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2004-07-23 15:31 tim |
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2004-11-02 11:59 tim |
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* samples/lipid/5x5.bass: modify 5x5.bass |
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* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
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branch new_design. |
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| 6 |
< |
2004-07-23 15:25 tim |
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> |
2004-11-02 11:59 tim |
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| 8 |
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* samples/water/tip3p_ice/: 200.in, tp3.bass: [no log message] |
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* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
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SimSnapshotManager.hpp: SimModel in progress |
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| 11 |
< |
2004-07-23 15:18 tim |
| 11 |
> |
2004-11-02 10:28 chrisfen |
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| 13 |
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* samples/: water/ssde/ssde.bass, argon/500.bass, |
| 14 |
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argon/argonNVT.bass: [no log message] |
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* src/: UseTheForce/DarkSide/shapes.F90, |
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primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes |
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looks like it's working |
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| 17 |
< |
2004-07-23 15:12 tim |
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> |
2004-11-02 10:27 tim |
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* samples/water/: dimer/two.in, spce/spce.in, ssd/ssd.in, |
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ssde/ssde.in, tip3p_ice/tp3.in, tip4p/tp4.in: add init files |
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* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
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functions for dealing with memory issue |
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| 22 |
< |
2004-07-23 15:10 tim |
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> |
2004-11-02 10:27 tim |
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| 24 |
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* samples/minimizer/: ssdEM.in, tip4p_two.in: add init file |
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* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
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added on branch new_design. |
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| 27 |
< |
2004-07-23 15:09 tim |
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> |
2004-11-02 10:23 tim |
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| 29 |
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* samples/argon/: NVT.bass, argonNVT.bass, argonNVT.in: rename |
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NVT.bass to argonNVT.bass |
| 29 |
> |
* src/: brains/SimModel.hpp, brains/Snapshot.hpp, |
| 30 |
> |
brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding |
| 31 |
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SimModel(something similar as SimInfo) |
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| 33 |
< |
2004-07-23 15:07 tim |
| 33 |
> |
2004-11-01 17:52 tim |
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< |
* samples/lipid/5x5.in: add 5x5.in |
| 35 |
> |
* src/: applications/simpleBuilder/MoLocator.hpp, |
| 36 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
| 37 |
> |
brains/DataStorage.hpp, brains/ForceFields.cpp, |
| 38 |
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brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp, |
| 39 |
> |
constraints/ZConstraint.cpp, integrators/Integrator.cpp, |
| 40 |
> |
integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp, |
| 41 |
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math/SquareMatrix3.hpp, math/Vector3.hpp, |
| 42 |
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minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp, |
| 43 |
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primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
| 44 |
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primitives/Molecule.cpp, primitives/Molecule.hpp, |
| 45 |
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primitives/RigidBody.hpp, primitives/Torsion.hpp, |
| 46 |
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restraints/Restraints.cpp, types/TorsionType.hpp, |
| 47 |
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utils/PropertyMap.hpp, utils/StringTokenizer.hpp, |
| 48 |
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visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp, |
| 49 |
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visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, |
| 50 |
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RigidBody and StuntDouble classes get compiled |
| 51 |
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| 52 |
< |
2004-07-23 15:06 tim |
| 52 |
> |
2004-11-01 16:40 tim |
| 53 |
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| 54 |
< |
* samples/alkane/: butane.in, init_butane.eor: add butane.in |
| 54 |
> |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
| 55 |
> |
on branch new_design. |
| 56 |
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| 57 |
< |
2004-07-23 14:57 gezelter |
| 57 |
> |
2004-11-01 16:40 tim |
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| 59 |
< |
* libBASS/Globals.cpp, samples/minimizer/ssdEM.bass, |
| 60 |
< |
samples/minimizer/tip4p_two.bass: changed minimizer keywords |
| 59 |
> |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
| 60 |
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branch new_design. |
| 61 |
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| 62 |
< |
2004-07-23 14:34 gezelter |
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> |
2004-11-01 16:40 tim |
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| 64 |
< |
* configure, ac-tools/configure.in: fixed typo |
| 64 |
> |
* src/primitives/Bond.hpp: file Bond.hpp was initially added on |
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branch new_design. |
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< |
2004-07-23 14:32 gezelter |
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> |
2004-11-01 16:40 tim |
| 68 |
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| 69 |
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* samples/minimizer/Makefile.in: fixed sample makefile |
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* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
| 70 |
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version of Bond, Bend and Torsion. |
| 71 |
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< |
2004-07-23 14:31 gezelter |
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> |
2004-11-01 16:37 tim |
| 73 |
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| 74 |
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* configure, ac-tools/configure.in, samples/minimizer/Makefile.in, |
| 75 |
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samples/minimizer/WATER.frc, samples/minimizer/ssdEM.bass, |
| 53 |
< |
samples/minimizer/tip4p_two.bass, samples/minimizer/water.mdl: |
| 54 |
< |
minimizer sample changes |
| 74 |
> |
* src/types/BendType.hpp: file BendType.hpp was initially added on |
| 75 |
> |
branch new_design. |
| 76 |
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| 77 |
< |
2004-07-23 14:15 gezelter |
| 77 |
> |
2004-11-01 16:37 tim |
| 78 |
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| 79 |
< |
* configure, ac-tools/configure.in: removed beadLipid |
| 79 |
> |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
| 80 |
> |
BondType, BendType, TorsionType |
| 81 |
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| 82 |
< |
2004-07-23 14:08 tim |
| 82 |
> |
2004-11-01 16:37 tim |
| 83 |
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| 84 |
< |
* samples/Makefile.in: remove beadLipid |
| 84 |
> |
* src/types/TorsionType.hpp: file TorsionType.hpp was initially |
| 85 |
> |
added on branch new_design. |
| 86 |
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| 87 |
< |
2004-07-23 14:03 chuckv |
| 87 |
> |
2004-11-01 16:37 tim |
| 88 |
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| 89 |
< |
* samples/metals/: Au_nanoparticle.eor, |
| 90 |
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Au_nanoparticle_coreshell_12-20.bass, |
| 68 |
< |
Au_nanoparticle_coreshell_12-20.in: Added core-shell nanoparticle |
| 69 |
< |
files. |
| 89 |
> |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
| 90 |
> |
branch new_design. |
| 91 |
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| 92 |
< |
2004-07-23 13:51 tim |
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> |
2004-11-01 15:15 tim |
| 93 |
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| 94 |
< |
* samples/water/tip4p/TP4init.in: remove TP4init.in |
| 94 |
> |
* src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
| 95 |
> |
CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
| 96 |
> |
GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp, |
| 97 |
> |
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: |
| 98 |
> |
break, break and break..... |
| 99 |
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| 100 |
< |
2004-07-23 13:50 tim |
| 100 |
> |
2004-11-01 14:57 tim |
| 101 |
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| 102 |
< |
* samples/water/tip4p/: Makefile.in, tp4.bass: change init file |
| 103 |
< |
name for tip4p and tip3p_ice |
| 102 |
> |
* test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, |
| 103 |
> |
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, |
| 104 |
> |
StuntDouble.hpp: these core classes get compiled |
| 105 |
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| 106 |
< |
2004-07-23 13:48 tim |
| 106 |
> |
2004-10-29 17:37 tim |
| 107 |
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| 108 |
< |
* samples/water/ssde/: Makefile.in, SSDEinit.in: [no log message] |
| 108 |
> |
* test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule |
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class |
| 110 |
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| 111 |
< |
2004-07-23 13:48 tim |
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> |
2004-10-29 17:28 chrisfen |
| 112 |
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| 113 |
< |
* samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass: change |
| 114 |
< |
init file name for ssd |
| 113 |
> |
* src/: UseTheForce/DarkSide/atype.F90, |
| 114 |
> |
UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, |
| 115 |
> |
types/ShapeAtomType.cpp: still debugging |
| 116 |
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| 117 |
< |
2004-07-23 13:46 tim |
| 117 |
> |
2004-10-29 17:28 chrisfen |
| 118 |
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| 119 |
< |
* samples/water/spce/: Makefile.in, SPCEinit.in, spce.bass: remove |
| 120 |
< |
SPCEInit.in |
| 119 |
> |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: |
| 120 |
> |
shapes rcut calculator added |
| 121 |
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| 122 |
< |
2004-07-23 13:45 tim |
| 122 |
> |
2004-10-29 17:27 chrisfen |
| 123 |
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| 124 |
< |
* samples/water/dimer/: Makefile.in, two.bass, two.init: change |
| 97 |
< |
names for init file |
| 124 |
> |
* samples/shape/linear.md: shorter run |
| 125 |
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| 126 |
< |
2004-07-23 13:40 tim |
| 126 |
> |
2004-10-29 15:54 tim |
| 127 |
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| 128 |
< |
* samples/lipid/: 5x5.bass, 5x5.eor, Makefile.in, init_5x5.eor: |
| 102 |
< |
change init file name in lipid directory |
| 128 |
> |
* test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. |
| 129 |
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| 130 |
< |
2004-07-23 13:36 tim |
| 130 |
> |
2004-10-29 11:22 tim |
| 131 |
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| 132 |
< |
* samples/argon/init_argon.eor: remove init_argon.eor |
| 132 |
> |
* test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, |
| 133 |
> |
ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove |
| 134 |
> |
some deprecated files |
| 135 |
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| 136 |
< |
2004-07-23 13:34 tim |
| 136 |
> |
2004-10-29 11:20 tim |
| 137 |
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| 138 |
< |
* samples/: alkane/Makefile.in, alkane/butane.bass, |
| 139 |
< |
alkane/butane.eor, argon/500.eor, argon/ar864.eor: [no log message] |
| 138 |
> |
* test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, |
| 139 |
> |
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: |
| 140 |
> |
More painful reconstruction is coming !!! |
| 141 |
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| 142 |
< |
2004-07-23 13:33 tim |
| 142 |
> |
2004-10-28 17:34 tim |
| 143 |
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| 144 |
< |
* samples/argon/Makefile.in: remove eor file |
| 144 |
> |
* src/brains/DataStorage.hpp, src/utils/next_combination.hpp, |
| 145 |
> |
test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, |
| 146 |
> |
test/brains/RigidBody.cpp, test/brains/RigidBody.hpp, |
| 147 |
> |
test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, |
| 148 |
> |
DirectionalAtom and RigidBody |
| 149 |
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| 150 |
< |
2004-07-23 13:31 tim |
| 150 |
> |
2004-10-28 17:26 tim |
| 151 |
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| 152 |
< |
* samples/argon/: Makefile.in, argon.bass, argon.eor, argonEM.bass: |
| 153 |
< |
