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2004-11-02 11:59 tim |
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2005-03-10 10:10 chrisfen |
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|
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* make/Makefile.in, samples/water/tip3p_ice/tp3.md, |
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src/brains/SimCreator.cpp, src/brains/SimInfo.hpp, |
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src/integrators/Integrator.cpp, src/integrators/Integrator.hpp, |
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src/integrators/VelocityVerletIntegrator.cpp, |
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src/integrators/VelocityVerletIntegrator.hpp, |
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src/io/DumpReader.cpp, src/io/Globals.cpp, src/io/Globals.hpp, |
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src/io/Makefile, src/io/ReadWrite.hpp, src/io/RestReader.cpp, |
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src/io/RestReader.hpp, src/io/RestWriter.cpp, |
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src/io/RestWriter.hpp, src/io/RestraintReader.cpp, |
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src/io/RestraintWriter.cpp, src/restraints/Makefile, |
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src/restraints/Restraints.cpp, src/restraints/Restraints.hpp, |
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src/restraints/ThermoIntegrationForceManager.cpp, |
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src/restraints/ThermoIntegrationForceManager.hpp: First commit of |
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the new restraints code |
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|
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2005-03-09 13:48 tim |
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|
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* src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding |
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IndexFinder |
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|
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2005-03-09 13:46 tim |
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|
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* src/: applications/dump2Xyz/Dump2XYZ.ggo, |
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applications/dump2Xyz/Dump2XYZCmd.c, |
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applications/dump2Xyz/Dump2XYZCmd.h, |
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selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp: |
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fix compilation issue |
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|
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2005-03-09 12:58 tim |
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|
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* forceFields/DUFF2.frc, scripts/filepp, |
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src/UseTheForce/EAM_FF.cpp, |
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src/io/MultipoleAtomTypesSectionParser.cpp, |
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src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug |
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in SectionParser (lineNo is not updated) |
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|
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2005-03-09 12:30 tim |
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|
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* src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, |
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applications/dump2Xyz/Dump2XYZ.ggo, |
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applications/dump2Xyz/Dump2XYZCmd.c, |
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applications/dump2Xyz/Dump2XYZCmd.h, brains/SimInfo.cpp, |
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brains/SimInfo.hpp, io/ChargeAtomTypesSectionParser.cpp, |
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io/ChargeAtomTypesSectionParser.hpp, |
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io/ElectrostaticAtomTypesSectionParser.cpp, |
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io/ElectrostaticAtomTypesSectionParser.hpp, io/Makefile, |
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io/MultipoleAtomTypesSectionParser.cpp, |
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io/MultipoleAtomTypesSectionParser.hpp, |
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io/SectionParserManager.cpp, selection/Makefile, |
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selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
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types/AtomType.cpp, types/DirectionalAtomType.cpp, |
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visitors/AtomVisitor.cpp, visitors/OtherVisitor.cpp, |
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visitors/OtherVisitor.hpp: adding IndexFinder which is used to |
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select the molecules; Seperate ElectrostaticAtomTypesSectionParser |
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into ChargeAtomTypesSectionParser and |
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MultipoleAtomTypesSectionParser;remove print dipole option from |
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Dump2XYZ; |
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|
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2005-03-09 12:28 tim |
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|
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* forceFields/DUFF2.frc: change the format of DUFF2 |
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|
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2005-03-09 10:44 gezelter |
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|
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* src/UseTheForce/DarkSide/: electrostatic.F90, |
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electrostatic_interface.F90, electrostatic_interface.h: new |
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electrostatic module |
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|
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2005-03-09 09:26 gezelter |
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|
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* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
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DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole |
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and fixed quadrupole stuff |
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|
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2005-03-09 09:25 gezelter |
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|
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* src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines |
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for outdated charge and dipole interfaces |
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|
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2005-03-08 16:08 gezelter |
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|
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* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in, |
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mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun |
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charge-dipole test cases |
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|
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2005-03-08 16:07 gezelter |
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|
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* src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp, |
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OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a |
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strange icc8 bug (we think). |
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|
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2005-03-08 16:07 gezelter |
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|
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* src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa! |
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|
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2005-03-08 16:07 gezelter |
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|
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* src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic |
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Unification Project |
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|
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2005-03-08 16:07 gezelter |
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|
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* src/io/Globals.cpp: Dunno |
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|
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2005-03-08 16:06 gezelter |
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|
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* src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using |
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OOPSE_itoa and checking a NULL left over from the LinkedList days |
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|
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2005-03-08 16:06 gezelter |
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|
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* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
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atype_interface.F90, atype_interface.h, charge.F90, |
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charge_interface.F90, charge_interface.h, dipole.F90, |
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dipole_interface.F90, dipole_interface.h: electrostatic unification |
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project fixed an uninitialized variable in Lennard Jones mixing map |
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|
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2005-03-08 16:05 gezelter |
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|
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* src/UseTheForce/doForces.F90: electrostatic unification project |
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|
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2005-03-08 16:05 gezelter |
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|
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* samples/water/dimer/: two.md, water.md: making some cool test |
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cases |
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|
129 |
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2005-03-08 16:05 gezelter |
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|
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* forceFields/DUFF2.frc: Added a charge for Chlorine |
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|
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2005-03-07 17:39 tim |
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|
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* src/: brains/SimInfo.cpp, io/DumpReader.cpp, |
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math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp, |
137 |
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primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp: |
138 |
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Fixing a bug in BitSet.cpp |
139 |
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|
140 |
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2005-03-04 10:28 gezelter |
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|
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* src/config.h.in: Cleaning up config.h.in by adding comments |
143 |
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|
144 |
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2005-03-04 10:28 gezelter |
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|
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* configure, ac-tools/configure.in, make/Makefile.in, |
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src/brains/SimCreator.cpp: SPRNG eradication project |
148 |
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|
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2005-03-03 09:40 tim |
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|
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* src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the |
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missing atom type problem) |
153 |
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|
154 |
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2005-03-02 11:29 tim |
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|
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* src/math/RandNumGen.hpp: adding base class of Random Number |
157 |
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generator |
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|
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2005-03-02 11:28 tim |
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|
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* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
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math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in |
163 |
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Velocitizer is not initialized which causes a seg fault |
164 |
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|
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2005-03-02 10:36 tim |
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|
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* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
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integrators/Velocitizer.hpp, math/Makefile, |
169 |
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math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
170 |
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math/ParallelRandNumGen.hpp, math/SeqRandNumGen.cpp, |
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math/SeqRandNumGen.hpp: remove default parameter from |
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MersenneTwister.hpp which causes all kinds of trouble. Refactory |
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random number generator |
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|
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2005-03-02 02:32 tim |
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|
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* test/math/testRandNumGen.cpp: Adding unit test for random number |
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generator |
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|
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2005-03-01 18:17 tim |
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|
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* src/brains/Thermo.hpp: fixed a file inclusion problem |
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|
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2005-03-01 18:17 tim |
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|
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* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
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OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp, |
188 |
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ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp, |
189 |
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RandNumGenTestCase.hpp: fixed compilation problem |
190 |
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|
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2005-03-01 18:02 tim |
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|
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* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
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integrators/Velocitizer.hpp, math/Makefile, |
195 |
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math/OOPSERandNumGen.hpp, math/ParallelRandNumGen.cpp, |
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math/ParallelRandNumGen.hpp, math/mt19937ar.c, |
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math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand |
198 |
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|
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2005-03-01 18:00 tim |
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|
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* test/math/: Makefile, ParallelandNumGenTestCase.cpp, |
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ParallelandNumGenTestCase.hpp: Change the name of test case |
203 |
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|
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2005-03-01 16:00 tim |
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|
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* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
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OOPSERandNumGenTestCase.hpp: adding testcase for random number |
208 |
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generator |
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|
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2005-03-01 15:10 tim |
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|
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* src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp, |
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integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp, |
214 |
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math/Polynomial.hpp, math/Quaternion.hpp, math/RectMatrix.hpp, |
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math/SquareMatrix.hpp, math/SquareMatrix3.hpp, math/Vector.hpp, |
216 |
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math/Vector3.hpp, minimizers/MinimizerCreator.hpp, |
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utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
218 |
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utils/TypeContainer.hpp, visitors/AtomVisitor.cpp, |
219 |
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visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4 |
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|
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2005-03-01 14:11 tim |
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|
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* src/: brains/SimCreator.cpp, brains/SimInfo.hpp, |
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integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
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math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding |
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OOPSERandNumGen |
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|
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2005-03-01 10:44 gezelter |
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|
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* make/Makefile.in: Fixed the damned build problem with the |
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libraries not being removed in make clean and make distclean (at |
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least we think it is fixed). |
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|
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2005-03-01 10:26 gezelter |
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|
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* src/math/MersenneTwister.hpp: Making small modifications to allow |
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for use on MPI machines |
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|
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2005-03-01 09:45 tim |
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|
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* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp, |
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integrators/Velocitizer.cpp, io/DumpReader.cpp, |
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math/MersenneTwister.hpp: adding MersenneTwister random number |
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generator |
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|
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2005-02-28 22:55 tim |
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|
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* src/math/MersenneTwister.hpp: Adding a modified version of |
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MersenneTwister.hpp |
250 |
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|
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2005-02-28 12:24 tim |
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|
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* doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png, |
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definition.jpg: selection expression |
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|
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2005-02-25 16:22 tim |
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|
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* src/: UseTheForce/DarkSide/LJ.F90, |
259 |
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UseTheForce/DarkSide/lj_interface.F90, |
260 |
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UseTheForce/DarkSide/lj_interface.h, |
261 |
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io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp, |
