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2004-11-04 14:48 tim |
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2005-09-28 11:55 tim |
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* src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid |
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divergence in rotation matrix to quaternion transformation |
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2005-09-28 11:32 gezelter |
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* src/primitives/RigidBody.cpp: Rotation matrix multiplication |
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order error |
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2005-09-28 11:32 gezelter |
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* src/io/DumpReader.cpp: tracking down quaternion bug |
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2005-09-28 11:32 gezelter |
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* forceFields/DUFF2.frc: Added DIP atom types for 2-point water |
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model |
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2005-09-27 15:02 tim |
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* src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix |
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to quaternion |
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2005-09-26 13:38 chuckv |
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* src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc |
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7 so derfc is external. Other compilers should treat erfc as |
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intrinsic. |
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2005-09-26 12:07 chuckv |
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* src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc |
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and declared it to be external to fix issure with ifc7. Hopefully |
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this will not cause a problem with other compilers where derfc is |
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an intrinsic function. |
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2005-09-26 11:42 chuckv |
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* src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype |
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in simulation module. We needed a seperate receive buffer. |
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2005-09-26 10:58 chuckv |
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* src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added |
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support for skinThickness keyword to Globals. |
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2005-09-26 10:56 tim |
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* src/io/DumpReader.cpp: fix a typo in DumpReader |
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2005-09-26 09:27 chrisfen |
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* samples/: minimizer/tip4p_two.md, |
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thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md, |
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water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md, |
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water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md, |
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water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md, |
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water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md, |
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water/tip4p/tp4.md: fixing up some samples |
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2005-09-24 12:39 chrisfen |
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* src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now |
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roughly the same speed as the old version when using dipoles |
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energies are now exactly the same between the old version of OOPSE |
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and this version |
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2005-09-24 12:38 chrisfen |
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* samples/water/ssdrf/ssdrf.md: turned rf on |
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2005-09-23 15:31 chuckv |
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* src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the |
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skin thickness and hardcode listSkin to be 1.0. We now get listskin |
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from skin. This will get fixed to where we can manually set skin |
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thickness. |
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2005-09-22 13:50 gezelter |
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* src/math/derfc.F90: added error function |
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2005-09-21 19:08 chuckv |
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* src/integrators/Velocitizer.cpp: Removed print statement for |
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angular momentum and inertia tensor from velocitizer. |
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2005-09-21 19:04 chuckv |
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* src/integrators/Velocitizer.cpp: Removed print statements for |
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remove angular momentum. |
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2005-09-21 18:45 chuckv |
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* src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ |
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(say we are using EAM), we probably shouldn't rebuild the LJ mixing |
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map. |
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2005-09-21 15:59 tim |
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* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: |
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DumpReader using pure c++ io |
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2005-09-21 12:20 chrisfen |
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* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a |
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defaultCutoff bug (HEMES!) |
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2005-09-20 17:13 gezelter |
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* make/Makefile.in: libz additions |
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2005-09-20 17:03 gezelter |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
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src/config.h.in: added check for zlib in configure |
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2005-09-20 16:22 tim |
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* src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, |
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gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter |
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2005-09-20 11:22 tim |
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* test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding |
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testcase for zipstream |
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2005-09-20 10:41 tim |
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* src/io/zipstream.hpp: adding zipstream.hpp |
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2005-09-20 10:34 chrisfen |
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* samples/: dipole/splitInWater.md, dipole/split_SSD.md, |
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dipole/twoSplitDipole.md, minimizer/ssdEM.md, |
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minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md, |
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zcons/zconsMoving.md: fixed up some sample md files |
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2005-09-19 18:21 chrisfen |
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* ChangeLog, samples/water/ssdrf/ssdrf.md, |
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src/UseTheForce/doForces.F90, |
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src/UseTheForce/DarkSide/electrostatic.F90, |
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src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp, |
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src/brains/fSimulation.h: Fixed bugs in reaction field, now it |
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appears as though it really is working... |
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2005-09-18 15:45 chrisfen |
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* ChangeLog, samples/water/ssdrf/ssdrf.md, |
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src/UseTheForce/doForces.F90, |
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src/UseTheForce/doForces_interface.F90, |
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src/UseTheForce/doForces_interface.h, |
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src/UseTheForce/DarkSide/electrostatic.F90, |
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src/UseTheForce/DarkSide/electrostatic_interface.h, |
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src/brains/SimInfo.cpp: reaction field seems to work now, still |
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need to do some testing... |
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2005-09-16 18:04 chuckv |
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* src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed |
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dump files. |
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2005-09-16 16:07 chrisfen |
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* src/: UseTheForce/doForces_interface.F90, |
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UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a |
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bug that ifc missed... |
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2005-09-16 15:36 chrisfen |
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* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
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fixing some summation method issues |
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2005-09-16 14:35 chrisfen |
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* src/brains/SimInfo.cpp: fixed a capitalization error |
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2005-09-16 14:34 chrisfen |
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* src/UseTheForce/: fElectrostaticSummationMethod.h, |
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DarkSide/fElectrostaticSummationMethod.h: moved a header file |
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around |
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2005-09-16 14:00 chrisfen |
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* src/: UseTheForce/DarkSide/electrostatic_interface.F90, |
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brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there |
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are known issues - particularly with reaction field... |
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2005-09-16 11:07 chrisfen |
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* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, |
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io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking |
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(cutting out the old way to do reaction field) |
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2005-09-15 17:05 gezelter |
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* src/UseTheForce/: doForces.F90, fCoulombicCorrection.h, |
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fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90, |
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DarkSide/electrostatic_interface.F90, |
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DarkSide/electrostatic_interface.h: Working on adding WOLF |
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2005-09-15 14:17 tim |
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* src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame |
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is called without calling getNFrames |
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2005-09-15 08:47 chrisfen |
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* src/UseTheForce/fCoulombicCorrection.h: forgot to add a header |
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2005-09-14 21:48 chuckv |
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* src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was |
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not initialized after creation. When maxval(gtypeMaxCutoff) was |
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called, the largest random garbage value was returned from the |
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array. |
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2005-09-14 19:14 chrisfen |
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* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, |
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io/Globals.hpp: changes to include the coulombicCorrection selector |
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2005-09-14 19:13 chrisfen |
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* src/UseTheForce/DarkSide/: Makefile, electrostatic.F90, |
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reactionField.F90: added in the undamped wolf, in the process of |
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doing the damped wolf |
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2005-09-14 19:13 chrisfen |
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* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
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doForces_interface.h, notifyCutoffs.F90: some changes to activate |
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the coulombicCorrection selector |
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2005-09-14 19:11 chrisfen |
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* samples/water/dimer/: cl.in, cl.md, water.md: just some testing |
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2005-09-14 19:11 chrisfen |
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* samples/argon/: 500.in, 500.md: Equilibrated the sample |
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2005-09-14 19:10 chrisfen |
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* forceFields/DUFF2.frc: re-added Cl- and Na+ |
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2005-09-14 15:31 chuckv |
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* src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup |
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eamAtypes instead of assuming a 1-1 correspondence to atypes. |
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2005-09-14 15:28 gezelter |
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* src/UseTheForce/doForces.F90: fix to put back calculation of r in |
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do_prepair |
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2005-09-14 14:02 gezelter |
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* src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the |
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createMixingMap routine. It should now set doShift correctly |
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2005-09-07 17:44 chuckv |
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* src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. |
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2005-09-07 17:23 chuckv |
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* src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi |
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logical variables |
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2005-09-07 17:08 gezelter |
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* src/UseTheForce/doForces.F90: bugfix on the grouptype finding |
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algorithm |
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2005-09-07 15:46 gezelter |
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* src/: UseTheForce/doForces.F90, |
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UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, |
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UseTheForce/notifyCutoffs_interface.F90, |
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UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp, |
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io/Globals.cpp, io/Globals.hpp: adding c-side interface to change |
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cutoff Policy |
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2005-09-07 14:18 gezelter |
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* src/UseTheForce/doForces.F90: Some bug hunting |
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2005-09-07 14:18 gezelter |
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* samples/argon/argonNVT.md: Just a longer test |
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2005-09-06 12:32 chuckv |
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* src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap |
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etc.. |
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2005-09-01 17:56 gezelter |
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* src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to |
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zero |
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2005-09-01 15:17 gezelter |
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* src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote |
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createGtypeCutoffMap |
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2005-08-30 13:23 chrisfen |
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* src/: UseTheForce/doForces.F90, |
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UseTheForce/doForces_interface.F90, |
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UseTheForce/doForces_interface.h, |
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UseTheForce/DarkSide/electrostatic.F90, |
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UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp, |
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brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some |
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changes for implementing the wolf potential |
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2005-08-26 17:39 chrisfen |
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* src/UseTheForce/DarkSide/eam.F90: updated getEAMCut |
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2005-08-26 16:30 chrisfen |
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* src/UseTheForce/: doForces.F90, DarkSide/eam.F90, |
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DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added |
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some probably nonfunctional get*cut routines |
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2005-08-26 15:34 chuckv |
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* src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. |
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2005-08-26 11:36 gezelter |
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* src/UseTheForce/doForces.F90: fixing some of the problems in the |
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interactionHash and gtypeCutoff routines |
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2005-08-17 10:26 gezelter |
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* src/UseTheForce/: doForces.F90, fCutoffPolicy.h, |
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DarkSide/simulation.F90: added fCutoffPolicy.h |
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2005-08-11 16:04 gezelter |
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* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in |
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progress |
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2005-08-10 14:17 gezelter |
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* src/primitives/StuntDouble.hpp: putting spaceballs back where |
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they belong |
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2005-08-09 17:33 gezelter |
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* src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard |
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Jones module |
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2005-08-09 17:33 gezelter |
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* src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky |
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2005-08-09 14:40 chuckv |
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* src/UseTheForce/doForces.F90: In process of re-write for group |
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based cutoff.... |
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2005-07-29 14:38 gezelter |
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* src/UseTheForce/doForces.F90: fixes in progress |
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2005-07-29 12:34 tim |
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* src/UseTheForce/doForces.F90: fix a bug which does not update |
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me_i and me_j correctly |
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2005-07-28 17:12 chuckv |
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* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed |
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cutoffs... Segfaults nicely now... |
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2005-07-20 12:04 gezelter |
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* configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text |
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error messages from pathscale compiler |
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| 389 |
> |
2005-07-13 11:48 tim |
| 390 |
> |
|
| 391 |
> |
* src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in |
| 392 |
> |
<functional> |
| 393 |
> |
|
| 394 |
> |
2005-07-13 10:54 tim |
| 395 |
> |
|
| 396 |
> |
* src/: UseTheForce/fSwitchingFunction.h, |
| 397 |
> |
UseTheForce/mpiComponentPlan.h, |
| 398 |
> |
UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h, |
| 399 |
> |
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
| 400 |
> |
io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c, |
| 401 |
> |
io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c, |
| 402 |
> |
io/parse_tree.h, math/MatVec3.c, utils/residentMem.c, |
| 403 |
> |
utils/simError.c, utils/simError.h: replace c++ style comment in c |
| 404 |
> |
files |
| 405 |
> |
|
| 406 |
> |
2005-07-03 15:53 chuckv |
| 407 |
> |
|
| 408 |
> |
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
| 409 |
> |
UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added |
| 410 |
> |
subroutine to set cuttoff for Interaction map and function in |
| 411 |
> |
simulation.F90 to determine if a particular atype is present in a |
| 412 |
> |
simulation. |
| 413 |
> |
|
| 414 |
> |
2005-06-28 08:58 gezelter |
| 415 |
> |
|
| 416 |
> |
* src/UseTheForce/doForces.F90: [no log message] |
| 417 |
> |
|
| 418 |
> |
2005-06-27 17:21 chuckv |
| 419 |
> |
|
| 420 |
> |
* src/UseTheForce/doForces.F90: More breaking and destruction of |
| 421 |
> |
force code. Does not build at this point... |
| 422 |
> |
|
| 423 |
> |
2005-06-27 16:01 gezelter |
| 424 |
> |
|
| 425 |
> |
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90, |
| 426 |
> |
UseTheForce/DarkSide/fInteractionMap.h, |
| 427 |
> |
UseTheForce/DarkSide/interactions.F90, utils/definitions.F90: |
| 428 |
> |
Breaky breaky! |
| 429 |
> |
|
| 430 |
> |
2005-06-20 11:03 gezelter |
| 431 |
> |
|
| 432 |
> |
* samples/water/ssd/ssd.md, |
| 433 |
> |
src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a |
| 434 |
> |
simulation |
| 435 |
> |
|
| 436 |
> |
2005-06-13 13:25 tim |
| 437 |
> |
|
| 438 |
> |
* src/: applications/staticProps/DensityPlot.cpp, |
| 439 |
> |
applications/staticProps/DensityPlot.hpp, |
| 440 |
> |
applications/staticProps/SCDOrderParameter.cpp, |
| 441 |
> |
applications/staticProps/StaticProps.cpp, |
| 442 |
> |
io/AtomTypesSectionParser.cpp: working version of DensityPlot |
| 443 |
> |
|
| 444 |
> |
2005-05-31 17:31 chuckv |
| 445 |
> |
|
| 446 |
> |
* src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to |
| 447 |
> |
remove angular momentum. |
| 448 |
> |
|
| 449 |
> |
2005-05-31 12:34 chuckv |
| 450 |
> |
|
| 451 |
> |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in |
| 452 |
> |
typo in nanorodBuilder. |
| 453 |
> |
|
| 454 |
> |
2005-05-30 09:01 chuckv |
| 455 |
> |
|
| 456 |
> |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 457 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, |
| 458 |
> |
brains/Stats.hpp, integrators/Velocitizer.cpp, |
| 459 |
> |
integrators/Velocitizer.hpp: Added method to remove system angular |
| 460 |
> |
momentum to velocitizer and added method to calculate system |
| 461 |
> |
angular momentum to siminfo. |
| 462 |
> |
|
| 463 |
> |
2005-05-29 16:16 chrisfen |
| 464 |
> |
|
| 465 |
> |
* src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed |
| 466 |
> |
balance from the Darkside (files) |
| 467 |
> |
|
| 468 |
> |
2005-05-29 16:15 chrisfen |
| 469 |
> |
|
| 470 |
> |
* src/UseTheForce/doForces.F90: Removed balance from doForces |
| 471 |
> |
|
| 472 |
> |
2005-05-29 16:15 chrisfen |
| 473 |
> |
|
| 474 |
> |
* samples/water/tap/: tap.in, tap.md: Updated tap sample |
| 475 |
> |
|
| 476 |
> |
2005-05-29 16:15 chrisfen |
| 477 |
> |
|
| 478 |
> |
* samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap |
| 479 |
> |
dimer for testing purposes |
| 480 |
> |
|
| 481 |
> |
2005-05-29 16:14 chrisfen |
| 482 |
> |
|
| 483 |
> |
* forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It |
| 484 |
> |
was apparently wiped earlier this month... |
| 485 |
> |
|
| 486 |
> |
2005-05-29 16:13 chrisfen |
| 487 |
> |
|
| 488 |
> |
* ChangeLog: ran make cvslog |
| 489 |
> |
|
| 490 |
> |
2005-05-28 19:16 tim |
| 491 |
> |
|
| 492 |
> |
* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding |
| 493 |
> |
AtomNameVisitor |
| 494 |
> |
|
| 495 |
> |
2005-05-28 19:09 tim |
| 496 |
> |
|
| 497 |
> |
* src/integrators/Integrator.cpp: dding resetIntegrator |
| 498 |
> |
|
| 499 |
> |
2005-05-28 19:06 tim |
| 500 |
> |
|
| 501 |
> |
* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, |
| 502 |
> |
NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, |
| 503 |
> |
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding |
| 504 |
> |
resetIntegrator |
| 505 |
> |
|
| 506 |
> |
2005-05-27 16:11 tim |
| 507 |
> |
|
| 508 |
> |
* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, |
| 509 |
> |
Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, |
| 510 |
> |
SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
| 511 |
> |
StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into |
| 512 |
> |
StaticProps |
| 513 |
> |
|
| 514 |
> |
2005-05-26 23:41 tim |
| 515 |
> |
|
| 516 |
> |
* src/: applications/staticProps/Makefile, |
| 517 |
> |
applications/staticProps/P2OrderParameter.cpp, |
| 518 |
> |
applications/staticProps/P2OrderParameter.hpp, |
| 519 |
> |
applications/staticProps/StaticProps.cpp, |
| 520 |
> |
applications/staticProps/StaticProps.ggo, |
| 521 |
> |
applications/staticProps/StaticPropsCmd.c, |
| 522 |
> |
applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, |
| 523 |
> |
utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps |
| 524 |
> |
|
| 525 |
> |
2005-05-26 17:45 tim |
| 526 |
> |
|
| 527 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 528 |
> |
applications/dump2Xyz/Dump2XYZCmd.c, |
| 529 |
> |
applications/dump2Xyz/Dump2XYZCmd.h, |
| 530 |
> |
applications/staticProps/Makefile, |
| 531 |
> |
applications/staticProps/P2OrderParameter.cpp, |
| 532 |
> |
applications/staticProps/P2OrderParameter.hpp, |
| 533 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
| 534 |
> |
applications/staticProps/RadialDistrFunc.hpp, |
| 535 |
> |
applications/staticProps/StaticAnalyser.hpp, |
| 536 |
> |
applications/staticProps/StaticProps.cpp, |
| 537 |
> |
applications/staticProps/StaticProps.ggo, |
| 538 |
> |
applications/staticProps/StaticPropsCmd.c, |
| 539 |
> |
applications/staticProps/StaticPropsCmd.h, visitors/Makefile, |
| 540 |
> |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding |
| 541 |
> |
AtomNameVisitor to convert atom name to its base name; |
| 542 |
> |
wrappingvisitor now wrap back to the center of the mass; adding |
| 543 |
> |
P2OrderParameter into StaticProps |
| 544 |
> |
|
| 545 |
> |
2005-05-22 16:36 chuckv |
| 546 |
> |
|
| 547 |
> |
* samples/metals/nanorod/Au_nanoparticle_FCC.md, |
| 548 |
> |
src/applications/nanoRodBuilder/Geometry.cpp, |
| 549 |
> |
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
| 550 |
> |
src/applications/nanoRodBuilder/GeometryFactory.cpp, |
| 551 |
> |
src/applications/nanoRodBuilder/GeometryFactory.hpp, |
| 552 |
> |
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 553 |
> |
src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
| 554 |
> |
tensor. |
| 555 |
> |
|
| 556 |
> |
2005-05-22 16:05 tim |
| 557 |
> |
|
| 558 |
> |
* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
| 559 |
> |
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
| 560 |
> |
io/Globals.hpp, io/SectionParserManager.cpp: adding keyword |
| 561 |
> |
printPressureTensor |
| 562 |
> |
|
| 563 |
> |
2005-05-20 14:27 tim |
| 564 |
> |
|
| 565 |
> |
* src/integrators/NPrT.cpp: NPrT in progress |
| 566 |
> |
|
| 567 |
> |
2005-05-20 11:01 tim |
| 568 |
> |
|
| 569 |
> |
* src/: integrators/NPrT.cpp, io/Globals.cpp, |
| 570 |
> |
utils/OOPSEConstant.hpp: NPrT in progress |
| 571 |
> |
|
| 572 |
> |
2005-05-19 16:31 tim |
| 573 |
> |
|
| 574 |
> |
* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, |
| 575 |
> |
integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, |
| 576 |
> |
io/Globals.hpp: NPAT is working |
| 577 |
> |
|
| 578 |
> |
2005-05-19 10:49 tim |
| 579 |
> |
|
| 580 |
> |
* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, |
| 581 |
> |
integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT |
| 582 |
> |
|
| 583 |
> |
2005-05-18 23:28 tim |
| 584 |
> |
|
| 585 |
> |
* src/: brains/Register.cpp, integrators/NPAT.cpp, |
| 586 |
> |
integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, |
| 587 |
> |
io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators |
| 588 |
> |
|
| 589 |
> |
2005-05-18 14:06 chrisfen |
| 590 |
> |
|
| 591 |
> |
* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just |
| 592 |
> |
some tap changes |
| 593 |
> |
|
| 594 |
> |
2005-05-18 13:31 chrisfen |
| 595 |
> |
|
| 596 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
| 597 |
> |
DarkSide/sticky.F90: Modifications to temper the dipolar strength |
| 598 |
> |
in the first solvation shell for tap |
| 599 |
> |
|
| 600 |
> |
2005-05-18 07:35 chrisfen |
| 601 |
> |
|
| 602 |
> |
* samples/water/tap/: tap.in, tap.md, water.md: added a tap example |
| 603 |
> |
for testing purposes |
| 604 |
> |
|
| 605 |
> |
2005-05-17 17:35 chrisfen |
| 606 |
> |
|
| 607 |
> |
* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, |
| 608 |
> |
samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, |
| 609 |
> |
src/UseTheForce/doForces.F90, |
| 610 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
| 611 |
> |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
| 612 |
> |
src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also |
| 613 |
> |
correcting changes to the previous merge that were not caught |
| 614 |
> |
|
| 615 |
> |
2005-05-16 23:20 chuckv |
| 616 |
> |
|
| 617 |
> |
* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: |
| 618 |
> |
Fixed merge issues between Kyle and Chris so OOPSE will actually |
| 619 |
> |
build. |
| 620 |
> |
|
| 621 |
> |
2005-05-16 22:46 kdaily |
| 622 |
> |
|
| 623 |
> |
* src/io/: GayBerneAtomTypesSectionParser.cpp, |
| 624 |
> |
GayBerneAtomTypesSectionParser.hpp, Makefile: help |
| 625 |
> |
|
| 626 |
> |
2005-05-16 21:08 kdaily |
| 627 |
> |
|
| 628 |
> |
* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, |
| 629 |
> |
src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, |
| 630 |
> |
src/types/DirectionalAtomType.cpp, |
| 631 |
> |
src/types/DirectionalAtomType.hpp: added gb |
| 632 |
> |
|
| 633 |
> |
2005-05-13 15:36 chrisfen |
| 634 |
> |
|
| 635 |
> |
* forceFields/DUFF2.frc: Better tap |
| 636 |
> |
|
| 637 |
> |
2005-05-12 14:43 chrisfen |
| 638 |
> |
|
| 639 |
> |
* forceFields/DUFF2.frc, samples/water/dimer/ssd.in, |
| 640 |
> |
samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, |
| 641 |
> |
src/applications/dump2Xyz/Dump2XYZ.cpp, |
| 642 |
> |
src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. |
| 643 |
> |
Need to parametrize. |
| 644 |
> |
|
| 645 |
> |
2005-05-11 18:15 chuckv |
| 646 |
> |
|
| 647 |
> |
* src/: io/ShapeAtomTypesSectionParser.cpp, |
| 648 |
> |
math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed |
| 649 |
> |
build issues under ifc7. |
| 650 |
> |
|
| 651 |
> |
2005-05-09 17:07 chuckv |
| 652 |
> |
|
| 653 |
> |
* src/applications/nanoRodBuilder/Geometry.hpp: More geometry |
| 654 |
> |
builder changes. |
| 655 |
> |
|
| 656 |
> |
2005-05-05 10:06 chrisfen |
| 657 |
> |
|
| 658 |
> |
* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED |
| 659 |
> |
to TAP |
| 660 |
> |
|
| 661 |
> |
2005-05-05 09:47 chrisfen |
| 662 |
> |
|
| 663 |
> |
* forceFields/DUFF2.frc, samples/water/ssde/ssde.md, |
| 664 |
> |
samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, |
| 665 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, |
| 666 |
> |
src/UseTheForce/DarkSide/atype.F90, |
| 667 |
> |
src/UseTheForce/DarkSide/atype_interface.F90, |
| 668 |
> |
src/UseTheForce/DarkSide/simulation.F90, |
| 669 |
> |
src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, |
| 670 |
> |
src/brains/fSimulation.h, src/io/Makefile, |
| 671 |
> |
src/io/StickyAtomTypesSectionParser.cpp, |
| 672 |
> |
src/io/StickyPowerAtomTypesSectionParser.cpp, |
| 673 |
> |
src/io/StickyPowerAtomTypesSectionParser.hpp, |
| 674 |
> |
src/types/AtomType.cpp, src/types/AtomType.hpp, |
| 675 |
> |
src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, |
| 676 |
> |
src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's |
| 677 |
> |
not parametrized, but OOPSE will now let me run it... |
| 678 |
> |
|
| 679 |
> |
2005-05-03 17:55 chuckv |
| 680 |
> |
|
| 681 |
> |
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
| 682 |
> |
GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: |
| 683 |
> |
Adding support for generic geometry to nanorodbuilder. |
| 684 |
> |
|
| 685 |
> |
2005-05-03 12:55 chuckv |
| 686 |
> |
|
| 687 |
> |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
| 688 |
> |
nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, |
| 689 |
> |
nanorodBuilderCmd.h: More changes to nanoRodBuilder.... |
| 690 |
> |
|
| 691 |
> |
2005-04-29 14:16 gezelter |
| 692 |
> |
|
| 693 |
> |
* make/Makefile.in: [no log message] |
| 694 |
> |
|
| 695 |
> |
2005-04-29 11:26 chrisfen |
| 696 |
> |
|
| 697 |
> |
* forceFields/DUFF2.frc, samples/water/spce/water.md, |
| 698 |
> |
samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, |
| 699 |
> |
samples/water/ssd-ion/water.md, samples/water/ssde/water.md, |
| 700 |
> |
samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, |
| 701 |
> |
samples/water/tip4p/water.md: Added TIP4P-Ew |
| 702 |
> |
|
| 703 |
> |
2005-04-27 19:24 chuckv |
| 704 |
> |
|
| 705 |
> |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
| 706 |
> |
GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, |
| 707 |
> |
nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with |
| 708 |
> |
nanoRodBuilder.... |
| 709 |
> |
|
| 710 |
> |
2005-04-27 15:13 chrisfen |
| 711 |
> |
|
| 712 |
> |
* samples/shape/Shapes.frc, samples/shape/linear.shape, |
| 713 |
> |
src/UseTheForce/DarkSide/atype.F90, |
| 714 |
> |
src/UseTheForce/DarkSide/shapes.F90, |
| 715 |
> |
src/UseTheForce/DarkSide/shapes_interface.F90, |
| 716 |
> |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of |
| 717 |
> |
write statements and am closer to a working shapes |
| 718 |
> |
|
| 719 |
> |
2005-04-22 16:57 chuckv |
| 720 |
> |
|
| 721 |
> |
* src/utils/Predicate.hpp: Fixed gcc4 bug... |
| 722 |
> |
|
| 723 |
> |
2005-04-22 16:52 tim |
| 724 |
> |
|
| 725 |
> |
* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, |
| 726 |
> |
Trim.hpp: adding CharClassificationFunctor to fix the locale |
| 727 |
> |
problem of c++ |
| 728 |
> |
|
| 729 |
> |
2005-04-21 09:12 chrisfen |
| 730 |
> |
|
| 731 |
> |
* samples/shape/Shapes.frc, samples/shape/linear.in, |
| 732 |
> |
samples/shape/linear.md, src/UseTheForce/ForceField.hpp, |
| 733 |
> |
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, |
| 734 |
> |
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
| 735 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, |
| 736 |
> |
src/UseTheForce/DarkSide/shapes.F90, |
| 737 |
> |
src/UseTheForce/DarkSide/shapes_interface.F90, |
| 738 |
> |
src/UseTheForce/DarkSide/shapes_interface.h, |
| 739 |
> |
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
| 740 |
> |
src/io/Makefile, src/io/SectionParser.cpp, |
| 741 |
> |
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
| 742 |
> |
src/io/ShapeAtomTypesSectionParser.cpp, |
| 743 |
> |
src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, |
| 744 |
> |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, |
| 745 |
> |
src/types/ShapeAtomType.hpp: Shapes is limping along with a array |
| 746 |
> |
bounds overwrite (I think...). At least the parser loads the |
| 747 |
> |
forcefield fine... |
| 748 |
> |
|
| 749 |
> |
2005-04-18 10:44 chrisfen |
| 750 |
> |
|
| 751 |
> |
* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on |
| 752 |
> |
Mac (capitalization confusion of filenames) |
| 753 |
> |
|
| 754 |
> |
2005-04-17 22:50 chrisfen |
| 755 |
> |
|
| 756 |
> |
* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, |
| 757 |
> |
UseTheForce/Shapes_FF.cpp, |
| 758 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
| 759 |
> |
io/ShapeAtomTypesSectionParser.cpp, |
| 760 |
> |
io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... |
| 761 |
> |
|
| 762 |
> |
2005-04-15 17:43 gezelter |
| 763 |
> |
|
| 764 |
> |
* README: gmake in case people forget |
| 765 |
> |
|
| 766 |
> |
2005-04-15 17:40 gezelter |
| 767 |
> |
|
| 768 |
> |
* src/applications/oopse/oopse.cpp: fixed the spacing on the |
| 769 |
> |
banner. Vanity. |
| 770 |
> |
|
| 771 |
> |
2005-04-15 17:22 gezelter |
| 772 |
> |
|
| 773 |
> |
* src/: config.h.in, applications/oopse/oopse.cpp: Version string |
| 774 |
> |
in banner (and version numbers in config.h) |
| 775 |
> |
|
| 776 |
> |
2005-04-15 17:22 gezelter |
| 777 |
> |
|
| 778 |
> |
* ChangeLog, LICENSE, README: Documentation changes |
| 779 |
> |
|
| 780 |
> |
2005-04-15 17:03 gezelter |
| 781 |
> |
|
| 782 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 783 |
> |
UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, |
| 784 |
> |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 785 |
> |
UseTheForce/ForceFieldCreator.hpp, |
| 786 |
> |
UseTheForce/ForceFieldFactory.cpp, |
| 787 |
> |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
| 788 |
> |
UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, |
| 789 |
> |
UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, |
| 790 |
> |
UseTheForce/notifyCutoffs.F90, |
| 791 |
> |
UseTheForce/notifyCutoffs_interface.F90, |
| 792 |
> |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
| 793 |
> |
UseTheForce/DarkSide/atype.F90, |
| 794 |
> |
UseTheForce/DarkSide/atype_interface.F90, |
| 795 |
> |
UseTheForce/DarkSide/eam.F90, |
| 796 |
> |
UseTheForce/DarkSide/eam_interface.F90, |
| 797 |
> |
UseTheForce/DarkSide/eam_interface.h, |
| 798 |
> |
UseTheForce/DarkSide/electrostatic.F90, |
| 799 |
> |
UseTheForce/DarkSide/electrostatic_interface.F90, |
| 800 |
> |
UseTheForce/DarkSide/electrostatic_interface.h, |
| 801 |
> |
UseTheForce/DarkSide/force_globals.F90, |
| 802 |
> |
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
| 803 |
> |
UseTheForce/DarkSide/lj_interface.F90, |
| 804 |
> |
UseTheForce/DarkSide/lj_interface.h, |
| 805 |
> |
UseTheForce/DarkSide/neighborLists.F90, |
| 806 |
> |
UseTheForce/DarkSide/reactionField.F90, |
| 807 |
> |
UseTheForce/DarkSide/shapes.F90, |
| 808 |
> |
UseTheForce/DarkSide/shapes_interface.F90, |
| 809 |
> |
UseTheForce/DarkSide/shapes_interface.h, |
| 810 |
> |
UseTheForce/DarkSide/simParallel.F90, |
| 811 |
> |
UseTheForce/DarkSide/simParallel_interface.F90, |
| 812 |
> |
UseTheForce/DarkSide/simParallel_interface.h, |
| 813 |
> |
UseTheForce/DarkSide/simulation.F90, |
| 814 |
> |
UseTheForce/DarkSide/simulation_interface.F90, |
| 815 |
> |
UseTheForce/DarkSide/simulation_interface.h, |
| 816 |
> |
UseTheForce/DarkSide/sticky.F90, |
| 817 |
> |
UseTheForce/DarkSide/sticky_interface.F90, |
| 818 |
> |
UseTheForce/DarkSide/sticky_interface.h, |
| 819 |
> |
UseTheForce/DarkSide/switcheroo.F90, |
| 820 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, |
| 821 |
> |
applications/dump2Xyz/Dump2XYZCmd.c, |
| 822 |
> |
applications/dump2Xyz/Dump2XYZCmd.h, |
| 823 |
> |
applications/dynamicProps/CrossTimeCorrFunc.cpp, |
| 824 |
> |
applications/dynamicProps/CrossTimeCorrFunc.hpp, |
| 825 |
> |
applications/dynamicProps/DipoleCorrFunc.cpp, |
| 826 |
> |
applications/dynamicProps/DipoleCorrFunc.hpp, |
| 827 |
> |
applications/dynamicProps/DynamicProps.cpp, |
| 828 |
> |
applications/dynamicProps/DynamicPropsCmd.c, |
| 829 |
> |
applications/dynamicProps/DynamicPropsCmd.h, |
| 830 |
> |
applications/dynamicProps/FrameTimeCorrFunc.hpp, |
| 831 |
> |
applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
| 832 |
> |
applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
| 833 |
> |
applications/dynamicProps/RCorrFunc.cpp, |
| 834 |
> |
applications/dynamicProps/RCorrFunc.hpp, |
| 835 |
> |
applications/dynamicProps/TimeCorrFunc.cpp, |
| 836 |
> |
applications/dynamicProps/TimeCorrFunc.hpp, |
| 837 |
> |
applications/dynamicProps/VCorrFunc.cpp, |
| 838 |
> |
applications/dynamicProps/VCorrFunc.hpp, |
| 839 |
> |
applications/nanoRodBuilder/GeometryBuilder.cpp, |
| 840 |
> |
applications/nanoRodBuilder/GeometryBuilder.hpp, |
| 841 |
> |
applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 842 |
> |
applications/nanoRodBuilder/nanorodBuilderCmd.c, |
| 843 |
> |
applications/nanoRodBuilder/nanorodBuilderCmd.h, |
| 844 |
> |
applications/oopse/oopse.cpp, |
| 845 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
| 846 |
> |
applications/simpleBuilder/simpleBuilderCmd.c, |
| 847 |
> |
applications/simpleBuilder/simpleBuilderCmd.h, |
| 848 |
> |
applications/staticProps/GofAngle2.cpp, |
| 849 |
> |
applications/staticProps/GofAngle2.hpp, |
| 850 |
> |
applications/staticProps/GofR.cpp, |
| 851 |
> |
applications/staticProps/GofR.hpp, |
| 852 |
> |
applications/staticProps/GofRAngle.cpp, |
| 853 |
> |
applications/staticProps/GofRAngle.hpp, |
| 854 |
> |
applications/staticProps/GofXyz.cpp, |
| 855 |
> |
applications/staticProps/GofXyz.hpp, |
| 856 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
| 857 |
> |
applications/staticProps/RadialDistrFunc.hpp, |
| 858 |
> |
applications/staticProps/StaticProps.cpp, |
| 859 |
> |
applications/staticProps/StaticPropsCmd.c, |
| 860 |
> |
applications/staticProps/StaticPropsCmd.h, |
| 861 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 862 |
> |
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
| 863 |
> |
brains/Exclude.hpp, brains/ForceManager.cpp, |
| 864 |
> |
brains/ForceManager.hpp, brains/MoleculeCreator.cpp, |
| 865 |
> |
brains/MoleculeCreator.hpp, brains/Register.cpp, |
| 866 |
> |
brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 867 |
> |
brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
| 868 |
> |
brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, |
| 869 |
> |
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, |
| 870 |
> |
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 871 |
> |
brains/fSimulation.h, constraints/ConstraintElem.hpp, |
| 872 |
> |
constraints/ConstraintPair.hpp, constraints/Rattle.cpp, |
| 873 |
> |
constraints/Rattle.hpp, constraints/ZconsStruct.hpp, |
| 874 |
> |
constraints/ZconstraintForceManager.cpp, |
| 875 |
> |
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
| 876 |
> |
integrators/DLM.hpp, integrators/Integrator.cpp, |
| 877 |
> |
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
| 878 |
> |
integrators/IntegratorFactory.cpp, |
| 879 |
> |
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
| 880 |
> |
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
| 881 |
> |
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
| 882 |
> |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
| 883 |
> |
integrators/NVT.cpp, integrators/NVT.hpp, |
| 884 |
> |
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
| 885 |
> |
integrators/Velocitizer.hpp, |
| 886 |
> |
integrators/VelocityVerletIntegrator.cpp, |
| 887 |
> |
integrators/VelocityVerletIntegrator.hpp, |
| 888 |
> |
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
| 889 |
> |
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
| 890 |
> |
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
| 891 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 892 |
> |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 893 |
> |
io/ChargeAtomTypesSectionParser.hpp, |
| 894 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
| 895 |
> |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
| 896 |
> |
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
| 897 |
> |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
| 898 |
> |
io/Globals.cpp, io/Globals.hpp, |
| 899 |
> |
io/LennardJonesAtomTypesSectionParser.cpp, |
| 900 |
> |
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
| 901 |
> |
io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, |
| 902 |
> |
io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, |
| 903 |
> |
io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, |
| 904 |
> |
io/SectionParser.cpp, io/SectionParser.hpp, |
| 905 |
> |
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
| 906 |
> |
io/StatWriter.cpp, io/StatWriter.hpp, |
| 907 |
> |
io/StickyAtomTypesSectionParser.cpp, |
| 908 |
> |
io/StickyAtomTypesSectionParser.hpp, |
| 909 |
> |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
| 910 |
> |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
| 911 |
> |
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, |
| 912 |
> |
io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, |
| 913 |
> |
io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, |
| 914 |
> |
io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, |
| 915 |
> |
lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, |
| 916 |
> |
lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
| 917 |
> |
lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, |
| 918 |
> |
lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, |
| 919 |
> |
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
| 920 |
> |
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
| 921 |
> |
math/ParallelRandNumGen.hpp, math/Polynomial.hpp, |
| 922 |
> |
math/Quaternion.hpp, math/RandNumGen.hpp, |
| 923 |
> |
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
| 924 |
> |
math/RectMatrix.hpp, math/SeqRandNumGen.cpp, |
| 925 |
> |
math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, |
| 926 |
> |
math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, |
| 927 |
> |
minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, |
| 928 |
> |
minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, |
| 929 |
> |
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
| 930 |
> |
minimizers/MinimizerFactory.hpp, |
| 931 |
> |
minimizers/MinimizerParameterSet.cpp, |
| 932 |
> |
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
| 933 |
> |
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
| 934 |
> |
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
| 935 |
> |
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
| 936 |
> |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
| 937 |
> |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 938 |
> |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
| 939 |
> |
primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, |
| 940 |
> |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
| 941 |
> |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
| 942 |
> |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
| 943 |
> |
primitives/Torsion.cpp, primitives/Torsion.hpp, |
| 944 |
> |
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
| 945 |
> |
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
| 946 |
> |
profiling/timing.F90, restraints/Restraints.cpp, |
| 947 |
> |
restraints/Restraints.hpp, |
| 948 |
> |
restraints/ThermoIntegrationForceManager.cpp, |
| 949 |
> |
restraints/ThermoIntegrationForceManager.hpp, |
| 950 |
> |
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
| 951 |
> |
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
| 952 |
> |
selection/NameFinder.cpp, selection/NameFinder.hpp, |
| 953 |
> |
selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, |
| 954 |
> |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
| 955 |
> |
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
| 956 |
> |
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, |
| 957 |
> |
selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, |
| 958 |
> |
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
| 959 |
> |
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
| 960 |
> |
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
| 961 |
> |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
| 962 |
> |
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
| 963 |
> |
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
| 964 |
> |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 965 |
> |
types/DirectionalAtomType.hpp, types/FixedBondType.hpp, |
| 966 |
> |
types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, |
| 967 |
> |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
| 968 |
> |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 969 |
> |
types/MorseBondType.hpp, types/OplsTorsionType.hpp, |
| 970 |
> |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
| 971 |
> |
types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, |
| 972 |
> |
types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, |
| 973 |
> |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
| 974 |
> |
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
| 975 |
> |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
| 976 |
> |
types/TorsionType.hpp, types/UreyBradleyBendType.hpp, |
| 977 |
> |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, |
| 978 |
> |
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
| 979 |
> |
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
| 980 |
> |
utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, |
| 981 |
> |
utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, |
| 982 |
> |
utils/PropertyMap.cpp, utils/PropertyMap.hpp, |
| 983 |
> |
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
| 984 |
> |
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
| 985 |
> |
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
| 986 |
> |
utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, |
| 987 |
> |
utils/any.hpp, utils/definitions.F90, utils/fError.c, |
| 988 |
> |
utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, |
| 989 |
> |
utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, |
| 990 |
> |
utils/residentMem.h, utils/simError.c, utils/simError.h, |
| 991 |
> |
utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, |
| 992 |
> |
visitors/AtomData.hpp, visitors/AtomVisitor.cpp, |
| 993 |
> |
visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, |
| 994 |
> |
visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, |
| 995 |
> |
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
| 996 |
> |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, |
| 997 |
> |
visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, |
| 998 |
> |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has |
| 999 |
> |
been drafted to perform our indentation services |
| 1000 |
> |
|
| 1001 |
> |
2005-04-15 17:03 gezelter |
| 1002 |
> |
|
| 1003 |
> |
* configure, ac-tools/configure.in: Jedi mind-trick warning |
| 1004 |
> |
messages have been added to make users ignore CGAL. |
| 1005 |
> |
|
| 1006 |
> |
2005-04-15 13:41 tim |
| 1007 |
> |
|
| 1008 |
> |
* make/Makefile.in: fix make install |
| 1009 |
> |
|
| 1010 |
> |
2005-04-15 13:41 tim |
| 1011 |
> |
|
| 1012 |
> |
* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: |
| 1013 |
> |
add Makefile of samples |
| 1014 |
> |
|
| 1015 |
> |
2005-04-15 13:33 tim |
| 1016 |
> |
|
| 1017 |
> |
* samples/: lipid/Makefile, water/dimer/Makefile, |
| 1018 |
> |
water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not |
| 1019 |
> |
installed correctly |
| 1020 |
> |
|
| 1021 |
> |
2005-04-14 16:41 gezelter |
| 1022 |
> |
|
| 1023 |
> |
* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1024 |
> |
make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, |
| 1025 |
> |
scripts/filepp, scripts/filepp.in: configure now searches for perl |
| 1026 |
> |
to use with filepp |
| 1027 |
> |
|
| 1028 |
> |
2005-04-14 16:20 gezelter |
| 1029 |
> |
|
| 1030 |
> |
* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |
| 1031 |
> |
MoLocator |
| 1032 |
> |
|
| 1033 |
> |
2005-04-14 14:12 gezelter |
| 1034 |
> |
|
| 1035 |
> |
* LICENSE: [no log message] |
| 1036 |
> |
|
| 1037 |
> |
2005-04-14 11:10 chuckv |
| 1038 |
> |
|
| 1039 |
> |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: |
| 1040 |
> |
nanorodbuilder now exit's when libCGAL is not present. |
| 1041 |
> |
|
| 1042 |
> |
2005-04-14 10:20 tim |
| 1043 |
> |
|
| 1044 |
> |
* src/io/make_nodes.h: fix one more warning message in make_nodes |
| 1045 |
> |
|
| 1046 |
> |
2005-04-13 18:36 chuckv |
| 1047 |
> |
|
| 1048 |
> |
* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed |
| 1049 |
> |
interface name for SGI Compiler |
| 1050 |
> |
|
| 1051 |
> |
2005-04-13 18:29 chrisfen |
| 1052 |
> |
|
| 1053 |
> |
* samples/water/ssde/ssde.md: oops... bad sample |
| 1054 |
> |
|
| 1055 |
> |
2005-04-13 18:00 chuckv |
| 1056 |
> |
|
| 1057 |
> |
* src/config.h.in: Change typo in CGAL. |
| 1058 |
> |
|
| 1059 |
> |
2005-04-13 17:43 tim |
| 1060 |
> |
|
| 1061 |
> |
* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, |
| 1062 |
> |
selection/SelectionCompiler.hpp: fix some warning messages |
| 1063 |
> |
|
| 1064 |
> |
2005-04-13 17:30 gezelter |
| 1065 |
> |
|
| 1066 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1067 |
> |
make/Makefile.in, src/config.h.in, |
| 1068 |
> |
src/applications/nanoRodBuilder/Makefile, |
| 1069 |
> |
src/applications/nanoRodBuilder/Makefile.in, |
| 1070 |
> |
src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL |
| 1071 |
> |
checks |
| 1072 |
> |
|
| 1073 |
> |
2005-04-13 15:36 chuckv |
| 1074 |
> |
|
| 1075 |
> |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, |
| 1076 |
> |
DarkSide/LJ.F90, DarkSide/electrostatic.F90, |
| 1077 |
> |
DarkSide/electrostatic_interface.F90, |
| 1078 |
> |
DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, |
| 1079 |
> |
DarkSide/lj_interface.h, DarkSide/sticky.F90, |
| 1080 |
> |
DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added |
| 1081 |
> |
destroy methods for Fortran modules. |
| 1082 |
> |
|
| 1083 |
> |
2005-04-13 15:17 chuckv |
| 1084 |
> |
|
| 1085 |
> |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, |
| 1086 |
> |
shapes_interface.h: Added destroy method to clean up memory |
| 1087 |
> |
|
| 1088 |
> |
2005-04-13 13:41 tim |
| 1089 |
> |
|
| 1090 |
> |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 1091 |
> |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 1092 |
> |
io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, |
| 1093 |
> |
primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, |
| 1094 |
> |
types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are |
| 1095 |
> |
fixed |
| 1096 |
> |
|
| 1097 |
> |
2005-04-12 17:44 chuckv |
| 1098 |
> |
|
| 1099 |
> |
* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed |
| 1100 |
> |
for nanoRodBuilder. |
| 1101 |
> |
|
| 1102 |
> |
2005-04-12 17:42 tim |
| 1103 |
> |
|
| 1104 |
> |
* src/applications/: nanoRodBuilder/nanorodBuilder.cpp, |
| 1105 |
> |
simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder |
| 1106 |
> |
and simpleBuilder(forget to delete lattice) |
| 1107 |
> |
|
| 1108 |
> |
2005-04-12 17:33 tim |
| 1109 |
> |
|
| 1110 |
> |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 1111 |
> |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: |
| 1112 |
> |
refactory lattice |
| 1113 |
> |
|
| 1114 |
> |
2005-04-12 17:07 tim |
| 1115 |
> |
|
| 1116 |
> |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, |
| 1117 |
> |
CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, |
| 1118 |
> |
Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory |
| 1119 |
> |
LatticeFactory and LatticeCreator |
| 1120 |
> |
|
| 1121 |
> |
2005-04-12 16:58 tim |
| 1122 |
> |
|
| 1123 |
> |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 1124 |
> |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, |
| 1125 |
> |
brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
| 1126 |
> |
lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, |
| 1127 |
> |
lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, |
| 1128 |
> |
lattice/Makefile: refactory LatticeFactory and LatticeCreator |
| 1129 |
> |
|
| 1130 |
> |
2005-04-12 16:28 gezelter |
| 1131 |
> |
|
| 1132 |
> |
* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, |
| 1133 |
> |
vector_class.F90: cleaned up vector_class memory leak fix by |
| 1134 |
> |
deallocating in reverse order of how we allocated. Also migrated |
| 1135 |
> |
MoLocator into utils directory |
| 1136 |
> |
|
| 1137 |
> |
2005-04-12 16:27 gezelter |
| 1138 |
> |
|
| 1139 |
> |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, |
| 1140 |
> |
Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
| 1141 |
> |
LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice |
| 1142 |
> |
directory |
| 1143 |
> |
|
| 1144 |
> |
2005-04-12 16:27 gezelter |
| 1145 |
> |
|
| 1146 |
> |
* src/applications/: nanoRodBuilder/BaseLattice.cpp, |
| 1147 |
> |
nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, |
| 1148 |
> |
nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, |
| 1149 |
> |
nanoRodBuilder/LatticeCreator.hpp, |
| 1150 |
> |
nanoRodBuilder/LatticeFactory.cpp, |
| 1151 |
> |
nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, |
| 1152 |
> |
nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, |
| 1153 |
> |
nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, |
| 1154 |
> |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
| 1155 |
> |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
| 1156 |
> |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
| 1157 |
> |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, |
| 1158 |
> |
simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, |
| 1159 |
> |
simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of |
| 1160 |
> |
these files are now redundant |
| 1161 |
> |
|
| 1162 |
> |
2005-04-12 16:27 gezelter |
| 1163 |
> |
|
| 1164 |
> |
* src/UseTheForce/DarkSide/: atype_interface.F90, |
| 1165 |
> |
atype_interface.h: cleaned up memory leak fix |
| 1166 |
> |
|
| 1167 |
> |
2005-04-12 16:26 gezelter |
| 1168 |
> |
|
| 1169 |
> |
* make/Makefile.in: added lattice subdirectory |
| 1170 |
> |
|
| 1171 |
> |
2005-04-12 15:57 chrisfen |
| 1172 |
> |
|
| 1173 |
> |
* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added |
| 1174 |
> |
a space by accident |
| 1175 |
> |
|
| 1176 |
> |
2005-04-12 15:56 chrisfen |
| 1177 |
> |
|
| 1178 |
> |
* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added |
| 1179 |
> |
quadrupole sample |
| 1180 |
> |
|
| 1181 |
> |
2005-04-12 15:56 chrisfen |
| 1182 |
> |
|
| 1183 |
> |
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating |
| 1184 |
> |
samples |
| 1185 |
> |
|
| 1186 |
> |
2005-04-12 13:30 tim |
| 1187 |
> |
|
| 1188 |
> |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom |
| 1189 |
> |
type in fortran side |
| 1190 |
> |
|
| 1191 |
> |
2005-04-12 12:45 chuckv |
| 1192 |
> |
|
| 1193 |
> |
* src/utils/vector_class.F90: Further changes to vector_class |
| 1194 |
> |
destroy function. |
| 1195 |
> |
|
| 1196 |
> |
2005-04-12 12:39 chuckv |
| 1197 |
> |
|
| 1198 |
> |
* src/utils/vector_class.F90: Fixed pointer memory leak in |
| 1199 |
> |
vector_class. |
| 1200 |
> |
|
| 1201 |
> |
2005-04-12 12:12 chuckv |
| 1202 |
> |
|
| 1203 |
> |
* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, |
| 1204 |
> |
DarkSide/atype_interface.F90, DarkSide/atype_interface.h, |
| 1205 |
> |
DarkSide/eam.F90, DarkSide/eam_interface.F90, |
| 1206 |
> |
DarkSide/eam_interface.h: Updates to deallocate object in fortran. |
| 1207 |
> |
|
| 1208 |
> |
2005-04-12 09:24 chrisfen |
| 1209 |
> |
|
| 1210 |
> |
* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI |
| 1211 |
> |
output |
| 1212 |
> |
|
| 1213 |
> |
2005-04-11 19:29 chuckv |
| 1214 |
> |
|
| 1215 |
> |
* src/: UseTheForce/DarkSide/atype.F90, |
| 1216 |
> |
applications/nanoRodBuilder/Makefile: Changes to delete atypes... |
| 1217 |
> |
|
| 1218 |
> |
2005-04-11 19:28 chuckv |
| 1219 |
> |
|
| 1220 |
> |
* src/utils/vector_class.F90: Added code to delete vector. |
| 1221 |
> |
|
| 1222 |
> |
2005-04-11 17:03 chuckv |
| 1223 |
> |
|
| 1224 |
> |
* samples/metals/nanorod/: Au_nanoparticle.md, |
| 1225 |
> |
Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why |
| 1226 |
> |
aren't these here? |
| 1227 |
> |
|
| 1228 |
> |
2005-04-11 16:58 tim |
| 1229 |
> |
|
| 1230 |
> |
* src/io/basic_ifstrstream.hpp: avoid multiple inherit in |
| 1231 |
> |
basic_ifstrstream |
| 1232 |
> |
|
| 1233 |
> |
2005-04-11 16:37 chuckv |
| 1234 |
> |
|
| 1235 |
> |
* make/Makefile.in, |
| 1236 |
> |
src/applications/nanoRodBuilder/BaseLattice.cpp, |
| 1237 |
> |
src/applications/nanoRodBuilder/BaseLattice.hpp, |
| 1238 |
> |
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
| 1239 |
> |
src/applications/nanoRodBuilder/GeometryBuilder.hpp, |
| 1240 |
> |
src/applications/nanoRodBuilder/Lattice.cpp, |
| 1241 |
> |
src/applications/nanoRodBuilder/Lattice.hpp, |
| 1242 |
> |
src/applications/nanoRodBuilder/LatticeCreator.cpp, |
| 1243 |
> |
src/applications/nanoRodBuilder/LatticeCreator.hpp, |
| 1244 |
> |
src/applications/nanoRodBuilder/LatticeFactory.cpp, |
| 1245 |
> |
src/applications/nanoRodBuilder/LatticeFactory.hpp, |
| 1246 |
> |
src/applications/nanoRodBuilder/Makefile, |
| 1247 |
> |
src/applications/nanoRodBuilder/MoLocator.cpp, |
| 1248 |
> |
src/applications/nanoRodBuilder/MoLocator.hpp, |
| 1249 |
> |
src/applications/nanoRodBuilder/nanoBuilder.ggo, |
| 1250 |
> |
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 1251 |
> |
src/applications/nanoRodBuilder/nanorodBuilder.ggo, |
| 1252 |
> |
src/applications/nanoRodBuilder/nanorodBuilderCmd.c, |
| 1253 |
> |
src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing |
| 1254 |
> |
nanoRodBuilder application (may not work yet). ((Doesn't work |
| 1255 |
> |
yet.)) (((May never work....))) |
| 1256 |
> |
|
| 1257 |
> |
2005-04-11 15:54 tim |
| 1258 |
> |
|
| 1259 |
> |
* src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete |
| 1260 |
> |
prepareVisitor in Dump2XYZ |
| 1261 |
> |
|
| 1262 |
> |
2005-04-11 15:19 chrisfen |
| 1263 |
> |
|
| 1264 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: fixing of the |
| 1265 |
> |
quadrupoles. look! it's divide by 3 like stone says! |
| 1266 |
> |
|
| 1267 |
> |
2005-04-11 15:18 chrisfen |
| 1268 |
> |
|
| 1269 |
> |
* forceFields/DUFF2.frc: fixing of the quadrupoles |
| 1270 |
> |
|
| 1271 |
> |
2005-04-11 15:16 tim |
| 1272 |
> |
|
| 1273 |
> |
* src/selection/Token.hpp: change the parameter name in |
| 1274 |
> |
constructors |
| 1275 |
> |
|
| 1276 |
> |
2005-04-11 14:49 gezelter |
| 1277 |
> |
|
| 1278 |
> |
* make/Makefile.in: One more bug fix for GNU make versions < 3.80 |
| 1279 |
> |
|
| 1280 |
> |
2005-04-11 14:06 gezelter |
| 1281 |
> |
|
| 1282 |
> |
* make/Makefile.in: Fixed the uc and lc functions for GNU make |
| 1283 |
> |
versions < 3.80 |
| 1284 |
> |
|
| 1285 |
> |
2005-04-11 11:13 gezelter |
| 1286 |
> |
|
| 1287 |
> |
* make/Makefile.in, src/UseTheForce/Makefile, |
| 1288 |
> |
src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added |
| 1289 |
> |
some stuff to clean out module files during "make clean" |
| 1290 |
> |
|
| 1291 |
> |
2005-04-08 17:13 chrisfen |
| 1292 |
> |
|
| 1293 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: quadrupole |
| 1294 |
> |
interactions should be working with a remaining question of |
| 1295 |
> |
interaction magnitude |
| 1296 |
> |
|
| 1297 |
> |
2005-04-08 17:12 chrisfen |
| 1298 |
> |
|
| 1299 |
> |
* samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with |
| 1300 |
> |
samples |
| 1301 |
> |
|
| 1302 |
> |
2005-04-08 13:48 chrisfen |
| 1303 |
> |
|
| 1304 |
> |
* samples/water/ssd/ssd.md: oops... messed up a sample |
| 1305 |
> |
|
| 1306 |
> |
2005-04-08 09:43 chrisfen |
| 1307 |
> |
|
| 1308 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix |
| 1309 |
> |
charge-dipole interactions |
| 1310 |
> |
|
| 1311 |
> |
2005-04-08 09:42 chrisfen |
| 1312 |
> |
|
| 1313 |
> |
* samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md, |
| 1314 |
> |
ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole |
| 1315 |
> |
|
| 1316 |
> |
2005-04-08 09:41 chrisfen |
| 1317 |
> |
|
| 1318 |
> |
* forceFields/DUFF2.frc: added Cl- and Na+ |
| 1319 |
> |
|
| 1320 |
> |
2005-04-06 18:59 tim |
| 1321 |
> |
|
| 1322 |
> |
* src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser |
| 1323 |
> |
|
| 1324 |
> |
2005-04-05 18:09 tim |
| 1325 |
> |
|
| 1326 |
> |
* src/selection/: NameFinder.cpp, SelectionCompiler.cpp, |
| 1327 |
> |
SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-' |
| 1328 |
> |
in atom type name;clean the code a little bit |
| 1329 |
> |
|
| 1330 |
> |
2005-03-29 16:00 tim |
| 1331 |
> |
|
| 1332 |
> |
* src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug |
| 1333 |
> |
in converting rotation matrix to quaternion |
| 1334 |
> |
|
| 1335 |
> |
2005-03-28 17:41 tim |
| 1336 |
> |
|
| 1337 |
> |
* src/visitors/LipidTransVisitor.cpp: fixed the wrapping |
| 1338 |
> |
|
| 1339 |
> |
2005-03-28 17:30 tim |
| 1340 |
> |
|
| 1341 |
> |
* src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do |
| 1342 |
> |
the wrapping |
| 1343 |
> |
|
| 1344 |
> |
2005-03-28 10:54 tim |
| 1345 |
> |
|
| 1346 |
> |
* src/applications/staticProps/GofXyz.cpp: fix a bug in getting the |
| 1347 |
> |
dimension of histogram |
| 1348 |
> |
|
| 1349 |
> |
2005-03-22 11:38 tim |
| 1350 |
> |
|
| 1351 |
> |
* make/Makefile.in, src/applications/dump2Xyz/Makefile, |
| 1352 |
> |
src/applications/dynamicProps/Makefile, |
| 1353 |
> |
src/applications/oopse/Makefile, |
| 1354 |
> |
src/applications/simpleBuilder/Makefile, |
| 1355 |
> |
src/applications/staticProps/Makefile: avoid building parallel |
| 1356 |
> |
executable for dump2XYZ, simpleBuilder, staticProps and |
| 1357 |
> |
dynamicProps |
| 1358 |
> |
|
| 1359 |
> |
2005-03-21 17:34 chrisfen |
| 1360 |
> |
|
| 1361 |
> |
* forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the |
| 1362 |
> |
forcefield files |
| 1363 |
> |
|
| 1364 |
> |
2005-03-21 15:51 chrisfen |
| 1365 |
> |
|
| 1366 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
| 1367 |
> |
DarkSide/reactionField.F90: Make sure electrostatic_module provides |
| 1368 |
> |
data for reaction_field |
| 1369 |
> |
|
| 1370 |
> |
2005-03-21 15:50 chrisfen |
| 1371 |
> |
|
| 1372 |
> |
* forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff. HE |
| 1373 |
> |
WILL CHANGE THIS BACK, RIGHT? |
| 1374 |
> |
|
| 1375 |
> |
2005-03-21 14:23 gezelter |
| 1376 |
> |
|
| 1377 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: constant back to |
| 1378 |
> |
correct value |
| 1379 |
> |
|
| 1380 |
> |
2005-03-21 14:22 gezelter |
| 1381 |
> |
|
| 1382 |
> |
* make/Makefile.in: fixed an install-related bug. |
| 1383 |
> |
$(InstallCommand) had been set to $(InstallData) |
| 1384 |
> |
|
| 1385 |
> |
2005-03-15 09:21 gezelter |
| 1386 |
> |
|
| 1387 |
> |
* src/integrators/Integrator.cpp: VelocityVerletIntegrator already |
| 1388 |
> |
deletes and Nullifies restWriter, so Integrator shouldn't do it. |
| 1389 |
> |
|
| 1390 |
> |
2005-03-15 09:20 gezelter |
| 1391 |
> |
|
| 1392 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos |
| 1393 |
> |
|
| 1394 |
> |
2005-03-13 02:39 gezelter |
| 1395 |
> |
|
| 1396 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: first run at |
| 1397 |
> |
charge-quadrupole interactions |
| 1398 |
> |
|
| 1399 |
> |
2005-03-12 14:12 chrisfen |
| 1400 |
> |
|
| 1401 |
> |
* samples/: Makefile.in, thermoIntegration/liquid/Makefile, |
| 1402 |
> |
thermoIntegration/solid/Makefile: forgot a couple of makefiles |
| 1403 |
> |
|
| 1404 |
> |
2005-03-12 14:05 chrisfen |
| 1405 |
> |
|
| 1406 |
> |
* samples/thermoIntegration/liquid/ssde.in, |
| 1407 |
> |
samples/thermoIntegration/liquid/ssde.md, |
| 1408 |
> |
samples/thermoIntegration/liquid/water.md, |
| 1409 |
> |
samples/thermoIntegration/solid/idealCrystal.in, |
| 1410 |
> |
samples/thermoIntegration/solid/ssde.in, |
| 1411 |
> |
samples/thermoIntegration/solid/ssde.md, |
| 1412 |
> |
samples/thermoIntegration/solid/ssde.zang0, |
| 1413 |
> |
samples/thermoIntegration/solid/water.md, |
| 1414 |
> |
samples/water/tip3p_ice/tp3.md, |
| 1415 |
> |
src/UseTheForce/DarkSide/sticky.F90, |
| 1416 |
> |
src/restraints/ThermoIntegrationForceManager.cpp: added some |
| 1417 |
> |
samples |
| 1418 |
> |
|
| 1419 |
> |
2005-03-11 12:50 tim |
| 1420 |
> |
|
| 1421 |
> |
* src/: brains/SimCreator.cpp, |
| 1422 |
> |
io/MultipoleAtomTypesSectionParser.cpp: fix a typo in |
| 1423 |
> |
MultipoleAtomTypesSectionParser |
| 1424 |
> |
|
| 1425 |
> |
2005-03-11 10:55 tim |
| 1426 |
> |
|
| 1427 |
> |
* src/brains/SimInfo.cpp: pairs inside cutoff group should not be |
| 1428 |
> |
excluded |
| 1429 |
> |
|
| 1430 |
> |
2005-03-11 10:53 gezelter |
| 1431 |
> |
|
| 1432 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for |
| 1433 |
> |
quadrupoles |
| 1434 |
> |
|
| 1435 |
> |
2005-03-11 10:52 gezelter |
| 1436 |
> |
|
| 1437 |
> |
* forceFields/DUFF2.frc: quadrupoles for SSD models |
| 1438 |
> |
|
| 1439 |
> |
2005-03-11 10:00 tim |
| 1440 |
> |
|
| 1441 |
> |
* ChangeLog, doc/SelectionExpression.html, |
| 1442 |
> |
doc/classoopse_1_1StuntDouble.png, doc/definition.jpg, |
| 1443 |
> |
doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png, |
| 1444 |
> |
src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp, |
| 1445 |
> |
src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp, |
| 1446 |
> |
src/selection/TokenMap.cpp: clean up SimInfo; modify the images of |
| 1447 |
> |
SelectionExpression.html |
| 1448 |
> |
|
| 1449 |
> |
2005-03-10 19:43 chrisfen |
| 1450 |
> |
|
| 1451 |
> |
* samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md, |
| 1452 |
> |
src/io/RestReader.cpp, src/restraints/Restraints.cpp, |
| 1453 |
> |
src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in |
| 1454 |
> |
MPI restraints |
| 1455 |
> |
|
| 1456 |
> |
2005-03-10 18:56 tim |
| 1457 |
> |
|
| 1458 |
> |
* doc/SelectionExpression.html, src/brains/SimInfo.cpp, |
| 1459 |
> |
src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody |
| 1460 |
> |
and cutoff group |
| 1461 |
> |
|
| 1462 |
> |
2005-03-10 17:06 gezelter |
| 1463 |
> |
|
| 1464 |
> |
* src/types/MorseBondType.hpp: fixed a doxygen problem |
| 1465 |
> |
|
| 1466 |
> |
2005-03-10 16:51 gezelter |
| 1467 |
> |
|
| 1468 |
> |
* samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with |
| 1469 |
> |
the split dipole test cases |
| 1470 |
> |
|
| 1471 |
> |
2005-03-10 16:51 gezelter |
| 1472 |
> |
|
| 1473 |
> |
* doc/SelectionExpression.html: updated some documentation |
| 1474 |
> |
|
| 1475 |
> |
2005-03-10 15:40 gezelter |
| 1476 |
> |
|
| 1477 |
> |
* src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp, |
| 1478 |
> |
Makefile: LinkedList removal project starts now |
| 1479 |
> |
|
| 1480 |
> |
2005-03-10 15:28 tim |
| 1481 |
> |
|
| 1482 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 1483 |
> |
io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp: |
| 1484 |
> |
using map to replace link list |
| 1485 |
> |
|
| 1486 |
> |
2005-03-10 14:11 tim |
| 1487 |
> |
|
| 1488 |
> |
* samples/dipole/: splitInWater.in, splitInWater.md: adding test |
| 1489 |
> |
case of split dipole |
| 1490 |
> |
|
| 1491 |
> |
2005-03-10 14:10 chrisfen |
| 1492 |
> |
|
| 1493 |
> |
* samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, |
| 1494 |
> |
src/io/RestWriter.cpp, |
| 1495 |
> |
src/restraints/ThermoIntegrationForceManager.cpp: Oops... MPI now |
| 1496 |
> |
builds... |
| 1497 |
> |
|
| 1498 |
> |
2005-03-10 13:44 tim |
| 1499 |
> |
|
| 1500 |
> |
* samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in, |
| 1501 |
> |
split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md: |
| 1502 |
> |
adding test case for split dipole |
| 1503 |
> |
|
| 1504 |
> |
2005-03-10 12:54 gezelter |
| 1505 |
> |
|
| 1506 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side |
| 1507 |
> |
support for split dipoles |
| 1508 |
> |
|
| 1509 |
> |
2005-03-10 11:27 chrisfen |
| 1510 |
> |
|
| 1511 |
> |
* samples/water/tip3p_ice/tp3.md, |
| 1512 |
> |
src/restraints/ThermoIntegrationForceManager.cpp: fixes to |
| 1513 |
> |
restraints |
| 1514 |
> |
|
| 1515 |
> |
2005-03-10 11:15 chrisfen |
| 1516 |
> |
|
| 1517 |
> |
* samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp, |
| 1518 |
> |
src/UseTheForce/ForceFields.hpp, |
| 1519 |
> |
src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints |
| 1520 |
> |
|
| 1521 |
> |
2005-03-10 11:14 tim |
| 1522 |
> |
|
| 1523 |
> |
* ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc, |
| 1524 |
> |
src/io/MultipoleAtomTypesSectionParser.cpp, |
| 1525 |
> |
src/selection/SelectionEvaluator.cpp: minor change |
| 1526 |
> |
|
| 1527 |
> |
2005-03-10 10:10 chrisfen |
| 1528 |
> |
|
| 1529 |
> |
* make/Makefile.in, samples/water/tip3p_ice/tp3.md, |
| 1530 |
> |
src/brains/SimCreator.cpp, src/brains/SimInfo.hpp, |
| 1531 |
> |
src/integrators/Integrator.cpp, src/integrators/Integrator.hpp, |
| 1532 |
> |
src/integrators/VelocityVerletIntegrator.cpp, |
| 1533 |
> |
src/integrators/VelocityVerletIntegrator.hpp, |
| 1534 |
> |
src/io/DumpReader.cpp, src/io/Globals.cpp, src/io/Globals.hpp, |
| 1535 |
> |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/RestReader.cpp, |
| 1536 |
> |
src/io/RestReader.hpp, src/io/RestWriter.cpp, |
| 1537 |
> |
src/io/RestWriter.hpp, src/io/RestraintReader.cpp, |
| 1538 |
> |
src/io/RestraintWriter.cpp, src/restraints/Makefile, |
| 1539 |
> |
src/restraints/Restraints.cpp, src/restraints/Restraints.hpp, |
| 1540 |
> |
src/restraints/ThermoIntegrationForceManager.cpp, |
| 1541 |
> |
src/restraints/ThermoIntegrationForceManager.hpp: First commit of |
| 1542 |
> |
the new restraints code |
| 1543 |
> |
|
| 1544 |
> |
2005-03-09 13:48 tim |
| 1545 |
> |
|
| 1546 |
> |
* src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding |
| 1547 |
> |
IndexFinder |
| 1548 |
> |
|
| 1549 |
> |
2005-03-09 13:46 tim |
| 1550 |
> |
|
| 1551 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.ggo, |
| 1552 |
> |
applications/dump2Xyz/Dump2XYZCmd.c, |
| 1553 |
> |
applications/dump2Xyz/Dump2XYZCmd.h, |
| 1554 |
> |
selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp: |
| 1555 |
> |
fix compilation issue |
| 1556 |
> |
|
| 1557 |
> |
2005-03-09 12:58 tim |
| 1558 |
> |
|
| 1559 |
> |
* forceFields/DUFF2.frc, scripts/filepp, |
| 1560 |
> |
src/UseTheForce/EAM_FF.cpp, |
| 1561 |
> |
src/io/MultipoleAtomTypesSectionParser.cpp, |
| 1562 |
> |
src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug |
| 1563 |
> |
in SectionParser (lineNo is not updated) |
| 1564 |
> |
|
| 1565 |
> |
2005-03-09 12:30 tim |
| 1566 |
> |
|
| 1567 |
> |
* src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, |
| 1568 |
> |
applications/dump2Xyz/Dump2XYZ.ggo, |
| 1569 |
> |
applications/dump2Xyz/Dump2XYZCmd.c, |
| 1570 |
> |
applications/dump2Xyz/Dump2XYZCmd.h, brains/SimInfo.cpp, |
| 1571 |
> |
brains/SimInfo.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 1572 |
> |
io/ChargeAtomTypesSectionParser.hpp, |
| 1573 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 1574 |
> |
io/ElectrostaticAtomTypesSectionParser.hpp, io/Makefile, |
| 1575 |
> |
io/MultipoleAtomTypesSectionParser.cpp, |
| 1576 |
> |
io/MultipoleAtomTypesSectionParser.hpp, |
| 1577 |
> |
io/SectionParserManager.cpp, selection/Makefile, |
| 1578 |
> |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
| 1579 |
> |
types/AtomType.cpp, types/DirectionalAtomType.cpp, |
| 1580 |
> |
visitors/AtomVisitor.cpp, visitors/OtherVisitor.cpp, |
| 1581 |
> |
visitors/OtherVisitor.hpp: adding IndexFinder which is used to |
| 1582 |
> |
select the molecules; Seperate ElectrostaticAtomTypesSectionParser |
| 1583 |
> |
into ChargeAtomTypesSectionParser and |
| 1584 |
> |
MultipoleAtomTypesSectionParser;remove print dipole option from |
| 1585 |
> |
Dump2XYZ; |
| 1586 |
> |
|
| 1587 |
> |
2005-03-09 12:28 tim |
| 1588 |
> |
|
| 1589 |
> |
* forceFields/DUFF2.frc: change the format of DUFF2 |
| 1590 |
> |
|
| 1591 |
> |
2005-03-09 10:44 gezelter |
| 1592 |
> |
|
| 1593 |
> |
* src/UseTheForce/DarkSide/: electrostatic.F90, |
| 1594 |
> |
electrostatic_interface.F90, electrostatic_interface.h: new |
| 1595 |
> |
electrostatic module |
| 1596 |
> |
|
| 1597 |
> |
2005-03-09 09:26 gezelter |
| 1598 |
> |
|
| 1599 |
> |
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
| 1600 |
> |
DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole |
| 1601 |
> |
and fixed quadrupole stuff |
| 1602 |
> |
|
| 1603 |
> |
2005-03-09 09:25 gezelter |
| 1604 |
> |
|
| 1605 |
> |
* src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines |
| 1606 |
> |
for outdated charge and dipole interfaces |
| 1607 |
> |
|
| 1608 |
> |
2005-03-08 16:08 gezelter |
| 1609 |
> |
|
| 1610 |
> |
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in, |
| 1611 |
> |
mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun |
| 1612 |
> |
charge-dipole test cases |
| 1613 |
> |
|
| 1614 |
> |
2005-03-08 16:07 gezelter |
| 1615 |
> |
|
| 1616 |
> |
* src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp, |
| 1617 |
> |
OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a |
| 1618 |
> |
strange icc8 bug (we think). |
| 1619 |
> |
|
| 1620 |
> |
2005-03-08 16:07 gezelter |
| 1621 |
> |
|
| 1622 |
> |
* src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa! |
| 1623 |
> |
|
| 1624 |
> |
2005-03-08 16:07 gezelter |
| 1625 |
> |
|
| 1626 |
> |
* src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic |
| 1627 |
> |
Unification Project |
| 1628 |
> |
|
| 1629 |
> |
2005-03-08 16:07 gezelter |
| 1630 |
> |
|
| 1631 |
> |
* src/io/Globals.cpp: Dunno |
| 1632 |
> |
|
| 1633 |
> |
2005-03-08 16:06 gezelter |
| 1634 |
> |
|
| 1635 |
> |
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using |
| 1636 |
> |
OOPSE_itoa and checking a NULL left over from the LinkedList days |
| 1637 |
> |
|
| 1638 |
> |
2005-03-08 16:06 gezelter |
| 1639 |
> |
|
| 1640 |
> |
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
| 1641 |
> |
atype_interface.F90, atype_interface.h, charge.F90, |
| 1642 |
> |
charge_interface.F90, charge_interface.h, dipole.F90, |
| 1643 |
> |
dipole_interface.F90, dipole_interface.h: electrostatic unification |
| 1644 |
> |
project fixed an uninitialized variable in Lennard Jones mixing map |
| 1645 |
> |
|
| 1646 |
> |
2005-03-08 16:05 gezelter |
| 1647 |
> |
|
| 1648 |
> |
* src/UseTheForce/doForces.F90: electrostatic unification project |
| 1649 |
> |
|
| 1650 |
> |
2005-03-08 16:05 gezelter |
| 1651 |
> |
|
| 1652 |
> |
* samples/water/dimer/: two.md, water.md: making some cool test |
| 1653 |
> |
cases |
| 1654 |
> |
|
| 1655 |
> |
2005-03-08 16:05 gezelter |
| 1656 |
> |
|
| 1657 |
> |
* forceFields/DUFF2.frc: Added a charge for Chlorine |
| 1658 |
> |
|
| 1659 |
> |
2005-03-07 17:39 tim |
| 1660 |
> |
|
| 1661 |
> |
* src/: brains/SimInfo.cpp, io/DumpReader.cpp, |
| 1662 |
> |
math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp, |
| 1663 |
> |
primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp: |
| 1664 |
> |
Fixing a bug in BitSet.cpp |
| 1665 |
> |
|
| 1666 |
> |
2005-03-04 10:28 gezelter |
| 1667 |
> |
|
| 1668 |
> |
* src/config.h.in: Cleaning up config.h.in by adding comments |
| 1669 |
> |
|
| 1670 |
> |
2005-03-04 10:28 gezelter |
| 1671 |
> |
|
| 1672 |
> |
* configure, ac-tools/configure.in, make/Makefile.in, |
| 1673 |
> |
src/brains/SimCreator.cpp: SPRNG eradication project |
| 1674 |
> |
|
| 1675 |
> |
2005-03-03 09:40 tim |
| 1676 |
> |
|
| 1677 |
> |
* src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the |
| 1678 |
> |
missing atom type problem) |
| 1679 |
> |
|
| 1680 |
> |
2005-03-02 11:29 tim |
| 1681 |
> |
|
| 1682 |
> |
* src/math/RandNumGen.hpp: adding base class of Random Number |
| 1683 |
> |
generator |
| 1684 |
> |
|
| 1685 |
> |
2005-03-02 11:28 tim |
| 1686 |
> |
|
| 1687 |
> |
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
| 1688 |
> |
math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in |
| 1689 |
> |
Velocitizer is not initialized which causes a seg fault |
| 1690 |
> |
|
| 1691 |
> |
2005-03-02 10:36 tim |
| 1692 |
> |
|
| 1693 |
> |
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
| 1694 |
> |
integrators/Velocitizer.hpp, math/Makefile, |
| 1695 |
> |
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
| 1696 |
> |
math/ParallelRandNumGen.hpp, math/SeqRandNumGen.cpp, |
| 1697 |
> |
math/SeqRandNumGen.hpp: remove default parameter from |
| 1698 |
> |
MersenneTwister.hpp which causes all kinds of trouble. Refactory |
| 1699 |
> |
random number generator |
| 1700 |
> |
|
| 1701 |
> |
2005-03-02 02:32 tim |
| 1702 |
> |
|
| 1703 |
> |
* test/math/testRandNumGen.cpp: Adding unit test for random number |
| 1704 |
> |
generator |
| 1705 |
> |
|
| 1706 |
> |
2005-03-01 18:17 tim |
| 1707 |
> |
|
| 1708 |
> |
* src/brains/Thermo.hpp: fixed a file inclusion problem |
| 1709 |
> |
|
| 1710 |
> |
2005-03-01 18:17 tim |
| 1711 |
> |
|
| 1712 |
> |
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
| 1713 |
> |
OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp, |
| 1714 |
> |
ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp, |
| 1715 |
> |
RandNumGenTestCase.hpp: fixed compilation problem |
| 1716 |
> |
|
| 1717 |
> |
2005-03-01 18:02 tim |
| 1718 |
> |
|
| 1719 |
> |
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
| 1720 |
> |
integrators/Velocitizer.hpp, math/Makefile, |
| 1721 |
> |
math/OOPSERandNumGen.hpp, math/ParallelRandNumGen.cpp, |
| 1722 |
> |
math/ParallelRandNumGen.hpp, math/mt19937ar.c, |
| 1723 |
> |
math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand |
| 1724 |
> |
|
| 1725 |
> |
2005-03-01 18:00 tim |
| 1726 |
> |
|
| 1727 |
> |
* test/math/: Makefile, ParallelandNumGenTestCase.cpp, |
| 1728 |
> |
ParallelandNumGenTestCase.hpp: Change the name of test case |
| 1729 |
> |
|
| 1730 |
> |
2005-03-01 16:00 tim |
| 1731 |
> |
|
| 1732 |
> |
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
| 1733 |
> |
OOPSERandNumGenTestCase.hpp: adding testcase for random number |
| 1734 |
> |
generator |
| 1735 |
> |
|
| 1736 |
> |
2005-03-01 15:10 tim |
| 1737 |
> |
|
| 1738 |
> |
* src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp, |
| 1739 |
> |
integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp, |
| 1740 |
> |
math/Polynomial.hpp, math/Quaternion.hpp, math/RectMatrix.hpp, |
| 1741 |
> |
math/SquareMatrix.hpp, math/SquareMatrix3.hpp, math/Vector.hpp, |
| 1742 |
> |
math/Vector3.hpp, minimizers/MinimizerCreator.hpp, |
| 1743 |
> |
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
| 1744 |
> |
utils/TypeContainer.hpp, visitors/AtomVisitor.cpp, |
| 1745 |
> |
visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4 |
| 1746 |
> |
|
| 1747 |
> |
2005-03-01 14:11 tim |
| 1748 |
> |
|
| 1749 |
> |
* src/: brains/SimCreator.cpp, brains/SimInfo.hpp, |
| 1750 |
> |
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
| 1751 |
> |
math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding |
| 1752 |
> |
OOPSERandNumGen |
| 1753 |
> |
|
| 1754 |
> |
2005-03-01 10:44 gezelter |
| 1755 |
> |
|
| 1756 |
> |
* make/Makefile.in: Fixed the damned build problem with the |
| 1757 |
> |
libraries not being removed in make clean and make distclean (at |
| 1758 |
> |
least we think it is fixed). |
| 1759 |
> |
|
| 1760 |
> |
2005-03-01 10:26 gezelter |
| 1761 |
> |
|
| 1762 |
> |
* src/math/MersenneTwister.hpp: Making small modifications to allow |
| 1763 |
> |
for use on MPI machines |
| 1764 |
> |
|
| 1765 |
> |
2005-03-01 09:45 tim |
| 1766 |
> |
|
| 1767 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp, |
| 1768 |
> |
integrators/Velocitizer.cpp, io/DumpReader.cpp, |
| 1769 |
> |
math/MersenneTwister.hpp: adding MersenneTwister random number |
| 1770 |
> |
generator |
| 1771 |
> |
|
| 1772 |
> |
2005-02-28 22:55 tim |
| 1773 |
> |
|
| 1774 |
> |
* src/math/MersenneTwister.hpp: Adding a modified version of |
| 1775 |
> |
MersenneTwister.hpp |
| 1776 |
> |
|
| 1777 |
> |
2005-02-28 12:24 tim |
| 1778 |
> |
|
| 1779 |
> |
* doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png, |
| 1780 |
> |
definition.jpg: selection expression |
| 1781 |
> |
|
| 1782 |
> |
2005-02-25 16:22 tim |
| 1783 |
> |
|
| 1784 |
> |
* src/: UseTheForce/DarkSide/LJ.F90, |
| 1785 |
> |
UseTheForce/DarkSide/lj_interface.F90, |
| 1786 |
> |
UseTheForce/DarkSide/lj_interface.h, |
| 1787 |
> |
io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp, |
| 1788 |
> |
types/AtomType.hpp: adding soft potential to LJ Module |
| 1789 |
> |
|
| 1790 |
> |
2005-02-25 11:38 tim |
| 1791 |
> |
|
| 1792 |
> |
* doc/SelectionExpression.html: adding documentation for selection |
| 1793 |
> |
expression |
| 1794 |
> |
|
| 1795 |
> |
2005-02-24 15:55 tim |
| 1796 |
> |
|
| 1797 |
> |
* src/: applications/simpleBuilder/simpleBuilder.cpp, |
| 1798 |
> |
integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp, |
| 1799 |
> |
io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp: |
| 1800 |
> |
adding basic_teebuf which can operate on multiple stream |
| 1801 |
> |
simutaneously. |
| 1802 |
> |
|
| 1803 |
> |
2005-02-22 14:26 chrisfen |
| 1804 |
> |
|
| 1805 |
> |
* samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf |
| 1806 |
> |
sample |
| 1807 |
> |
|
| 1808 |
> |
2005-02-22 13:56 tim |
| 1809 |
> |
|
| 1810 |
> |
* src/: UseTheForce/DarkSide/reactionField.F90, |
| 1811 |
> |
primitives/RigidBody.cpp: reactionfield get fixed |
| 1812 |
> |
|
| 1813 |
> |
2005-02-21 11:57 tim |
| 1814 |
> |
|
| 1815 |
> |
* src/: applications/staticProps/GofRAngle.cpp, |
| 1816 |
> |
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix |
| 1817 |
> |
a bug in GofRAngle |
| 1818 |
> |
|
| 1819 |
> |
2005-02-21 10:28 tim |
| 1820 |
> |
|
| 1821 |
> |
* src/primitives/Molecule.cpp: Fix for compilation on the Sun |
| 1822 |
> |
|
| 1823 |
> |
2005-02-21 10:22 tim |
| 1824 |
> |
|
| 1825 |
> |
* src/utils/next_combination.hpp: fix for compilation on the Sun |
| 1826 |
> |
|
| 1827 |
> |
2005-02-21 10:21 tim |
| 1828 |
> |
|
| 1829 |
> |
* src/utils/GenericData.hpp: fix problem in sun |
| 1830 |
> |
|
| 1831 |
> |
2005-02-18 18:07 tim |
| 1832 |
> |
|
| 1833 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 1834 |
> |
applications/dump2Xyz/Dump2XYZ.ggo, |
| 1835 |
> |
applications/dump2Xyz/Dump2XYZCmd.c, |
| 1836 |
> |
applications/dump2Xyz/Dump2XYZCmd.h, |
| 1837 |
> |
applications/dynamicProps/RCorrFunc.cpp, |
| 1838 |
> |
applications/staticProps/GofXyz.cpp, |
| 1839 |
> |
applications/staticProps/GofXyz.hpp, |
| 1840 |
> |
applications/staticProps/StaticProps.cpp, |
| 1841 |
> |
applications/staticProps/StaticProps.ggo, |
| 1842 |
> |
applications/staticProps/StaticPropsCmd.c, |
| 1843 |
> |
applications/staticProps/StaticPropsCmd.h, |
| 1844 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 1845 |
> |
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
| 1846 |
> |
visitors/Makefile: adding LipidTransVisitor, GofXyz is working now |
| 1847 |
> |
|
| 1848 |
> |
2005-02-18 10:58 gezelter |
| 1849 |
> |
|
| 1850 |
> |
* src/brains/Register.cpp: Corrected filename collision for EAM on |
| 1851 |
> |
Mac OS X |
| 1852 |
> |
|
| 1853 |
> |
2005-02-18 10:58 gezelter |
| 1854 |
> |
|
| 1855 |
> |
* src/applications/oopse/oopse.cpp: Updated copyright information |
| 1856 |
> |
|
| 1857 |
> |
2005-02-18 10:58 gezelter |
| 1858 |
> |
|
| 1859 |
> |
* src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp, |
| 1860 |
> |
Makefile: corrected filename collision for EAM on operating systems |
| 1861 |
> |
which are not case sensitive (aka Mac OS X) |
| 1862 |
> |
|
| 1863 |
> |
2005-02-17 15:15 tim |
| 1864 |
> |
|
| 1865 |
> |
* src/applications/staticProps/GofXyz.cpp: more bug get fixed |
| 1866 |
> |
|
| 1867 |
> |
2005-02-17 14:50 tim |
| 1868 |
> |
|
| 1869 |
> |
* src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug |
| 1870 |
> |
in GofXyz |
| 1871 |
> |
|
| 1872 |
> |
2005-02-17 14:09 tim |
| 1873 |
> |
|
| 1874 |
> |
* src/applications/staticProps/RadialDistrFunc.hpp: make |
| 1875 |
> |
processHistogram non-abstrct function |
| 1876 |
> |
|
| 1877 |
> |
2005-02-17 13:41 tim |
| 1878 |
> |
|
| 1879 |
> |
* src/applications/staticProps/GofXyz.cpp: [no log message] |
| 1880 |
> |
|
| 1881 |
> |
2005-02-17 13:30 tim |
| 1882 |
> |
|
| 1883 |
> |
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
| 1884 |
> |
GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: |
| 1885 |
> |
finish GofXyz |
| 1886 |
> |
|
| 1887 |
> |
2005-02-17 11:21 tim |
| 1888 |
> |
|
| 1889 |
> |
* src/applications/staticProps/: GofAngle2.cpp, GofR.cpp, |
| 1890 |
> |
GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial |
| 1891 |
> |
distribution function |
| 1892 |
> |
|
| 1893 |
> |
2005-02-17 10:23 tim |
| 1894 |
> |
|
| 1895 |
> |
* src/utils/BitSet.hpp: forget the const correctness for BitSet |
| 1896 |
> |
|
| 1897 |
> |
2005-02-17 10:18 tim |
| 1898 |
> |
|
| 1899 |
> |
* src/: brains/BlockSnapshotManager.cpp, |
| 1900 |
> |
selection/DistanceFinder.cpp: The change of interface of BitSet |
| 1901 |
> |
cause a bug in SelectionEvaluation |
| 1902 |
> |
|
| 1903 |
> |
2005-02-16 16:13 tim |
| 1904 |
> |
|
| 1905 |
> |
* src/utils/residentMem.c: return residentMem in byte |
| 1906 |
> |
|
| 1907 |
> |
2005-02-16 16:00 tim |
| 1908 |
> |
|
| 1909 |
> |
* src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix |
| 1910 |
> |
a bug in writing out the value of cosang |
| 1911 |
> |
|
| 1912 |
> |
2005-02-16 15:43 tim |
| 1913 |
> |
|
| 1914 |
> |
* src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to |
| 1915 |
> |
estimate avaliable memory |
| 1916 |
> |
|
| 1917 |
> |
2005-02-16 15:30 tim |
| 1918 |
> |
|
| 1919 |
> |
* src/: applications/staticProps/GofAngle2.cpp, |
| 1920 |
> |
applications/staticProps/GofAngle2.hpp, |
| 1921 |
> |
applications/staticProps/GofR.cpp, |
| 1922 |
> |
applications/staticProps/GofR.hpp, |
| 1923 |
> |
applications/staticProps/GofRAngle.cpp, |
| 1924 |
> |
applications/staticProps/GofRAngle.hpp, |
| 1925 |
> |
applications/staticProps/GofXyz.cpp, |
| 1926 |
> |
applications/staticProps/GofXyz.hpp, |
| 1927 |
> |
applications/staticProps/StaticProps.cpp, |
| 1928 |
> |
applications/staticProps/StaticProps.ggo, |
| 1929 |
> |
applications/staticProps/StaticPropsCmd.c, |
| 1930 |
> |
applications/staticProps/StaticPropsCmd.h, |
| 1931 |
> |
brains/BlockSnapshotManager.cpp: change the default bin number |
| 1932 |
> |
|
| 1933 |
> |
2005-02-16 14:36 tim |
| 1934 |
> |
|
| 1935 |
> |
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
| 1936 |
> |
applications/dynamicProps/RCorrFunc.cpp, |
| 1937 |
> |
applications/dynamicProps/TimeCorrFunc.cpp, |
| 1938 |
> |
applications/dynamicProps/VCorrFunc.cpp, |
| 1939 |
> |
applications/staticProps/GofAngle2.cpp, |
| 1940 |
> |
applications/staticProps/GofR.cpp, |
| 1941 |
> |
applications/staticProps/GofR.hpp, |
| 1942 |
> |
applications/staticProps/GofRAngle.cpp, |
| 1943 |
> |
applications/staticProps/GofRAngle.hpp, |
| 1944 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
| 1945 |
> |
applications/staticProps/RadialDistrFunc.hpp, |
| 1946 |
> |
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
| 1947 |
> |
utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output |
| 1948 |
> |
files;fix the problem of counting in staticProps |
| 1949 |
> |
|
| 1950 |
> |
2005-02-15 14:39 tim |
| 1951 |
> |
|
| 1952 |
> |
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
| 1953 |
> |
BlockSnapshotManager |
| 1954 |
> |
|
| 1955 |
> |
2005-02-15 14:36 tim |
| 1956 |
> |
|
| 1957 |
> |
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
| 1958 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
| 1959 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 1960 |
> |
selection/SelectionEvaluator.cpp: BlockSnapshotManager is using |
| 1961 |
> |
reference counting now |
| 1962 |
> |
|
| 1963 |
> |
2005-02-15 12:49 tim |
| 1964 |
> |
|
| 1965 |
> |
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
| 1966 |
> |
replace std::make_pair by VariablesType::value_type to make Sun |
| 1967 |
> |
Compiler happy |
| 1968 |
> |
|
| 1969 |
> |
2005-02-15 12:35 tim |
| 1970 |
> |
|
| 1971 |
> |
* src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to |
| 1972 |
> |
TokenMap, using TokenMapType::value_type instead of std::make_pair |
| 1973 |
> |
to make Sun compiler happy |
| 1974 |
> |
|
| 1975 |
> |
2005-02-15 12:24 tim |
| 1976 |
> |
|
| 1977 |
> |
* src/applications/staticProps/: GofRAngle.cpp, |
| 1978 |
> |
RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps |
| 1979 |
> |
|
| 1980 |
> |
2005-02-15 12:11 tim |
| 1981 |
> |
|
| 1982 |
> |
* src/: applications/staticProps/GofR.cpp, |
| 1983 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
| 1984 |
> |
applications/staticProps/RadialDistrFunc.hpp, |
| 1985 |
> |
brains/BlockSnapshotManager.cpp, utils/BitSet.cpp: (1) adding |
| 1986 |
> |
#ifdef __RWSTD to make sun compiler happy (2) fix pair density |
| 1987 |
> |
calculation problem when two selections intersect with each other |
| 1988 |
> |
|
| 1989 |
> |
2005-02-15 10:24 gezelter |
| 1990 |
> |
|
| 1991 |
> |
* src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy |
| 1992 |
> |
xlc++ |
| 1993 |
> |
|
| 1994 |
> |
2005-02-15 10:17 gezelter |
| 1995 |
> |
|
| 1996 |
> |
* configure, ac-tools/configure.in, src/config.h.in, |
| 1997 |
> |
src/utils/residentMem.c: [no log message] |
| 1998 |
> |
|
| 1999 |
> |
2005-02-15 01:17 gezelter |
| 2000 |
> |
|
| 2001 |
> |
* src/utils/residentMem.c: bug fix for null termination |
| 2002 |
> |
|
| 2003 |
> |
2005-02-15 01:11 gezelter |
| 2004 |
> |
|
| 2005 |
> |
* configure, ac-tools/configure.in, src/utils/residentMem.c: |
| 2006 |
> |
bugfixing residentMem |
| 2007 |
> |
|
| 2008 |
> |
2005-02-15 00:59 gezelter |
| 2009 |
> |
|
| 2010 |
> |
* configure, ac-tools/configure.in, src/config.h.in, |
| 2011 |
> |
src/utils/residentMem.c: bugfixes for residentMem on LINUX |
| 2012 |
> |
|
| 2013 |
> |
2005-02-15 00:08 gezelter |
| 2014 |
> |
|
| 2015 |
> |
* src/utils/Makefile.in: added residentMem |
| 2016 |
> |
|
| 2017 |
> |
2005-02-15 00:05 gezelter |
| 2018 |
> |
|
| 2019 |
> |
* configure, ac-tools/configure.in, make/Makefile.in, |
| 2020 |
> |
src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c, |
| 2021 |
> |
src/utils/residentMem.h: modifications to estimate memory in use by |
| 2022 |
> |
other processes autoconf fixes ps syntax checking config.h file |
| 2023 |
> |
cleaning |
| 2024 |
> |
|
| 2025 |
> |
2005-02-14 18:26 gezelter |
| 2026 |
> |
|
| 2027 |
> |
* configure, ac-tools/configure.in, make/Makefile.in: ps niceness |
| 2028 |
> |
|
| 2029 |
> |
2005-02-14 18:16 gezelter |
| 2030 |
> |
|
| 2031 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps |
| 2032 |
> |
strangeness |
| 2033 |
> |
|
| 2034 |
> |
2005-02-14 14:42 tim |
| 2035 |
> |
|
| 2036 |
> |
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
| 2037 |
> |
BlockSnapshotManager.hpp |
| 2038 |
> |
|
| 2039 |
> |
2005-02-14 13:51 tim |
| 2040 |
> |
|
| 2041 |
> |
* src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo, |
| 2042 |
> |
StaticPropsCmd.c: default length for staticProps is 1/2 smallest |
| 2043 |
> |
length of first frame |
| 2044 |
> |
|
| 2045 |
> |
2005-02-14 13:12 tim |
| 2046 |
> |
|
| 2047 |
> |
* src/integrators/VelocityVerletIntegrator.cpp: fix a bug in |
| 2048 |
> |
VelocityVerletIntegrator : last frame is written twice |
| 2049 |
> |
|
| 2050 |
> |
2005-02-14 12:57 tim |
| 2051 |
> |
|
| 2052 |
> |
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
| 2053 |
> |
brains/SimInfo.cpp, primitives/RigidBody.cpp, |
| 2054 |
> |
primitives/StuntDouble.hpp: begin bug fix |
| 2055 |
> |
|
| 2056 |
> |
2005-02-14 12:35 tim |
| 2057 |
> |
|
| 2058 |
> |
* src/applications/dynamicProps/: CorrelationFunction.cpp, |
| 2059 |
> |
CorrelationFunction.hpp, CrossTimeCorrFunc.cpp, |
| 2060 |
> |
CrossTimeCorrFunc.hpp, DipoleCorrFunc.cpp, DipoleCorrFunc.hpp, |
| 2061 |
> |
DynamicProps.cpp, FrameTimeCorrFunc.hpp, Makefile, |
| 2062 |
> |
ParticleTimeCorrFunc.cpp, ParticleTimeCorrFunc.hpp, RCorrFunc.cpp, |
| 2063 |
> |
RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp, |
| 2064 |
> |
VCorrFunc.hpp: refactory CorrelationFunction |
| 2065 |
> |
|
| 2066 |
> |
2005-02-14 10:18 gezelter |
| 2067 |
> |
|
| 2068 |
> |
* src/applications/dynamicProps/CorrelationFunction.cpp: bug fix |
| 2069 |
> |
and start of switch for type of correlation function |
| 2070 |
> |
|
| 2071 |
> |
2005-02-13 16:18 tim |
| 2072 |
> |
|
| 2073 |
> |
* src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in |
| 2074 |
> |
calculating bytes per stuntdouble |
| 2075 |
> |
|
| 2076 |
> |
2005-02-13 16:03 tim |
| 2077 |
> |
|
| 2078 |
> |
* src/applications/dynamicProps/CorrelationFunction.cpp: more fix |
| 2079 |
> |
|
| 2080 |
> |
2005-02-13 15:57 tim |
| 2081 |
> |
|
| 2082 |
> |
* src/applications/dynamicProps/CorrelationFunction.cpp: fixed a |
| 2083 |
> |
bug in CorrelationFunction |
| 2084 |
> |
|
| 2085 |
> |
2005-02-13 15:36 tim |
| 2086 |
> |
|
| 2087 |
> |
* src/: applications/staticProps/GofR.cpp, |
| 2088 |
> |
applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a |
| 2089 |
> |
bug in SimInfo::getCutoff() |
| 2090 |
> |
|
| 2091 |
> |
2005-02-13 15:08 tim |
| 2092 |
> |
|
| 2093 |
> |
* make/Makefile.in: adding staticProps and dynamicProps into |
| 2094 |
> |
Makefile.in |
| 2095 |
> |
|
| 2096 |
> |
2005-02-13 15:05 tim |
| 2097 |
> |
|
| 2098 |
> |
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
| 2099 |
> |
applications/dynamicProps/CorrelationFunction.hpp, |
| 2100 |
> |
applications/staticProps/StaticProps.cpp, |
| 2101 |
> |
applications/staticProps/StaticProps.ggo, |
| 2102 |
> |
applications/staticProps/StaticPropsCmd.c, |
| 2103 |
> |
applications/staticProps/StaticPropsCmd.h, brains/SimInfo.cpp, |
| 2104 |
> |
brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length |
| 2105 |
> |
defaults to the cutoff radius |
| 2106 |
> |
|
| 2107 |
> |
2005-02-13 14:14 tim |
| 2108 |
> |
|
| 2109 |
> |
* src/utils/Algorithm.hpp: adding Algorithm.hpp |
| 2110 |
> |
|
| 2111 |
> |
2005-02-13 14:10 tim |
| 2112 |
> |
|
| 2113 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 2114 |
> |
applications/dynamicProps/CorrelationFunction.cpp, |
| 2115 |
> |
applications/dynamicProps/CorrelationFunction.hpp, |
| 2116 |
> |
applications/dynamicProps/DynamicProps.cpp, |
| 2117 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 2118 |
> |
integrators/Integrator.cpp, integrators/Integrator.hpp, |
| 2119 |
> |
integrators/VelocityVerletIntegrator.cpp, |
| 2120 |
> |
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.cpp, |
| 2121 |
> |
io/LennardJonesAtomTypesSectionParser.cpp, minimizers/PRCG.cpp, |
| 2122 |
> |
utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h, |
| 2123 |
> |
visitors/OtherVisitor.cpp: dynamicProps get built |
| 2124 |
> |
|
| 2125 |
> |
2005-02-13 10:56 tim |
| 2126 |
> |
|
| 2127 |
> |
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
| 2128 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 2129 |
> |
brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in |
| 2130 |
> |
progress |
| 2131 |
> |
|
| 2132 |
> |
2005-02-13 03:04 tim |
| 2133 |
> |
|
| 2134 |
> |
* src/: applications/dynamicProps/CorrelationFunction.hpp, |
| 2135 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 2136 |
> |
brains/Makefile, brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
| 2137 |
> |
brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more |
| 2138 |
> |
work in dynamicProps |
| 2139 |
> |
|
| 2140 |
> |
2005-02-13 02:25 tim |
| 2141 |
> |
|
| 2142 |
> |
* src/applications/dynamicProps/DynamicProps.cpp: adding |
| 2143 |
> |
dynamicProps |
| 2144 |
> |
|
| 2145 |
> |
2005-02-13 02:14 tim |
| 2146 |
> |
|
| 2147 |
> |
* src/applications/dynamicProps/: DynamicPropsCmd.c, |
| 2148 |
> |
DynamicPropsCmd.h: adding command line option to DynamicProps |
| 2149 |
> |
|
| 2150 |
> |
2005-02-13 02:13 tim |
| 2151 |
> |
|
| 2152 |
> |
* src/applications/dynamicProps/: DynamicProps.ggo, Makefile: |
| 2153 |
> |
adding command line option for DynamicProps |
| 2154 |
> |
|
| 2155 |
> |
2005-02-13 01:57 tim |
| 2156 |
> |
|
| 2157 |
> |
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
| 2158 |
> |
applications/dynamicProps/CorrelationFunction.hpp, |
| 2159 |
> |
applications/dynamicProps/DipoleCorrFunc.cpp, |
| 2160 |
> |
applications/dynamicProps/DipoleCorrFunc.hpp, |
| 2161 |
> |
applications/dynamicProps/RCorrFunc.cpp, |
| 2162 |
> |
applications/dynamicProps/RCorrFunc.hpp, |
| 2163 |
> |
applications/dynamicProps/VCorrFunc.cpp, |
| 2164 |
> |
applications/dynamicProps/VCorrFunc.hpp, |
| 2165 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
| 2166 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 2167 |
> |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
| 2168 |
> |
brains/SnapshotManager.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
| 2169 |
> |
primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding |
| 2170 |
> |
dynamicProps |
| 2171 |
> |
|
| 2172 |
> |
2005-02-12 15:09 tim |
| 2173 |
> |
|
| 2174 |
> |
* src/selection/SelectionManager.cpp: adding SelectionManager.cpp |
| 2175 |
> |
|
| 2176 |
> |
2005-02-11 17:41 tim |
| 2177 |
> |
|
| 2178 |
> |
* src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one |
| 2179 |
> |
more constructor to Snapshot to create customized DataStorage |
| 2180 |
> |
|
| 2181 |
> |
2005-02-11 17:39 tim |
| 2182 |
> |
|
| 2183 |
> |
* src/selection/: DistanceFinder.hpp, Makefile, |
| 2184 |
> |
SelectionManager.hpp: adding beginSelected, nextSelected method to |
| 2185 |
> |
SelectionManager |
| 2186 |
> |
|
| 2187 |
> |
2005-02-11 17:36 tim |
| 2188 |
> |
|
| 2189 |
> |
* src/config.h.in, configure: adding support for physmem |
| 2190 |
> |
|
| 2191 |
> |
2005-02-11 17:35 tim |
| 2192 |
> |
|
| 2193 |
> |
* ac-tools/configure.in: adding supprot for physmem |
| 2194 |
> |
|
| 2195 |
> |
2005-02-11 17:35 tim |
| 2196 |
> |
|
| 2197 |
> |
* src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding |
| 2198 |
> |
physmem |
| 2199 |
> |
|
| 2200 |
> |
2005-02-10 17:37 tim |
| 2201 |
> |
|
| 2202 |
> |
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
| 2203 |
> |
GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp, |
| 2204 |
> |
GofXyz.hpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
| 2205 |
> |
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
| 2206 |
> |
StaticPropsCmd.h: more work in StaticProps |
| 2207 |
> |
|
| 2208 |
> |
2005-02-10 13:14 tim |
| 2209 |
> |
|
| 2210 |
> |
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
| 2211 |
> |
GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, |
| 2212 |
> |
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofXyz.cpp, GofXyz.hpp, |
| 2213 |
> |
Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
| 2214 |
> |
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
| 2215 |
> |
StaticPropsCmd.h: change the filenames |
| 2216 |
> |
|
| 2217 |
> |
2005-02-10 09:15 tim |
| 2218 |
> |
|
| 2219 |
> |
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
| 2220 |
> |
GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp, |
| 2221 |
> |
RadialDistrFunc.hpp: adding GofRAngle |
| 2222 |
> |
|
| 2223 |
> |
2005-02-09 13:21 tim |
| 2224 |
> |
|
| 2225 |
> |
* src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some |
| 2226 |
> |
useless files |
| 2227 |
> |
|
| 2228 |
> |
2005-02-09 13:12 tim |
| 2229 |
> |
|
| 2230 |
> |
* src/applications/staticProps/: GofR.cpp, Makefile, |
| 2231 |
> |
RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress |
| 2232 |
> |
|
| 2233 |
> |
2005-02-09 12:08 tim |
| 2234 |
> |
|
| 2235 |
> |
* src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp, |
| 2236 |
> |
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h, |
| 2237 |
> |
RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR |
| 2238 |
> |
|
| 2239 |
> |
2005-02-07 17:39 tim |
| 2240 |
> |
|
| 2241 |
> |
* src/primitives/Molecule.hpp: add getRigidBodyAt function into |
| 2242 |
> |
Molecule class |
| 2243 |
> |
|
| 2244 |
> |
2005-02-07 17:38 tim |
| 2245 |
> |
|
| 2246 |
> |
* src/applications/dump2Xyz/Dump2XYZCmd.c: update help info |
| 2247 |
> |
|
| 2248 |
> |
2005-02-07 17:36 tim |
| 2249 |
> |
|
| 2250 |
> |
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
| 2251 |
> |
SelectionCompiler.cpp: support select internal index selection, for |
| 2252 |
> |
example, select DMPC.3 |
| 2253 |
> |
|
| 2254 |
> |
2005-02-07 16:11 tim |
| 2255 |
> |
|
| 2256 |
> |
* src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update |
| 2257 |
> |
help info for Dump2XYZ |
| 2258 |
> |
|
| 2259 |
> |
2005-02-07 15:39 chrisfen |
| 2260 |
> |
|
| 2261 |
> |
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
| 2262 |
> |
selection librarys added |
| 2263 |
> |
|
| 2264 |
> |
2005-02-07 15:31 tim |
| 2265 |
> |
|
| 2266 |
> |
* src/selection/Makefile, make/Makefile.in: adding Makefile |
| 2267 |
> |
|
| 2268 |
> |
2005-02-07 15:20 chrisfen |
| 2269 |
> |
|
| 2270 |
> |
* src/utils/wildcards.hpp: issue commented out in wildcards |
| 2271 |
> |
|
| 2272 |
> |
2005-02-07 15:06 tim |
| 2273 |
> |
|
| 2274 |
> |
* src/selection/SelectionEvaluator.cpp: forget to reset the pc |
| 2275 |
> |
which cause reevaluate return NULL |
| 2276 |
> |
|
| 2277 |
> |
2005-02-07 14:14 tim |
| 2278 |
> |
|
| 2279 |
> |
* src/brains/: SimCreator.cpp, SimSnapshotManager.cpp, |
| 2280 |
> |
SimSnapshotManager.hpp: fix a bug in determing the global index for |
| 2281 |
> |
rigidbodies |
| 2282 |
> |
|
| 2283 |
> |
2005-02-07 14:13 tim |
| 2284 |
> |
|
| 2285 |
> |
* src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change |
| 2286 |
> |
in Bitset |
| 2287 |
> |
|
| 2288 |
> |
2005-02-07 14:13 tim |
| 2289 |
> |
|
| 2290 |
> |
* src/selection/: DistanceFinder.cpp, DistanceFinder.hpp, |
| 2291 |
> |
SelectionCompiler.cpp, SelectionCompiler.hpp, |
| 2292 |
> |
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp, |
| 2293 |
> |
TokenMap.cpp: selection library is working |
| 2294 |
> |
|
| 2295 |
> |
2005-02-04 17:46 tim |
| 2296 |
> |
|
| 2297 |
> |
* src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor |
| 2298 |
> |
|
| 2299 |
> |
2005-02-04 17:45 tim |
| 2300 |
> |
|
| 2301 |
> |
* src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor |
| 2302 |
> |
and XYZVisitor now use selection library |
| 2303 |
> |
|
| 2304 |
> |
2005-02-04 17:44 tim |
| 2305 |
> |
|
| 2306 |
> |
* src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp: |
| 2307 |
> |
adding SelectionManager into SimInfo |
| 2308 |
> |
|
| 2309 |
> |
2005-02-04 17:43 tim |
| 2310 |
> |
|
| 2311 |
> |
* src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, |
| 2312 |
> |
Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of |
| 2313 |
> |
selection library |
| 2314 |
> |
|
| 2315 |
> |
2005-02-04 17:42 tim |
| 2316 |
> |
|
| 2317 |
> |
* src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change |
| 2318 |
> |
in BitSet |
| 2319 |
> |
|
| 2320 |
> |
2005-02-04 17:41 tim |
| 2321 |
> |
|
| 2322 |
> |
* src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing |
| 2323 |
> |
implementation |
| 2324 |
> |
|
| 2325 |
> |
2005-02-04 17:39 tim |
| 2326 |
> |
|
| 2327 |
> |
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
| 2328 |
> |
SelectionCompiler.cpp, SelectionCompiler.hpp, |
| 2329 |
> |
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
| 2330 |
> |
SelectionManager.hpp, Token.hpp: half of the selection utility is |
| 2331 |
> |
working need to debug within keyword and atomproperty keyword |
| 2332 |
> |
|
| 2333 |
> |
2005-02-04 00:42 tim |
| 2334 |
> |
|
| 2335 |
> |
* src/selection/: NameFinder.cpp, NameFinder.hpp: selection library |
| 2336 |
> |
get built |
| 2337 |
> |
|
| 2338 |
> |
2005-02-04 00:42 tim |
| 2339 |
> |
|
| 2340 |
> |
* src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet |
| 2341 |
> |
|
| 2342 |
> |
2005-02-04 00:26 tim |
| 2343 |
> |
|
| 2344 |
> |
* src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp: |
| 2345 |
> |
remove some useless files |
| 2346 |
> |
|
| 2347 |
> |
2005-02-03 23:57 tim |
| 2348 |
> |
|
| 2349 |
> |
* src/: primitives/RigidBody.hpp, selection/NameFinder.cpp, |
| 2350 |
> |
selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp: |
| 2351 |
> |
adding wildcard class; NameFinder is finished |
| 2352 |
> |
|
| 2353 |
> |
2005-02-03 18:14 tim |
| 2354 |
> |
|
| 2355 |
> |
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
| 2356 |
> |
SelectionCompiler.cpp, SelectionCompiler.hpp, |
| 2357 |
> |
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
| 2358 |
> |
SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in |
| 2359 |
> |
selection library |
| 2360 |
> |
|
| 2361 |
> |
2005-02-03 09:04 tim |
| 2362 |
> |
|
| 2363 |
> |
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
| 2364 |
> |
selection in progress |
| 2365 |
> |
|
| 2366 |
> |
2005-02-02 18:13 tim |
| 2367 |
> |
|
| 2368 |
> |
* src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp, |
| 2369 |
> |
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp, |
| 2370 |
> |
Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in |
| 2371 |
> |
progress, except SelectionEvaluator, other files are compiled |
| 2372 |
> |
|
| 2373 |
> |
2005-02-02 18:12 tim |
| 2374 |
> |
|
| 2375 |
> |
* src/utils/: Makefile.in, any.hpp: adding boost::any |
| 2376 |
> |
|
| 2377 |
> |
2005-02-02 07:51 tim |
| 2378 |
> |
|
| 2379 |
> |
* src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp |
| 2380 |
> |
|
| 2381 |
> |
2005-02-01 17:49 tim |
| 2382 |
> |
|
| 2383 |
> |
* src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp, |
| 2384 |
> |
selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, |
| 2385 |
> |
selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, |
| 2386 |
> |
selection/Token.hpp: Selection in progress |
| 2387 |
> |
|
| 2388 |
> |
2005-02-01 01:55 tim |
| 2389 |
> |
|
| 2390 |
> |
* src/: selection/SelectionCompiler.hpp, |
| 2391 |
> |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
| 2392 |
> |
selection/SelectionManager.hpp, selection/Token.hpp, |
| 2393 |
> |
utils/BitSet.cpp, utils/BitSet.hpp: adding selection library |
| 2394 |
> |
|
| 2395 |
> |
2005-01-26 10:26 tim |
| 2396 |
> |
|
| 2397 |
> |
* src/integrators/: Integrator.cpp, Integrator.hpp, |
| 2398 |
> |
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget |
| 2399 |
> |
to add eorWriter |
| 2400 |
> |
|
| 2401 |
> |
2005-01-26 10:15 tim |
| 2402 |
> |
|
| 2403 |
> |
* src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp: |
| 2404 |
> |
(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the |
| 2405 |
> |
wrong column of electroframe |
| 2406 |
> |
|
| 2407 |
> |
2005-01-25 16:59 tim |
| 2408 |
> |
|
| 2409 |
> |
* src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in |
| 2410 |
> |
SimInfo, use number of cutoff stamp as counter to loop over |
| 2411 |
> |
rigidbody stamp |
| 2412 |
> |
|
| 2413 |
> |
2005-01-25 12:45 tim |
| 2414 |
> |
|
| 2415 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 2416 |
> |
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
| 2417 |
> |
integrators/DLM.cpp, io/AtomTypesSectionParser.cpp, |
| 2418 |
> |
io/BendTypesSectionParser.cpp, io/BondTypesSectionParser.cpp, |
| 2419 |
> |
io/DirectionalAtomTypesSectionParser.cpp, io/DumpReader.cpp, |
| 2420 |
> |
io/EAMAtomTypesSectionParser.cpp, |
| 2421 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, io/Globals.cpp, |
| 2422 |
> |
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
| 2423 |
> |
io/StickyAtomTypesSectionParser.cpp, |
| 2424 |
> |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
| 2425 |
> |
math/SquareMatrix.hpp, primitives/DirectionalAtom.cpp, |
| 2426 |
> |
primitives/DirectionalAtom.hpp, primitives/GhostTorsion.cpp, |
| 2427 |
> |
primitives/GhostTorsion.hpp, primitives/Makefile, |
| 2428 |
> |
primitives/RigidBody.cpp, types/MakeStamps.cpp: (1) complete |
| 2429 |
> |
section parser's error message (2) add GhostTorsion (3) accumulate |
| 2430 |
> |
inertial tensor from the directional atoms before calculate |
| 2431 |
> |
rigidbody's inertial tensor |
| 2432 |
> |
|
| 2433 |
> |
2005-01-17 17:17 tim |
| 2434 |
> |
|
| 2435 |
> |
* forceFields/DUFF2.frc: forget to set dipole for lipid head group |
| 2436 |
> |
|
| 2437 |
> |
2005-01-17 11:58 tim |
| 2438 |
> |
|
| 2439 |
> |
* src/integrators/NVT.cpp: fix a bug in loading initial extended |
| 2440 |
> |
system parameters |
| 2441 |
> |
|
| 2442 |
> |
2005-01-17 11:05 tim |
| 2443 |
> |
|
| 2444 |
> |
* src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT |
| 2445 |
> |
|
| 2446 |
> |
2005-01-14 17:02 tim |
| 2447 |
> |
|
| 2448 |
> |
* src/UseTheForce/WATER.cpp: remove WATER.cpp |
| 2449 |
> |
|
| 2450 |
> |
2005-01-14 16:37 tim |
| 2451 |
> |
|
| 2452 |
> |
* forceFields/Makefile: sync Makefile |
| 2453 |
> |
|
| 2454 |
> |
2005-01-14 16:13 gezelter |
| 2455 |
> |
|
| 2456 |
> |
* make/Makefile.in, src/Makefile, src/UseTheForce/Makefile, |
| 2457 |
> |
src/UseTheForce/DarkSide/Makefile, src/applications/Makefile, |
| 2458 |
> |
src/applications/dump2Xyz/Makefile, |
| 2459 |
> |
src/applications/oopse/Makefile, |
| 2460 |
> |
src/applications/simpleBuilder/Makefile, src/brains/Makefile, |
| 2461 |
> |
src/constraints/Makefile, src/integrators/Makefile, |
| 2462 |
> |
src/io/Makefile, src/math/Makefile, src/minimizers/Makefile, |
| 2463 |
> |
src/primitives/Makefile, src/profiling/Makefile, |
| 2464 |
> |
src/restraints/Makefile, src/types/Makefile, src/utils/Makefile.in, |
| 2465 |
> |
src/visitors/Makefile: moved Package variable into subdirectory |
| 2466 |
> |
makefiles to speed up the building process |
| 2467 |
> |
|
| 2468 |
> |
2005-01-14 15:48 gezelter |
| 2469 |
> |
|
| 2470 |
> |
* src/applications/oopse/oopse.cpp: Fixed publication details in |
| 2471 |
> |
banner |
| 2472 |
> |
|
| 2473 |
> |
2005-01-14 15:48 gezelter |
| 2474 |
> |
|
| 2475 |
> |
* src/UseTheForce/DarkSide/: simParallel_interface.F90, |
| 2476 |
> |
simParallel_interface.h: added dummy subroutine to avoid empty |
| 2477 |
> |
unit, synchronized this dummy routine between C and fortran |
| 2478 |
> |
|
| 2479 |
> |
2005-01-14 15:31 gezelter |
| 2480 |
> |
|
| 2481 |
> |
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90, |
| 2482 |
> |
notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90, |
| 2483 |
> |
DarkSide/Makefile, DarkSide/atype.F90, |
| 2484 |
> |
DarkSide/atype_interface.F90, DarkSide/charge.F90, |
| 2485 |
> |
DarkSide/charge_interface.F90, DarkSide/dipole.F90, |
| 2486 |
> |
DarkSide/dipole_interface.F90, DarkSide/eam.F90, |
| 2487 |
> |
DarkSide/eam_interface.F90, DarkSide/gb.F90, |
| 2488 |
> |
DarkSide/gb_interface.F90, DarkSide/lj_interface.F90, |
| 2489 |
> |
DarkSide/shapes.F90, DarkSide/shapes_interface.F90, |
| 2490 |
> |
DarkSide/simParallel.F90, DarkSide/simParallel_interface.F90, |
| 2491 |
> |
DarkSide/simulation.F90, DarkSide/simulation_interface.F90, |
| 2492 |
> |
DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating |
| 2493 |
> |
modules and C/Fortran interface subroutines |
| 2494 |
> |
|
| 2495 |
> |
2005-01-14 15:15 gezelter |
| 2496 |
> |
|
| 2497 |
> |
* configure, ac-tools/aclocal.m4: more fixes for gnugetopt |
| 2498 |
> |
|
| 2499 |
> |
2005-01-14 15:09 gezelter |
| 2500 |
> |
|
| 2501 |
> |
* configure, ac-tools/configure.in, src/config.h.in, |
| 2502 |
> |
src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt |
| 2503 |
> |
|
| 2504 |
> |
2005-01-14 11:49 tim |
| 2505 |
> |
|
| 2506 |
> |
* src/: io/EAMAtomTypesSectionParser.cpp, |
| 2507 |
> |
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
| 2508 |
> |
utils/StringUtils.hpp: using c library to do conversion instead of |
| 2509 |
> |
using iostream due to a bug in libstdc++(GCC 3.2) |
| 2510 |
> |
|
| 2511 |
> |
2005-01-13 21:40 tim |
| 2512 |
> |
|
| 2513 |
> |
* src/brains/SimSetup.cpp: no message |
| 2514 |
> |
|
| 2515 |
> |
2005-01-13 20:56 tim |
| 2516 |
> |
|
| 2517 |
> |
* src/primitives/Molecule.hpp: fix a bug in global index |
| 2518 |
> |
|
| 2519 |
> |
2005-01-13 20:04 tim |
| 2520 |
> |
|
| 2521 |
> |
* src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include |
| 2522 |
> |
Integrator.hpp in Minimizer |
| 2523 |
> |
|
| 2524 |
> |
2005-01-13 17:14 gezelter |
| 2525 |
> |
|
| 2526 |
> |
* src/utils/Makefile: compile getopt and getopt1 if we need to |
