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2003-08-26 15:37 tim |
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2003-10-24 18:17 mmeineke |
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* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
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MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
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latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
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QuickBass, MoLocator, and latticeBuilder into a Builder Library |
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overhauled latticeBilayer into its own program. Removed sysBuild |
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from the Makefile |
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2003-10-24 13:36 gezelter |
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* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
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latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
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builder |
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2003-10-24 13:35 gezelter |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
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merge problem |
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2003-10-23 15:57 mmeineke |
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* samples/metals/Makefile.in: added eam ForceField files to the |
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init |
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fixed an eam mpi parmeter setup bug |
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added the init file to the makefile |
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2003-10-23 15:57 mmeineke |
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* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
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to the init |
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fixed an eam mpi parmeter setup bug |
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2003-10-23 15:57 mmeineke |
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* forceFields/Makefile.in: added eam ForceField files to the init |
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2003-10-22 17:17 mmeineke |
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* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
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NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
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integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
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no box skew allowed. |
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2003-10-21 15:33 mmeineke |
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* libBASS/Globals.cpp, libBASS/Globals.hpp, |
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libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
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staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
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* useInitTime = false: sets the origin time to 0.0 regardless |
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of the time stamp in the .init file * default=> useInitTime = |
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true; |
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2003-10-17 17:19 mmeineke |
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* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
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Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
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staticProps.cpp, obj/placeholder: added the staticProps directory |
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to the build list for both configure and configure.in |
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fixed a number of bugs in the staticProps code. gofr is now |
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working. |
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2003-10-17 17:18 mmeineke |
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* ac-tools/configure.in: added the staticProps directory to the |
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build list for both configure and configure.in |
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2003-10-17 17:17 mmeineke |
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* configure: added the staticProps directory to the build list |
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2003-10-16 15:16 mmeineke |
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* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
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Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
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use linked lists instead of a vector. |
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Fixed the makefile to build DumpReader.cpp |
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Removed a comment output in Exclude.cpp |
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Modified DumpWriter and Integrator to write an eor file every time |
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a frame is written. This lets the .eor file represent the last |
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written frame of a simulation. |
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2003-10-10 13:10 mmeineke |
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* props/AllCorr.cpp, props/AllCorr.hpp, props/CorrWrap.cpp, |
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props/CorrWrap.hpp, props/GofR.cpp, props/PairCorrList.cpp, |
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props/PairCorrList.hpp, props/PairCorrType.cpp, |
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props/PairCorrType.hpp, props/staticProps.cpp, |
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staticProps/AllCorr.cpp, staticProps/AllCorr.hpp, |
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staticProps/CorrWrap.cpp, staticProps/CorrWrap.hpp, |
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staticProps/GofR.cpp, staticProps/Makefile.in, |
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staticProps/PairCorrList.cpp, staticProps/PairCorrList.hpp, |
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staticProps/PairCorrType.cpp, staticProps/PairCorrType.hpp, |
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staticProps/staticProps.cpp: removed the props directory, and moved |
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everything over to staticProps |
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2003-10-09 18:09 mmeineke |
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* libmdtools/Atom.hpp, props/AllCorr.cpp, props/AllCorr.hpp, |
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props/CorrWrap.cpp, props/CorrWrap.hpp, props/GofR.cpp, |
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props/PairCorrType.cpp, props/PairCorrType.hpp, |
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props/staticProps.cpp: Contiuned work on staticProps. should be in |
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a position where it will compile and run first runs. |
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2003-10-04 14:46 chuckv |
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* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
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samples/metals/Au.bass: Fixed bug in calc_eam. |
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2003-10-04 14:08 chuckv |
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* samples/metals/init_au.in: added Au init file for eam. |
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2003-10-03 18:11 mmeineke |
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* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
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entahlpy from the statwriter and thermo. |
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2003-10-03 18:02 mmeineke |
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* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
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PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
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staticProps.cpp: changed the formating ogf the error statements in |
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simError |
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added a function to get the maxCutoff |
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near completion of the staticProps code. still needs the pair loop, |
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and the loop to allocate and read each frame. |
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2003-10-03 18:02 mmeineke |
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* libmdtools/SimInfo.hpp: changed the formating ogf the error |
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statements in simError |
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added a function to get the maxCutoff |
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2003-10-03 18:01 mmeineke |
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* libBASS/simError.c: changed the formating ogf the error |
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statements in simError |
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2003-10-02 18:06 mmeineke |
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* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
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PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
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staticProps.cpp: finishing up the constructs needed to get this |
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program up and running |
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2003-09-30 12:00 mmeineke |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
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f90Flags so they are no longer overwritten by the compiler. |
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2003-09-29 18:06 mmeineke |
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* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
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for conifig.in |
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fixed wrappers to extern "C" |
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2003-09-29 18:06 mmeineke |
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* ac-tools/configure.in: added mpif90 mod check back same for |
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conifig.in |
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2003-09-29 18:05 mmeineke |
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* configure: added mpif90 mod check back |
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2003-09-29 17:16 mmeineke |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
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libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
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libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
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libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
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libBASS/ZconStamp.cpp, libBASS/simError.c, |
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libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
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libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
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libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
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found with SUN's SUNWspro.s1s7 |
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2003-09-29 13:38 mmeineke |
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* libmdtools/GenericData.hpp: light change in syntax. no |
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signifigant change. |
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2003-09-25 17:17 mmeineke |
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* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
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additional remarks from icc -w3 (extra verbose output) |
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2003-09-25 15:27 mmeineke |
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* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
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libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
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libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
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libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
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libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
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libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
| 208 |
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libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
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libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
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libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
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libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
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gcc -Wall and g++ -Wall |
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2003-09-25 14:54 gezelter |
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* configure, ac-tools/configure.in: fixed a bug in configure |
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2003-09-25 12:42 gezelter |
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* Makefile.in, configure, ac-tools/aclocal.m4, |
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ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
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src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
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fixes for configure |
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2003-09-24 15:34 mmeineke |
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* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
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that it is called before the first Statistics are written. |
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2003-09-23 16:36 gezelter |
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* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
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bunch of Make.dep files to CVS |
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2003-09-23 16:34 mmeineke |
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* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
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SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
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Some small syntax cleaning in NPTfm and SimSetup |
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2003-09-22 19:07 tim |
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* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
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SimInfo.hpp: fix bug in calculating maxCutoff |
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2003-09-22 17:23 mmeineke |
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* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
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Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
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Converted NPTf to work with the NPT base class. |
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Removed NPTfm and NPTim from cvs |
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2003-09-19 16:00 mmeineke |
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* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
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NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
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class. NPTi is up to date. NPTf is not. |
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2003-09-19 12:03 mmeineke |
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* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
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makefile |
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2003-09-19 12:01 gezelter |
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* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
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2003-09-19 12:01 gezelter |
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* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
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(nearly) conserved quantities for both NPTi and NPTf |
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2003-09-19 11:20 mmeineke |
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* utils/Makefile.in: fixed a typo in the makefile. |
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2003-09-19 10:55 gezelter |
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* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
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samples/water/ssd.bass: [no log message] |
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2003-09-19 10:22 tim |
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* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
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2003-09-17 10:22 mmeineke |
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* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
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work with constraints. |
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2003-09-16 16:02 tim |
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* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
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SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
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fixed conserved quantity in NPT (Still some small bug) |
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NPTi appears very stable. |
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2003-09-15 12:52 tim |
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* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
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libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
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libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
| 307 |
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libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
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libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
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libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
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utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
| 311 |
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statWriter fix bug of vector wrapping at NPTi |
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2003-09-12 16:51 mmeineke |
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* props/: AllCorr.cpp, AllCorr.hpp, GofR.cpp, PairCorrType.cpp, |
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PairCorrType.hpp: added AllCorr. It eill still need some work |
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2003-09-12 12:20 gezelter |
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* libmdtools/: Make.dep, Makefile.in: Added integrators to |
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Makefile.in |
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2003-09-12 12:20 gezelter |
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* ChangeLog: Entered changes for configure into ChangeLog |
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2003-09-10 17:28 mmeineke |
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* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more |
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work on getting gofR working. |
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2003-09-09 17:50 mmeineke |
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* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the |
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beginings of the GofR pair correlation. |
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added identification of identI in matchI. |
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2003-09-09 16:35 mmeineke |
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* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
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NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog |
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added two new NPT integrators, they still need work. |
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2003-09-09 16:34 mmeineke |
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* ChangeLog: updated the ChangeLog |
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2003-09-05 18:45 gezelter |
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* libmdtools/Make.dep: dependency on config.h |
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2003-09-05 18:36 gezelter |
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* configure, ac-tools/aclocal.m4: fixed sprng problem |
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2003-09-05 17:29 gezelter |
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* samples/metals/Makefile.in: New Makefile for metals sample |
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2003-09-05 17:27 gezelter |
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* Makefile, Makefile.in, ac-tools/aclocal.m4, |
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ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, |
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forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 367 |
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libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
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libBASS/Makefile.in, libmdtools/Integrator.hpp, |
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libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep, |
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libmdtools/Makefile, libmdtools/Makefile.in, |
| 371 |
> |
libmdtools/calc_eam.F90, libmdtools/config.h.in, |
| 372 |
> |
libmdtools/definitions_module.F90, libmdtools/fInfo.c, |
| 373 |
> |
libmdtools/fortranWrappers.cpp, |
| 374 |
> |
libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, |
| 375 |
> |
libmdtools/simulation_module.F90, samples/Makefile, |
| 376 |
> |
samples/Makefile.in, samples/alkane/Makefile, |
| 377 |
> |
samples/alkane/Makefile.in, samples/argon/Makefile, |
| 378 |
> |
samples/argon/Makefile.in, samples/argon/argon.bass, |
| 379 |
> |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
| 380 |
> |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
| 381 |
> |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
| 382 |
> |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
| 383 |
> |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
| 384 |
> |
autoconf / configure method of configuring OOPSE |
| 385 |
> |
|
| 386 |
> |
2003-09-04 17:48 mmeineke |
| 387 |
> |
|
| 388 |
> |
* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 389 |
> |
libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, |
| 390 |
> |
libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp, |
| 391 |
> |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile: |
| 392 |
> |
added resetTime to the Global namespace. |
| 393 |
> |
|
| 394 |
> |
added ability to reset the integrators in the NVT and NPT family. |
| 395 |
> |
|
| 396 |
> |
2003-09-04 17:48 mmeineke |
| 397 |
> |
|
| 398 |
> |
* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global |
| 399 |
> |
namespace. |
| 400 |
> |
|
| 401 |
> |
2003-09-02 10:30 tim |
| 402 |
> |
|
| 403 |
> |
* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, |
| 404 |
> |
ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of |
| 405 |
> |
PolicyByMass |
| 406 |
> |
|
| 407 |
> |
2003-08-28 17:09 tim |
| 408 |
> |
|
| 409 |
> |
* ChangeLog, libmdtools/GenericData.cpp, |
| 410 |
> |
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
| 411 |
> |
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
| 412 |
> |
|
| 413 |
> |
2003-08-28 12:59 mmeineke |
| 414 |
> |
|
| 415 |
> |
* props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp: |
| 416 |
> |
added the first functional parts of the PairCorrType Abstract |
| 417 |
> |
classes. |
| 418 |
> |
|
| 419 |
> |
2003-08-27 15:23 tim |
| 420 |
> |
|
| 421 |
> |
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
| 422 |
> |
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
| 423 |
> |
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
| 424 |
> |
turn on the optimization flag, it causes a seg fault |
| 425 |
> |
|
| 426 |
> |
2003-08-27 12:25 gezelter |
| 427 |
> |
|
| 428 |
> |
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
| 429 |
> |
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
| 430 |
> |
stress tensor parallel bug. |
| 431 |
> |
|
| 432 |
> |
2003-08-27 12:16 tim |
| 433 |
> |
|
| 434 |
> |
* ChangeLog, libmdtools/DUFF.cpp, |
| 435 |
> |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
| 436 |
> |
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
| 437 |
> |
molMembershipList use global index instead of local index |
| 438 |
> |
|
| 439 |
> |
2003-08-26 16:37 tim |
| 440 |
|
|
| 441 |
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
| 442 |
|
mpiSimulation.cpp: set default force substraction policy to |
| 443 |
|
PolicyByMass |
| 444 |
|
|
| 445 |
< |
2003-08-26 15:29 tim |
| 445 |
> |
2003-08-26 16:29 tim |
| 446 |
|
|
| 447 |
|
* libmdtools/Integrator.cpp: [no log message] |
| 448 |
|
|
| 449 |
< |
2003-08-26 15:13 mmeineke |
| 449 |
> |
2003-08-26 16:13 mmeineke |
| 450 |
|
|
| 451 |
|
* utils/sysbuilder/bilayerSys.cpp: added define statemewnt to |
| 452 |
|
Statwriter and Dumpwriter to handle files larger than 2 gb. |
| 455 |
|
|
| 456 |
|
hard coding some system init into bilayer.sys |
| 457 |
|
|
| 458 |
< |
2003-08-26 15:12 mmeineke |
| 458 |
> |
2003-08-26 16:12 mmeineke |
| 459 |
|
|
| 460 |
|
* libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: |
| 461 |
|
added define statemewnt to Statwriter and Dumpwriter to handle |
| 463 |
|
|
| 464 |
|
commented out some print statements in Zconstraint |
| 465 |
|
|
| 466 |
< |
2003-08-26 15:02 tim |
| 466 |
> |
2003-08-26 16:02 tim |
| 467 |
|
|
| 468 |
|
* libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed |
| 469 |
|
and check the seed which is specified by user at least contains 9 |
| 470 |
|
digits |
| 471 |
|
|
| 472 |
< |
2003-08-26 13:32 mmeineke |
| 472 |
> |
2003-08-26 14:32 mmeineke |
| 473 |
|
|
| 474 |
|
* libmdtools/DUFF.cpp: changed the Makefiel a litle. |
| 475 |
|
|
| 477 |
|
constucted in MPI. (The MPI struct had 6 doubles declared versus |
| 478 |
|
the actual 11) |
| 479 |
|
|
| 480 |
< |
2003-08-26 13:30 mmeineke |
| 480 |
> |
2003-08-26 14:30 mmeineke |
| 481 |
|
|
| 482 |
|
* Makefile: changed the Makefiel a litle. |
| 483 |
|
|
| 484 |
< |
2003-08-25 17:17 gezelter |
| 484 |
> |
2003-08-25 18:17 gezelter |
| 485 |
|
|
| 486 |
|
* utils/sysbuilder/Makefile: More FreeBSD fixes |
| 487 |
|
|
| 488 |
< |
2003-08-25 16:51 gezelter |
| 488 |
> |
2003-08-25 17:51 gezelter |
| 489 |
|
|
| 490 |
|
* libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, |
| 491 |
|
libmdtools/Makefile, src/Makefile: [no log message] |
| 492 |
|
|
| 493 |
< |
2003-08-22 15:04 mmeineke |
| 493 |
> |
2003-08-22 16:04 mmeineke |
| 494 |
|
|
| 495 |
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on |
| 496 |
|
frequency of output dumps. |
| 497 |
|
|
| 498 |
< |
2003-08-20 17:23 tim |
| 498 |
> |
2003-08-20 18:23 tim |
| 499 |
|
|
| 500 |
|
* libBASS/Globals.hpp, libmdtools/SimInfo.hpp, |
| 501 |
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
| 503 |
|
if he does not specify any value for seed, oopse will take the |
| 504 |
|
value of seconds of system time as seed |
| 505 |
|
|
| 506 |
< |
2003-08-20 14:42 mmeineke |
| 506 |
> |
2003-08-20 15:42 mmeineke |
| 507 |
|
|
| 508 |
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 509 |
|
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, |
| 516 |
|
fixed a bug where ghostbend atom b was not being set. ( recent bug |
| 517 |
|
from SimState conversion) |
| 518 |
|
|
| 519 |
< |
2003-08-20 14:41 mmeineke |
| 519 |
> |
2003-08-20 15:41 mmeineke |
| 520 |
|
|
| 521 |
|
* libBASS/Globals.hpp: updated the Changelog. |
| 522 |
|
|
| 523 |
|
added some bug fixes for setting the random number generator seed |
| 524 |
|
value. |
| 525 |
|
|
| 526 |
< |
2003-08-20 14:41 mmeineke |
| 526 |
> |
2003-08-20 15:41 mmeineke |
| 527 |
|
|
| 528 |
|
* ChangeLog: updated the Changelog. |
| 529 |
|
|
| 530 |
< |
2003-08-20 14:11 tim |
| 530 |
> |
2003-08-20 15:11 tim |
| 531 |
|
|
| 532 |
|
* libBASS/Globals.cpp, libmdtools/DUFF.cpp, |
| 533 |
|
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost |
| 534 |
|
bend class |
| 535 |
|
|
| 536 |
< |
2003-08-20 10:13 mmeineke |
| 536 |
> |
2003-08-20 11:13 mmeineke |
| 537 |
|
|
| 538 |
|
* utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in |
| 539 |
|
make links. added -f to ln -s. |
| 540 |
|
|
| 541 |
< |
2003-08-20 09:50 tim |
| 541 |
> |
2003-08-20 10:50 tim |
| 542 |
|
|
| 543 |
|
* libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] |
| 544 |
|
|
| 545 |
< |
2003-08-20 09:34 tim |
| 545 |
> |
2003-08-20 10:34 tim |
| 546 |
|
|
| 547 |
|
* libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp, |
| 548 |
|
ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg |
| 549 |
|
printing |
| 550 |
|
|
| 551 |
< |
2003-08-18 15:59 chuckv |
| 551 |
> |
2003-08-18 16:59 chuckv |
| 552 |
|
|
| 553 |
|
* utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 554 |
|
latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, |
| 555 |
|
sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. |
| 556 |
|
Nanobuilder still broke. |
| 557 |
|
|
| 558 |
< |
2003-08-15 14:24 tim |
| 558 |
> |
2003-08-15 15:24 tim |
| 559 |
|
|
| 560 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 561 |
|
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
| 564 |
|
libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint |
| 565 |
|
Method |
| 566 |
|
|
| 567 |
< |
2003-08-14 11:16 tim |
| 567 |
> |
2003-08-14 12:16 tim |
| 568 |
|
|
| 569 |
|
* libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint |
| 570 |
|
with average force substraction strategy |
| 571 |
|
|
| 572 |
< |
2003-08-13 16:20 chuckv |
| 572 |
> |
2003-08-13 17:20 chuckv |
| 573 |
|
|
| 574 |
|
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some |
| 575 |
|
profiling code -DPROFILE. |
| 576 |
|
|
| 577 |
< |
2003-08-13 14:21 tim |
| 577 |
> |
2003-08-13 15:21 tim |
| 578 |
|
|
| 579 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 580 |
|
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 581 |
|
libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic |
| 582 |
|
potential & z-contraint method |
| 583 |
|
|
| 584 |
< |
2003-08-12 16:44 mmeineke |
| 584 |
> |
2003-08-12 17:44 mmeineke |
| 585 |
|
|
| 586 |
|
* libBASS/BASS_interface.cpp, libBASS/Globals.hpp, |
| 587 |
|
libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 590 |
|
annoying bug in Directional Atom, where mu was getting written to |
| 591 |
|
pseudorandom memory location. |
| 592 |
|
|
| 593 |
< |
2003-08-12 14:56 tim |
| 593 |
> |
2003-08-12 15:56 tim |
| 594 |
|
|
| 595 |
|
* libBASS/BASS_interface.cpp, libBASS/Globals.cpp, |
| 596 |
|
libBASS/Globals.hpp, libmdtools/Atom.hpp, |
| 597 |
|
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
| 598 |
|
libmdtools/SimSetup.cpp: debugging globals |
| 599 |
|
|
| 600 |
< |
2003-08-12 13:40 gezelter |
| 600 |
> |
2003-08-12 14:40 gezelter |
| 601 |
|
|
| 602 |
|
* forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes |
| 603 |
|
and new atypes in LJFF |
| 604 |
|
|
| 605 |
< |
2003-08-12 13:15 gezelter |
| 605 |
> |
2003-08-12 14:15 gezelter |
| 606 |
|
|
| 607 |
|
* forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older |
| 608 |
|
stuff... |
| 609 |
|
|
| 610 |
< |
2003-08-12 13:14 chuckv |
| 610 |
> |
2003-08-12 14:14 chuckv |
| 611 |
|
|
| 612 |
|
* utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. |
| 613 |
|
|
| 614 |
< |
2003-08-12 13:04 chuckv |
| 614 |
> |
2003-08-12 14:04 chuckv |
| 615 |
|
|
| 616 |
|
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: |
| 617 |
|
Missed del of files before. |
| 618 |
|
|
| 619 |
< |
2003-08-12 13:03 chuckv |
| 619 |
> |
2003-08-12 14:03 chuckv |
| 620 |
|
|
| 621 |
|
* utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log |
| 622 |
|
message] |
| 623 |
|
|
| 624 |
< |
2003-08-12 13:01 chuckv |
| 624 |
> |
2003-08-12 14:01 chuckv |
| 625 |
|
|
| 626 |
|
* utils/sysbuilder/Makefile: commit makefile |
| 627 |
|
|
| 628 |
< |
2003-08-12 12:51 tim |
| 628 |
> |
2003-08-12 13:51 tim |
| 629 |
|
|
| 630 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 631 |
|
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
| 633 |
|
libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added |
| 634 |
|
harmonical potential to z-constraint method |
| 635 |
|
|
| 636 |
< |
2003-08-11 17:31 chuckv |
| 636 |
> |
2003-08-11 18:31 chuckv |
| 637 |
|
|
| 638 |
|
* utils/Makefile: Changed makefile to only build quicklate. |
| 639 |
|
|
| 640 |
< |
2003-08-11 17:25 chuckv |
| 640 |
> |
2003-08-11 18:25 chuckv |
| 641 |
|
|
| 642 |
|
* ac-tools/configure.in: added utils/sysbuilder to be built. |
| 643 |
|
|
| 644 |
< |
2003-08-11 17:12 chuckv |
| 644 |
> |
2003-08-11 18:12 chuckv |
| 645 |
|
|
| 646 |
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 647 |
|
bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, |
| 655 |
|
sysbuilder into a subdirectory. Fixed some of sysbuilder to work |
| 656 |
|
with new atom allocation in libmdtools. |
| 657 |
|
|
| 658 |
< |
2003-08-11 14:41 tim |
| 658 |
> |
2003-08-11 15:41 tim |
| 659 |
|
|
| 660 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp: added method of |
| 661 |
|
moving zconstraint molecules to specified positions |
| 662 |
|
|
| 663 |
< |
2003-08-11 14:39 tim |
| 663 |
> |
2003-08-11 15:39 tim |
| 664 |
|
|
| 665 |
|
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] |
| 666 |
|
|
| 667 |
< |
2003-08-11 14:38 mmeineke |
| 667 |
> |
2003-08-11 15:38 mmeineke |
| 668 |
|
|
| 669 |
|
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
| 670 |
|
libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, |
| 675 |
|
libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint |
| 676 |
|
into the BASS language syntax. |
| 677 |
|
|
| 678 |
< |
2003-08-11 13:29 mmeineke |
| 678 |
> |
2003-08-11 14:29 mmeineke |
| 679 |
|
|
| 680 |
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of |
| 681 |
|
degrees of freedom to account for zConstreints |
| 682 |
|
|
| 683 |
< |
2003-08-08 16:22 chuckv |
| 683 |
> |
2003-08-08 17:22 chuckv |
| 684 |
|
|
| 685 |
|
* libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, |
| 686 |
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
| 687 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
| 688 |
|
works..... |
| 689 |
|
|
| 690 |
< |
2003-08-08 13:32 mmeineke |
| 690 |
> |
2003-08-08 14:32 mmeineke |
| 691 |
|
|
| 692 |
|
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
| 693 |
|
moved frameCount's functionality into DumpReader. also split props |
| 694 |
|
into staticProps and dynamicProps. (currently only have |
| 695 |
|
staticProps) |
| 696 |
|
|
| 697 |
< |
2003-08-08 12:48 mmeineke |
| 697 |
> |
2003-08-08 13:48 mmeineke |
| 698 |
|
|
| 699 |
|
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
| 700 |
|
instance of Atom::setZ and Atom::getZ in ZConstaint. |
| 701 |
|
|
| 702 |
< |
2003-08-07 16:47 mmeineke |
| 702 |
> |
2003-08-07 17:47 mmeineke |
| 703 |
|
|
| 704 |
|
* libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
| 705 |
|
DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, |
| 708 |
|
SimState.hpp, Torsion.cpp: switched SimInfo to use a system |
| 709 |
|
configuration from SimState rather than arrays from Atom |
| 710 |
|
|
| 711 |
< |
2003-08-06 19:47 chuckv |
| 711 |
> |
2003-08-06 20:47 chuckv |
| 712 |
|
|
| 713 |
|
* libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, |
| 714 |
|
libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, |
| 715 |
|
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
| 716 |
|
samples/metals/Au.bass: Bug fixes for eam... |
| 717 |
|
|
| 718 |
< |
2003-08-01 11:18 tim |
| 718 |
> |
2003-08-01 12:18 tim |
| 719 |
|
|
| 720 |
|
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of |
| 721 |
|
Z-Constraint |
| 722 |
|
|
| 723 |
< |
2003-07-31 14:59 tim |
| 723 |
> |
2003-07-31 15:59 tim |
| 724 |
|
|
| 725 |
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 726 |
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 727 |
|
libmdtools/ZConstraint.cpp: add index range checking into |
| 728 |
|
ZConstraint |
| 729 |
|
|
| 730 |
< |
2003-07-31 10:38 tim |
| 730 |
> |
2003-07-31 11:38 tim |
| 731 |
|
|
| 732 |
|
* libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters |
| 733 |
|
to the globals |
| 734 |
|
|
| 735 |
< |
2003-07-31 10:35 tim |
| 735 |
> |
2003-07-31 11:35 tim |
| 736 |
|
|
| 737 |
|
* libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, |
| 738 |
|
Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, |
| 740 |
|
SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: |
| 741 |
|
Added Z constraint. |
| 742 |
|
|
| 743 |
< |
2003-07-30 16:17 chuckv |
| 743 |
> |
2003-07-30 17:17 chuckv |
| 744 |
|
|
| 745 |
|
* libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, |
| 746 |
|
libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, |
| 747 |
|
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, |
| 748 |
|
samples/metals/Au.bass: More bug fixes for eam. |
| 749 |
|
|
| 750 |
< |
2003-07-29 11:32 mmeineke |
| 750 |
> |
2003-07-29 12:32 mmeineke |
| 751 |
|
|
| 752 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
| 753 |
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 754 |
|
props/frameCount.c, props/frameCount.h, props/props.cpp, |
| 755 |
|
src/Makefile: working on the props code |
| 756 |
|
|
| 757 |
< |
2003-07-29 11:32 mmeineke |
| 757 |
> |
2003-07-29 12:32 mmeineke |
| 758 |
|
|
| 759 |
|
* libBASS/Globals.cpp: [no log message] |
| 760 |
|
|
| 761 |
< |
2003-07-25 15:05 chuckv |
| 761 |
> |
2003-07-25 16:05 chuckv |
| 762 |
|
|
| 763 |
|
* samples/metals/: Au.bass, metals.mdl: Added bass models for |
| 764 |
|
metals |
| 765 |
|
|
| 766 |
< |
2003-07-25 15:00 chuckv |
| 766 |
> |
2003-07-25 16:00 chuckv |
| 767 |
|
|
| 768 |
|
* libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, |
| 769 |
|
notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. |
| 770 |
|
|
| 771 |
< |
2003-07-24 16:22 chuckv |
| 771 |
> |
2003-07-24 17:22 chuckv |
| 772 |
|
|
| 773 |
|
* ac-tools/configure.in: Changed configure to look for both upper |
| 774 |
|
and lower cass .mod files |
| 775 |
|
|
| 776 |
< |
2003-07-24 14:57 chuckv |
| 776 |
> |
2003-07-24 15:57 chuckv |
| 777 |
|
|
| 778 |
|
* libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for |
| 779 |
|
eam and do_forces. |
| 780 |
|
|
| 781 |
< |
2003-07-23 17:13 chuckv |
| 781 |
> |
2003-07-23 18:13 chuckv |
| 782 |
|
|
| 783 |
|
* libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, |
| 784 |
|
force_globals.F90, simulation_module.F90, status_module.F90: |
| 785 |
|
Finished most code for eam.... |
| 786 |
|
|
| 787 |
< |
2003-07-22 16:49 mmeineke |
| 787 |
> |
2003-07-22 17:49 mmeineke |
| 788 |
|
|
| 789 |
|
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan |
| 790 |
|
function to the DumpReader. It should now save the start of each |
| 791 |
|
frame in a vector. |
| 792 |
|
|
| 793 |
< |
2003-07-22 15:05 mmeineke |
| 793 |
> |
2003-07-22 16:05 mmeineke |
| 794 |
|
|
| 795 |
|
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes |
| 796 |
|
to read dump files |
| 797 |
|
|
| 798 |
< |
2003-07-22 14:54 tim |
| 798 |
> |
2003-07-22 15:54 tim |
| 799 |
|
|
| 800 |
|
* libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, |
| 801 |
|
Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, |
| 802 |
|
NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log |
| 803 |
|
message] |
| 804 |
|
|
| 805 |
< |
2003-07-22 11:41 mmeineke |
| 805 |
> |
2003-07-22 12:41 mmeineke |
| 806 |
|
|
| 807 |
|
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, |
| 808 |
|
SimSetup.cpp: Fixed a current time initialization bug in |
| 809 |
|
InitFromFile. |
| 810 |
|
|
| 811 |
< |
2003-07-21 16:27 mmeineke |
| 811 |
> |
2003-07-21 17:27 mmeineke |
| 812 |
|
|
| 813 |
|
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, |
| 814 |
|
Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and |
| 815 |
|
friends to accomadate random file access |
| 816 |
|
|
| 817 |
< |
2003-07-21 11:23 mmeineke |
| 817 |
> |
2003-07-21 12:23 mmeineke |
| 818 |
|
|
| 819 |
|
* libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no |
| 820 |
|
one sets it. |
| 821 |
|
|
| 822 |
< |
2003-07-21 11:23 mmeineke |
| 822 |
> |
2003-07-21 12:23 mmeineke |
| 823 |
|
|
| 824 |
|
* libmdtools/: InitializeFromFile.cpp, Integrator.cpp, |
| 825 |
|
ReadWrite.hpp: fixed Initializefrom file to start the simulation |
| 826 |
|
from the time specified in the init file. |
| 827 |
|
|
| 828 |
< |
2003-07-17 16:49 gezelter |
| 828 |
> |
2003-07-17 17:49 gezelter |
| 829 |
|
|
| 830 |
|
* libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, |
| 831 |
|
DumpReader.cpp: Started work on a DumpReader |
| 832 |
|
|
| 833 |
< |
2003-07-17 15:38 gezelter |
| 833 |
> |
2003-07-17 16:38 gezelter |
| 834 |
|
|
| 835 |
|
* libmdtools/calc_sticky_pair.F90: Fixes for SSD/E |
| 836 |
|
|
| 837 |
< |
2003-07-17 15:32 gezelter |
| 837 |
> |
2003-07-17 16:32 gezelter |
| 838 |
|
|
| 839 |
|
* forceFields/DUFF.frc, libmdtools/DUFF.cpp, |
| 840 |
|
libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: |
| 841 |
|
Changes for SSD/E |
| 842 |
|
|
| 843 |
< |
2003-07-17 14:38 mmeineke |
| 843 |
> |
2003-07-17 15:38 mmeineke |
| 844 |
|
|
| 845 |
|
* libmdtools/do_Forces.F90: commented out an eam line |
| 846 |
|
|
| 847 |
< |
2003-07-17 14:32 chuckv |
| 847 |
> |
2003-07-17 15:32 chuckv |
| 848 |
|
|
| 849 |
|
* libmdtools/atype_module.F90: fixed spelling issue |
| 850 |
|
|
| 851 |
< |
2003-07-17 14:29 chuckv |
| 851 |
> |
2003-07-17 15:29 chuckv |
| 852 |
|
|
| 853 |
|
* libmdtools/: fInfo.c, status_module.F90: added info module |
| 854 |
|
|
| 855 |
< |
2003-07-17 14:25 chuckv |
| 855 |
> |
2003-07-17 15:25 chuckv |
| 856 |
|
|
| 857 |
|
* libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, |
| 858 |
|
atype_module.F90, calc_eam.F90, do_Forces.F90, |
| 859 |
|
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
| 860 |
|
mpiSimulation_module.F90: Added massive changes for eam.... |
| 861 |
|
|
| 862 |
< |
2003-07-16 16:49 chuckv |
| 862 |
> |
2003-07-16 17:49 chuckv |
| 863 |
|
|
| 864 |
|
* libmdtools/EAM_FF.cpp: More up to date version of EAM_FF |
| 865 |
|
|
| 866 |
< |
2003-07-16 16:30 mmeineke |
| 866 |
> |
2003-07-16 17:30 mmeineke |
| 867 |
|
|
| 868 |
|
* libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, |
| 869 |
|
SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 874 |
|
notifyCutoffs in Fortran notifies those who need the information of |
| 875 |
|
any changes to cutoffs. |
| 876 |
|
|
| 877 |
< |
2003-07-16 12:35 gezelter |
| 877 |
> |
2003-07-16 13:35 gezelter |
| 878 |
|
|
| 879 |
|
* utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. |
| 880 |
|
quickLate is now somewhat more intelligent about periodic |
| 881 |
|
boundaries and wrapping. |
| 882 |
|
|
| 883 |
< |
2003-07-16 11:40 chuckv |
| 883 |
> |
2003-07-16 12:40 chuckv |
| 884 |
|
|
| 885 |
|
* libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists |
| 886 |
|
|
| 887 |
< |
2003-07-16 10:34 mmeineke |
| 887 |
> |
2003-07-16 11:34 mmeineke |
| 888 |
|
|
| 889 |
|
* scripts/cleanSrc: added a quick wipe-and-update script for quick |
| 890 |
|
rebuilds on BoB |
| 891 |
|
|
| 892 |
< |
2003-07-15 21:11 gezelter |
| 892 |
> |
2003-07-15 22:11 gezelter |
| 893 |
|
|
| 894 |
|
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, |
| 895 |
|
SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more |
| 896 |
|
fixes for box changes |
| 897 |
|
|
| 898 |
< |
2003-07-15 17:29 mmeineke |
| 898 |
> |
2003-07-15 18:29 mmeineke |
| 899 |
|
|
| 900 |
|
* libmdtools/simulation_module.F90: removed some debugging print |
| 901 |
|
statements. |
| 902 |
|
|
| 903 |
< |
2003-07-15 17:22 mmeineke |
| 903 |
> |
2003-07-15 18:22 mmeineke |
| 904 |
|
|
| 905 |
|
* libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 906 |
|
do_Forces.F90, simulation_module.F90: fixed a long lived bug in |
| 909 |
|
cutoff region to be to small. Also led to the removal of the taper |
| 910 |
|
region to buffer the dipole cutoff. |
| 911 |
|
|
| 912 |
< |
2003-07-15 16:34 mmeineke |
| 912 |
> |
2003-07-15 17:34 mmeineke |
| 913 |
|
|
| 914 |
|
* libmdtools/: SimInfo.cpp, simulation_module.F90: working on |
| 915 |
|
fixing ssd bug |
| 916 |
|
|
| 917 |
< |
2003-07-15 14:56 gezelter |
| 917 |
> |
2003-07-15 15:56 gezelter |
| 918 |
|
|
| 919 |
|
* libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes |
| 920 |
|
for the NPT ensembles |
| 921 |
|
|
| 922 |
< |
2003-07-15 13:52 mmeineke |
| 922 |
> |
2003-07-15 14:52 mmeineke |
| 923 |
|
|
| 924 |
|
* libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up |
| 925 |
|
simSetup |
| 926 |
|
|
| 927 |
< |
2003-07-15 12:57 mmeineke |
| 927 |
> |
2003-07-15 13:57 mmeineke |
| 928 |
|
|
| 929 |
|
* libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, |
| 930 |
|
SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: |
| 931 |
|
fixed some bugs, Changed entry_plug to info where appropriate |
| 932 |
|
|
| 933 |
< |
2003-07-15 12:25 chuckv |
| 933 |
> |
2003-07-15 13:25 chuckv |
| 934 |
|
|
| 935 |
|
* utils/sysBuild.ggo: added more command line arguments |
| 936 |
|
|
| 937 |
< |
2003-07-15 12:11 gezelter |
| 937 |
> |
2003-07-15 13:11 gezelter |
| 938 |
|
|
| 939 |
|
* samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: |
| 940 |
|
Fixing force field line |
| 941 |
|
|
| 942 |
< |
2003-07-15 12:10 gezelter |
| 942 |
> |
2003-07-15 13:10 gezelter |
| 943 |
|
|
| 944 |
|
* libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, |
| 945 |
|
calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
| 946 |
|
calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure |
| 947 |
|
tensor |
| 948 |
|
|
| 949 |
< |
2003-07-15 10:50 gezelter |
| 949 |
> |
2003-07-15 11:50 gezelter |
| 950 |
|
|
| 951 |
|
* libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes |
| 952 |
|
|
| 953 |
< |
2003-07-15 10:42 gezelter |
| 953 |
> |
2003-07-15 11:42 gezelter |
| 954 |
|
|
| 955 |
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: |
| 956 |
|
removed old outdated code |
| 957 |
|
|
| 958 |
< |
2003-07-15 09:45 gezelter |
| 958 |
> |
2003-07-15 10:45 gezelter |
| 959 |
|
|
| 960 |
|
* libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx |
| 961 |
|
|
| 962 |
< |
2003-07-15 09:28 gezelter |
| 962 |
> |
2003-07-15 10:28 gezelter |
| 963 |
|
|
| 964 |
|
* libmdtools/Molecule.cpp: removing get_vx |
| 965 |
|
|
| 966 |
< |
2003-07-14 22:28 gezelter |
| 966 |
> |
2003-07-14 23:28 gezelter |
| 967 |
|
|
| 968 |
|
* libmdtools/NPTfm.cpp: Added NPTfm |
| 969 |
|
|
| 970 |
< |
2003-07-14 22:27 gezelter |
| 970 |
> |
2003-07-14 23:27 gezelter |
| 971 |
|
|
| 972 |
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
| 973 |
|
Bugfix in NPTim, fixes for NPTfm |
| 974 |
|
|
| 975 |
< |
2003-07-14 22:08 gezelter |
| 975 |
> |
2003-07-14 23:08 gezelter |
| 976 |
|
|
| 977 |
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
| 978 |
|
Checking in changes for NPTim |
| 979 |
|
|
| 980 |
< |
2003-07-14 18:06 gezelter |
| 980 |
> |
2003-07-14 19:06 gezelter |
| 981 |
|
|
| 982 |
|
* utils/Makefile: Broken SysBuilder |
| 983 |
|
|
| 984 |
< |
2003-07-14 18:06 gezelter |
| 984 |
> |
2003-07-14 19:06 gezelter |
| 985 |
|
|
| 986 |
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
| 987 |
|
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
| 988 |
|
for samples |
| 989 |
|
|
| 990 |
< |
2003-07-14 18:06 gezelter |
| 990 |
> |
2003-07-14 19:06 gezelter |
| 991 |
|
|
| 992 |
|
* libmdtools/: Integrator.cpp, do_Forces.F90: Removed some |
| 993 |
|
debugging write statements |
| 994 |
|
|
| 995 |
< |
2003-07-14 17:38 gezelter |
| 995 |
> |
2003-07-14 18:38 gezelter |
| 996 |
|
|
| 997 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, |
| 998 |
|
NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom |
| 999 |
|
|
| 1000 |
< |
2003-07-14 16:48 mmeineke |
| 1000 |
> |
2003-07-14 17:48 mmeineke |
| 1001 |
|
|
| 1002 |
|
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get |
| 1003 |
|
and set routines to Atom and DirectionalAtom |
| 1004 |
|
|
| 1005 |
< |
2003-07-14 16:35 chuckv |
| 1005 |
> |
2003-07-14 17:35 chuckv |
| 1006 |
|
|
| 1007 |
|
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, |
| 1008 |
|
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder |
| 1009 |
|
that takes different cmd line arguments. |
| 1010 |
|
|
| 1011 |
< |
2003-07-14 16:28 mmeineke |
| 1011 |
> |
2003-07-14 17:28 mmeineke |
| 1012 |
|
|
| 1013 |
|
* libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, |
| 1014 |
|
ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, |
| 1015 |
|
SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors |
| 1016 |
|
were not being updated |
| 1017 |
|
|
| 1018 |
< |
2003-07-14 10:04 gezelter |
| 1018 |
> |
2003-07-14 11:04 gezelter |
| 1019 |
|
|
| 1020 |
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on |
| 1021 |
|
NPTim |
| 1022 |
|
|
| 1023 |
< |
2003-07-14 09:55 mmeineke |
| 1023 |
> |
2003-07-14 10:55 mmeineke |
| 1024 |
|
|
| 1025 |
|
* forceFields/DUFF.frc: Switched the bond in the force field back |
| 1026 |
|
to constrained, to preserve energy |
| 1027 |
|
|
| 1028 |
< |
2003-07-11 17:34 mmeineke |
| 1028 |
> |
2003-07-11 18:34 mmeineke |
| 1029 |
|
|
| 1030 |
|
* libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, |
| 1031 |
|
Integrator.hpp: working on som integrator bugs |
| 1032 |
|
|
| 1033 |
< |
2003-07-11 10:26 gezelter |
| 1033 |
> |
2003-07-11 11:26 gezelter |
| 1034 |
|
|
| 1035 |
|
* libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting |
| 1036 |
|
to worry about all the strtok() calls in our code |
| 1037 |
|
|
| 1038 |
< |
2003-07-11 09:49 gezelter |
| 1038 |
> |
2003-07-11 10:49 gezelter |
| 1039 |
|
|
| 1040 |
|
* utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness |
| 1041 |
|
|
| 1042 |
< |
2003-07-10 20:15 gezelter |
| 1042 |
> |
2003-07-10 21:15 gezelter |
| 1043 |
|
|
| 1044 |
|
* libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and |
| 1045 |
|
eor. |
| 1046 |
|
|
| 1047 |
< |
2003-07-10 17:15 mmeineke |
| 1047 |
> |
2003-07-10 18:15 mmeineke |
| 1048 |
|
|
| 1049 |
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, |
| 1050 |
|
SimInfo.cpp, Thermo.cpp: fixed some bugs |
| 1051 |
|
|
| 1052 |
< |
2003-07-10 14:53 chuckv |
| 1052 |
> |
2003-07-10 15:53 chuckv |
| 1053 |
|
|
| 1054 |
|
* utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, |
| 1055 |
|
nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added |
| 1056 |
|
nanoBuilder and a general Lattice builder. |
| 1057 |
|
|
| 1058 |
< |
2003-07-10 12:10 gezelter |
| 1058 |
> |
2003-07-10 13:10 gezelter |
| 1059 |
|
|
| 1060 |
|
* libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, |
| 1061 |
|
Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff |
| 1062 |
|
|
| 1063 |
< |
2003-07-09 17:14 mmeineke |
| 1063 |
> |
2003-07-09 18:14 mmeineke |
| 1064 |
|
|
| 1065 |
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
| 1066 |
|
Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, |
| 1067 |
|
SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the |
| 1068 |
|
caclulation of HmatInverse. |
| 1069 |
|
|
| 1070 |
< |
2003-07-09 10:34 mmeineke |
| 1070 |
> |
2003-07-09 11:34 mmeineke |
| 1071 |
|
|
| 1072 |
|
* libBASS/MoleculeStamp.hpp: starting some work for xlate |
| 1073 |
|
|
| 1074 |
< |
2003-07-09 10:33 mmeineke |
| 1074 |
> |
2003-07-09 11:33 mmeineke |
| 1075 |
|
|
| 1076 |
|
* libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff |
| 1077 |
|
|
| 1078 |
< |
2003-07-09 08:56 gezelter |
| 1078 |
> |
2003-07-09 09:56 gezelter |
| 1079 |
|
|
| 1080 |
|
* libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf |
| 1081 |
|
|
| 1082 |
< |
2003-07-09 08:56 gezelter |
| 1082 |
> |
2003-07-09 09:56 gezelter |
| 1083 |
|
|
| 1084 |
|
* libBASS/Globals.cpp: Removed Qmass |
| 1085 |
|
|
| 1086 |
< |
2003-07-08 21:15 gezelter |
| 1086 |
> |
2003-07-08 22:15 gezelter |
| 1087 |
|
|
| 1088 |
|
* libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf |
| 1089 |
|
and NPTi |
| 1090 |
|
|
| 1091 |
< |
2003-07-08 20:41 gezelter |
| 1091 |
> |
2003-07-08 21:41 gezelter |
| 1092 |
|
|
| 1093 |
|
* libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf |
| 1094 |
|
|
| 1095 |
< |
2003-07-08 16:10 gezelter |
| 1095 |
> |
2003-07-08 17:10 gezelter |
| 1096 |
|
|
| 1097 |
|
* libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] |
| 1098 |
|
|
| 1099 |
< |
2003-07-08 16:06 gezelter |
| 1099 |
> |
2003-07-08 17:06 gezelter |
| 1100 |
|
|
| 1101 |
|
* libmdtools/NPTi.cpp: fixed box scaling |
| 1102 |
|
|
| 1103 |
< |
2003-07-08 15:56 gezelter |
| 1103 |
> |
2003-07-08 16:56 gezelter |
| 1104 |
|
|
| 1105 |
|
* libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, |
| 1106 |
|
SimInfo.hpp, Thermo.cpp: NPTi |
| 1107 |
|
|
| 1108 |
< |
2003-07-03 14:41 mmeineke |
| 1108 |
> |
2003-07-03 15:41 mmeineke |
| 1109 |
|
|
| 1110 |
|
* libBASS/Makefile, libmdtools/Makefile, src/Makefile, |
| 1111 |
|
utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy |
| 1112 |
|
scripts in the makefiles |
| 1113 |
|
|
| 1114 |
< |
2003-07-02 16:26 mmeineke |
| 1114 |
> |
2003-07-02 17:26 mmeineke |
| 1115 |
|
|
| 1116 |
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
| 1117 |
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 1122 |
|
utils/Makefile: fixed the bugs introduced by switching the periodic |
| 1123 |
|
box to a matrix |
| 1124 |
|
|
| 1125 |
< |
2003-07-01 17:39 gezelter |
| 1125 |
> |
2003-07-01 18:39 gezelter |
| 1126 |
|
|
| 1127 |
|
* libmdtools/do_Forces.F90: Fortran flexi-BOX |
| 1128 |
|
|
| 1129 |
< |
2003-07-01 17:29 gezelter |
| 1129 |
> |
2003-07-01 18:29 gezelter |
| 1130 |
|
|
| 1131 |
|
* libmdtools/simulation_module.F90: Fixes for flexi-BOX |
| 1132 |
|
|
| 1133 |
< |
2003-07-01 16:33 mmeineke |
| 1133 |
> |
2003-07-01 17:33 mmeineke |
| 1134 |
|
|
| 1135 |
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, |
| 1136 |
|
fortranWrapDefines.hpp, simulation_module.F90: working on adding |
| 1137 |
|
the box matrix to everything. |
| 1138 |
|
|
| 1139 |
< |
2003-06-30 17:03 mmeineke |
| 1139 |
> |
2003-06-30 18:03 mmeineke |
| 1140 |
|
|
| 1141 |
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 1142 |
|
src/oopse.cpp: |
| 1143 |
|
Updated the ChangeLog, and Converted most of the SImInfo to use |
| 1144 |
|
non-Isotropic boxes. wrapVector needs to be finished. |
| 1145 |
|
|
| 1146 |
< |
2003-06-25 16:12 mmeineke |
| 1146 |
> |
2003-06-25 17:12 mmeineke |
| 1147 |
|
|
| 1148 |
|
* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
| 1149 |
|
to Harmonic bonds in the DUFF frc file |
| 1150 |
|
|
| 1151 |
|
fixed constraints. |
| 1152 |
|
|
| 1153 |
< |
2003-06-25 16:11 mmeineke |
| 1153 |
> |
2003-06-25 17:11 mmeineke |
| 1154 |
|
|
| 1155 |
|
* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
| 1156 |
|
the DUFF frc file |
| 1157 |
|
|
| 1158 |
< |
2003-06-24 17:51 gezelter |
| 1158 |
> |
2003-06-24 18:51 gezelter |
| 1159 |
|
|
| 1160 |
|
* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
| 1161 |
|
|
| 1162 |
< |
2003-06-24 14:57 mmeineke |
| 1162 |
> |
2003-06-24 15:57 mmeineke |
| 1163 |
|
|
| 1164 |
|
* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
| 1165 |
|
libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
| 1166 |
|
the DUFF forcefield and BondExtensions.cpp |
| 1167 |
|
|
| 1168 |
< |
2003-06-23 16:24 mmeineke |
| 1168 |
> |
2003-06-23 17:24 mmeineke |
| 1169 |
|
|
| 1170 |
|
* libmdtools/Integrator.cpp: Doing some work to debug the |
| 1171 |
|
constraint code. |
| 1172 |
|
|
| 1173 |
< |
2003-06-20 15:50 gezelter |
| 1173 |
> |
2003-06-20 16:50 gezelter |
| 1174 |
|
|
| 1175 |
|
* libmdtools/Integrator.hpp: NPT fix |
| 1176 |
|
|
| 1177 |
< |
2003-06-20 15:29 mmeineke |
| 1177 |
> |
2003-06-20 16:29 mmeineke |
| 1178 |
|
|
| 1179 |
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 1180 |
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 1183 |
|
libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
| 1184 |
|
integrator and NVT seem to be working now. |
| 1185 |
|
|
| 1186 |
< |
2003-06-20 11:49 gezelter |
| 1186 |
> |
2003-06-20 12:49 gezelter |
| 1187 |
|
|
| 1188 |
|
* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
| 1189 |
|
|
| 1190 |
< |
2003-06-19 17:02 mmeineke |
| 1190 |
> |
2003-06-19 18:02 mmeineke |
| 1191 |
|
|
| 1192 |
|
* forceFields/DUFF.frc, forceFields/LJFF.frc, |
| 1193 |
|
forceFields/LJ_FF.frc, forceFields/Makefile, |
| 1198 |
|
libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
| 1199 |
|
forcefield names. |
| 1200 |
|
|
| 1201 |
< |
2003-06-19 14:21 mmeineke |
| 1201 |
> |
2003-06-19 15:21 mmeineke |
| 1202 |
|
|
| 1203 |
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
| 1204 |
|
finished the basics of the integrator and SimSetup.cpp |
| 1205 |
|
|
| 1206 |
< |
2003-06-19 14:11 mmeineke |
| 1206 |
> |
2003-06-19 15:11 mmeineke |
| 1207 |
|
|
| 1208 |
|
* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
| 1209 |
|
up / get it to work with the new Integrator. |
| 1210 |
|
|
| 1211 |
< |
2003-06-18 17:20 mmeineke |
| 1211 |
> |
2003-06-18 18:20 mmeineke |
| 1212 |
|
|
| 1213 |
|
* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
| 1214 |
|
output times. |
| 1215 |
|
|
| 1216 |
< |
2003-06-17 16:56 mmeineke |
| 1216 |
> |
2003-06-17 17:56 mmeineke |
| 1217 |
|
|
| 1218 |
|
* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
| 1219 |
|
fro the ghost Bend in TraPPE_Ex |
| 1220 |
|
|
| 1221 |
|
some work on the integrator. ( incomplete) |
| 1222 |
|
|
| 1223 |
< |
2003-06-17 16:55 mmeineke |
| 1223 |
> |
2003-06-17 17:55 mmeineke |
| 1224 |
|
|
| 1225 |
|
* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
| 1226 |
|
Bend in TraPPE_Ex |
| 1227 |
|
|
| 1228 |
< |
2003-06-04 16:06 mmeineke |
| 1228 |
> |
2003-06-04 17:06 mmeineke |
| 1229 |
|
|
| 1230 |
|
* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
| 1231 |
|
constrainB to the Symplectic integrator |
| 1232 |
|
|
| 1233 |
< |
2003-05-30 16:32 mmeineke |
| 1233 |
> |
2003-05-30 17:32 mmeineke |
| 1234 |
|
|
| 1235 |
|
* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
| 1236 |
|
the basic integrator. |
| 1237 |
|
|
| 1238 |
|
bilayerSys.cpp altered for building tb3. |
| 1239 |
|
|
| 1240 |
< |
2003-05-30 16:31 mmeineke |
| 1240 |
> |
2003-05-30 17:31 mmeineke |
| 1241 |
|
|
| 1242 |
|
* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
| 1243 |
|
TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
| 1244 |
|
modifiying Symplectic to become the basic integrator. |
| 1245 |
|
|
| 1246 |
< |
2003-05-30 15:19 mmeineke |
| 1246 |
> |
2003-05-30 16:19 mmeineke |
| 1247 |
|
|
| 1248 |
|
* libmdtools/Integrator.hpp: added some member variables for |
| 1249 |
|
position, velocity, etc. |
| 1250 |
|
|
| 1251 |
< |
2003-05-30 14:07 mmeineke |
| 1251 |
> |
2003-05-30 15:07 mmeineke |
| 1252 |
|
|
| 1253 |
|
* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
| 1254 |
|
is now derived from Integrator |
| 1255 |
|
|
| 1256 |
< |
2003-05-20 11:44 mmeineke |
| 1256 |
> |
2003-05-20 12:44 mmeineke |
| 1257 |
|
|
| 1258 |
|
* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
| 1259 |
|
|
| 1260 |
< |
2003-05-17 11:57 mmeineke |
| 1260 |
> |
2003-05-17 12:57 mmeineke |
| 1261 |
|
|
| 1262 |
|
* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
| 1263 |
|
working |
| 1264 |
|
|
| 1265 |
< |
2003-05-16 16:37 mmeineke |
| 1265 |
> |
2003-05-16 17:37 mmeineke |
| 1266 |
|
|
| 1267 |
|
* utils/bilayerSys.cpp: still working on the bilayer code |
| 1268 |
|
|
| 1269 |
< |
2003-05-16 09:28 mmeineke |
| 1269 |
> |
2003-05-16 10:28 mmeineke |
| 1270 |
|
|
| 1271 |
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
| 1272 |
|
work to overhaul sysbuild. |
| 1273 |
|
|
| 1274 |
< |
2003-05-13 16:23 mmeineke |
| 1274 |
> |
2003-05-13 17:23 mmeineke |
| 1275 |
|
|
| 1276 |
|
* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
| 1277 |
|
|
| 1278 |
< |
2003-05-13 15:47 mmeineke |
| 1278 |
> |
2003-05-13 16:47 mmeineke |
| 1279 |
|
|
| 1280 |
|
* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
| 1281 |
|
beadLipid/water.mdl: Added bead lipid model to the sample directory |
| 1282 |
|
|
| 1283 |
< |
2003-05-13 15:34 mmeineke |
| 1283 |
> |
2003-05-13 16:34 mmeineke |
| 1284 |
|
|
| 1285 |
|
* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
| 1286 |
|
the Trappe extended force field |
| 1287 |
|
|
| 1288 |
< |
2003-05-13 12:01 mmeineke |
| 1288 |
> |
2003-05-13 13:01 mmeineke |
| 1289 |
|
|
| 1290 |
|
* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
| 1291 |
|
TraPPe_Ex forceField |
| 1292 |
|
|
| 1293 |
< |
2003-05-09 14:51 mmeineke |
| 1293 |
> |
2003-05-09 15:51 mmeineke |
| 1294 |
|
|
| 1295 |
|
* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
| 1296 |
|
there were some duplicate entries |
| 1297 |
|
|
| 1298 |
|
added a two chain lipid to the lipid.mdl in sample |
| 1299 |
|
|
| 1300 |
< |
2003-05-09 14:51 mmeineke |
| 1300 |
> |
2003-05-09 15:51 mmeineke |
| 1301 |
|
|
| 1302 |
|
* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
| 1303 |
|
there were some duplicate entries |
| 1304 |
|
|
| 1305 |
< |
2003-05-09 11:56 mmeineke |
| 1305 |
> |
2003-05-09 12:56 mmeineke |
| 1306 |
|
|
| 1307 |
|
* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
| 1308 |
|
configure script |
| 1309 |
|
|
| 1310 |
|
added the CH branching group to the TraPPE_Ex fource field |
| 1311 |
|
|
| 1312 |
< |
2003-05-09 11:55 mmeineke |
| 1312 |
> |
2003-05-09 12:55 mmeineke |
| 1313 |
|
|
| 1314 |
|
* ac-tools/configure.in: added the utils subdirectory to the |
| 1315 |
|
configure script |
| 1316 |
|
|
| 1317 |
< |
2003-04-25 11:02 mmeineke |
| 1317 |
> |
2003-04-25 12:02 mmeineke |
| 1318 |
|
|
| 1319 |
|
* utils/bilayerSys.cpp: i quick fix to th distance in the random |
| 1320 |
|
bilayer builder |
| 1321 |
|
|
| 1322 |
< |
2003-04-24 21:00 mmeineke |
| 1322 |
> |
2003-04-24 22:00 mmeineke |
| 1323 |
|
|
| 1324 |
|
* libmdtools/f_verlet_constrained.F90: added a new test for |
| 1325 |
|
constraint failure |
| 1326 |
|
|
| 1327 |
< |
2003-04-17 16:54 mmeineke |
| 1327 |
> |
2003-04-17 17:54 mmeineke |
| 1328 |
|
|
| 1329 |
|
* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
| 1330 |
|
utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
| 1331 |
|
utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
| 1332 |
|
build our systems |
| 1333 |
|
|
| 1334 |
< |
2003-04-16 16:11 mmeineke |
| 1334 |
> |
2003-04-16 17:11 mmeineke |
| 1335 |
|
|
| 1336 |
|
* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
| 1337 |
|
|
| 1338 |
< |
2003-04-15 16:47 mmeineke |
| 1338 |
> |
2003-04-15 17:47 mmeineke |
| 1339 |
|
|
| 1340 |
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
| 1341 |
|
and sysBuild both will build now. woot! |
| 1342 |
|
|
| 1343 |
< |
2003-04-15 16:20 mmeineke |
| 1343 |
> |
2003-04-15 17:20 mmeineke |
| 1344 |
|
|
| 1345 |
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 1346 |
|
bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
| 1349 |
|
|
| 1350 |
|
MoLocator.cpp is currently empty |
| 1351 |
|
|
| 1352 |
< |
2003-04-15 15:40 chuckv |
| 1352 |
> |
2003-04-15 16:40 chuckv |
| 1353 |
|
|
| 1354 |
|
* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
| 1355 |
|
forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
| 1356 |
|
forceFields/pdu3.eam, forceFields/ptu3.eam, |
| 1357 |
|
libmdtools/ForceFields.hpp: Added eam force files... |
| 1358 |
|
|
| 1359 |
< |
2003-04-15 11:37 chuckv |
| 1359 |
> |
2003-04-15 12:37 chuckv |
| 1360 |
|
|
| 1361 |
|
* libmdtools/EAM_FF.cpp: More eam work. |
| 1362 |
|
|
| 1363 |
< |
2003-04-14 16:22 mmeineke |
| 1363 |
> |
2003-04-14 17:22 mmeineke |
| 1364 |
|
|
| 1365 |
|
* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
| 1366 |
|
utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
| 1367 |
|
working on the system builder |
| 1368 |
|
|
| 1369 |
< |
2003-04-14 16:16 chuckv |
| 1369 |
> |
2003-04-14 17:16 chuckv |
| 1370 |
|
|
| 1371 |
|
* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
| 1372 |
|
ordering on NVT calculation in integrators. |
| 1373 |
|
|
| 1374 |
< |
2003-04-14 14:51 mmeineke |
| 1374 |
> |
2003-04-14 15:51 mmeineke |
| 1375 |
|
|
| 1376 |
|
* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
| 1377 |
|
obj/placeHolder: working on a system builder |
| 1378 |
|
|
| 1379 |
< |
2003-04-14 14:04 mmeineke |
| 1379 |
> |
2003-04-14 15:04 mmeineke |
| 1380 |
|
|
| 1381 |
|
* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
| 1382 |
|
|
| 1383 |
|
added sysBuild to the utils Makefile |
| 1384 |
|
|
| 1385 |
< |
2003-04-14 14:03 mmeineke |
| 1385 |
> |
2003-04-14 15:03 mmeineke |
| 1386 |
|
|
| 1387 |
|
* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
| 1388 |
|
Ghost bends to the TraPPE_Ex forceField |
| 1389 |
|
|
| 1390 |
< |
2003-04-14 13:19 chuckv |
| 1390 |
> |
2003-04-14 14:19 chuckv |
| 1391 |
|
|
| 1392 |
|
* libmdtools/calc_eam.F90: Added first mangling of EAM. |
| 1393 |
|
|
| 1394 |
< |
2003-04-11 13:46 mmeineke |
| 1394 |
> |
2003-04-11 14:46 mmeineke |
| 1395 |
|
|
| 1396 |
|
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
| 1397 |
|