262 |
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types/AtomType.hpp: adding soft potential to LJ Module |
263 |
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|
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2005-02-25 11:38 tim |
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|
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* doc/SelectionExpression.html: adding documentation for selection |
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expression |
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2005-02-24 15:55 tim |
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|
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* src/: applications/simpleBuilder/simpleBuilder.cpp, |
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integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp, |
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io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp: |
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adding basic_teebuf which can operate on multiple stream |
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simutaneously. |
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|
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2005-02-22 13:56 tim |
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|
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* src/: UseTheForce/DarkSide/reactionField.F90, |
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primitives/RigidBody.cpp: reactionfield get fixed |
281 |
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|
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2005-02-21 11:57 tim |
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|
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* src/: applications/staticProps/GofRAngle.cpp, |
285 |
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visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix |
286 |
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a bug in GofRAngle |
287 |
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|
288 |
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2005-02-21 10:28 tim |
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|
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* src/primitives/Molecule.cpp: Fix for compilation on the Sun |
291 |
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2005-02-21 10:22 tim |
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|
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* src/utils/next_combination.hpp: fix for compilation on the Sun |
295 |
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2005-02-21 10:21 tim |
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|
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* src/utils/GenericData.hpp: fix problem in sun |
299 |
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2005-02-18 18:07 tim |
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|
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* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
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applications/dump2Xyz/Dump2XYZ.ggo, |
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applications/dump2Xyz/Dump2XYZCmd.c, |
305 |
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applications/dump2Xyz/Dump2XYZCmd.h, |
306 |
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applications/dynamicProps/RCorrFunc.cpp, |
307 |
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applications/staticProps/GofXyz.cpp, |
308 |
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applications/staticProps/GofXyz.hpp, |
309 |
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applications/staticProps/StaticProps.cpp, |
310 |
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applications/staticProps/StaticProps.ggo, |
311 |
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applications/staticProps/StaticPropsCmd.c, |
312 |
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applications/staticProps/StaticPropsCmd.h, |
313 |
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io/ElectrostaticAtomTypesSectionParser.cpp, |
314 |
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visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
315 |
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visitors/Makefile: adding LipidTransVisitor, GofXyz is working now |
316 |
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|
317 |
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2005-02-18 10:58 gezelter |
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|
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* src/brains/Register.cpp: Corrected filename collision for EAM on |
320 |
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Mac OS X |
321 |
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322 |
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2005-02-18 10:58 gezelter |
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* src/applications/oopse/oopse.cpp: Updated copyright information |
325 |
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2005-02-18 10:58 gezelter |
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|
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* src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp, |
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Makefile: corrected filename collision for EAM on operating systems |
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which are not case sensitive (aka Mac OS X) |
331 |
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|
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2005-02-17 15:15 tim |
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* src/applications/staticProps/GofXyz.cpp: more bug get fixed |
335 |
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2005-02-17 14:50 tim |
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|
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* src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug |
339 |
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in GofXyz |
340 |
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|
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2005-02-17 14:09 tim |
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|
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* src/applications/staticProps/RadialDistrFunc.hpp: make |
344 |
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processHistogram non-abstrct function |
345 |
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2005-02-17 13:41 tim |
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* src/applications/staticProps/GofXyz.cpp: [no log message] |
349 |
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2005-02-17 13:30 tim |
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* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
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GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: |
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finish GofXyz |
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356 |
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2005-02-17 11:21 tim |
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* src/applications/staticProps/: GofAngle2.cpp, GofR.cpp, |
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GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial |
360 |
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distribution function |
361 |
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362 |
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2005-02-17 10:23 tim |
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* src/utils/BitSet.hpp: forget the const correctness for BitSet |
365 |
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366 |
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2005-02-17 10:18 tim |
367 |
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|
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* src/: brains/BlockSnapshotManager.cpp, |
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selection/DistanceFinder.cpp: The change of interface of BitSet |
370 |
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cause a bug in SelectionEvaluation |
371 |
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|
372 |
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2005-02-16 16:13 tim |
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* src/utils/residentMem.c: return residentMem in byte |
375 |
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2005-02-16 16:00 tim |
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|
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* src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix |
379 |
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a bug in writing out the value of cosang |
380 |
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|
381 |
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2005-02-16 15:43 tim |
382 |
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|
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* src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to |
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estimate avaliable memory |
385 |
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386 |
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2005-02-16 15:30 tim |
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|
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* src/: applications/staticProps/GofAngle2.cpp, |
389 |
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applications/staticProps/GofAngle2.hpp, |
390 |
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applications/staticProps/GofR.cpp, |
391 |
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applications/staticProps/GofR.hpp, |
392 |
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applications/staticProps/GofRAngle.cpp, |
393 |
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applications/staticProps/GofRAngle.hpp, |
394 |
> |
applications/staticProps/GofXyz.cpp, |
395 |
> |
applications/staticProps/GofXyz.hpp, |
396 |
> |
applications/staticProps/StaticProps.cpp, |
397 |
> |
applications/staticProps/StaticProps.ggo, |
398 |
> |
applications/staticProps/StaticPropsCmd.c, |
399 |
> |
applications/staticProps/StaticPropsCmd.h, |
400 |
> |
brains/BlockSnapshotManager.cpp: change the default bin number |
401 |
> |
|
402 |
> |
2005-02-16 14:36 tim |
403 |
> |
|
404 |
> |
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
405 |
> |
applications/dynamicProps/RCorrFunc.cpp, |
406 |
> |
applications/dynamicProps/TimeCorrFunc.cpp, |
407 |
> |
applications/dynamicProps/VCorrFunc.cpp, |
408 |
> |
applications/staticProps/GofAngle2.cpp, |
409 |
> |
applications/staticProps/GofR.cpp, |
410 |
> |
applications/staticProps/GofR.hpp, |
411 |
> |
applications/staticProps/GofRAngle.cpp, |
412 |
> |
applications/staticProps/GofRAngle.hpp, |
413 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
414 |
> |
applications/staticProps/RadialDistrFunc.hpp, |
415 |
> |
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
416 |
> |
utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output |
417 |
> |
files;fix the problem of counting in staticProps |
418 |
> |
|
419 |
> |
2005-02-15 14:39 tim |
420 |
> |
|
421 |
> |
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
422 |
> |
BlockSnapshotManager |
423 |
> |
|
424 |
> |
2005-02-15 14:36 tim |
425 |
> |
|
426 |
> |
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
427 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
428 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
429 |
> |
selection/SelectionEvaluator.cpp: BlockSnapshotManager is using |
430 |
> |
reference counting now |
431 |
> |
|
432 |
> |
2005-02-15 12:49 tim |
433 |
> |
|
434 |
> |
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
435 |
> |
replace std::make_pair by VariablesType::value_type to make Sun |
436 |
> |
Compiler happy |
437 |
> |
|
438 |
> |
2005-02-15 12:35 tim |
439 |
> |
|
440 |
> |
* src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to |
441 |
> |
TokenMap, using TokenMapType::value_type instead of std::make_pair |
442 |
> |
to make Sun compiler happy |
443 |
> |
|
444 |
> |
2005-02-15 12:24 tim |
445 |
> |
|
446 |
> |
* src/applications/staticProps/: GofRAngle.cpp, |
447 |
> |
RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps |
448 |
> |
|
449 |
> |
2005-02-15 12:11 tim |
450 |
> |
|
451 |
> |
* src/: applications/staticProps/GofR.cpp, |
452 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
453 |
> |
applications/staticProps/RadialDistrFunc.hpp, |
454 |
> |
brains/BlockSnapshotManager.cpp, utils/BitSet.cpp: (1) adding |
455 |
> |
#ifdef __RWSTD to make sun compiler happy (2) fix pair density |
456 |
> |
calculation problem when two selections intersect with each other |
457 |
> |
|
458 |
> |
2005-02-15 10:24 gezelter |
459 |
> |
|
460 |
> |
* src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy |
461 |
> |
xlc++ |
462 |
> |
|
463 |
> |
2005-02-15 10:17 gezelter |
464 |
> |
|
465 |
> |
* configure, ac-tools/configure.in, src/config.h.in, |
466 |
> |
src/utils/residentMem.c: [no log message] |
467 |
> |
|
468 |
> |
2005-02-15 01:17 gezelter |
469 |
> |
|
470 |
> |
* src/utils/residentMem.c: bug fix for null termination |
471 |
> |
|
472 |
> |
2005-02-15 01:11 gezelter |
473 |
> |
|
474 |
> |
* configure, ac-tools/configure.in, src/utils/residentMem.c: |
475 |
> |
bugfixing residentMem |
476 |
> |
|
477 |
> |
2005-02-15 00:59 gezelter |
478 |
> |
|
479 |
> |
* configure, ac-tools/configure.in, src/config.h.in, |
480 |
> |
src/utils/residentMem.c: bugfixes for residentMem on LINUX |
481 |
> |
|
482 |
> |
2005-02-15 00:08 gezelter |
483 |
> |
|
484 |
> |
* src/utils/Makefile.in: added residentMem |
485 |
> |
|
486 |
> |
2005-02-15 00:05 gezelter |
487 |
> |
|
488 |
> |
* configure, ac-tools/configure.in, make/Makefile.in, |
489 |
> |
src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c, |
490 |
> |
src/utils/residentMem.h: modifications to estimate memory in use by |
491 |
> |
other processes autoconf fixes ps syntax checking config.h file |
492 |
> |
cleaning |
493 |
> |
|
494 |
> |
2005-02-14 18:26 gezelter |
495 |
> |
|
496 |
> |
* configure, ac-tools/configure.in, make/Makefile.in: ps niceness |
497 |
> |
|
498 |
> |
2005-02-14 18:16 gezelter |
499 |
> |
|
500 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps |
501 |
> |
strangeness |
502 |
> |
|
503 |
> |
2005-02-14 14:42 tim |
504 |
> |
|
505 |
> |
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
506 |
> |
BlockSnapshotManager.hpp |
507 |
> |
|
508 |
> |
2005-02-14 13:51 tim |
509 |
> |
|
510 |
> |
* src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo, |
511 |
> |
StaticPropsCmd.c: default length for staticProps is 1/2 smallest |
512 |
> |
length of first frame |
513 |
> |
|
514 |
> |
2005-02-14 13:12 tim |
515 |
> |
|
516 |
> |
* src/integrators/VelocityVerletIntegrator.cpp: fix a bug in |
517 |
> |
VelocityVerletIntegrator : last frame is written twice |
518 |
> |
|
519 |
> |
2005-02-14 12:57 tim |
520 |
> |
|
521 |
> |
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
522 |
> |
brains/SimInfo.cpp, primitives/RigidBody.cpp, |
523 |
> |
primitives/StuntDouble.hpp: begin bug fix |
524 |
> |
|
525 |
> |
2005-02-14 12:35 tim |
526 |
> |
|
527 |
> |
* src/applications/dynamicProps/: CorrelationFunction.cpp, |
528 |
> |
CorrelationFunction.hpp, CrossTimeCorrFunc.cpp, |
529 |
> |
CrossTimeCorrFunc.hpp, DipoleCorrFunc.cpp, DipoleCorrFunc.hpp, |
530 |
> |
DynamicProps.cpp, FrameTimeCorrFunc.hpp, Makefile, |
531 |
> |
ParticleTimeCorrFunc.cpp, ParticleTimeCorrFunc.hpp, RCorrFunc.cpp, |
532 |
> |
RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp, |
533 |
> |
VCorrFunc.hpp: refactory CorrelationFunction |
534 |
> |
|
535 |
> |
2005-02-14 10:18 gezelter |
536 |
> |
|
537 |
> |
* src/applications/dynamicProps/CorrelationFunction.cpp: bug fix |
538 |
> |
and start of switch for type of correlation function |
539 |
> |
|
540 |
> |
2005-02-13 16:18 tim |
541 |
> |
|
542 |
> |
* src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in |
543 |
> |
calculating bytes per stuntdouble |
544 |
> |
|
545 |
> |
2005-02-13 16:03 tim |
546 |
> |
|
547 |
> |
* src/applications/dynamicProps/CorrelationFunction.cpp: more fix |
548 |
> |
|
549 |
> |
2005-02-13 15:57 tim |
550 |
> |
|
551 |
> |
* src/applications/dynamicProps/CorrelationFunction.cpp: fixed a |
552 |
> |
bug in CorrelationFunction |
553 |
> |
|
554 |
> |
2005-02-13 15:36 tim |
555 |
> |
|
556 |
> |
* src/: applications/staticProps/GofR.cpp, |
557 |
> |
applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a |
558 |
> |
bug in SimInfo::getCutoff() |
559 |
> |
|
560 |
> |
2005-02-13 15:08 tim |
561 |
> |
|
562 |
> |
* make/Makefile.in: adding staticProps and dynamicProps into |
563 |
> |
Makefile.in |
564 |
> |
|
565 |
> |
2005-02-13 15:05 tim |
566 |
> |
|
567 |
> |
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
568 |
> |
applications/dynamicProps/CorrelationFunction.hpp, |
569 |
> |
applications/staticProps/StaticProps.cpp, |
570 |
> |
applications/staticProps/StaticProps.ggo, |
571 |
> |
applications/staticProps/StaticPropsCmd.c, |
572 |
> |
applications/staticProps/StaticPropsCmd.h, brains/SimInfo.cpp, |
573 |
> |
brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length |
574 |
> |
defaults to the cutoff radius |
575 |
> |
|
576 |
> |
2005-02-13 14:14 tim |
577 |
> |
|
578 |
> |
* src/utils/Algorithm.hpp: adding Algorithm.hpp |
579 |
> |
|
580 |
> |
2005-02-13 14:10 tim |
581 |
> |
|
582 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
583 |
> |
applications/dynamicProps/CorrelationFunction.cpp, |
584 |
> |
applications/dynamicProps/CorrelationFunction.hpp, |
585 |
> |
applications/dynamicProps/DynamicProps.cpp, |
586 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
587 |
> |
integrators/Integrator.cpp, integrators/Integrator.hpp, |
588 |
> |
integrators/VelocityVerletIntegrator.cpp, |
589 |
> |
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.cpp, |
590 |
> |
io/LennardJonesAtomTypesSectionParser.cpp, minimizers/PRCG.cpp, |
591 |
> |
utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h, |
592 |
> |
visitors/OtherVisitor.cpp: dynamicProps get built |
593 |
> |
|
594 |
> |
2005-02-13 10:56 tim |
595 |
> |
|
596 |
> |
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
597 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
598 |
> |
brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in |
599 |
> |
progress |
600 |
> |
|
601 |
> |
2005-02-13 03:04 tim |
602 |
> |
|
603 |
> |
* src/: applications/dynamicProps/CorrelationFunction.hpp, |
604 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
605 |
> |
brains/Makefile, brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
606 |
> |
brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more |
607 |
> |
work in dynamicProps |
608 |
> |
|
609 |
> |
2005-02-13 02:25 tim |
610 |
> |
|
611 |
> |
* src/applications/dynamicProps/DynamicProps.cpp: adding |
612 |
> |
dynamicProps |
613 |
> |
|
614 |
> |
2005-02-13 02:14 tim |
615 |
> |
|
616 |
> |
* src/applications/dynamicProps/: DynamicPropsCmd.c, |
617 |
> |
DynamicPropsCmd.h: adding command line option to DynamicProps |
618 |
> |
|
619 |
> |
2005-02-13 02:13 tim |
620 |
> |
|
621 |
> |
* src/applications/dynamicProps/: DynamicProps.ggo, Makefile: |
622 |
> |
adding command line option for DynamicProps |
623 |
> |
|
624 |
> |
2005-02-13 01:57 tim |
625 |
> |
|
626 |
> |
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
627 |
> |
applications/dynamicProps/CorrelationFunction.hpp, |
628 |
> |
applications/dynamicProps/DipoleCorrFunc.cpp, |
629 |
> |
applications/dynamicProps/DipoleCorrFunc.hpp, |
630 |
> |
applications/dynamicProps/RCorrFunc.cpp, |
631 |
> |
applications/dynamicProps/RCorrFunc.hpp, |
632 |
> |
applications/dynamicProps/VCorrFunc.cpp, |
633 |
> |
applications/dynamicProps/VCorrFunc.hpp, |
634 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
635 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
636 |
> |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
637 |
> |
brains/SnapshotManager.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
638 |
> |
primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding |
639 |
> |
dynamicProps |
640 |
> |
|
641 |
> |
2005-02-12 15:09 tim |
642 |
> |
|
643 |
> |
* src/selection/SelectionManager.cpp: adding SelectionManager.cpp |
644 |
> |
|
645 |
> |
2005-02-11 17:41 tim |
646 |
> |
|
647 |
> |
* src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one |
648 |
> |
more constructor to Snapshot to create customized DataStorage |
649 |
> |
|
650 |
> |
2005-02-11 17:39 tim |
651 |
> |
|
652 |
> |
* src/selection/: DistanceFinder.hpp, Makefile, |
653 |
> |
SelectionManager.hpp: adding beginSelected, nextSelected method to |
654 |
> |
SelectionManager |
655 |
> |
|
656 |
> |
2005-02-11 17:36 tim |
657 |
> |
|
658 |
> |
* src/config.h.in, configure: adding support for physmem |
659 |
> |
|
660 |
> |
2005-02-11 17:35 tim |
661 |
> |
|
662 |
> |
* ac-tools/configure.in: adding supprot for physmem |
663 |
> |
|
664 |
> |
2005-02-11 17:35 tim |
665 |
> |
|
666 |
> |
* src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding |
667 |
> |
physmem |
668 |
> |
|
669 |
> |
2005-02-10 17:37 tim |
670 |
> |
|
671 |
> |
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
672 |
> |
GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp, |
673 |
> |
GofXyz.hpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
674 |
> |
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
675 |
> |
StaticPropsCmd.h: more work in StaticProps |
676 |
> |
|
677 |
> |
2005-02-10 13:14 tim |
678 |
> |
|
679 |
> |
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
680 |
> |
GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, |
681 |
> |
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofXyz.cpp, GofXyz.hpp, |
682 |
> |
Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
683 |
> |
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
684 |
> |
StaticPropsCmd.h: change the filenames |
685 |
> |
|
686 |
> |
2005-02-10 09:15 tim |
687 |
> |
|
688 |
> |
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
689 |
> |
GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp, |
690 |
> |
RadialDistrFunc.hpp: adding GofRAngle |
691 |
> |
|
692 |
> |
2005-02-09 13:21 tim |
693 |
> |
|
694 |
> |
* src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some |
695 |
> |
useless files |
696 |
> |
|
697 |
> |
2005-02-09 13:12 tim |
698 |
> |
|
699 |
> |
* src/applications/staticProps/: GofR.cpp, Makefile, |
700 |
> |
RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress |
701 |
> |
|
702 |
> |
2005-02-09 12:08 tim |
703 |
> |
|
704 |
> |
* src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp, |
705 |
> |
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h, |
706 |
> |
RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR |
707 |
> |
|
708 |
> |
2005-02-07 17:39 tim |
709 |
> |
|
710 |
> |
* src/primitives/Molecule.hpp: add getRigidBodyAt function into |
711 |
> |
Molecule class |
712 |
> |
|
713 |
> |
2005-02-07 17:38 tim |
714 |
> |
|
715 |
> |
* src/applications/dump2Xyz/Dump2XYZCmd.c: update help info |
716 |
> |
|
717 |
> |
2005-02-07 17:36 tim |
718 |
> |
|
719 |
> |
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
720 |
> |
SelectionCompiler.cpp: support select internal index selection, for |
721 |
> |
example, select DMPC.3 |
722 |
> |
|
723 |
> |
2005-02-07 16:11 tim |
724 |
> |
|
725 |
> |
* src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update |
726 |
> |
help info for Dump2XYZ |
727 |
> |
|
728 |
> |
2005-02-07 15:39 chrisfen |
729 |
> |
|
730 |
> |
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
731 |
> |
selection librarys added |
732 |
> |
|
733 |
> |
2005-02-07 15:31 tim |
734 |
> |
|
735 |
> |
* src/selection/Makefile, make/Makefile.in: adding Makefile |
736 |
> |
|
737 |
> |
2005-02-07 15:20 chrisfen |
738 |
> |
|
739 |
> |
* src/utils/wildcards.hpp: issue commented out in wildcards |
740 |
> |
|
741 |
> |
2005-02-07 15:06 tim |
742 |
> |
|
743 |
> |
* src/selection/SelectionEvaluator.cpp: forget to reset the pc |
744 |
> |
which cause reevaluate return NULL |
745 |
> |
|
746 |
> |
2005-02-07 14:14 tim |
747 |
> |
|
748 |
> |
* src/brains/: SimCreator.cpp, SimSnapshotManager.cpp, |
749 |
> |
SimSnapshotManager.hpp: fix a bug in determing the global index for |
750 |
> |
rigidbodies |
751 |
> |
|
752 |
> |
2005-02-07 14:13 tim |
753 |
> |
|
754 |
> |
* src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change |
755 |
> |
in Bitset |
756 |
> |
|
757 |
> |
2005-02-07 14:13 tim |
758 |
> |
|
759 |
> |
* src/selection/: DistanceFinder.cpp, DistanceFinder.hpp, |
760 |
> |
SelectionCompiler.cpp, SelectionCompiler.hpp, |
761 |
> |
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp, |
762 |
> |
TokenMap.cpp: selection library is working |
763 |
> |
|
764 |
> |
2005-02-04 17:46 tim |
765 |
> |
|
766 |
> |
* src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor |
767 |
> |
|
768 |
> |
2005-02-04 17:45 tim |
769 |
> |
|
770 |
> |
* src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor |
771 |
> |
and XYZVisitor now use selection library |
772 |
> |
|
773 |
> |
2005-02-04 17:44 tim |
774 |
> |
|
775 |
> |
* src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp: |
776 |
> |
adding SelectionManager into SimInfo |
777 |
> |
|
778 |
> |
2005-02-04 17:43 tim |
779 |
> |
|
780 |
> |
* src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, |
781 |
> |
Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of |
782 |
> |
selection library |
783 |
> |
|
784 |
> |
2005-02-04 17:42 tim |
785 |
> |
|
786 |
> |
* src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change |
787 |
> |
in BitSet |
788 |
> |
|
789 |
> |
2005-02-04 17:41 tim |
790 |
> |
|
791 |
> |
* src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing |
792 |
> |
implementation |
793 |
> |
|
794 |
> |
2005-02-04 17:39 tim |
795 |
> |
|
796 |
> |
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
797 |
> |
SelectionCompiler.cpp, SelectionCompiler.hpp, |
798 |
> |
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
799 |
> |
SelectionManager.hpp, Token.hpp: half of the selection utility is |
800 |
> |
working need to debug within keyword and atomproperty keyword |
801 |
> |
|
802 |
> |
2005-02-04 00:42 tim |
803 |
> |
|
804 |
> |
* src/selection/: NameFinder.cpp, NameFinder.hpp: selection library |
805 |
> |
get built |
806 |
> |
|
807 |
> |
2005-02-04 00:42 tim |
808 |
> |
|
809 |
> |
* src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet |
810 |
> |
|
811 |
> |
2005-02-04 00:26 tim |
812 |
> |
|
813 |
> |
* src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp: |
814 |
> |
remove some useless files |
815 |
> |
|
816 |
> |
2005-02-03 23:57 tim |
817 |
> |
|
818 |
> |
* src/: primitives/RigidBody.hpp, selection/NameFinder.cpp, |
819 |
> |
selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp: |
820 |
> |
adding wildcard class; NameFinder is finished |
821 |
> |
|
822 |
> |
2005-02-03 18:14 tim |
823 |
> |
|
824 |
> |
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
825 |
> |
SelectionCompiler.cpp, SelectionCompiler.hpp, |
826 |
> |
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
827 |
> |
SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in |
828 |
> |
selection library |
829 |
> |
|
830 |
> |
2005-02-03 09:04 tim |
831 |
> |
|
832 |
> |
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
833 |
> |
selection in progress |
834 |
> |
|
835 |
> |
2005-02-02 18:13 tim |
836 |
> |
|
837 |
> |
* src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp, |
838 |
> |
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp, |
839 |
> |
Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in |
840 |
> |
progress, except SelectionEvaluator, other files are compiled |
841 |
> |
|
842 |
> |
2005-02-02 18:12 tim |
843 |
> |
|
844 |
> |
* src/utils/: Makefile.in, any.hpp: adding boost::any |
845 |
> |
|
846 |
> |
2005-02-02 07:51 tim |
847 |
> |
|
848 |
> |
* src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp |
849 |
> |
|
850 |
> |
2005-02-01 17:49 tim |
851 |
> |
|
852 |
> |
* src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp, |
853 |
> |
selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, |
854 |
> |
selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, |
855 |
> |
selection/Token.hpp: Selection in progress |
856 |
> |
|
857 |
> |
2005-02-01 01:55 tim |
858 |
> |
|
859 |
> |
* src/: selection/SelectionCompiler.hpp, |
860 |
> |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
861 |
> |
selection/SelectionManager.hpp, selection/Token.hpp, |
862 |
> |
utils/BitSet.cpp, utils/BitSet.hpp: adding selection library |
863 |
> |
|
864 |
> |
2005-01-26 10:26 tim |
865 |
> |
|
866 |
> |
* src/integrators/: Integrator.cpp, Integrator.hpp, |
867 |
> |
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget |
868 |
> |
to add eorWriter |
869 |
> |
|
870 |
> |
2005-01-26 10:15 tim |
871 |
> |
|
872 |
> |
* src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp: |
873 |
> |
(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the |
874 |
> |
wrong column of electroframe |
875 |
> |
|
876 |
> |
2005-01-25 16:59 tim |
877 |
> |
|
878 |
> |
* src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in |
879 |
> |
SimInfo, use number of cutoff stamp as counter to loop over |
880 |
> |
rigidbody stamp |
881 |
> |
|
882 |
> |
2005-01-25 12:45 tim |
883 |
> |
|
884 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
885 |
> |
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
886 |
> |
integrators/DLM.cpp, io/AtomTypesSectionParser.cpp, |
887 |
> |
io/BendTypesSectionParser.cpp, io/BondTypesSectionParser.cpp, |
888 |
> |
io/DirectionalAtomTypesSectionParser.cpp, io/DumpReader.cpp, |
889 |
> |
io/EAMAtomTypesSectionParser.cpp, |
890 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, io/Globals.cpp, |
891 |
> |
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
892 |
> |
io/StickyAtomTypesSectionParser.cpp, |
893 |
> |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
894 |
> |
math/SquareMatrix.hpp, primitives/DirectionalAtom.cpp, |
895 |
> |
primitives/DirectionalAtom.hpp, primitives/GhostTorsion.cpp, |
896 |
> |
primitives/GhostTorsion.hpp, primitives/Makefile, |
897 |
> |
primitives/RigidBody.cpp, types/MakeStamps.cpp: (1) complete |
898 |
> |
section parser's error message (2) add GhostTorsion (3) accumulate |
899 |
> |
inertial tensor from the directional atoms before calculate |
900 |
> |
rigidbody's inertial tensor |
901 |
> |
|
902 |
> |
2005-01-17 17:17 tim |
903 |
> |
|
904 |
> |
* forceFields/DUFF2.frc: forget to set dipole for lipid head group |
905 |
> |
|
906 |
> |
2005-01-17 11:58 tim |
907 |
> |
|
908 |
> |
* src/integrators/NVT.cpp: fix a bug in loading initial extended |
909 |
> |
system parameters |
910 |
> |
|
911 |
> |
2005-01-17 11:05 tim |
912 |
> |
|
913 |
> |
* src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT |
914 |
> |
|
915 |
> |
2005-01-14 17:02 tim |
916 |
> |
|
917 |
> |
* src/UseTheForce/WATER.cpp: remove WATER.cpp |
918 |
> |
|
919 |
> |
2005-01-14 16:37 tim |
920 |
> |
|
921 |
> |
* forceFields/Makefile: sync Makefile |
922 |
> |
|
923 |
> |
2005-01-14 16:13 gezelter |
924 |
> |
|
925 |
> |
* make/Makefile.in, src/Makefile, src/UseTheForce/Makefile, |
926 |
> |
src/UseTheForce/DarkSide/Makefile, src/applications/Makefile, |
927 |
> |
src/applications/dump2Xyz/Makefile, |
928 |
> |
src/applications/oopse/Makefile, |
929 |
> |
src/applications/simpleBuilder/Makefile, src/brains/Makefile, |
930 |
> |
src/constraints/Makefile, src/integrators/Makefile, |
931 |
> |
src/io/Makefile, src/math/Makefile, src/minimizers/Makefile, |
932 |
> |
src/primitives/Makefile, src/profiling/Makefile, |
933 |
> |
src/restraints/Makefile, src/types/Makefile, src/utils/Makefile.in, |
934 |
> |
src/visitors/Makefile: moved Package variable into subdirectory |
935 |
> |
makefiles to speed up the building process |
936 |
> |
|
937 |
> |
2005-01-14 15:48 gezelter |
938 |
> |
|
939 |
> |
* src/applications/oopse/oopse.cpp: Fixed publication details in |
940 |
> |
banner |
941 |
> |
|
942 |
> |
2005-01-14 15:48 gezelter |
943 |
> |
|
944 |
> |
* src/UseTheForce/DarkSide/: simParallel_interface.F90, |
945 |
> |
simParallel_interface.h: added dummy subroutine to avoid empty |
946 |
> |
unit, synchronized this dummy routine between C and fortran |
947 |
> |
|
948 |
> |
2005-01-14 15:31 gezelter |
949 |
> |
|
950 |
> |
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90, |
951 |
> |
notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90, |
952 |
> |
DarkSide/Makefile, DarkSide/atype.F90, |
953 |
> |
DarkSide/atype_interface.F90, DarkSide/charge.F90, |
954 |
> |
DarkSide/charge_interface.F90, DarkSide/dipole.F90, |
955 |
> |
DarkSide/dipole_interface.F90, DarkSide/eam.F90, |
956 |
> |
DarkSide/eam_interface.F90, DarkSide/gb.F90, |
957 |
> |
DarkSide/gb_interface.F90, DarkSide/lj_interface.F90, |
958 |
> |
DarkSide/shapes.F90, DarkSide/shapes_interface.F90, |
959 |
> |
DarkSide/simParallel.F90, DarkSide/simParallel_interface.F90, |
960 |
> |
DarkSide/simulation.F90, DarkSide/simulation_interface.F90, |
961 |
> |
DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating |
962 |
> |
modules and C/Fortran interface subroutines |
963 |
> |
|
964 |
> |
2005-01-14 15:15 gezelter |
965 |
> |
|
966 |
> |
* configure, ac-tools/aclocal.m4: more fixes for gnugetopt |
967 |
> |
|
968 |
> |
2005-01-14 15:09 gezelter |
969 |
> |
|
970 |
> |
* configure, ac-tools/configure.in, src/config.h.in, |
971 |
> |
src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt |
972 |
> |
|
973 |
> |
2005-01-14 11:49 tim |
974 |
> |
|
975 |
> |
* src/: io/EAMAtomTypesSectionParser.cpp, |
976 |
> |
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
977 |
> |
utils/StringUtils.hpp: using c library to do conversion instead of |
978 |
> |
using iostream due to a bug in libstdc++(GCC 3.2) |
979 |
> |
|
980 |
> |
2005-01-13 21:40 tim |
981 |
> |
|
982 |
> |
* src/brains/SimSetup.cpp: no message |
983 |
> |
|
984 |
> |
2005-01-13 20:56 tim |
985 |
> |
|
986 |
> |
* src/primitives/Molecule.hpp: fix a bug in global index |
987 |
> |
|
988 |
> |
2005-01-13 20:04 tim |
989 |
> |
|
990 |
> |
* src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include |
991 |
> |
Integrator.hpp in Minimizer |
992 |
> |
|
993 |
> |
2005-01-13 17:14 gezelter |
994 |
> |
|
995 |
> |
* src/utils/Makefile: compile getopt and getopt1 if we need to |
996 |
> |
|
997 |
> |
2005-01-13 16:56 gezelter |
998 |
> |
|
999 |
> |
* make/Makefile.in: template flags |
1000 |
> |
|
1001 |
> |
2005-01-13 16:48 gezelter |
1002 |
> |
|
1003 |
> |
* src/applications/oopse/Makefile: formatting |
1004 |
> |
|
1005 |
> |
2005-01-13 16:48 gezelter |
1006 |
> |
|
1007 |
> |
* make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir |
1008 |
> |
target |
1009 |
> |
|
1010 |
> |
2005-01-13 14:40 tim |
1011 |
> |
|
1012 |
> |
* src/: UseTheForce/fSwitchingFunction.h, |
1013 |
> |
UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile, |
1014 |
> |
math/Makefile, math/RectMatrix.hpp, math/Vector.hpp, |
1015 |
> |
primitives/RigidBody.cpp, types/AtomTypeProperties.h, |
1016 |
> |
types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform |
1017 |
> |
|
1018 |
> |
2005-01-13 13:26 tim |
1019 |
> |
|
1020 |
> |
* make/Makefile.in: change the order of linking (object file comes |
1021 |
> |
first and then follow by user built library) |
1022 |
> |
|
1023 |
> |
2005-01-12 18:24 tim |
1024 |
> |
|
1025 |
> |
* src/io/DumpWriter.cpp: remove useless debug info |
1026 |
> |
|
1027 |
> |
2005-01-12 18:21 tim |
1028 |
> |
|
1029 |
> |
* src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix |
1030 |
> |
|
1031 |
> |
2005-01-12 18:17 tim |
1032 |
> |
|
1033 |
> |
* make/: Makefile.in, Makefile.in: missing tab |
1034 |
> |
|
1035 |
> |
2005-01-12 18:15 tim |
1036 |
> |
|
1037 |
> |
* src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor |
1038 |
> |
get fixed |
1039 |
> |
|
1040 |
> |
2005-01-12 17:40 gezelter |
1041 |
> |
|
1042 |
> |
* make/Makefile.in, src/UseTheForce/DUFF.cpp, |
1043 |
> |
src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp, |
1044 |
> |
src/UseTheForce/EAM.hpp, src/UseTheForce/EAM_FF.cpp, |
1045 |
> |
src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp, |
1046 |
> |
src/UseTheForce/ForceFieldCreator.hpp, |
1047 |
> |
src/UseTheForce/ForceFieldFactory.cpp, |
1048 |
> |
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/LJFF.cpp, |
1049 |
> |
src/UseTheForce/Makefile, src/UseTheForce/Shapes_FF.cpp, |
1050 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/doForces_interface.h, |
1051 |
> |
src/UseTheForce/fSwitchingFunction.h, |
1052 |
> |
src/UseTheForce/mpiComponentPlan.h, |
1053 |
> |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
1054 |
> |
src/UseTheForce/notifyCutoffs.F90, |
1055 |
> |
src/UseTheForce/notifyCutoffs_interface.h, |
1056 |
> |
src/UseTheForce/DarkSide/LJ.F90, |
1057 |
> |
src/UseTheForce/DarkSide/atype.F90, |
1058 |
> |
src/UseTheForce/DarkSide/atype_interface.h, |
1059 |
> |
src/UseTheForce/DarkSide/charge.F90, |
1060 |
> |
src/UseTheForce/DarkSide/charge_interface.h, |
1061 |
> |
src/UseTheForce/DarkSide/dipole.F90, |
1062 |
> |
src/UseTheForce/DarkSide/dipole_interface.h, |
1063 |
> |
src/UseTheForce/DarkSide/eam.F90, |
1064 |
> |
src/UseTheForce/DarkSide/eam_interface.h, |
1065 |
> |
src/UseTheForce/DarkSide/force_globals.F90, |
1066 |
> |
src/UseTheForce/DarkSide/gb.F90, |
1067 |
> |
src/UseTheForce/DarkSide/gb_interface.h, |
1068 |
> |
src/UseTheForce/DarkSide/lj_interface.h, |
1069 |
> |
src/UseTheForce/DarkSide/neighborLists.F90, |
1070 |
> |
src/UseTheForce/DarkSide/reactionField.F90, |
1071 |
> |
src/UseTheForce/DarkSide/shapes.F90, |
1072 |
> |
src/UseTheForce/DarkSide/shapes_interface.h, |
1073 |
> |
src/UseTheForce/DarkSide/simParallel.F90, |
1074 |
> |
src/UseTheForce/DarkSide/simParallel_interface.h, |
1075 |
> |
src/UseTheForce/DarkSide/simulation.F90, |
1076 |
> |
src/UseTheForce/DarkSide/simulation_interface.h, |
1077 |
> |
src/UseTheForce/DarkSide/sticky.F90, |
1078 |
> |
src/UseTheForce/DarkSide/sticky_interface.h, |
1079 |
> |
src/UseTheForce/DarkSide/switcheroo.F90, |
1080 |
> |
src/applications/Makedepend, src/applications/quickLate.c, |
1081 |
> |
src/applications/dump2Xyz/Dump2XYZ.cpp, |
1082 |
> |
src/applications/oopse/oopse.cpp, |
1083 |
> |
src/applications/simpleBuilder/BaseLattice.cpp, |
1084 |
> |
src/applications/simpleBuilder/BaseLattice.hpp, |
1085 |
> |
src/applications/simpleBuilder/Lattice.cpp, |
1086 |
> |
src/applications/simpleBuilder/Lattice.hpp, |
1087 |
> |
src/applications/simpleBuilder/LatticeCreator.cpp, |
1088 |
> |
src/applications/simpleBuilder/LatticeCreator.hpp, |
1089 |
> |
src/applications/simpleBuilder/LatticeFactory.cpp, |
1090 |
> |
src/applications/simpleBuilder/LatticeFactory.hpp, |
1091 |
> |
src/applications/simpleBuilder/MoLocator.cpp, |
1092 |
> |
src/applications/simpleBuilder/MoLocator.hpp, |
1093 |
> |
src/applications/simpleBuilder/simpleBuilder.cpp, |
1094 |
> |
src/brains/DataStorage.cpp, src/brains/DataStorage.hpp, |
1095 |
> |
src/brains/Exclude.cpp, src/brains/Exclude.hpp, |
1096 |
> |
src/brains/ForceManager.cpp, src/brains/ForceManager.hpp, |
1097 |
> |
src/brains/Makefile, src/brains/Migrator.hpp, |
1098 |
> |
src/brains/MoleculeCreator.cpp, src/brains/MoleculeCreator.hpp, |
1099 |
> |
src/brains/Register.cpp, src/brains/Register.hpp, |
1100 |
> |
src/brains/SimCreator.cpp, src/brains/SimCreator.hpp, |
1101 |
> |
src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
1102 |
> |
src/brains/SimModel.hpp, src/brains/SimSetup.hpp, |
1103 |
> |
src/brains/SimSnapshotManager.cpp, |
1104 |
> |
src/brains/SimSnapshotManager.hpp, src/brains/SimState.cpp, |
1105 |
> |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
1106 |
> |
src/brains/SkipList.hpp, src/brains/Snapshot.cpp, |
1107 |
> |
src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp, |
1108 |
> |
src/brains/Stats.cpp, src/brains/Stats.hpp, src/brains/Thermo.cpp, |
1109 |
> |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
1110 |
> |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
1111 |
> |
src/constraints/AbstractClasses.hpp, |
1112 |
> |
src/constraints/ConstraintElem.hpp, |
1113 |
> |
src/constraints/ConstraintPair.hpp, src/constraints/Makefile, |
1114 |
> |
src/constraints/Rattle.cpp, src/constraints/Rattle.hpp, |
1115 |
> |
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
1116 |
> |
src/constraints/ZconsStruct.hpp, |
1117 |
> |
src/constraints/ZconstraintForceManager.cpp, |
1118 |
> |
src/constraints/ZconstraintForceManager.hpp, |
1119 |
> |
src/integrators/AbstractClasses.hpp, |
1120 |
> |
src/integrators/AllIntegrator.hpp, src/integrators/DLM.cpp, |
1121 |
> |
src/integrators/DLM.hpp, src/integrators/Integrator.cpp, |
1122 |
> |
src/integrators/Integrator.hpp, |
1123 |
> |
src/integrators/IntegratorCreator.hpp, |
1124 |
> |
src/integrators/IntegratorFactory.cpp, |
1125 |
> |
src/integrators/IntegratorFactory.hpp, src/integrators/Makefile, |
1126 |
> |
src/integrators/NPT.cpp, src/integrators/NPT.hpp, |
1127 |
> |
src/integrators/NPTf.cpp, src/integrators/NPTf.hpp, |
1128 |
> |
src/integrators/NPTi.cpp, src/integrators/NPTi.hpp, |
1129 |
> |
src/integrators/NPTxyz.cpp, src/integrators/NPTxyz.hpp, |
1130 |
> |
src/integrators/NVE.cpp, src/integrators/NVE.hpp, |
1131 |
> |
src/integrators/NVT.cpp, src/integrators/NVT.hpp, |
1132 |
> |
src/integrators/RotationAlgorithm.hpp, |
1133 |
> |
src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp, |
1134 |
> |
src/integrators/VelocityVerletIntegrator.cpp, |
1135 |
> |
src/integrators/VelocityVerletIntegrator.hpp, |
1136 |
> |
src/io/AtomTypesSectionParser.cpp, |
1137 |
> |
src/io/AtomTypesSectionParser.hpp, src/io/BASS_interface.cpp, |
1138 |
> |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
1139 |
> |
src/io/BendTypesSectionParser.cpp, |
1140 |
> |
src/io/BendTypesSectionParser.hpp, |
1141 |
> |
src/io/BondTypesSectionParser.cpp, |
1142 |
> |
src/io/BondTypesSectionParser.hpp, |
1143 |
> |
src/io/DirectionalAtomTypesSectionParser.cpp, |
1144 |
> |
src/io/DirectionalAtomTypesSectionParser.hpp, |
1145 |
> |
src/io/DumpReader.cpp, src/io/DumpReader.hpp, |
1146 |
> |
src/io/DumpWriter.cpp, src/io/DumpWriter.hpp, |
1147 |
> |
src/io/EAMAtomTypesSectionParser.cpp, |
1148 |
> |
src/io/EAMAtomTypesSectionParser.hpp, |
1149 |
> |
src/io/ElectrostaticAtomTypesSectionParser.cpp, |
1150 |
> |
src/io/ElectrostaticAtomTypesSectionParser.hpp, src/io/Globals.cpp, |
1151 |
> |
src/io/Globals.hpp, src/io/InitializeFromFile.cpp, |
1152 |
> |
src/io/LennardJonesAtomTypesSectionParser.cpp, |
1153 |
> |
src/io/LennardJonesAtomTypesSectionParser.hpp, |
1154 |
> |
src/io/LinkedAssign.cpp, src/io/LinkedAssign.hpp, |
1155 |
> |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
1156 |
> |
src/io/Makefile, src/io/SectionParser.cpp, |
1157 |
> |
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
1158 |
> |
src/io/SectionParserManager.hpp, src/io/StatWriter.cpp, |
1159 |
> |
src/io/StatWriter.hpp, src/io/StickyAtomTypesSectionParser.cpp, |
1160 |
> |
src/io/StickyAtomTypesSectionParser.hpp, |
1161 |
> |
src/io/TorsionTypesSectionParser.cpp, |
1162 |
> |
src/io/TorsionTypesSectionParser.hpp, src/io/ZConsReader.cpp, |
1163 |
> |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
1164 |
> |
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
1165 |
> |
src/io/interface.c, src/io/make_nodes.c, src/io/make_nodes.h, |
1166 |
> |
src/io/mpiBASS.c, src/io/mpiBASS.h, src/io/node_list.h, |
1167 |
> |
src/io/parse_interface.h, src/io/parse_me.h, src/io/parse_tree.c, |
1168 |
> |
src/io/parse_tree.h, src/math/ChebyshevPolynomials.cpp, |
1169 |
> |
src/math/ChebyshevPolynomials.hpp, src/math/MatVec3.c, |
1170 |
> |
src/math/MatVec3.h, src/math/Polynomial.hpp, |
1171 |
> |
src/math/Quaternion.hpp, src/math/RealSphericalHarmonic.cpp, |
1172 |
> |
src/math/RealSphericalHarmonic.hpp, src/math/RectMatrix.hpp, |
1173 |
> |
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
1174 |
> |
src/math/Vector.hpp, src/math/Vector3.hpp, |
1175 |
> |
src/math/randomSPRNG.cpp, src/math/randomSPRNG.hpp, |
1176 |
> |
src/minimizers/CGFamilyMinimizer.cpp, |
1177 |
> |
src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Makefile, |
1178 |
> |
src/minimizers/Minimizer.cpp, src/minimizers/Minimizer.hpp, |
1179 |
> |
src/minimizers/MinimizerCreator.hpp, |
1180 |
> |
src/minimizers/MinimizerFactory.cpp, |
1181 |
> |
src/minimizers/MinimizerFactory.hpp, |
