| 1 |
mmeineke |
568 |
2003-06-25 16:12 mmeineke |
| 2 |
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| 3 |
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* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
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to Harmonic bonds in the DUFF frc file |
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| 6 |
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fixed constraints. |
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2003-06-25 16:11 mmeineke |
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| 10 |
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* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
| 11 |
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the DUFF frc file |
| 12 |
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| 13 |
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2003-06-24 17:51 gezelter |
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| 15 |
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* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
| 16 |
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| 17 |
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2003-06-24 14:57 mmeineke |
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| 19 |
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* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
| 20 |
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libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
| 21 |
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the DUFF forcefield and BondExtensions.cpp |
| 22 |
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| 23 |
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2003-06-23 16:24 mmeineke |
| 24 |
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* libmdtools/Integrator.cpp: Doing some work to debug the |
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constraint code. |
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| 28 |
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2003-06-20 15:50 gezelter |
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* libmdtools/Integrator.hpp: NPT fix |
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2003-06-20 15:29 mmeineke |
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* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 35 |
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libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 36 |
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libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, |
| 37 |
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libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, |
| 38 |
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libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
| 39 |
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integrator and NVT seem to be working now. |
| 40 |
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| 41 |
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2003-06-20 11:49 gezelter |
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* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
| 44 |
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| 45 |
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2003-06-19 17:02 mmeineke |
| 46 |
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| 47 |
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* forceFields/DUFF.frc, forceFields/LJFF.frc, |
| 48 |
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forceFields/LJ_FF.frc, forceFields/Makefile, |
| 49 |
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forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, |
| 50 |
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libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, |
| 51 |
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libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 52 |
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libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, |
| 53 |
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libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
| 54 |
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forcefield names. |
| 55 |
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| 56 |
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2003-06-19 14:21 mmeineke |
| 57 |
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| 58 |
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* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
| 59 |
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finished the basics of the integrator and SimSetup.cpp |
| 60 |
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| 61 |
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2003-06-19 14:11 mmeineke |
| 62 |
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| 63 |
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* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
| 64 |
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up / get it to work with the new Integrator. |
| 65 |
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| 66 |
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2003-06-18 17:20 mmeineke |
| 67 |
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| 68 |
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* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
| 69 |
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output times. |
| 70 |
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| 71 |
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2003-06-17 16:56 mmeineke |
| 72 |
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| 73 |
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* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
| 74 |
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fro the ghost Bend in TraPPE_Ex |
| 75 |
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| 76 |
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some work on the integrator. ( incomplete) |
| 77 |
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| 78 |
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2003-06-17 16:55 mmeineke |
| 79 |
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| 80 |
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* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
| 81 |
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Bend in TraPPE_Ex |
| 82 |
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| 83 |
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2003-06-04 16:06 mmeineke |
| 84 |
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| 85 |
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* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
| 86 |
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constrainB to the Symplectic integrator |
