
1807 |
+ |
routines for the sysbuilder to work with simSetup |
1808 |
+ |
|
1809 |
+ |
2003-10-27 11:20 gezelter |
1810 |
+ |
|
1811 |
+ |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
1812 |
+ |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
1813 |
+ |
|
1814 |
+ |
2003-10-24 17:17 mmeineke |
1815 |
+ |
|
1816 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1817 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
1818 |
+ |
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
1819 |
+ |
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
1820 |
+ |
overhauled latticeBilayer into its own program. Removed sysBuild |
1821 |
+ |
from the Makefile |
1822 |
+ |
|
1823 |
+ |
2003-10-24 12:36 gezelter |
1824 |
+ |
|
1825 |
+ |
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
1826 |
+ |
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
1827 |
+ |
builder |
1828 |
+ |
|
1829 |
+ |
2003-10-24 12:35 gezelter |
1830 |
+ |
|
1831 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
1832 |
+ |
merge problem |
1833 |
+ |
|
1834 |
+ |
2003-10-23 14:57 mmeineke |
1835 |
+ |
|
1836 |
+ |
* samples/metals/Makefile.in: added eam ForceField files to the |
1837 |
+ |
init |
1838 |
+ |
|
1839 |
+ |
fixed an eam mpi parmeter setup bug |
1840 |
+ |
|
1841 |
+ |
added the init file to the makefile |
1842 |
+ |
|
1843 |
+ |
2003-10-23 14:57 mmeineke |
1844 |
+ |
|
1845 |
+ |
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
1846 |
+ |
to the init |
1847 |
+ |
|
1848 |
+ |
fixed an eam mpi parmeter setup bug |
1849 |
+ |
|
1850 |
+ |
2003-10-23 14:57 mmeineke |
1851 |
+ |
|
1852 |
+ |
* forceFields/Makefile.in: added eam ForceField files to the init |
1853 |
+ |
|
1854 |
+ |
2003-10-22 16:17 mmeineke |
1855 |
+ |
|
1856 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
1857 |
+ |
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
1858 |
+ |
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
1859 |
+ |
no box skew allowed. |
1860 |
+ |
|
1861 |
+ |
2003-10-21 14:33 mmeineke |
1862 |
+ |
|
1863 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1864 |
+ |
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
1865 |
+ |
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
1866 |
+ |
* useInitTime = false: sets the origin time to 0.0 regardless |
1867 |
+ |
of the time stamp in the .init file * default=> useInitTime = |
1868 |
+ |
true; |
1869 |
+ |
|
1870 |
+ |
2003-10-17 16:19 mmeineke |
1871 |
+ |
|
1872 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
1873 |
+ |
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1874 |
+ |
staticProps.cpp, obj/placeholder: added the staticProps directory |
1875 |
+ |
to the build list for both configure and configure.in |
1876 |
+ |
|
1877 |
+ |
fixed a number of bugs in the staticProps code. gofr is now |
1878 |
+ |
working. |
1879 |
+ |
|
1880 |
+ |
2003-10-17 16:18 mmeineke |
1881 |
+ |
|
1882 |
+ |
* ac-tools/configure.in: added the staticProps directory to the |
1883 |
+ |
build list for both configure and configure.in |
1884 |
+ |
|
1885 |
+ |
2003-10-17 16:17 mmeineke |
1886 |
+ |
|
1887 |
+ |
* configure: added the staticProps directory to the build list |
1888 |
+ |
|
1889 |
+ |
2003-10-16 14:16 mmeineke |
1890 |
+ |
|
1891 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
1892 |
+ |
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
1893 |
+ |
use linked lists instead of a vector. |
1894 |
+ |
|
1895 |
+ |
Fixed the makefile to build DumpReader.cpp |
1896 |
+ |
|
1897 |
+ |
Removed a comment output in Exclude.cpp |
1898 |
+ |
|
1899 |
+ |
Modified DumpWriter and Integrator to write an eor file every time |
1900 |
+ |
a frame is written. This lets the .eor file represent the last |
1901 |
+ |
written frame of a simulation. |
1902 |
+ |
|
1903 |
+ |
2003-10-10 12:10 mmeineke |
1904 |
+ |
|
1905 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
1906 |
+ |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
1907 |
+ |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1908 |
+ |
staticProps.cpp: removed the props directory, and moved everything |
1909 |
+ |
over to staticProps |
1910 |
+ |
|
1911 |
+ |
2003-10-09 17:09 mmeineke |
1912 |
+ |
|
1913 |
+ |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
1914 |
+ |
a position where it will compile and run first runs. |
1915 |
+ |
|
1916 |
+ |
2003-10-04 13:46 chuckv |
1917 |
+ |
|
1918 |
+ |
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
1919 |
+ |
samples/metals/Au.bass: Fixed bug in calc_eam. |
1920 |
+ |
|
1921 |
+ |
2003-10-04 13:08 chuckv |
1922 |
+ |
|
1923 |
+ |
* samples/metals/init_au.in: added Au init file for eam. |
1924 |
+ |
|
1925 |
+ |
2003-10-03 17:11 mmeineke |
1926 |
+ |
|
1927 |
+ |
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
1928 |
+ |
entahlpy from the statwriter and thermo. |
1929 |
+ |
|
1930 |
+ |
2003-10-03 17:02 mmeineke |
1931 |
+ |
|
1932 |
+ |
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
1933 |
+ |
statements in simError |
1934 |
+ |
|
1935 |
+ |
added a function to get the maxCutoff |
1936 |
+ |
|
1937 |
+ |
2003-10-03 17:01 mmeineke |
1938 |
+ |
|
1939 |
+ |
* libBASS/simError.c: changed the formating ogf the error |
1940 |
+ |
statements in simError |
1941 |
+ |
|
1942 |
+ |
2003-09-30 11:00 mmeineke |
1943 |
+ |
|
1944 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
1945 |
+ |
f90Flags so they are no longer overwritten by the compiler. |
1946 |
+ |
|
1947 |
+ |
2003-09-29 17:06 mmeineke |
1948 |
+ |
|
1949 |
+ |
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
1950 |
+ |
for conifig.in |
1951 |
+ |
|
1952 |
+ |
fixed wrappers to extern "C" |
1953 |
+ |
|
1954 |
+ |
2003-09-29 17:06 mmeineke |
1955 |
+ |
|
1956 |
+ |
* ac-tools/configure.in: added mpif90 mod check back same for |
1957 |
+ |
conifig.in |
1958 |
+ |
|
1959 |
+ |
2003-09-29 17:05 mmeineke |
1960 |
+ |
|
1961 |
+ |
* configure: added mpif90 mod check back |
1962 |
+ |
|
1963 |
+ |
2003-09-29 16:16 mmeineke |
1964 |
+ |
|
1965 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1966 |
+ |
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
1967 |
+ |
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
1968 |
+ |
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
1969 |
+ |
libBASS/ZconStamp.cpp, libBASS/simError.c, |
1970 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
1971 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
1972 |
+ |
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
1973 |
+ |
found with SUN's SUNWspro.s1s7 |
1974 |
+ |
|
1975 |
+ |
2003-09-29 12:38 mmeineke |
1976 |
+ |
|
1977 |
+ |
* libmdtools/GenericData.hpp: light change in syntax. no |
1978 |
+ |
signifigant change. |
1979 |
+ |
|
1980 |
+ |
2003-09-25 16:17 mmeineke |
1981 |
+ |
|
1982 |
+ |
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
1983 |
+ |
additional remarks from icc -w3 (extra verbose output) |
1984 |
+ |
|
1985 |
+ |
2003-09-25 14:27 mmeineke |
1986 |
+ |
|
1987 |
+ |
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1988 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
1989 |
+ |
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
1990 |
+ |
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
1991 |
+ |
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
1992 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
1993 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1994 |
+ |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1995 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
1996 |
+ |
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
1997 |
+ |
gcc -Wall and g++ -Wall |
1998 |
+ |
|
1999 |
+ |
2003-09-25 13:54 gezelter |
2000 |
+ |
|
2001 |
+ |
* configure, ac-tools/configure.in: fixed a bug in configure |
2002 |
+ |
|
2003 |
+ |
2003-09-25 11:42 gezelter |
2004 |
+ |
|
2005 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
2006 |
+ |
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
2007 |
+ |
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
2008 |
+ |
fixes for configure |
2009 |
+ |
|
2010 |
+ |
2003-09-24 14:34 mmeineke |
2011 |
+ |
|
2012 |
+ |
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
2013 |
+ |
that it is called before the first Statistics are written. |
2014 |
+ |
|
2015 |
+ |
2003-09-23 15:36 gezelter |
2016 |
+ |
|
2017 |
+ |
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
2018 |
+ |
bunch of Make.dep files to CVS |
2019 |
+ |
|
2020 |
+ |
2003-09-23 15:34 mmeineke |
2021 |
+ |
|
2022 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
2023 |
+ |
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
2024 |
+ |
|
2025 |
+ |
Some small syntax cleaning in NPTfm and SimSetup |
2026 |
+ |
|
2027 |
+ |
2003-09-22 18:07 tim |
2028 |
+ |
|
2029 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
2030 |
+ |
SimInfo.hpp: fix bug in calculating maxCutoff |
2031 |
+ |
|
2032 |
+ |
2003-09-22 16:23 mmeineke |
2033 |
+ |
|
2034 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
2035 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
2036 |
+ |
Converted NPTf to work with the NPT base class. |
2037 |
+ |
|
2038 |
+ |
Removed NPTfm and NPTim from cvs |
2039 |
+ |
|
2040 |
+ |
2003-09-19 15:00 mmeineke |
2041 |
+ |
|
2042 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
2043 |
+ |
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
2044 |
+ |
class. NPTi is up to date. NPTf is not. |
2045 |
+ |
|
2046 |
+ |
2003-09-19 11:03 mmeineke |
2047 |
+ |
|
2048 |
+ |
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
2049 |
+ |
makefile |
2050 |
+ |
|
2051 |
+ |
2003-09-19 11:01 gezelter |
2052 |
+ |
|
2053 |
+ |
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
2054 |
+ |
|
2055 |
+ |
2003-09-19 11:01 gezelter |
2056 |
+ |
|
2057 |
+ |
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
2058 |
+ |
(nearly) conserved quantities for both NPTi and NPTf |
2059 |
+ |
|
2060 |
+ |
2003-09-19 10:20 mmeineke |
2061 |
+ |
|
2062 |
+ |
* utils/Makefile.in: fixed a typo in the makefile. |
2063 |
+ |
|
2064 |
+ |
2003-09-19 09:55 gezelter |
2065 |
+ |
|
2066 |
+ |
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
2067 |
+ |
samples/water/ssd.bass: [no log message] |
2068 |
+ |
|
2069 |
+ |
2003-09-19 09:22 tim |
2070 |
+ |
|
2071 |
+ |
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
2072 |
+ |
|
2073 |
+ |
2003-09-17 09:22 mmeineke |
2074 |
+ |
|
2075 |
+ |
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
2076 |
+ |
work with constraints. |
2077 |
+ |
|
2078 |
+ |
2003-09-16 15:02 tim |
2079 |
+ |
|
2080 |
+ |
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
2081 |
+ |
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
2082 |
+ |
|
2083 |
+ |
fixed conserved quantity in NPT (Still some small bug) |
2084 |
+ |
|
2085 |
+ |
NPTi appears very stable. |
2086 |
+ |
|
2087 |
+ |
2003-09-15 11:52 tim |
2088 |
+ |
|
2089 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
2090 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
2091 |
+ |
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
2092 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
2093 |
+ |
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
2094 |
+ |
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
2095 |
+ |
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
2096 |
+ |
statWriter fix bug of vector wrapping at NPTi |
2097 |
+ |
|
2098 |
+ |
2003-09-12 11:20 gezelter |
2099 |
+ |
|
2100 |
+ |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
2101 |
+ |
Makefile.in |
2102 |
+ |
|
2103 |
+ |
2003-09-12 11:20 gezelter |
2104 |
+ |
|
2105 |
+ |
* ChangeLog: Entered changes for configure into ChangeLog |
2106 |
+ |
|
2107 |
|
2003-09-09 15:35 mmeineke |
2108 |
|
|
2109 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
2178 |
|
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
2179 |
|
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
2180 |
|
|
87 |
– |
2003-08-28 11:59 mmeineke |
88 |
– |
|
89 |
– |
* props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp: |
90 |
– |
added the first functional parts of the PairCorrType Abstract |
91 |
– |
classes. |
92 |
– |
|
2181 |
|
2003-08-27 14:23 tim |
2182 |
|
|
2183 |
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
2448 |
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
2449 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
2450 |
|
works..... |
363 |
– |
|
364 |
– |
2003-08-08 13:32 mmeineke |
365 |
– |
|
366 |
– |
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
367 |
– |
moved frameCount's functionality into DumpReader. also split props |
368 |
– |
into staticProps and dynamicProps. (currently only have |
369 |
– |
staticProps) |
2451 |
|
|
2452 |
|
2003-08-08 12:48 mmeineke |
2453 |
|
|
2505 |
|
2003-07-29 11:32 mmeineke |
2506 |
|
|
2507 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
2508 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
2509 |
< |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
429 |
< |
src/Makefile: working on the props code |
2508 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
2509 |
> |
working on the props code |
2510 |
|
|
2511 |
|
2003-07-29 11:32 mmeineke |
2512 |
|
|
3643 |
|
|
3644 |
|
2003-03-24 20:07 gezelter |
3645 |
|
|
3646 |
< |
* samples/Makefile, tests/Makefile: moving tests to samples |
3646 |
> |
* samples/Makefile: moving tests to samples |
3647 |
|
|
3648 |
|
2003-03-24 20:06 gezelter |
3649 |
|
|
3650 |
< |
* samples/alkane/Makefile, samples/alkane/alkanes.mdl, |
3651 |
< |
samples/alkane/butane.bass, samples/alkane/init_butane.eor, |
3652 |
< |
samples/argon/Makefile, samples/argon/argon.bass, |
3653 |
< |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
3654 |
< |
samples/lipid/5x5.bass, samples/lipid/Makefile, |
3655 |
< |
samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, |
3656 |
< |
samples/lipid/water.mdl, samples/water/Makefile, |
1577 |
< |
samples/water/init_ssd.eor, samples/water/ssd.bass, |
1578 |
< |
samples/water/water.mdl, tests/alkane/Makefile, |
1579 |
< |
tests/alkane/alkanes.mdl, tests/alkane/butane.bass, |
1580 |
< |
tests/alkane/init_butane.eor, tests/argon/Makefile, |
1581 |
< |
tests/argon/argon.bass, tests/argon/init_argon.eor, |
1582 |
< |
tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile, |
1583 |
< |
tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl, |
1584 |
< |
tests/lipid/water.mdl, tests/water/Makefile, |
1585 |
< |
tests/water/init_ssd.eor, tests/water/ssd.bass, |
1586 |
< |
tests/water/water.mdl: moved tests to samples |
3650 |
> |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
3651 |
> |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
3652 |
> |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
3653 |
> |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
3654 |
> |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
3655 |
> |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
3656 |
> |
samples |
3657 |
|
|
3658 |
|
2003-03-24 19:51 gezelter |
3659 |
|
|
3661 |
|
|
3662 |
|
2003-03-24 19:46 gezelter |
3663 |
|
|
3664 |
< |
* ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile, |
1595 |
< |
tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile: |
1596 |
< |
Added makefiles in tests directories |
3664 |
> |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
3665 |
|
|
3666 |
|
2003-03-24 16:55 gezelter |
3667 |
|
|
3678 |
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
3679 |
|
do_Forces.F90: little bug fixes here and there |
3680 |
|
|
1613 |
– |
2003-03-24 11:04 mmeineke |
1614 |
– |
|
1615 |
– |
* tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon |
1616 |
– |
test simulation |
1617 |
– |
|
1618 |
– |
2003-03-24 11:02 mmeineke |
1619 |
– |
|
1620 |
– |
* tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl, |
1621 |
– |
lipid/water.mdl, water/init_ssd.eor, water/ssd.bass, |
1622 |
– |
water/water.mdl: [no log message] |
1623 |
– |
|
1624 |
– |
2003-03-24 11:02 mmeineke |
1625 |
– |
|
1626 |
– |
* tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added |
1627 |
– |
some test bass files for experimenting with |
1628 |
– |
|
3681 |
|
2003-03-24 10:26 mmeineke |
3682 |
|
|
3683 |
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
3787 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
3788 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
3789 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
3790 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
3791 |
< |
revision |
3790 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
3791 |
> |
Tree |
3792 |
|
|
3793 |
|
2003-03-21 12:42 mmeineke |
3794 |
|
|
3845 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
3846 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
3847 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
3848 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
3849 |
< |
Tree |
3848 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
3849 |
> |
revision |
3850 |
|
|