1182 |
> |
src/minimizers/MinimizerParameterSet.cpp, |
1183 |
> |
src/minimizers/MinimizerParameterSet.hpp, |
1184 |
> |
src/minimizers/OOPSEMinimizer.cpp, |
1185 |
> |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
1186 |
> |
src/minimizers/PRCG.hpp, src/minimizers/SDMinimizer.cpp, |
1187 |
> |
src/minimizers/SDMinimizer.hpp, src/primitives/AbstractClasses.hpp, |
1188 |
> |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
1189 |
> |
src/primitives/Bend.cpp, src/primitives/Bend.hpp, |
1190 |
> |
src/primitives/BendExtensions.cpp, src/primitives/Bond.cpp, |
1191 |
> |
src/primitives/Bond.hpp, src/primitives/BondExtensions.cpp, |
1192 |
> |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
1193 |
> |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
1194 |
> |
src/primitives/GhostBend.hpp, src/primitives/Makefile, |
1195 |
> |
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
1196 |
> |
src/primitives/RigidBody.cpp, src/primitives/RigidBody.hpp, |
1197 |
> |
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
1198 |
> |
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
1199 |
> |
src/primitives/Torsion.hpp, src/primitives/TorsionExtensions.cpp, |
1200 |
> |
src/primitives/UreyBradleyBend.cpp, |
1201 |
> |
src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp, |
1202 |
> |
src/profiling/mdProfile.hpp, src/types/AtomStamp.cpp, |
1203 |
> |
src/types/AtomStamp.hpp, src/types/AtomType.cpp, |
1204 |
> |
src/types/AtomType.hpp, src/types/AtomTypeProperties.h, |
1205 |
> |
src/types/BendStamp.cpp, src/types/BendStamp.hpp, |
1206 |
> |
src/types/BendType.hpp, src/types/BondStamp.cpp, |
1207 |
> |
src/types/BondStamp.hpp, src/types/BondType.hpp, |
1208 |
> |
src/types/CharmmTorsionType.cpp, src/types/CharmmTorsionType.hpp, |
1209 |
> |
src/types/Component.cpp, src/types/Component.hpp, |
1210 |
> |
src/types/CubicBendType.hpp, src/types/CubicBondType.hpp, |
1211 |
> |
src/types/CubicTorsionType.hpp, src/types/CutoffGroupStamp.cpp, |
1212 |
> |
src/types/CutoffGroupStamp.hpp, src/types/DirectionalAtomType.cpp, |
1213 |
> |
src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp, |
1214 |
> |
src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp, |
1215 |
> |
src/types/MakeStamps.cpp, src/types/MakeStamps.hpp, |
1216 |
> |
src/types/Makefile, src/types/MoleculeStamp.cpp, |
1217 |
> |
src/types/MoleculeStamp.hpp, src/types/MorseBondType.hpp, |
1218 |
> |
src/types/OplsTorsionType.hpp, src/types/PolynomialBendType.hpp, |
1219 |
> |
src/types/PolynomialBondType.hpp, |
1220 |
> |
src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp, |
1221 |
> |
src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp, |
1222 |
> |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
1223 |
> |
src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp, |
1224 |
> |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
1225 |
> |
src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp, |
1226 |
> |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
1227 |
> |
src/utils/GenericData.hpp, src/utils/GenericFactory.hpp, |
1228 |
> |
src/utils/LocalIndexManager.hpp, src/utils/Makefile, |
1229 |
> |
src/utils/MemoryUtils.hpp, src/utils/NumericConstant.hpp, |
1230 |
> |
src/utils/OOPSEConstant.hpp, src/utils/PropertyMap.cpp, |
1231 |
> |
src/utils/PropertyMap.hpp, src/utils/StreamTokenizer.cpp, |
1232 |
> |
src/utils/StreamTokenizer.hpp, src/utils/StringTokenizer.cpp, |
1233 |
> |
src/utils/StringTokenizer.hpp, src/utils/StringUtils.cpp, |
1234 |
> |
src/utils/StringUtils.hpp, src/utils/Trim.cpp, src/utils/Trim.hpp, |
1235 |
> |
src/utils/Tuple.hpp, src/utils/TupleMatcher.hpp, |
1236 |
> |
src/utils/TypeContainer.hpp, src/utils/TypeInfo.hpp, |
1237 |
> |
src/utils/Utility.cpp, src/utils/Utility.hpp, |
1238 |
> |
src/utils/definitions.F90, src/utils/fError.c, |
1239 |
> |
src/utils/next_combination.hpp, src/utils/oopseMPI.F90, |
1240 |
> |
src/utils/simError.c, src/utils/simError.h, src/utils/status.F90, |
1241 |
> |
src/utils/vector_class.F90, src/visitors/AtomData.hpp, |
1242 |
> |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
1243 |
> |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
1244 |
> |
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
1245 |
> |
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
1246 |
> |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
1247 |
> |
src/visitors/ZconsVisitor.hpp: merging new_design branch into |
1248 |
> |
OOPSE-2.0 |
1249 |
> |
|
1250 |
> |
2005-01-12 13:13 tim |
1251 |
> |
|
1252 |
> |
* src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp, |
1253 |
> |
utils/TypeContainer.hpp: forget to include <algorithm> |
1254 |
> |
|
1255 |
> |
2005-01-12 12:25 tim |
1256 |
> |
|
1257 |
> |
* forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc, |
1258 |
> |
newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force |
1259 |
> |
fields |
1260 |
> |
|
1261 |
> |
2005-01-12 12:14 tim |
1262 |
> |
|
1263 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
1264 |
> |
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
1265 |
> |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
1266 |
> |
UseTheForce/ForceFieldCreator.hpp, |
1267 |
> |
UseTheForce/ForceFieldFactory.cpp, |
1268 |
> |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
1269 |
> |
UseTheForce/doForces.F90, UseTheForce/doForces_interface.h, |
1270 |
> |
UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h, |
1271 |
> |
UseTheForce/notifyCutoffs.F90, |
1272 |
> |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
1273 |
> |
UseTheForce/DarkSide/atype.F90, |
1274 |
> |
UseTheForce/DarkSide/atype_interface.h, |
1275 |
> |
UseTheForce/DarkSide/charge.F90, |
1276 |
> |
UseTheForce/DarkSide/charge_interface.h, |
1277 |
> |
UseTheForce/DarkSide/dipole.F90, |
1278 |
> |
UseTheForce/DarkSide/dipole_interface.h, |
1279 |
> |
UseTheForce/DarkSide/eam.F90, UseTheForce/DarkSide/eam_interface.h, |
1280 |
> |
UseTheForce/DarkSide/force_globals.F90, |
1281 |
> |
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
1282 |
> |
UseTheForce/DarkSide/lj_interface.h, |
1283 |
> |
UseTheForce/DarkSide/neighborLists.F90, |
1284 |
> |
UseTheForce/DarkSide/reactionField.F90, |
1285 |
> |
UseTheForce/DarkSide/shapes.F90, |
1286 |
> |
UseTheForce/DarkSide/shapes_interface.h, |
1287 |
> |
UseTheForce/DarkSide/simParallel.F90, |
1288 |
> |
UseTheForce/DarkSide/simParallel_interface.h, |
1289 |
> |
UseTheForce/DarkSide/simulation.F90, |
1290 |
> |
UseTheForce/DarkSide/simulation_interface.h, |
1291 |
> |
UseTheForce/DarkSide/sticky.F90, |
1292 |
> |
UseTheForce/DarkSide/sticky_interface.h, |
1293 |
> |
UseTheForce/DarkSide/switcheroo.F90, |
1294 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
1295 |
> |
applications/simpleBuilder/BaseLattice.cpp, |
1296 |
> |
applications/simpleBuilder/BaseLattice.hpp, |
1297 |
> |
applications/simpleBuilder/Lattice.cpp, |
1298 |
> |
applications/simpleBuilder/Lattice.hpp, |
1299 |
> |
applications/simpleBuilder/LatticeCreator.cpp, |
1300 |
> |
applications/simpleBuilder/LatticeCreator.hpp, |
1301 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
1302 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
1303 |
> |
applications/simpleBuilder/MoLocator.cpp, |
1304 |
> |
applications/simpleBuilder/MoLocator.hpp, |
1305 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
1306 |
> |
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
1307 |
> |
brains/Exclude.hpp, brains/ForceManager.cpp, |
1308 |
> |
brains/ForceManager.hpp, brains/Makefile, brains/Migrator.hpp, |
1309 |
> |
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
1310 |
> |
brains/Register.cpp, brains/Register.hpp, brains/SimCreator.cpp, |
1311 |
> |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
1312 |
> |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
1313 |
> |
brains/SkipList.cpp, brains/SkipList.hpp, brains/SnapShot.cpp, |
1314 |
> |
brains/Snapshot.cpp, brains/Snapshot.hpp, |
1315 |
> |
brains/SnapshotManager.hpp, brains/Stats.cpp, brains/Stats.hpp, |
1316 |
> |
brains/Thermo.cpp, brains/Thermo.hpp, brains/fSimulation.h, |
1317 |
> |
constraints/ConstraintElem.hpp, constraints/ConstraintPair.hpp, |
1318 |
> |
constraints/Rattle.cpp, constraints/Rattle.hpp, |
1319 |
> |
constraints/ZconsStruct.hpp, |
1320 |
> |
constraints/ZconstraintForceManager.cpp, |
1321 |
> |
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
1322 |
> |
integrators/DLM.hpp, integrators/Integrator.cpp, |
1323 |
> |
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
1324 |
> |
integrators/IntegratorFactory.cpp, |
1325 |
> |
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
1326 |
> |
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
1327 |
> |
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
1328 |
> |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
1329 |
> |
integrators/NVT.cpp, integrators/NVT.hpp, |
1330 |
> |
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
1331 |
> |
integrators/Velocitizer.hpp, |
1332 |
> |
integrators/VelocityVerletIntegrator.cpp, |
1333 |
> |
integrators/VelocityVerletIntegrator.hpp, |
1334 |
> |
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
1335 |
> |
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
1336 |
> |
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
1337 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
1338 |
> |
io/BondTypesSectionParser.hpp, |
1339 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
1340 |
> |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
1341 |
> |
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
1342 |
> |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
1343 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
1344 |
> |
io/ElectrostaticAtomTypesSectionParser.hpp, io/Globals.cpp, |
1345 |
> |
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
1346 |
> |
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
1347 |
> |
io/LinkedAssign.hpp, io/LinkedCommand.cpp, io/LinkedCommand.hpp, |
1348 |
> |
io/SectionParser.cpp, io/SectionParser.hpp, |
1349 |
> |
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
1350 |
> |
io/StatWriter.cpp, io/StatWriter.hpp, |
1351 |
> |
io/StickyAtomTypesSectionParser.cpp, |
1352 |
> |
io/StickyAtomTypesSectionParser.hpp, |
1353 |
> |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
1354 |
> |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
1355 |
> |
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/interface.c, |
1356 |
> |
io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, |
1357 |
> |
io/node_list.h, io/parse_interface.h, io/parse_me.h, |
1358 |
> |
io/parse_tree.c, io/parse_tree.h, math/ChebyshevPolynomials.cpp, |
1359 |
> |
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
1360 |
> |
math/Polynomial.hpp, math/Quaternion.hpp, |
1361 |
> |
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
1362 |
> |
math/RectMatrix.hpp, math/SquareMatrix.hpp, math/SquareMatrix3.hpp, |
1363 |
> |
math/Vector.hpp, math/Vector3.hpp, math/randomSPRNG.cpp, |
1364 |
> |
math/randomSPRNG.hpp, minimizers/CGFamilyMinimizer.cpp, |
1365 |
> |
minimizers/CGFamilyMinimizer.hpp, minimizers/Minimizer.cpp, |
1366 |
> |
minimizers/Minimizer.hpp, minimizers/MinimizerCreator.hpp, |
1367 |
> |
minimizers/MinimizerFactory.cpp, minimizers/MinimizerFactory.hpp, |
1368 |
> |
minimizers/MinimizerParameterSet.cpp, |
1369 |
> |
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
1370 |
> |
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
1371 |
> |
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
1372 |
> |
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
1373 |
> |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
1374 |
> |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
1375 |
> |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
1376 |
> |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
1377 |
> |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
1378 |
> |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
1379 |
> |
primitives/Torsion.cpp, primitives/Torsion.hpp, |
1380 |
> |
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
1381 |
> |
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
1382 |
> |
restraints/Restraints.cpp, restraints/Restraints.hpp, |
1383 |
> |
types/AtomStamp.cpp, types/AtomStamp.hpp, types/AtomType.cpp, |
1384 |
> |
types/AtomType.hpp, types/AtomTypeProperties.h, |
1385 |
> |
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
1386 |
> |
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
1387 |
> |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
1388 |
> |
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
1389 |
> |
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
1390 |
> |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
1391 |
> |
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp, |
1392 |
> |
types/FixedBondType.hpp, types/HarmonicBendType.hpp, |
1393 |
> |
types/HarmonicBondType.hpp, types/MakeStamps.cpp, |
1394 |
> |
types/MakeStamps.hpp, types/MoleculeStamp.cpp, |
1395 |
> |
types/MoleculeStamp.hpp, types/MorseBondType.hpp, |
1396 |
> |
types/OplsTorsionType.hpp, types/PolynomialBendType.hpp, |
1397 |
> |
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
1398 |
> |
types/QuarticBendType.hpp, types/QuarticBondType.hpp, |
1399 |
> |
types/QuarticTorsionType.hpp, types/RigidBodyStamp.cpp, |
1400 |
> |
types/RigidBodyStamp.hpp, types/ShapeAtomType.cpp, |
1401 |
> |
types/ShapeAtomType.hpp, types/TorsionStamp.cpp, |
1402 |
> |
types/TorsionStamp.hpp, types/TorsionType.hpp, |
1403 |
> |
types/UreyBradleyBendType.hpp, types/ZconStamp.cpp, |
1404 |
> |
types/ZconStamp.hpp, utils/GenericData.hpp, |
1405 |
> |
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
1406 |
> |
utils/MemoryUtils.hpp, utils/NumericConstant.hpp, |
1407 |
> |
utils/OOPSEConstant.hpp, utils/PropertyMap.cpp, |
1408 |
> |
utils/PropertyMap.hpp, utils/StringTokenizer.cpp, |
1409 |
> |
utils/StringTokenizer.hpp, utils/StringUtils.cpp, |
1410 |
> |
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
1411 |
> |
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
1412 |
> |
utils/Utility.cpp, utils/Utility.hpp, utils/definitions.F90, |
1413 |
> |
utils/fError.c, utils/next_combination.hpp, utils/oopseMPI.F90, |
1414 |
> |
utils/simError.c, utils/simError.h, utils/status.F90, |
1415 |
> |
utils/vector_class.F90, visitors/AtomData.hpp, |
1416 |
> |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp, |
1417 |
> |
visitors/BaseVisitor.hpp, visitors/CompositeVisitor.cpp, |
1418 |
> |
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
1419 |
> |
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
1420 |
> |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
1421 |
> |
visitors/ZconsVisitor.hpp: change license |
1422 |
> |
|
1423 |
> |
2005-01-12 12:14 tim |
1424 |
> |
|
1425 |
> |
* src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on |
1426 |
> |
branch new_design. |
1427 |
> |
|
1428 |
> |
2005-01-11 16:03 tim |
1429 |
> |
|
1430 |
> |
* src/: constraints/ZconstraintForceManager.cpp, |
1431 |
> |
constraints/ZconstraintForceManager.hpp, |
1432 |
> |
minimizers/MinimizerParameterSet.cpp, |
1433 |
> |
minimizers/MinimizerParameterSet.hpp: change const static double |
1434 |
> |
data member to const double |
1435 |
> |
|
1436 |
> |
2005-01-11 15:50 tim |
1437 |
> |
|
1438 |
> |
* src/io/basic_ifstrstream.hpp: forget namespace qualifier std:: |
1439 |
> |
|
1440 |
> |
2005-01-11 15:39 tim |
1441 |
> |
|
1442 |
> |
* src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h: |
1443 |
> |
change data type from logical to integer in AtomTypeProperties.h |
1444 |
> |
|
1445 |
> |
2005-01-11 11:36 tim |
1446 |
> |
|
1447 |
> |
* forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding |
1448 |
> |
new format of EAM force field |
1449 |
> |
|
1450 |
> |
2005-01-11 11:24 tim |
1451 |
> |
|
1452 |
> |
* src/UseTheForce/DUFF.cpp: change default name of DUFF force field |
1453 |
> |
to DUFF2.frc |
1454 |
> |
|
1455 |
> |
2005-01-11 11:23 tim |
1456 |
> |
|
1457 |
> |
* forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to |
1458 |
> |
DUFF2.frc |
1459 |
> |
|
1460 |
> |
2005-01-11 11:09 tim |
1461 |
> |
|
1462 |
> |
* make/Makefile.in: adding constraints and minimizers into |
1463 |
> |
Makefile.in |
1464 |
> |
|
1465 |
> |
2005-01-11 11:03 tim |
1466 |
> |
|
1467 |
> |
* src/io/: ChargeAtomTypesSectionParser.cpp, |
1468 |
> |
ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp, |
1469 |
> |
DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless |
1470 |
> |
files |
1471 |
> |
|
1472 |
> |
2005-01-11 10:59 tim |
1473 |
> |
|
1474 |
> |
* src/io/ZConsWriter.cpp: [no log message] |
1475 |
> |
|
1476 |
> |
2005-01-11 10:53 tim |
1477 |
> |
|
1478 |
> |
* src/UseTheForce/EAM.cpp: minor fix |
1479 |
> |
|
1480 |
> |
2005-01-11 10:52 tim |
1481 |
> |
|
1482 |
> |
* src/constraints/Rattle.cpp: file Rattle.cpp was initially added |
1483 |
> |
on branch new_design. |
1484 |
> |
|
1485 |
> |
2005-01-11 10:52 tim |
1486 |
> |
|
1487 |
> |
* src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm |
1488 |
> |
|
1489 |
> |
2005-01-11 10:52 tim |
1490 |
> |
|
1491 |
> |
* src/constraints/Rattle.hpp: file Rattle.hpp was initially added |
1492 |
> |
on branch new_design. |
1493 |
> |
|
1494 |
> |
2005-01-11 10:47 tim |
1495 |
> |
|
1496 |
> |
* make/Makefile.in: forget a '$' sign |
1497 |
> |
|
1498 |
> |
2005-01-11 10:46 tim |
1499 |
> |
|
1500 |
> |
* make/Makefile.in: missing tab in rules |
1501 |
> |
|
1502 |
> |
2005-01-10 17:04 tim |
1503 |
> |
|
1504 |
> |
* src/: UseTheForce/ForceFieldCreator.cpp, |
1505 |
> |
UseTheForce/ForceFieldCreator.hpp, |
1506 |
> |
UseTheForce/ForceFieldFactory.cpp, |
1507 |
> |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
1508 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
1509 |
> |
applications/simpleBuilder/simpleBuilder.cpp, brains/Makefile, |
1510 |
> |
brains/Register.cpp, brains/Register.hpp, |
1511 |
> |
integrators/IntegratorCreator.cpp, |
1512 |
> |
integrators/IntegratorCreator.hpp, |
1513 |
> |
integrators/IntegratorFactory.cpp, |
1514 |
> |
integrators/IntegratorFactory.hpp, integrators/Makefile, |
1515 |
> |
integrators/NPTi.cpp, integrators/NVE.cpp, integrators/NVT.cpp, |
1516 |
> |
minimizers/Makefile, minimizers/MinimizerCreator.cpp, |
1517 |
> |
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
1518 |
> |
minimizers/MinimizerFactory.hpp: create a register module to |
1519 |
> |
register force fields, integrators and minimizers |
1520 |
> |
|
1521 |
> |
2005-01-10 17:04 tim |
1522 |
> |
|
1523 |
> |
* src/brains/Register.cpp: file Register.cpp was initially added on |
1524 |
> |
branch new_design. |
1525 |
> |
|
1526 |
> |
2005-01-10 17:04 tim |
1527 |
> |
|
1528 |
> |
* src/brains/Register.hpp: file Register.hpp was initially added on |
1529 |
> |
branch new_design. |
1530 |
> |
|
1531 |
> |
2005-01-10 15:52 tim |
1532 |
> |
|
1533 |
> |
* src/: UseTheForce/ForceFieldFactory.cpp, |
1534 |
> |
applications/oopse/oopse.cpp, brains/ForceManager.hpp, |
1535 |
> |
constraints/ZconstraintForceManager.cpp, |
1536 |
> |
constraints/ZconstraintForceManager.hpp, |
1537 |
> |
integrators/IntegratorFactory.cpp, |
1538 |
> |
integrators/VelocityVerletIntegrator.cpp, io/ZConsReader.cpp, |
1539 |
> |
io/ZConsWriter.cpp, minimizers/MinimizerFactory.cpp, |
1540 |
> |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint |
1541 |
> |
method is working now |
1542 |
> |
|
1543 |
> |
2005-01-10 13:05 tim |
1544 |
> |
|
1545 |
> |
* src/: constraints/ConstraintElem.hpp, |
1546 |
> |
constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp, |
1547 |
> |
constraints/ZconstraintForceManager.cpp, |
1548 |
> |
constraints/ZconstraintForceManager.hpp, io/ZConsReader.cpp, |
1549 |
> |
io/ZConsReader.hpp, io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
1550 |
> |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in |
1551 |
> |
zconstraint |
1552 |
> |
|
1553 |
> |
2005-01-10 13:05 tim |
1554 |
> |
|
1555 |
> |
* src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was |
1556 |
> |
initially added on branch new_design. |
1557 |
> |
|
1558 |
> |
2005-01-07 16:50 tim |
1559 |
> |
|
1560 |
> |
* src/: applications/simpleBuilder/BaseLattice.hpp, |
1561 |
> |
applications/simpleBuilder/Lattice.hpp, |
1562 |
> |
applications/simpleBuilder/LatticeCreator.hpp, |
1563 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
1564 |
> |
applications/simpleBuilder/MoLocator.hpp, brains/ForceManager.hpp, |
1565 |
> |
constraints/ConstraintElem.hpp, constraints/Makefile, |
1566 |
> |
constraints/ZConstraint.cpp, constraints/ZconsData.hpp, |
1567 |
> |
constraints/ZconstraintForceManager.cpp, |
1568 |
> |
constraints/ZconstraintForceManager.hpp, |
1569 |
> |
integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp, |
1570 |
> |
utils/NumericConstant.hpp: ZConstraintForceManager in progress |
1571 |
> |
|
1572 |
> |
2005-01-07 16:50 tim |
1573 |
> |
|
1574 |
> |
* src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was |
1575 |
> |
initially added on branch new_design. |
1576 |
> |
|
1577 |
> |
2005-01-07 16:50 tim |
1578 |
> |
|
1579 |
> |
* src/constraints/ZconstraintForceManager.cpp: file |
1580 |
> |
ZconstraintForceManager.cpp was initially added on branch |
1581 |
> |
new_design. |
1582 |
> |
|
1583 |
> |
2005-01-07 16:50 tim |
1584 |
> |
|
1585 |
> |
* src/constraints/ZconstraintForceManager.hpp: file |
1586 |
> |
ZconstraintForceManager.hpp was initially added on branch |
1587 |
> |
new_design. |
1588 |
> |
|
1589 |
> |
2005-01-06 17:31 tim |
1590 |
> |
|
1591 |
> |
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
1592 |
> |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
1593 |
> |
constraints/ConstraintPair.hpp, integrators/Integrator.cpp, |
1594 |
> |
integrators/NPTi.cpp, integrators/VelocityVerletIntegrator.cpp, |
1595 |
> |
io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp: |
1596 |
> |
constraint is almost working |
1597 |
> |
|
1598 |
> |
2005-01-05 19:36 tim |
1599 |
> |
|
1600 |
> |
* src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is |
1601 |
> |
working |
1602 |
> |
|
1603 |
> |
2005-01-05 19:16 tim |
1604 |
> |
|
1605 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
1606 |
> |
applications/oopse/oopse.cpp, |
1607 |
> |
applications/simpleBuilder/BaseLattice.cpp, |
1608 |
> |
applications/simpleBuilder/Lattice.cpp, |