| 87 |
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| 88 |
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2003-05-30 16:32 mmeineke |
| 89 |
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| 90 |
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* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
| 91 |
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the basic integrator. |
| 92 |
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| 93 |
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bilayerSys.cpp altered for building tb3. |
| 94 |
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| 95 |
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2003-05-30 16:31 mmeineke |
| 96 |
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| 97 |
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* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
| 98 |
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TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
| 99 |
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modifiying Symplectic to become the basic integrator. |
| 100 |
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| 101 |
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2003-05-30 15:19 mmeineke |
| 102 |
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| 103 |
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* libmdtools/Integrator.hpp: added some member variables for |
| 104 |
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position, velocity, etc. |
| 105 |
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| 106 |
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2003-05-30 14:07 mmeineke |
| 107 |
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| 108 |
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* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
| 109 |
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is now derived from Integrator |
| 110 |
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| 111 |
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2003-05-20 11:44 mmeineke |
| 112 |
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| 113 |
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* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
| 114 |
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| 115 |
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2003-05-17 11:57 mmeineke |
| 116 |
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| 117 |
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* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
| 118 |
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working |
| 119 |
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| 120 |
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2003-05-16 16:37 mmeineke |
| 121 |
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| 122 |
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* utils/bilayerSys.cpp: still working on the bilayer code |
| 123 |
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| 124 |
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2003-05-16 09:28 mmeineke |
| 125 |
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| 126 |
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* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
| 127 |
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work to overhaul sysbuild. |
| 128 |
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| 129 |
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2003-05-13 16:23 mmeineke |
| 130 |
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| 131 |
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* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
| 132 |
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| 133 |
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2003-05-13 15:47 mmeineke |
| 134 |
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| 135 |
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* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
| 136 |
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beadLipid/water.mdl: Added bead lipid model to the sample directory |
| 137 |
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| 138 |
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2003-05-13 15:34 mmeineke |
| 139 |
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| 140 |
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* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
| 141 |
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the Trappe extended force field |
| 142 |
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| 143 |
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2003-05-13 12:01 mmeineke |
| 144 |
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| 145 |
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* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
| 146 |
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TraPPe_Ex forceField |
| 147 |
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| 148 |
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2003-05-09 14:51 mmeineke |
| 149 |
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| 150 |
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* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
| 151 |
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there were some duplicate entries |
| 152 |
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| 153 |
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added a two chain lipid to the lipid.mdl in sample |
| 154 |
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| 155 |
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2003-05-09 14:51 mmeineke |
| 156 |
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| 157 |
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* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
| 158 |
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there were some duplicate entries |
| 159 |
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| 160 |
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2003-05-09 11:56 mmeineke |
| 161 |
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| 162 |
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* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
| 163 |
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configure script |
| 164 |
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| 165 |
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added the CH branching group to the TraPPE_Ex fource field |
| 166 |
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| 167 |
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2003-05-09 11:55 mmeineke |
| 168 |
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| 169 |
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* ac-tools/configure.in: added the utils subdirectory to the |