change names for argon |
| 152 |
> |
* ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, |
| 153 |
> |
src/applications/simpleBuilder/MoLocator.cpp, |
| 154 |
> |
src/applications/simpleBuilder/Vector3d.hpp, |
| 155 |
> |
src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: |
| 156 |
> |
remove old Vector3d.hpp from application/simpleBuilder |
| 157 |
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| 158 |
< |
2004-07-23 11:47 tim |
| 158 |
> |
2004-10-28 16:42 tim |
| 159 |
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| 160 |
< |
* samples/water/ssde/SSDEinit.in: [no log message] |
| 160 |
> |
* src/utils/next_combination.hpp: Minor change in next_combination |
| 161 |
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| 162 |
< |
2004-07-23 11:45 tim |
| 162 |
> |
2004-10-28 16:28 tim |
| 163 |
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| 164 |
< |
* samples/water/ssde/SSDEinit.in: add init file for ssde |
| 164 |
> |
* src/utils/next_combination.hpp, |
| 165 |
> |
test/utils/NextCombinationTestCase.cpp, |
| 166 |
> |
test/utils/ReplaceWildCardTestCase.cpp: Done with combination |
| 167 |
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| 168 |
< |
2004-07-23 11:43 chuckv |
| 168 |
> |
2004-10-28 16:11 tim |
| 169 |
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| 170 |
< |
* libmdtools/calc_eam.F90: Fixed bug in calc_eam with mixtures and |
| 171 |
< |
cutoffs associated with mixture. |
| 170 |
> |
* src/utils/next_combination.hpp: change documentation of |
| 171 |
> |
next_combination.hpp |
| 172 |
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| 173 |
< |
2004-07-23 10:35 tim |
| 173 |
> |
2004-10-28 15:41 tim |
| 174 |
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| 175 |
< |
* libmdtools/: AtomVisitor.cpp, AtomVisitor.hpp: support SSD_E |
| 176 |
< |
SSD_RF SSD1 |
| 175 |
> |
* ChangeLog, src/utils/next_combination.hpp, |
| 176 |
> |
test/utils/NextCombinationTestCase.cpp, |
| 177 |
> |
test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working |
| 178 |
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| 179 |
< |
2004-07-23 09:53 tim |
| 179 |
> |
2004-10-28 15:01 tim |
| 180 |
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| 181 |
< |
* libmdtools/AtomVisitor.cpp: SSDVisitor support SSD_RF, SSD_E, |
| 143 |
< |
SSD1 now |
| 181 |
> |
* src/utils/next_combination.hpp: adding replace wildcard function |
| 182 |
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| 183 |
< |
2004-07-23 09:19 tim |
| 183 |
> |
2004-10-28 14:33 tim |
| 184 |
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| 185 |
< |
* libmdtools/ZConsReader.cpp: remove ^M from ZConsReader.cpp |
| 185 |
> |
* src/utils/next_combination.hpp: Minor change |
| 186 |
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| 187 |
< |
2004-07-23 09:18 tim |
| 187 |
> |
2004-10-28 14:06 tim |
| 188 |
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| 189 |
< |
* samples/lipid/5x5.bass: remove unsupport keyword |
| 189 |
> |
* ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, |
| 190 |
> |
src/applications/simpleBuilder/simpleBuilder.cpp, |
| 191 |
> |
src/utils/next_combination.hpp, test/utils/Makefile, |
| 192 |
> |
test/utils/NextCombinationTestCase.cpp, |
| 193 |
> |
test/utils/ReplaceWildCardTestCase.cpp, |
| 194 |
> |
test/utils/next_combination.hpp: STL next_permutation like |
| 195 |
> |
next_combination is working |
| 196 |
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| 197 |
< |
2004-07-22 16:01 chuckv |
| 197 |
> |
2004-10-28 12:22 chrisfen |
| 198 |
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| 199 |
< |
* samples/metals/: init_Au_bulk.in, init_Au_nanoparticle.in: |
| 156 |
< |
Changed init files to be more OOPSE like... |
| 199 |
> |
* src/UseTheForce/WATER.cpp: fix of setDipoles |
| 200 |
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| 201 |
< |
2004-07-22 10:11 gezelter |
| 201 |
> |
2004-10-28 12:20 gezelter |
| 202 |
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| 203 |
< |
* configure, ac-tools/configure.in: added sample directory |
| 203 |
> |
* src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the |
| 204 |
> |
shapeFile |
| 205 |
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| 206 |
< |
2004-07-22 10:06 chrisfen |
| 206 |
> |
2004-10-28 12:20 gezelter |
| 207 |
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| 208 |
< |
* src/Makefile.in: fixed icc7 incompatibility in linking |
| 208 |
> |
* samples/shape/linear.md: forgot the orientation line |
| 209 |
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| 210 |
< |
2004-07-21 17:03 chrisfen |
| 210 |
> |
2004-10-28 11:56 gezelter |
| 211 |
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| 212 |
< |
* samples/water/: Makefile.in, tip3p_ice/200.in, |
| 213 |
< |
tip3p_ice/Makefile.in, tip3p_ice/tp3.bass, tip3p_ice/water.mdl: |
| 214 |
< |
Added tip3p_ice to Makefile |
| 212 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 213 |
> |
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
| 214 |
> |
UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate |
| 215 |
> |
declaration foo |
| 216 |
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| 217 |
< |
2004-07-21 16:46 chuckv |
| 217 |
> |
2004-10-28 11:55 gezelter |
| 218 |
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| 219 |
< |
* samples/metals/: Au.bass, Au.eor, Au_bulk_FBD.bass, |
| 175 |
< |
Au_bulk_voter.bass, Au_nanoparticle.bass, Au_nanoparticle.eor, |
| 176 |
< |
init_Au_bulk.in, init_Au_nanoparticle.in, init_au.in: Added sample |
| 177 |
< |
files for bulk metals and a bass file for both voter and FBD |
| 178 |
< |
formulations of EAM. |
| 219 |
> |
* samples/lipid/5x5.md: uncommented .in line |
| 220 |
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| 221 |
< |
2004-07-21 14:53 gezelter |
| 221 |
> |
2004-10-28 10:42 tim |
| 222 |
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| 223 |
< |
* samples/water/dimer/two.bass: Checked a bug where eor file wasn't |
| 224 |
< |
being written at the end of the run |
| 223 |
> |
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
| 224 |
> |
NextCombinationTestCase.hpp, next_combination.hpp: next_combination |
| 225 |
> |
in progress |
| 226 |
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| 227 |
< |
2004-07-21 14:53 gezelter |
| 227 |
> |
2004-10-28 10:15 tim |
| 228 |
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| 229 |
< |
* libmdtools/Integrator.cpp: Fixed a bug where eor file wasn't |
| 230 |
< |
being written at the end of the run |
| 229 |
> |
* test/utils/: NextCombinationTestCase.cpp, |
| 230 |
> |
NextCombinationTestCase.hpp: adding next_combination test case |
| 231 |
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| 232 |
< |
2004-07-21 09:11 gezelter |
| 232 |
> |
2004-10-28 10:02 tim |
| 233 |
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| 234 |
< |
* README: [no log message] |
| 234 |
> |
* test/utils/next_combination.hpp: STL Compatible combination |
| 235 |
> |
sequence generator |
| 236 |
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| 237 |
< |
2004-07-21 09:08 gezelter |
| 237 |
> |
2004-10-28 01:23 tim |
| 238 |
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| 239 |
< |
* samples/argon/machines: cleaning up for export |
| 239 |
> |
* test/utils/: GenerateCombination.hpp, |
| 240 |
> |
ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp |
| 241 |
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| 242 |
< |
2004-07-21 09:04 gezelter |
| 242 |
> |
2004-10-28 01:16 tim |
| 243 |
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| 244 |
< |
* NEWS, README: cleaning up for export |
| 244 |
> |
* test/utils/GenerateCombination.hpp: a STL next_permutaion like |
| 245 |
> |
next_combination function. |
| 246 |
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| 247 |
< |
2004-07-21 08:45 gezelter |
| 247 |
> |
2004-10-27 22:27 tim |
| 248 |
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|
| 249 |
< |
* configure, ac-tools/configure.in: removing staticProps from cvs |
| 205 |
< |
tree |
| 249 |
> |
* test/utils/ReplaceWildCard.hpp: no message |
| 250 |
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|
| 251 |
< |
2004-07-20 12:07 gezelter |
| 251 |
> |
2004-10-27 22:14 tim |
| 252 |
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|
| 253 |
< |
* configure, ac-tools/aclocal.m4, utils/Makefile.in, |
| 254 |
< |
utils/quickLate.c, utils/sysbuilder/Makefile.in: [no log message] |
| 253 |
> |
* test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: |
| 254 |
> |
ReplaceWildCard(recursive version) is working, need refactoring. An |
| 255 |
> |
iterative version is on the way |
| 256 |
|
|
| 257 |
< |
2004-07-20 10:17 gezelter |
| 257 |
> |
2004-10-27 21:28 tim |
| 258 |
|
|
| 259 |
< |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 260 |
< |
third-party/gnugetopt.h, utils/getopt.c, utils/getopt1.c, |
| 216 |
< |
utils/gnugetopt.h: fixing getopt_long |
| 259 |
> |
* test/utils/: Makefile, ReplaceWildCard.hpp, |
| 260 |
> |
ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress |
| 261 |
|
|
| 262 |
< |
2004-07-19 16:58 gezelter |
| 262 |
> |
2004-10-27 21:08 tim |
| 263 |
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|
| 264 |
< |
* configure, ac-tools/configure.in, libmdtools/ReadWrite.hpp, |
| 265 |
< |
libmdtools/ZConsWriter.hpp, src/Makefile.in, |
| 222 |
< |
third-party/gnugetopt.h, utils/Dump2XYZCmd.c, utils/Make.dep, |
| 223 |
< |
utils/Makefile.in, utils/sysbuilder/Makefile.in, |
| 224 |
< |
utils/sysbuilder/latticeBuilder.cpp: [no log message] |
| 264 |
> |
* test/utils/: ReplaceWildCardTestCase.cpp, |
| 265 |
> |
ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard |
| 266 |
|
|
| 267 |
< |
2004-07-19 16:52 tim |
| 267 |
> |
2004-10-27 18:17 tim |
| 268 |
|
|
| 269 |
< |
* utils/quickLate.c: minor fix of format string in quicklate.c |
| 269 |
> |
* test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need |
| 270 |
> |
test |
| 271 |
|
|
| 272 |
< |
2004-07-19 16:30 tim |
| 272 |
> |
2004-10-27 01:25 tim |
| 273 |
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|
| 274 |
< |
* utils/zsub: remove zsub from cvs tree |
| 274 |
> |
* src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild |
| 275 |
> |
char matching is on the way |
| 276 |
|
|
| 277 |
< |
2004-07-19 16:25 tim |
| 277 |
> |
2004-10-27 01:07 tim |
| 278 |
|
|
| 279 |
< |
* libmdtools/ZConstraint.cpp, utils/Dump2XYZ.cpp: remove some |
| 237 |
< |
comment lines |
| 279 |
> |
* src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 |
| 280 |
|
|
| 281 |
< |
2004-07-19 16:00 tim |
| 281 |
> |
2004-10-26 22:00 gezelter |
| 282 |
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|
| 283 |
< |
* libmdtools/OOPSEMinimizer.hpp: remove an extra semicolon from |
| 242 |
< |
OOPSEMinimizer.hpp |
| 283 |
> |
* src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix |
| 284 |
|
|
| 285 |
< |
2004-07-19 13:55 gezelter |
| 285 |
> |
2004-10-26 21:20 gezelter |
| 286 |
|
|
| 287 |
< |
* libBASS/y.tab.h: Shouldn't have been in CVS |
| 287 |
> |
* src/UseTheForce/ForceFields.hpp: subclass foo |
| 288 |
|
|
| 289 |
< |
2004-07-19 13:54 gezelter |
| 289 |
> |
2004-10-26 21:16 gezelter |
| 290 |
|
|
| 291 |
< |
* libBASS/y.tab.h, libmdtools/ForceFields.cpp: Fix for |
| 292 |
< |
thermodynamic integration of rigid bodies |
| 291 |
> |
* src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> |
| 292 |
> |
string conversion |
| 293 |
|
|
| 294 |
< |
2004-07-19 12:00 gezelter |
| 294 |
> |
2004-10-26 19:01 gezelter |
| 295 |
|
|
| 296 |
< |
* libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: These can be |
| 297 |
< |
generated via lex and yacc at compile time |
| 296 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 297 |
> |
UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, |
| 298 |
> |
brains/SimSetup.hpp: char* -> string |
| 299 |
|
|
| 300 |
< |
2004-07-19 11:47 gezelter |
| 300 |
> |
2004-10-26 17:25 gezelter |
| 301 |
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|
| 302 |
< |
* libBASS/BASSlex.c, libBASS/BASSyacc.c, libBASS/BASSyacc.h, |
| 303 |
< |
libBASS/make_nodes.c, libBASS/y.tab.h, libmdtools/Makefile.in, |
| 304 |
< |
libmdtools/MatVec3.c, src/Makefile.in: [no log message] |
| 302 |
> |
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, |
| 303 |
> |
Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, |
| 304 |
> |
ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some |
| 305 |
> |
isXXX |
| 306 |
|
|
| 307 |
< |
2004-07-19 11:32 gezelter |
| 307 |
> |
2004-10-26 17:25 gezelter |
| 308 |
|
|
| 309 |
< |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 310 |
< |
third-party/gnugetopt.h, utils/Makefile.in, |
| 268 |
< |
utils/sysbuilder/Makefile.in: changes for gnu getopt and fixed |
| 269 |
< |
SPRNG configure script |
| 309 |
> |
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
| 310 |
> |
define name collision |
| 311 |
|
|
| 312 |
< |
2004-07-16 16:49 gezelter |
| 312 |
> |
2004-10-26 17:24 gezelter |
| 313 |
|
|
| 314 |
< |
* libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: fixing for machines |
| 315 |
< |
that don't have lex and yacc |
| 314 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 315 |
> |
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
| 316 |
> |
UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp, |
| 317 |
> |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
| 318 |
> |
UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: |
| 319 |
> |
forcefield refactoring for shapes |
| 320 |
|
|
| 321 |
< |
2004-07-16 15:55 gezelter |
| 321 |
> |
2004-10-26 17:24 gezelter |
| 322 |
|
|
| 323 |
< |
* Makefile: Makefiles don't belong in cvs repository |
| 323 |
> |
* samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, |
| 324 |
> |
Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, |
| 325 |
> |
linear.md, linear.shape, toluene.shape: adding sample shape |
| 326 |
> |
directory |
| 327 |
|
|
| 328 |
< |
2004-07-16 15:54 gezelter |
| 328 |
> |
2004-10-26 17:19 tim |
| 329 |
|
|
| 330 |
< |
* Makefile, forceFields/Makefile, libBASS/Makefile, |