1609 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
1610 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
1611 |
> |
applications/simpleBuilder/MoLocator.cpp, |
1612 |
> |
applications/simpleBuilder/MoLocator.hpp, |
1613 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
1614 |
> |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.hpp, |
1615 |
> |
minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder |
1616 |
> |
in progress |
1617 |
> |
|
1618 |
> |
2005-01-05 12:35 tim |
1619 |
> |
|
1620 |
> |
* src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp |
1621 |
> |
was initially added on branch new_design. |
1622 |
> |
|
1623 |
> |
2005-01-05 12:35 tim |
1624 |
> |
|
1625 |
> |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
1626 |
> |
Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, |
1627 |
> |
MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp, |
1628 |
> |
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp, |
1629 |
> |
SDMinimizer.hpp: minimizer in progress |
1630 |
> |
|
1631 |
> |
2005-01-05 12:35 tim |
1632 |
> |
|
1633 |
> |
* src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially |
1634 |
> |
added on branch new_design. |
1635 |
> |
|
1636 |
> |
2005-01-05 12:35 tim |
1637 |
> |
|
1638 |
> |
* src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp |
1639 |
> |
was initially added on branch new_design. |
1640 |
> |
|
1641 |
> |
2005-01-05 12:35 tim |
1642 |
> |
|
1643 |
> |
* src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp |
1644 |
> |
was initially added on branch new_design. |
1645 |
> |
|
1646 |
> |
2005-01-05 12:35 tim |
1647 |
> |
|
1648 |
> |
* src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially |
1649 |
> |
added on branch new_design. |
1650 |
> |
|
1651 |
> |
2005-01-05 12:35 tim |
1652 |
> |
|
1653 |
> |
* src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp |
1654 |
> |
was initially added on branch new_design. |
1655 |
> |
|
1656 |
> |
2005-01-04 17:18 tim |
1657 |
> |
|
1658 |
> |
* src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was |
1659 |
> |
initially added on branch new_design. |
1660 |
> |
|
1661 |
> |
2005-01-04 17:18 tim |
1662 |
> |
|
1663 |
> |
* src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
1664 |
> |
brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, |
1665 |
> |
brains/Thermo.cpp, constraints/ConstraintPair.hpp, |
1666 |
> |
constraints/Makefile, integrators/NPT.cpp, integrators/NVE.cpp, |
1667 |
> |
integrators/NVT.cpp, integrators/VelocityVerletIntegrator.cpp, |
1668 |
> |
integrators/VelocityVerletIntegrator.hpp, io/DumpReader.cpp, |
1669 |
> |
primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in |
1670 |
> |
progress |
1671 |
> |
|
1672 |
> |
2005-01-04 17:18 tim |
1673 |
> |
|
1674 |
> |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
1675 |
> |
Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, |
1676 |
> |
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, |
1677 |
> |
SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress |
1678 |
> |
|
1679 |
> |
2005-01-04 17:18 tim |
1680 |
> |
|
1681 |
> |
* src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp |
1682 |
> |
was initially added on branch new_design. |
1683 |
> |
|
1684 |
> |
2005-01-04 17:18 tim |
1685 |
> |
|
1686 |
> |
* src/minimizers/MinimizerParameterSet.cpp: file |
1687 |
> |
MinimizerParameterSet.cpp was initially added on branch new_design. |
1688 |
> |
|
1689 |
> |
2005-01-04 17:18 tim |
1690 |
> |
|
1691 |
> |
* src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was |
1692 |
> |
initially added on branch new_design. |
1693 |
> |
|
1694 |
> |
2005-01-04 17:18 tim |
1695 |
> |
|
1696 |
> |
* src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on |
1697 |
> |
branch new_design. |
1698 |
> |
|
1699 |
> |
2004-12-20 15:50 chuckv |
1700 |
> |
|
1701 |
> |
* make/Makefile.in: Fixed Makefile test bug under OSX and possibly |
1702 |
> |
other BSD's, replaced test -f *.mod with ls function since BSD test |
1703 |
> |
apparently doesn't support wildcards. |
1704 |
> |
|
1705 |
> |
2004-12-20 15:36 tim |
1706 |
> |
|
1707 |
> |
* make/Makefile.in: fix a test command incompatiable problem |
1708 |
> |
|
1709 |
> |
2004-12-20 14:49 tim |
1710 |
> |
|
1711 |
> |
* src/integrators/NPTi.cpp: NPT is working now |
1712 |
> |
|
1713 |
> |
2004-12-16 14:20 tim |
1714 |
> |
|
1715 |
> |
* src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the |
1716 |
> |
invalid stamp id |
1717 |
> |
|
1718 |
> |
2004-12-16 14:00 tim |
1719 |
> |
|
1720 |
> |
* forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, |
1721 |
> |
newEAM.u6.frc: adding new EAM force field files |
1722 |
> |
|
1723 |
> |
2004-12-16 13:55 tim |
1724 |
> |
|
1725 |
> |
* src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays |
1726 |
> |
in EAM parameter file is incorrect |
1727 |
> |
|
1728 |
> |
2004-12-16 12:27 tim |
1729 |
> |
|
1730 |
> |
* src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
1731 |
> |
brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp, |
1732 |
> |
utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM |
1733 |
> |
|
1734 |
> |
2004-12-15 17:34 tim |
1735 |
> |
|
1736 |
> |
* src/: applications/simpleBuilder/BaseLattice.cpp, |
1737 |
> |
applications/simpleBuilder/BaseLattice.hpp, |
1738 |
> |
applications/simpleBuilder/Lattice.cpp, |
1739 |
> |
applications/simpleBuilder/Lattice.hpp, |
1740 |
> |
applications/simpleBuilder/LatticeCreator.cpp, |
1741 |
> |
applications/simpleBuilder/LatticeCreator.hpp, |
1742 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
1743 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
1744 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
1745 |
> |
io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream |
1746 |
> |
|
1747 |
> |
2004-12-15 16:07 tim |
1748 |
> |
|
1749 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
1750 |
> |
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile, |
1751 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp: |
1752 |
> |
add EAM Force Field |
1753 |
> |
|
1754 |
> |
2004-12-15 14:40 tim |
1755 |
> |
|
1756 |
> |
* src/applications/oopse/oopse.cpp: add more force fields |
1757 |
> |
|
1758 |
> |
2004-12-15 11:44 tim |
1759 |
> |
|
1760 |
> |
* src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget |
1761 |
> |
to call All_reduce in MPI version) |
1762 |
> |
|
1763 |
> |
2004-12-15 11:13 tim |
1764 |
> |
|
1765 |
> |
* src/: brains/SimCreator.cpp, brains/SimInfo.cpp, |
1766 |
> |
io/DumpReader.cpp: MPI in NVE is working |
1767 |
> |
|
1768 |
> |
2004-12-14 16:57 tim |
1769 |
> |
|
1770 |
> |
* src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader. |
1771 |
> |
Master nodes does not brocast the total number of frames |
1772 |
> |
|
1773 |
> |
2004-12-14 14:08 tim |
1774 |
> |
|
1775 |
> |
* src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp, |
1776 |
> |
integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
1777 |
> |
minimizers/CGFamilyMinimizer.cpp, |
1778 |
> |
minimizers/MinimizerParameterSet.hpp, |
1779 |
> |
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
1780 |
> |
minimizers/SDMinimizer.cpp: more fix in MPI version |
1781 |
> |
|
1782 |
> |
2004-12-13 17:30 tim |
1783 |
> |
|
1784 |
> |
* src/: UseTheForce/DarkSide/simParallel.F90, |
1785 |
> |
applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
1786 |
> |
brains/SimInfo.cpp, brains/Snapshot.hpp, brains/Thermo.cpp, |
1787 |
> |
integrators/DLM.cpp, integrators/Integrator.cpp, |
1788 |
> |
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
1789 |
> |
integrators/NPTxyz.cpp, integrators/NVT.cpp, io/DumpReader.cpp, |
1790 |
> |
io/DumpWriter.cpp, io/EAMAtomTypesSectionParser.cpp, |
1791 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, io/SectionParser.hpp, |
1792 |
> |
io/ZConsWriter.cpp, io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, |
1793 |
> |
math/SquareMatrix3.hpp, primitives/Bend.hpp, primitives/Bond.hpp, |
1794 |
> |
primitives/RigidBody.cpp, primitives/StuntDouble.cpp, |
1795 |
> |
primitives/StuntDouble.hpp, types/CutoffGroupStamp.cpp, |
1796 |
> |
utils/LocalIndexManager.hpp, utils/PropertyMap.cpp, |
1797 |
> |
utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version |
1798 |
> |
is built |
1799 |
> |
|
1800 |
> |
2004-12-10 13:41 tim |
1801 |
> |
|
1802 |
> |
* src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp |
1803 |
> |
|
1804 |
> |
2004-12-10 11:14 tim |
1805 |
> |
|
1806 |
> |
* src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp, |
1807 |
> |
primitives/StuntDouble.hpp: forget to zero out the torque. Sticky |
1808 |
> |
and Dipole is working now |
1809 |
> |
|
1810 |
> |
2004-12-09 18:15 tim |
1811 |
> |
|
1812 |
> |
* src/: UseTheForce/DarkSide/dipole.F90, |
1813 |
> |
UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp: |
1814 |
> |
fix an index problem in eFrame matrix |
1815 |
> |
|
1816 |
> |
2004-12-09 18:09 tim |
1817 |
> |
|
1818 |
> |
* src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when |
1819 |
> |
initializing the new Charge AtomType |
1820 |
> |
|
1821 |
> |
2004-12-09 16:15 tim |
1822 |
> |
|
1823 |
> |
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90, |
1824 |
> |
types/DirectionalAtomType.cpp: sticky module get compiled |
1825 |
> |
|
1826 |
> |
2004-12-09 15:43 gezelter |
1827 |
> |
|
1828 |
> |
* src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90, |
1829 |
> |
reactionField.F90: u_l -> eFrame for electrostatics u_l -> A for |
1830 |
> |
GB |
1831 |
> |
|
1832 |
> |
2004-12-09 15:42 gezelter |
1833 |
> |
|
1834 |
> |
* src/UseTheForce/doForces.F90: u_l -> eFrame |
1835 |
> |
|
1836 |
> |
2004-12-09 15:27 gezelter |
1837 |
> |
|
1838 |
> |
* src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky |
1839 |
> |
module now has the option for multiple sticky types |
1840 |
> |
|
1841 |
> |
2004-12-09 15:27 gezelter |
1842 |
> |
|
1843 |
> |
* src/UseTheForce/doForces.F90: sticky |
1844 |
> |
|
1845 |
> |
2004-12-09 11:22 tim |
1846 |
> |
|
1847 |
> |
* src/integrators/: NPT.cpp, NVT.cpp: fix an interface |
1848 |
> |
inconsistency in lab2Bidy |
1849 |
> |
|
1850 |
> |
2004-12-09 10:45 tim |
1851 |
> |
|
1852 |
> |
* src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug |
1853 |
> |
in calculating torque in rigid body |
1854 |
> |
|
1855 |
> |
2004-12-08 15:37 tim |
1856 |
> |
|
1857 |
> |
* src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h, |
1858 |
> |
brains/SnapShot.cpp, brains/Snapshot.hpp, |
1859 |
> |
integrators/Integrator.cpp, |
1860 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp: |
1861 |
> |
fix a parsing bug in ElectroStaticAtomTypesSectionParser |
1862 |
> |
|
1863 |
> |
2004-12-08 12:03 tim |
1864 |
> |
|
1865 |
> |
* src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane |
1866 |
> |
in NVT is working |
1867 |
> |
|
1868 |
> |
2004-12-07 18:08 tim |
1869 |
> |
|
1870 |
> |
* src/: UseTheForce/Makefile, brains/SimInfo.hpp, |
1871 |
> |
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
1872 |
> |
integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp, |
1873 |
> |
io/DumpWriter.cpp: NPT in progress |
1874 |
> |
|
1875 |
> |
2004-12-07 09:43 tim |
1876 |
> |
|
1877 |
> |
* test/utils/: Makefile, NextCombinationTestCase.hpp: [no log |
1878 |
> |
message] |
1879 |
> |
|
1880 |
> |
2004-12-07 00:12 tim |
1881 |
> |
|
1882 |
> |
* src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in |
1883 |
> |
UseInitXSstate |
1884 |
> |
|
1885 |
> |
2004-12-07 00:00 tim |
1886 |
> |
|
1887 |
> |
* src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message |
1888 |
> |
|
1889 |
> |
2004-12-06 23:47 tim |
1890 |
> |
|
1891 |
> |
* src/types/DirectionalAtomType.cpp: [no log message] |
1892 |
> |
|
1893 |
> |
2004-12-06 21:18 tim |
1894 |
> |
|
1895 |
> |
* forceFields/newDUFF.frc: merge WATER force field into DUFF |
1896 |
> |
|
1897 |
> |
2004-12-06 20:33 tim |
1898 |
> |
|
1899 |
> |
* forceFields/newDUFF.frc: change the force constant of bonds |
1900 |
> |
|
1901 |
> |
2004-12-06 18:29 tim |
1902 |
> |
|
1903 |
> |
* src/: UseTheForce/DarkSide/charge.F90, |
1904 |
> |
UseTheForce/DarkSide/charge_interface.h, |
1905 |
> |
UseTheForce/DarkSide/dipole.F90, |
1906 |
> |
UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp: |
1907 |
> |
fix atom type ident in Charge and Dipole Module |
1908 |
> |
|
1909 |
> |
2004-12-06 17:56 tim |
1910 |
> |
|
1911 |
> |
* src/primitives/Torsion.cpp: butane is working now |
1912 |
> |
|
1913 |
> |
2004-12-06 15:15 tim |
1914 |
> |
|
1915 |
> |
* src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp, |
1916 |
> |
primitives/Bond.hpp, primitives/Torsion.cpp: short range |
1917 |
> |
interaction for butane is correct.Still something wrong with long |
1918 |
> |
range one |
1919 |
> |
|
1920 |
> |
2004-12-05 23:49 tim |
1921 |
> |
|
1922 |
> |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
1923 |
> |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
1924 |
> |
io/BendTypesSectionParser.cpp, math/Polynomial.hpp, |
1925 |
> |
primitives/Atom.hpp, utils/NumericConstant.hpp, |
1926 |
> |
utils/TypeContainer.hpp: fix a bug in Exclude List |
1927 |
> |
|
1928 |
> |
2004-12-05 17:21 tim |
1929 |
> |
|
1930 |
> |
* forceFields/newDUFF.frc: minor fix in DUFF |
1931 |
> |
|
1932 |
> |
2004-12-05 17:02 tim |
1933 |
> |
|
1934 |
> |
* src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp, |
1935 |
> |
utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp: |
1936 |
> |
fix a bug in filling MolMembership |
1937 |
> |
|
1938 |
> |
2004-12-05 12:12 tim |
1939 |
> |
|
1940 |
> |
* forceFields/newDUFF.frc: minor fix in force field file |
1941 |
> |
|
1942 |
> |
2004-12-05 12:09 tim |
1943 |
> |
|
1944 |
> |
* src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, |
1945 |
> |
integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp |
1946 |
> |
|
1947 |
> |
2004-12-04 15:09 tim |
1948 |
> |
|
1949 |
> |
* src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp, |
1950 |
> |
math/Vector3.hpp: NVE is working now, get the same result as |
1951 |
> |
OOPSE-1.0 |
1952 |
> |
|
1953 |
> |
2004-12-04 14:29 tim |
1954 |
> |
|
1955 |
> |
* src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy |
1956 |
> |
|
1957 |
> |
2004-12-04 14:24 gezelter |
1958 |
> |
|
1959 |
> |
* src/primitives/: Bend.cpp, Torsion.cpp: What? |
1960 |
> |
|
1961 |
> |
2004-12-04 14:24 gezelter |
1962 |
> |
|
1963 |
> |
* src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion |
1964 |
> |
|
1965 |
> |
2004-12-04 00:24 tim |
1966 |
> |
|
1967 |
> |
* src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp, |
1968 |
> |
integrators/Integrator.hpp, |
1969 |
> |
integrators/VelocityVerletIntegrator.cpp, primitives/Torsion.cpp, |
1970 |
> |
utils/TypeContainer.hpp: NVE conserved energy, however, potential |
1971 |
> |
is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf |
1972 |
> |
and NPTxyz to test integrator Step 2 SSD in NVE to test DLM, |
1973 |
> |
dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step |
1974 |
> |
4 EAM Step 5 Shape Step 6 Constraint & Restraint |
1975 |
> |
|
1976 |
> |
2004-12-03 19:01 tim |
1977 |
> |
|
1978 |
> |
* src/: UseTheForce/DarkSide/LJ.F90, |
1979 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp, |
1980 |
> |
integrators/VelocityVerletIntegrator.cpp, |
1981 |
> |
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
1982 |
> |
io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working, |
1983 |
> |
energy of NVE is not conserved |
1984 |
> |
|
1985 |
> |
2004-12-03 17:36 tim |
1986 |
> |
|
1987 |
> |
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
1988 |
> |
primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running |
1989 |
> |
|
1990 |
> |
2004-12-03 16:30 tim |
1991 |
> |
|
1992 |
> |
* src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp, |
1993 |
> |
brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile, |
1994 |
> |
integrators/NVE.cpp, primitives/Molecule.cpp, |
1995 |
> |
primitives/Molecule.hpp, primitives/StuntDouble.hpp, |
1996 |
> |
primitives/Torsion.hpp: more missing function get implemented |
1997 |
> |
|
1998 |
> |
2004-12-03 15:30 tim |
1999 |
> |
|
2000 |
> |
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp, |
2001 |
> |
SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo |
2002 |
> |
|
2003 |
> |
2004-12-03 12:59 tim |
2004 |
> |
|
2005 |
> |
* src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
2006 |
> |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
2007 |
> |
integrators/NPT.cpp, integrators/NPTi.cpp, integrators/NVT.cpp, |
2008 |
> |
io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp, |
2009 |
> |
io/SectionParserManager.cpp, utils/LocalIndexManager.hpp, |
2010 |
> |
utils/TypeContainer.hpp: begin to fix bugs |
2011 |
> |
|
2012 |
> |
2004-12-02 19:26 tim |
2013 |
> |
|
2014 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
2015 |
> |
UseTheForce/ForceFieldCreator.cpp, |
2016 |
> |
UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp, |
2017 |
> |
integrators/IntegratorCreator.cpp, |
2018 |
> |
integrators/IntegratorFactory.cpp, io/SectionParserManager.cpp, |
2019 |
> |
io/SectionParserManager.hpp, utils/Makefile, |
2020 |
> |
utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a |
2021 |
> |
bug in countTokens in StringTokenizer |
2022 |
> |
|
2023 |
> |
2004-12-02 19:26 tim |
2024 |
> |
|
2025 |
> |
* src/utils/Trim.cpp: file Trim.cpp was initially added on branch |
2026 |
> |
new_design. |
2027 |
> |
|
2028 |
> |
2004-12-02 19:06 tim |
2029 |
> |
|
2030 |
> |
* forceFields/newDUFF.frc: minor fix |
2031 |
> |
|
2032 |
> |
2004-12-02 18:15 tim |
2033 |
> |
|
2034 |
> |
* forceFields/newDUFF.frc: new ForceField format |
2035 |
> |
|
2036 |
> |
2004-12-02 17:15 tim |
2037 |
> |
|
2038 |
> |
* src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp |
2039 |
> |
was initially added on branch new_design. |
2040 |
> |
|
2041 |
> |
2004-12-02 17:15 tim |
2042 |
> |
|
2043 |
> |
* src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp |
2044 |
> |
was initially added on branch new_design. |
2045 |
> |
|
2046 |
> |
2004-12-02 17:15 tim |
2047 |
> |
|
2048 |
> |
* src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp |
2049 |
> |
was initially added on branch new_design. |
2050 |
> |
|
2051 |
> |
2004-12-02 17:15 tim |
2052 |
> |
|
2053 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
2054 |
> |
UseTheForce/ForceFieldCreator.cpp, |
2055 |
> |
UseTheForce/ForceFieldCreator.hpp, |
2056 |
> |
UseTheForce/ForceFieldFactory.cpp, |
2057 |
> |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
2058 |
> |
applications/oopse/oopse.cpp, integrators/IntegratorCreator.cpp, |
2059 |
> |
integrators/IntegratorCreator.hpp, |
2060 |
> |
integrators/IntegratorFactory.cpp, |
2061 |
> |
integrators/IntegratorFactory.hpp, integrators/Makefile, |
2062 |
> |
integrators/NPTf.cpp, integrators/NPTf.hpp, integrators/NPTi.cpp, |
2063 |
> |
integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
2064 |
> |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
2065 |
> |
integrators/NVT.cpp, integrators/NVT.hpp, |
2066 |
> |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
2067 |
> |
types/Makefile: refine factory pattern to make it initialized |
2068 |
> |
correctly |
2069 |
> |
|
2070 |
> |
2004-12-02 17:15 tim |
2071 |
> |
|
2072 |
> |
* src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp |
2073 |
> |
was initially added on branch new_design. |
2074 |
> |
|
2075 |
> |
2004-12-02 11:53 tim |
2076 |
> |
|
2077 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, |
2078 |
> |
types/DirectionalAtomType.cpp, types/Makefile: oopse get built |
2079 |
> |
|
2080 |
> |
2004-12-02 11:04 tim |
2081 |
> |
|
2082 |
> |
* src/: applications/simpleBuilder/LatticeCreator.cpp, |
2083 |
> |
applications/simpleBuilder/LatticeCreator.hpp, |
2084 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
2085 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
2086 |
> |
applications/simpleBuilder/simpleBuilder.cpp, brains/Exclude.cpp, |
2087 |
> |
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
2088 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp, |
2089 |
> |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
2090 |
> |
brains/SnapshotManager.hpp, brains/Stats.cpp, |
2091 |
> |
constraints/ZconsData.hpp, io/DumpWriter.cpp, io/LinkedAssign.hpp, |
2092 |
> |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp, |
2093 |
> |
io/basic_ifstrstream.hpp, primitives/Bend.hpp, |
2094 |
> |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
2095 |
> |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
2096 |
> |
types/OplsTorsionType.hpp, types/ShapeAtomType.hpp, |
2097 |
> |
utils/PropertyMap.hpp, utils/TypeContainer.hpp, |
2098 |
> |
visitors/AtomVisitor.cpp, visitors/CompositeVisitor.cpp, |
2099 |
> |
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
2100 |
> |
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
2101 |
> |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still |
2102 |
> |
have two linking problem |
2103 |
> |
|
2104 |
> |
2004-12-02 00:17 tim |
2105 |
> |
|
2106 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
2107 |
> |
applications/simpleBuilder/Lattice.cpp, |
2108 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
2109 |
> |
constraints/ZConstraint.cpp, io/DumpWriter.cpp, io/ZConsReader.cpp, |
2110 |
> |
io/ZConsWriter.cpp, minimizers/CGFamilyMinimizer.cpp, |
2111 |
> |
minimizers/OOPSEMinimizer.cpp, minimizers/SDMinimizer.cpp, |
2112 |
> |
restraints/Restraints.cpp, visitors/AtomVisitor.cpp, |
2113 |
> |
visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp, |
2114 |
> |
visitors/ZconsVisitor.cpp: change endl to std::endl |
2115 |
> |
|
2116 |
> |
2004-12-02 00:14 tim |
2117 |
> |
|
2118 |
> |
* src/: UseTheForce/Shapes_FF.cpp, |
2119 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, |
2120 |
> |
applications/simpleBuilder/BaseLattice.hpp, |
2121 |
> |
applications/simpleBuilder/Lattice.hpp, |
2122 |
> |
applications/simpleBuilder/LatticeCreator.hpp, |
2123 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
2124 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
2125 |
> |
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
2126 |
> |
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
2127 |
> |
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
2128 |
> |
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