simulation_module.F90: fixed a memory bug in Fortran, where |
| 1398 |
|
molMembershipArray was declared nLocal instead of nGlobal. |
| 1399 |
|
|
| 1400 |
< |
2003-04-11 10:16 gezelter |
| 1400 |
> |
2003-04-11 11:16 gezelter |
| 1401 |
|
|
| 1402 |
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 1403 |
|
SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
| 1404 |
|
fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
| 1405 |
|
for NPT |
| 1406 |
|
|
| 1407 |
< |
2003-04-10 15:08 mmeineke |
| 1407 |
> |
2003-04-10 16:08 mmeineke |
| 1408 |
|
|
| 1409 |
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
| 1410 |
|
globalIndex counter to Molecule |
| 1411 |
|
|
| 1412 |
< |
2003-04-10 11:35 gezelter |
| 1412 |
> |
2003-04-10 12:35 gezelter |
| 1413 |
|
|
| 1414 |
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
| 1415 |
|
ConstantStress |
| 1416 |
|
|
| 1417 |
< |
2003-04-10 11:27 mmeineke |
| 1417 |
> |
2003-04-10 12:27 mmeineke |
| 1418 |
|
|
| 1419 |
|
* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
| 1420 |
|
caused a miscalculation of nLocal. |
| 1421 |
|
|
| 1422 |
< |
2003-04-10 11:21 mmeineke |
| 1422 |
> |
2003-04-10 12:21 mmeineke |
| 1423 |
|
|
| 1424 |
|
* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
| 1425 |
|
do_Forces.F90: fixed a bug in symplectic, where presure was only |
| 1426 |
|
being calculated the first time through. |
| 1427 |
|
|
| 1428 |
< |
2003-04-09 11:20 chuckv |
| 1428 |
> |
2003-04-09 12:20 chuckv |
| 1429 |
|
|
| 1430 |
|
* samples/alkane/alkanes.mdl: added pentane to the alkane model |
| 1431 |
|
file |
| 1432 |
|
|
| 1433 |
< |
2003-04-09 08:59 gezelter |
| 1433 |
> |
2003-04-09 09:59 gezelter |
| 1434 |
|
|
| 1435 |
|
* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
| 1436 |
|
Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
| 1437 |
|
|
| 1438 |
< |
2003-04-08 23:06 gezelter |
| 1438 |
> |
2003-04-09 00:06 gezelter |
| 1439 |
|
|
| 1440 |
|
* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
| 1441 |
|
ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 1445 |
|
fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
| 1446 |
|
NVT |
| 1447 |
|
|
| 1448 |
< |
2003-04-08 17:38 chuckv |
| 1448 |
> |
2003-04-08 18:38 chuckv |
| 1449 |
|
|
| 1450 |
|
* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
| 1451 |
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
| 1453 |
|
libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
| 1454 |
|
(kinda)... |
| 1455 |
|
|
| 1456 |
< |
2003-04-08 16:35 gezelter |
| 1456 |
> |
2003-04-08 17:35 gezelter |
| 1457 |
|
|
| 1458 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 1459 |
|
libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
| 1460 |
|
libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
| 1461 |
|
|
| 1462 |
< |
2003-04-08 12:16 chuckv |
| 1462 |
> |
2003-04-08 13:16 chuckv |
| 1463 |
|
|
| 1464 |
|
* libmdtools/: do_Forces.F90, neighborLists.F90, |
| 1465 |
|
simulation_module.F90: Moved expand neighborlist to init_FF. |
| 1466 |
|
|
| 1467 |
< |
2003-04-08 10:20 chuckv |
| 1467 |
> |
2003-04-08 11:20 chuckv |
| 1468 |
|
|
| 1469 |
|
* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
| 1470 |
|
NVT |
| 1471 |
|
|
| 1472 |
< |
2003-04-08 09:39 gezelter |
| 1472 |
> |
2003-04-08 10:39 gezelter |
| 1473 |
|
|
| 1474 |
|
* libmdtools/Verlet.cpp: fixes for nvt / npt |
| 1475 |
|
|
| 1476 |
< |
2003-04-08 09:34 gezelter |
| 1476 |
> |
2003-04-08 10:34 gezelter |
| 1477 |
|
|
| 1478 |
|
* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
| 1479 |
|
Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
| 1480 |
|
|
| 1481 |
< |
2003-04-08 07:50 gezelter |
| 1481 |
> |
2003-04-08 08:50 gezelter |
| 1482 |
|
|
| 1483 |
|
* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
| 1484 |
|
|
| 1485 |
< |
2003-04-08 07:44 gezelter |
| 1485 |
> |
2003-04-08 08:44 gezelter |
| 1486 |
|
|
| 1487 |
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
| 1488 |
|
Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
| 1489 |
|
NVT and NPT ensembles |
| 1490 |
|
|
| 1491 |
< |
2003-04-07 16:42 gezelter |
| 1491 |
> |
2003-04-07 17:42 gezelter |
| 1492 |
|
|
| 1493 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 1494 |
|
libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
| 1495 |
|
libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
| 1496 |
|
|
| 1497 |
< |
2003-04-07 16:20 mmeineke |
| 1497 |
> |
2003-04-07 17:20 mmeineke |
| 1498 |
|
|
| 1499 |
|
* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
| 1500 |
|
portion of SSD. |
| 1501 |
|
|
| 1502 |
< |
2003-04-07 16:16 mmeineke |
| 1502 |
> |
2003-04-07 17:16 mmeineke |
| 1503 |
|
|
| 1504 |
|
* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
| 1505 |
|
doing some testing in sticky through Symplectic. |
| 1506 |
|
|
| 1507 |
< |
2003-04-07 15:51 gezelter |
| 1507 |
> |
2003-04-07 16:51 gezelter |
| 1508 |
|
|
| 1509 |
|
* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
| 1510 |
|
|
| 1511 |
< |
2003-04-07 15:50 chuckv |
| 1511 |
> |
2003-04-07 16:50 chuckv |
| 1512 |
|
|
| 1513 |
|
* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
| 1514 |
|
tau and virial. |
| 1515 |
|
|
| 1516 |
< |
2003-04-07 15:06 mmeineke |
| 1516 |
> |
2003-04-07 16:06 mmeineke |
| 1517 |
|
|
| 1518 |
|
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
| 1519 |
|
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
| 1520 |
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
| 1521 |
|
src/Makefile: bug fixes |
| 1522 |
|
|
| 1523 |
< |
2003-04-07 11:56 gezelter |
| 1523 |
> |
2003-04-07 12:56 gezelter |
| 1524 |
|
|
| 1525 |
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
| 1526 |
|
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
| 1527 |
|
Many fixes to add extended system |
| 1528 |
|
|
| 1529 |
< |
2003-04-07 09:30 gezelter |
| 1529 |
> |
2003-04-07 10:30 gezelter |
| 1530 |
|
|
| 1531 |
|
* src/Makefile: Fixed a bug caused by my experimentation |
| 1532 |
|
|
| 1533 |
< |
2003-04-07 09:30 gezelter |
| 1533 |
> |
2003-04-07 10:30 gezelter |
| 1534 |
|
|
| 1535 |
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
| 1536 |
|
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
| 1537 |
|
Added ExtendedSystem infrastructure for NPT and NVT calculations |
| 1538 |
|
|
| 1539 |
< |
2003-04-07 09:30 gezelter |
| 1539 |
> |
2003-04-07 10:30 gezelter |
| 1540 |
|
|
| 1541 |
|
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
| 1542 |
|
|
| 1889 |
|
|
| 1890 |
|
2003-03-24 20:07 gezelter |
| 1891 |
|
|
| 1892 |
< |
* samples/Makefile: moving tests to samples |
| 1892 |
> |
* samples/Makefile, tests/Makefile: moving tests to samples |
| 1893 |
|
|
| 1894 |
|
2003-03-24 20:06 gezelter |
| 1895 |
|
|
| 1896 |
< |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
| 1897 |
< |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
| 1898 |
< |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
| 1899 |
< |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
| 1900 |
< |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
| 1901 |
< |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
| 1902 |
< |
samples |
| 1896 |
> |
* samples/alkane/Makefile, samples/alkane/alkanes.mdl, |
| 1897 |
> |
samples/alkane/butane.bass, samples/alkane/init_butane.eor, |
| 1898 |
> |
samples/argon/Makefile, samples/argon/argon.bass, |
| 1899 |
> |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
| 1900 |
> |
samples/lipid/5x5.bass, samples/lipid/Makefile, |
| 1901 |
> |
samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, |
| 1902 |
> |
samples/lipid/water.mdl, samples/water/Makefile, |
| 1903 |
> |
samples/water/init_ssd.eor, samples/water/ssd.bass, |
| 1904 |
> |
samples/water/water.mdl, tests/alkane/Makefile, |
| 1905 |
> |
tests/alkane/alkanes.mdl, tests/alkane/butane.bass, |
| 1906 |
> |
tests/alkane/init_butane.eor, tests/argon/Makefile, |
| 1907 |
> |
tests/argon/argon.bass, tests/argon/init_argon.eor, |
| 1908 |
> |
tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile, |
| 1909 |
> |
tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl, |
| 1910 |
> |
tests/lipid/water.mdl, tests/water/Makefile, |
| 1911 |
> |
tests/water/init_ssd.eor, tests/water/ssd.bass, |
| 1912 |
> |
tests/water/water.mdl: moved tests to samples |
| 1913 |
|
|
| 1914 |
|
2003-03-24 19:51 gezelter |
| 1915 |
|
|
| 1917 |
|
|
| 1918 |
|
2003-03-24 19:46 gezelter |
| 1919 |
|
|
| 1920 |
< |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
| 1920 |
> |
* ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile, |
| 1921 |
> |
tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile: |
| 1922 |
> |
Added makefiles in tests directories |
| 1923 |
|
|
| 1924 |
|
2003-03-24 16:55 gezelter |
| 1925 |
|
|
| 1936 |
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
| 1937 |
|
do_Forces.F90: little bug fixes here and there |
| 1938 |
|
|
| 1939 |
+ |
2003-03-24 11:04 mmeineke |
| 1940 |
+ |
|
| 1941 |
+ |
* tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon |
| 1942 |
+ |
test simulation |
| 1943 |
+ |
|
| 1944 |
+ |
2003-03-24 11:02 mmeineke |
| 1945 |
+ |
|
| 1946 |
+ |
* tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl, |
| 1947 |
+ |
lipid/water.mdl, water/init_ssd.eor, water/ssd.bass, |
| 1948 |
+ |
water/water.mdl: [no log message] |
| 1949 |
+ |
|
| 1950 |
+ |
2003-03-24 11:02 mmeineke |
| 1951 |
+ |
|
| 1952 |
+ |
* tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added |
| 1953 |
+ |
some test bass files for experimenting with |
| 1954 |
+ |
|
| 1955 |
|
2003-03-24 10:26 mmeineke |
| 1956 |
|
|
| 1957 |
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