| 2527 |
> |
|
| 2528 |
> |
2005-01-13 16:56 gezelter |
| 2529 |
> |
|
| 2530 |
> |
* make/Makefile.in: template flags |
| 2531 |
> |
|
| 2532 |
> |
2005-01-13 16:48 gezelter |
| 2533 |
> |
|
| 2534 |
> |
* src/applications/oopse/Makefile: formatting |
| 2535 |
> |
|
| 2536 |
> |
2005-01-13 16:48 gezelter |
| 2537 |
> |
|
| 2538 |
> |
* make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir |
| 2539 |
> |
target |
| 2540 |
> |
|
| 2541 |
> |
2005-01-13 14:40 tim |
| 2542 |
> |
|
| 2543 |
> |
* src/: UseTheForce/fSwitchingFunction.h, |
| 2544 |
> |
UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile, |
| 2545 |
> |
math/Makefile, math/RectMatrix.hpp, math/Vector.hpp, |
| 2546 |
> |
primitives/RigidBody.cpp, types/AtomTypeProperties.h, |
| 2547 |
> |
types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform |
| 2548 |
> |
|
| 2549 |
> |
2005-01-13 13:26 tim |
| 2550 |
> |
|
| 2551 |
> |
* make/Makefile.in: change the order of linking (object file comes |
| 2552 |
> |
first and then follow by user built library) |
| 2553 |
> |
|
| 2554 |
> |
2005-01-12 18:24 tim |
| 2555 |
> |
|
| 2556 |
> |
* src/io/DumpWriter.cpp: remove useless debug info |
| 2557 |
> |
|
| 2558 |
> |
2005-01-12 18:21 tim |
| 2559 |
> |
|
| 2560 |
> |
* src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix |
| 2561 |
> |
|
| 2562 |
> |
2005-01-12 18:17 tim |
| 2563 |
> |
|
| 2564 |
> |
* make/: Makefile.in, Makefile.in: missing tab |
| 2565 |
> |
|
| 2566 |
> |
2005-01-12 18:15 tim |
| 2567 |
> |
|
| 2568 |
> |
* src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor |
| 2569 |
> |
get fixed |
| 2570 |
> |
|
| 2571 |
> |
2005-01-12 17:40 gezelter |
| 2572 |
> |
|
| 2573 |
> |
* make/Makefile.in, src/UseTheForce/DUFF.cpp, |
| 2574 |
> |
src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp, |
| 2575 |
> |
src/UseTheForce/EAM.hpp, src/UseTheForce/EAM_FF.cpp, |
| 2576 |
> |
src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp, |
| 2577 |
> |
src/UseTheForce/ForceFieldCreator.hpp, |
| 2578 |
> |
src/UseTheForce/ForceFieldFactory.cpp, |
| 2579 |
> |
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/LJFF.cpp, |
| 2580 |
> |
src/UseTheForce/Makefile, src/UseTheForce/Shapes_FF.cpp, |
| 2581 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/doForces_interface.h, |
| 2582 |
> |
src/UseTheForce/fSwitchingFunction.h, |
| 2583 |
> |
src/UseTheForce/mpiComponentPlan.h, |
| 2584 |
> |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 2585 |
> |
src/UseTheForce/notifyCutoffs.F90, |
| 2586 |
> |
src/UseTheForce/notifyCutoffs_interface.h, |
| 2587 |
> |
src/UseTheForce/DarkSide/LJ.F90, |
| 2588 |
> |
src/UseTheForce/DarkSide/atype.F90, |
| 2589 |
> |
src/UseTheForce/DarkSide/atype_interface.h, |
| 2590 |
> |
src/UseTheForce/DarkSide/charge.F90, |
| 2591 |
> |
src/UseTheForce/DarkSide/charge_interface.h, |
| 2592 |
> |
src/UseTheForce/DarkSide/dipole.F90, |
| 2593 |
> |
src/UseTheForce/DarkSide/dipole_interface.h, |
| 2594 |
> |
src/UseTheForce/DarkSide/eam.F90, |
| 2595 |
> |
src/UseTheForce/DarkSide/eam_interface.h, |
| 2596 |
> |
src/UseTheForce/DarkSide/force_globals.F90, |
| 2597 |
> |
src/UseTheForce/DarkSide/gb.F90, |
| 2598 |
> |
src/UseTheForce/DarkSide/gb_interface.h, |
| 2599 |
> |
src/UseTheForce/DarkSide/lj_interface.h, |
| 2600 |
> |
src/UseTheForce/DarkSide/neighborLists.F90, |
| 2601 |
> |
src/UseTheForce/DarkSide/reactionField.F90, |
| 2602 |
> |
src/UseTheForce/DarkSide/shapes.F90, |
| 2603 |
> |
src/UseTheForce/DarkSide/shapes_interface.h, |
| 2604 |
> |
src/UseTheForce/DarkSide/simParallel.F90, |
| 2605 |
> |
src/UseTheForce/DarkSide/simParallel_interface.h, |
| 2606 |
> |
src/UseTheForce/DarkSide/simulation.F90, |
| 2607 |
> |
src/UseTheForce/DarkSide/simulation_interface.h, |
| 2608 |
> |
src/UseTheForce/DarkSide/sticky.F90, |
| 2609 |
> |
src/UseTheForce/DarkSide/sticky_interface.h, |
| 2610 |
> |
src/UseTheForce/DarkSide/switcheroo.F90, |
| 2611 |
> |
src/applications/Makedepend, src/applications/quickLate.c, |
| 2612 |
> |
src/applications/dump2Xyz/Dump2XYZ.cpp, |
| 2613 |
> |
src/applications/oopse/oopse.cpp, |
| 2614 |
> |
src/applications/simpleBuilder/BaseLattice.cpp, |
| 2615 |
> |
src/applications/simpleBuilder/BaseLattice.hpp, |
| 2616 |
> |
src/applications/simpleBuilder/Lattice.cpp, |
| 2617 |
> |
src/applications/simpleBuilder/Lattice.hpp, |
| 2618 |
> |
src/applications/simpleBuilder/LatticeCreator.cpp, |
| 2619 |
> |
src/applications/simpleBuilder/LatticeCreator.hpp, |
| 2620 |
> |
src/applications/simpleBuilder/LatticeFactory.cpp, |
| 2621 |
> |
src/applications/simpleBuilder/LatticeFactory.hpp, |
| 2622 |
> |
src/applications/simpleBuilder/MoLocator.cpp, |
| 2623 |
> |
src/applications/simpleBuilder/MoLocator.hpp, |
| 2624 |
> |
src/applications/simpleBuilder/simpleBuilder.cpp, |
| 2625 |
> |
src/brains/DataStorage.cpp, src/brains/DataStorage.hpp, |
| 2626 |
> |
src/brains/Exclude.cpp, src/brains/Exclude.hpp, |
| 2627 |
> |
src/brains/ForceManager.cpp, src/brains/ForceManager.hpp, |
| 2628 |
> |
src/brains/Makefile, src/brains/Migrator.hpp, |
| 2629 |
> |
src/brains/MoleculeCreator.cpp, src/brains/MoleculeCreator.hpp, |
| 2630 |
> |
src/brains/Register.cpp, src/brains/Register.hpp, |
| 2631 |
> |
src/brains/SimCreator.cpp, src/brains/SimCreator.hpp, |
| 2632 |
> |
src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
| 2633 |
> |
src/brains/SimModel.hpp, src/brains/SimSetup.hpp, |
| 2634 |
> |
src/brains/SimSnapshotManager.cpp, |
| 2635 |
> |
src/brains/SimSnapshotManager.hpp, src/brains/SimState.cpp, |
| 2636 |
> |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 2637 |
> |
src/brains/SkipList.hpp, src/brains/Snapshot.cpp, |
| 2638 |
> |
src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp, |
| 2639 |
> |
src/brains/Stats.cpp, src/brains/Stats.hpp, src/brains/Thermo.cpp, |
| 2640 |
> |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 2641 |
> |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 2642 |
> |
src/constraints/AbstractClasses.hpp, |
| 2643 |
> |
src/constraints/ConstraintElem.hpp, |
| 2644 |
> |
src/constraints/ConstraintPair.hpp, src/constraints/Makefile, |
| 2645 |
> |
src/constraints/Rattle.cpp, src/constraints/Rattle.hpp, |
| 2646 |
> |
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
| 2647 |
> |
src/constraints/ZconsStruct.hpp, |
| 2648 |
> |
src/constraints/ZconstraintForceManager.cpp, |
| 2649 |
> |
src/constraints/ZconstraintForceManager.hpp, |
| 2650 |
> |
src/integrators/AbstractClasses.hpp, |
| 2651 |
> |
src/integrators/AllIntegrator.hpp, src/integrators/DLM.cpp, |
| 2652 |
> |
src/integrators/DLM.hpp, src/integrators/Integrator.cpp, |
| 2653 |
> |
src/integrators/Integrator.hpp, |
| 2654 |
> |
src/integrators/IntegratorCreator.hpp, |
| 2655 |
> |
src/integrators/IntegratorFactory.cpp, |
| 2656 |
> |
src/integrators/IntegratorFactory.hpp, src/integrators/Makefile, |
| 2657 |
> |
src/integrators/NPT.cpp, src/integrators/NPT.hpp, |
| 2658 |
> |
src/integrators/NPTf.cpp, src/integrators/NPTf.hpp, |
| 2659 |
> |
src/integrators/NPTi.cpp, src/integrators/NPTi.hpp, |
| 2660 |
> |
src/integrators/NPTxyz.cpp, src/integrators/NPTxyz.hpp, |
| 2661 |
> |
src/integrators/NVE.cpp, src/integrators/NVE.hpp, |
| 2662 |
> |
src/integrators/NVT.cpp, src/integrators/NVT.hpp, |
| 2663 |
> |
src/integrators/RotationAlgorithm.hpp, |
| 2664 |
> |
src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp, |
| 2665 |
> |
src/integrators/VelocityVerletIntegrator.cpp, |
| 2666 |
> |
src/integrators/VelocityVerletIntegrator.hpp, |
| 2667 |
> |
src/io/AtomTypesSectionParser.cpp, |
| 2668 |
> |
src/io/AtomTypesSectionParser.hpp, src/io/BASS_interface.cpp, |
| 2669 |
> |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 2670 |
> |
src/io/BendTypesSectionParser.cpp, |
| 2671 |
> |
src/io/BendTypesSectionParser.hpp, |
| 2672 |
> |
src/io/BondTypesSectionParser.cpp, |
| 2673 |
> |
src/io/BondTypesSectionParser.hpp, |
| 2674 |
> |
src/io/DirectionalAtomTypesSectionParser.cpp, |
| 2675 |
> |
src/io/DirectionalAtomTypesSectionParser.hpp, |
| 2676 |
> |
src/io/DumpReader.cpp, src/io/DumpReader.hpp, |
| 2677 |
> |
src/io/DumpWriter.cpp, src/io/DumpWriter.hpp, |
| 2678 |
> |
src/io/EAMAtomTypesSectionParser.cpp, |
| 2679 |
> |
src/io/EAMAtomTypesSectionParser.hpp, |
| 2680 |
> |
src/io/ElectrostaticAtomTypesSectionParser.cpp, |
| 2681 |
> |
src/io/ElectrostaticAtomTypesSectionParser.hpp, src/io/Globals.cpp, |
| 2682 |
> |
src/io/Globals.hpp, src/io/InitializeFromFile.cpp, |
| 2683 |
> |
src/io/LennardJonesAtomTypesSectionParser.cpp, |
| 2684 |
> |
src/io/LennardJonesAtomTypesSectionParser.hpp, |
| 2685 |
> |
src/io/LinkedAssign.cpp, src/io/LinkedAssign.hpp, |
| 2686 |
> |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 2687 |
> |
src/io/Makefile, src/io/SectionParser.cpp, |
| 2688 |
> |
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
| 2689 |
> |
src/io/SectionParserManager.hpp, src/io/StatWriter.cpp, |
| 2690 |
> |
src/io/StatWriter.hpp, src/io/StickyAtomTypesSectionParser.cpp, |
| 2691 |
> |
src/io/StickyAtomTypesSectionParser.hpp, |
| 2692 |
> |
src/io/TorsionTypesSectionParser.cpp, |
| 2693 |
> |
src/io/TorsionTypesSectionParser.hpp, src/io/ZConsReader.cpp, |
| 2694 |
> |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 2695 |
> |
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
| 2696 |
> |
src/io/interface.c, src/io/make_nodes.c, src/io/make_nodes.h, |
| 2697 |
> |
src/io/mpiBASS.c, src/io/mpiBASS.h, src/io/node_list.h, |
| 2698 |
> |
src/io/parse_interface.h, src/io/parse_me.h, src/io/parse_tree.c, |
| 2699 |
> |
src/io/parse_tree.h, src/math/ChebyshevPolynomials.cpp, |
| 2700 |
> |
src/math/ChebyshevPolynomials.hpp, src/math/MatVec3.c, |
| 2701 |
> |
src/math/MatVec3.h, src/math/Polynomial.hpp, |
| 2702 |
> |
src/math/Quaternion.hpp, src/math/RealSphericalHarmonic.cpp, |
| 2703 |
> |
src/math/RealSphericalHarmonic.hpp, src/math/RectMatrix.hpp, |
| 2704 |
> |
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
| 2705 |
> |
src/math/Vector.hpp, src/math/Vector3.hpp, |
| 2706 |
> |
src/math/randomSPRNG.cpp, src/math/randomSPRNG.hpp, |
| 2707 |
> |
src/minimizers/CGFamilyMinimizer.cpp, |
| 2708 |
> |
src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Makefile, |
| 2709 |
> |
src/minimizers/Minimizer.cpp, src/minimizers/Minimizer.hpp, |
| 2710 |
> |
src/minimizers/MinimizerCreator.hpp, |
| 2711 |
> |
src/minimizers/MinimizerFactory.cpp, |
| 2712 |
> |
src/minimizers/MinimizerFactory.hpp, |
| 2713 |
> |
src/minimizers/MinimizerParameterSet.cpp, |
| 2714 |
> |
src/minimizers/MinimizerParameterSet.hpp, |
| 2715 |
> |
src/minimizers/OOPSEMinimizer.cpp, |
| 2716 |
> |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 2717 |
> |
src/minimizers/PRCG.hpp, src/minimizers/SDMinimizer.cpp, |
| 2718 |
> |
src/minimizers/SDMinimizer.hpp, src/primitives/AbstractClasses.hpp, |
| 2719 |
> |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 2720 |
> |
src/primitives/Bend.cpp, src/primitives/Bend.hpp, |
| 2721 |
> |
src/primitives/BendExtensions.cpp, src/primitives/Bond.cpp, |
| 2722 |
> |
src/primitives/Bond.hpp, src/primitives/BondExtensions.cpp, |
| 2723 |
> |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 2724 |
> |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 2725 |
> |
src/primitives/GhostBend.hpp, src/primitives/Makefile, |
| 2726 |
> |
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
| 2727 |
> |
src/primitives/RigidBody.cpp, src/primitives/RigidBody.hpp, |
| 2728 |
> |
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
| 2729 |
> |
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
| 2730 |
> |
src/primitives/Torsion.hpp, src/primitives/TorsionExtensions.cpp, |
| 2731 |
> |
src/primitives/UreyBradleyBend.cpp, |
| 2732 |
> |
src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp, |
| 2733 |
> |
src/profiling/mdProfile.hpp, src/types/AtomStamp.cpp, |
| 2734 |
> |
src/types/AtomStamp.hpp, src/types/AtomType.cpp, |
| 2735 |
> |
src/types/AtomType.hpp, src/types/AtomTypeProperties.h, |
| 2736 |
> |
src/types/BendStamp.cpp, src/types/BendStamp.hpp, |
| 2737 |
> |
src/types/BendType.hpp, src/types/BondStamp.cpp, |
| 2738 |
> |
src/types/BondStamp.hpp, src/types/BondType.hpp, |
| 2739 |
> |
src/types/CharmmTorsionType.cpp, src/types/CharmmTorsionType.hpp, |
| 2740 |
> |
src/types/Component.cpp, src/types/Component.hpp, |
| 2741 |
> |
src/types/CubicBendType.hpp, src/types/CubicBondType.hpp, |
| 2742 |
> |
src/types/CubicTorsionType.hpp, src/types/CutoffGroupStamp.cpp, |
| 2743 |
> |
src/types/CutoffGroupStamp.hpp, src/types/DirectionalAtomType.cpp, |
| 2744 |
> |
src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp, |
| 2745 |
> |
src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp, |
| 2746 |
> |
src/types/MakeStamps.cpp, src/types/MakeStamps.hpp, |
| 2747 |
> |
src/types/Makefile, src/types/MoleculeStamp.cpp, |
| 2748 |
> |
src/types/MoleculeStamp.hpp, src/types/MorseBondType.hpp, |
| 2749 |
> |
src/types/OplsTorsionType.hpp, src/types/PolynomialBendType.hpp, |
| 2750 |
> |
src/types/PolynomialBondType.hpp, |
| 2751 |
> |
src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp, |
| 2752 |
> |
src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp, |
| 2753 |
> |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 2754 |
> |
src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp, |
| 2755 |
> |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 2756 |
> |
src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp, |
| 2757 |
> |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 2758 |
> |
src/utils/GenericData.hpp, src/utils/GenericFactory.hpp, |
| 2759 |
> |
src/utils/LocalIndexManager.hpp, src/utils/Makefile, |
| 2760 |
> |
src/utils/MemoryUtils.hpp, src/utils/NumericConstant.hpp, |
| 2761 |
> |
src/utils/OOPSEConstant.hpp, src/utils/PropertyMap.cpp, |
| 2762 |
> |
src/utils/PropertyMap.hpp, src/utils/StreamTokenizer.cpp, |
| 2763 |
> |
src/utils/StreamTokenizer.hpp, src/utils/StringTokenizer.cpp, |
| 2764 |
> |
src/utils/StringTokenizer.hpp, src/utils/StringUtils.cpp, |
| 2765 |
> |
src/utils/StringUtils.hpp, src/utils/Trim.cpp, src/utils/Trim.hpp, |
| 2766 |
> |
src/utils/Tuple.hpp, src/utils/TupleMatcher.hpp, |
| 2767 |
> |
src/utils/TypeContainer.hpp, src/utils/TypeInfo.hpp, |
| 2768 |
> |
src/utils/Utility.cpp, src/utils/Utility.hpp, |
| 2769 |
> |
src/utils/definitions.F90, src/utils/fError.c, |
| 2770 |
> |
src/utils/next_combination.hpp, src/utils/oopseMPI.F90, |
| 2771 |
> |
src/utils/simError.c, src/utils/simError.h, src/utils/status.F90, |
| 2772 |
> |
src/utils/vector_class.F90, src/visitors/AtomData.hpp, |
| 2773 |
> |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 2774 |
> |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 2775 |
> |
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
| 2776 |
> |
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
| 2777 |
> |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 2778 |
> |
src/visitors/ZconsVisitor.hpp: merging new_design branch into |
| 2779 |
> |
OOPSE-2.0 |
| 2780 |
> |
|
| 2781 |
> |
2005-01-12 13:13 tim |
| 2782 |
> |
|
| 2783 |
> |
* src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp, |
| 2784 |
> |
utils/TypeContainer.hpp: forget to include <algorithm> |
| 2785 |
> |
|
| 2786 |
> |
2005-01-12 12:25 tim |
| 2787 |
> |
|
| 2788 |
> |
* forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc, |
| 2789 |
> |
newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force |
| 2790 |
> |
fields |
| 2791 |
> |
|
| 2792 |
> |
2005-01-12 12:14 tim |
| 2793 |
> |
|
| 2794 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 2795 |
> |
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
| 2796 |
> |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 2797 |
> |
UseTheForce/ForceFieldCreator.hpp, |
| 2798 |
> |
UseTheForce/ForceFieldFactory.cpp, |
| 2799 |
> |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
| 2800 |
> |
UseTheForce/doForces.F90, UseTheForce/doForces_interface.h, |
| 2801 |
> |
UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h, |
| 2802 |
> |
UseTheForce/notifyCutoffs.F90, |
| 2803 |
> |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
| 2804 |
> |
UseTheForce/DarkSide/atype.F90, |
| 2805 |
> |
UseTheForce/DarkSide/atype_interface.h, |
| 2806 |
> |
UseTheForce/DarkSide/charge.F90, |
| 2807 |
> |
UseTheForce/DarkSide/charge_interface.h, |
| 2808 |
> |
UseTheForce/DarkSide/dipole.F90, |
| 2809 |
> |
UseTheForce/DarkSide/dipole_interface.h, |
| 2810 |
> |
UseTheForce/DarkSide/eam.F90, UseTheForce/DarkSide/eam_interface.h, |
| 2811 |
> |
UseTheForce/DarkSide/force_globals.F90, |
| 2812 |
> |
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
| 2813 |
> |
UseTheForce/DarkSide/lj_interface.h, |
| 2814 |
> |
UseTheForce/DarkSide/neighborLists.F90, |
| 2815 |
> |
UseTheForce/DarkSide/reactionField.F90, |
| 2816 |
> |
UseTheForce/DarkSide/shapes.F90, |
| 2817 |
> |
UseTheForce/DarkSide/shapes_interface.h, |
| 2818 |
> |
UseTheForce/DarkSide/simParallel.F90, |
| 2819 |
> |
UseTheForce/DarkSide/simParallel_interface.h, |
| 2820 |
> |
UseTheForce/DarkSide/simulation.F90, |
| 2821 |
> |
UseTheForce/DarkSide/simulation_interface.h, |
| 2822 |
> |
UseTheForce/DarkSide/sticky.F90, |
| 2823 |
> |
UseTheForce/DarkSide/sticky_interface.h, |
| 2824 |
> |
UseTheForce/DarkSide/switcheroo.F90, |
| 2825 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
| 2826 |
> |
applications/simpleBuilder/BaseLattice.cpp, |
| 2827 |
> |
applications/simpleBuilder/BaseLattice.hpp, |
| 2828 |
> |
applications/simpleBuilder/Lattice.cpp, |
| 2829 |
> |
applications/simpleBuilder/Lattice.hpp, |
| 2830 |
> |
applications/simpleBuilder/LatticeCreator.cpp, |
| 2831 |
> |
applications/simpleBuilder/LatticeCreator.hpp, |
| 2832 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
| 2833 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
| 2834 |
> |
applications/simpleBuilder/MoLocator.cpp, |
| 2835 |
> |
applications/simpleBuilder/MoLocator.hpp, |
| 2836 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
| 2837 |
> |
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
| 2838 |
> |
brains/Exclude.hpp, brains/ForceManager.cpp, |
| 2839 |
> |
brains/ForceManager.hpp, brains/Makefile, brains/Migrator.hpp, |
| 2840 |
> |
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
| 2841 |
> |
brains/Register.cpp, brains/Register.hpp, brains/SimCreator.cpp, |
| 2842 |
> |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 2843 |
> |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
| 2844 |
> |
brains/SkipList.cpp, brains/SkipList.hpp, brains/SnapShot.cpp, |
| 2845 |
> |
brains/Snapshot.cpp, brains/Snapshot.hpp, |
| 2846 |
> |
brains/SnapshotManager.hpp, brains/Stats.cpp, brains/Stats.hpp, |
| 2847 |
> |
brains/Thermo.cpp, brains/Thermo.hpp, brains/fSimulation.h, |
| 2848 |
> |
constraints/ConstraintElem.hpp, constraints/ConstraintPair.hpp, |
| 2849 |
> |
constraints/Rattle.cpp, constraints/Rattle.hpp, |
| 2850 |
> |
constraints/ZconsStruct.hpp, |
| 2851 |
> |
constraints/ZconstraintForceManager.cpp, |
| 2852 |
> |
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
| 2853 |
> |
integrators/DLM.hpp, integrators/Integrator.cpp, |
| 2854 |
> |
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
| 2855 |
> |
integrators/IntegratorFactory.cpp, |
| 2856 |
> |
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
| 2857 |
> |
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
| 2858 |
> |
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
| 2859 |
> |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
| 2860 |
> |
integrators/NVT.cpp, integrators/NVT.hpp, |
| 2861 |
> |
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
| 2862 |
> |
integrators/Velocitizer.hpp, |
| 2863 |
> |
integrators/VelocityVerletIntegrator.cpp, |
| 2864 |
> |
integrators/VelocityVerletIntegrator.hpp, |
| 2865 |
> |
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
| 2866 |
> |
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
| 2867 |
> |
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
| 2868 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 2869 |
> |
io/BondTypesSectionParser.hpp, |
| 2870 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
| 2871 |
> |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
| 2872 |
> |
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
| 2873 |
> |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
| 2874 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 2875 |
> |
io/ElectrostaticAtomTypesSectionParser.hpp, io/Globals.cpp, |
| 2876 |
> |
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
| 2877 |
> |
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
| 2878 |
> |
io/LinkedAssign.hpp, io/LinkedCommand.cpp, io/LinkedCommand.hpp, |
| 2879 |
> |
io/SectionParser.cpp, io/SectionParser.hpp, |
| 2880 |
> |
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
| 2881 |
> |
io/StatWriter.cpp, io/StatWriter.hpp, |
| 2882 |
> |
io/StickyAtomTypesSectionParser.cpp, |
| 2883 |
> |
io/StickyAtomTypesSectionParser.hpp, |
| 2884 |
> |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
| 2885 |
> |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
| 2886 |
> |
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/interface.c, |
| 2887 |
> |
io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, |
| 2888 |
> |
io/node_list.h, io/parse_interface.h, io/parse_me.h, |
| 2889 |
> |
io/parse_tree.c, io/parse_tree.h, math/ChebyshevPolynomials.cpp, |
| 2890 |
> |
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
| 2891 |
> |
math/Polynomial.hpp, math/Quaternion.hpp, |
| 2892 |
> |
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
| 2893 |
> |
math/RectMatrix.hpp, math/SquareMatrix.hpp, math/SquareMatrix3.hpp, |
| 2894 |
> |
math/Vector.hpp, math/Vector3.hpp, math/randomSPRNG.cpp, |
| 2895 |
> |
math/randomSPRNG.hpp, minimizers/CGFamilyMinimizer.cpp, |
| 2896 |
> |
minimizers/CGFamilyMinimizer.hpp, minimizers/Minimizer.cpp, |
| 2897 |
> |
minimizers/Minimizer.hpp, minimizers/MinimizerCreator.hpp, |
| 2898 |
> |
minimizers/MinimizerFactory.cpp, minimizers/MinimizerFactory.hpp, |
| 2899 |
> |
minimizers/MinimizerParameterSet.cpp, |
| 2900 |
> |
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
| 2901 |
> |
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
| 2902 |
> |
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
| 2903 |
> |
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
| 2904 |
> |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
| 2905 |
> |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 2906 |
> |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
| 2907 |
> |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
| 2908 |
> |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
| 2909 |
> |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
| 2910 |
> |
primitives/Torsion.cpp, primitives/Torsion.hpp, |
| 2911 |
> |
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
| 2912 |
> |
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
| 2913 |
> |
restraints/Restraints.cpp, restraints/Restraints.hpp, |
| 2914 |
> |
types/AtomStamp.cpp, types/AtomStamp.hpp, types/AtomType.cpp, |
| 2915 |
> |
types/AtomType.hpp, types/AtomTypeProperties.h, |
| 2916 |
> |
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
| 2917 |
> |
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
| 2918 |
> |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
| 2919 |
> |
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
| 2920 |
> |
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
| 2921 |
> |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 2922 |
> |
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp, |
| 2923 |
> |
types/FixedBondType.hpp, types/HarmonicBendType.hpp, |
| 2924 |
> |
types/HarmonicBondType.hpp, types/MakeStamps.cpp, |
| 2925 |
> |
types/MakeStamps.hpp, types/MoleculeStamp.cpp, |
| 2926 |
> |
types/MoleculeStamp.hpp, types/MorseBondType.hpp, |
| 2927 |
> |
types/OplsTorsionType.hpp, types/PolynomialBendType.hpp, |
| 2928 |
> |
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
| 2929 |
> |
types/QuarticBendType.hpp, types/QuarticBondType.hpp, |
| 2930 |
> |
types/QuarticTorsionType.hpp, types/RigidBodyStamp.cpp, |
| 2931 |
> |
types/RigidBodyStamp.hpp, types/ShapeAtomType.cpp, |
| 2932 |
> |
types/ShapeAtomType.hpp, types/TorsionStamp.cpp, |
| 2933 |
> |
types/TorsionStamp.hpp, types/TorsionType.hpp, |
| 2934 |
> |
types/UreyBradleyBendType.hpp, types/ZconStamp.cpp, |
| 2935 |
> |
types/ZconStamp.hpp, utils/GenericData.hpp, |
| 2936 |
> |
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
| 2937 |
> |
utils/MemoryUtils.hpp, utils/NumericConstant.hpp, |
| 2938 |
> |
utils/OOPSEConstant.hpp, utils/PropertyMap.cpp, |
| 2939 |
> |
utils/PropertyMap.hpp, utils/StringTokenizer.cpp, |
| 2940 |
> |
utils/StringTokenizer.hpp, utils/StringUtils.cpp, |
| 2941 |
> |
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
| 2942 |
> |
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
| 2943 |
> |
utils/Utility.cpp, utils/Utility.hpp, utils/definitions.F90, |
| 2944 |
> |
utils/fError.c, utils/next_combination.hpp, utils/oopseMPI.F90, |
| 2945 |
> |
utils/simError.c, utils/simError.h, utils/status.F90, |
| 2946 |
> |
utils/vector_class.F90, visitors/AtomData.hpp, |
| 2947 |
> |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp, |
| 2948 |
> |
visitors/BaseVisitor.hpp, visitors/CompositeVisitor.cpp, |
| 2949 |
> |
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
| 2950 |
> |
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 2951 |
> |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
| 2952 |
> |
visitors/ZconsVisitor.hpp: change license |
| 2953 |
> |
|
| 2954 |
> |
2005-01-12 12:14 tim |
| 2955 |
> |
|
| 2956 |
> |
* src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on |
| 2957 |
> |
branch new_design. |
| 2958 |
> |
|
| 2959 |
> |
2005-01-11 16:03 tim |
| 2960 |
> |
|
| 2961 |
> |
* src/: constraints/ZconstraintForceManager.cpp, |
| 2962 |
> |
constraints/ZconstraintForceManager.hpp, |
| 2963 |
> |
minimizers/MinimizerParameterSet.cpp, |
| 2964 |
> |
minimizers/MinimizerParameterSet.hpp: change const static double |
| 2965 |
> |
data member to const double |
| 2966 |
> |
|
| 2967 |
> |
2005-01-11 15:50 tim |
| 2968 |
> |
|
| 2969 |
> |
* src/io/basic_ifstrstream.hpp: forget namespace qualifier std:: |
| 2970 |
> |
|
| 2971 |
> |
2005-01-11 15:39 tim |
| 2972 |
> |
|
| 2973 |
> |
* src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h: |
| 2974 |
> |
change data type from logical to integer in AtomTypeProperties.h |
| 2975 |
> |
|
| 2976 |
> |
2005-01-11 11:36 tim |
| 2977 |
> |
|
| 2978 |
> |
* forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding |
| 2979 |
> |
new format of EAM force field |
| 2980 |
> |
|
| 2981 |
> |
2005-01-11 11:24 tim |
| 2982 |
> |
|
| 2983 |
> |
* src/UseTheForce/DUFF.cpp: change default name of DUFF force field |
| 2984 |
> |
to DUFF2.frc |
| 2985 |
> |
|
| 2986 |
> |
2005-01-11 11:23 tim |
| 2987 |
> |
|
| 2988 |
> |
* forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to |
| 2989 |
> |
DUFF2.frc |
| 2990 |
> |
|
| 2991 |
> |
2005-01-11 11:09 tim |
| 2992 |
> |
|
| 2993 |
> |
* make/Makefile.in: adding constraints and minimizers into |
| 2994 |
> |
Makefile.in |
| 2995 |
> |
|
| 2996 |
> |
2005-01-11 11:03 tim |
| 2997 |
> |
|
| 2998 |
> |
* src/io/: ChargeAtomTypesSectionParser.cpp, |
| 2999 |
> |
ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp, |
| 3000 |
> |
DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless |
| 3001 |
> |
files |
| 3002 |
> |
|
| 3003 |
> |
2005-01-11 10:59 tim |
| 3004 |
> |
|
| 3005 |
> |
* src/io/ZConsWriter.cpp: [no log message] |
| 3006 |
> |
|
| 3007 |
> |
2005-01-11 10:53 tim |
| 3008 |
> |
|
| 3009 |
> |
* src/UseTheForce/EAM.cpp: minor fix |
| 3010 |
> |
|
| 3011 |
> |
2005-01-11 10:52 tim |
| 3012 |
> |
|
| 3013 |
> |
* src/constraints/Rattle.hpp: file Rattle.hpp was initially added |
| 3014 |
> |
on branch new_design. |
| 3015 |
> |
|
| 3016 |
> |
2005-01-11 10:52 tim |
| 3017 |
> |
|
| 3018 |
> |
* src/constraints/Rattle.cpp: file Rattle.cpp was initially added |
| 3019 |
> |
on branch new_design. |
| 3020 |
> |
|
| 3021 |
> |
2005-01-11 10:52 tim |
| 3022 |
> |
|
| 3023 |
> |
* src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm |
| 3024 |
> |
|
| 3025 |
> |
2005-01-11 10:47 tim |
| 3026 |
> |
|
| 3027 |
> |
* make/Makefile.in: forget a '$' sign |
| 3028 |
> |
|
| 3029 |
> |
2005-01-11 10:46 tim |
| 3030 |
> |
|
| 3031 |
> |
* make/Makefile.in: missing tab in rules |
| 3032 |
> |
|
| 3033 |
> |
2005-01-10 17:04 tim |
| 3034 |
> |
|
| 3035 |
> |
* src/: UseTheForce/ForceFieldCreator.cpp, |
| 3036 |
> |
UseTheForce/ForceFieldCreator.hpp, |
| 3037 |
> |
UseTheForce/ForceFieldFactory.cpp, |
| 3038 |
> |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
| 3039 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
| 3040 |
> |
applications/simpleBuilder/simpleBuilder.cpp, brains/Makefile, |
| 3041 |
> |
brains/Register.cpp, brains/Register.hpp, |
| 3042 |
> |
integrators/IntegratorCreator.cpp, |
| 3043 |
> |
integrators/IntegratorCreator.hpp, |
| 3044 |
> |
integrators/IntegratorFactory.cpp, |
| 3045 |
> |
integrators/IntegratorFactory.hpp, integrators/Makefile, |
| 3046 |
> |
integrators/NPTi.cpp, integrators/NVE.cpp, integrators/NVT.cpp, |
| 3047 |
> |
minimizers/Makefile, minimizers/MinimizerCreator.cpp, |
| 3048 |
> |
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
| 3049 |
> |
minimizers/MinimizerFactory.hpp: create a register module to |
| 3050 |
> |
register force fields, integrators and minimizers |
| 3051 |
> |
|
| 3052 |
> |
2005-01-10 17:04 tim |
| 3053 |
> |
|
| 3054 |
> |
* src/brains/Register.cpp: file Register.cpp was initially added on |
| 3055 |
> |
branch new_design. |
| 3056 |
> |
|
| 3057 |
> |
2005-01-10 17:04 tim |
| 3058 |
> |
|
| 3059 |
> |
* src/brains/Register.hpp: file Register.hpp was initially added on |
| 3060 |
> |
branch new_design. |
| 3061 |
> |
|
| 3062 |
> |
2005-01-10 15:52 tim |
| 3063 |
> |
|
| 3064 |
> |
* src/: UseTheForce/ForceFieldFactory.cpp, |
| 3065 |
> |
applications/oopse/oopse.cpp, brains/ForceManager.hpp, |
| 3066 |
> |
constraints/ZconstraintForceManager.cpp, |
| 3067 |
> |
constraints/ZconstraintForceManager.hpp, |
| 3068 |
> |
integrators/IntegratorFactory.cpp, |
| 3069 |
> |
integrators/VelocityVerletIntegrator.cpp, io/ZConsReader.cpp, |
| 3070 |
> |
io/ZConsWriter.cpp, minimizers/MinimizerFactory.cpp, |
| 3071 |
> |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint |
| 3072 |
> |
method is working now |
| 3073 |
> |
|
| 3074 |
> |
2005-01-10 13:05 tim |
| 3075 |
> |
|
| 3076 |
> |
* src/: constraints/ConstraintElem.hpp, |
| 3077 |
> |
constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp, |
| 3078 |
> |
constraints/ZconstraintForceManager.cpp, |
| 3079 |
> |
constraints/ZconstraintForceManager.hpp, io/ZConsReader.cpp, |
| 3080 |
> |
io/ZConsReader.hpp, io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
| 3081 |
> |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in |
| 3082 |
> |
zconstraint |
| 3083 |
> |
|
| 3084 |
> |
2005-01-10 13:05 tim |
| 3085 |
> |
|
| 3086 |
> |
* src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was |
| 3087 |
> |
initially added on branch new_design. |
| 3088 |
> |
|
| 3089 |
> |
2005-01-07 16:50 tim |
| 3090 |
> |
|
| 3091 |
> |
* src/constraints/ZconstraintForceManager.cpp: file |
| 3092 |
> |
ZconstraintForceManager.cpp was initially added on branch |
| 3093 |
> |
new_design. |
| 3094 |
> |
|
| 3095 |
> |
2005-01-07 16:50 tim |
| 3096 |
> |
|
| 3097 |
> |
* src/constraints/ZconstraintForceManager.hpp: file |
| 3098 |
> |
ZconstraintForceManager.hpp was initially added on branch |
| 3099 |
> |
new_design. |
| 3100 |
> |
|
| 3101 |
> |
2005-01-07 16:50 tim |
| 3102 |
> |
|
| 3103 |
> |
* src/: applications/simpleBuilder/BaseLattice.hpp, |
| 3104 |
> |
applications/simpleBuilder/Lattice.hpp, |
| 3105 |
> |
applications/simpleBuilder/LatticeCreator.hpp, |
| 3106 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
| 3107 |
> |
applications/simpleBuilder/MoLocator.hpp, brains/ForceManager.hpp, |
| 3108 |
> |
constraints/ConstraintElem.hpp, constraints/Makefile, |
| 3109 |
> |
constraints/ZConstraint.cpp, constraints/ZconsData.hpp, |
| 3110 |
> |
constraints/ZconstraintForceManager.cpp, |
| 3111 |
> |
constraints/ZconstraintForceManager.hpp, |
| 3112 |
> |
integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp, |
| 3113 |
> |
utils/NumericConstant.hpp: ZConstraintForceManager in progress |
| 3114 |
> |
|
| 3115 |
> |
2005-01-07 16:50 tim |
| 3116 |
> |
|
| 3117 |
> |
* src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was |
| 3118 |
> |
initially added on branch new_design. |
| 3119 |
> |
|
| 3120 |
> |
2005-01-06 17:31 tim |
| 3121 |
> |
|
| 3122 |
> |
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
| 3123 |
> |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 3124 |
> |
constraints/ConstraintPair.hpp, integrators/Integrator.cpp, |
| 3125 |
> |
integrators/NPTi.cpp, integrators/VelocityVerletIntegrator.cpp, |
| 3126 |
> |
io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp: |
| 3127 |
> |
constraint is almost working |
| 3128 |
> |
|
| 3129 |
> |
2005-01-05 19:36 tim |
| 3130 |
> |
|
| 3131 |
> |
* src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is |
| 3132 |
> |
working |
| 3133 |
> |
|
| 3134 |
> |
2005-01-05 19:16 tim |
| 3135 |
> |
|
| 3136 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 3137 |
> |
applications/oopse/oopse.cpp, |
| 3138 |
> |
applications/simpleBuilder/BaseLattice.cpp, |
| 3139 |
> |
applications/simpleBuilder/Lattice.cpp, |
| 3140 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
| 3141 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
| 3142 |
> |
applications/simpleBuilder/MoLocator.cpp, |
| 3143 |
> |
applications/simpleBuilder/MoLocator.hpp, |
| 3144 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
| 3145 |
> |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.hpp, |
| 3146 |
> |
minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder |
| 3147 |
> |
in progress |
| 3148 |
> |
|
| 3149 |
> |
2005-01-05 12:35 tim |
| 3150 |
> |
|
| 3151 |
> |
* src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp |
| 3152 |
> |
was initially added on branch new_design. |
| 3153 |
> |
|
| 3154 |
> |
2005-01-05 12:35 tim |
| 3155 |
> |
|
| 3156 |
> |
* src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially |
| 3157 |
> |
added on branch new_design. |
| 3158 |
> |
|
| 3159 |
> |
2005-01-05 12:35 tim |
| 3160 |
> |
|
| 3161 |
> |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
| 3162 |
> |
Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, |
| 3163 |
> |
MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp, |
| 3164 |
> |
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp, |
| 3165 |
> |
SDMinimizer.hpp: minimizer in progress |
| 3166 |
> |
|
| 3167 |
> |
2005-01-05 12:35 tim |
| 3168 |
> |
|
| 3169 |
> |
* src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp |
| 3170 |
> |
was initially added on branch new_design. |
| 3171 |
> |
|
| 3172 |
> |
2005-01-05 12:35 tim |
| 3173 |
> |
|
| 3174 |
> |
* src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp |
| 3175 |
> |
was initially added on branch new_design. |
| 3176 |
> |
|
| 3177 |
> |
2005-01-05 12:35 tim |
| 3178 |
> |
|
| 3179 |
> |
* src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp |
| 3180 |
> |
was initially added on branch new_design. |
| 3181 |
> |
|
| 3182 |
> |
2005-01-05 12:35 tim |
| 3183 |
> |
|
| 3184 |
> |
* src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially |
| 3185 |
> |
added on branch new_design. |
| 3186 |
> |
|
| 3187 |
> |
2005-01-04 17:18 tim |
| 3188 |
> |
|
| 3189 |
> |
* src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
| 3190 |
> |
brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, |
| 3191 |
> |
brains/Thermo.cpp, constraints/ConstraintPair.hpp, |
| 3192 |
> |
constraints/Makefile, integrators/NPT.cpp, integrators/NVE.cpp, |
| 3193 |
> |
integrators/NVT.cpp, integrators/VelocityVerletIntegrator.cpp, |
| 3194 |
> |
integrators/VelocityVerletIntegrator.hpp, io/DumpReader.cpp, |
| 3195 |
> |
primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in |
| 3196 |
> |
progress |
| 3197 |
> |
|
| 3198 |
> |
2005-01-04 17:18 tim |
| 3199 |
> |
|
| 3200 |
> |
* src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was |
| 3201 |
> |
initially added on branch new_design. |
| 3202 |
> |
|
| 3203 |
> |
2005-01-04 17:18 tim |
| 3204 |
> |
|
| 3205 |
> |
* src/minimizers/MinimizerParameterSet.cpp: file |
| 3206 |
> |
MinimizerParameterSet.cpp was initially added on branch new_design. |
| 3207 |
> |
|
| 3208 |
> |
2005-01-04 17:18 tim |
| 3209 |
> |
|
| 3210 |
> |
* src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was |
| 3211 |
> |
initially added on branch new_design. |
| 3212 |
> |
|
| 3213 |
> |
2005-01-04 17:18 tim |
| 3214 |
> |
|
| 3215 |
> |
* src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp |
| 3216 |
> |
was initially added on branch new_design. |
| 3217 |
> |
|
| 3218 |
> |
2005-01-04 17:18 tim |
| 3219 |
> |
|
| 3220 |
> |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
| 3221 |
> |
Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, |
| 3222 |
> |
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, |
| 3223 |
> |
SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress |
| 3224 |
> |
|
| 3225 |
> |
2005-01-04 17:18 tim |
| 3226 |
> |
|
| 3227 |
> |
* src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on |
| 3228 |
> |
branch new_design. |
| 3229 |
> |
|
| 3230 |
> |
2004-12-20 15:50 chuckv |
| 3231 |
> |
|
| 3232 |
> |
* make/Makefile.in: Fixed Makefile test bug under OSX and possibly |
| 3233 |
> |
other BSD's, replaced test -f *.mod with ls function since BSD test |
| 3234 |
> |
apparently doesn't support wildcards. |
| 3235 |
> |
|
| 3236 |
> |
2004-12-20 15:36 tim |
| 3237 |
> |
|
| 3238 |
> |
* make/Makefile.in: fix a test command incompatiable problem |
| 3239 |
> |
|
| 3240 |
> |
2004-12-20 14:49 tim |
| 3241 |
> |
|
| 3242 |
> |
* src/integrators/NPTi.cpp: NPT is working now |
| 3243 |
> |
|
| 3244 |
> |
2004-12-16 14:20 tim |
| 3245 |
> |
|
| 3246 |
> |
* src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the |
| 3247 |
> |
invalid stamp id |
| 3248 |
> |
|
| 3249 |
> |
2004-12-16 14:00 tim |
| 3250 |
> |
|
| 3251 |
> |
* forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, |
| 3252 |
> |
newEAM.u6.frc: adding new EAM force field files |
| 3253 |
> |
|
| 3254 |
> |
2004-12-16 13:55 tim |
| 3255 |
> |
|
| 3256 |
> |
* src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays |
| 3257 |
> |
in EAM parameter file is incorrect |
| 3258 |
> |
|
| 3259 |
> |
2004-12-16 12:27 tim |
| 3260 |
> |
|
| 3261 |
> |
* src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
| 3262 |
> |
brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp, |
| 3263 |
> |
utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM |
| 3264 |
> |
|
| 3265 |
> |
2004-12-15 17:34 tim |
| 3266 |
> |
|
| 3267 |
> |
* src/: applications/simpleBuilder/BaseLattice.cpp, |
| 3268 |
> |
applications/simpleBuilder/BaseLattice.hpp, |
| 3269 |
> |
applications/simpleBuilder/Lattice.cpp, |
| 3270 |
> |
applications/simpleBuilder/Lattice.hpp, |
| 3271 |
> |
applications/simpleBuilder/LatticeCreator.cpp, |
| 3272 |
> |
applications/simpleBuilder/LatticeCreator.hpp, |
| 3273 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
| 3274 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
| 3275 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
| 3276 |
> |
io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream |
| 3277 |
> |
|
| 3278 |
> |
2004-12-15 16:07 tim |
| 3279 |
> |
|
| 3280 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 3281 |
> |
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile, |
| 3282 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp: |
| 3283 |
> |
add EAM Force Field |
| 3284 |
> |
|
| 3285 |
> |
2004-12-15 14:40 tim |
| 3286 |
> |
|
| 3287 |
> |
* src/applications/oopse/oopse.cpp: add more force fields |
| 3288 |
> |
|
| 3289 |
> |
2004-12-15 11:44 tim |
| 3290 |
> |
|
| 3291 |
> |
* src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget |
| 3292 |
> |
to call All_reduce in MPI version) |
| 3293 |
> |
|
| 3294 |
> |
2004-12-15 11:13 tim |
| 3295 |
> |
|
| 3296 |
> |
* src/: brains/SimCreator.cpp, brains/SimInfo.cpp, |
| 3297 |
> |
io/DumpReader.cpp: MPI in NVE is working |
| 3298 |
> |
|
| 3299 |
> |
2004-12-14 16:57 tim |
| 3300 |
> |
|
| 3301 |
> |
* src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader. |
| 3302 |
> |
Master nodes does not brocast the total number of frames |
| 3303 |
> |
|
| 3304 |
> |
2004-12-14 14:08 tim |
| 3305 |
> |
|
| 3306 |
> |
* src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp, |
| 3307 |
> |
integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
| 3308 |
> |
minimizers/CGFamilyMinimizer.cpp, |
| 3309 |
> |
minimizers/MinimizerParameterSet.hpp, |
| 3310 |
> |
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
| 3311 |
> |
minimizers/SDMinimizer.cpp: more fix in MPI version |
| 3312 |
> |
|
| 3313 |
> |
2004-12-13 17:30 tim |
| 3314 |
> |
|
| 3315 |
> |
* src/: UseTheForce/DarkSide/simParallel.F90, |
| 3316 |
> |
applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
| 3317 |
> |
brains/SimInfo.cpp, brains/Snapshot.hpp, brains/Thermo.cpp, |
| 3318 |
> |
integrators/DLM.cpp, integrators/Integrator.cpp, |
| 3319 |
> |
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
| 3320 |
> |
integrators/NPTxyz.cpp, integrators/NVT.cpp, io/DumpReader.cpp, |
| 3321 |
> |
io/DumpWriter.cpp, io/EAMAtomTypesSectionParser.cpp, |
| 3322 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, io/SectionParser.hpp, |
| 3323 |
> |
io/ZConsWriter.cpp, io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, |
| 3324 |
> |
math/SquareMatrix3.hpp, primitives/Bend.hpp, primitives/Bond.hpp, |
| 3325 |
> |
primitives/RigidBody.cpp, primitives/StuntDouble.cpp, |
| 3326 |
> |
primitives/StuntDouble.hpp, types/CutoffGroupStamp.cpp, |
| 3327 |
> |
utils/LocalIndexManager.hpp, utils/PropertyMap.cpp, |
| 3328 |
> |
utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version |
| 3329 |
> |
is built |
| 3330 |
> |
|
| 3331 |
> |
2004-12-10 13:41 tim |
| 3332 |
> |
|
| 3333 |
> |
* src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp |
| 3334 |
> |
|
| 3335 |
> |
2004-12-10 11:14 tim |
| 3336 |
> |
|
| 3337 |
> |
* src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp, |
| 3338 |
> |
primitives/StuntDouble.hpp: forget to zero out the torque. Sticky |
| 3339 |
> |
and Dipole is working now |
| 3340 |
> |
|
| 3341 |
> |
2004-12-09 18:15 tim |
| 3342 |
> |
|
| 3343 |
> |
* src/: UseTheForce/DarkSide/dipole.F90, |
| 3344 |
> |
UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp: |
| 3345 |
> |
fix an index problem in eFrame matrix |
| 3346 |
> |
|
| 3347 |
> |
2004-12-09 18:09 tim |
| 3348 |
> |
|
| 3349 |
> |
* src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when |
| 3350 |
> |
initializing the new Charge AtomType |
| 3351 |
> |
|
| 3352 |
> |
2004-12-09 16:15 tim |
| 3353 |
> |
|
| 3354 |
> |
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90, |
| 3355 |
> |
types/DirectionalAtomType.cpp: sticky module get compiled |
| 3356 |
> |
|
| 3357 |
> |
2004-12-09 15:43 gezelter |
| 3358 |
> |
|
| 3359 |
> |
* src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90, |
| 3360 |
> |
reactionField.F90: u_l -> eFrame for electrostatics u_l -> A for |
| 3361 |
> |
GB |
| 3362 |
> |
|
| 3363 |
> |
2004-12-09 15:42 gezelter |
| 3364 |
> |
|
| 3365 |
> |
* src/UseTheForce/doForces.F90: u_l -> eFrame |
| 3366 |
> |
|
| 3367 |
> |
2004-12-09 15:27 gezelter |
| 3368 |
> |
|
| 3369 |
> |
* src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky |
| 3370 |
> |
module now has the option for multiple sticky types |
| 3371 |
> |
|
| 3372 |
> |
2004-12-09 15:27 gezelter |
| 3373 |
> |
|
| 3374 |
> |
* src/UseTheForce/doForces.F90: sticky |
| 3375 |
> |
|
| 3376 |
> |
2004-12-09 11:22 tim |
| 3377 |
> |
|
| 3378 |
> |
* src/integrators/: NPT.cpp, NVT.cpp: fix an interface |
| 3379 |
> |
inconsistency in lab2Bidy |
| 3380 |
> |
|
| 3381 |
> |
2004-12-09 10:45 tim |
| 3382 |
> |
|
| 3383 |
> |
* src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug |
| 3384 |
> |
in calculating torque in rigid body |
| 3385 |
> |
|
| 3386 |
> |
2004-12-08 15:37 tim |
| 3387 |
> |
|
| 3388 |
> |
* src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h, |
| 3389 |
> |
brains/SnapShot.cpp, brains/Snapshot.hpp, |
| 3390 |
> |
integrators/Integrator.cpp, |
| 3391 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp: |
| 3392 |
> |
fix a parsing bug in ElectroStaticAtomTypesSectionParser |
| 3393 |
> |
|
| 3394 |
> |
2004-12-08 12:03 tim |
| 3395 |
> |
|
| 3396 |
> |
* src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane |
| 3397 |
> |
in NVT is working |
| 3398 |
> |
|
| 3399 |
> |
2004-12-07 18:08 tim |
| 3400 |
> |
|
| 3401 |
> |
* src/: UseTheForce/Makefile, brains/SimInfo.hpp, |
| 3402 |
> |
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
| 3403 |
> |
integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp, |
| 3404 |
> |
io/DumpWriter.cpp: NPT in progress |
| 3405 |
> |
|
| 3406 |
> |
2004-12-07 09:43 tim |
| 3407 |
> |
|
| 3408 |
> |
* test/utils/: Makefile, NextCombinationTestCase.hpp: [no log |
| 3409 |
> |
message] |
| 3410 |
> |
|
| 3411 |
> |
2004-12-07 00:12 tim |
| 3412 |
> |
|
| 3413 |
> |
* src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in |
| 3414 |
> |
UseInitXSstate |
| 3415 |
> |
|
| 3416 |
> |
2004-12-07 00:00 tim |
| 3417 |
> |
|
| 3418 |
> |
* src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message |
| 3419 |
> |
|
| 3420 |
> |
2004-12-06 23:47 tim |
| 3421 |
> |
|
| 3422 |
> |
* src/types/DirectionalAtomType.cpp: [no log message] |
| 3423 |
> |
|
| 3424 |
> |
2004-12-06 21:18 tim |
| 3425 |
> |
|
| 3426 |
> |
* forceFields/newDUFF.frc: merge WATER force field into DUFF |
| 3427 |
> |
|
| 3428 |
> |
2004-12-06 20:33 tim |
| 3429 |
> |
|
| 3430 |
> |
* forceFields/newDUFF.frc: change the force constant of bonds |
| 3431 |
> |
|
| 3432 |
> |
2004-12-06 18:29 tim |
| 3433 |
> |
|
| 3434 |
> |
* src/: UseTheForce/DarkSide/charge.F90, |
| 3435 |
> |
UseTheForce/DarkSide/charge_interface.h, |
| 3436 |
> |
UseTheForce/DarkSide/dipole.F90, |
| 3437 |
> |
UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp: |
| 3438 |
> |
fix atom type ident in Charge and Dipole Module |
| 3439 |
> |
|
| 3440 |
> |
2004-12-06 17:56 tim |
| 3441 |
> |
|
| 3442 |
> |
* src/primitives/Torsion.cpp: butane is working now |
| 3443 |
> |
|
| 3444 |
> |
2004-12-06 15:15 tim |
| 3445 |
> |
|
| 3446 |
> |
* src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp, |
| 3447 |
> |
primitives/Bond.hpp, primitives/Torsion.cpp: short range |
| 3448 |
> |
interaction for butane is correct.Still something wrong with long |
| 3449 |
> |
range one |
| 3450 |
> |
|
| 3451 |
> |
2004-12-05 23:49 tim |
| 3452 |
> |
|
| 3453 |
> |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
| 3454 |
> |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 3455 |
> |
io/BendTypesSectionParser.cpp, math/Polynomial.hpp, |
| 3456 |
> |
primitives/Atom.hpp, utils/NumericConstant.hpp, |
| 3457 |
> |
utils/TypeContainer.hpp: fix a bug in Exclude List |
| 3458 |
> |
|
| 3459 |
> |
2004-12-05 17:21 tim |
| 3460 |
> |
|
| 3461 |
> |
* forceFields/newDUFF.frc: minor fix in DUFF |
| 3462 |
> |
|
| 3463 |
> |
2004-12-05 17:02 tim |
| 3464 |
> |
|
| 3465 |
> |
* src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp, |
| 3466 |
> |
utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp: |
| 3467 |
> |
fix a bug in filling MolMembership |
| 3468 |
> |
|
| 3469 |
> |
2004-12-05 12:12 tim |
| 3470 |
> |
|
| 3471 |
> |
* forceFields/newDUFF.frc: minor fix in force field file |
| 3472 |
> |
|
| 3473 |
> |
2004-12-05 12:09 tim |
| 3474 |
> |
|
| 3475 |
> |
* src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, |
| 3476 |
> |
integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp |
| 3477 |
> |
|
| 3478 |
> |
2004-12-04 15:09 tim |
| 3479 |
> |
|
| 3480 |
> |
* src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp, |
| 3481 |
> |
math/Vector3.hpp: NVE is working now, get the same result as |
| 3482 |
> |
OOPSE-1.0 |
| 3483 |
> |
|
| 3484 |
> |
2004-12-04 14:29 tim |
| 3485 |
> |
|
| 3486 |
> |
* src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy |
| 3487 |
> |
|
| 3488 |
> |
2004-12-04 14:24 gezelter |
| 3489 |
> |
|
| 3490 |
> |
* src/primitives/: Bend.cpp, Torsion.cpp: What? |
| 3491 |
> |
|
| 3492 |
> |
2004-12-04 14:24 gezelter |
| 3493 |
> |
|
| 3494 |
> |
* src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion |
| 3495 |
> |
|
| 3496 |
> |
2004-12-04 00:24 tim |
| 3497 |
> |
|
| 3498 |
> |
* src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp, |
| 3499 |
> |
integrators/Integrator.hpp, |
| 3500 |
> |
integrators/VelocityVerletIntegrator.cpp, primitives/Torsion.cpp, |
| 3501 |
> |
utils/TypeContainer.hpp: NVE conserved energy, however, potential |
| 3502 |
> |
is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf |
| 3503 |
> |
and NPTxyz to test integrator Step 2 SSD in NVE to test DLM, |
| 3504 |
> |
dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step |
| 3505 |
> |
4 EAM Step 5 Shape Step 6 Constraint & Restraint |
| 3506 |
> |
|
| 3507 |
> |
2004-12-03 19:01 tim |
| 3508 |
> |
|
| 3509 |
> |
* src/: UseTheForce/DarkSide/LJ.F90, |
| 3510 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp, |
| 3511 |
> |
integrators/VelocityVerletIntegrator.cpp, |
| 3512 |
> |
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
| 3513 |
> |
io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working, |
| 3514 |
> |
energy of NVE is not conserved |
| 3515 |
> |
|
| 3516 |
> |
2004-12-03 17:36 tim |
| 3517 |
> |
|
| 3518 |
> |
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
| 3519 |
> |
primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running |
| 3520 |
> |
|
| 3521 |
> |
2004-12-03 16:30 tim |
| 3522 |
> |
|
| 3523 |
> |
* src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp, |
| 3524 |
> |
brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile, |
| 3525 |
> |
integrators/NVE.cpp, primitives/Molecule.cpp, |
| 3526 |
> |
primitives/Molecule.hpp, primitives/StuntDouble.hpp, |
| 3527 |
> |
primitives/Torsion.hpp: more missing function get implemented |
| 3528 |
> |
|
| 3529 |
> |
2004-12-03 15:30 tim |
| 3530 |
> |
|
| 3531 |
> |
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp, |
| 3532 |
> |
SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo |
| 3533 |
> |
|
| 3534 |
> |
2004-12-03 12:59 tim |
| 3535 |
> |
|
| 3536 |
> |
* src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
| 3537 |
> |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 3538 |
> |
integrators/NPT.cpp, integrators/NPTi.cpp, integrators/NVT.cpp, |
| 3539 |
> |
io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp, |
| 3540 |
> |
io/SectionParserManager.cpp, utils/LocalIndexManager.hpp, |
| 3541 |
> |
utils/TypeContainer.hpp: begin to fix bugs |
| 3542 |
> |
|
| 3543 |
> |
2004-12-02 19:26 tim |
| 3544 |
> |
|
| 3545 |
> |
* src/utils/Trim.cpp: file Trim.cpp was initially added on branch |
| 3546 |
> |
new_design. |
| 3547 |
> |
|
| 3548 |
> |
2004-12-02 19:26 tim |
| 3549 |
> |
|
| 3550 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 3551 |
> |
UseTheForce/ForceFieldCreator.cpp, |
| 3552 |
> |
UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp, |
| 3553 |
> |
integrators/IntegratorCreator.cpp, |
| 3554 |
> |
integrators/IntegratorFactory.cpp, io/SectionParserManager.cpp, |
| 3555 |
> |
io/SectionParserManager.hpp, utils/Makefile, |
| 3556 |
> |
utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a |
| 3557 |
> |
bug in countTokens in StringTokenizer |
| 3558 |
> |
|
| 3559 |
> |
2004-12-02 19:06 tim |
| 3560 |
> |
|
| 3561 |
> |
* forceFields/newDUFF.frc: minor fix |
| 3562 |
> |
|
| 3563 |
> |
2004-12-02 18:15 tim |
| 3564 |
> |
|
| 3565 |
> |
* forceFields/newDUFF.frc: new ForceField format |
| 3566 |
> |
|
| 3567 |
> |
2004-12-02 17:15 tim |
| 3568 |
> |
|
| 3569 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 3570 |
> |
UseTheForce/ForceFieldCreator.cpp, |
| 3571 |
> |
UseTheForce/ForceFieldCreator.hpp, |
| 3572 |
> |
UseTheForce/ForceFieldFactory.cpp, |
| 3573 |
> |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
| 3574 |
> |
applications/oopse/oopse.cpp, integrators/IntegratorCreator.cpp, |
| 3575 |
> |
integrators/IntegratorCreator.hpp, |
| 3576 |
> |
integrators/IntegratorFactory.cpp, |
| 3577 |
> |
integrators/IntegratorFactory.hpp, integrators/Makefile, |
| 3578 |
> |
integrators/NPTf.cpp, integrators/NPTf.hpp, integrators/NPTi.cpp, |
| 3579 |
> |
integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
| 3580 |
> |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
| 3581 |
> |
integrators/NVT.cpp, integrators/NVT.hpp, |
| 3582 |
> |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
| 3583 |
> |
types/Makefile: refine factory pattern to make it initialized |
| 3584 |
> |
correctly |
| 3585 |
> |
|
| 3586 |
> |
2004-12-02 17:15 tim |
| 3587 |
> |
|
| 3588 |
> |
* src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp |
| 3589 |
> |
was initially added on branch new_design. |
| 3590 |
> |
|
| 3591 |
> |
2004-12-02 17:15 tim |
| 3592 |
> |
|
| 3593 |
> |
* src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp |
| 3594 |
> |
was initially added on branch new_design. |
| 3595 |
> |
|
| 3596 |
> |
2004-12-02 17:15 tim |
| 3597 |
> |
|
| 3598 |
> |
* src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp |
| 3599 |
> |
was initially added on branch new_design. |
| 3600 |
> |
|
| 3601 |
> |
2004-12-02 17:15 tim |
| 3602 |
> |
|
| 3603 |
> |
* src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp |
| 3604 |
> |
was initially added on branch new_design. |
| 3605 |
> |
|
| 3606 |
> |
2004-12-02 11:53 tim |
| 3607 |
> |
|
| 3608 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, |
| 3609 |
> |
types/DirectionalAtomType.cpp, types/Makefile: oopse get built |
| 3610 |
> |
|
| 3611 |
> |
2004-12-02 11:04 tim |
| 3612 |
> |
|
| 3613 |
> |
* src/: applications/simpleBuilder/LatticeCreator.cpp, |
| 3614 |
> |
applications/simpleBuilder/LatticeCreator.hpp, |
| 3615 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
| 3616 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
| 3617 |
> |
applications/simpleBuilder/simpleBuilder.cpp, brains/Exclude.cpp, |
| 3618 |
> |
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
| 3619 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 3620 |
> |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
| 3621 |
> |
brains/SnapshotManager.hpp, brains/Stats.cpp, |
| 3622 |
> |
constraints/ZconsData.hpp, io/DumpWriter.cpp, io/LinkedAssign.hpp, |
| 3623 |
> |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp, |
| 3624 |
> |
io/basic_ifstrstream.hpp, primitives/Bend.hpp, |
| 3625 |
> |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
| 3626 |
> |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 3627 |
> |
types/OplsTorsionType.hpp, types/ShapeAtomType.hpp, |
| 3628 |
> |
utils/PropertyMap.hpp, utils/TypeContainer.hpp, |
| 3629 |
> |
visitors/AtomVisitor.cpp, visitors/CompositeVisitor.cpp, |
| 3630 |
> |
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
| 3631 |
> |
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 3632 |
> |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still |
| 3633 |
> |
have two linking problem |
| 3634 |
> |
|
| 3635 |
> |
2004-12-02 00:17 tim |
| 3636 |
> |
|
| 3637 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 3638 |
> |
applications/simpleBuilder/Lattice.cpp, |
| 3639 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
| 3640 |
> |
constraints/ZConstraint.cpp, io/DumpWriter.cpp, io/ZConsReader.cpp, |
| 3641 |
> |
io/ZConsWriter.cpp, minimizers/CGFamilyMinimizer.cpp, |
| 3642 |
> |
minimizers/OOPSEMinimizer.cpp, minimizers/SDMinimizer.cpp, |
| 3643 |
> |
restraints/Restraints.cpp, visitors/AtomVisitor.cpp, |
| 3644 |
> |
visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp, |
| 3645 |
> |
visitors/ZconsVisitor.cpp: change endl to std::endl |
| 3646 |
> |
|
| 3647 |
> |
2004-12-02 00:14 tim |
| 3648 |
> |
|
| 3649 |
> |
* src/: UseTheForce/Shapes_FF.cpp, |
| 3650 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, |
| 3651 |
> |
applications/simpleBuilder/BaseLattice.hpp, |
| 3652 |
> |
applications/simpleBuilder/Lattice.hpp, |
| 3653 |
> |
applications/simpleBuilder/LatticeCreator.hpp, |
| 3654 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
| 3655 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
| 3656 |
> |
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
| 3657 |
> |
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
| 3658 |
> |
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
| 3659 |
> |
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
| 3660 |
> |
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 3661 |
> |
visitors/RigidBodyVisitor.hpp: minor fix |
| 3662 |
> |
|
| 3663 |
> |
2004-12-02 00:09 tim |
| 3664 |
> |
|
| 3665 |
> |
* src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp: |
| 3666 |
> |
remove StreamTokenizer |
| 3667 |
> |
|
| 3668 |
> |
2004-12-02 00:06 tim |
| 3669 |
> |
|
| 3670 |
> |
* src/: UseTheForce/Shapes_FF.cpp, |
| 3671 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
| 3672 |
> |
applications/simpleBuilder/simpleBuilder.cpp, brains/Thermo.cpp, |
| 3673 |
> |
io/ZConsWriter.cpp, math/randomSPRNG.cpp, |
| 3674 |
> |
restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using |
| 3675 |
> |
namespace std in .cpp file |
| 3676 |
> |
|
| 3677 |
> |
2004-12-02 00:04 tim |
| 3678 |
> |
|
| 3679 |
> |
* src/: UseTheForce/Shapes_FF.cpp, |
| 3680 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, |
| 3681 |
> |
applications/simpleBuilder/BaseLattice.hpp, |
| 3682 |
> |
applications/simpleBuilder/Lattice.cpp, |
| 3683 |
> |
applications/simpleBuilder/Lattice.hpp, |
| 3684 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
| 3685 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
| 3686 |
> |
applications/simpleBuilder/MoLocator.cpp, |
| 3687 |
> |
applications/simpleBuilder/MoLocator.hpp, brains/SkipList.cpp, |
| 3688 |
> |
brains/SkipList.hpp, constraints/ZconsData.hpp, io/ZConsReader.cpp, |
| 3689 |
> |
io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
| 3690 |
> |
minimizers/MinimizerParameterSet.hpp, |
| 3691 |
> |
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
| 3692 |
> |
minimizers/PRCG.cpp, primitives/Atom.cpp, primitives/RigidBody.cpp, |
| 3693 |
> |
restraints/Restraints.cpp, restraints/Restraints.hpp, |
| 3694 |
> |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 3695 |
> |
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
| 3696 |
> |
utils/GenericData.hpp, visitors/CompositeVisitor.cpp, |
| 3697 |
> |
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 3698 |
> |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding |
| 3699 |
> |
qulified name prefix std |
| 3700 |
> |
|
| 3701 |
> |
2004-12-01 23:55 tim |
| 3702 |
> |
|
| 3703 |
> |
* src/: UseTheForce/Shapes_FF.cpp, |
| 3704 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, |
| 3705 |
> |
applications/simpleBuilder/BaseLattice.hpp, |
| 3706 |
> |
applications/simpleBuilder/Lattice.hpp, |
| 3707 |
> |
applications/simpleBuilder/LatticeCreator.hpp, |
| 3708 |
> |
applications/simpleBuilder/LatticeFactory.cpp, |
| 3709 |
> |
applications/simpleBuilder/LatticeFactory.hpp, |
| 3710 |
> |
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
| 3711 |
> |
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
| 3712 |
> |
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
| 3713 |
> |
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
| 3714 |
> |
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 3715 |
> |
visitors/RigidBodyVisitor.hpp: replace string by std::string |
| 3716 |
> |
|
| 3717 |
> |
2004-12-01 22:12 tim |
| 3718 |
> |
|
| 3719 |
> |
* make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp, |
| 3720 |
> |
src/applications/simpleBuilder/BaseLattice.hpp, |
| 3721 |
> |
src/applications/simpleBuilder/Lattice.hpp, |
| 3722 |
> |
src/applications/simpleBuilder/LatticeCreator.hpp, |
| 3723 |
> |
src/applications/simpleBuilder/LatticeFactory.hpp, |
| 3724 |
> |
src/applications/simpleBuilder/MoLocator.hpp, |
| 3725 |
> |
src/brains/SimInfo.cpp, src/brains/SkipList.hpp, |
| 3726 |
> |
src/brains/Snapshot.hpp, src/constraints/ZconsData.hpp, |
| 3727 |
> |
src/integrators/IntegratorFactory.hpp, src/io/Globals.hpp, |
| 3728 |
> |
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
| 3729 |
> |
src/minimizers/OOPSEMinimizer.hpp, src/primitives/StuntDouble.hpp, |
| 3730 |
> |
src/types/MoleculeStamp.hpp, src/types/ShapeAtomType.hpp, |
| 3731 |
> |
src/utils/Makefile, src/utils/StringUtils.cpp, |
| 3732 |
> |
src/utils/StringUtils.hpp, src/utils/TypeInfo.hpp, |
| 3733 |
> |
src/utils/Utility.cpp, src/visitors/CompositeVisitor.hpp, |
| 3734 |
> |
src/visitors/RigidBodyVisitor.hpp, test/brains/DirectionalAtom.cpp, |
| 3735 |
> |
test/brains/RigidBody.cpp: replace misuse of using namespace std in |
| 3736 |
> |
header files |
| 3737 |
> |
|
| 3738 |
> |
2004-12-01 21:23 tim |
| 3739 |
> |
|
| 3740 |
> |
* src/: primitives/Atom.hpp, primitives/RigidBody.hpp, |
| 3741 |
> |
primitives/StuntDouble.hpp, utils/TypeContainer.hpp, |
| 3742 |
> |
utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp: |
| 3743 |
> |
begin to fix linking problem |
| 3744 |
> |
|
| 3745 |
> |
2004-12-01 21:08 tim |
| 3746 |
> |
|
| 3747 |
> |
* src/: applications/oopse/oopse.cpp, brains/Stats.cpp, |
| 3748 |
> |
brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile, |
| 3749 |
> |
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
| 3750 |
> |
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
| 3751 |
> |
integrators/NPTxyz.cpp, integrators/VelocityVerletIntegrator.hpp, |
| 3752 |
> |
math/SquareMatrix3.hpp, primitives/Atom.hpp, |
| 3753 |
> |
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
| 3754 |
> |
utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled, |
| 3755 |
> |
still has some linking problem |
| 3756 |
> |
|
| 3757 |
> |
2004-12-01 19:26 tim |
| 3758 |
> |
|
| 3759 |
> |
* src/: integrators/NVT.cpp, integrators/NVT.hpp, |
| 3760 |
> |
utils/OOPSEConstant.hpp: NVT get built |
| 3761 |
> |
|
| 3762 |
> |
2004-12-01 19:09 tim |
| 3763 |
> |
|
| 3764 |
> |
* src/integrators/DLM.cpp: file DLM.cpp was initially added on |
| 3765 |
> |
branch new_design. |
| 3766 |
> |
|
| 3767 |
> |
2004-12-01 19:09 tim |
| 3768 |
> |
|
| 3769 |
> |
* src/integrators/DLM.hpp: file DLM.hpp was initially added on |
| 3770 |
> |
branch new_design. |
| 3771 |
> |
|
| 3772 |
> |
2004-12-01 19:09 tim |
| 3773 |
> |
|
| 3774 |
> |
* src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, |
| 3775 |
> |
brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
| 3776 |
> |
brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp, |
| 3777 |
> |
integrators/Integrator.hpp, integrators/Makefile, |
| 3778 |
> |
integrators/NVE.cpp, integrators/NVE.hpp, |
| 3779 |
> |
integrators/RotationAlgorithm.hpp, |
| 3780 |
> |
integrators/VelocityVerletIntegrator.cpp, |
| 3781 |
> |
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE |
| 3782 |
> |
get built |
| 3783 |
> |
|
| 3784 |
> |
2004-12-01 19:09 tim |
| 3785 |
> |
|
| 3786 |
> |
* src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp |
| 3787 |
> |
was initially added on branch new_design. |
| 3788 |
> |
|
| 3789 |
> |
2004-12-01 17:45 tim |
| 3790 |
> |
|
| 3791 |
> |
* src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp, |
| 3792 |
> |
integrators/IntegratorFactory.cpp, |
| 3793 |
> |
integrators/IntegratorFactory.hpp, integrators/Makefile, |
| 3794 |
> |
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
| 3795 |
> |
integrators/VelocityVerletIntegrator.cpp, |
| 3796 |
> |
integrators/VelocityVerletIntegrator.hpp, io/DumpWrite.hpp, |
| 3797 |
> |
io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp, |
| 3798 |
> |
io/StatWriter.hpp: rename DumpWrite to DumpWriter |
| 3799 |
> |
|
| 3800 |
> |
2004-12-01 17:45 tim |
| 3801 |
> |
|
| 3802 |
> |
* src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on |
| 3803 |
> |
branch new_design. |
| 3804 |
> |
|
| 3805 |
> |
2004-12-01 15:05 tim |
| 3806 |
> |
|
| 3807 |
> |
* src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp, |
| 3808 |
> |
io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile, |
| 3809 |
> |
utils/Utility.cpp, utils/Utility.hpp, visitors/AtomData.hpp, |
| 3810 |
> |
visitors/BaseVisitor.hpp, visitors/OtherVisitor.cpp, |
| 3811 |
> |
visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp, |
| 3812 |
> |
visitors/ZconsVisitor.hpp: visitors get built |
| 3813 |
> |
|
| 3814 |
> |
2004-12-01 14:32 chrisfen |
| 3815 |
> |
|
| 3816 |
> |
* samples/water/tip3p_ice/tp3.md: fixed a sample |
| 3817 |
> |
|
| 3818 |
> |
2004-12-01 14:10 tim |
| 3819 |
> |
|
| 3820 |
> |
* src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp, |
| 3821 |
> |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 3822 |
> |
src/types/AtomType.hpp, src/utils/Utility.hpp, |
| 3823 |
> |
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
| 3824 |
> |
src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp: |
| 3825 |
> |
spell check |
| 3826 |
> |
|
| 3827 |
> |
2004-12-01 13:42 tim |
| 3828 |
> |
|
| 3829 |
> |
* src/: UseTheForce/DarkSide/atype.F90, |
| 3830 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 3831 |
> |
io/ElectrostaticAtomTypesSectionParser.hpp, primitives/Atom.hpp, |
| 3832 |
> |
primitives/DirectionalAtom.cpp, primitives/RigidBody.cpp, |
| 3833 |
> |
primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator |
| 3834 |
> |
and constraint, other directories get built |
| 3835 |
> |
|
| 3836 |
> |
2004-12-01 12:38 tim |
| 3837 |
> |
|
| 3838 |
> |
* src/: brains/DataStorage.cpp, brains/DataStorage.hpp, |
| 3839 |
> |
brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
| 3840 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 3841 |
> |
io/ElectrostaticAtomTypesSectionParser.hpp, |
| 3842 |
> |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 3843 |
> |
primitives/GhostBend.cpp, primitives/RigidBody.cpp, |
| 3844 |
> |
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
| 3845 |
> |
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
| 3846 |
> |
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
| 3847 |
> |
refactory AtomType |
| 3848 |
> |
|
| 3849 |
> |
2004-11-30 22:11 tim |
| 3850 |
> |
|
| 3851 |
> |
* src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change |
| 3852 |
> |
|
| 3853 |
> |
2004-11-30 21:30 tim |
| 3854 |
> |
|
| 3855 |
> |
* src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change |
| 3856 |
> |
NumericConstant |
| 3857 |
> |
|
| 3858 |
> |
2004-11-30 21:24 tim |
| 3859 |
> |
|
| 3860 |
> |
* src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp, |
| 3861 |
> |
primitives/RigidBody.cpp: minor fix |
| 3862 |
> |
|
| 3863 |
> |
2004-11-30 18:14 tim |
| 3864 |
> |
|
| 3865 |
> |
* src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
| 3866 |
> |
io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile, |
| 3867 |
> |
io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io |
| 3868 |
> |
get built, next is integrator |
| 3869 |
> |
|
| 3870 |
> |
2004-11-30 17:43 tim |
| 3871 |
> |
|
| 3872 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 3873 |
> |
UseTheForce/ForceField.hpp, brains/SimCreator.cpp, |
| 3874 |
> |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 3875 |
> |
io/BASS_interface.cpp, primitives/StuntDouble.hpp, |
| 3876 |
> |
utils/StringUtils.hpp: brains get built |
| 3877 |
> |
|
| 3878 |
> |
2004-11-30 15:50 tim |
| 3879 |
> |
|
| 3880 |
> |
* src/: brains/ForceManager.cpp, brains/Makefile, |
| 3881 |
> |
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
| 3882 |
> |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
| 3883 |
> |
utils/StringUtils.hpp: brains get built, io is next |
| 3884 |
> |
|
| 3885 |
> |
2004-11-30 14:58 tim |
| 3886 |
> |
|
| 3887 |
> |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
| 3888 |
> |
brains/ForceManager.cpp, brains/ForceManager.hpp, |
| 3889 |
> |
brains/MoleculeCreator.cpp, brains/SimCreator.hpp, |
| 3890 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 3891 |
> |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
| 3892 |
> |
brains/SnapShot.cpp, brains/Stats.cpp, brains/Stats.hpp, |
| 3893 |
> |
brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, |
| 3894 |
> |
math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo |
| 3895 |
> |
|
| 3896 |
> |
2004-11-30 14:58 tim |
| 3897 |
> |
|
| 3898 |
> |
* src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially |
| 3899 |
> |
added on branch new_design. |
| 3900 |
> |
|
| 3901 |
> |
2004-11-30 12:54 tim |
| 3902 |
> |
|
| 3903 |
> |
* src/: primitives/Bend.hpp, primitives/Bond.hpp, |
| 3904 |
> |
primitives/StuntDouble.hpp, primitives/Torsion.hpp, |
| 3905 |
> |
utils/LocalIndexManager.hpp: more get fixed |
| 3906 |
> |
|
| 3907 |
> |
2004-11-30 00:03 tim |
| 3908 |
> |
|
| 3909 |
> |
* src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was |
| 3910 |
> |
initially added on branch new_design. |
| 3911 |
> |
|
| 3912 |
> |
2004-11-30 00:03 tim |
| 3913 |
> |
|
| 3914 |
> |
* src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename |
| 3915 |
> |
LocalndexManager.hpp to LocalIndexManager.hpp |
| 3916 |
> |
|
| 3917 |
> |
2004-11-29 23:43 tim |
| 3918 |
> |
|
| 3919 |
> |
* src/: io/BendTypesSectionParser.cpp, |
| 3920 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 3921 |
> |
io/BondTypesSectionParser.hpp, io/SectionParserManager.cpp, |
| 3922 |
> |
io/SectionParserManager.hpp, io/TorsionTypesSectionParser.cpp, |
| 3923 |
> |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
| 3924 |
> |
types/PolynomialTorsionType.hpp: Section Parsers get compiled |
| 3925 |
> |
|
| 3926 |
> |
2004-11-29 23:14 tim |
| 3927 |
> |
|
| 3928 |
> |
* src/: io/BendTypesSectionParser.cpp, |
| 3929 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 3930 |
> |
io/BondTypesSectionParser.hpp, io/TorsionTypesSectionParser.cpp, |
| 3931 |
> |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor |
| 3932 |
> |
fixed |
| 3933 |
> |
|
| 3934 |
> |
2004-11-29 22:49 tim |
| 3935 |
> |
|
| 3936 |
> |
* src/: io/TorsionTypesSectionParser.cpp, |
| 3937 |
> |
io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp, |
| 3938 |
> |
types/CubicTorsionType.hpp, types/PolynomialBendType.hpp, |
| 3939 |
> |
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
| 3940 |
> |
types/QuarticTorsionType.hpp: minor fixed |
| 3941 |
> |
|
| 3942 |
> |
2004-11-29 22:32 tim |
| 3943 |
> |
|
| 3944 |
> |
* src/: io/TorsionTypesSectionParser.cpp, |
| 3945 |
> |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
| 3946 |
> |
types/PolynomialTorsionType.hpp: #inlcude statement can not be |
| 3947 |
> |
embedded |
| 3948 |
> |
|
| 3949 |
> |
2004-11-29 16:42 tim |
| 3950 |
> |
|
| 3951 |
> |
* test/math/: Makefile, PolynomialTestCase.cpp, |
| 3952 |
> |
PolynomialTestCase.hpp: add PolynomialTestCase |
| 3953 |
> |
|
| 3954 |
> |
2004-11-29 16:42 tim |
| 3955 |
> |
|
| 3956 |
> |
* src/math/Polynomial.hpp: Polynomial passes unit test |
| 3957 |
> |
|
| 3958 |
> |
2004-11-29 15:03 tim |
| 3959 |
> |
|
| 3960 |
> |
* src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename |
| 3961 |
> |
QuarticTorsion.hpp to QuarticTorsionType.hpp |
| 3962 |
> |
|
| 3963 |
> |
2004-11-29 15:03 tim |
| 3964 |
> |
|
| 3965 |
> |
* src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was |
| 3966 |
> |
initially added on branch new_design. |
| 3967 |
> |
|
| 3968 |
> |
2004-11-29 14:56 tim |
| 3969 |
> |
|
| 3970 |
> |
* src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was |
| 3971 |
> |
initially added on branch new_design. |
| 3972 |
> |
|
| 3973 |
> |
2004-11-29 14:56 tim |
| 3974 |
> |
|
| 3975 |
> |
* src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add |
| 3976 |
> |
CubicTorsionType and QuarticTorsionType |
| 3977 |
> |
|
| 3978 |
> |
2004-11-29 14:56 tim |
| 3979 |
> |
|
| 3980 |
> |
* src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was |
| 3981 |
> |
initially added on branch new_design. |
| 3982 |
> |
|
| 3983 |
> |
2004-11-29 13:00 tim |
| 3984 |
> |
|
| 3985 |
> |
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
| 3986 |
> |
types/CubicBendType.hpp, types/CubicBondType.hpp, |
| 3987 |
> |
types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get |
| 3988 |
> |
fixed |
| 3989 |
> |
|
| 3990 |
> |
2004-11-29 12:59 tim |
| 3991 |
> |
|
| 3992 |
> |
* src/utils/Trim.hpp: file Trim.hpp was initially added on branch |
| 3993 |
> |
new_design. |
| 3994 |
> |
|
| 3995 |
> |
2004-11-29 12:59 tim |
| 3996 |
> |
|
| 3997 |
> |
* src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim |
| 3998 |
> |
Algorithm for std::string |
| 3999 |
> |
|
| 4000 |
> |
2004-11-29 10:52 tim |
| 4001 |
> |
|
| 4002 |
> |
* src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove |
| 4003 |
> |
some useless files |
| 4004 |
> |
|
| 4005 |
> |
2004-11-29 10:50 tim |
| 4006 |
> |
|
| 4007 |
> |
* src/io/: BondTypesSectionParser.cpp, |
| 4008 |
> |
ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp, |
| 4009 |
> |
ElectrostaticAtomTypesSectionParser.cpp, |
| 4010 |
> |
HarmonicBondTypesSectionParser.cpp, |
| 4011 |
> |
HarmonicBondTypesSectionParser.hpp, |
| 4012 |
> |
LennardJonesAtomTypesSectionParser.cpp, Makefile, |
| 4013 |
> |
SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp, |
| 4014 |
> |
StickyAtomTypesSectionParser.hpp: more files get fixed |
| 4015 |
> |
|
| 4016 |
> |
2004-11-29 10:27 tim |
| 4017 |
> |
|
| 4018 |
> |
* src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp, |
| 4019 |
> |
DirectionalAtomTypesSectionParser.cpp, |
| 4020 |
> |
EAMAtomTypesSectionParser.cpp, EAMAtomTypesSectionParser.hpp, |
| 4021 |
> |
Makefile, SectionParser.cpp, SectionParser.hpp, |
| 4022 |
> |
SectionParserManager.cpp, SectionParserManager.hpp: part of io get |
| 4023 |
> |
built |
| 4024 |
> |
|
| 4025 |
> |
2004-11-29 09:49 tim |
| 4026 |
> |
|
| 4027 |
> |
* src/types/UreyBradleyBendType.hpp: types get built |
| 4028 |
> |
|
| 4029 |
> |
2004-11-29 09:40 tim |
| 4030 |
> |
|
| 4031 |
> |
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp: |
| 4032 |
> |
types get built |
| 4033 |
> |
|
| 4034 |
> |
2004-11-25 21:13 tim |
| 4035 |
> |
|
| 4036 |
> |
* src/: UseTheForce/ForceField.hpp, |
| 4037 |
> |
io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp, |
| 4038 |
> |
types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some |
| 4039 |
> |
files |
| 4040 |
|
|
| 4041 |
< |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
| 4042 |
< |
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
| 4043 |
< |
class |
| 4041 |
> |
2004-11-25 15:18 tim |
| 4042 |
> |
|
| 4043 |
> |
* src/types/QuarticBondType.hpp: file QuarticBondType.hpp was |
| 4044 |
> |
initially added on branch new_design. |
| 4045 |
> |
|
| 4046 |
> |
2004-11-25 15:18 tim |
| 4047 |
> |
|
| 4048 |
> |
* src/: io/AtomTypesSectionParser.cpp, |
| 4049 |
> |
io/BondTypesSectionParser.cpp, |
| 4050 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
| 4051 |
> |
types/QuadraticBendType.hpp, types/QuadraticBondType.hpp, |
| 4052 |
> |
types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some |
| 4053 |
> |
files |
| 4054 |
> |
|
| 4055 |
> |
2004-11-25 15:18 tim |
| 4056 |
> |
|
| 4057 |
> |
* src/types/QuarticBendType.hpp: file QuarticBendType.hpp was |
| 4058 |
> |
initially added on branch new_design. |
| 4059 |
> |
|
| 4060 |
> |
2004-11-24 17:12 tim |
| 4061 |
> |
|
| 4062 |
> |
* src/: io/AtomTypesSectionParser.cpp, |
| 4063 |
> |
io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp, |
| 4064 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 4065 |
> |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 4066 |
> |
io/ChargeAtomTypesSectionParser.hpp, |
| 4067 |
> |
io/DipoleAtomTypesSectionParser.cpp, |
| 4068 |
> |
io/DipoleAtomTypesSectionParser.hpp, |
| 4069 |
> |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
| 4070 |
> |
io/DumpReader.hpp, io/EAMAtomTypesSectionParser.cpp, |
| 4071 |
> |
io/EAMAtomTypesSectionParser.hpp, |
| 4072 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 4073 |
> |
io/ElectrostaticAtomTypesSectionParser.hpp, |
| 4074 |
> |
io/HarmonicBondTypesSectionParser.hpp, |
| 4075 |
> |
io/LennardJonesAtomTypesSectionParser.cpp, |
| 4076 |
> |
io/LennardJonesAtomTypesSectionParser.hpp, io/Makefile, |
| 4077 |
> |
io/SectionParser.hpp, io/SectionParserManager.hpp, |
| 4078 |
> |
io/StickyAtomTypesSectionParser.cpp, |
| 4079 |
> |
io/StickyAtomTypesSectionParser.hpp, |
| 4080 |
> |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
| 4081 |
> |
utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built |
| 4082 |
> |
|
| 4083 |
> |
2004-11-24 16:33 tim |
| 4084 |
> |
|
| 4085 |
> |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp, |
| 4086 |
> |
ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp, |
| 4087 |
> |
LJFF.cpp, Makefile: UseTheForce get built |
| 4088 |
> |
|
| 4089 |
> |
2004-11-24 15:55 tim |
| 4090 |
> |
|
| 4091 |
> |
* src/: math/RectMatrix.hpp, primitives/Bend.cpp, |
| 4092 |
> |
primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp, |
| 4093 |
> |
primitives/Makefile, primitives/Molecule.cpp, |
| 4094 |
> |
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
| 4095 |
> |
primitives/StuntDouble.hpp, primitives/Torsion.cpp, |
| 4096 |
> |
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
| 4097 |
> |
primitives/UreyBradleyBend.hpp: types and primitives get built |
| 4098 |
> |
|
| 4099 |
> |
2004-11-24 14:49 tim |
| 4100 |
> |
|
| 4101 |
> |
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
| 4102 |
> |
StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint |
| 4103 |
> |
StringTokenizerTestCase |
| 4104 |
> |
|
| 4105 |
> |
2004-11-24 14:49 tim |
| 4106 |
> |
|
| 4107 |
> |
* src/utils/: GenericData.hpp, StringTokenizer.cpp, |
| 4108 |
> |
StringTokenizer.hpp: StringTokenizer passes unit test |
| 4109 |
> |
|
| 4110 |
> |
2004-11-24 13:20 tim |
| 4111 |
> |
|
| 4112 |
> |
* ChangeLog, make/Makefile.in, src/UseTheForce/Makefile, |
| 4113 |
> |
src/io/Makefile, src/primitives/Makefile, src/utils/Makefile: |
| 4114 |
> |
change Makefile |
| 4115 |
> |
|
| 4116 |
> |
2004-11-24 13:06 chrisfen |
| 4117 |
> |
|
| 4118 |
> |
* src/io/RestraintReader.cpp: improved restraints - mpi should work |
| 4119 |
> |
fine |
| 4120 |
> |
|
| 4121 |
> |
2004-11-24 13:06 chrisfen |
| 4122 |
> |
|
| 4123 |
> |
* src/integrators/Integrator.cpp: improved restraints |
| 4124 |
> |
|
| 4125 |
> |
2004-11-24 13:05 chrisfen |
| 4126 |
> |
|
| 4127 |
> |
* samples/water/tip3p_ice/tp3.md: oops... |
| 4128 |
> |
|
| 4129 |
> |
2004-11-24 12:42 tim |
| 4130 |
> |
|
| 4131 |
> |
* src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, |
| 4132 |
> |
brains/DataStorage.hpp, brains/SimCreator.cpp, |
| 4133 |
> |
brains/SimCreator.hpp, integrators/Integrator.hpp, |
| 4134 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 4135 |
> |
primitives/DirectionalAtom.cpp: add SetForceManager method to |
| 4136 |
> |
integrator |
| 4137 |
> |
|
| 4138 |
> |
2004-11-23 18:12 tim |
| 4139 |
> |
|
| 4140 |
> |
* src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, |
| 4141 |
> |
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
| 4142 |
> |
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
| 4143 |
> |
integrators/NPTxyz.cpp, integrators/NPTxyz.hpp, |
| 4144 |
> |
integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp, |
| 4145 |
> |
integrators/NVT.hpp, integrators/Velocitizer.cpp, |
| 4146 |
> |
integrators/VelocityVerletIntegrator.cpp, |
| 4147 |
> |
integrators/VelocityVerletIntegrator.hpp, |
| 4148 |
> |
types/UreyBradleyBendType.hpp: refactory NPT integrator |
| 4149 |
> |
|
| 4150 |
> |
2004-11-23 17:50 chrisfen |
| 4151 |
> |
|
| 4152 |
> |
* samples/water/tip3p_ice/tp3.md: Back to normal... Oh... |
| 4153 |
> |
Restraints should work in parallel now |
| 4154 |
> |
|
| 4155 |
> |
2004-11-23 17:48 chrisfen |
| 4156 |
> |
|
| 4157 |
> |
* src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 4158 |
> |
brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
| 4159 |
> |
integrators/Integrator.cpp, integrators/Integrator.hpp, |
| 4160 |
> |
io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp, |
| 4161 |
> |
io/RestraintReader.cpp, io/RestraintWriter.cpp, |
| 4162 |
> |
restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements |
| 4163 |
> |
to restraints |
| 4164 |
> |
|
| 4165 |
> |
2004-11-23 17:47 chrisfen |
| 4166 |
> |
|
| 4167 |
> |
* samples/water/tip3p_ice/tp3.md: just some testing changes, I'll |
| 4168 |
> |
return to the original on next commit |
| 4169 |
> |
|
| 4170 |
> |
2004-11-23 12:53 tim |
| 4171 |
> |
|
| 4172 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 4173 |
> |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 4174 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
| 4175 |
> |
io/ChargeAtomTypesSectionParser.cpp, |
| 4176 |
> |
io/DirectionalAtomTypesSectionParser.hpp, |
| 4177 |
> |
io/EAMAtomTypesSectionParser.cpp, |
| 4178 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 4179 |
> |
io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
| 4180 |
> |
io/SectionParser.hpp, types/DirectionalAtomType.cpp, |
| 4181 |
> |
utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser |
| 4182 |
> |
|
| 4183 |
> |
2004-11-23 12:53 tim |
| 4184 |
> |
|
| 4185 |
> |
* src/io/ElectrostaticAtomTypesSectionParser.hpp: file |
| 4186 |
> |
ElectrostaticAtomTypesSectionParser.hpp was initially added on |
| 4187 |
> |
branch new_design. |
| 4188 |
> |
|
| 4189 |
> |
2004-11-23 12:53 tim |
| 4190 |
> |
|
| 4191 |
> |
* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
| 4192 |
> |
ElectrostaticAtomTypesSectionParser.cpp was initially added on |
| 4193 |
> |
branch new_design. |
| 4194 |
> |
|
| 4195 |
> |
2004-11-23 01:03 tim |
| 4196 |
> |
|
| 4197 |
> |
* src/: io/EAMAtomTypesSectionParser.cpp, |
| 4198 |
> |
io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, |
| 4199 |
> |
types/AtomType.hpp, types/DirectionalAtomType.cpp, |
| 4200 |
> |
types/DirectionalAtomType.hpp: add EAM AtomType Section Parser |
| 4201 |
> |
|
| 4202 |
> |
2004-11-23 01:03 tim |
| 4203 |
> |
|
| 4204 |
> |
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
| 4205 |
> |
was initially added on branch new_design. |
| 4206 |
> |
|
| 4207 |
> |
2004-11-23 01:03 tim |
| 4208 |
> |
|
| 4209 |
> |
* src/io/EAMAtomTypesSectionParser.hpp: file |
| 4210 |
> |
EAMAtomTypesSectionParser.hpp was initially added on branch |
| 4211 |
> |
new_design. |
| 4212 |
> |
|
| 4213 |
> |
2004-11-23 01:03 tim |
| 4214 |
> |
|
| 4215 |
> |
* src/io/EAMAtomTypesSectionParser.cpp: file |
| 4216 |
> |
EAMAtomTypesSectionParser.cpp was initially added on branch |
| 4217 |
> |
new_design. |
| 4218 |
> |
|
| 4219 |
> |
2004-11-22 23:35 tim |
| 4220 |
> |
|
| 4221 |
> |
* src/io/TorsionTypesSectionParser.hpp: file |
| 4222 |
> |
TorsionTypesSectionParser.hpp was initially added on branch |
| 4223 |
> |
new_design. |
| 4224 |
> |
|
| 4225 |
> |
2004-11-22 23:35 tim |
| 4226 |
> |
|
| 4227 |
> |
* src/io/BendTypesSectionParser.hpp: file |
| 4228 |
> |
BendTypesSectionParser.hpp was initially added on branch |
| 4229 |
> |
new_design. |
| 4230 |
> |
|
| 4231 |
> |
2004-11-22 23:35 tim |
| 4232 |
> |
|
| 4233 |
> |
* src/io/BondTypesSectionParser.hpp: file |
| 4234 |
> |
BondTypesSectionParser.hpp was initially added on branch |
| 4235 |
> |
new_design. |
| 4236 |
> |
|
| 4237 |
> |
2004-11-22 23:35 tim |
| 4238 |
> |
|
| 4239 |
> |
* src/io/BondTypesSectionParser.cpp: file |
| 4240 |
> |
BondTypesSectionParser.cpp was initially added on branch |
| 4241 |
> |
new_design. |
| 4242 |
> |
|
| 4243 |
> |
2004-11-22 23:35 tim |
| 4244 |
> |
|
| 4245 |
> |
* src/io/TorsionTypesSectionParser.cpp: file |
| 4246 |
> |
TorsionTypesSectionParser.cpp was initially added on branch |
| 4247 |
> |
new_design. |
| 4248 |
> |
|
| 4249 |
> |
2004-11-22 23:35 tim |
| 4250 |
> |
|
| 4251 |
> |
* src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, |
| 4252 |
> |
BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, |
| 4253 |
> |
TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add |
| 4254 |
> |
BondTypesSectionParser, BendTypesSectionParser and |
| 4255 |
> |
TorsionTypeSectionParser |
| 4256 |
> |
|
| 4257 |
> |
2004-11-22 23:35 tim |
| 4258 |
> |
|
| 4259 |
> |
* src/io/BendTypesSectionParser.cpp: file |
| 4260 |
> |
BendTypesSectionParser.cpp was initially added on branch |
| 4261 |
> |
new_design. |
| 4262 |
> |
|
| 4263 |
> |
2004-11-22 18:04 tim |
| 4264 |
> |
|
| 4265 |
> |
* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in |
| 4266 |
> |
DUFF and EAM |
| 4267 |
> |
|
| 4268 |
> |
2004-11-22 18:02 tim |
| 4269 |
> |
|
| 4270 |
> |
* src/io/: DirectionalAtomTypesParser.hpp, |
| 4271 |
> |
DirectionalAtomTypesSectionParser.hpp: adding section parsers |
| 4272 |
> |
|
| 4273 |
> |
2004-11-22 18:02 tim |
| 4274 |
> |
|
| 4275 |
> |
* src/io/DirectionalAtomTypesSectionParser.hpp: file |
| 4276 |
> |
DirectionalAtomTypesSectionParser.hpp was initially added on branch |
| 4277 |
> |
new_design. |
| 4278 |
> |
|
| 4279 |
> |
2004-11-22 15:55 tim |
| 4280 |
> |
|
| 4281 |
> |
* src/io/DipoleAtomTypesSectionParser.hpp: file |
| 4282 |
> |
DipoleAtomTypesSectionParser.hpp was initially added on branch |
| 4283 |
> |
new_design. |
| 4284 |
> |
|
| 4285 |
> |
2004-11-22 15:55 tim |
| 4286 |
> |
|
| 4287 |
> |
* src/io/AtomTypesSectionParser.hpp: file |
| 4288 |
> |
AtomTypesSectionParser.hpp was initially added on branch |
| 4289 |
> |
new_design. |
| 4290 |
> |
|
| 4291 |
> |
2004-11-22 15:55 tim |
| 4292 |
> |
|
| 4293 |
> |
* src/io/HarmonicBondTypesSectionParser.hpp: file |
| 4294 |
> |
HarmonicBondTypesSectionParser.hpp was initially added on branch |
| 4295 |
> |
new_design. |
| 4296 |
|
|
| 4297 |
+ |
2004-11-22 15:55 tim |
| 4298 |
+ |
|
| 4299 |
+ |
* src/io/StickyAtomTypesSectionParser.cpp: file |
| 4300 |
+ |
StickyAtomTypesSectionParser.cpp was initially added on branch |
| 4301 |
+ |
new_design. |
| 4302 |
+ |
|
| 4303 |
+ |
2004-11-22 15:55 tim |
| 4304 |
+ |
|
| 4305 |
+ |
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
| 4306 |
+ |
LennardJonesAtomTypesSectionParser.hpp was initially added on |
| 4307 |
+ |
branch new_design. |
| 4308 |
+ |
|
| 4309 |
+ |
2004-11-22 15:55 tim |
| 4310 |
+ |
|
| 4311 |
+ |
* src/io/HarmonicBondTypesSectionParser.cpp: file |
| 4312 |
+ |
HarmonicBondTypesSectionParser.cpp was initially added on branch |
| 4313 |
+ |
new_design. |
| 4314 |
+ |
|
| 4315 |
+ |
2004-11-22 15:55 tim |
| 4316 |
+ |
|
| 4317 |
+ |
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
| 4318 |
+ |
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
| 4319 |
+ |
new_design. |
| 4320 |
+ |
|
| 4321 |
+ |
2004-11-22 15:55 tim |
| 4322 |
+ |
|
| 4323 |
+ |
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
| 4324 |
+ |
was initially added on branch new_design. |
| 4325 |
+ |
|
| 4326 |
+ |
2004-11-22 15:55 tim |
| 4327 |
+ |
|
| 4328 |
+ |
* src/io/AtomTypesSectionParser.cpp: file |
| 4329 |
+ |
AtomTypesSectionParser.cpp was initially added on branch |
| 4330 |
+ |
new_design. |
| 4331 |
+ |
|
| 4332 |
+ |
2004-11-22 15:55 tim |
| 4333 |
+ |
|
| 4334 |
+ |
* src/io/ChargeAtomTypesSectionParser.cpp: file |
| 4335 |
+ |
ChargeAtomTypesSectionParser.cpp was initially added on branch |
| 4336 |
+ |
new_design. |
| 4337 |
+ |
|
| 4338 |
+ |
2004-11-22 15:55 tim |
| 4339 |
+ |
|
| 4340 |
+ |
* src/io/DipoleAtomTypesSectionParser.cpp: file |
| 4341 |
+ |
DipoleAtomTypesSectionParser.cpp was initially added on branch |
| 4342 |
+ |
new_design. |
| 4343 |
+ |
|
| 4344 |
+ |
2004-11-22 15:55 tim |
| 4345 |
+ |
|
| 4346 |
+ |
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
| 4347 |
+ |
LennardJonesAtomTypesSectionParser.cpp was initially added on |
| 4348 |
+ |
branch new_design. |
| 4349 |
+ |
|
| 4350 |
+ |
2004-11-22 15:55 tim |
| 4351 |
+ |
|
| 4352 |
+ |
* src/io/ChargeAtomTypesSectionParser.hpp: file |
| 4353 |
+ |
ChargeAtomTypesSectionParser.hpp was initially added on branch |
| 4354 |
+ |
new_design. |
| 4355 |
+ |
|
| 4356 |
+ |
2004-11-22 15:55 tim |
| 4357 |
+ |
|
| 4358 |
+ |
* src/io/StickyAtomTypesSectionParser.hpp: file |
| 4359 |
+ |
StickyAtomTypesSectionParser.hpp was initially added on branch |
| 4360 |
+ |
new_design. |
| 4361 |
+ |
|
| 4362 |
+ |
2004-11-22 15:55 tim |
| 4363 |
+ |
|
| 4364 |
+ |
* src/io/SectionParser.hpp: file SectionParser.hpp was initially |
| 4365 |
+ |
added on branch new_design. |
| 4366 |
+ |
|
| 4367 |
+ |
2004-11-22 15:55 tim |
| 4368 |
+ |
|
| 4369 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
| 4370 |
+ |
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
| 4371 |
+ |
brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
| 4372 |
+ |
integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
| 4373 |
+ |
io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 4374 |
+ |
io/ChargeAtomTypesSectionParser.hpp, |
| 4375 |
+ |
io/DipoleAtomTypesSectionParser.cpp, |
| 4376 |
+ |
io/DipoleAtomTypesSectionParser.hpp, |
| 4377 |
+ |
io/DirectionalAtomTypesParser.hpp, |
| 4378 |
+ |
io/DirectionalAtomTypesSectionParser.cpp, |
| 4379 |
+ |
io/HarmonicBondTypesSectionParser.cpp, |
| 4380 |
+ |
io/HarmonicBondTypesSectionParser.hpp, |
| 4381 |
+ |
io/LennardJonesAtomTypesSectionParser.cpp, |
| 4382 |
+ |
io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
| 4383 |
+ |
io/SectionParser.hpp, io/SectionParserManager.cpp, |
| 4384 |
+ |
io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
| 4385 |
+ |
io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
| 4386 |
+ |
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
| 4387 |
+ |
utils/GenericData.hpp: adding section parsers |
| 4388 |
+ |
|
| 4389 |
+ |
2004-11-22 15:55 tim |
| 4390 |
+ |
|
| 4391 |
+ |
* src/io/DirectionalAtomTypesParser.hpp: file |
| 4392 |
+ |
DirectionalAtomTypesParser.hpp was initially added on branch |
| 4393 |
+ |
new_design. |
| 4394 |
+ |
|
| 4395 |
+ |
2004-11-22 15:55 tim |
| 4396 |
+ |
|
| 4397 |
+ |
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
| 4398 |
+ |
was initially added on branch new_design. |
| 4399 |
+ |
|
| 4400 |
+ |
2004-11-22 15:55 tim |
| 4401 |
+ |
|
| 4402 |
+ |
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
| 4403 |
+ |
added on branch new_design. |
| 4404 |
+ |
|
| 4405 |
+ |
2004-11-19 17:12 tim |
| 4406 |
+ |
|
| 4407 |
+ |
* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
| 4408 |
+ |
added on branch new_design. |
| 4409 |
+ |
|
| 4410 |
+ |
2004-11-19 17:12 tim |
| 4411 |
+ |
|
| 4412 |
+ |
* src/: brains/SimState.cpp, brains/SimState.hpp, |
| 4413 |
+ |
io/InitializeFromFile.cpp, types/FixBondType.hpp, |
| 4414 |
+ |
types/FixedBondType.hpp: remove more useless files |
| 4415 |
+ |
|
| 4416 |
+ |
2004-11-19 16:47 tim |
| 4417 |
+ |
|
| 4418 |
+ |
* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, |
| 4419 |
+ |
integrators/Integrator.cpp, applications/Makedepend: remove more |
| 4420 |
+ |
useless files |
| 4421 |
+ |
|
| 4422 |
+ |
2004-11-19 16:38 tim |
| 4423 |
+ |
|
| 4424 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 4425 |
+ |
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
| 4426 |
+ |
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
| 4427 |
+ |
integrators/NVT.hpp: refactory integrator |
| 4428 |
+ |
|
| 4429 |
+ |
2004-11-19 16:38 tim |
| 4430 |
+ |
|
| 4431 |
+ |
* src/integrators/NPTi.hpp: file NPTi.hpp was initially added on |
| 4432 |
+ |
branch new_design. |
| 4433 |
+ |
|
| 4434 |
+ |
2004-11-19 16:38 tim |
| 4435 |
+ |
|
| 4436 |
+ |
* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
| 4437 |
+ |
branch new_design. |
| 4438 |
+ |
|
| 4439 |
+ |
2004-11-19 16:38 tim |
| 4440 |
+ |
|
| 4441 |
+ |
* src/integrators/NPT.hpp: file NPT.hpp was initially added on |
| 4442 |
+ |
branch new_design. |
| 4443 |
+ |
|
| 4444 |
+ |
2004-11-19 16:38 tim |
| 4445 |
+ |
|
| 4446 |
+ |
* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
| 4447 |
+ |
on branch new_design. |
| 4448 |
+ |
|
| 4449 |
+ |
2004-11-19 16:38 tim |
| 4450 |
+ |
|
| 4451 |
+ |
* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
| 4452 |
+ |
branch new_design. |
| 4453 |
+ |
|
| 4454 |
+ |
2004-11-19 15:37 tim |
| 4455 |
+ |
|
| 4456 |
+ |
* forceFields/newDUFF.frc: new DUFF forcefield |
| 4457 |
+ |
|
| 4458 |
+ |
2004-11-19 15:23 tim |
| 4459 |
+ |
|
| 4460 |
+ |
* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
| 4461 |
+ |
branch new_design. |
| 4462 |
+ |
|
| 4463 |
+ |
2004-11-19 15:23 tim |
| 4464 |
+ |
|
| 4465 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, |
| 4466 |
+ |
UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, |
| 4467 |
+ |
utils/TypeContainer.hpp: add EAM |
| 4468 |
+ |
|
| 4469 |
+ |
2004-11-19 15:23 tim |
| 4470 |
+ |
|
| 4471 |
+ |
* src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on |
| 4472 |
+ |
branch new_design. |
| 4473 |
+ |
|
| 4474 |
+ |
2004-11-19 13:02 tim |
| 4475 |
+ |
|
| 4476 |
+ |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except |
| 4477 |
+ |
error checking |
| 4478 |
+ |
|
| 4479 |
+ |
2004-11-19 12:56 tim |
| 4480 |
+ |
|
| 4481 |
+ |
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
| 4482 |
+ |
was initially added on branch new_design. |
| 4483 |
+ |
|
| 4484 |
+ |
2004-11-19 12:56 tim |
| 4485 |
+ |
|
| 4486 |
+ |
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
| 4487 |
+ |
was initially added on branch new_design. |
| 4488 |
+ |
|
| 4489 |
+ |
2004-11-19 12:56 tim |
| 4490 |
+ |
|
| 4491 |
+ |
* src/types/FixBondType.hpp: file FixBondType.hpp was initially |
| 4492 |
+ |
added on branch new_design. |
| 4493 |
+ |
|
| 4494 |
+ |
2004-11-19 12:56 tim |
| 4495 |
+ |
|
| 4496 |
+ |
* src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, |
| 4497 |
+ |
UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, |
| 4498 |
+ |
UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, |
| 4499 |
+ |
integrators/IntegratorFactory.cpp, |
| 4500 |
+ |
integrators/IntegratorFactory.hpp, integrators/NVE.hpp, |
| 4501 |
+ |
integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp, |
| 4502 |
+ |
utils/StringTokenizer.cpp: DUFF is almost done except error |
| 4503 |
+ |
checking |
| 4504 |
+ |
|
| 4505 |
+ |
2004-11-18 19:11 tim |
| 4506 |
+ |
|
| 4507 |
+ |
* src/UseTheForce/DUFF.cpp: adding DUFF parser |
| 4508 |
+ |
|
| 4509 |
+ |
2004-11-18 18:26 tim |
| 4510 |
+ |
|
| 4511 |
+ |
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
| 4512 |
+ |
initially added on branch new_design. |
| 4513 |
+ |
|
| 4514 |
+ |
2004-11-18 18:26 tim |
| 4515 |
+ |
|
| 4516 |
+ |
* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, |
| 4517 |
+ |
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
| 4518 |
+ |
integrators/VelocityVerletIntegrator.cpp, |
| 4519 |
+ |
integrators/VelocityVerletIntegrator.hpp, |
| 4520 |
+ |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
| 4521 |
+ |
types/CubicBendType.hpp, types/CubicBondType.hpp, |
| 4522 |
+ |
types/HarmonicBondType.hpp, types/QuadraticBendType.hpp, |
| 4523 |
+ |
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding |
| 4524 |
+ |
DUFF parser |
| 4525 |
+ |
|
| 4526 |
+ |
2004-11-18 16:42 tim |
| 4527 |
+ |
|
| 4528 |
+ |
* forceFields/newDUFF.frc: adding new format DUFF force field |
| 4529 |
+ |
|
| 4530 |
+ |
2004-11-18 10:57 chrisfen |
| 4531 |
+ |
|
| 4532 |
+ |
* src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that |
| 4533 |
+ |
slowed down the force loop |
| 4534 |
+ |
|
| 4535 |
+ |
2004-11-18 00:42 tim |
| 4536 |
+ |
|
| 4537 |
+ |
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
| 4538 |
+ |
initially added on branch new_design. |
| 4539 |
+ |
|
| 4540 |
+ |
2004-11-18 00:42 tim |
| 4541 |
+ |
|
| 4542 |
+ |
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
| 4543 |
+ |
initially added on branch new_design. |
| 4544 |
+ |
|
| 4545 |
+ |
2004-11-18 00:42 tim |
| 4546 |
+ |
|
| 4547 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, |
| 4548 |
+ |
primitives/Bend.cpp, utils/NumericConstant.cpp, |
| 4549 |
+ |
utils/NumericConstant.hpp: Adding NumericConstant class |
| 4550 |
+ |
|
| 4551 |
+ |
2004-11-17 23:16 tim |
| 4552 |
+ |
|
| 4553 |
+ |
* src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, |
| 4554 |
+ |
UseTheForce/ForceFields.hpp: remove more junk files |
| 4555 |
+ |
|
| 4556 |
+ |
2004-11-17 23:12 tim |
| 4557 |
+ |
|
| 4558 |
+ |
* src/: brains/ForceFields.cpp, brains/SimSetup.cpp, |
| 4559 |
+ |
brains/SimSetup.hpp, constraints/AbstractClasses.hpp, |
| 4560 |
+ |
integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp, |
| 4561 |
+ |
primitives/AbstractClasses.hpp, primitives/Bond.cpp, |
| 4562 |
+ |
primitives/BondExtensions.cpp, primitives/SRI.hpp, |
| 4563 |
+ |
primitives/TorsionExtensions.cpp: remove some junk files |
| 4564 |
+ |
|
| 4565 |
+ |
2004-11-17 23:07 tim |
| 4566 |
+ |
|
| 4567 |
+ |
* src/primitives/BendExtensions.cpp: remove some junk files |
| 4568 |
+ |
|
| 4569 |
+ |
2004-11-17 23:04 tim |
| 4570 |
+ |
|
| 4571 |
+ |
* src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, |
| 4572 |
+ |
QuadraticBondType.hpp: refine QudraticBond |
| 4573 |
+ |
|
| 4574 |
+ |
2004-11-17 22:57 tim |
| 4575 |
+ |
|
| 4576 |
+ |
* src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp |
| 4577 |
+ |
|
| 4578 |
+ |
2004-11-17 22:57 tim |
| 4579 |
+ |
|
| 4580 |
+ |
* src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was |
| 4581 |
+ |
initially added on branch new_design. |
| 4582 |
+ |
|
| 4583 |
+ |
2004-11-17 16:47 tim |
| 4584 |
+ |
|
| 4585 |
+ |
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
| 4586 |
+ |
was initially added on branch new_design. |
| 4587 |
+ |
|
| 4588 |
+ |
2004-11-17 16:47 tim |
| 4589 |
+ |
|
| 4590 |
+ |
* src/types/CubicBendType.hpp: file CubicBendType.hpp was initially |
| 4591 |
+ |
added on branch new_design. |
| 4592 |
+ |
|
| 4593 |
+ |
2004-11-17 16:47 tim |
| 4594 |
+ |
|
| 4595 |
+ |
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
| 4596 |
+ |
added on branch new_design. |
| 4597 |
+ |
|
| 4598 |
+ |
2004-11-17 16:47 tim |
| 4599 |
+ |
|
| 4600 |
+ |
* src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was |
| 4601 |
+ |
initially added on branch new_design. |
| 4602 |
+ |
|
| 4603 |
+ |
2004-11-17 16:47 tim |
| 4604 |
+ |
|
| 4605 |
+ |
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
| 4606 |
+ |
initially added on branch new_design. |
| 4607 |
+ |
|
| 4608 |
+ |
2004-11-17 16:47 tim |
| 4609 |
+ |
|
| 4610 |
+ |
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
| 4611 |
+ |
initially added on branch new_design. |
| 4612 |
+ |
|
| 4613 |
+ |
2004-11-17 16:47 tim |
| 4614 |
+ |
|
| 4615 |
+ |
* src/types/CubicBondType.hpp: file CubicBondType.hpp was initially |
| 4616 |
+ |
added on branch new_design. |
| 4617 |
+ |
|
| 4618 |
+ |
2004-11-17 16:47 tim |
| 4619 |
+ |
|
| 4620 |
+ |
* src/: math/ChebyshevPolynomials.cpp, |
| 4621 |
+ |
math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, |
| 4622 |
+ |
primitives/Bend.hpp, primitives/GhostBend.cpp, |
| 4623 |
+ |
primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp, |
| 4624 |
+ |
primitives/UreyBradleyBend.hpp, types/BondType.hpp, |
| 4625 |
+ |
types/CubicBendType.hpp, types/CubicBondType.hpp, |
| 4626 |
+ |
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
| 4627 |
+ |
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: |
| 4628 |
+ |
UreyBradleyBend and GhostBend |
| 4629 |
+ |
|
| 4630 |
+ |
2004-11-17 13:58 tim |
| 4631 |
+ |
|
| 4632 |
+ |
* src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp |
| 4633 |
+ |
was initially added on branch new_design. |
| 4634 |
+ |
|
| 4635 |
+ |
2004-11-17 13:58 tim |
| 4636 |
+ |
|
| 4637 |
+ |
* src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp |
| 4638 |
+ |
was initially added on branch new_design. |
| 4639 |
+ |
|
| 4640 |
+ |
2004-11-17 13:58 tim |
| 4641 |
+ |
|
| 4642 |
+ |
* src/: math/ChebyshevPolynomials.cpp, |
| 4643 |
+ |
math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, |
| 4644 |
+ |
primitives/Bond.hpp, types/CharmmTorsionType.hpp, |
| 4645 |
+ |
types/OplsTorsionType.hpp, types/PolynomialBondType.hpp, |
| 4646 |
+ |
types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types |
| 4647 |
+ |
stuff and Chebyshev Polynomial |
| 4648 |
+ |
|
| 4649 |
+ |
2004-11-17 13:58 tim |
| 4650 |
+ |
|
| 4651 |
+ |
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
| 4652 |
+ |
initially added on branch new_design. |
| 4653 |
+ |
|
| 4654 |
+ |
2004-11-17 01:37 tim |
| 4655 |
+ |
|
| 4656 |
+ |
* src/types/PolynomialTorsionType.hpp: file |
| 4657 |
+ |
PolynomialTorsionType.hpp was initially added on branch new_design. |
| 4658 |
+ |
|
| 4659 |
+ |
2004-11-17 01:37 tim |
| 4660 |
+ |
|
| 4661 |
+ |
* src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was |
| 4662 |
+ |
initially added on branch new_design. |
| 4663 |
+ |
|
| 4664 |
+ |
2004-11-17 01:37 tim |
| 4665 |
+ |
|
| 4666 |
+ |
* src/: math/Polynomial.hpp, primitives/Bend.cpp, |
| 4667 |
+ |
primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, |
| 4668 |
+ |
types/BondType.hpp, types/CharmmTorsionType.cpp, |
| 4669 |
+ |
types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp, |
| 4670 |
+ |
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
| 4671 |
+ |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
| 4672 |
+ |
types/PolynomialTorsionType.hpp, types/TorsionType.hpp, |
| 4673 |
+ |
utils/StringTokenizer.hpp: add PolynomialBondType, |
| 4674 |
+ |
PolynomialBendType, PolynomialTorsionType, HarmonicBendType and |
| 4675 |
+ |
CharmmTorsionType. Need to refine the design and add document for |
| 4676 |
+ |
them |
| 4677 |
+ |
|
| 4678 |
+ |
2004-11-17 01:37 tim |
| 4679 |
+ |
|
| 4680 |
+ |
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
| 4681 |
+ |
initially added on branch new_design. |
| 4682 |
+ |
|
| 4683 |
+ |
2004-11-17 01:37 tim |
| 4684 |
+ |
|
| 4685 |
+ |
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
| 4686 |
+ |
initially added on branch new_design. |
| 4687 |
+ |
|
| 4688 |
+ |
2004-11-17 01:37 tim |
| 4689 |
+ |
|
| 4690 |
+ |
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
| 4691 |
+ |
initially added on branch new_design. |
| 4692 |
+ |
|
| 4693 |
+ |
2004-11-16 20:11 tim |
| 4694 |
+ |
|
| 4695 |
+ |
* src/types/: BendType.hpp, PolynomialBondType.hpp, |
| 4696 |
+ |
TorsionType.hpp: add PolynomialBondType |
| 4697 |
+ |
|
| 4698 |
+ |
2004-11-16 20:11 tim |
| 4699 |
+ |
|
| 4700 |
+ |
* src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was |
| 4701 |
+ |
initially added on branch new_design. |
| 4702 |
+ |
|
| 4703 |
+ |
2004-11-16 18:20 tim |
| 4704 |
+ |
|
| 4705 |
+ |
* src/math/Polynomial.hpp: file Polynomial.hpp was initially added |
| 4706 |
+ |
on branch new_design. |
| 4707 |
+ |
|
| 4708 |
+ |
2004-11-16 18:20 tim |
| 4709 |
+ |
|
| 4710 |
+ |
* src/math/Polynomial.hpp: Adding Polynomial class |
| 4711 |
+ |
|
| 4712 |
+ |
2004-11-16 17:04 gezelter |
| 4713 |
+ |
|
| 4714 |
+ |
* src/types/MorseBondType.hpp: file MorseBondType.hpp was initially |
| 4715 |
+ |
added on branch new_design. |
| 4716 |
+ |
|
| 4717 |
+ |
2004-11-16 17:04 gezelter |
| 4718 |
+ |
|
| 4719 |
+ |
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
| 4720 |
+ |
initially added on branch new_design. |
| 4721 |
+ |
|
| 4722 |
+ |
2004-11-16 17:04 gezelter |
| 4723 |
+ |
|
| 4724 |
+ |
* src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, |
| 4725 |
+ |
MorseBondType.hpp, TorsionType.hpp: added some new stuff |
| 4726 |
+ |
|
| 4727 |
+ |
2004-11-16 15:36 tim |
| 4728 |
+ |
|
| 4729 |
+ |
* src/: primitives/Bend.cpp, primitives/Bend.hpp, |
| 4730 |
+ |
primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, |
| 4731 |
+ |
types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and |
| 4732 |
+ |
TorsionType |
| 4733 |
+ |
|
| 4734 |
+ |
2004-11-15 21:07 tim |
| 4735 |
+ |
|
| 4736 |
+ |
* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on |
| 4737 |
+ |
branch new_design. |
| 4738 |
+ |
|
| 4739 |
+ |
2004-11-15 21:07 tim |
| 4740 |
+ |
|
| 4741 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 4742 |
+ |
UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, |
| 4743 |
+ |
utils/StringTokenizer.cpp: adding DUFF class; adding checking |
| 4744 |
+ |
statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer |
| 4745 |
+ |
|
| 4746 |
+ |
2004-11-15 18:00 tim |
| 4747 |
+ |
|
| 4748 |
+ |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 4749 |
+ |
UseTheForce/ForceFieldFactory.cpp, |
| 4750 |
+ |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, |
| 4751 |
+ |
UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, |
| 4752 |
+ |
types/AtomType.hpp: adding ForceFieldFactory and LJFF classes |
| 4753 |
+ |
|
| 4754 |
+ |
2004-11-15 18:00 tim |
| 4755 |
+ |
|
| 4756 |
+ |
* src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp |
| 4757 |
+ |
was initially added on branch new_design. |
| 4758 |
+ |
|
| 4759 |
+ |
2004-11-15 18:00 tim |
| 4760 |
+ |
|
| 4761 |
+ |
* src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp |
| 4762 |
+ |
was initially added on branch new_design. |
| 4763 |
+ |
|
| 4764 |
+ |
2004-11-15 18:00 tim |
| 4765 |
+ |
|
| 4766 |
+ |
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
| 4767 |
+ |
branch new_design. |
| 4768 |
+ |
|
| 4769 |
+ |
2004-11-15 13:02 tim |
| 4770 |
+ |
|
| 4771 |
+ |
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
| 4772 |
+ |
initially added on branch new_design. |
| 4773 |
+ |
|
| 4774 |
+ |
2004-11-15 13:02 tim |
| 4775 |
+ |
|
| 4776 |
+ |
* src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on |
| 4777 |
+ |
branch new_design. |
| 4778 |
+ |
|
| 4779 |
+ |
2004-11-15 13:02 tim |
| 4780 |
+ |
|
| 4781 |
+ |
* src/io/DumpReader.hpp: file DumpReader.hpp was initially added on |
| 4782 |
+ |
branch new_design. |
| 4783 |
+ |
|
| 4784 |
+ |
2004-11-15 13:02 tim |
| 4785 |
+ |
|
| 4786 |
+ |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 4787 |
+ |
brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
| 4788 |
+ |
integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, |
| 4789 |
+ |
io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, |
| 4790 |
+ |
DumpWriter.Next Step is LJFF and integrators |
| 4791 |
+ |
|
| 4792 |
+ |
2004-11-13 00:08 tim |
| 4793 |
+ |
|
| 4794 |
+ |
* src/: brains/ForceManager.cpp, brains/ForceManager.hpp, |
| 4795 |
+ |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 4796 |
+ |
brains/SimInfo.hpp, primitives/Molecule.cpp, |
| 4797 |
+ |
primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, |
| 4798 |
+ |
refactory, refactory |
| 4799 |
+ |
|
| 4800 |
+ |
2004-11-12 17:43 tim |
| 4801 |
+ |
|
| 4802 |
+ |
* src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, |
| 4803 |
+ |
StringTokenizer.cpp: bug fix in hasMoreTokens |
| 4804 |
+ |
|
| 4805 |
+ |
2004-11-12 17:28 tim |
| 4806 |
+ |
|
| 4807 |
+ |
* src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was |
| 4808 |
+ |
initially added on branch new_design. |
| 4809 |
+ |
|
| 4810 |
+ |
2004-11-12 17:28 tim |
| 4811 |
+ |
|
| 4812 |
+ |
* src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding |
| 4813 |
+ |
StringUtils, a c-style strtok like class, need unit test |
| 4814 |
+ |
|
| 4815 |
+ |
2004-11-12 12:40 tim |
| 4816 |
+ |
|
| 4817 |
+ |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 4818 |
+ |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 4819 |
+ |
brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test |
| 4820 |
+ |
|
| 4821 |
+ |
2004-11-12 02:05 tim |
| 4822 |
+ |
|
| 4823 |
+ |
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
| 4824 |
+ |
primitives/CutoffGroup.hpp, primitives/Molecule.cpp: |
| 4825 |
+ |
MoleculeCreator forget to create CutoffGroups for free atoms |
| 4826 |
+ |
|
| 4827 |
+ |
2004-11-12 01:19 tim |
| 4828 |
+ |
|
| 4829 |
+ |
* src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
| 4830 |
+ |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 4831 |
+ |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
| 4832 |
+ |
io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: |
| 4833 |
+ |
OOPSE = Object-Obfuscated Parallel Simulation Engine |
| 4834 |
+ |
|
| 4835 |
+ |
2004-11-11 16:48 chrisfen |
| 4836 |
+ |
|
| 4837 |
+ |
* samples/water/tip3p_ice/tp3.md: working sample |
| 4838 |
+ |
|
| 4839 |
+ |
2004-11-11 16:47 chrisfen |
| 4840 |
+ |
|
| 4841 |
+ |
* src/restraints/Restraints.cpp: working towards parallel |
| 4842 |
+ |
restraints |
| 4843 |
+ |
|
| 4844 |
+ |
2004-11-11 16:47 chrisfen |
| 4845 |
+ |
|
| 4846 |
+ |
* src/integrators/Integrator.cpp: Commented out some write |
| 4847 |
+ |
statements |
| 4848 |
+ |
|
| 4849 |
+ |
2004-11-11 16:46 chrisfen |
| 4850 |
+ |
|
| 4851 |
+ |
* src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some |
| 4852 |
+ |
write statements |
| 4853 |
+ |
|
| 4854 |
+ |
2004-11-11 16:46 chrisfen |
| 4855 |
+ |
|
| 4856 |
+ |
* samples/water/tip3p_ice/tp3.md: Fun with ice |
| 4857 |
+ |
|
| 4858 |
+ |
2004-11-11 11:41 tim |
| 4859 |
+ |
|
| 4860 |
+ |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
| 4861 |
+ |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 4862 |
+ |
brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h, |
| 4863 |
+ |
brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp, |
| 4864 |
+ |
io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove |
| 4865 |
+ |
useless mpiSimulation |
| 4866 |
+ |
|
| 4867 |
+ |
2004-11-11 11:41 tim |
| 4868 |
+ |
|
| 4869 |
+ |
* src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on |
| 4870 |
+ |
branch new_design. |
| 4871 |
+ |
|
| 4872 |
+ |
2004-11-10 17:50 tim |
| 4873 |
+ |
|
| 4874 |
+ |
* src/: brains/ForceManager.cpp, brains/SimInfo.cpp, |
| 4875 |
+ |
brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, |
| 4876 |
+ |
integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo |
| 4877 |
+ |
|
| 4878 |
+ |
2004-11-10 17:01 tim |
| 4879 |
+ |
|
| 4880 |
+ |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
| 4881 |
+ |
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
| 4882 |
+ |
brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 4883 |
+ |
brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp, |
| 4884 |
+ |
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
| 4885 |
+ |
io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp, |
| 4886 |
+ |
visitors/AtomVisitor.cpp: another painful day (1) SimCreator, |
| 4887 |
+ |
SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom |
| 4888 |
+ |
File will be removed) (3) ForceField (at least LJ) and BondType, |
| 4889 |
+ |
BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & |
| 4890 |
+ |
Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint |
| 4891 |
+ |
|
| 4892 |
+ |
2004-11-10 09:52 tim |
| 4893 |
+ |
|
| 4894 |
+ |
* src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a |
| 4895 |
+ |
configurable StatWriter |
| 4896 |
+ |
|
| 4897 |
+ |
2004-11-10 09:52 tim |
| 4898 |
+ |
|
| 4899 |
+ |
* src/io/StatWriter.hpp: file StatWriter.hpp was initially added on |
| 4900 |
+ |
branch new_design. |
| 4901 |
+ |
|
| 4902 |
+ |
2004-11-09 21:58 tim |
| 4903 |
+ |
|
| 4904 |
+ |
* src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation |
| 4905 |
+ |
in progress |
| 4906 |
+ |
|
| 4907 |
+ |
2004-11-09 18:11 tim |
| 4908 |
+ |
|
| 4909 |
+ |
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
| 4910 |
+ |
added on branch new_design. |
| 4911 |
+ |
|
| 4912 |
+ |
2004-11-09 18:11 tim |
| 4913 |
+ |
|
| 4914 |
+ |
* src/integrators/VelocityVerletIntegrator.cpp: file |
| 4915 |
+ |
VelocityVerletIntegrator.cpp was initially added on branch |
| 4916 |
+ |
new_design. |
| 4917 |
+ |
|
| 4918 |
+ |
2004-11-09 18:11 tim |
| 4919 |
+ |
|
| 4920 |
+ |
* src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, |
| 4921 |
+ |
brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 4922 |
+ |
brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, |
| 4923 |
+ |
brains/mpiSimulation.hpp, integrators/Integrator.hpp, |
| 4924 |
+ |
integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, |
| 4925 |
+ |
integrators/VelocityVerletIntegrator.hpp: adding ForceManager |
| 4926 |
+ |
|
| 4927 |
+ |
2004-11-09 18:11 tim |
| 4928 |
+ |
|
| 4929 |
+ |
* src/brains/ForceManager.hpp: file ForceManager.hpp was initially |
| 4930 |
+ |
added on branch new_design. |
| 4931 |
+ |
|
| 4932 |
+ |
2004-11-09 18:11 tim |
| 4933 |
+ |
|
| 4934 |
+ |
* src/integrators/NVE.cpp: file NVE.cpp was initially added on |
| 4935 |
+ |
branch new_design. |
| 4936 |
+ |
|
| 4937 |
+ |
2004-11-08 20:08 tim |
| 4938 |
+ |
|
| 4939 |
+ |
* src/integrators/VelocityVerletIntegrator.hpp: file |
| 4940 |
+ |
VelocityVerletIntegrator.hpp was initially added on branch |
| 4941 |
+ |
new_design. |
| 4942 |
+ |
|
| 4943 |
+ |
2004-11-08 20:08 tim |
| 4944 |
+ |
|
| 4945 |
+ |
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
| 4946 |
+ |
branch new_design. |
| 4947 |
+ |
|
| 4948 |
+ |
2004-11-08 20:08 tim |
| 4949 |
+ |
|
| 4950 |
+ |
* src/: brains/Exclude.hpp, brains/Stats.hpp, |
| 4951 |
+ |
integrators/Integrator.hpp, integrators/NVE.hpp, |
| 4952 |
+ |
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
| 4953 |
+ |
utils/TypeContainer.hpp: More to break |
| 4954 |
+ |
|
| 4955 |
+ |
2004-11-06 00:21 tim |
| 4956 |
+ |
|
| 4957 |
+ |
* src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially |
| 4958 |
+ |
added on branch new_design. |
| 4959 |
+ |
|
| 4960 |
+ |
2004-11-06 00:21 tim |
| 4961 |
+ |
|
| 4962 |
+ |
* src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, |
| 4963 |
+ |
UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, |
| 4964 |
+ |
utils/TypeContainer.hpp, utils/next_combination.hpp: adding |
| 4965 |
+ |
ForceField and TypeContainer classes |
| 4966 |
+ |
|
| 4967 |
+ |
2004-11-05 18:38 tim |
| 4968 |
+ |
|
| 4969 |
+ |
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
| 4970 |
+ |
initially added on branch new_design. |
| 4971 |
+ |
|
| 4972 |
+ |
2004-11-05 18:38 tim |
| 4973 |
+ |
|
| 4974 |
+ |
* src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was |
| 4975 |
+ |
initially added on branch new_design. |
| 4976 |
+ |
|
| 4977 |
+ |
2004-11-05 18:38 tim |
| 4978 |
+ |
|
| 4979 |
+ |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
| 4980 |
+ |
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
| 4981 |
+ |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 4982 |
+ |
brains/SimInfo.hpp, primitives/Molecule.hpp, |
| 4983 |
+ |
utils/LocalndexManager.hpp: Fix Exclude class etc. |
| 4984 |
+ |
|
| 4985 |
+ |
2004-11-05 16:45 chrisfen |
| 4986 |
+ |
|
| 4987 |
+ |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 4988 |
+ |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the |
| 4989 |
+ |
linear visitor |
| 4990 |
+ |
|
| 4991 |
+ |
2004-11-05 16:04 chrisfen |
| 4992 |
+ |
|
| 4993 |
+ |
* src/UseTheForce/DarkSide/shapes.F90: current status of the |
| 4994 |
+ |
debugging process |
| 4995 |
+ |
|
| 4996 |
+ |
2004-11-05 16:04 chrisfen |
| 4997 |
+ |
|
| 4998 |
+ |
* make/Makefile.in: included visitors and minimizer |
| 4999 |
+ |
|
| 5000 |
+ |
2004-11-05 16:03 chrisfen |
| 5001 |
+ |
|
| 5002 |
+ |
* ChangeLog: new changes |
| 5003 |
+ |
|
| 5004 |
+ |
2004-11-04 21:56 tim |
| 5005 |
+ |
|
| 5006 |
+ |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
| 5007 |
+ |
primitives/Molecule.hpp: Pain...... |
| 5008 |
+ |
|
| 5009 |
+ |
2004-11-04 15:55 tim |
| 5010 |
+ |
|
| 5011 |
+ |
* ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, |
| 5012 |
+ |
src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, |
| 5013 |
+ |
src/brains/Stats.hpp: time to break SimSetup |
| 5014 |
+ |
|
| 5015 |
+ |
2004-11-04 15:51 gezelter |
| 5016 |
+ |
|
| 5017 |
+ |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new |
| 5018 |
+ |
classes in progress |
| 5019 |
+ |
|
| 5020 |
|
2004-11-04 14:48 tim |
| 5021 |
|
|
| 5022 |
|
* src/brains/Stats.cpp: file Stats.cpp was initially added on |
| 5027 |
|
* src/brains/Stats.hpp: file Stats.hpp was initially added on |
| 5028 |
|
branch new_design. |
| 5029 |
|
|
| 5030 |
+ |
2004-11-04 14:48 tim |
| 5031 |
+ |
|
| 5032 |
+ |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
| 5033 |
+ |
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
| 5034 |
+ |
class |
| 5035 |
+ |
|
| 5036 |
|
2004-11-04 11:22 gezelter |
| 5037 |
|
|
| 5038 |
|
* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
| 5067 |
|
|
| 5068 |
|
2004-11-03 14:56 tim |
| 5069 |
|
|
| 51 |
– |
* src/brains/SimCreator.cpp: file SimCreator.cpp was initially |
| 52 |
– |
added on branch new_design. |
| 53 |
– |
|
| 54 |
– |
2004-11-03 14:56 tim |
| 55 |
– |
|
| 5070 |
|
* src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator |
| 5071 |
|
class(similar as SimSetup) |
| 5072 |
|
|
| 5075 |
|
* src/brains/SimCreator.hpp: file SimCreator.hpp was initially |
| 5076 |
|
added on branch new_design. |
| 5077 |
|
|
| 5078 |
+ |
2004-11-03 14:56 tim |
| 5079 |
+ |
|
| 5080 |
+ |
* src/brains/SimCreator.cpp: file SimCreator.cpp was initially |
| 5081 |
+ |
added on branch new_design. |
| 5082 |
+ |
|
| 5083 |
|
2004-11-03 13:00 tim |
| 5084 |
|
|
| 5085 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 5107 |
|
|
| 5108 |
|
2004-11-02 17:41 tim |
| 5109 |
|
|
| 5110 |
+ |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
| 5111 |
+ |
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
| 5112 |
+ |
Need unit test |
| 5113 |
+ |
|
| 5114 |
+ |
2004-11-02 17:41 tim |
| 5115 |
+ |
|
| 5116 |
|
* src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was |
| 5117 |
|
initially added on branch new_design. |
| 5118 |
|
|
| 5121 |
|
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
| 5122 |
|
branch new_design. |
| 5123 |
|
|
| 5124 |
< |
2004-11-02 17:41 tim |
| 5124 |
> |
2004-11-02 11:59 tim |
| 5125 |
|
|
| 5126 |
< |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
| 5127 |
< |
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
| 103 |
< |
Need unit test |
| 5126 |
> |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
| 5127 |
> |
branch new_design. |
| 5128 |
|
|
| 5129 |
|
2004-11-02 11:59 tim |
| 5130 |
|
|
| 5131 |
|
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
| 5132 |
|
SimSnapshotManager.hpp: SimModel in progress |
| 5133 |
|
|
| 110 |
– |
2004-11-02 11:59 tim |
| 111 |
– |
|
| 112 |
– |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
| 113 |
– |
branch new_design. |
| 114 |
– |
|
| 5134 |
|
2004-11-02 10:28 chrisfen |
| 5135 |
|
|
| 5136 |
|
* src/: UseTheForce/DarkSide/shapes.F90, |
| 5139 |
|
|
| 5140 |
|
2004-11-02 10:27 tim |
| 5141 |
|
|
| 5142 |
< |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
| 5143 |
< |
added on branch new_design. |
| 5142 |
> |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
| 5143 |
> |
functions for dealing with memory issue |
| 5144 |
|
|
| 5145 |
|
2004-11-02 10:27 tim |
| 5146 |
|
|
| 5147 |
< |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
| 5148 |
< |
functions for dealing with memory issue |
| 5147 |
> |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
| 5148 |
> |
added on branch new_design. |
| 5149 |
|
|
| 5150 |
|
2004-11-02 10:23 tim |
| 5151 |
|
|