2129 |
> |
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
2130 |
> |
visitors/RigidBodyVisitor.hpp: minor fix |
2131 |
> |
|
2132 |
> |
2004-12-02 00:09 tim |
2133 |
> |
|
2134 |
> |
* src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp: |
2135 |
> |
remove StreamTokenizer |
2136 |
> |
|
2137 |
> |
2004-12-02 00:06 tim |
2138 |
> |
|
2139 |
> |
* src/: UseTheForce/Shapes_FF.cpp, |
2140 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
2141 |
> |
applications/simpleBuilder/simpleBuilder.cpp, brains/Thermo.cpp, |
2142 |
> |
io/ZConsWriter.cpp, math/randomSPRNG.cpp, |
2143 |
> |
restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using |
2144 |
> |
namespace std in .cpp file |
2145 |
> |
|
2146 |
> |
2004-12-02 00:04 tim |
2147 |
> |
|
2148 |
> |
* src/: UseTheForce/Shapes_FF.cpp, |
2149 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, |
2150 |
> |
applications/simpleBuilder/BaseLattice.hpp, |
2151 |
> |
applications/simpleBuilder/Lattice.cpp, |
2152 |
> |
applications/simpleBuilder/Lattice.hpp, |
2153 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
2154 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
2155 |
> |
applications/simpleBuilder/MoLocator.cpp, |
2156 |
> |
applications/simpleBuilder/MoLocator.hpp, brains/SkipList.cpp, |
2157 |
> |
brains/SkipList.hpp, constraints/ZconsData.hpp, io/ZConsReader.cpp, |
2158 |
> |
io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
2159 |
> |
minimizers/MinimizerParameterSet.hpp, |
2160 |
> |
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
2161 |
> |
minimizers/PRCG.cpp, primitives/Atom.cpp, primitives/RigidBody.cpp, |
2162 |
> |
restraints/Restraints.cpp, restraints/Restraints.hpp, |
2163 |
> |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
2164 |
> |
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
2165 |
> |
utils/GenericData.hpp, visitors/CompositeVisitor.cpp, |
2166 |
> |
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
2167 |
> |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding |
2168 |
> |
qulified name prefix std |
2169 |
> |
|
2170 |
> |
2004-12-01 23:55 tim |
2171 |
> |
|
2172 |
> |
* src/: UseTheForce/Shapes_FF.cpp, |
2173 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, |
2174 |
> |
applications/simpleBuilder/BaseLattice.hpp, |
2175 |
> |
applications/simpleBuilder/Lattice.hpp, |
2176 |
> |
applications/simpleBuilder/LatticeCreator.hpp, |
2177 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
2178 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
2179 |
> |
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
2180 |
> |
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
2181 |
> |
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
2182 |
> |
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
2183 |
> |
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
2184 |
> |
visitors/RigidBodyVisitor.hpp: replace string by std::string |
2185 |
> |
|
2186 |
> |
2004-12-01 22:12 tim |
2187 |
> |
|
2188 |
> |
* make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp, |
2189 |
> |
src/applications/simpleBuilder/BaseLattice.hpp, |
2190 |
> |
src/applications/simpleBuilder/Lattice.hpp, |
2191 |
> |
src/applications/simpleBuilder/LatticeCreator.hpp, |
2192 |
> |
src/applications/simpleBuilder/LatticeFactory.hpp, |
2193 |
> |
src/applications/simpleBuilder/MoLocator.hpp, |
2194 |
> |
src/brains/SimInfo.cpp, src/brains/SkipList.hpp, |
2195 |
> |
src/brains/Snapshot.hpp, src/constraints/ZconsData.hpp, |
2196 |
> |
src/integrators/IntegratorFactory.hpp, src/io/Globals.hpp, |
2197 |
> |
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
2198 |
> |
src/minimizers/OOPSEMinimizer.hpp, src/primitives/StuntDouble.hpp, |
2199 |
> |
src/types/MoleculeStamp.hpp, src/types/ShapeAtomType.hpp, |
2200 |
> |
src/utils/Makefile, src/utils/StringUtils.cpp, |
2201 |
> |
src/utils/StringUtils.hpp, src/utils/TypeInfo.hpp, |
2202 |
> |
src/utils/Utility.cpp, src/visitors/CompositeVisitor.hpp, |
2203 |
> |
src/visitors/RigidBodyVisitor.hpp, test/brains/DirectionalAtom.cpp, |
2204 |
> |
test/brains/RigidBody.cpp: replace misuse of using namespace std in |
2205 |
> |
header files |
2206 |
> |
|
2207 |
> |
2004-12-01 21:23 tim |
2208 |
> |
|
2209 |
> |
* src/: primitives/Atom.hpp, primitives/RigidBody.hpp, |
2210 |
> |
primitives/StuntDouble.hpp, utils/TypeContainer.hpp, |
2211 |
> |
utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp: |
2212 |
> |
begin to fix linking problem |
2213 |
> |
|
2214 |
> |
2004-12-01 21:08 tim |
2215 |
> |
|
2216 |
> |
* src/: applications/oopse/oopse.cpp, brains/Stats.cpp, |
2217 |
> |
brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile, |
2218 |
> |
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
2219 |
> |
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
2220 |
> |
integrators/NPTxyz.cpp, integrators/VelocityVerletIntegrator.hpp, |
2221 |
> |
math/SquareMatrix3.hpp, primitives/Atom.hpp, |
2222 |
> |
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
2223 |
> |
utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled, |
2224 |
> |
still has some linking problem |
2225 |
> |
|
2226 |
> |
2004-12-01 19:26 tim |
2227 |
> |
|
2228 |
> |
* src/: integrators/NVT.cpp, integrators/NVT.hpp, |
2229 |
> |
utils/OOPSEConstant.hpp: NVT get built |
2230 |
> |
|
2231 |
> |
2004-12-01 19:09 tim |
2232 |
> |
|
2233 |
> |
* src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp |
2234 |
> |
was initially added on branch new_design. |
2235 |
> |
|
2236 |
> |
2004-12-01 19:09 tim |
2237 |
> |
|
2238 |
> |
* src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, |
2239 |
> |
brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
2240 |
> |
brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp, |
2241 |
> |
integrators/Integrator.hpp, integrators/Makefile, |
2242 |
> |
integrators/NVE.cpp, integrators/NVE.hpp, |
2243 |
> |
integrators/RotationAlgorithm.hpp, |
2244 |
> |
integrators/VelocityVerletIntegrator.cpp, |
2245 |
> |
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE |
2246 |
> |
get built |
2247 |
> |
|
2248 |
> |
2004-12-01 19:09 tim |
2249 |
> |
|
2250 |
> |
* src/integrators/DLM.hpp: file DLM.hpp was initially added on |
2251 |
> |
branch new_design. |
2252 |
> |
|
2253 |
> |
2004-12-01 19:09 tim |
2254 |
> |
|
2255 |
> |
* src/integrators/DLM.cpp: file DLM.cpp was initially added on |
2256 |
> |
branch new_design. |
2257 |
> |
|
2258 |
> |
2004-12-01 17:45 tim |
2259 |
> |
|
2260 |
> |
* src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp, |
2261 |
> |
integrators/IntegratorFactory.cpp, |
2262 |
> |
integrators/IntegratorFactory.hpp, integrators/Makefile, |
2263 |
> |
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
2264 |
> |
integrators/VelocityVerletIntegrator.cpp, |
2265 |
> |
integrators/VelocityVerletIntegrator.hpp, io/DumpWrite.hpp, |
2266 |
> |
io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp, |
2267 |
> |
io/StatWriter.hpp: rename DumpWrite to DumpWriter |
2268 |
> |
|
2269 |
> |
2004-12-01 17:45 tim |
2270 |
> |
|
2271 |
> |
* src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on |
2272 |
> |
branch new_design. |
2273 |
> |
|
2274 |
> |
2004-12-01 15:05 tim |
2275 |
> |
|
2276 |
> |
* src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp, |
2277 |
> |
io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile, |
2278 |
> |
utils/Utility.cpp, utils/Utility.hpp, visitors/AtomData.hpp, |
2279 |
> |
visitors/BaseVisitor.hpp, visitors/OtherVisitor.cpp, |
2280 |
> |
visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp, |
2281 |
> |
visitors/ZconsVisitor.hpp: visitors get built |
2282 |
> |
|
2283 |
> |
2004-12-01 14:32 chrisfen |
2284 |
> |
|
2285 |
> |
* samples/water/tip3p_ice/tp3.md: fixed a sample |
2286 |
> |
|
2287 |
> |
2004-12-01 14:10 tim |
2288 |
> |
|
2289 |
> |
* src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp, |
2290 |
> |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
2291 |
> |
src/types/AtomType.hpp, src/utils/Utility.hpp, |
2292 |
> |
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
2293 |
> |
src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp: |
2294 |
> |
spell check |
2295 |
> |
|
2296 |
> |
2004-12-01 13:42 tim |
2297 |
> |
|
2298 |
> |
* src/: UseTheForce/DarkSide/atype.F90, |
2299 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
2300 |
> |
io/ElectrostaticAtomTypesSectionParser.hpp, primitives/Atom.hpp, |
2301 |
> |
primitives/DirectionalAtom.cpp, primitives/RigidBody.cpp, |
2302 |
> |
primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator |
2303 |
> |
and constraint, other directories get built |
2304 |
> |
|
2305 |
> |
2004-12-01 12:38 tim |
2306 |
> |
|
2307 |
> |
* src/: brains/DataStorage.cpp, brains/DataStorage.hpp, |
2308 |
> |
brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
2309 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
2310 |
> |
io/ElectrostaticAtomTypesSectionParser.hpp, |
2311 |
> |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
2312 |
> |
primitives/GhostBend.cpp, primitives/RigidBody.cpp, |
2313 |
> |
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
2314 |
> |
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
2315 |
> |
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
2316 |
> |
refactory AtomType |
2317 |
> |
|
2318 |
> |
2004-11-30 22:11 tim |
2319 |
> |
|
2320 |
> |
* src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change |
2321 |
> |
|
2322 |
> |
2004-11-30 21:30 tim |
2323 |
> |
|
2324 |
> |
* src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change |
2325 |
> |
NumericConstant |
2326 |
> |
|
2327 |
> |
2004-11-30 21:24 tim |
2328 |
> |
|
2329 |
> |
* src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp, |
2330 |
> |
primitives/RigidBody.cpp: minor fix |
2331 |
> |
|
2332 |
> |
2004-11-30 18:14 tim |
2333 |
> |
|
2334 |
> |
* src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
2335 |
> |
io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile, |
2336 |
> |
io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io |
2337 |
> |
get built, next is integrator |
2338 |
> |
|
2339 |
> |
2004-11-30 17:43 tim |
2340 |
> |
|
2341 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
2342 |
> |
UseTheForce/ForceField.hpp, brains/SimCreator.cpp, |
2343 |
> |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
2344 |
> |
io/BASS_interface.cpp, primitives/StuntDouble.hpp, |
2345 |
> |
utils/StringUtils.hpp: brains get built |
2346 |
> |
|
2347 |
> |
2004-11-30 15:50 tim |
2348 |
> |
|
2349 |
> |
* src/: brains/ForceManager.cpp, brains/Makefile, |
2350 |
> |
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
2351 |
> |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
2352 |
> |
utils/StringUtils.hpp: brains get built, io is next |
2353 |
> |
|
2354 |
> |
2004-11-30 14:58 tim |
2355 |
> |
|
2356 |
> |
* src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially |
2357 |
> |
added on branch new_design. |
2358 |
> |
|
2359 |
> |
2004-11-30 14:58 tim |
2360 |
> |
|
2361 |
> |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
2362 |
> |
brains/ForceManager.cpp, brains/ForceManager.hpp, |
2363 |
> |
brains/MoleculeCreator.cpp, brains/SimCreator.hpp, |
2364 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp, |
2365 |
> |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
2366 |
> |
brains/SnapShot.cpp, brains/Stats.cpp, brains/Stats.hpp, |
2367 |
> |
brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, |
2368 |
> |
math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo |
2369 |
> |
|
2370 |
> |
2004-11-30 12:54 tim |
2371 |
> |
|
2372 |
> |
* src/: primitives/Bend.hpp, primitives/Bond.hpp, |
2373 |
> |
primitives/StuntDouble.hpp, primitives/Torsion.hpp, |
2374 |
> |
utils/LocalIndexManager.hpp: more get fixed |
2375 |
> |
|
2376 |
> |
2004-11-30 00:03 tim |
2377 |
> |
|
2378 |
> |
* src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename |
2379 |
> |
LocalndexManager.hpp to LocalIndexManager.hpp |
2380 |
> |
|
2381 |
> |
2004-11-30 00:03 tim |
2382 |
> |
|
2383 |
> |
* src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was |
2384 |
> |
initially added on branch new_design. |
2385 |
> |
|
2386 |
> |
2004-11-29 23:43 tim |
2387 |
> |
|
2388 |
> |
* src/: io/BendTypesSectionParser.cpp, |
2389 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
2390 |
> |
io/BondTypesSectionParser.hpp, io/SectionParserManager.cpp, |
2391 |
> |
io/SectionParserManager.hpp, io/TorsionTypesSectionParser.cpp, |
2392 |
> |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
2393 |
> |
types/PolynomialTorsionType.hpp: Section Parsers get compiled |
2394 |
> |
|
2395 |
> |
2004-11-29 23:14 tim |
2396 |
> |
|
2397 |
> |
* src/: io/BendTypesSectionParser.cpp, |
2398 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
2399 |
> |
io/BondTypesSectionParser.hpp, io/TorsionTypesSectionParser.cpp, |
2400 |
> |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor |
2401 |
> |
fixed |
2402 |
> |
|
2403 |
> |
2004-11-29 22:49 tim |
2404 |
> |
|
2405 |
> |
* src/: io/TorsionTypesSectionParser.cpp, |
2406 |
> |
io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp, |
2407 |
> |
types/CubicTorsionType.hpp, types/PolynomialBendType.hpp, |
2408 |
> |
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
2409 |
> |
types/QuarticTorsionType.hpp: minor fixed |
2410 |
> |
|
2411 |
> |
2004-11-29 22:32 tim |
2412 |
> |
|
2413 |
> |
* src/: io/TorsionTypesSectionParser.cpp, |
2414 |
> |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
2415 |
> |
types/PolynomialTorsionType.hpp: #inlcude statement can not be |
2416 |
> |
embedded |
2417 |
> |
|
2418 |
> |
2004-11-29 16:42 tim |
2419 |
> |
|
2420 |
> |
* test/math/: Makefile, PolynomialTestCase.cpp, |
2421 |
> |
PolynomialTestCase.hpp: add PolynomialTestCase |
2422 |
> |
|
2423 |
> |
2004-11-29 16:42 tim |
2424 |
> |
|
2425 |
> |
* src/math/Polynomial.hpp: Polynomial passes unit test |
2426 |
> |
|
2427 |
> |
2004-11-29 15:03 tim |
2428 |
> |
|
2429 |
> |
* src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename |
2430 |
> |
QuarticTorsion.hpp to QuarticTorsionType.hpp |
2431 |
> |
|
2432 |
> |
2004-11-29 15:03 tim |
2433 |
> |
|
2434 |
> |
* src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was |
2435 |
> |
initially added on branch new_design. |
2436 |
> |
|
2437 |
> |
2004-11-29 14:56 tim |
2438 |
> |
|
2439 |
> |
* src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was |
2440 |
> |
initially added on branch new_design. |
2441 |
> |
|
2442 |
> |
2004-11-29 14:56 tim |
2443 |
> |
|
2444 |
> |
* src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add |
2445 |
> |
CubicTorsionType and QuarticTorsionType |
2446 |
> |
|
2447 |
> |
2004-11-29 14:56 tim |
2448 |
> |
|
2449 |
> |
* src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was |
2450 |
> |
initially added on branch new_design. |
2451 |
> |
|
2452 |
> |
2004-11-29 13:00 tim |
2453 |
> |
|
2454 |
> |
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
2455 |
> |
types/CubicBendType.hpp, types/CubicBondType.hpp, |
2456 |
> |
types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get |
2457 |
> |
fixed |
2458 |
> |
|
2459 |
> |
2004-11-29 12:59 tim |
2460 |
> |
|
2461 |
> |
* src/utils/Trim.hpp: file Trim.hpp was initially added on branch |
2462 |
> |
new_design. |
2463 |
> |
|
2464 |
> |
2004-11-29 12:59 tim |
2465 |
> |
|
2466 |
> |
* src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim |
2467 |
> |
Algorithm for std::string |
2468 |
> |
|
2469 |
> |
2004-11-29 10:52 tim |
2470 |
> |
|
2471 |
> |
* src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove |
2472 |
> |
some useless files |
2473 |
> |
|
2474 |
> |
2004-11-29 10:50 tim |
2475 |
> |
|
2476 |
> |
* src/io/: BondTypesSectionParser.cpp, |
2477 |
> |
ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp, |
2478 |
> |
ElectrostaticAtomTypesSectionParser.cpp, |
2479 |
> |
HarmonicBondTypesSectionParser.cpp, |
2480 |
> |
HarmonicBondTypesSectionParser.hpp, |
2481 |
> |
LennardJonesAtomTypesSectionParser.cpp, Makefile, |
2482 |
> |
SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp, |
2483 |
> |
StickyAtomTypesSectionParser.hpp: more files get fixed |
2484 |
> |
|
2485 |
> |
2004-11-29 10:27 tim |
2486 |
> |
|
2487 |
> |
* src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp, |
2488 |
> |
DirectionalAtomTypesSectionParser.cpp, |
2489 |
> |
EAMAtomTypesSectionParser.cpp, EAMAtomTypesSectionParser.hpp, |
2490 |
> |
Makefile, SectionParser.cpp, SectionParser.hpp, |
2491 |
> |
SectionParserManager.cpp, SectionParserManager.hpp: part of io get |
2492 |
> |
built |
2493 |
> |
|
2494 |
> |
2004-11-29 09:49 tim |
2495 |
> |
|
2496 |
> |
* src/types/UreyBradleyBendType.hpp: types get built |
2497 |
> |
|
2498 |
> |
2004-11-29 09:40 tim |
2499 |
> |
|
2500 |
> |
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp: |
2501 |
> |
types get built |
2502 |
> |
|
2503 |
> |
2004-11-25 21:13 tim |
2504 |
> |
|
2505 |
> |
* src/: UseTheForce/ForceField.hpp, |
2506 |
> |
io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp, |
2507 |
> |
types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some |
2508 |
> |
files |
2509 |
> |
|
2510 |
> |
2004-11-25 15:18 tim |
2511 |
> |
|
2512 |
> |
* src/: io/AtomTypesSectionParser.cpp, |
2513 |
> |
io/BondTypesSectionParser.cpp, |
2514 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
2515 |
> |
types/QuadraticBendType.hpp, types/QuadraticBondType.hpp, |
2516 |
> |
types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some |
2517 |
> |
files |
2518 |
> |
|
2519 |
> |
2004-11-25 15:18 tim |
2520 |
> |
|
2521 |
> |
* src/types/QuarticBendType.hpp: file QuarticBendType.hpp was |
2522 |
> |
initially added on branch new_design. |
2523 |
> |
|
2524 |
> |
2004-11-25 15:18 tim |
2525 |
> |
|
2526 |
> |
* src/types/QuarticBondType.hpp: file QuarticBondType.hpp was |
2527 |
> |
initially added on branch new_design. |
2528 |
> |
|
2529 |
> |
2004-11-24 17:12 tim |
2530 |
> |
|
2531 |
> |
* src/: io/AtomTypesSectionParser.cpp, |
2532 |
> |
io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp, |
2533 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
2534 |
> |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
2535 |
> |
io/ChargeAtomTypesSectionParser.hpp, |
2536 |
> |
io/DipoleAtomTypesSectionParser.cpp, |
2537 |
> |
io/DipoleAtomTypesSectionParser.hpp, |
2538 |
> |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
2539 |
> |
io/DumpReader.hpp, io/EAMAtomTypesSectionParser.cpp, |
2540 |
> |
io/EAMAtomTypesSectionParser.hpp, |
2541 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
2542 |
> |
io/ElectrostaticAtomTypesSectionParser.hpp, |
2543 |
> |
io/HarmonicBondTypesSectionParser.hpp, |
2544 |
> |
io/LennardJonesAtomTypesSectionParser.cpp, |
2545 |
> |
io/LennardJonesAtomTypesSectionParser.hpp, io/Makefile, |
2546 |
> |
io/SectionParser.hpp, io/SectionParserManager.hpp, |
2547 |
> |
io/StickyAtomTypesSectionParser.cpp, |
2548 |
> |
io/StickyAtomTypesSectionParser.hpp, |
2549 |
> |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
2550 |
> |
utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built |
2551 |
> |
|
2552 |
> |
2004-11-24 16:33 tim |
2553 |
> |
|
2554 |
> |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp, |
2555 |
> |
ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp, |
2556 |
> |
LJFF.cpp, Makefile: UseTheForce get built |
2557 |
> |
|
2558 |
> |
2004-11-24 15:55 tim |
2559 |
> |
|
2560 |
> |
* src/: math/RectMatrix.hpp, primitives/Bend.cpp, |
2561 |
> |
primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp, |
2562 |
> |
primitives/Makefile, primitives/Molecule.cpp, |
2563 |
> |
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
2564 |
> |
primitives/StuntDouble.hpp, primitives/Torsion.cpp, |
2565 |
> |
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
2566 |
> |
primitives/UreyBradleyBend.hpp: types and primitives get built |
2567 |
> |
|
2568 |
> |
2004-11-24 14:49 tim |
2569 |
> |
|
2570 |
> |
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
2571 |
> |
StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint |
2572 |
> |
StringTokenizerTestCase |
2573 |
> |
|
2574 |
> |
2004-11-24 14:49 tim |
2575 |
> |
|
2576 |
> |
* src/utils/: GenericData.hpp, StringTokenizer.cpp, |
2577 |
> |
StringTokenizer.hpp: StringTokenizer passes unit test |
2578 |
> |
|
2579 |
> |
2004-11-24 13:20 tim |
2580 |
> |
|
2581 |
> |
* ChangeLog, make/Makefile.in, src/UseTheForce/Makefile, |
2582 |
> |
src/io/Makefile, src/primitives/Makefile, src/utils/Makefile: |
2583 |
> |
change Makefile |
2584 |
> |
|
2585 |
> |
2004-11-24 13:06 chrisfen |
2586 |
> |
|
2587 |
> |
* src/io/RestraintReader.cpp: improved restraints - mpi should work |
2588 |
> |
fine |
2589 |
> |
|
2590 |
> |
2004-11-24 13:06 chrisfen |
2591 |
> |
|
2592 |
> |
* src/integrators/Integrator.cpp: improved restraints |
2593 |
> |
|
2594 |
> |
2004-11-24 13:05 chrisfen |
2595 |
> |
|
2596 |
> |
* samples/water/tip3p_ice/tp3.md: oops... |
2597 |
> |
|
2598 |
> |
2004-11-24 12:42 tim |
2599 |
> |
|
2600 |
> |
* src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, |
2601 |
> |
brains/DataStorage.hpp, brains/SimCreator.cpp, |
2602 |
> |
brains/SimCreator.hpp, integrators/Integrator.hpp, |
2603 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
2604 |
> |
primitives/DirectionalAtom.cpp: add SetForceManager method to |
2605 |
> |
integrator |
2606 |
> |
|
2607 |
> |
2004-11-23 18:12 tim |
2608 |
> |
|
2609 |
> |
* src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, |
2610 |
> |
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
2611 |
> |
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
2612 |
> |
integrators/NPTxyz.cpp, integrators/NPTxyz.hpp, |
2613 |
> |
integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp, |
2614 |
> |
integrators/NVT.hpp, integrators/Velocitizer.cpp, |
2615 |
> |
integrators/VelocityVerletIntegrator.cpp, |
2616 |
> |
integrators/VelocityVerletIntegrator.hpp, |
2617 |
> |
types/UreyBradleyBendType.hpp: refactory NPT integrator |
2618 |
> |
|
2619 |
> |
2004-11-23 17:50 chrisfen |
2620 |
> |
|
2621 |
> |
* samples/water/tip3p_ice/tp3.md: Back to normal... Oh... |
2622 |
> |
Restraints should work in parallel now |
2623 |
> |
|
2624 |
> |
2004-11-23 17:48 chrisfen |
2625 |
> |
|
2626 |
> |
* src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
2627 |
> |
brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