| 331 |
< |
libmdtools/Makefile, samples/Makefile, src/Makefile, |
| 332 |
< |
third-party/Makefile, utils/Makefile, utils/sysbuilder/Makefile: |
| 333 |
< |
Makefiles don't belong in repository |
| 330 |
> |
* ChangeLog, src/brains/DataStorage.cpp, |
| 331 |
> |
src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, |
| 332 |
> |
test/brains/DataStorageTestCase.cpp, |
| 333 |
> |
test/brains/DataStorageTestCase.hpp, test/brains/Makefile: |
| 334 |
> |
DataStorage passes unit test |
| 335 |
|
|
| 336 |
< |
2004-07-16 15:49 gezelter |
| 336 |
> |
2004-10-26 13:03 chrisfen |
| 337 |
|
|
| 338 |
< |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
| 339 |
< |
metals/Makefile: Makefiles don't belong in repository |
| 338 |
> |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: |
| 339 |
> |
Changes to help advance shapes |
| 340 |
|
|
| 341 |
< |
2004-07-16 15:20 chrisfen |
| 341 |
> |
2004-10-26 13:02 chrisfen |
| 342 |
|
|
| 343 |
< |
* Makefile, configure, ac-tools/configure.in, forceFields/Makefile, |
| 344 |
< |
libBASS/Makefile, libmdtools/Makefile, samples/alkane/Makefile, |
| 296 |
< |
samples/argon/Makefile, samples/lipid/Makefile, |
| 297 |
< |
samples/metals/Makefile, src/Makefile, utils/Makefile, |
| 298 |
< |
utils/sysbuilder/Makefile: Updated configure for new samples |
| 343 |
> |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to |
| 344 |
> |
Shapes force field reader |
| 345 |
|
|
| 346 |
< |
2004-07-16 14:57 chrisfen |
| 346 |
> |
2004-10-26 12:28 tim |
| 347 |
|
|
| 348 |
< |
* samples/water/tip4p/Makefile.in: tip4p makefile.in added |
| 348 |
> |
* src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and |
| 349 |
> |
SnapshotTestCase in progress |
| 350 |
|
|
| 351 |
< |
2004-07-16 14:57 chrisfen |
| 351 |
> |
2004-10-25 17:46 tim |
| 352 |
|
|
| 353 |
< |
* samples/water/ssde/: 256init.in, Makefile.in, ssde.bass: ssde |
| 354 |
< |
makefile.in added |
| 353 |
> |
* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
| 354 |
> |
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
| 355 |
> |
src/math/Vector3.hpp, test/brains/StuntDouble.hpp, |
| 356 |
> |
test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, |
| 357 |
> |
test/math/VectorTestCase.cpp: add getArray function to RectMatrix |
| 358 |
> |
and Vector classes |
| 359 |
|
|
| 360 |
< |
2004-07-16 14:57 chrisfen |
| 360 |
> |
2004-10-25 12:03 tim |
| 361 |
|
|
| 362 |
< |
* samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass, |
| 363 |
< |
water.mdl: ssd files sorted added |
| 362 |
> |
* ChangeLog, src/utils/GenericFactory.hpp, |
| 363 |
> |
test/utils/GenericFactoryTestCase.cpp, |
| 364 |
> |
test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding |
| 365 |
> |
GenericFactory Test Case. GenericFactory now can bed used to creat |
| 366 |
> |
ForcefieldFactory and IntegratorFactory etc. |
| 367 |
|
|
| 368 |
< |
2004-07-16 14:57 chrisfen |
| 368 |
> |
2004-10-24 23:08 tim |
| 369 |
|
|
| 370 |
< |
* samples/water/spce/Makefile.in: spce makefile.in added |
| 370 |
> |
* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, |
| 371 |
> |
brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, |
| 372 |
> |
brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes |
| 373 |
> |
get reconstructed |
| 374 |
|
|
| 375 |
< |
2004-07-16 14:56 chrisfen |
| 375 |
> |
2004-10-24 02:55 tim |
| 376 |
|
|
| 377 |
< |
* samples/water/dimer/: Makefile.in, two.bass, two.init, water.mdl: |
| 321 |
< |
dimer files added |
| 377 |
> |
* src/utils/GenericFactory.hpp: GenericFactory pass unit test |
| 378 |
|
|
| 379 |
< |
2004-07-16 14:56 chrisfen |
| 379 |
> |
2004-10-23 18:09 tim |
| 380 |
|
|
| 381 |
< |
* samples/water/: 200.in, Makefile, Makefile.in, init_ssd.eor, |
| 382 |
< |
spce.bass, spce.eor, ssd.bass, ssd.eor, tim.bass, tim.eor, |
| 383 |
< |
tim.init, tim.xyz, tip3p.bass, tip3p.eor, tip3p.init, two.bass, |
| 328 |
< |
two.eor, two.init, two.xyz, water.mdl: Cleaned up this file |
| 329 |
< |
considerably |
| 381 |
> |
* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, |
| 382 |
> |
StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, |
| 383 |
> |
RigidBody.cpp: Refactoring in progress |
| 384 |
|
|
| 385 |
< |
2004-07-16 13:57 gezelter |
| 385 |
> |
2004-10-22 18:09 tim |
| 386 |
|
|
| 387 |
< |
* AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README, |
| 388 |
< |
configure, ac-tools/Make.conf.in, ac-tools/aclocal.m4, |
| 389 |
< |
ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in, |
| 390 |
< |
ac-tools/fortran90.m4, ac-tools/install-sh, ac-tools/shtool, |
| 391 |
< |
forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl, |
| 392 |
< |
forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl, |
| 393 |
< |
forceFields/Au.VC.funcfl, forceFields/Au.u3.funcfl, |
| 387 |
> |
* ChangeLog, src/brains/Snapshot.hpp, |
| 388 |
> |
src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, |
| 389 |
> |
test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, |
| 390 |
> |
test/brains/StuntDouble.hpp: more work in Snapshot |
| 391 |
> |
|
| 392 |
> |
2004-10-22 17:59 chrisfen |
| 393 |
> |
|
| 394 |
> |
* src/: UseTheForce/LJFF.cpp, |
| 395 |
> |
UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear |
| 396 |
> |
god! It runs and conserves energy! |
| 397 |
> |
|
| 398 |
> |
2004-10-22 17:54 chrisfen |
| 399 |
> |
|
| 400 |
> |
* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY |
| 401 |
> |
|
| 402 |
> |
2004-10-22 17:53 chrisfen |
| 403 |
> |
|
| 404 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 405 |
> |
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
| 406 |
> |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
| 407 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey |
| 408 |
> |
breakey |
| 409 |
> |
|
| 410 |
> |
2004-10-22 17:53 chrisfen |
| 411 |
> |
|
| 412 |
> |
* make/Makefile.in: compiler flags |
| 413 |
> |
|
| 414 |
> |
2004-10-22 16:20 gezelter |
| 415 |
> |
|
| 416 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 417 |
> |
UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, |
| 418 |
> |
brains/fSimulation.h, types/AtomType.hpp, |
| 419 |
> |
types/DirectionalAtomType.hpp: fixey fixey |
| 420 |
> |
|
| 421 |
> |
2004-10-22 15:22 gezelter |
| 422 |
> |
|
| 423 |
> |
* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, |
| 424 |
> |
charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, |
| 425 |
> |
lj_interface.h, shapes.F90, simulation.F90: Added un-busticated |
| 426 |
> |
fortran files and c/Fortran interfaces |
| 427 |
> |
|
| 428 |
> |
2004-10-22 15:21 gezelter |
| 429 |
> |
|
| 430 |
> |
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
| 431 |
> |
DirectionalAtomType.hpp, Makefile: More on AtomType and |
| 432 |
> |
DirectionalAtomType |
| 433 |
> |
|
| 434 |
> |
2004-10-22 09:47 gezelter |
| 435 |
> |
|
| 436 |
> |
* src/types/AtomType.hpp: Adding AtomType |
| 437 |
> |
|
| 438 |
> |
2004-10-21 16:31 tim |
| 439 |
> |
|
| 440 |
> |
* ChangeLog, src/brains/Snapshot.hpp, |
| 441 |
> |
src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, |
| 442 |
> |
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
| 443 |
> |
src/math/Vector.hpp, src/math/Vector3.hpp, |
| 444 |
> |
test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: |
| 445 |
> |
Snapshot and SnapshotManager in progress |
| 446 |
> |
|
| 447 |
> |
2004-10-21 16:30 tim |
| 448 |
> |
|
| 449 |
> |
* test/brains/: BrainsTest.cpp, Makefile, |
| 450 |
> |
SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, |
| 451 |
> |
SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for |
| 452 |
> |
Snapshot and snapshotManager. |
| 453 |
> |
|
| 454 |
> |
2004-10-21 15:15 gezelter |
| 455 |
> |
|
| 456 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 457 |
> |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 458 |
> |
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
| 459 |
> |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
| 460 |
> |
UseTheForce/doForces_interface.h, UseTheForce/fForceField.h, |
| 461 |
> |
UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h, |
| 462 |
> |
brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. |
| 463 |
> |
Fixey Fixey. |
| 464 |
> |
|
| 465 |
> |
2004-10-21 11:32 tim |
| 466 |
> |
|
| 467 |
> |
* src/utils/GenericData.cpp, src/utils/Makefile, |
| 468 |
> |
test/utils/Makefile, test/utils/UtilTest: remove some junk files |
| 469 |
> |
|
| 470 |
> |
2004-10-21 11:24 tim |
| 471 |
> |
|
| 472 |
> |
* test/utils/GenericData.hpp: remove backup of GenericData.hpp |
| 473 |
> |
|
| 474 |
> |
2004-10-21 11:22 tim |
| 475 |
> |
|
| 476 |
> |
* ChangeLog, src/brains/SimSetup.cpp, |
| 477 |
> |
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
| 478 |
> |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 479 |
> |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 480 |
> |
src/integrators/NVT.cpp, src/io/DumpReader.cpp, |
| 481 |
> |
src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp, |
| 482 |
> |
src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp, |
| 483 |
> |
src/utils/GenericData.cpp, src/utils/GenericData.hpp, |
| 484 |
> |
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
| 485 |
> |
src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 486 |
> |
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
| 487 |
> |
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
| 488 |
> |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 489 |
> |
src/visitors/ZconsVisitor.hpp: replace old GebericData with new |
| 490 |
> |
GenericData |
| 491 |
> |
|
| 492 |
> |
2004-10-21 10:25 chuckv |
| 493 |
> |
|
| 494 |
> |
* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj |
| 495 |
> |
module. |
| 496 |
> |
|
| 497 |
> |
2004-10-21 10:24 chuckv |
| 498 |
> |
|
| 499 |
> |
* src/UseTheForce/DarkSide/lj_interface.h: Added interface for |
| 500 |
> |
fortran lj module. |
| 501 |
> |
|
| 502 |
> |
2004-10-20 17:54 tim |
| 503 |
> |
|
| 504 |
> |
* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, |
| 505 |
> |
test/utils/GenericDataTestCase.cpp, test/utils/Makefile, |
| 506 |
> |
test/utils/PropertyMapTestCase.cpp, |
| 507 |
> |
test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: |
| 508 |
> |
GenericData and PropertyMap pass unit test. |
| 509 |
> |
|
| 510 |
> |
2004-10-20 16:52 gezelter |
| 511 |
> |
|
| 512 |
> |
* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, |
| 513 |
> |
DarkSide/sticky_interface.h: fixed a fortran name problem |
| 514 |
> |
|
| 515 |
> |
2004-10-20 16:38 tim |
| 516 |
> |
|
| 517 |
> |
* test/utils/: GenericData.hpp, GenericDataTestCase.cpp, |
| 518 |
> |
GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, |
| 519 |
> |
UtilTest, UtilTest.cpp: adding generic data test case |
| 520 |
> |
|
| 521 |
> |
2004-10-20 16:16 chuckv |
| 522 |
> |
|
| 523 |
> |
* configure, ac-tools/aclocal.m4, |
| 524 |
> |
src/UseTheForce/DarkSide/Makefile, |
| 525 |
> |
src/UseTheForce/DarkSide/mpiSimulation.F90, |
| 526 |
> |
src/UseTheForce/DarkSide/mpiSimulation_interface.h, |
| 527 |
> |
src/UseTheForce/DarkSide/simParallel.F90, |
| 528 |
> |
src/UseTheForce/DarkSide/simParallel_interface.h, |
| 529 |
> |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: |
| 530 |
> |
Fortran/C++ interface de-obfuscation project appears to be |
| 531 |
> |
complete! Woo hoo! |
| 532 |
> |
|
| 533 |
> |
2004-10-20 15:47 chuckv |
| 534 |
> |
|
| 535 |
> |
* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, |
| 536 |
> |
fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project |
| 537 |
> |
continues |
| 538 |
> |
|
| 539 |
> |
2004-10-20 15:46 chuckv |
| 540 |
> |
|
| 541 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 542 |
> |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 543 |
> |
UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, |
| 544 |
> |
UseTheForce/doForces_interface.h, |
| 545 |
> |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, |
| 546 |
> |
UseTheForce/DarkSide/atype_interface.h, |
| 547 |
> |
UseTheForce/DarkSide/eam_interface.h, |
| 548 |
> |
UseTheForce/DarkSide/gb_interface.h, |
| 549 |
> |
UseTheForce/DarkSide/mpiSimulation_interface.h, |
| 550 |
> |
UseTheForce/DarkSide/shapes_interface.h, |
| 551 |
> |
UseTheForce/DarkSide/simulation_interface.h, |
| 552 |
> |
UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, |
| 553 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface |
| 554 |
> |
de-obfuscation project (It is a very long story) |
| 555 |
> |
|
| 556 |
> |
2004-10-20 13:07 tim |
| 557 |
> |
|
| 558 |
> |
* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
| 559 |
> |
test/math/SquareMatrix3TestCase.cpp, |
| 560 |
> |
test/math/SquareMatrixTestCase.cpp, |
| 561 |
> |
test/math/SquareMatrixTestCase.hpp: Math library pass the unit test |
| 562 |
> |
|
| 563 |
> |
2004-10-20 00:52 tim |
| 564 |
> |
|
| 565 |
> |
* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
| 566 |
> |
SnapshotManager in design phase |
| 567 |
> |
|
| 568 |
> |
2004-10-19 23:54 gezelter |
| 569 |
> |
|
| 570 |
> |
* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
| 571 |
> |
problem prevented linking |
| 572 |
> |
|
| 573 |
> |
2004-10-19 23:54 gezelter |
| 574 |
> |
|
| 575 |
> |
* src/UseTheForce/Shapes_FF.cpp: fixed include |
| 576 |
> |
|
| 577 |
> |
2004-10-19 23:26 gezelter |
| 578 |
> |
|
| 579 |
> |
* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
| 580 |
> |
oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
| 581 |
> |
more fortran name mangling |
| 582 |
> |
|
| 583 |
> |
2004-10-19 23:23 gezelter |
| 584 |
> |
|
| 585 |
> |
* src/profiling/timing.F90: yet more fortran renaming |
| 586 |
> |
|
| 587 |
> |
2004-10-19 23:19 gezelter |
| 588 |
> |
|
| 589 |
> |
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
| 590 |
> |
do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
| 591 |
> |
notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
| 592 |
> |
wrappers.F90: Fortran name cleanup continues |
| 593 |
> |
|
| 594 |
> |
2004-10-19 23:12 gezelter |
| 595 |
> |
|
| 596 |
> |
* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
| 597 |
> |
broken fortran stuff |
| 598 |
> |
|
| 599 |
> |
2004-10-19 23:02 gezelter |
| 600 |
> |
|
| 601 |
> |
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
| 602 |
> |
atype_interface.h, atype_module.F90, atype_module_interface.h, |
| 603 |
> |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
| 604 |
> |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
| 605 |
> |
calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, |
| 606 |
> |
eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, |
| 607 |
> |
gb_interface.h, gb_module_interface.h, mpiSimulation.F90, |
| 608 |
> |
mpiSimulation_interface.h, mpiSimulation_module.F90, |
| 609 |
> |
mpisimulation_module_interface.h, reactionField.F90, shapes.F90, |
| 610 |
> |
shapes_interface.h, shapes_module.h, simulation.F90, |
| 611 |
> |
simulation_interface.h, simulation_module.F90, |
| 612 |
> |
simulation_module_interface.h, sticky.F90, sticky_interface.h, |
| 613 |
> |
sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
| 614 |
> |
name sanity on the fortran side |
| 615 |
> |
|
| 616 |
> |
2004-10-19 19:18 tim |
| 617 |
> |
|
| 618 |
> |
* test/math/SquareMatrix3TestCase.hpp: [no log message] |
| 619 |
> |
|
| 620 |
> |
2004-10-19 18:01 tim |
| 621 |
> |
|
| 622 |
> |
* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
| 623 |
> |
src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
| 624 |
> |
except diagonalize(), all of functions in math library pass the |
| 625 |
> |
test |
| 626 |
> |
|
| 627 |
> |
2004-10-19 17:43 chuckv |
| 628 |
> |
|
| 629 |
> |
* src/UseTheForce/do_Forces.h: Added correct prototypes for |
| 630 |
> |
C-fortran interface functions. |
| 631 |
> |
|
| 632 |
> |
2004-10-19 17:37 chuckv |
| 633 |
> |
|
| 634 |
> |
* src/UseTheForce/DarkSide/: atype_module_interface.h, |
| 635 |
> |
eam_module_inteface.h, gb_module_interface.h, |
| 636 |
> |
mpisimulation_module_interface.h, simulation_module_interface.h, |
| 637 |
> |
sticky_pair_module_interface.h: Added correct prototypes for |
| 638 |
> |
C-fortran interface functions. |
| 639 |
> |
|
| 640 |
> |
2004-10-19 16:28 tim |
| 641 |
> |
|
| 642 |
> |
* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
| 643 |
> |
src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
| 644 |
> |
test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, |
| 645 |
> |
test/math/RectMatrixTestCase.cpp, |
| 646 |
> |
test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, |
| 647 |
> |
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
| 648 |
> |
bugs get fixed at math library |
| 649 |
> |
|
| 650 |
> |
2004-10-19 15:43 chuckv |
| 651 |
> |
|
| 652 |
> |
* src/UseTheForce/: DarkSide/atype_module_interface.h, |
| 653 |
> |
DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
| 654 |
> |
DarkSide/mpisimulation_module_interface.h, |
| 655 |
> |
DarkSide/simulation_module_interface.h, |
| 656 |
> |
DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, |
| 657 |
> |
DarkSide/atype_module.F90, DarkSide/calc_gb.F90, |
| 658 |
> |
DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, |
| 659 |
> |
DarkSide/simulation_module.F90, do_Forces.F90, |
| 660 |
> |
fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, |
| 661 |
> |
notifycutoffs_module_interface.h: Added new files for fortran |
| 662 |
> |
interface. |
| 663 |
> |
|
| 664 |
> |
2004-10-19 15:43 gezelter |
| 665 |
> |
|
| 666 |
> |
* src/UseTheForce/Makefile: regressing |
| 667 |
> |
|
| 668 |
> |
2004-10-19 15:40 gezelter |
| 669 |
> |
|
| 670 |
> |
* src/: UseTheForce/DarkSide/calc_shapes.F90, |
| 671 |
> |
UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
| 672 |
> |
working on shapes for portability |
| 673 |
> |
|
| 674 |
> |
2004-10-19 15:40 gezelter |
| 675 |
> |
|
| 676 |
> |
* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
| 677 |
> |
|
| 678 |
> |
2004-10-19 13:21 chrisfen |
| 679 |
> |
|
| 680 |
> |
* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
| 681 |
> |
findBegin |
| 682 |
> |
|
| 683 |
> |
2004-10-18 23:34 tim |
| 684 |
> |
|
| 685 |
> |
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
| 686 |
> |
are fixed in Vector class |
| 687 |
> |
|
| 688 |
> |
2004-10-18 23:28 tim |
| 689 |
> |
|
| 690 |
> |
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
| 691 |
> |
some bugs in RectMatrixTestCase |
| 692 |
> |
|
| 693 |
> |
2004-10-18 23:21 tim |
| 694 |
> |
|
| 695 |
> |
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
| 696 |
> |
test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
| 697 |
> |
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
| 698 |
> |
test/math/VectorTestCase.hpp: implement more test cases |
| 699 |
> |
|
| 700 |
> |
2004-10-18 18:13 tim |
| 701 |
> |
|
| 702 |
> |
* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
| 703 |
> |
src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
| 704 |
> |
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
| 705 |
> |
src/utils/StringTokenizer.hpp, test/math/Makefile, |
| 706 |
> |
test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
| 707 |
> |
tests on math library |
| 708 |
> |
|
| 709 |
> |
2004-10-18 16:03 tim |
| 710 |
> |
|
| 711 |
> |
* test/math/: Makefile, QuaternionTestCase.cpp, |
| 712 |
> |
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
| 713 |
> |
SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
| 714 |
> |
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
| 715 |
> |
more testing units |
| 716 |
> |
|
| 717 |
> |
2004-10-18 12:07 tim |
| 718 |
> |
|
| 719 |
> |
* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
| 720 |
> |
math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
| 721 |
> |
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
| 722 |
> |
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
| 723 |
> |
|
| 724 |
> |
2004-10-18 11:30 gezelter |
| 725 |
> |
|
| 726 |
> |
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
| 727 |
> |
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
| 728 |
> |
\phi) |
| 729 |
> |
|
| 730 |
> |
2004-10-18 11:29 gezelter |
| 731 |
> |
|
| 732 |
> |
* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
| 733 |
> |
types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
| 734 |
> |
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
| 735 |
> |
Shapes into OOPSE |
| 736 |
> |
|
| 737 |
> |
2004-10-18 10:21 gezelter |
| 738 |
> |
|
| 739 |
> |
* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
| 740 |
> |
|
| 741 |
> |
2004-10-18 00:23 tim |
| 742 |
> |
|
| 743 |
> |
* test/math/VectorTestCase.hpp: adding vector test case |
| 744 |
> |
|
| 745 |
> |
2004-10-18 00:23 tim |
| 746 |
> |
|
| 747 |
> |
* src/utils/GenericFactory.hpp: adding generic factory and vector |
| 748 |
> |
test case |
| 749 |
> |
|
| 750 |
> |
2004-10-16 20:19 tim |
| 751 |
> |
|
| 752 |
> |
* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
| 753 |
> |
SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
| 754 |
> |
progress |
| 755 |
> |
|
| 756 |
> |
2004-10-15 20:31 tim |
| 757 |
> |
|
| 758 |
> |
* src/math/Quaternion.hpp: add quaternion class |
| 759 |
> |
|
| 760 |
> |
2004-10-15 16:11 tim |
| 761 |
> |
|
| 762 |
> |
* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
| 763 |
> |
IfstrstreamTestCase.hpp: adding test file |
| 764 |
> |
|
| 765 |
> |
2004-10-15 16:10 tim |
| 766 |
> |
|
| 767 |
> |
* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
| 768 |
> |
|
| 769 |
> |
2004-10-15 15:42 tim |
| 770 |
> |
|
| 771 |
> |
* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
| 772 |
> |
|
| 773 |
> |
2004-10-15 15:35 tim |
| 774 |
> |
|
| 775 |
> |
* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
| 776 |
> |
|
| 777 |
> |
2004-10-15 15:34 tim |
| 778 |
> |
|
| 779 |
> |
* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
| 780 |
> |
namespace oopse |
| 781 |
> |
|
| 782 |
> |
2004-10-15 14:38 chuckv |
| 783 |
> |
|
| 784 |
> |
* configure, ac-tools/aclocal.m4: Changed optimization flags for |
| 785 |
> |
XLF and XLC. |
| 786 |
> |
|
| 787 |
> |
2004-10-15 13:28 tim |
| 788 |
> |
|
| 789 |
> |
* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
| 790 |
> |
adding ifstrstream test case |
| 791 |
> |
|
| 792 |
> |
2004-10-15 13:20 tim |
| 793 |
> |
|
| 794 |
> |
* src/io/basic_ifstrstream.hpp: fix include |
| 795 |
> |
|
| 796 |
> |
2004-10-15 13:18 tim |
| 797 |
> |
|
| 798 |
> |
* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
| 799 |
> |
|
| 800 |
> |
2004-10-15 13:17 tim |
| 801 |
> |
|
| 802 |
> |
* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
| 803 |
> |
|
| 804 |
> |
2004-10-15 13:16 tim |
| 805 |
> |
|
| 806 |
> |
* test/io/: Makefile, ifstrstreamTestCase.cpp, |
| 807 |
> |
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
| 808 |
> |
|
| 809 |
> |
2004-10-15 10:37 tim |
| 810 |
> |
|
| 811 |
> |
* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
| 812 |
> |
ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
| 813 |
> |
|
| 814 |
> |
2004-10-15 10:20 tim |
| 815 |
> |
|
| 816 |
> |
* src/io/basic_ifstrstream.hpp: add checkFilename Option |
| 817 |
> |
|
| 818 |
> |
2004-10-15 10:19 tim |
| 819 |
> |
|
| 820 |
> |
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
| 821 |
> |
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
| 822 |
> |
SquareMatrixTestCase class |
| 823 |
> |
|
| 824 |
> |
2004-10-15 02:52 tim |
| 825 |
> |
|
| 826 |
> |
* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
| 827 |
> |
|
| 828 |
> |
2004-10-14 18:28 tim |
| 829 |
> |
|
| 830 |
> |
* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
| 831 |
> |
Vector.hpp: math library in progress |
| 832 |
> |
|
| 833 |
> |
2004-10-14 18:27 tim |
| 834 |
> |
|
| 835 |
> |
* src/io/FileReader.hpp: FileReader in progress |
| 836 |
> |
|
| 837 |
> |
2004-10-13 18:53 tim |
| 838 |
> |
|
| 839 |
> |
* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
| 840 |
> |
test in isOrthogonal of SquareMatrix is failed by some reasons |
| 841 |
> |
|
| 842 |
> |
2004-10-13 17:28 tim |
| 843 |
> |
|
| 844 |
> |
* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
| 845 |
> |
class |
| 846 |
> |
|
| 847 |
> |
2004-10-13 17:27 tim |
| 848 |
> |
|
| 849 |
> |
* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
| 850 |
> |
RectMatrixTestCase.hpp: adding testing unit |
| 851 |
> |
|
| 852 |
> |
2004-10-13 17:24 tim |
| 853 |
> |
|
| 854 |
> |
* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
| 855 |
> |
|
| 856 |
> |
2004-10-13 01:51 tim |
| 857 |
> |
|
| 858 |
> |
* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
| 859 |
> |
Vector3.hpp: refactory vector and matrix classes |
| 860 |
> |
|
| 861 |
> |
2004-10-13 01:50 tim |
| 862 |
> |
|
| 863 |
> |
* src/math/Vector3d.hpp: Remove some Makefile.in |
| 864 |
> |
|
| 865 |
> |
2004-10-12 18:57 tim |
| 866 |
> |
|
| 867 |
> |
* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
| 868 |
> |
Matrix3x3d.hpp |
| 869 |
> |
|
| 870 |
> |
2004-10-12 14:08 tim |
| 871 |
> |
|
| 872 |
> |
* doc/: cppstyle.html, style.css: adding c++ coding style |
| 873 |
> |
|
| 874 |
> |
2004-10-11 17:15 tim |
| 875 |
> |
|
| 876 |
> |
* src/: constraints/AbstractClasses.hpp, |
| 877 |
> |
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
| 878 |
> |
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
| 879 |
> |
|
| 880 |
> |
2004-10-11 16:54 tim |
| 881 |
> |
|
| 882 |
> |
* scripts/filepp: fix a bug in filepp |
| 883 |
> |
|
| 884 |
> |
2004-10-11 16:13 tim |
| 885 |
> |
|
| 886 |
> |
* make/Makefile.in: using filepp to generate dependencies instead |
| 887 |
> |
of compilers |
| 888 |
> |
|
| 889 |
> |
2004-10-11 16:10 tim |
| 890 |
> |
|
| 891 |
> |
* scripts/filepp: filepp can be used to generate dependencies for |
| 892 |
> |
c/c++ now |
| 893 |
> |
|
| 894 |
> |
2004-10-11 13:40 tim |
| 895 |
> |
|
| 896 |
> |
* make/Makefile.in: remove -module from F90Options |
| 897 |
> |
|
| 898 |
> |
2004-10-11 13:01 tim |
| 899 |
> |
|
| 900 |
> |
* make/Makefile.in: adding rules to move fortran 90 module to |
| 901 |
> |
target directory |
| 902 |
> |
|
| 903 |
> |
2004-10-11 10:43 gezelter |
| 904 |
> |
|
| 905 |
> |
* make/Makefile.in: fixed makefile.in |
| 906 |
> |
|
| 907 |
> |
2004-10-11 09:51 tim |
| 908 |
> |
|
| 909 |
> |
* scripts/filepp: remove "use bytes" which causes problem in sgi |
| 910 |
> |
machine |
| 911 |
> |
|
| 912 |
> |
2004-10-11 09:26 tim |
| 913 |
> |
|
| 914 |
> |
* forceFields/Makefile: add Makefile |
| 915 |
> |
|
| 916 |
> |
2004-10-11 09:23 tim |
| 917 |
> |
|
| 918 |
> |
* samples/: water/dimer/Makefile, water/spce/Makefile, |
| 919 |
> |
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
| 920 |
> |
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
| 921 |
> |
directory |
| 922 |
> |
|
| 923 |
> |
2004-10-11 09:23 tim |
| 924 |
> |
|
| 925 |
> |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
| 926 |
> |
Makefile |
| 927 |
> |
|
| 928 |
> |
2004-10-09 01:01 tim |
| 929 |
> |
|
| 930 |
> |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
| 931 |
> |
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
| 932 |
> |
Remove some Makefile.in |
| 933 |
> |
|
| 934 |
> |
2004-10-08 18:15 tim |
| 935 |
> |
|
| 936 |
> |
* make/Makefile.in: [no log message] |
| 937 |
> |
|
| 938 |
> |
2004-10-08 17:51 tim |
| 939 |
> |
|
| 940 |
> |
* make/Makefile.in: fix make install |
| 941 |
> |
|
| 942 |
> |
2004-10-08 17:10 tim |
| 943 |
> |
|
| 944 |
> |
* make/Makefile.in: adding make install |
| 945 |
> |
|
| 946 |
> |
2004-10-08 17:04 tim |
| 947 |
> |
|
| 948 |
> |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
| 949 |
> |
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
| 950 |
> |
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
| 951 |
> |
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
| 952 |
> |
water/ssde/Makefile, water/ssde/Makefile.in, |
| 953 |
> |
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
| 954 |
> |
water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
| 955 |
> |
zcons/Makefile.in: add Makefile to sample directory |
| 956 |
> |
|
| 957 |
> |
2004-10-06 18:03 gezelter |
| 958 |
> |
|
| 959 |
> |
* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
| 960 |
> |
stuff |
| 961 |
> |
|
| 962 |
> |
2004-10-06 18:03 gezelter |
| 963 |
> |
|
| 964 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 965 |
> |
make/Doxyfile, src/applications/getopt.c, |
| 966 |
> |
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
| 967 |
> |
build fixes |
| 968 |
> |
|
| 969 |
> |
2004-10-06 17:20 tim |
| 970 |
> |
|
| 971 |
> |
* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
| 972 |
> |
|
| 973 |
> |
2004-10-06 17:19 tim |
| 974 |
> |
|
| 975 |
> |
* scripts/filepp: filepp can handle different fortran module case |
| 976 |
> |
and suffix |
| 977 |
> |
|
| 978 |
> |
2004-10-06 16:27 gezelter |
| 979 |
> |
|
| 980 |
> |
* src/restraints/Restraints.cpp: Chris doesn't know about the |
| 981 |
> |
OOPSE-2.0 directory structure yet |
| 982 |
> |
|
| 983 |
> |
2004-10-06 16:27 gezelter |
| 984 |
> |
|
| 985 |
> |
* ChangeLog: Yeah yeah, we'lll get around to it later |
| 986 |
> |
|
| 987 |
> |
2004-10-06 16:22 gezelter |
| 988 |
> |
|
| 989 |
> |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 990 |
> |
make/Makefile.in: cleaning up build process |
| 991 |
> |
|
| 992 |
> |
2004-10-06 15:01 chrisfen |
| 993 |
> |
|
| 994 |
> |
* src/restraints/Restraints.cpp: made the file reading in |
| 995 |
> |
restraints more intelligent - no longer gives uninformative seg |
| 996 |
> |
faults |
| 997 |
> |
|
| 998 |
> |
2004-10-06 14:55 gezelter |
| 999 |
> |
|
| 1000 |
> |
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
| 1001 |
> |
|
| 1002 |
> |
2004-10-06 14:51 gezelter |
| 1003 |
> |
|
| 1004 |
> |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
| 1005 |
> |
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
| 1006 |
> |
|
| 1007 |
> |
2004-10-06 13:53 tim |
| 1008 |
> |
|
| 1009 |
> |
* make/: Makefile, Makefile.in: fix make statistics |
| 1010 |
> |
|
| 1011 |
> |
2004-10-06 13:18 tim |
| 1012 |
> |
|
| 1013 |
> |
* make/: Makefile, Makefile.in: adding GNU make functions to |
| 1014 |
> |
combine all of the static libraries to a big library |
| 1015 |
> |
|
| 1016 |
> |
2004-10-05 17:57 tim |
| 1017 |
> |
|
| 1018 |
> |
* make/: Makefile, Makefile.in: adding shared library flag |
| 1019 |
> |
|
| 1020 |
> |
2004-10-05 14:37 tim |
| 1021 |
> |
|
| 1022 |
> |
* src/: Makefile, UseTheForce/Makefile, |
| 1023 |
> |
UseTheForce/mpiSimulation_module.F90, |
| 1024 |
> |
UseTheForce/DarkSide/Makefile, |
| 1025 |
> |
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
| 1026 |
> |
mpiSimulation_module to DarkSide |
| 1027 |
> |
|
| 1028 |
> |
2004-10-05 14:35 tim |
| 1029 |
> |
|
| 1030 |
> |
* make/: Makefile, Makefile.in: building MPI version;using static |
| 1031 |
> |
library instead of shared library |
| 1032 |
> |
|
| 1033 |
> |
2004-10-05 09:14 tim |
| 1034 |
> |
|
| 1035 |
> |
* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
| 1036 |
> |
to filepp |
| 1037 |
> |
|
| 1038 |
> |
2004-10-04 15:56 tim |
| 1039 |
> |
|
| 1040 |
> |
* make/: Makefile, Makefile.in: add make cvslog |
| 1041 |
> |
|
| 1042 |
> |
2004-10-04 11:24 gezelter |
| 1043 |
> |
|
| 1044 |
> |
* make/: Makefile, Makefile.in: more work on the parallel build |
| 1045 |
> |
|
| 1046 |
> |
2004-10-04 11:06 gezelter |
| 1047 |
> |
|
| 1048 |
> |
* make/: Makefile, Makefile.in: changes to backport declare flags |
| 1049 |
> |
|
| 1050 |
> |
2004-10-04 10:27 gezelter |
| 1051 |
> |
|
| 1052 |
> |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
| 1053 |
> |
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
| 1054 |
> |
shapes |
| 1055 |
> |
|
| 1056 |
> |
2004-10-01 23:40 tim |
| 1057 |
> |
|
| 1058 |
> |
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
| 1059 |
> |
|
| 1060 |
> |
2004-10-01 23:22 tim |
| 1061 |
> |
|
| 1062 |
> |
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
| 1063 |
> |
|
| 1064 |
> |
2004-10-01 16:59 tim |
| 1065 |
> |
|
| 1066 |
> |
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
| 1067 |
> |
|
| 1068 |
> |
2004-10-01 16:22 gezelter |
| 1069 |
> |
|
| 1070 |
> |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
| 1071 |
> |
few minor build changes |
| 1072 |
> |
|
| 1073 |
> |
2004-10-01 16:11 tim |
| 1074 |
> |
|
| 1075 |
> |
* scripts/filepp: adding fortran90 make dependency tool |
| 1076 |
> |
|
| 1077 |
> |
2004-09-30 10:41 tim |
| 1078 |
> |
|
| 1079 |
> |
* make/: Makefile, Makefile.in: make clean is smart enough to only |
| 1080 |
> |
remove object files belong to current package. turn off silent |
| 1081 |
> |
mode |
| 1082 |
> |
|
| 1083 |
> |
2004-09-29 16:55 tim |
| 1084 |
> |
|
| 1085 |
> |
* src/: Makefile, UseTheForce/Makefile, |
| 1086 |
> |
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
| 1087 |
> |
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
| 1088 |
> |
brains/Makedepend, brains/Makefile, constraints/Makefile, |
| 1089 |
> |
integrators/Makefile, io/Makefile, math/Makefile, |
| 1090 |
> |
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
| 1091 |
> |
restraints/Makefile, types/Makefile, utils/Makefile, |
| 1092 |
> |
visitors/Makefile: define DEV_ROOT as relative path |
| 1093 |
> |
|
| 1094 |
> |
2004-09-29 16:54 tim |
| 1095 |
> |
|
| 1096 |
> |
* make/: Makefile, Makefile.in: get the relative path by shell |
| 1097 |
> |
script |
| 1098 |
> |
|
| 1099 |
> |
2004-09-29 16:32 tim |
| 1100 |
> |
|
| 1101 |
> |
* make/Makefile: eliminate DEV_ROOT by relative path |
| 1102 |
> |
|
| 1103 |
> |
2004-09-29 13:37 tim |
| 1104 |
> |
|
| 1105 |
> |
* make/Makefile.in: add PackageLibs; fix dependency rule |
| 1106 |
> |
|
| 1107 |
> |
2004-09-29 12:57 gezelter |
| 1108 |
> |
|
| 1109 |
> |
* configure, ac-tools/configure.in: updates |
| 1110 |
> |
|
| 1111 |
> |
2004-09-29 12:56 gezelter |
| 1112 |
> |
|
| 1113 |
> |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
| 1114 |
> |
|
| 1115 |
> |
2004-09-29 12:46 tim |
| 1116 |
> |
|
| 1117 |
> |
* Makefile: If makefile does not exist, print error message |
| 1118 |
> |
|
| 1119 |
> |
2004-09-29 12:12 tim |
| 1120 |
> |
|
| 1121 |
> |
* make/: Make.conf.in, Makefile: fix dependencies rule |
| 1122 |
> |
|
| 1123 |
> |
2004-09-29 10:58 gezelter |
| 1124 |
> |
|
| 1125 |
> |
* Makefile, make/Makefile: still working on build process |
| 1126 |
> |
|
| 1127 |
> |
2004-09-29 10:00 tim |
| 1128 |
> |
|
| 1129 |
> |
* make/Makefile: add print statment to rules |
| 1130 |
> |
|
| 1131 |
> |
2004-09-29 09:59 tim |
| 1132 |
> |
|
| 1133 |
> |
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
| 1134 |
> |
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
| 1135 |
> |
applications/simpleBuilder/Makefile, brains/Makefile, |
| 1136 |
> |
constraints/Makefile, integrators/Makefile, io/Makefile, |
| 1137 |
> |
math/Makefile, minimizers/Makefile, primitives/Makefile, |
| 1138 |
> |
profiling/Makefile, restraints/Makefile, types/Makefile, |
| 1139 |
> |
utils/Makefile, visitors/Makefile: change Makefile to relative path |
| 1140 |
> |
|
| 1141 |
> |
2004-09-28 21:55 tim |
| 1142 |
> |
|
| 1143 |
> |
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
| 1144 |
> |
which cause headache in bulding libutils |
| 1145 |
> |
|
| 1146 |
> |
2004-09-28 18:24 tim |
| 1147 |
> |
|
| 1148 |
> |
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
| 1149 |
> |
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
| 1150 |
> |
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
| 1151 |
> |
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
| 1152 |
> |
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
| 1153 |
> |
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
| 1154 |
> |
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
| 1155 |
> |
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
| 1156 |
> |
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
| 1157 |
> |
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
| 1158 |
> |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
| 1159 |
> |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
| 1160 |
> |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
| 1161 |
> |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
| 1162 |
> |
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
| 1163 |
> |
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
| 1164 |
> |
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
| 1165 |
> |
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
| 1166 |
> |
change directory structure of application. Every executable file is |
| 1167 |
> |
replaced in seperate directory |
| 1168 |
> |
|
| 1169 |
> |
2004-09-28 17:15 gezelter |
| 1170 |
> |
|
| 1171 |
> |
* lib/dummy: Keep that lib around, please. |
| 1172 |
> |
|
| 1173 |
> |
2004-09-28 17:14 gezelter |
| 1174 |
> |
|
| 1175 |
> |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
| 1176 |
> |
starting a configure version |
| 1177 |
> |
|
| 1178 |
> |
2004-09-28 16:08 tim |
| 1179 |
> |
|
| 1180 |
> |
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
| 1181 |
> |
UseTheForce/DarkSide/Makefile, |
| 1182 |
> |
UseTheForce/DarkSide/notifyCutoffs.F90, |
| 1183 |
> |
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
| 1184 |
> |
brains/Makefile, brains/simulation_module.F90: move fortran files |
| 1185 |
> |
around to solve dependency problem |
| 1186 |
> |
|
| 1187 |
> |
2004-09-28 15:43 tim |
| 1188 |
> |
|
| 1189 |
> |
* Makefile, src/UseTheForce/ForceFields.hpp, |
| 1190 |
> |
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
| 1191 |
> |
src/applications/Makedepend, src/applications/Makefile, |
| 1192 |
> |
src/brains/Makedepend, src/brains/simulation_module.F90, |
| 1193 |
> |
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
| 1194 |
> |
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
| 1195 |
> |
src/utils/Makefile: [no log message] |
| 1196 |
> |
|
| 1197 |
> |
2004-09-28 15:41 tim |
| 1198 |
> |
|
| 1199 |
> |
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
| 1200 |
> |
problem |
| 1201 |
> |
|
| 1202 |
> |
2004-09-28 11:13 tim |
| 1203 |
> |
|
| 1204 |
> |
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
| 1205 |
> |
src/io/Makefile: add yacc and lex rules |
| 1206 |
> |
|
| 1207 |
> |
2004-09-27 15:24 tim |
| 1208 |
> |
|
| 1209 |
> |
* make/Makefile: adding include path to F90Options |
| 1210 |
> |
|
| 1211 |
> |
2004-09-27 15:13 tim |
| 1212 |
> |
|
| 1213 |
> |
* make/Makefile: change suffix from .cc to .cpp |
| 1214 |
> |
|
| 1215 |
> |
2004-09-24 11:27 tim |
| 1216 |
> |
|
| 1217 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 1218 |
> |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 1219 |
> |
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
| 1220 |
> |
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
| 1221 |
> |
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
| 1222 |
> |
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
| 1223 |
> |
UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 1224 |
> |
UseTheForce/DarkSide/notifyCutoffs.F90, |
| 1225 |
> |
UseTheForce/DarkSide/switch_module.F90, |
| 1226 |
> |
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
| 1227 |
> |
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
| 1228 |
> |
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
| 1229 |
> |
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
| 1230 |
> |
applications/MoLocator.cpp, applications/MoLocator.hpp, |
| 1231 |
> |
applications/cmdline.c, applications/nanoBuilder.cpp, |
| 1232 |
> |
applications/oopse.cpp, applications/simpleBuilder.cpp, |
| 1233 |
> |
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
| 1234 |
> |
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 1235 |
> |
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
| 1236 |
> |
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 1237 |
> |
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
| 1238 |
> |
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
| 1239 |
> |
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
| 1240 |
> |
integrators/Integrator.hpp, integrators/NPT.cpp, |
| 1241 |
> |
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
| 1242 |
> |
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
| 1243 |
> |
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
| 1244 |
> |
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
| 1245 |
> |
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
| 1246 |
> |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
| 1247 |
> |
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
| 1248 |
> |
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
| 1249 |
> |
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
| 1250 |
> |
math/MatVec3.h, math/randomSPRNG.cpp, |
| 1251 |
> |
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
| 1252 |
> |
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
| 1253 |
> |
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
| 1254 |
> |
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
| 1255 |
> |
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
| 1256 |
> |
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
| 1257 |
> |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 1258 |
> |
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
| 1259 |
> |
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
| 1260 |
> |
primitives/RigidBody.hpp, primitives/SRI.hpp, |
| 1261 |
> |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
| 1262 |
> |
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
| 1263 |
> |
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
| 1264 |
> |
restraints/Restraints.hpp, types/AtomStamp.cpp, |
| 1265 |
> |
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
| 1266 |
> |
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
| 1267 |
> |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 1268 |
> |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
| 1269 |
> |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 1270 |
> |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
| 1271 |
> |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
| 1272 |
> |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
| 1273 |
> |
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
| 1274 |
> |
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
| 1275 |
> |
utils/simError.c, visitors/AtomVisitor.cpp, |
| 1276 |
> |
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
| 1277 |
> |
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
| 1278 |
> |
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 1279 |
> |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
| 1280 |
> |
visitors/ZconsVisitor.hpp: change the #include in source files |
| 1281 |
> |
|
| 1282 |
> |
2004-09-23 23:16 gezelter |
| 1283 |
> |
|
| 1284 |
> |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 1285 |
> |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
| 1286 |
> |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
| 1287 |
> |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
| 1288 |
> |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
| 1289 |
> |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
| 1290 |
> |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
| 1291 |
> |
src/UseTheForce/fForceField.h, |
| 1292 |
> |
src/UseTheForce/fSwitchingFunction.h, |
| 1293 |
> |
src/UseTheForce/fortranWrapDefines.hpp, |
| 1294 |
> |
src/UseTheForce/fortranWrappers.cpp, |
| 1295 |
> |
src/UseTheForce/fortranWrappers.hpp, |
| 1296 |
> |
src/UseTheForce/mpiComponentPlan.h, |
| 1297 |
> |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 1298 |
> |
src/UseTheForce/mpiSimulation_module.F90, |
| 1299 |
> |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
| 1300 |
> |
src/UseTheForce/DarkSide/atype_module.F90, |
| 1301 |
> |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 1302 |
> |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
| 1303 |
> |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
| 1304 |
> |
src/UseTheForce/DarkSide/calc_eam.F90, |
| 1305 |
> |
src/UseTheForce/DarkSide/calc_gb.F90, |
| 1306 |
> |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
| 1307 |
> |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
| 1308 |
> |
src/UseTheForce/DarkSide/force_globals.F90, |
| 1309 |
> |
src/UseTheForce/DarkSide/neighborLists.F90, |
| 1310 |
> |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
| 1311 |
> |
src/UseTheForce/DarkSide/switch_module.F90, |
| 1312 |
> |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 1313 |
> |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
| 1314 |
> |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
| 1315 |
> |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
| 1316 |
> |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 1317 |
> |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
| 1318 |
> |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 1319 |
> |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
| 1320 |
> |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
| 1321 |
> |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
| 1322 |
> |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
| 1323 |
> |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
| 1324 |
> |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
| 1325 |
> |
src/types/BondStamp.hpp, src/types/Component.cpp, |
| 1326 |
> |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
| 1327 |
> |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
| 1328 |
> |
src/types/MakeStamps.hpp, src/types/Makefile, |
| 1329 |
> |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
| 1330 |
> |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 1331 |
> |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 1332 |
> |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 1333 |
> |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
| 1334 |
> |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
| 1335 |
> |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
| 1336 |
> |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
| 1337 |
> |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
| 1338 |
> |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 1339 |
> |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
| 1340 |
> |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 1341 |
> |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 1342 |
> |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
| 1343 |
> |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
| 1344 |
> |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
| 1345 |
> |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
| 1346 |
> |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
| 1347 |
> |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
| 1348 |
> |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
| 1349 |
> |
src/minimizers/OOPSEMinimizer.cpp, |
| 1350 |
> |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 1351 |
> |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
| 1352 |
> |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 1353 |
> |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
| 1354 |
> |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
| 1355 |
> |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 1356 |
> |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 1357 |
> |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
| 1358 |
> |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
| 1359 |
> |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
| 1360 |
> |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
| 1361 |
> |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
| 1362 |
> |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
| 1363 |
> |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
| 1364 |
> |
src/utils/GenericData.hpp, src/utils/Makefile, |
| 1365 |
> |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
| 1366 |
> |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
| 1367 |
> |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
| 1368 |
> |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
| 1369 |
> |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
| 1370 |
> |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
| 1371 |
> |
src/utils/simError.c, src/utils/simError.h, |
| 1372 |
> |
src/utils/status_module.F90, src/utils/vector_class.F90, |
| 1373 |
> |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 1374 |
> |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 1375 |
> |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
| 1376 |
> |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 1377 |
> |
src/visitors/RigidBodyVisitor.cpp, |
| 1378 |
> |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 1379 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
| 1380 |
> |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 1381 |
> |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 1382 |
> |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 1383 |
> |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
| 1384 |
> |
samples/zcons/Makefile.in, samples/zcons/water.md, |
| 1385 |
> |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
| 1386 |
> |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
| 1387 |
> |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
| 1388 |
> |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
| 1389 |
> |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
| 1390 |
> |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
| 1391 |
> |
src/applications/LatticeCreator.cpp, |
| 1392 |
> |
src/applications/LatticeCreator.hpp, |
| 1393 |
> |
src/applications/LatticeFactory.cpp, |
| 1394 |
> |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
| 1395 |
> |
src/applications/Makefile, src/applications/MoLocator.cpp, |
| 1396 |
> |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
| 1397 |
> |
src/applications/cmdline.c, src/applications/cmdline.h, |
| 1398 |
> |
src/applications/getopt.c, src/applications/getopt1.c, |
| 1399 |
> |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
| 1400 |
> |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
| 1401 |
> |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
| 1402 |
> |
src/applications/simpleBuilder.ggo, |
| 1403 |
> |
src/applications/simpleBuilderCmd.c, |
| 1404 |
> |
src/integrators/AbstractClasses.hpp, |
| 1405 |
> |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
| 1406 |
> |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
| 1407 |
> |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 1408 |
> |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 1409 |
> |
src/integrators/NVT.cpp, src/profiling/Makefile, |
| 1410 |
> |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
| 1411 |
> |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
| 1412 |
> |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
| 1413 |
> |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
| 1414 |
> |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
| 1415 |
> |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
| 1416 |
> |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
| 1417 |
> |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
| 1418 |
> |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
| 1419 |
> |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
| 1420 |
> |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
| 1421 |
> |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
| 1422 |
> |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
| 1423 |
> |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
| 1424 |
> |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 1425 |
> |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 1426 |
> |
samples/alkane/butane.in, samples/alkane/butane.md, |
| 1427 |
> |
samples/argon/500.in, samples/argon/500.md, |
| 1428 |
> |
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 1429 |
> |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 1430 |
> |
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 1431 |
> |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 1432 |
> |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 1433 |
> |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
| 1434 |
> |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
| 1435 |
> |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
| 1436 |
> |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
| 1437 |
> |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
| 1438 |
> |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
| 1439 |
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
| 1440 |
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
| 1441 |
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
| 1442 |
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
| 1443 |
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
| 1444 |
< |
forceFields/LJFF.frc, forceFields/Makefile, |
| 1445 |
< |
forceFields/Makefile.in, forceFields/Ni.VC.funcfl, |
| 1446 |
< |
forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl, |
| 1447 |
< |
forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 1448 |
< |
forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl, |
| 1449 |
< |
forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl, |
| 1450 |
< |
forceFields/WATER.frc, libBASS/AtomStamp.cpp, |
| 1451 |
< |
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
| 1452 |
< |
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
| 1453 |
< |
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
| 1454 |
< |
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
| 1455 |
< |
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
| 357 |
< |
libBASS/Component.cpp, libBASS/Component.hpp, |
| 358 |
< |
libBASS/CutoffGroupStamp.cpp, libBASS/CutoffGroupStamp.hpp, |
| 359 |
< |
libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
| 360 |
< |
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
| 361 |
< |
libBASS/LinkedCommand.hpp, libBASS/Make.dep, |
| 362 |
< |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
| 363 |
< |
libBASS/Makefile.in, libBASS/MoleculeStamp.cpp, |
| 364 |
< |
libBASS/MoleculeStamp.hpp, libBASS/RigidBodyStamp.cpp, |
| 365 |
< |
libBASS/RigidBodyStamp.hpp, libBASS/TorsionStamp.cpp, |
| 366 |
< |
libBASS/TorsionStamp.hpp, libBASS/ZconStamp.cpp, |
| 367 |
< |
libBASS/ZconStamp.hpp, libBASS/config.h.in, libBASS/fError.c, |
| 368 |
< |
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
| 369 |
< |
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
| 370 |
< |
libBASS/parse_interface.h, libBASS/parse_me.h, |
| 371 |
< |
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
| 372 |
< |
libBASS/simError.h, libBASS/y.tab.h, libBASS/MPIobj/dummy, |
| 373 |
< |
libBASS/obj/dummy, libmdtools/AbstractClasses.hpp, |
| 374 |
< |
libmdtools/AllIntegrator.hpp, libmdtools/Atom.cpp, |
| 375 |
< |
libmdtools/Atom.hpp, libmdtools/AtomVisitor.cpp, |
| 376 |
< |
libmdtools/AtomVisitor.hpp, libmdtools/BaseVisitor.hpp, |
| 377 |
< |
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
| 378 |
< |
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
| 379 |
< |
libmdtools/CGFamilyMinimizer.cpp, libmdtools/CompositeVisitor.cpp, |
| 380 |
< |
libmdtools/CompositeVisitor.hpp, libmdtools/CutoffGroup.hpp, |
| 381 |
< |
libmdtools/DUFF.cpp, libmdtools/DirectionalAtom.cpp, |
| 382 |
< |
libmdtools/DirectionalAtom.hpp, libmdtools/DumpReader.cpp, |
| 383 |
< |
libmdtools/DumpWriter.cpp, libmdtools/EAM_FF.cpp, |
| 384 |
< |
libmdtools/Euler3.cpp, libmdtools/Euler3.hpp, |
| 385 |
< |
libmdtools/Exclude.cpp, libmdtools/Exclude.hpp, |
| 386 |
< |
libmdtools/ForceFields.cpp, libmdtools/ForceFields.hpp, |
| 387 |
< |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
| 388 |
< |
libmdtools/GhostBend.cpp, libmdtools/InitializeFromFile.cpp, |
| 389 |
< |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 390 |
< |
libmdtools/LJFF.cpp, libmdtools/Make.dep, libmdtools/Makefile, |
| 391 |
< |
libmdtools/Makefile.in, libmdtools/MatVec3.c, libmdtools/MatVec3.h, |
| 392 |
< |
libmdtools/MinimizerParameterSet.hpp, libmdtools/Molecule.cpp, |
| 393 |
< |
libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
| 394 |
< |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
| 395 |
< |
libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, |
| 396 |
< |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
| 397 |
< |
libmdtools/PRCG.cpp, libmdtools/ReadWrite.hpp, |
| 398 |
< |
libmdtools/Restraints.cpp, libmdtools/Restraints.hpp, |
| 399 |
< |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
| 400 |
< |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
| 401 |
< |
libmdtools/SDMinimizer.cpp, libmdtools/SRI.hpp, |
| 402 |
< |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 403 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 404 |
< |
libmdtools/SimState.cpp, libmdtools/SimState.hpp, |
| 405 |
< |
libmdtools/SkipList.cpp, libmdtools/SkipList.hpp, |
| 406 |
< |
libmdtools/StatWriter.cpp, libmdtools/StreamTokenizer.cpp, |
| 407 |
< |
libmdtools/StreamTokenizer.hpp, libmdtools/StringUtils.c, |
| 408 |
< |
libmdtools/StringUtils.h, libmdtools/StuntDouble.cpp, |
| 409 |
< |
libmdtools/StuntDouble.hpp, libmdtools/Thermo.cpp, |
| 410 |
< |
libmdtools/Thermo.hpp, libmdtools/Torsion.cpp, |
| 411 |
< |
libmdtools/TorsionExtensions.cpp, libmdtools/TypeInfo.hpp, |
| 412 |
< |
libmdtools/Utility.cpp, libmdtools/Utility.hpp, |
| 413 |
< |
libmdtools/WATER.cpp, libmdtools/ZConsReader.cpp, |
| 414 |
< |
libmdtools/ZConsReader.hpp, libmdtools/ZConsWriter.cpp, |
| 415 |
< |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp, |
| 416 |
< |
libmdtools/ZconsVisitor.cpp, libmdtools/ZconsVisitor.hpp, |
| 417 |
< |
libmdtools/atype_module.F90, libmdtools/calc_LJ_FF.F90, |
| 418 |
< |
libmdtools/calc_charge_charge.F90, |
| 419 |
< |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, |
| 420 |
< |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
| 421 |
< |
libmdtools/calc_sticky_pair.F90, libmdtools/config.h.in, |
| 422 |
< |
libmdtools/definitions_module.F90, libmdtools/do_Forces.F90, |
| 423 |
< |
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
| 424 |
< |
libmdtools/fSwitchingFunction.h, libmdtools/forceFactory.hpp, |
| 425 |
< |
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
| 426 |
< |
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
| 427 |
< |
libmdtools/mdProfile.cpp, libmdtools/mdProfile.hpp, |
| 428 |
< |
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
| 429 |
< |
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
| 430 |
< |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 431 |
< |
libmdtools/neighborLists.F90, libmdtools/notifyCutoffs.F90, |
| 432 |
< |
libmdtools/oopseMPI_module.F90, libmdtools/randomSPRNG.cpp, |
| 433 |
< |
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
| 434 |
< |
libmdtools/status_module.F90, libmdtools/switch_module.F90, |
| 435 |
< |
libmdtools/timing.F90, libmdtools/vector_class.F90, |
| 436 |
< |
libmdtools/wrappers.F90, libmdtools/MPIobj/dummy, |
| 437 |
< |
libmdtools/obj/dummy, samples/Makefile, samples/Makefile.in, |
| 438 |
< |
samples/alkane/Makefile, samples/alkane/Makefile.in, |
| 439 |
< |
samples/alkane/alkanes.mdl, samples/alkane/butane.bass, |
| 440 |
< |
samples/alkane/butane.eor, samples/alkane/init_butane.eor, |
| 441 |
< |
samples/argon/500.bass, samples/argon/500.eor, |
| 442 |
< |
samples/argon/500.in, samples/argon/Makefile, |
| 443 |
< |
samples/argon/Makefile.in, samples/argon/NVT.bass, |
| 444 |
< |
samples/argon/ar864.bass, samples/argon/ar864.eor, |
| 445 |
< |
samples/argon/ar864.in, samples/argon/argon.bass, |
| 446 |
< |
samples/argon/argon.eor, samples/argon/argonEM.bass, |
| 447 |
< |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
| 448 |
< |
samples/argon/machines, samples/lipid/5x5.bass, |
| 449 |
< |
samples/lipid/5x5.eor, samples/lipid/Makefile, |
| 450 |
< |
samples/lipid/Makefile.in, samples/lipid/init_5x5.eor, |
| 451 |
< |
samples/lipid/lipid.mdl, samples/lipid/water.mdl, |
| 452 |
< |
samples/metals/Au.bass, samples/metals/Au.eor, |
| 453 |
< |
samples/metals/Makefile, samples/metals/Makefile.in, |
| 454 |
< |
samples/metals/init_au.in, samples/metals/metals.mdl, |
| 455 |
< |
samples/water/200.in, samples/water/Makefile, |
| 456 |
< |
samples/water/Makefile.in, samples/water/init_ssd.eor, |
| 457 |
< |
samples/water/spce.bass, samples/water/spce.eor, |
| 458 |
< |
samples/water/ssd.bass, samples/water/ssd.eor, |
| 459 |
< |
samples/water/tim.bass, samples/water/tim.eor, |
| 460 |
< |
samples/water/tim.init, samples/water/tim.xyz, |
| 461 |
< |
samples/water/tip3p.bass, samples/water/tip3p.eor, |
| 462 |
< |
samples/water/tip3p.init, samples/water/two.bass, |
| 463 |
< |
samples/water/two.eor, samples/water/two.init, |
| 464 |
< |
samples/water/two.xyz, samples/water/water.mdl, |
| 465 |
< |
samples/water/spce/SPCEinit.in, samples/water/spce/spce.bass, |
| 466 |
< |
samples/water/spce/water.mdl, samples/water/ssde/256init.in, |
| 467 |
< |
samples/water/ssde/ssde.bass, samples/water/ssde/water.mdl, |
| 468 |
< |
samples/water/tip4p/TP4init.in, samples/water/tip4p/tp4.bass, |
| 469 |
< |
samples/water/tip4p/water.mdl, scripts/cleanSrc, scripts/cvs2cl.pl, |
| 470 |
< |
scripts/sfmakedepend, src/Make.dep, src/Makefile, src/Makefile.in, |
| 471 |
< |
src/oopse.cpp, src/oose.cpp, src/MPIobj/dummy, src/obj/dummy, |
| 472 |
< |
third-party/Makefile, third-party/Makefile.in, |
| 473 |
< |
third-party/mt19937ar.c, utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, |
| 474 |
< |
utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h, utils/Make.dep, |
| 475 |
< |
utils/Makefile, utils/Makefile.in, utils/quickLate.c, utils/zsub, |
| 476 |
< |
utils/MPIobj/placeHolder, utils/obj/placeHolder, |
| 477 |
< |
utils/sysbuilder/Make.dep, utils/sysbuilder/Makefile, |
| 478 |
< |
utils/sysbuilder/Makefile.in, utils/sysbuilder/MoLocator.cpp, |
| 479 |
< |
utils/sysbuilder/MoLocator.hpp, utils/sysbuilder/cmdline.c, |
| 480 |
< |
utils/sysbuilder/cmdline.h, utils/sysbuilder/latticeBilayer.cpp, |
| 481 |
< |
utils/sysbuilder/latticeBuilder.cpp, |
| 482 |
< |
utils/sysbuilder/latticeBuilder.hpp, |
| 483 |
< |
utils/sysbuilder/nanoBuilder.cpp, utils/sysbuilder/nanoBuilder.hpp, |
| 484 |
< |
utils/sysbuilder/randomBilayer.cpp, utils/sysbuilder/sysBuild.cpp, |
| 485 |
< |
utils/sysbuilder/sysBuild.ggo, utils/sysbuilder/sysBuild.hpp, |
| 486 |
< |
utils/sysbuilder/MPIobj/placeHolder, |
| 487 |
< |
utils/sysbuilder/obj/placeHolder: Initial import of OOPSE-1.0 |
| 488 |
< |
source tree |
| 1444 |
> |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
| 1445 |
> |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
| 1446 |
> |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
| 1447 |
> |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
| 1448 |
> |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
| 1449 |
> |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 1450 |
> |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 1451 |
> |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
| 1452 |
> |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
| 1453 |
> |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
| 1454 |
> |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 1455 |
> |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
| 1456 |
|
|
| 1457 |
< |
2004-07-16 13:57 gezelter |
| 1457 |
> |
2004-09-23 23:16 gezelter |
| 1458 |
|
|
| 1459 |
< |
* AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README, |
| 1460 |
< |
configure, ac-tools/Make.conf.in, ac-tools/aclocal.m4, |
| 1461 |
< |
ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in, |
| 1462 |
< |
ac-tools/fortran90.m4, ac-tools/install-sh, ac-tools/shtool, |
| 1463 |
< |
forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl, |
| 1464 |
< |
forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl, |
| 1465 |
< |
forceFields/Au.VC.funcfl, forceFields/Au.u3.funcfl, |
| 1459 |
> |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 1460 |
> |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
| 1461 |
> |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
| 1462 |
> |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
| 1463 |
> |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
| 1464 |
> |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
| 1465 |
> |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
| 1466 |
> |
src/UseTheForce/fForceField.h, |
| 1467 |
> |
src/UseTheForce/fSwitchingFunction.h, |
| 1468 |
> |
src/UseTheForce/fortranWrapDefines.hpp, |
| 1469 |
> |
src/UseTheForce/fortranWrappers.cpp, |
| 1470 |
> |
src/UseTheForce/fortranWrappers.hpp, |
| 1471 |
> |
src/UseTheForce/mpiComponentPlan.h, |
| 1472 |
> |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 1473 |
> |
src/UseTheForce/mpiSimulation_module.F90, |
| 1474 |
> |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
| 1475 |
> |
src/UseTheForce/DarkSide/atype_module.F90, |
| 1476 |
> |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 1477 |
> |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
| 1478 |
> |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
| 1479 |
> |
src/UseTheForce/DarkSide/calc_eam.F90, |
| 1480 |
> |
src/UseTheForce/DarkSide/calc_gb.F90, |
| 1481 |
> |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
| 1482 |
> |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
| 1483 |
> |
src/UseTheForce/DarkSide/force_globals.F90, |
| 1484 |
> |
src/UseTheForce/DarkSide/neighborLists.F90, |
| 1485 |
> |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
| 1486 |
> |
src/UseTheForce/DarkSide/switch_module.F90, |
| 1487 |
> |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 1488 |
> |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
| 1489 |
> |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
| 1490 |
> |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
| 1491 |
> |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 1492 |
> |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
| 1493 |
> |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 1494 |
> |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
| 1495 |
> |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
| 1496 |
> |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
| 1497 |
> |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
| 1498 |
> |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
| 1499 |
> |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
| 1500 |
> |
src/types/BondStamp.hpp, src/types/Component.cpp, |
| 1501 |
> |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
| 1502 |
> |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
| 1503 |
> |
src/types/MakeStamps.hpp, src/types/Makefile, |
| 1504 |
> |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
| 1505 |
> |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 1506 |
> |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 1507 |
> |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 1508 |
> |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
| 1509 |
> |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
| 1510 |
> |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
| 1511 |
> |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
| 1512 |
> |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
| 1513 |
> |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 1514 |
> |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
| 1515 |
> |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 1516 |
> |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 1517 |
> |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
| 1518 |
> |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
| 1519 |
> |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
| 1520 |
> |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
| 1521 |
> |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
| 1522 |
> |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
| 1523 |
> |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
| 1524 |
> |
src/minimizers/OOPSEMinimizer.cpp, |
| 1525 |
> |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 1526 |
> |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
| 1527 |
> |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 1528 |
> |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
| 1529 |
> |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
| 1530 |
> |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 1531 |
> |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 1532 |
> |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
| 1533 |
> |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
| 1534 |
> |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
| 1535 |
> |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
| 1536 |
> |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
| 1537 |
> |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
| 1538 |
> |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
| 1539 |
> |
src/utils/GenericData.hpp, src/utils/Makefile, |
| 1540 |
> |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
| 1541 |
> |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
| 1542 |
> |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
| 1543 |
> |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
| 1544 |
> |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
| 1545 |
> |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
| 1546 |
> |
src/utils/simError.c, src/utils/simError.h, |
| 1547 |
> |
src/utils/status_module.F90, src/utils/vector_class.F90, |
| 1548 |
> |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 1549 |
> |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 1550 |
> |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
| 1551 |
> |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 1552 |
> |
src/visitors/RigidBodyVisitor.cpp, |
| 1553 |
> |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 1554 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
| 1555 |
> |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 1556 |
> |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 1557 |
> |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 1558 |
> |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
| 1559 |
> |
samples/zcons/Makefile.in, samples/zcons/water.md, |
| 1560 |
> |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
| 1561 |
> |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
| 1562 |
> |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
| 1563 |
> |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
| 1564 |
> |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
| 1565 |
> |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
| 1566 |
> |
src/applications/LatticeCreator.cpp, |
| 1567 |
> |
src/applications/LatticeCreator.hpp, |
| 1568 |
> |
src/applications/LatticeFactory.cpp, |
| 1569 |
> |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
| 1570 |
> |
src/applications/Makefile, src/applications/MoLocator.cpp, |
| 1571 |
> |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
| 1572 |
> |
src/applications/cmdline.c, src/applications/cmdline.h, |
| 1573 |
> |
src/applications/getopt.c, src/applications/getopt1.c, |
| 1574 |
> |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
| 1575 |
> |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
| 1576 |
> |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
| 1577 |
> |
src/applications/simpleBuilder.ggo, |
| 1578 |
> |
src/applications/simpleBuilderCmd.c, |
| 1579 |
> |
src/integrators/AbstractClasses.hpp, |
| 1580 |
> |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
| 1581 |
> |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
| 1582 |
> |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 1583 |
> |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 1584 |
> |
src/integrators/NVT.cpp, src/profiling/Makefile, |
| 1585 |
> |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
| 1586 |
> |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
| 1587 |
> |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
| 1588 |
> |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
| 1589 |
> |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
| 1590 |
> |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
| 1591 |
> |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
| 1592 |
> |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
| 1593 |
> |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
| 1594 |
> |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
| 1595 |
> |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
| 1596 |
> |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
| 1597 |
> |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
| 1598 |
> |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
| 1599 |
> |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 1600 |
> |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 1601 |
> |
samples/alkane/butane.in, samples/alkane/butane.md, |
| 1602 |
> |
samples/argon/500.in, samples/argon/500.md, |
| 1603 |
> |
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 1604 |
> |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 1605 |
> |
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 1606 |
> |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 1607 |
> |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 1608 |
> |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
| 1609 |
> |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
| 1610 |
> |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
| 1611 |
> |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
| 1612 |
> |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
| 1613 |
> |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
| 1614 |
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
| 1615 |
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
| 1616 |
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
| 1617 |
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
| 1618 |
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
| 1619 |
< |
forceFields/LJFF.frc, forceFields/Makefile, |
| 1620 |
< |
forceFields/Makefile.in, forceFields/Ni.VC.funcfl, |
| 1621 |
< |
forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl, |
| 1622 |
< |
forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 1623 |
< |
forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl, |
| 1624 |
< |
forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl, |
| 1625 |
< |
forceFields/WATER.frc, libBASS/AtomStamp.cpp, |
| 1626 |
< |
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
| 1627 |
< |
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
| 1628 |
< |
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
| 1629 |
< |
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
| 1630 |
< |
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
| 516 |
< |
libBASS/Component.cpp, libBASS/Component.hpp, |
| 517 |
< |
libBASS/CutoffGroupStamp.cpp, libBASS/CutoffGroupStamp.hpp, |
| 518 |
< |
libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
| 519 |
< |
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
| 520 |
< |
libBASS/LinkedCommand.hpp, libBASS/Make.dep, |
| 521 |
< |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
| 522 |
< |
libBASS/Makefile.in, libBASS/MoleculeStamp.cpp, |
| 523 |
< |
libBASS/MoleculeStamp.hpp, libBASS/RigidBodyStamp.cpp, |
| 524 |
< |
libBASS/RigidBodyStamp.hpp, libBASS/TorsionStamp.cpp, |
| 525 |
< |
libBASS/TorsionStamp.hpp, libBASS/ZconStamp.cpp, |
| 526 |
< |
libBASS/ZconStamp.hpp, libBASS/config.h.in, libBASS/fError.c, |
| 527 |
< |
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
| 528 |
< |
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
| 529 |
< |
libBASS/parse_interface.h, libBASS/parse_me.h, |
| 530 |
< |
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
| 531 |
< |
libBASS/simError.h, libBASS/y.tab.h, libBASS/MPIobj/dummy, |
| 532 |
< |
libBASS/obj/dummy, libmdtools/AbstractClasses.hpp, |
| 533 |
< |
libmdtools/AllIntegrator.hpp, libmdtools/Atom.cpp, |
| 534 |
< |
libmdtools/Atom.hpp, libmdtools/AtomVisitor.cpp, |
| 535 |
< |
libmdtools/AtomVisitor.hpp, libmdtools/BaseVisitor.hpp, |
| 536 |
< |
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
| 537 |
< |
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
| 538 |
< |
libmdtools/CGFamilyMinimizer.cpp, libmdtools/CompositeVisitor.cpp, |
| 539 |
< |
libmdtools/CompositeVisitor.hpp, libmdtools/CutoffGroup.hpp, |
| 540 |
< |
libmdtools/DUFF.cpp, libmdtools/DirectionalAtom.cpp, |
| 541 |
< |
libmdtools/DirectionalAtom.hpp, libmdtools/DumpReader.cpp, |
| 542 |
< |
libmdtools/DumpWriter.cpp, libmdtools/EAM_FF.cpp, |
| 543 |
< |
libmdtools/Euler3.cpp, libmdtools/Euler3.hpp, |
| 544 |
< |
libmdtools/Exclude.cpp, libmdtools/Exclude.hpp, |
| 545 |
< |
libmdtools/ForceFields.cpp, libmdtools/ForceFields.hpp, |
| 546 |
< |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
| 547 |
< |
libmdtools/GhostBend.cpp, libmdtools/InitializeFromFile.cpp, |
| 548 |
< |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 549 |
< |
libmdtools/LJFF.cpp, libmdtools/Make.dep, libmdtools/Makefile, |
| 550 |
< |
libmdtools/Makefile.in, libmdtools/MatVec3.c, libmdtools/MatVec3.h, |
| 551 |
< |
libmdtools/MinimizerParameterSet.hpp, libmdtools/Molecule.cpp, |
| 552 |
< |
libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
| 553 |
< |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
| 554 |
< |
libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, |
| 555 |
< |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
| 556 |
< |
libmdtools/PRCG.cpp, libmdtools/ReadWrite.hpp, |
| 557 |
< |
libmdtools/Restraints.cpp, libmdtools/Restraints.hpp, |
| 558 |
< |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
| 559 |
< |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
| 560 |
< |
libmdtools/SDMinimizer.cpp, libmdtools/SRI.hpp, |
| 561 |
< |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 562 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 563 |
< |
libmdtools/SimState.cpp, libmdtools/SimState.hpp, |
| 564 |
< |
libmdtools/SkipList.cpp, libmdtools/SkipList.hpp, |
| 565 |
< |
libmdtools/StatWriter.cpp, libmdtools/StreamTokenizer.cpp, |
| 566 |
< |
libmdtools/StreamTokenizer.hpp, libmdtools/StringUtils.c, |
| 567 |
< |
libmdtools/StringUtils.h, libmdtools/StuntDouble.cpp, |
| 568 |
< |
libmdtools/StuntDouble.hpp, libmdtools/Thermo.cpp, |
| 569 |
< |
libmdtools/Thermo.hpp, libmdtools/Torsion.cpp, |
| 570 |
< |
libmdtools/TorsionExtensions.cpp, libmdtools/TypeInfo.hpp, |
| 571 |
< |
libmdtools/Utility.cpp, libmdtools/Utility.hpp, |
| 572 |
< |
libmdtools/WATER.cpp, libmdtools/ZConsReader.cpp, |
| 573 |
< |
libmdtools/ZConsReader.hpp, libmdtools/ZConsWriter.cpp, |
| 574 |
< |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp, |
| 575 |
< |
libmdtools/ZconsVisitor.cpp, libmdtools/ZconsVisitor.hpp, |
| 576 |
< |
libmdtools/atype_module.F90, libmdtools/calc_LJ_FF.F90, |
| 577 |
< |
libmdtools/calc_charge_charge.F90, |
| 578 |
< |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, |
| 579 |
< |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
| 580 |
< |
libmdtools/calc_sticky_pair.F90, libmdtools/config.h.in, |
| 581 |
< |
libmdtools/definitions_module.F90, libmdtools/do_Forces.F90, |
| 582 |
< |
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
| 583 |
< |
libmdtools/fSwitchingFunction.h, libmdtools/forceFactory.hpp, |
| 584 |
< |
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
| 585 |
< |
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
| 586 |
< |
libmdtools/mdProfile.cpp, libmdtools/mdProfile.hpp, |
| 587 |
< |
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
| 588 |
< |
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
| 589 |
< |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 590 |
< |
libmdtools/neighborLists.F90, libmdtools/notifyCutoffs.F90, |
| 591 |
< |
libmdtools/oopseMPI_module.F90, libmdtools/randomSPRNG.cpp, |
| 592 |
< |
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
| 593 |
< |
libmdtools/status_module.F90, libmdtools/switch_module.F90, |
| 594 |
< |
libmdtools/timing.F90, libmdtools/vector_class.F90, |
| 595 |
< |
libmdtools/wrappers.F90, libmdtools/MPIobj/dummy, |
| 596 |
< |
libmdtools/obj/dummy, samples/Makefile, samples/Makefile.in, |
| 597 |
< |
samples/alkane/Makefile, samples/alkane/Makefile.in, |
| 598 |
< |
samples/alkane/alkanes.mdl, samples/alkane/butane.bass, |
| 599 |
< |
samples/alkane/butane.eor, samples/alkane/init_butane.eor, |
| 600 |
< |
samples/argon/500.bass, samples/argon/500.eor, |
| 601 |
< |
samples/argon/500.in, samples/argon/Makefile, |
| 602 |
< |
samples/argon/Makefile.in, samples/argon/NVT.bass, |
| 603 |
< |
samples/argon/ar864.bass, samples/argon/ar864.eor, |
| 604 |
< |
samples/argon/ar864.in, samples/argon/argon.bass, |
| 605 |
< |
samples/argon/argon.eor, samples/argon/argonEM.bass, |
| 606 |
< |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
| 607 |
< |
samples/argon/machines, samples/lipid/5x5.bass, |
| 608 |
< |
samples/lipid/5x5.eor, samples/lipid/Makefile, |
| 609 |
< |
samples/lipid/Makefile.in, samples/lipid/init_5x5.eor, |
| 610 |
< |
samples/lipid/lipid.mdl, samples/lipid/water.mdl, |
| 611 |
< |
samples/metals/Au.bass, samples/metals/Au.eor, |
| 612 |
< |
samples/metals/Makefile, samples/metals/Makefile.in, |
| 613 |
< |
samples/metals/init_au.in, samples/metals/metals.mdl, |
| 614 |
< |
samples/water/200.in, samples/water/Makefile, |
| 615 |
< |
samples/water/Makefile.in, samples/water/init_ssd.eor, |
| 616 |
< |
samples/water/spce.bass, samples/water/spce.eor, |
| 617 |
< |
samples/water/ssd.bass, samples/water/ssd.eor, |
| 618 |
< |
samples/water/tim.bass, samples/water/tim.eor, |
| 619 |
< |
samples/water/tim.init, samples/water/tim.xyz, |
| 620 |
< |
samples/water/tip3p.bass, samples/water/tip3p.eor, |
| 621 |
< |
samples/water/tip3p.init, samples/water/two.bass, |
| 622 |
< |
samples/water/two.eor, samples/water/two.init, |
| 623 |
< |
samples/water/two.xyz, samples/water/water.mdl, |
| 624 |
< |
samples/water/spce/SPCEinit.in, samples/water/spce/spce.bass, |
| 625 |
< |
samples/water/spce/water.mdl, samples/water/ssde/256init.in, |
| 626 |
< |
samples/water/ssde/ssde.bass, samples/water/ssde/water.mdl, |
| 627 |
< |
samples/water/tip4p/TP4init.in, samples/water/tip4p/tp4.bass, |
| 628 |
< |
samples/water/tip4p/water.mdl, scripts/cleanSrc, scripts/cvs2cl.pl, |
| 629 |
< |
scripts/sfmakedepend, src/Make.dep, src/Makefile, src/Makefile.in, |
| 630 |
< |
src/oopse.cpp, src/oose.cpp, src/MPIobj/dummy, src/obj/dummy, |
| 631 |
< |
third-party/Makefile, third-party/Makefile.in, |
| 632 |
< |
third-party/mt19937ar.c, utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, |
| 633 |
< |
utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h, utils/Make.dep, |
| 634 |
< |
utils/Makefile, utils/Makefile.in, utils/quickLate.c, utils/zsub, |
| 635 |
< |
utils/MPIobj/placeHolder, utils/obj/placeHolder, |
| 636 |
< |
utils/sysbuilder/Make.dep, utils/sysbuilder/Makefile, |
| 637 |
< |
utils/sysbuilder/Makefile.in, utils/sysbuilder/MoLocator.cpp, |
| 638 |
< |
utils/sysbuilder/MoLocator.hpp, utils/sysbuilder/cmdline.c, |
| 639 |
< |
utils/sysbuilder/cmdline.h, utils/sysbuilder/latticeBilayer.cpp, |
| 640 |
< |
utils/sysbuilder/latticeBuilder.cpp, |
| 641 |
< |
utils/sysbuilder/latticeBuilder.hpp, |
| 642 |
< |
utils/sysbuilder/nanoBuilder.cpp, utils/sysbuilder/nanoBuilder.hpp, |
| 643 |
< |
utils/sysbuilder/randomBilayer.cpp, utils/sysbuilder/sysBuild.cpp, |
| 644 |
< |
utils/sysbuilder/sysBuild.ggo, utils/sysbuilder/sysBuild.hpp, |
| 645 |
< |
utils/sysbuilder/MPIobj/placeHolder, |
| 646 |
< |
utils/sysbuilder/obj/placeHolder: Initial revision |
| 1619 |
> |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
| 1620 |
> |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
| 1621 |
> |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
| 1622 |
> |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
| 1623 |
> |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
| 1624 |
> |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 1625 |
> |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 1626 |
> |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
| 1627 |
> |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
| 1628 |
> |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
| 1629 |
> |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 1630 |
> |
forceFields/Pt.VC.funcfl: Initial revision |
| 1631 |
|
|