| 170 |
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configure script |
| 171 |
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| 172 |
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2003-04-25 11:02 mmeineke |
| 173 |
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| 174 |
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* utils/bilayerSys.cpp: i quick fix to th distance in the random |
| 175 |
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bilayer builder |
| 176 |
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| 177 |
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2003-04-24 21:00 mmeineke |
| 178 |
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| 179 |
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* libmdtools/f_verlet_constrained.F90: added a new test for |
| 180 |
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constraint failure |
| 181 |
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| 182 |
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2003-04-17 16:54 mmeineke |
| 183 |
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| 184 |
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* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
| 185 |
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utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
| 186 |
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utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
| 187 |
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build our systems |
| 188 |
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| 189 |
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2003-04-16 16:11 mmeineke |
| 190 |
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| 191 |
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* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
| 192 |
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| 193 |
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2003-04-15 16:47 mmeineke |
| 194 |
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| 195 |
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* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
| 196 |
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and sysBuild both will build now. woot! |
| 197 |
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| 198 |
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2003-04-15 16:20 mmeineke |
| 199 |
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| 200 |
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* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 201 |
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bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
| 202 |
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| 203 |
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sysBuild still need to write the bass file. |
| 204 |
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| 205 |
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MoLocator.cpp is currently empty |
| 206 |
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| 207 |
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2003-04-15 15:40 chuckv |
| 208 |
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| 209 |
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* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
| 210 |
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forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
| 211 |
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forceFields/pdu3.eam, forceFields/ptu3.eam, |
| 212 |
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libmdtools/ForceFields.hpp: Added eam force files... |
| 213 |
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| 214 |
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2003-04-15 11:37 chuckv |
| 215 |
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| 216 |
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* libmdtools/EAM_FF.cpp: More eam work. |
| 217 |
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| 218 |
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2003-04-14 16:22 mmeineke |
| 219 |
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| 220 |
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* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
| 221 |
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utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
| 222 |
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working on the system builder |
| 223 |
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| 224 |
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2003-04-14 16:16 chuckv |
| 225 |
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| 226 |
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* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
| 227 |
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ordering on NVT calculation in integrators. |
| 228 |
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| 229 |
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2003-04-14 14:51 mmeineke |
| 230 |
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| 231 |
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* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
| 232 |
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obj/placeHolder: working on a system builder |
| 233 |
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| 234 |
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2003-04-14 14:04 mmeineke |
| 235 |
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| 236 |
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* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
| 237 |
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| 238 |
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added sysBuild to the utils Makefile |
| 239 |
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| 240 |
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2003-04-14 14:03 mmeineke |
| 241 |
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| 242 |
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* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
| 243 |
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Ghost bends to the TraPPE_Ex forceField |
| 244 |
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| 245 |
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2003-04-14 13:19 chuckv |
| 246 |
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| 247 |
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* libmdtools/calc_eam.F90: Added first mangling of EAM. |
| 248 |
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| 249 |
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2003-04-11 13:46 mmeineke |
| 250 |
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| 251 |
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* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
| 252 |
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simulation_module.F90: fixed a memory bug in Fortran, where |
| 253 |
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molMembershipArray was declared nLocal instead of nGlobal. |
| 254 |
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| 255 |
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2003-04-11 10:16 gezelter |
| 256 |
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| 257 |
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* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 258 |
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SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
| 259 |
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fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
| 260 |
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for NPT |
| 261 |
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| 262 |
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2003-04-10 15:08 mmeineke |
| 263 |
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| 264 |
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* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
| 265 |
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globalIndex counter to Molecule |
| 266 |
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| 267 |
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2003-04-10 11:35 gezelter |
| 268 |
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| 269 |
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* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
| 270 |
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ConstantStress |
| 271 |
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| 272 |
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2003-04-10 11:27 mmeineke |
| 273 |
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| 274 |
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* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
| 275 |
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caused a miscalculation of nLocal. |
| 276 |
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| 277 |
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2003-04-10 11:21 mmeineke |
| 278 |
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| 279 |
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* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
| 280 |
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do_Forces.F90: fixed a bug in symplectic, where presure was only |
| 281 |
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being calculated the first time through. |
| 282 |
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| 283 |
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2003-04-09 11:20 chuckv |
| 284 |
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| 285 |
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* samples/alkane/alkanes.mdl: added pentane to the alkane model |
| 286 |
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file |
| 287 |
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| 288 |
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2003-04-09 08:59 gezelter |
| 289 |
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| 290 |
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* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
| 291 |
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Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
| 292 |
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| 293 |
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2003-04-08 23:06 gezelter |
| 294 |
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| 295 |
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* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
| 296 |
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ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 297 |
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SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, |
| 298 |
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Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
| 299 |
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calc_reaction_field.F90, calc_sticky_pair.F90, |
| 300 |
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fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
| 301 |
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NVT |
| 302 |
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| 303 |
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2003-04-08 17:38 chuckv |
| 304 |
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| 305 |
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* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
| 306 |
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libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
| 307 |
|
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libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 308 |
|
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libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
| 309 |
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(kinda)... |
| 310 |
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| 311 |
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2003-04-08 16:35 gezelter |
| 312 |
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| 313 |
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* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 314 |
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libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
| 315 |
|
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libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
| 316 |
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| 317 |
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2003-04-08 12:16 chuckv |
| 318 |
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| 319 |
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* libmdtools/: do_Forces.F90, neighborLists.F90, |
| 320 |
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simulation_module.F90: Moved expand neighborlist to init_FF. |
| 321 |
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| 322 |
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2003-04-08 10:20 chuckv |
| 323 |
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| 324 |
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* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
| 325 |
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NVT |
| 326 |
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| 327 |
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2003-04-08 09:39 gezelter |
| 328 |
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| 329 |
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* libmdtools/Verlet.cpp: fixes for nvt / npt |
| 330 |
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| 331 |
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2003-04-08 09:34 gezelter |
| 332 |
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| 333 |
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* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
| 334 |
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Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
| 335 |
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| 336 |
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2003-04-08 07:50 gezelter |
| 337 |
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| 338 |
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* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
| 339 |
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| 340 |
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2003-04-08 07:44 gezelter |
| 341 |
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| 342 |
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* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
| 343 |
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Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
| 344 |
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NVT and NPT ensembles |
| 345 |
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| 346 |
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2003-04-07 16:42 gezelter |
| 347 |
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| 348 |
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* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 349 |
|
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libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
| 350 |
|
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libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
| 351 |
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| 352 |
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2003-04-07 16:20 mmeineke |
| 353 |
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| 354 |
|
|
* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
| 355 |
|
|
portion of SSD. |
| 356 |
|
|
|
| 357 |
|
|
2003-04-07 16:16 mmeineke |
| 358 |
|
|
|
| 359 |
|
|
* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
| 360 |
|
|
doing some testing in sticky through Symplectic. |
| 361 |
|
|
|
| 362 |
|
|
2003-04-07 15:51 gezelter |
| 363 |
|
|
|
| 364 |
|
|
* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
| 365 |
|
|
|
| 366 |
|
|
2003-04-07 15:50 chuckv |
| 367 |
|
|
|
| 368 |
|
|
* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
| 369 |
|
|
tau and virial. |
| 370 |
|
|
|
| 371 |
|
|
2003-04-07 15:06 mmeineke |
| 372 |
|
|
|
| 373 |
|
|
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
| 374 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
| 375 |
|
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
| 376 |
|
|
src/Makefile: bug fixes |
| 377 |
|
|
|
| 378 |
|
|
2003-04-07 11:56 gezelter |
| 379 |
|
|
|
| 380 |
|
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
| 381 |
|
|
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
| 382 |
|
|
Many fixes to add extended system |
| 383 |
|
|
|
| 384 |
|
|
2003-04-07 09:30 gezelter |
| 385 |
|
|
|
| 386 |
|
|
* src/Makefile: Fixed a bug caused by my experimentation |
| 387 |
|
|
|
| 388 |
|
|
2003-04-07 09:30 gezelter |
| 389 |
|
|
|
| 390 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
| 391 |
|
|
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
| 392 |
|
|
Added ExtendedSystem infrastructure for NPT and NVT calculations |
| 393 |
|
|
|
| 394 |
|
|
2003-04-07 09:30 gezelter |
| 395 |
|
|
|
| 396 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
| 397 |
|
|
|
| 398 |
|
|
2003-04-04 23:07 gezelter |
| 399 |
|
|
|
| 400 |
|
|
* src/Makefile: final mods to try a fortran compiler |
| 401 |
|
|
|
| 402 |
|
|
2003-04-04 22:39 gezelter |
| 403 |
|
|
|
| 404 |
|
|
* libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, |
| 405 |
|
|
fortranWrapDefines.hpp: Bug fixes for simulation module rewrites |
| 406 |
|
|
|
| 407 |
|
|
2003-04-04 21:56 gezelter |
| 408 |
|
|
|
| 409 |
|
|
* libmdtools/: Makefile, atype_module.F90, do_Forces.F90, |
| 410 |
|
|
fortranWrappers.cpp, wrappers.F90: bug fixes for compilation |
| 411 |
|
|
|
| 412 |
|
|
2003-04-04 21:45 gezelter |
| 413 |
|
|
|
| 414 |
|
|
* libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug |
| 415 |
|
|
fixes to fortran wrappers |
| 416 |
|
|
|
| 417 |
|
|
2003-04-04 17:22 chuckv |
| 418 |
|
|
|
| 419 |
|
|
* libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 420 |
|
|
calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, |
| 421 |
|
|
do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, |
| 422 |
|
|
simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets |
| 423 |
|
|
smarter, fortran gets dumber... |
| 424 |
|
|
|
| 425 |
|
|
2003-04-04 14:57 mmeineke |
| 426 |
|
|
|
| 427 |
|
|
* libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, |
| 428 |
|
|
neighborLists.F90: fixed a memory read bug in neighborlist |
| 429 |
|
|
|
| 430 |
|
|
2003-04-04 14:47 gezelter |
| 431 |
|
|
|
| 432 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
| 433 |
|
|
SimInfo.hpp, Thermo.cpp: Changes for Extended System |
| 434 |
|
|
|
| 435 |
|
|
2003-04-04 14:16 gezelter |
| 436 |
|
|
|
| 437 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
| 438 |
|
|
SimInfo.hpp: Fixes for ExtendedSystem |
| 439 |
|
|
|
| 440 |
|
|
2003-04-03 20:57 gezelter |
| 441 |
|
|
|
| 442 |
|
|
* libmdtools/ExtendedSystem.hpp: Added extended system header |
| 443 |
|
|
|
| 444 |
|
|
2003-04-03 20:57 gezelter |
| 445 |
|
|
|
| 446 |
|
|
* libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes |
| 447 |
|
|
for extended system code |
| 448 |
|
|
|
| 449 |
|
|
2003-04-03 18:49 gezelter |
| 450 |
|
|
|
| 451 |
|
|
* libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to |
| 452 |
|
|
extendedsystem |
| 453 |
|
|
|
| 454 |
|
|
2003-04-03 17:19 mmeineke |
| 455 |
|
|
|
| 456 |
|
|
* libmdtools/Molecule.hpp: added some little fixes here and there. |
| 457 |
|
|
|
| 458 |
|
|
2003-04-03 17:01 mmeineke |
| 459 |
|
|
|
| 460 |
|
|
* libmdtools/TraPPE_ExFF.cpp: fixed a possible call before |
| 461 |
|
|
initialize bug. |
| 462 |
|
|
|
| 463 |
|
|
2003-04-03 16:12 mmeineke |
| 464 |
|
|
|
| 465 |
|
|
* libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just |
| 466 |
|
|
little things like deleteing unused variables and such. |
| 467 |
|
|
|
| 468 |
|
|
2003-04-03 15:57 mmeineke |
| 469 |
|
|
|
| 470 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to |
| 471 |
|
|
simError.h also some fixes to Molecule.hpp |
| 472 |
|
|
|
| 473 |
|
|
2003-04-03 15:57 mmeineke |
| 474 |
|
|
|
| 475 |
|
|
* libBASS/simError.h: a few fixes to simError.h |
| 476 |
|
|
|
| 477 |
|
|
2003-04-03 15:21 mmeineke |
| 478 |
|
|
|
| 479 |
|
|
* libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, |
| 480 |
|
|
libBASS/simError.h, libmdtools/DumpWriter.cpp, |
| 481 |
|
|
libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, |
| 482 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, |
| 483 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, |
| 484 |
|
|
src/Makefile, src/oopse.cpp: fixed some small things with |
| 485 |
|
|
simError.h |
| 486 |
|
|
|
| 487 |
|
|
2003-04-03 15:19 gezelter |
| 488 |
|
|
|
| 489 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT |
| 490 |
|
|
|
| 491 |
|
|
2003-04-03 14:58 gezelter |
| 492 |
|
|
|
| 493 |
|
|
* libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for |
| 494 |
|
|
now) |
| 495 |
|
|
|
| 496 |
|
|
2003-04-03 08:42 gezelter |
| 497 |
|
|
|
| 498 |
|
|
* README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: |
| 499 |
|
|
Changed Readme, added some files |
| 500 |
|
|
|
| 501 |
|
|
2003-04-02 17:19 mmeineke |
| 502 |
|
|
|
| 503 |
|
|
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, |
| 504 |
|
|
Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: |
| 505 |
|
|
dipoles mostly work, but there is a memory leak somewhere. |
| 506 |
|
|
|
| 507 |
|
|
2003-04-02 10:01 mmeineke |
| 508 |
|
|
|
| 509 |
|
|
* libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting |
| 510 |
|
|
the proper atomIdents. |
| 511 |
|
|
|
| 512 |
|
|
2003-04-01 11:50 chuckv |
| 513 |
|
|
|
| 514 |
|
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
| 515 |
|
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
| 516 |
|
|
samples/argon/argon.bass: more bug fixes.... |
| 517 |
|
|
|
| 518 |
|
|
2003-04-01 11:49 mmeineke |
| 519 |
|
|
|
| 520 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed |
| 521 |
|
|
DumpWriter to be more robust to errors. also added a little |
| 522 |
|
|
namespace to InitFromFile to wrap it's helper functions in MPI |
| 523 |
|
|
|
| 524 |
|
|
2003-03-31 17:09 chuckv |
| 525 |
|
|
|
| 526 |
|
|
* libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local |
| 527 |
|
|
not zeroed. |
| 528 |
|
|
|
| 529 |
|
|
2003-03-31 16:50 chuckv |
| 530 |
|
|
|
| 531 |
|
|
* libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, |
| 532 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
| 533 |
|
|
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
| 534 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
| 535 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, |
| 536 |
|
|
samples/alkane/butane.bass: Fixes in MPI force calc and in |
| 537 |
|
|
Trappe_Ex parsing. |
| 538 |
|
|
|
| 539 |
|
|
2003-03-28 17:34 chuckv |
| 540 |
|
|
|
| 541 |
|
|
* libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp |
| 542 |
|
|
|
| 543 |
|
|
2003-03-28 16:45 chuckv |
| 544 |
|
|
|
| 545 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
| 546 |
|
|
libmdtools/InitializeFromFile.cpp: Bug fixes in read-write |
| 547 |
|
|
routines. |
| 548 |
|
|
|
| 549 |
|
|
2003-03-28 14:33 mmeineke |
| 550 |
|
|
|
| 551 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, |
| 552 |
|
|
Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a |
| 553 |
|
|
bug where the Excludes were not being created properly |
| 554 |
|
|
|
| 555 |
|
|
2003-03-28 14:30 chuckv |
| 556 |
|
|
|
| 557 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
| 558 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, |
| 559 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes |
| 560 |
|
|
and debugging mpi read write from file. |
| 561 |
|
|
|
| 562 |
|
|
2003-03-28 10:28 mmeineke |
| 563 |
|
|
|
| 564 |
|
|
* libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range |
| 565 |
|
|
interactions in Trappe |
| 566 |
|
|
|
| 567 |
|
|
2003-03-27 18:33 chuckv |
| 568 |
|
|
|
| 569 |
|
|
* libmdtools/: SimSetup.cpp, mpiSimulation.cpp, |
| 570 |
|
|
mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. |
| 571 |
|
|
|
| 572 |
|
|
2003-03-27 17:16 mmeineke |
| 573 |
|
|
|
| 574 |
|
|
* libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where |
| 575 |
|
|
excludes were not being initialized |
| 576 |
|
|
|
| 577 |
|
|
2003-03-27 16:52 mmeineke |
| 578 |
|
|
|
| 579 |
|
|
* src/Makefile: [no log message] |
| 580 |
|
|
|
| 581 |
|
|
2003-03-27 16:52 mmeineke |
| 582 |
|
|
|
| 583 |
|
|
* libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. |
| 584 |
|
|
|
| 585 |
|
|
2003-03-27 16:07 mmeineke |
| 586 |
|
|
|
| 587 |
|
|
* libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, |
| 588 |
|
|
Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, |
| 589 |
|
|
Verlet.cpp: fixed the compile time bugs, Source builds and links |
| 590 |
|
|
|
| 591 |
|
|
2003-03-27 15:48 mmeineke |
| 592 |
|
|
|
| 593 |
|
|
* libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few |
| 594 |
|
|
more bugs. |
| 595 |
|
|
|
| 596 |
|
|
2003-03-27 15:40 mmeineke |
| 597 |
|
|
|
| 598 |
|
|
* libmdtools/Molecule.cpp: added the Molecule.cpp file |
| 599 |
|
|
|
| 600 |
|
|
2003-03-27 15:39 mmeineke |
| 601 |
|
|
|
| 602 |
|
|
* libmdtools/: Makefile, Molecule.hpp: fixed the makefile |
| 603 |
|
|
|
| 604 |
|
|
2003-03-27 15:36 mmeineke |
| 605 |
|
|
|
| 606 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
| 607 |
|
|
ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, |
| 608 |
|
|
SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs |
| 609 |
|
|
|
| 610 |
|
|
2003-03-27 15:12 mmeineke |
| 611 |
|
|
|
| 612 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
| 613 |
|
|
Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, |
| 614 |
|
|
Verlet.cpp: I have implemeted Molecules everywhere I could remember |
| 615 |
|
|
to. will now attempt to compile. |
| 616 |
|
|
|
| 617 |
|
|
2003-03-27 14:21 mmeineke |
| 618 |
|
|
|
| 619 |
|
|
* libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, |
| 620 |
|
|
SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished |
| 621 |
|
|
updating SimSetup to initialize and use the new MPI division of |
| 622 |
|
|
labour, and Molecule class |
| 623 |
|
|
|
| 624 |
|
|
2003-03-27 12:55 mmeineke |
| 625 |
|
|
|
| 626 |
|
|
* libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to |
| 627 |
|
|
use Molecule |
| 628 |
|
|
|
| 629 |
|
|
2003-03-27 12:32 mmeineke |
| 630 |
|
|
|
| 631 |
|
|
* libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, |
| 632 |
|
|
SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been |
| 633 |
|
|
converted to the new Molecule model. TraPPE_Ex is currently being |
| 634 |
|
|
updated. SimSetups routines are writtten, but not yet called. |
| 635 |
|
|
|
| 636 |
|
|
2003-03-27 10:07 gezelter |
| 637 |
|
|
|
| 638 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
| 639 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom |
| 640 |
|
|
numbering in MPI |
| 641 |
|
|
|
| 642 |
|
|
2003-03-27 09:30 mmeineke |
| 643 |
|
|
|
| 644 |
|
|
* libmdtools/mpiSimulation.cpp: little bug fixes here and there. |
| 645 |
|
|
|
| 646 |
|
|
2003-03-26 20:49 gezelter |
| 647 |
|
|
|
| 648 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to |
| 649 |
|
|
fileio for MPI |
| 650 |
|
|
|
| 651 |
|
|
2003-03-26 18:14 gezelter |
| 652 |
|
|
|
| 653 |
|
|
* libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, |
| 654 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug |
| 655 |
|
|
fixes many bug fixes |
| 656 |
|
|
|
| 657 |
|
|
2003-03-26 17:24 gezelter |
| 658 |
|
|
|
| 659 |
|
|
* libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on |
| 660 |
|
|
sequence of atoms on the other processors. Node 0 now fires |
| 661 |
|
|
potatoes at other processors to get them to send french fries back. |
| 662 |
|
|
|
| 663 |
|
|
2003-03-26 17:02 mmeineke |
| 664 |
|
|
|
| 665 |
|
|
* libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for |
| 666 |
|
|
making the molecules is in place. ForceField needs to be updated |
| 667 |
|
|
next. |
| 668 |
|
|
|
| 669 |
|
|
2003-03-26 16:54 mmeineke |
| 670 |
|
|
|
| 671 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of |
| 672 |
|
|
the "static" bugs in Atom and Exclude |
| 673 |
|
|
|
| 674 |
|
|
2003-03-26 16:50 mmeineke |
| 675 |
|
|
|
| 676 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, |
| 677 |
|
|
SimSetup.cpp: still working on the SimSetup routine. also fixed |
| 678 |
|
|
some things in Exclude.hpp |
| 679 |
|
|
|
| 680 |
|
|
2003-03-26 16:24 gezelter |
| 681 |
|
|
|
| 682 |
|
|
* libmdtools/Makefile: Added Atom.cpp and Exclude.cpp |
| 683 |
|
|
|
| 684 |
|
|
2003-03-26 16:23 gezelter |
| 685 |
|
|
|
| 686 |
|
|
* libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom |
| 687 |
|
|
and Exclude list |
| 688 |
|
|
|
| 689 |
|
|
2003-03-26 16:04 gezelter |
| 690 |
|
|
|
| 691 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and |
| 692 |
|
|
delete ranges of atoms |
| 693 |
|
|
|
| 694 |
|
|
2003-03-26 15:45 mmeineke |
| 695 |
|
|
|
| 696 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class |
| 697 |
|
|
with static arrays similar to the Atom class |
| 698 |
|
|
|
| 699 |
|
|
2003-03-26 15:22 mmeineke |
| 700 |
|
|
|
| 701 |
|
|
* libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm |
| 702 |
|
|
overhauling the molecule class to contain it's own bonds, bends, |
| 703 |
|
|
and torsions. |
| 704 |
|
|
|
| 705 |
|
|
may god have mercy on my soul. |
| 706 |
|
|
|
| 707 |
|
|
2003-03-26 14:34 chuckv |
| 708 |
|
|
|
| 709 |
|
|
* libmdtools/mpiSimulation.cpp: Finished globalIndex. |
| 710 |
|
|
|
| 711 |
|
|
2003-03-26 13:02 gezelter |
| 712 |
|
|
|
| 713 |
|
|
* libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, |
| 714 |
|
|
mpiSimulation.hpp: MPI stuff for passing out molecules |
| 715 |
|
|
|
| 716 |
|
|
2003-03-26 11:12 chuckv |
| 717 |
|
|
|
| 718 |
|
|
* libmdtools/mpiSimulation.cpp: working on load balancing |
| 719 |
|
|
|
| 720 |
|
|
2003-03-26 10:37 chuckv |
| 721 |
|
|
|
| 722 |
|
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
| 723 |
|
|
samples/argon/argon.bass: Fixes for Parallel thermalization |
| 724 |
|
|
|
| 725 |
|
|
2003-03-26 09:55 mmeineke |
| 726 |
|
|
|
| 727 |
|
|
* libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in |
| 728 |
|
|
THermo.cpp |
| 729 |
|
|
|
| 730 |
|
|
2003-03-25 17:54 chuckv |
| 731 |
|
|
|
| 732 |
|
|
* libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation |
| 733 |
|
|
of potential energy and temperature. |
| 734 |
|
|
|
| 735 |
|
|
2003-03-25 09:29 mmeineke |
| 736 |
|
|
|
| 737 |
|
|
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
| 738 |
|
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
| 739 |
|
|
|
| 740 |
|
|
2003-03-25 09:29 mmeineke |
| 741 |
|
|
|
| 742 |
|
|
* libBASS/MPIobj/dummy: added dummy files to keep the build |
| 743 |
|
|
deirectories from being pruned. |
| 744 |
|
|
|
| 745 |
|
|
2003-03-24 20:07 gezelter |
| 746 |
|
|
|
| 747 |
|
|
* samples/Makefile: moving tests to samples |
| 748 |
|
|
|
| 749 |
|
|
2003-03-24 20:06 gezelter |
| 750 |
|
|
|
| 751 |
|
|
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
| 752 |
|
|
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
| 753 |
|
|
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
| 754 |
|
|
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
| 755 |
|
|
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
| 756 |
|
|
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
| 757 |
|
|
samples |
| 758 |
|
|
|
| 759 |
|
|
2003-03-24 19:51 gezelter |
| 760 |
|
|
|
| 761 |
|
|
* ac-tools/configure.in: Tests are becoming samples |
| 762 |
|
|
|
| 763 |
|
|
2003-03-24 19:46 gezelter |
| 764 |
|
|
|
| 765 |
|
|
* ac-tools/Make.conf.in: Added makefiles in tests directories |
| 766 |
|
|
|
| 767 |
|
|
2003-03-24 16:55 gezelter |
| 768 |
|
|
|
| 769 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp, |
| 770 |
|
|
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, |
| 771 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90, |
| 772 |
|
|
libmdtools/calc_reaction_field.F90, |
| 773 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 774 |
|
|
libmdtools/simulation_module.F90: electrostatic changes for dipole |
| 775 |
|
|
/ RF separation |
| 776 |
|
|
|
| 777 |
|
|
2003-03-24 13:33 mmeineke |
| 778 |
|
|
|
| 779 |
|
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
| 780 |
|
|
do_Forces.F90: little bug fixes here and there |
| 781 |
|
|
|
| 782 |
|
|
2003-03-24 10:26 mmeineke |
| 783 |
|
|
|
| 784 |
|
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
| 785 |
|
|
where short range interactions were not being calculated. |
| 786 |
|
|
|
| 787 |
|
|
removed some debug print statements |
| 788 |
|
|
|
| 789 |
|
|
2003-03-21 17:11 chuckv |
| 790 |
|
|
|
| 791 |
|
|
* libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90, |
| 792 |
|
|
do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90: |
| 793 |
|
|
various write statements for debugging |
| 794 |
|
|
|
| 795 |
|
|
2003-03-21 16:26 chuckv |
| 796 |
|
|
|
| 797 |
|
|
* forceFields/Makefile: added links to the makefile in forceFields |
| 798 |
|
|
|
| 799 |
|
|
2003-03-21 15:52 gezelter |
| 800 |
|
|
|
| 801 |
|
|
* ac-tools/Make.conf.in, ac-tools/configure.in, |
| 802 |
|
|
libmdtools/Makefile: Fixed F_MACH_DEP bug |
| 803 |
|
|
|
| 804 |
|
|
2003-03-21 15:37 gezelter |
| 805 |
|
|
|
| 806 |
|
|
* ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in, |
| 807 |
|
|
ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile, |
| 808 |
|
|
libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend, |
| 809 |
|
|
src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org, |
| 810 |
|
|
autoconf fixes |
| 811 |
|
|
|
| 812 |
gezelter |
385 |
2003-03-21 14:58 gezelter |
| 813 |
mmeineke |
377 |
|
| 814 |
gezelter |
385 |
* LICENSE: Added license file |
| 815 |
|
|
|
| 816 |
|
|
2003-03-21 14:55 gezelter |
| 817 |
|
|
|
| 818 |
|
|
* forceFields/Makefile: Fixed makefile |
| 819 |
|
|
|
| 820 |
|
|
2003-03-21 14:49 gezelter |
| 821 |
|
|
|
| 822 |
|
|
* forceFields/Makefile: Makefile for forceFields |
| 823 |
|
|
|
| 824 |
|
|
2003-03-21 14:42 gezelter |
| 825 |
|
|
|
| 826 |
|
|
* README: Readme changes |
| 827 |
|
|
|
| 828 |
|
|
2003-03-21 12:52 mmeineke |
| 829 |
|
|
|
| 830 |
|
|
* src/Makefile: [no log message] |
| 831 |
|
|
|
| 832 |
|
|
2003-03-21 12:52 mmeineke |
| 833 |
|
|
|
| 834 |
|
|
* libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends |
| 835 |
|
|
|
| 836 |
|
|
2003-03-21 12:42 mmeineke |
| 837 |
|
|
|
| 838 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
| 839 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 840 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
| 841 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
| 842 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
| 843 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
| 844 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
| 845 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
| 846 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
| 847 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
| 848 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
| 849 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
| 850 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
| 851 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
| 852 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
| 853 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
| 854 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
| 855 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
| 856 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
| 857 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
| 858 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
| 859 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
| 860 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
| 861 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
| 862 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
| 863 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
| 864 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
| 865 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
| 866 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
| 867 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
| 868 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
| 869 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
| 870 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
| 871 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
| 872 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 873 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 874 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
| 875 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
| 876 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
| 877 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
| 878 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
| 879 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
| 880 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
| 881 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 882 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
| 883 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
| 884 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
| 885 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
| 886 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
| 887 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
| 888 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 889 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
| 890 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
| 891 |
|
|
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
| 892 |
|
|
Tree |
| 893 |
|
|
|
| 894 |
|
|
2003-03-21 12:42 mmeineke |
| 895 |
|
|
|
| 896 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
| 897 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 898 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
| 899 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
| 900 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
| 901 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
| 902 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
| 903 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
| 904 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
| 905 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
| 906 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
| 907 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
| 908 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
| 909 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
| 910 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
| 911 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
| 912 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
| 913 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
| 914 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
| 915 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
| 916 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
| 917 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
| 918 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
| 919 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
| 920 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
| 921 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
| 922 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
| 923 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
| 924 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
| 925 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
| 926 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
| 927 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
| 928 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
| 929 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
| 930 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 931 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 932 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
| 933 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
| 934 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
| 935 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
| 936 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
| 937 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
| 938 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
| 939 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 940 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
| 941 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
| 942 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
| 943 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
| 944 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
| 945 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
| 946 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 947 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
| 948 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
| 949 |
|
|
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
| 950 |
|
|
revision |
| 951 |
|
|
|