2628 |
> |
integrators/Integrator.cpp, integrators/Integrator.hpp, |
2629 |
> |
io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp, |
2630 |
> |
io/RestraintReader.cpp, io/RestraintWriter.cpp, |
2631 |
> |
restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements |
2632 |
> |
to restraints |
2633 |
> |
|
2634 |
> |
2004-11-23 17:47 chrisfen |
2635 |
|
|
2636 |
< |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
2636 |
> |
* samples/water/tip3p_ice/tp3.md: just some testing changes, I'll |
2637 |
> |
return to the original on next commit |
2638 |
> |
|
2639 |
> |
2004-11-23 12:53 tim |
2640 |
> |
|
2641 |
> |
* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
2642 |
> |
ElectrostaticAtomTypesSectionParser.cpp was initially added on |
2643 |
|
branch new_design. |
2644 |
|
|
2645 |
+ |
2004-11-23 12:53 tim |
2646 |
+ |
|
2647 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
2648 |
+ |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
2649 |
+ |
applications/simpleBuilder/simpleBuilder.cpp, |
2650 |
+ |
io/ChargeAtomTypesSectionParser.cpp, |
2651 |
+ |
io/DirectionalAtomTypesSectionParser.hpp, |
2652 |
+ |
io/EAMAtomTypesSectionParser.cpp, |
2653 |
+ |
io/ElectrostaticAtomTypesSectionParser.cpp, |
2654 |
+ |
io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
2655 |
+ |
io/SectionParser.hpp, types/DirectionalAtomType.cpp, |
2656 |
+ |
utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser |
2657 |
+ |
|
2658 |
+ |
2004-11-23 12:53 tim |
2659 |
+ |
|
2660 |
+ |
* src/io/ElectrostaticAtomTypesSectionParser.hpp: file |
2661 |
+ |
ElectrostaticAtomTypesSectionParser.hpp was initially added on |
2662 |
+ |
branch new_design. |
2663 |
+ |
|
2664 |
+ |
2004-11-23 01:03 tim |
2665 |
+ |
|
2666 |
+ |
* src/io/EAMAtomTypesSectionParser.cpp: file |
2667 |
+ |
EAMAtomTypesSectionParser.cpp was initially added on branch |
2668 |
+ |
new_design. |
2669 |
+ |
|
2670 |
+ |
2004-11-23 01:03 tim |
2671 |
+ |
|
2672 |
+ |
* src/: io/EAMAtomTypesSectionParser.cpp, |
2673 |
+ |
io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, |
2674 |
+ |
types/AtomType.hpp, types/DirectionalAtomType.cpp, |
2675 |
+ |
types/DirectionalAtomType.hpp: add EAM AtomType Section Parser |
2676 |
+ |
|
2677 |
+ |
2004-11-23 01:03 tim |
2678 |
+ |
|
2679 |
+ |
* src/io/EAMAtomTypesSectionParser.hpp: file |
2680 |
+ |
EAMAtomTypesSectionParser.hpp was initially added on branch |
2681 |
+ |
new_design. |
2682 |
+ |
|
2683 |
+ |
2004-11-23 01:03 tim |
2684 |
+ |
|
2685 |
+ |
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
2686 |
+ |
was initially added on branch new_design. |
2687 |
+ |
|
2688 |
+ |
2004-11-22 23:35 tim |
2689 |
+ |
|
2690 |
+ |
* src/io/TorsionTypesSectionParser.cpp: file |
2691 |
+ |
TorsionTypesSectionParser.cpp was initially added on branch |
2692 |
+ |
new_design. |
2693 |
+ |
|
2694 |
+ |
2004-11-22 23:35 tim |
2695 |
+ |
|
2696 |
+ |
* src/io/BendTypesSectionParser.hpp: file |
2697 |
+ |
BendTypesSectionParser.hpp was initially added on branch |
2698 |
+ |
new_design. |
2699 |
+ |
|
2700 |
+ |
2004-11-22 23:35 tim |
2701 |
+ |
|
2702 |
+ |
* src/io/BondTypesSectionParser.cpp: file |
2703 |
+ |
BondTypesSectionParser.cpp was initially added on branch |
2704 |
+ |
new_design. |
2705 |
+ |
|
2706 |
+ |
2004-11-22 23:35 tim |
2707 |
+ |
|
2708 |
+ |
* src/io/BondTypesSectionParser.hpp: file |
2709 |
+ |
BondTypesSectionParser.hpp was initially added on branch |
2710 |
+ |
new_design. |
2711 |
+ |
|
2712 |
+ |
2004-11-22 23:35 tim |
2713 |
+ |
|
2714 |
+ |
* src/io/TorsionTypesSectionParser.hpp: file |
2715 |
+ |
TorsionTypesSectionParser.hpp was initially added on branch |
2716 |
+ |
new_design. |
2717 |
+ |
|
2718 |
+ |
2004-11-22 23:35 tim |
2719 |
+ |
|
2720 |
+ |
* src/io/BendTypesSectionParser.cpp: file |
2721 |
+ |
BendTypesSectionParser.cpp was initially added on branch |
2722 |
+ |
new_design. |
2723 |
+ |
|
2724 |
+ |
2004-11-22 23:35 tim |
2725 |
+ |
|
2726 |
+ |
* src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, |
2727 |
+ |
BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, |
2728 |
+ |
TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add |
2729 |
+ |
BondTypesSectionParser, BendTypesSectionParser and |
2730 |
+ |
TorsionTypeSectionParser |
2731 |
+ |
|
2732 |
+ |
2004-11-22 18:04 tim |
2733 |
+ |
|
2734 |
+ |
* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in |
2735 |
+ |
DUFF and EAM |
2736 |
+ |
|
2737 |
+ |
2004-11-22 18:02 tim |
2738 |
+ |
|
2739 |
+ |
* src/io/DirectionalAtomTypesSectionParser.hpp: file |
2740 |
+ |
DirectionalAtomTypesSectionParser.hpp was initially added on branch |
2741 |
+ |
new_design. |
2742 |
+ |
|
2743 |
+ |
2004-11-22 18:02 tim |
2744 |
+ |
|
2745 |
+ |
* src/io/: DirectionalAtomTypesParser.hpp, |
2746 |
+ |
DirectionalAtomTypesSectionParser.hpp: adding section parsers |
2747 |
+ |
|
2748 |
+ |
2004-11-22 15:55 tim |
2749 |
+ |
|
2750 |
+ |
* src/io/DirectionalAtomTypesParser.hpp: file |
2751 |
+ |
DirectionalAtomTypesParser.hpp was initially added on branch |
2752 |
+ |
new_design. |
2753 |
+ |
|
2754 |
+ |
2004-11-22 15:55 tim |
2755 |
+ |
|
2756 |
+ |
* src/io/HarmonicBondTypesSectionParser.hpp: file |
2757 |
+ |
HarmonicBondTypesSectionParser.hpp was initially added on branch |
2758 |
+ |
new_design. |
2759 |
+ |
|
2760 |
+ |
2004-11-22 15:55 tim |
2761 |
+ |
|
2762 |
+ |
* src/io/ChargeAtomTypesSectionParser.hpp: file |
2763 |
+ |
ChargeAtomTypesSectionParser.hpp was initially added on branch |
2764 |
+ |
new_design. |
2765 |
+ |
|
2766 |
+ |
2004-11-22 15:55 tim |
2767 |
+ |
|
2768 |
+ |
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
2769 |
+ |
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
2770 |
+ |
new_design. |
2771 |
+ |
|
2772 |
+ |
2004-11-22 15:55 tim |
2773 |
+ |
|
2774 |
+ |
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
2775 |
+ |
LennardJonesAtomTypesSectionParser.cpp was initially added on |
2776 |
+ |
branch new_design. |
2777 |
+ |
|
2778 |
+ |
2004-11-22 15:55 tim |
2779 |
+ |
|
2780 |
+ |
* src/io/DipoleAtomTypesSectionParser.cpp: file |
2781 |
+ |
DipoleAtomTypesSectionParser.cpp was initially added on branch |
2782 |
+ |
new_design. |
2783 |
+ |
|
2784 |
+ |
2004-11-22 15:55 tim |
2785 |
+ |
|
2786 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
2787 |
+ |
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
2788 |
+ |
brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
2789 |
+ |
integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
2790 |
+ |
io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
2791 |
+ |
io/ChargeAtomTypesSectionParser.hpp, |
2792 |
+ |
io/DipoleAtomTypesSectionParser.cpp, |
2793 |
+ |
io/DipoleAtomTypesSectionParser.hpp, |
2794 |
+ |
io/DirectionalAtomTypesParser.hpp, |
2795 |
+ |
io/DirectionalAtomTypesSectionParser.cpp, |
2796 |
+ |
io/HarmonicBondTypesSectionParser.cpp, |
2797 |
+ |
io/HarmonicBondTypesSectionParser.hpp, |
2798 |
+ |
io/LennardJonesAtomTypesSectionParser.cpp, |
2799 |
+ |
io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
2800 |
+ |
io/SectionParser.hpp, io/SectionParserManager.cpp, |
2801 |
+ |
io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
2802 |
+ |
io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
2803 |
+ |
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
2804 |
+ |
utils/GenericData.hpp: adding section parsers |
2805 |
+ |
|
2806 |
+ |
2004-11-22 15:55 tim |
2807 |
+ |
|
2808 |
+ |
* src/io/DipoleAtomTypesSectionParser.hpp: file |
2809 |
+ |
DipoleAtomTypesSectionParser.hpp was initially added on branch |
2810 |
+ |
new_design. |
2811 |
+ |
|
2812 |
+ |
2004-11-22 15:55 tim |
2813 |
+ |
|
2814 |
+ |
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
2815 |
+ |
added on branch new_design. |
2816 |
+ |
|
2817 |
+ |
2004-11-22 15:55 tim |
2818 |
+ |
|
2819 |
+ |
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
2820 |
+ |
was initially added on branch new_design. |
2821 |
+ |
|
2822 |
+ |
2004-11-22 15:55 tim |
2823 |
+ |
|
2824 |
+ |
* src/io/AtomTypesSectionParser.cpp: file |
2825 |
+ |
AtomTypesSectionParser.cpp was initially added on branch |
2826 |
+ |
new_design. |
2827 |
+ |
|
2828 |
+ |
2004-11-22 15:55 tim |
2829 |
+ |
|
2830 |
+ |
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
2831 |
+ |
LennardJonesAtomTypesSectionParser.hpp was initially added on |
2832 |
+ |
branch new_design. |
2833 |
+ |
|
2834 |
+ |
2004-11-22 15:55 tim |
2835 |
+ |
|
2836 |
+ |
* src/io/HarmonicBondTypesSectionParser.cpp: file |
2837 |
+ |
HarmonicBondTypesSectionParser.cpp was initially added on branch |
2838 |
+ |
new_design. |
2839 |
+ |
|
2840 |
+ |
2004-11-22 15:55 tim |
2841 |
+ |
|
2842 |
+ |
* src/io/AtomTypesSectionParser.hpp: file |
2843 |
+ |
AtomTypesSectionParser.hpp was initially added on branch |
2844 |
+ |
new_design. |
2845 |
+ |
|
2846 |
+ |
2004-11-22 15:55 tim |
2847 |
+ |
|
2848 |
+ |
* src/io/StickyAtomTypesSectionParser.cpp: file |
2849 |
+ |
StickyAtomTypesSectionParser.cpp was initially added on branch |
2850 |
+ |
new_design. |
2851 |
+ |
|
2852 |
+ |
2004-11-22 15:55 tim |
2853 |
+ |
|
2854 |
+ |
* src/io/SectionParser.hpp: file SectionParser.hpp was initially |
2855 |
+ |
added on branch new_design. |
2856 |
+ |
|
2857 |
+ |
2004-11-22 15:55 tim |
2858 |
+ |
|
2859 |
+ |
* src/io/ChargeAtomTypesSectionParser.cpp: file |
2860 |
+ |
ChargeAtomTypesSectionParser.cpp was initially added on branch |
2861 |
+ |
new_design. |
2862 |
+ |
|
2863 |
+ |
2004-11-22 15:55 tim |
2864 |
+ |
|
2865 |
+ |
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
2866 |
+ |
was initially added on branch new_design. |
2867 |
+ |
|
2868 |
+ |
2004-11-22 15:55 tim |
2869 |
+ |
|
2870 |
+ |
* src/io/StickyAtomTypesSectionParser.hpp: file |
2871 |
+ |
StickyAtomTypesSectionParser.hpp was initially added on branch |
2872 |
+ |
new_design. |
2873 |
+ |
|
2874 |
+ |
2004-11-19 17:12 tim |
2875 |
+ |
|
2876 |
+ |
* src/: brains/SimState.cpp, brains/SimState.hpp, |
2877 |
+ |
io/InitializeFromFile.cpp, types/FixBondType.hpp, |
2878 |
+ |
types/FixedBondType.hpp: remove more useless files |
2879 |
+ |
|
2880 |
+ |
2004-11-19 17:12 tim |
2881 |
+ |
|
2882 |
+ |
* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
2883 |
+ |
added on branch new_design. |
2884 |
+ |
|
2885 |
+ |
2004-11-19 16:47 tim |
2886 |
+ |
|
2887 |
+ |
* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, |
2888 |
+ |
integrators/Integrator.cpp, applications/Makedepend: remove more |
2889 |
+ |
useless files |
2890 |
+ |
|
2891 |
+ |
2004-11-19 16:38 tim |
2892 |
+ |
|
2893 |
+ |
* src/integrators/NPTi.hpp: file NPTi.hpp was initially added on |
2894 |
+ |
branch new_design. |
2895 |
+ |
|
2896 |
+ |
2004-11-19 16:38 tim |
2897 |
+ |
|
2898 |
+ |
* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
2899 |
+ |
on branch new_design. |
2900 |
+ |
|
2901 |
+ |
2004-11-19 16:38 tim |
2902 |
+ |
|
2903 |
+ |
* src/integrators/NPT.hpp: file NPT.hpp was initially added on |
2904 |
+ |
branch new_design. |
2905 |
+ |
|
2906 |
+ |
2004-11-19 16:38 tim |
2907 |
+ |
|
2908 |
+ |
* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
2909 |
+ |
branch new_design. |
2910 |
+ |
|
2911 |
+ |
2004-11-19 16:38 tim |
2912 |
+ |
|
2913 |
+ |
* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
2914 |
+ |
branch new_design. |
2915 |
+ |
|
2916 |
+ |
2004-11-19 16:38 tim |
2917 |
+ |
|
2918 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
2919 |
+ |
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
2920 |
+ |
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
2921 |
+ |
integrators/NVT.hpp: refactory integrator |
2922 |
+ |
|
2923 |
+ |
2004-11-19 15:37 tim |
2924 |
+ |
|
2925 |
+ |
* forceFields/newDUFF.frc: new DUFF forcefield |
2926 |
+ |
|
2927 |
+ |
2004-11-19 15:23 tim |
2928 |
+ |
|
2929 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, |
2930 |
+ |
UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, |
2931 |
+ |
utils/TypeContainer.hpp: add EAM |
2932 |
+ |
|
2933 |
+ |
2004-11-19 15:23 tim |
2934 |
+ |
|
2935 |
+ |
* src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on |
2936 |
+ |
branch new_design. |
2937 |
+ |
|
2938 |
+ |
2004-11-19 15:23 tim |
2939 |
+ |
|
2940 |
+ |
* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
2941 |
+ |
branch new_design. |
2942 |
+ |
|
2943 |
+ |
2004-11-19 13:02 tim |
2944 |
+ |
|
2945 |
+ |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except |
2946 |
+ |
error checking |
2947 |
+ |
|
2948 |
+ |
2004-11-19 12:56 tim |
2949 |
+ |
|
2950 |
+ |
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
2951 |
+ |
was initially added on branch new_design. |
2952 |
+ |
|
2953 |
+ |
2004-11-19 12:56 tim |
2954 |
+ |
|
2955 |
+ |
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
2956 |
+ |
was initially added on branch new_design. |
2957 |
+ |
|
2958 |
+ |
2004-11-19 12:56 tim |
2959 |
+ |
|
2960 |
+ |
* src/types/FixBondType.hpp: file FixBondType.hpp was initially |
2961 |
+ |
added on branch new_design. |
2962 |
+ |
|
2963 |
+ |
2004-11-19 12:56 tim |
2964 |
+ |
|
2965 |
+ |
* src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, |
2966 |
+ |
UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, |
2967 |
+ |
UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, |
2968 |
+ |
integrators/IntegratorFactory.cpp, |
2969 |
+ |
integrators/IntegratorFactory.hpp, integrators/NVE.hpp, |
2970 |
+ |
integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp, |
2971 |
+ |
utils/StringTokenizer.cpp: DUFF is almost done except error |
2972 |
+ |
checking |
2973 |
+ |
|
2974 |
+ |
2004-11-18 19:11 tim |
2975 |
+ |
|
2976 |
+ |
* src/UseTheForce/DUFF.cpp: adding DUFF parser |
2977 |
+ |
|
2978 |
+ |
2004-11-18 18:26 tim |
2979 |
+ |
|
2980 |
+ |
* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, |
2981 |
+ |
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
2982 |
+ |
integrators/VelocityVerletIntegrator.cpp, |
2983 |
+ |
integrators/VelocityVerletIntegrator.hpp, |
2984 |
+ |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
2985 |
+ |
types/CubicBendType.hpp, types/CubicBondType.hpp, |
2986 |
+ |
types/HarmonicBondType.hpp, types/QuadraticBendType.hpp, |
2987 |
+ |
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding |
2988 |
+ |
DUFF parser |
2989 |
+ |
|
2990 |
+ |
2004-11-18 18:26 tim |
2991 |
+ |
|
2992 |
+ |
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
2993 |
+ |
initially added on branch new_design. |
2994 |
+ |
|
2995 |
+ |
2004-11-18 16:42 tim |
2996 |
+ |
|
2997 |
+ |
* forceFields/newDUFF.frc: adding new format DUFF force field |
2998 |
+ |
|
2999 |
+ |
2004-11-18 10:57 chrisfen |
3000 |
+ |
|
3001 |
+ |
* src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that |
3002 |
+ |
slowed down the force loop |
3003 |
+ |
|
3004 |
+ |
2004-11-18 00:42 tim |
3005 |
+ |
|
3006 |
+ |
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
3007 |
+ |
initially added on branch new_design. |
3008 |
+ |
|
3009 |
+ |
2004-11-18 00:42 tim |
3010 |
+ |
|
3011 |
+ |
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
3012 |
+ |
initially added on branch new_design. |
3013 |
+ |
|
3014 |
+ |
2004-11-18 00:42 tim |
3015 |
+ |
|
3016 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, |
3017 |
+ |
primitives/Bend.cpp, utils/NumericConstant.cpp, |
3018 |
+ |
utils/NumericConstant.hpp: Adding NumericConstant class |
3019 |
+ |
|
3020 |
+ |
2004-11-17 23:16 tim |
3021 |
+ |
|
3022 |
+ |
* src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, |
3023 |
+ |
UseTheForce/ForceFields.hpp: remove more junk files |
3024 |
+ |
|
3025 |
+ |
2004-11-17 23:12 tim |
3026 |
+ |
|
3027 |
+ |
* src/: brains/ForceFields.cpp, brains/SimSetup.cpp, |
3028 |
+ |
brains/SimSetup.hpp, constraints/AbstractClasses.hpp, |
3029 |
+ |
integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp, |
3030 |
+ |
primitives/AbstractClasses.hpp, primitives/Bond.cpp, |
3031 |
+ |
primitives/BondExtensions.cpp, primitives/SRI.hpp, |
3032 |
+ |
primitives/TorsionExtensions.cpp: remove some junk files |
3033 |
+ |
|
3034 |
+ |
2004-11-17 23:07 tim |
3035 |
+ |
|
3036 |
+ |
* src/primitives/BendExtensions.cpp: remove some junk files |
3037 |
+ |
|
3038 |
+ |
2004-11-17 23:04 tim |
3039 |
+ |
|
3040 |
+ |
* src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, |
3041 |
+ |
QuadraticBondType.hpp: refine QudraticBond |
3042 |
+ |
|
3043 |
+ |
2004-11-17 22:57 tim |
3044 |
+ |
|
3045 |
+ |
* src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp |
3046 |
+ |
|
3047 |
+ |
2004-11-17 22:57 tim |
3048 |
+ |
|
3049 |
+ |
* src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was |
3050 |
+ |
initially added on branch new_design. |
3051 |
+ |
|
3052 |
+ |
2004-11-17 16:47 tim |
3053 |
+ |
|
3054 |
+ |
* src/types/CubicBendType.hpp: file CubicBendType.hpp was initially |
3055 |
+ |
added on branch new_design. |
3056 |
+ |
|
3057 |
+ |
2004-11-17 16:47 tim |
3058 |
+ |
|
3059 |
+ |
* src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was |
3060 |
+ |
initially added on branch new_design. |
3061 |
+ |
|
3062 |
+ |
2004-11-17 16:47 tim |
3063 |
+ |
|
3064 |
+ |
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
3065 |
+ |
initially added on branch new_design. |
3066 |
+ |
|
3067 |
+ |
2004-11-17 16:47 tim |
3068 |
+ |
|
3069 |
+ |
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
3070 |
+ |
initially added on branch new_design. |
3071 |
+ |
|
3072 |
+ |
2004-11-17 16:47 tim |
3073 |
+ |
|
3074 |
+ |
* src/types/CubicBondType.hpp: file CubicBondType.hpp was initially |
3075 |
+ |
added on branch new_design. |
3076 |
+ |
|
3077 |
+ |
2004-11-17 16:47 tim |
3078 |
+ |
|
3079 |
+ |
* src/: math/ChebyshevPolynomials.cpp, |
3080 |
+ |
math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, |
3081 |
+ |
primitives/Bend.hpp, primitives/GhostBend.cpp, |
3082 |
+ |
primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp, |
3083 |
+ |
primitives/UreyBradleyBend.hpp, types/BondType.hpp, |
3084 |
+ |
types/CubicBendType.hpp, types/CubicBondType.hpp, |
3085 |
+ |
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
3086 |
+ |
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: |
3087 |
+ |
UreyBradleyBend and GhostBend |
3088 |
+ |
|
3089 |
+ |
2004-11-17 16:47 tim |
3090 |
+ |
|
3091 |
+ |
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
3092 |
+ |
added on branch new_design. |
3093 |
+ |
|
3094 |
+ |
2004-11-17 16:47 tim |
3095 |
+ |
|
3096 |
+ |
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
3097 |
+ |
was initially added on branch new_design. |
3098 |
+ |
|
3099 |
+ |
2004-11-17 13:58 tim |
3100 |
+ |
|
3101 |
+ |
* src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp |
3102 |
+ |
was initially added on branch new_design. |
3103 |
+ |
|
3104 |
+ |
2004-11-17 13:58 tim |
3105 |
+ |
|
3106 |
+ |
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
3107 |
+ |
initially added on branch new_design. |
3108 |
+ |
|
3109 |
+ |
2004-11-17 13:58 tim |
3110 |
+ |
|
3111 |
+ |
* src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp |
3112 |
+ |
was initially added on branch new_design. |
3113 |
+ |
|
3114 |
+ |
2004-11-17 13:58 tim |
3115 |
+ |
|
3116 |
+ |
* src/: math/ChebyshevPolynomials.cpp, |
3117 |
+ |
math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, |
3118 |
+ |
primitives/Bond.hpp, types/CharmmTorsionType.hpp, |
3119 |
+ |
types/OplsTorsionType.hpp, types/PolynomialBondType.hpp, |
3120 |
+ |
types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types |
3121 |
+ |
stuff and Chebyshev Polynomial |
3122 |
+ |
|
3123 |
+ |
2004-11-17 01:37 tim |
3124 |
+ |
|
3125 |
+ |
* src/types/PolynomialTorsionType.hpp: file |
3126 |
+ |
PolynomialTorsionType.hpp was initially added on branch new_design. |
3127 |
+ |
|
3128 |
+ |
2004-11-17 01:37 tim |
3129 |
+ |
|
3130 |
+ |
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
3131 |
+ |
initially added on branch new_design. |
3132 |
+ |
|
3133 |
+ |
2004-11-17 01:37 tim |
3134 |
+ |
|
3135 |
+ |
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
3136 |
+ |
initially added on branch new_design. |
3137 |
+ |
|
3138 |
+ |
2004-11-17 01:37 tim |
3139 |
+ |
|
3140 |
+ |
* src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was |
3141 |
+ |
initially added on branch new_design. |
3142 |
+ |
|
3143 |
+ |
2004-11-17 01:37 tim |
3144 |
+ |
|
3145 |
+ |
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
3146 |
+ |
initially added on branch new_design. |
3147 |
+ |
|
3148 |
+ |
2004-11-17 01:37 tim |
3149 |
+ |
|
3150 |
+ |
* src/: math/Polynomial.hpp, primitives/Bend.cpp, |
3151 |
+ |
primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, |
3152 |
+ |
types/BondType.hpp, types/CharmmTorsionType.cpp, |
3153 |
+ |
types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp, |
3154 |
+ |
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
3155 |
+ |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
3156 |
+ |
types/PolynomialTorsionType.hpp, types/TorsionType.hpp, |
3157 |
+ |
utils/StringTokenizer.hpp: add PolynomialBondType, |
3158 |
+ |
PolynomialBendType, PolynomialTorsionType, HarmonicBendType and |
3159 |
+ |
CharmmTorsionType. Need to refine the design and add document for |
3160 |
+ |
them |
3161 |
+ |
|
3162 |
+ |
2004-11-16 20:11 tim |
3163 |
+ |
|
3164 |
+ |
* src/types/: BendType.hpp, PolynomialBondType.hpp, |
3165 |
+ |
TorsionType.hpp: add PolynomialBondType |
3166 |
+ |
|
3167 |
+ |
2004-11-16 20:11 tim |
3168 |
+ |
|
3169 |
+ |
* src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was |
3170 |
+ |
initially added on branch new_design. |
3171 |
+ |
|
3172 |
+ |
2004-11-16 18:20 tim |
3173 |
+ |
|
3174 |
+ |
* src/math/Polynomial.hpp: Adding Polynomial class |
3175 |
+ |
|
3176 |
+ |
2004-11-16 18:20 tim |
3177 |
+ |
|
3178 |
+ |
* src/math/Polynomial.hpp: file Polynomial.hpp was initially added |
3179 |
+ |
on branch new_design. |
3180 |
+ |
|
3181 |
+ |
2004-11-16 17:04 gezelter |
3182 |
+ |
|
3183 |
+ |
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
3184 |
+ |
initially added on branch new_design. |
3185 |
+ |
|
3186 |
+ |
2004-11-16 17:04 gezelter |
3187 |
+ |
|
3188 |
+ |
* src/types/MorseBondType.hpp: file MorseBondType.hpp was initially |
3189 |
+ |
added on branch new_design. |
3190 |
+ |
|
3191 |
+ |
2004-11-16 17:04 gezelter |
3192 |
+ |
|
3193 |
+ |
* src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, |
3194 |
+ |
MorseBondType.hpp, TorsionType.hpp: added some new stuff |
3195 |
+ |
|
3196 |
+ |
2004-11-16 15:36 tim |
3197 |
+ |
|
3198 |
+ |
* src/: primitives/Bend.cpp, primitives/Bend.hpp, |
3199 |
+ |
primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, |
3200 |
+ |
types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and |
3201 |
+ |
TorsionType |
3202 |
+ |
|
3203 |
+ |
2004-11-15 21:07 tim |
3204 |
+ |
|
3205 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
3206 |
+ |
UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, |
3207 |
+ |
utils/StringTokenizer.cpp: adding DUFF class; adding checking |
3208 |
+ |
statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer |
3209 |
+ |
|
3210 |
+ |
2004-11-15 21:07 tim |
3211 |
+ |
|
3212 |
+ |
* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on |
3213 |
+ |
branch new_design. |
3214 |
+ |
|
3215 |
+ |
2004-11-15 18:00 tim |
3216 |
+ |
|
3217 |
+ |
* src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp |
3218 |
+ |
was initially added on branch new_design. |
3219 |
+ |
|
3220 |
+ |
2004-11-15 18:00 tim |
3221 |
+ |
|
3222 |
+ |
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
3223 |
+ |
branch new_design. |
3224 |
+ |
|
3225 |
+ |
2004-11-15 18:00 tim |
3226 |
+ |
|
3227 |
+ |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
3228 |
+ |
UseTheForce/ForceFieldFactory.cpp, |
3229 |
+ |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, |
3230 |
+ |
UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, |
3231 |
+ |
types/AtomType.hpp: adding ForceFieldFactory and LJFF classes |
3232 |
+ |
|
3233 |
+ |
2004-11-15 18:00 tim |
3234 |
+ |
|
3235 |
+ |
* src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp |
3236 |
+ |
was initially added on branch new_design. |
3237 |
+ |
|
3238 |
+ |
2004-11-15 13:02 tim |
3239 |
+ |
|
3240 |
+ |
* src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on |
3241 |
+ |
branch new_design. |
3242 |
+ |
|
3243 |
+ |
2004-11-15 13:02 tim |
3244 |
+ |
|
3245 |
+ |
* src/io/DumpReader.hpp: file DumpReader.hpp was initially added on |
3246 |
+ |
branch new_design. |
3247 |
+ |
|
3248 |
+ |
2004-11-15 13:02 tim |
3249 |
+ |
|
3250 |
+ |
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
3251 |
+ |
initially added on branch new_design. |
3252 |
+ |
|
3253 |
+ |
2004-11-15 13:02 tim |
3254 |
+ |
|
3255 |
+ |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, |
3256 |
+ |
brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
3257 |
+ |
integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, |
3258 |
+ |
io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, |
3259 |
+ |
DumpWriter.Next Step is LJFF and integrators |
3260 |
+ |
|
3261 |
+ |
2004-11-13 00:08 tim |
3262 |
+ |
|
3263 |
+ |
* src/: brains/ForceManager.cpp, brains/ForceManager.hpp, |
3264 |
+ |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
3265 |
+ |
brains/SimInfo.hpp, primitives/Molecule.cpp, |
3266 |
+ |
primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, |
3267 |
+ |
refactory, refactory |
3268 |
+ |
|
3269 |
+ |
2004-11-12 17:43 tim |
3270 |
+ |
|
3271 |
+ |
* src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, |
3272 |
+ |
StringTokenizer.cpp: bug fix in hasMoreTokens |
3273 |
+ |
|
3274 |
+ |
2004-11-12 17:28 tim |
3275 |
+ |
|
3276 |
+ |
* src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was |
3277 |
+ |
initially added on branch new_design. |
3278 |
+ |
|
3279 |
+ |
2004-11-12 17:28 tim |
3280 |
+ |
|
3281 |
+ |
* src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding |
3282 |
+ |
StringUtils, a c-style strtok like class, need unit test |
3283 |
+ |
|
3284 |
+ |
2004-11-12 12:40 tim |
3285 |
+ |
|
3286 |
+ |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
3287 |
+ |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
3288 |
+ |
brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test |
3289 |
+ |
|
3290 |
+ |
2004-11-12 02:05 tim |
3291 |
+ |
|
3292 |
+ |
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
3293 |
+ |
primitives/CutoffGroup.hpp, primitives/Molecule.cpp: |
3294 |
+ |
MoleculeCreator forget to create CutoffGroups for free atoms |
3295 |
+ |
|
3296 |
+ |
2004-11-12 01:19 tim |
3297 |
+ |
|
3298 |
+ |
* src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
3299 |
+ |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
3300 |
+ |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
3301 |
+ |
io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: |
3302 |
+ |
OOPSE = Object-Obfuscated Parallel Simulation Engine |
3303 |
+ |
|
3304 |
+ |
2004-11-11 16:48 chrisfen |
3305 |
+ |
|
3306 |
+ |
* samples/water/tip3p_ice/tp3.md: working sample |
3307 |
+ |
|
3308 |
+ |
2004-11-11 16:47 chrisfen |
3309 |
+ |
|
3310 |
+ |
* src/restraints/Restraints.cpp: working towards parallel |
3311 |
+ |
restraints |
3312 |
+ |
|
3313 |
+ |
2004-11-11 16:47 chrisfen |
3314 |
+ |
|
3315 |
+ |
* src/integrators/Integrator.cpp: Commented out some write |
3316 |
+ |
statements |
3317 |
+ |
|
3318 |
+ |
2004-11-11 16:46 chrisfen |
3319 |
+ |
|
3320 |
+ |
* src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some |
3321 |
+ |
write statements |
3322 |
+ |
|
3323 |
+ |
2004-11-11 16:46 chrisfen |
3324 |
+ |
|
3325 |
+ |
* samples/water/tip3p_ice/tp3.md: Fun with ice |
3326 |
+ |
|
3327 |
+ |
2004-11-11 11:41 tim |
3328 |
+ |
|
3329 |
+ |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
3330 |
+ |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
3331 |
+ |
brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h, |
3332 |
+ |
brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp, |
3333 |
+ |
io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove |
3334 |
+ |
useless mpiSimulation |
3335 |
+ |
|
3336 |
+ |
2004-11-11 11:41 tim |
3337 |
+ |
|
3338 |
+ |
* src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on |
3339 |
+ |
branch new_design. |
3340 |
+ |
|
3341 |
+ |
2004-11-10 17:50 tim |
3342 |
+ |
|
3343 |
+ |
* src/: brains/ForceManager.cpp, brains/SimInfo.cpp, |
3344 |
+ |
brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, |
3345 |
+ |
integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo |
3346 |
+ |
|
3347 |
+ |
2004-11-10 17:01 tim |
3348 |
+ |
|
3349 |
+ |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
3350 |
+ |
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
3351 |
+ |
brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
3352 |
+ |
brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp, |
3353 |
+ |
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
3354 |
+ |
io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp, |
3355 |
+ |
visitors/AtomVisitor.cpp: another painful day (1) SimCreator, |
3356 |
+ |
SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom |
3357 |
+ |
File will be removed) (3) ForceField (at least LJ) and BondType, |
3358 |
+ |
BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & |
3359 |
+ |
Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint |
3360 |
+ |
|
3361 |
+ |
2004-11-10 09:52 tim |
3362 |
+ |
|
3363 |
+ |
* src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a |
3364 |
+ |
configurable StatWriter |
3365 |
+ |
|
3366 |
+ |
2004-11-10 09:52 tim |
3367 |
+ |
|
3368 |
+ |
* src/io/StatWriter.hpp: file StatWriter.hpp was initially added on |
3369 |
+ |
branch new_design. |
3370 |
+ |
|
3371 |
+ |
2004-11-09 21:58 tim |
3372 |
+ |
|
3373 |
+ |
* src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation |
3374 |
+ |
in progress |
3375 |
+ |
|
3376 |
+ |
2004-11-09 18:11 tim |
3377 |
+ |
|
3378 |
+ |
* src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, |
3379 |
+ |
brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
3380 |
+ |
brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, |
3381 |
+ |
brains/mpiSimulation.hpp, integrators/Integrator.hpp, |
3382 |
+ |
integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, |
3383 |
+ |
integrators/VelocityVerletIntegrator.hpp: adding ForceManager |
3384 |
+ |
|
3385 |
+ |
2004-11-09 18:11 tim |
3386 |
+ |
|
3387 |
+ |
* src/brains/ForceManager.hpp: file ForceManager.hpp was initially |
3388 |
+ |
added on branch new_design. |
3389 |
+ |
|
3390 |
+ |
2004-11-09 18:11 tim |
3391 |
+ |
|
3392 |
+ |
* src/integrators/VelocityVerletIntegrator.cpp: file |
3393 |
+ |
VelocityVerletIntegrator.cpp was initially added on branch |
3394 |
+ |
new_design. |
3395 |
+ |
|
3396 |
+ |
2004-11-09 18:11 tim |
3397 |
+ |
|
3398 |
+ |
* src/integrators/NVE.cpp: file NVE.cpp was initially added on |
3399 |
+ |
branch new_design. |
3400 |
+ |
|
3401 |
+ |
2004-11-09 18:11 tim |
3402 |
+ |
|
3403 |
+ |
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
3404 |
+ |
added on branch new_design. |
3405 |
+ |
|
3406 |
+ |
2004-11-08 20:08 tim |
3407 |
+ |
|
3408 |
+ |
* src/integrators/VelocityVerletIntegrator.hpp: file |
3409 |
+ |
VelocityVerletIntegrator.hpp was initially added on branch |
3410 |
+ |
new_design. |
3411 |
+ |
|
3412 |
+ |
2004-11-08 20:08 tim |
3413 |
+ |
|
3414 |
+ |
* src/: brains/Exclude.hpp, brains/Stats.hpp, |
3415 |
+ |
integrators/Integrator.hpp, integrators/NVE.hpp, |
3416 |
+ |
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
3417 |
+ |
utils/TypeContainer.hpp: More to break |
3418 |
+ |
|
3419 |
+ |
2004-11-08 20:08 tim |
3420 |
+ |
|
3421 |
+ |
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
3422 |
+ |
branch new_design. |
3423 |
+ |
|
3424 |
+ |
2004-11-06 00:21 tim |
3425 |
+ |
|
3426 |
+ |
* src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially |
3427 |
+ |
added on branch new_design. |
3428 |
+ |
|
3429 |
+ |
2004-11-06 00:21 tim |
3430 |
+ |
|
3431 |
+ |
* src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, |
3432 |
+ |
UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, |
3433 |
+ |
utils/TypeContainer.hpp, utils/next_combination.hpp: adding |
3434 |
+ |
ForceField and TypeContainer classes |
3435 |
+ |
|
3436 |
+ |
2004-11-05 18:38 tim |
3437 |
+ |
|
3438 |
+ |
* src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was |
3439 |
+ |
initially added on branch new_design. |
3440 |
+ |
|
3441 |
+ |
2004-11-05 18:38 tim |
3442 |
+ |
|
3443 |
+ |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
3444 |
+ |
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
3445 |
+ |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
3446 |
+ |
brains/SimInfo.hpp, primitives/Molecule.hpp, |
3447 |
+ |
utils/LocalndexManager.hpp: Fix Exclude class etc. |
3448 |
+ |
|
3449 |
+ |
2004-11-05 18:38 tim |
3450 |
+ |
|
3451 |
+ |
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
3452 |
+ |
initially added on branch new_design. |
3453 |
+ |
|
3454 |
+ |
2004-11-05 16:45 chrisfen |
3455 |
+ |
|
3456 |
+ |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
3457 |
+ |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the |
3458 |
+ |
linear visitor |
3459 |
+ |
|
3460 |
+ |
2004-11-05 16:04 chrisfen |
3461 |
+ |
|
3462 |
+ |
* src/UseTheForce/DarkSide/shapes.F90: current status of the |
3463 |
+ |
debugging process |
3464 |
+ |
|
3465 |
+ |
2004-11-05 16:04 chrisfen |
3466 |
+ |
|
3467 |
+ |
* make/Makefile.in: included visitors and minimizer |
3468 |
+ |
|
3469 |
+ |
2004-11-05 16:03 chrisfen |
3470 |
+ |
|
3471 |
+ |
* ChangeLog: new changes |
3472 |
+ |
|
3473 |
+ |
2004-11-04 21:56 tim |
3474 |
+ |
|
3475 |
+ |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
3476 |
+ |
primitives/Molecule.hpp: Pain...... |
3477 |
+ |
|
3478 |
+ |
2004-11-04 15:55 tim |
3479 |
+ |
|
3480 |
+ |
* ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, |
3481 |
+ |
src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, |
3482 |
+ |
src/brains/Stats.hpp: time to break SimSetup |
3483 |
+ |
|
3484 |
+ |
2004-11-04 15:51 gezelter |
3485 |
+ |
|
3486 |
+ |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new |
3487 |
+ |
classes in progress |
3488 |
+ |
|
3489 |
+ |
2004-11-04 14:48 tim |
3490 |
+ |
|
3491 |
+ |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
3492 |
+ |
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
3493 |
+ |
class |
3494 |
+ |
|
3495 |
+ |
2004-11-04 14:48 tim |
3496 |
+ |
|
3497 |
+ |
* src/brains/Stats.cpp: file Stats.cpp was initially added on |
3498 |
+ |
branch new_design. |
3499 |
+ |
|
3500 |
+ |
2004-11-04 14:48 tim |
3501 |
+ |
|
3502 |
+ |
* src/brains/Stats.hpp: file Stats.hpp was initially added on |
3503 |
+ |
branch new_design. |
3504 |
+ |
|
3505 |
+ |
2004-11-04 11:22 gezelter |
3506 |
+ |
|
3507 |
+ |
* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
3508 |
+ |
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and |
3509 |
+ |
linearAxis are virtual in StuntDouble, but are implemented by |
3510 |
+ |
DirectionalAtom and RigidBody In StuntDouble, they should return |
3511 |
+ |
false and "-1" but there should be logic to figure them out in the |
3512 |
+ |
other two classes |
3513 |
+ |
|
3514 |
+ |
2004-11-04 11:20 gezelter |
3515 |
+ |
|
3516 |
+ |
* src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't |
3517 |
+ |
remember what I did |
3518 |
+ |
|
3519 |
+ |
2004-11-04 11:20 gezelter |
3520 |
+ |
|
3521 |
+ |
* src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky |
3522 |
+ |
|
3523 |
+ |
2004-11-04 11:20 gezelter |
3524 |
+ |
|
3525 |
+ |
* src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX |
3526 |
+ |
in the entry_plug so that it only is set if the atoms really are in |
3527 |
+ |
the simulation |
3528 |
+ |
|
3529 |
+ |
2004-11-04 11:20 gezelter |
3530 |
+ |
|
3531 |
+ |
* samples/water/ssd/ssd.md: testing force fields |
3532 |
+ |
|
3533 |
+ |
2004-11-04 11:19 gezelter |
3534 |
+ |
|
3535 |
+ |
* samples/shape/linear.in: testing shapes |
3536 |
+ |
|
3537 |
+ |
2004-11-03 14:56 tim |
3538 |
+ |
|
3539 |
+ |
* src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator |
3540 |
+ |
class(similar as SimSetup) |
3541 |
+ |
|
3542 |
+ |
2004-11-03 14:56 tim |
3543 |
+ |
|
3544 |
+ |
* src/brains/SimCreator.hpp: file SimCreator.hpp was initially |
3545 |
+ |
added on branch new_design. |
3546 |
+ |
|
3547 |
+ |
2004-11-03 14:56 tim |
3548 |
+ |
|
3549 |
+ |
* src/brains/SimCreator.cpp: file SimCreator.cpp was initially |
3550 |
+ |
added on branch new_design. |
3551 |
+ |
|
3552 |
+ |
2004-11-03 13:00 tim |
3553 |
+ |
|
3554 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
3555 |
+ |
UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, |
3556 |
+ |
UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp, |
3557 |
+ |
brains/DataStorage.hpp, primitives/Atom.hpp, |
3558 |
+ |
primitives/DirectionalAtom.hpp, restraints/Restraints.hpp, |
3559 |
+ |
visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get |
3560 |
+ |
compiled. Still a long way to go ...... |
3561 |
+ |
|
3562 |
+ |
2004-11-03 11:08 tim |
3563 |
+ |
|
3564 |
+ |
* ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
3565 |
+ |
src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, |
3566 |
+ |
src/integrators/NPTf.cpp, src/integrators/NPTi.cpp, |
3567 |
+ |
src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp, |
3568 |
+ |
src/io/ZConsReader.cpp, src/primitives/Bend.cpp, |
3569 |
+ |
src/primitives/Bond.cpp, src/primitives/GhostBend.cpp, |
3570 |
+ |
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
3571 |
+ |
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
3572 |
+ |
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
3573 |
+ |
src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp, |
3574 |
+ |
src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, |
3575 |
+ |
src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... |
3576 |
+ |
|
3577 |
+ |
2004-11-02 17:41 tim |
3578 |
+ |
|
3579 |
+ |
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
3580 |
+ |
branch new_design. |
3581 |
+ |
|
3582 |
+ |
2004-11-02 17:41 tim |
3583 |
+ |
|
3584 |
+ |
* src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was |
3585 |
+ |
initially added on branch new_design. |
3586 |
+ |
|
3587 |
+ |
2004-11-02 17:41 tim |
3588 |
+ |
|
3589 |
+ |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
3590 |
+ |
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
3591 |
+ |
Need unit test |
3592 |
+ |
|
3593 |
|
2004-11-02 11:59 tim |
3594 |
|
|
3595 |
|
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
3596 |
|
SimSnapshotManager.hpp: SimModel in progress |
3597 |
|
|
3598 |
+ |
2004-11-02 11:59 tim |
3599 |
+ |
|
3600 |
+ |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
3601 |
+ |
branch new_design. |
3602 |
+ |
|
3603 |
|
2004-11-02 10:28 chrisfen |
3604 |
|
|
3605 |
|
* src/: UseTheForce/DarkSide/shapes.F90, |
3608 |
|
|
3609 |
|
2004-11-02 10:27 tim |
3610 |
|
|
3611 |
< |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
3612 |
< |
functions for dealing with memory issue |
3611 |
> |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
3612 |
> |
added on branch new_design. |
3613 |
|
|
3614 |
|
2004-11-02 10:27 tim |
3615 |
|
|
3616 |
< |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
3617 |
< |
added on branch new_design. |
3616 |
> |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
3617 |
> |
functions for dealing with memory issue |
3618 |
|
|
3619 |
|
2004-11-02 10:23 tim |
3620 |
|
|
3643 |
|
|
3644 |
|
2004-11-01 16:40 tim |
3645 |
|
|
3646 |
< |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
3647 |
< |
on branch new_design. |
3646 |
> |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
3647 |
> |
branch new_design. |
3648 |
|
|
3649 |
|
2004-11-01 16:40 tim |
3650 |
|
|
3651 |
< |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
3652 |
< |
branch new_design. |
3651 |
> |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
3652 |
> |
version of Bond, Bend and Torsion. |
3653 |
|
|
3654 |
|
2004-11-01 16:40 tim |
3655 |
|
|
3658 |
|
|
3659 |
|
2004-11-01 16:40 tim |
3660 |
|
|
3661 |
< |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
3662 |
< |
version of Bond, Bend and Torsion. |
3661 |
> |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
3662 |
> |
on branch new_design. |
3663 |
|
|
3664 |
|
2004-11-01 16:37 tim |
3665 |
|
|
3668 |
|
|
3669 |
|
2004-11-01 16:37 tim |
3670 |
|
|
3671 |
< |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
3672 |
< |
BondType, BendType, TorsionType |
3671 |
> |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
3672 |
> |
branch new_design. |
3673 |
|
|
3674 |
|
2004-11-01 16:37 tim |
3675 |
|
|
3678 |
|
|
3679 |
|
2004-11-01 16:37 tim |
3680 |
|
|
3681 |
< |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
3682 |
< |
branch new_design. |
3681 |
> |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
3682 |
> |
BondType, BendType, TorsionType |
3683 |
|
|
3684 |
|
2004-11-01 15:15 tim |
3685 |
|
|
4512 |
|
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
4513 |
|
directory |
4514 |
|
|
923 |
– |
2004-10-11 09:23 tim |
924 |
– |
|
925 |
– |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
926 |
– |
Makefile |
927 |
– |
|
4515 |
|
2004-10-09 01:01 tim |
4516 |
|
|
4517 |
< |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
4518 |
< |
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
932 |
< |
Remove some Makefile.in |
4517 |
> |
* samples/: alkane/Makefile.in, lipid/Makefile.in, |
4518 |
> |
metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in |
4519 |
|
|
4520 |
|
2004-10-08 18:15 tim |
4521 |
|
|
4531 |
|
|
4532 |
|
2004-10-08 17:04 tim |
4533 |
|
|
4534 |
< |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
4535 |
< |
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
4536 |
< |
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
4534 |
> |
* samples/: alkane/Makefile, lipid/Makefile, metals/Makefile, |
4535 |
> |
minimizer/Makefile, water/Makefile.in, water/dimer/Makefile, |
4536 |
> |
water/dimer/Makefile.in, water/spce/Makefile, |
4537 |
|
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
4538 |
|
water/ssde/Makefile, water/ssde/Makefile.in, |
4539 |
|
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
4696 |
|
|
4697 |
|
2004-09-29 12:56 gezelter |
4698 |
|
|
4699 |
< |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
4699 |
> |
* make/: Make.conf.in, Makefile.in, _files/style.css: Working on |
4700 |
> |
make stuff |
4701 |
|
|
4702 |
|
2004-09-29 12:46 tim |
4703 |
|
|
4963 |
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
4964 |
|
src/visitors/RigidBodyVisitor.cpp, |
4965 |
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
4966 |
< |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
4966 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
4967 |
> |
make/_files/style.css, samples/Makefile.in, |
4968 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
4969 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
4970 |
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
5012 |
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
5013 |
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
5014 |
|
samples/alkane/butane.in, samples/alkane/butane.md, |
1427 |
– |
samples/argon/500.in, samples/argon/500.md, |
1428 |
– |
samples/argon/Makefile.in, samples/argon/ar864.in, |
1429 |
– |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
1430 |
– |
samples/argon/argonNVT.md, samples/argon/lj.md, |
5015 |
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
5016 |
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
5017 |
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
5135 |
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
5136 |
|
src/visitors/RigidBodyVisitor.cpp, |
5137 |
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
5138 |
< |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
5138 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
5139 |
> |
make/_files/style.css, samples/Makefile.in, |
5140 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
5141 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
5142 |
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
5184 |
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
5185 |
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
5186 |
|
samples/alkane/butane.in, samples/alkane/butane.md, |
1602 |
– |
samples/argon/500.in, samples/argon/500.md, |
1603 |
– |
samples/argon/Makefile.in, samples/argon/ar864.in, |
1604 |
– |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
1605 |
– |
samples/argon/argonNVT.md, samples/argon/lj.md, |
5187 |
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
5188 |
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
5189 |
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |