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2004-11-04 21:56 tim |
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* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
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primitives/Molecule.hpp: Pain...... |
| 5 |
|
| 6 |
2004-11-04 15:55 tim |
| 7 |
|
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* ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, |
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src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, |
| 10 |
src/brains/Stats.hpp: time to break SimSetup |
| 11 |
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| 12 |
2004-11-04 15:51 gezelter |
| 13 |
|
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* src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new |
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classes in progress |
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2004-11-04 14:48 tim |
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|
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* src/brains/Stats.cpp: file Stats.cpp was initially added on |
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branch new_design. |
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2004-11-04 14:48 tim |
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* src/brains/Stats.hpp: file Stats.hpp was initially added on |
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branch new_design. |
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2004-11-04 14:48 tim |
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|
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* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
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SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
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class |
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| 33 |
2004-11-04 11:22 gezelter |
| 34 |
|
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* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
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RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and |
| 37 |
linearAxis are virtual in StuntDouble, but are implemented by |
| 38 |
DirectionalAtom and RigidBody In StuntDouble, they should return |
| 39 |
false and "-1" but there should be logic to figure them out in the |
| 40 |
other two classes |
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|
| 42 |
2004-11-04 11:20 gezelter |
| 43 |
|
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* src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't |
| 45 |
remember what I did |
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| 47 |
2004-11-04 11:20 gezelter |
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* src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky |
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| 51 |
2004-11-04 11:20 gezelter |
| 52 |
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* src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX |
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in the entry_plug so that it only is set if the atoms really are in |
| 55 |
the simulation |
| 56 |
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| 57 |
2004-11-04 11:20 gezelter |
| 58 |
|
| 59 |
* samples/water/ssd/ssd.md: testing force fields |
| 60 |
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| 61 |
2004-11-04 11:19 gezelter |
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* samples/shape/linear.in: testing shapes |
| 64 |
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| 65 |
2004-11-03 14:56 tim |
| 66 |
|
| 67 |
* src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator |
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class(similar as SimSetup) |
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|
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2004-11-03 14:56 tim |
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|
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* src/brains/SimCreator.hpp: file SimCreator.hpp was initially |
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added on branch new_design. |
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2004-11-03 14:56 tim |
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|
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* src/brains/SimCreator.cpp: file SimCreator.cpp was initially |
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added on branch new_design. |
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| 80 |
2004-11-03 13:00 tim |
| 81 |
|
| 82 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 83 |
UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, |
| 84 |
UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp, |
| 85 |
brains/DataStorage.hpp, primitives/Atom.hpp, |
| 86 |
primitives/DirectionalAtom.hpp, restraints/Restraints.hpp, |
| 87 |
visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get |
| 88 |
compiled. Still a long way to go ...... |
| 89 |
|
| 90 |
2004-11-03 11:08 tim |
| 91 |
|
| 92 |
* ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
| 93 |
src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, |
| 94 |
src/integrators/NPTf.cpp, src/integrators/NPTi.cpp, |
| 95 |
src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp, |
| 96 |
src/io/ZConsReader.cpp, src/primitives/Bend.cpp, |
| 97 |
src/primitives/Bond.cpp, src/primitives/GhostBend.cpp, |
| 98 |
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
| 99 |
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
| 100 |
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
| 101 |
src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp, |
| 102 |
src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, |
| 103 |
src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... |
| 104 |
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| 105 |
2004-11-02 17:41 tim |
| 106 |
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| 107 |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
| 108 |
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
| 109 |
Need unit test |
| 110 |
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| 111 |
2004-11-02 17:41 tim |
| 112 |
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| 113 |
* src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was |
| 114 |
initially added on branch new_design. |
| 115 |
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| 116 |
2004-11-02 17:41 tim |
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|
| 118 |
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
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branch new_design. |
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2004-11-02 11:59 tim |
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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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| 126 |
2004-11-02 11:59 tim |
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* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
| 129 |
SimSnapshotManager.hpp: SimModel in progress |
| 130 |
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| 131 |
2004-11-02 10:28 chrisfen |
| 132 |
|
| 133 |
* src/: UseTheForce/DarkSide/shapes.F90, |
| 134 |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes |
| 135 |
looks like it's working |
| 136 |
|
| 137 |
2004-11-02 10:27 tim |
| 138 |
|
| 139 |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
| 140 |
functions for dealing with memory issue |
| 141 |
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| 142 |
2004-11-02 10:27 tim |
| 143 |
|
| 144 |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
| 145 |
added on branch new_design. |
| 146 |
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| 147 |
2004-11-02 10:23 tim |
| 148 |
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| 149 |
* src/: brains/SimModel.hpp, brains/Snapshot.hpp, |
| 150 |
brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding |
| 151 |
SimModel(something similar as SimInfo) |
| 152 |
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| 153 |
2004-11-01 17:52 tim |
| 154 |
|
| 155 |
* src/: applications/simpleBuilder/MoLocator.hpp, |
| 156 |
applications/simpleBuilder/simpleBuilder.cpp, |
| 157 |
brains/DataStorage.hpp, brains/ForceFields.cpp, |
| 158 |
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp, |
| 159 |
constraints/ZConstraint.cpp, integrators/Integrator.cpp, |
| 160 |
integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp, |
| 161 |
math/SquareMatrix3.hpp, math/Vector3.hpp, |
| 162 |
minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp, |
| 163 |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
| 164 |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
| 165 |
primitives/RigidBody.hpp, primitives/Torsion.hpp, |
| 166 |
restraints/Restraints.cpp, types/TorsionType.hpp, |
| 167 |
utils/PropertyMap.hpp, utils/StringTokenizer.hpp, |
| 168 |
visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp, |
| 169 |
visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, |
| 170 |
RigidBody and StuntDouble classes get compiled |
| 171 |
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| 172 |
2004-11-01 16:40 tim |
| 173 |
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| 174 |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
| 175 |
on branch new_design. |
| 176 |
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| 177 |
2004-11-01 16:40 tim |
| 178 |
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| 179 |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
| 180 |
branch new_design. |
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| 182 |
2004-11-01 16:40 tim |
| 183 |
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| 184 |
* src/primitives/Bond.hpp: file Bond.hpp was initially added on |
| 185 |
branch new_design. |
| 186 |
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| 187 |
2004-11-01 16:40 tim |
| 188 |
|
| 189 |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
| 190 |
version of Bond, Bend and Torsion. |
| 191 |
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| 192 |
2004-11-01 16:37 tim |
| 193 |
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| 194 |
* src/types/BendType.hpp: file BendType.hpp was initially added on |
| 195 |
branch new_design. |
| 196 |
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| 197 |
2004-11-01 16:37 tim |
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| 199 |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
| 200 |
BondType, BendType, TorsionType |
| 201 |
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| 202 |
2004-11-01 16:37 tim |
| 203 |
|
| 204 |
* src/types/TorsionType.hpp: file TorsionType.hpp was initially |
| 205 |
added on branch new_design. |
| 206 |
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| 207 |
2004-11-01 16:37 tim |
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| 209 |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
| 210 |
branch new_design. |
| 211 |
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| 212 |
2004-11-01 15:15 tim |
| 213 |
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| 214 |
* src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
| 215 |
CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
| 216 |
GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp, |
| 217 |
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: |
| 218 |
break, break and break..... |
| 219 |
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| 220 |
2004-11-01 14:57 tim |
| 221 |
|
| 222 |
* test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, |
| 223 |
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, |
| 224 |
StuntDouble.hpp: these core classes get compiled |
| 225 |
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| 226 |
2004-10-29 17:37 tim |
| 227 |
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| 228 |
* test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule |
| 229 |
class |
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| 231 |
2004-10-29 17:28 chrisfen |
| 232 |
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| 233 |
* src/: UseTheForce/DarkSide/atype.F90, |
| 234 |
UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, |
| 235 |
types/ShapeAtomType.cpp: still debugging |
| 236 |
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| 237 |
2004-10-29 17:28 chrisfen |
| 238 |
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| 239 |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: |
| 240 |
shapes rcut calculator added |
| 241 |
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| 242 |
2004-10-29 17:27 chrisfen |
| 243 |
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| 244 |
* samples/shape/linear.md: shorter run |
| 245 |
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| 246 |
2004-10-29 15:54 tim |
| 247 |
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| 248 |
* test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. |
| 249 |
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| 250 |
2004-10-29 11:22 tim |
| 251 |
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| 252 |
* test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, |
| 253 |
ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove |
| 254 |
some deprecated files |
| 255 |
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| 256 |
2004-10-29 11:20 tim |
| 257 |
|
| 258 |
* test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, |
| 259 |
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: |
| 260 |
More painful reconstruction is coming !!! |
| 261 |
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| 262 |
2004-10-28 17:34 tim |
| 263 |
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| 264 |
* src/brains/DataStorage.hpp, src/utils/next_combination.hpp, |
| 265 |
test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, |
| 266 |
test/brains/RigidBody.cpp, test/brains/RigidBody.hpp, |
| 267 |
test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, |
| 268 |
DirectionalAtom and RigidBody |
| 269 |
|
| 270 |
2004-10-28 17:26 tim |
| 271 |
|
| 272 |
* ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, |
| 273 |
src/applications/simpleBuilder/MoLocator.cpp, |
| 274 |
src/applications/simpleBuilder/Vector3d.hpp, |
| 275 |
src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: |
| 276 |
remove old Vector3d.hpp from application/simpleBuilder |
| 277 |
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| 278 |
2004-10-28 16:42 tim |
| 279 |
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| 280 |
* src/utils/next_combination.hpp: Minor change in next_combination |
| 281 |
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| 282 |
2004-10-28 16:28 tim |
| 283 |
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| 284 |
* src/utils/next_combination.hpp, |
| 285 |
test/utils/NextCombinationTestCase.cpp, |
| 286 |
test/utils/ReplaceWildCardTestCase.cpp: Done with combination |
| 287 |
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| 288 |
2004-10-28 16:11 tim |
| 289 |
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| 290 |
* src/utils/next_combination.hpp: change documentation of |
| 291 |
next_combination.hpp |
| 292 |
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| 293 |
2004-10-28 15:41 tim |
| 294 |
|
| 295 |
* ChangeLog, src/utils/next_combination.hpp, |
| 296 |
test/utils/NextCombinationTestCase.cpp, |
| 297 |
test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working |
| 298 |
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| 299 |
2004-10-28 15:01 tim |
| 300 |
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| 301 |
* src/utils/next_combination.hpp: adding replace wildcard function |
| 302 |
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| 303 |
2004-10-28 14:33 tim |
| 304 |
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| 305 |
* src/utils/next_combination.hpp: Minor change |
| 306 |
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| 307 |
2004-10-28 14:06 tim |
| 308 |
|
| 309 |
* ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, |
| 310 |
src/applications/simpleBuilder/simpleBuilder.cpp, |
| 311 |
src/utils/next_combination.hpp, test/utils/Makefile, |
| 312 |
test/utils/NextCombinationTestCase.cpp, |
| 313 |
test/utils/ReplaceWildCardTestCase.cpp, |
| 314 |
test/utils/next_combination.hpp: STL next_permutation like |
| 315 |
next_combination is working |
| 316 |
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| 317 |
2004-10-28 12:22 chrisfen |
| 318 |
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| 319 |
* src/UseTheForce/WATER.cpp: fix of setDipoles |
| 320 |
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| 321 |
2004-10-28 12:20 gezelter |
| 322 |
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| 323 |
* src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the |
| 324 |
shapeFile |
| 325 |
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| 326 |
2004-10-28 12:20 gezelter |
| 327 |
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| 328 |
* samples/shape/linear.md: forgot the orientation line |
| 329 |
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| 330 |
2004-10-28 11:56 gezelter |
| 331 |
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| 332 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 333 |
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
| 334 |
UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate |
| 335 |
declaration foo |
| 336 |
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| 337 |
2004-10-28 11:55 gezelter |
| 338 |
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| 339 |
* samples/lipid/5x5.md: uncommented .in line |
| 340 |
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| 341 |
2004-10-28 10:42 tim |
| 342 |
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| 343 |
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
| 344 |
NextCombinationTestCase.hpp, next_combination.hpp: next_combination |
| 345 |
in progress |
| 346 |
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| 347 |
2004-10-28 10:15 tim |
| 348 |
|
| 349 |
* test/utils/: NextCombinationTestCase.cpp, |
| 350 |
NextCombinationTestCase.hpp: adding next_combination test case |
| 351 |
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| 352 |
2004-10-28 10:02 tim |
| 353 |
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| 354 |
* test/utils/next_combination.hpp: STL Compatible combination |
| 355 |
sequence generator |
| 356 |
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| 357 |
2004-10-28 01:23 tim |
| 358 |
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| 359 |
* test/utils/: GenerateCombination.hpp, |
| 360 |
ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp |
| 361 |
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| 362 |
2004-10-28 01:16 tim |
| 363 |
|
| 364 |
* test/utils/GenerateCombination.hpp: a STL next_permutaion like |
| 365 |
next_combination function. |
| 366 |
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| 367 |
2004-10-27 22:27 tim |
| 368 |
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| 369 |
* test/utils/ReplaceWildCard.hpp: no message |
| 370 |
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| 371 |
2004-10-27 22:14 tim |
| 372 |
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| 373 |
* test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: |
| 374 |
ReplaceWildCard(recursive version) is working, need refactoring. An |
| 375 |
iterative version is on the way |
| 376 |
|
| 377 |
2004-10-27 21:28 tim |
| 378 |
|
| 379 |
* test/utils/: Makefile, ReplaceWildCard.hpp, |
| 380 |
ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress |
| 381 |
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| 382 |
2004-10-27 21:08 tim |
| 383 |
|
| 384 |
* test/utils/: ReplaceWildCardTestCase.cpp, |
| 385 |
ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard |
| 386 |
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| 387 |
2004-10-27 18:17 tim |
| 388 |
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| 389 |
* test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need |
| 390 |
test |
| 391 |
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| 392 |
2004-10-27 01:25 tim |
| 393 |
|
| 394 |
* src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild |
| 395 |
char matching is on the way |
| 396 |
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| 397 |
2004-10-27 01:07 tim |
| 398 |
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| 399 |
* src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 |
| 400 |
|
| 401 |
2004-10-26 22:00 gezelter |
| 402 |
|
| 403 |
* src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix |
| 404 |
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| 405 |
2004-10-26 21:20 gezelter |
| 406 |
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| 407 |
* src/UseTheForce/ForceFields.hpp: subclass foo |
| 408 |
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| 409 |
2004-10-26 21:16 gezelter |
| 410 |
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| 411 |
* src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> |
| 412 |
string conversion |
| 413 |
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| 414 |
2004-10-26 19:01 gezelter |
| 415 |
|
| 416 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 417 |
UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, |
| 418 |
brains/SimSetup.hpp: char* -> string |
| 419 |
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| 420 |
2004-10-26 17:25 gezelter |
| 421 |
|
| 422 |
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, |
| 423 |
Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, |
| 424 |
ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some |
| 425 |
isXXX |
| 426 |
|
| 427 |
2004-10-26 17:25 gezelter |
| 428 |
|
| 429 |
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
| 430 |
define name collision |
| 431 |
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| 432 |
2004-10-26 17:24 gezelter |
| 433 |
|
| 434 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 435 |
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
| 436 |
UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp, |
| 437 |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
| 438 |
UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: |
| 439 |
forcefield refactoring for shapes |
| 440 |
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| 441 |
2004-10-26 17:24 gezelter |
| 442 |
|
| 443 |
* samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, |
| 444 |
Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, |
| 445 |
linear.md, linear.shape, toluene.shape: adding sample shape |
| 446 |
directory |
| 447 |
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| 448 |
2004-10-26 17:19 tim |
| 449 |
|
| 450 |
* ChangeLog, src/brains/DataStorage.cpp, |
| 451 |
src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, |
| 452 |
test/brains/DataStorageTestCase.cpp, |
| 453 |
test/brains/DataStorageTestCase.hpp, test/brains/Makefile: |
| 454 |
DataStorage passes unit test |
| 455 |
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| 456 |
2004-10-26 13:03 chrisfen |
| 457 |
|
| 458 |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: |
| 459 |
Changes to help advance shapes |
| 460 |
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| 461 |
2004-10-26 13:02 chrisfen |
| 462 |
|
| 463 |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to |
| 464 |
Shapes force field reader |
| 465 |
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| 466 |
2004-10-26 12:28 tim |
| 467 |
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| 468 |
* src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and |
| 469 |
SnapshotTestCase in progress |
| 470 |
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| 471 |
2004-10-25 17:46 tim |
| 472 |
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| 473 |
* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
| 474 |
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
| 475 |
src/math/Vector3.hpp, test/brains/StuntDouble.hpp, |
| 476 |
test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, |
| 477 |
test/math/VectorTestCase.cpp: add getArray function to RectMatrix |
| 478 |
and Vector classes |
| 479 |
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| 480 |
2004-10-25 12:03 tim |
| 481 |
|
| 482 |
* ChangeLog, src/utils/GenericFactory.hpp, |
| 483 |
test/utils/GenericFactoryTestCase.cpp, |
| 484 |
test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding |
| 485 |
GenericFactory Test Case. GenericFactory now can bed used to creat |
| 486 |
ForcefieldFactory and IntegratorFactory etc. |
| 487 |
|
| 488 |
2004-10-24 23:08 tim |
| 489 |
|
| 490 |
* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, |
| 491 |
brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, |
| 492 |
brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes |
| 493 |
get reconstructed |
| 494 |
|
| 495 |
2004-10-24 02:55 tim |
| 496 |
|
| 497 |
* src/utils/GenericFactory.hpp: GenericFactory pass unit test |
| 498 |
|
| 499 |
2004-10-23 18:09 tim |
| 500 |
|
| 501 |
* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, |
| 502 |
StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, |
| 503 |
RigidBody.cpp: Refactoring in progress |
| 504 |
|
| 505 |
2004-10-22 18:09 tim |
| 506 |
|
| 507 |
* ChangeLog, src/brains/Snapshot.hpp, |
| 508 |
src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, |
| 509 |
test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, |
| 510 |
test/brains/StuntDouble.hpp: more work in Snapshot |
| 511 |
|
| 512 |
2004-10-22 17:59 chrisfen |
| 513 |
|
| 514 |
* src/: UseTheForce/LJFF.cpp, |
| 515 |
UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear |
| 516 |
god! It runs and conserves energy! |
| 517 |
|
| 518 |
2004-10-22 17:54 chrisfen |
| 519 |
|
| 520 |
* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY |
| 521 |
|
| 522 |
2004-10-22 17:53 chrisfen |
| 523 |
|
| 524 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 525 |
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
| 526 |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
| 527 |
brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey |
| 528 |
breakey |
| 529 |
|
| 530 |
2004-10-22 17:53 chrisfen |
| 531 |
|
| 532 |
* make/Makefile.in: compiler flags |
| 533 |
|
| 534 |
2004-10-22 16:20 gezelter |
| 535 |
|
| 536 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 537 |
UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, |
| 538 |
brains/fSimulation.h, types/AtomType.hpp, |
| 539 |
types/DirectionalAtomType.hpp: fixey fixey |
| 540 |
|
| 541 |
2004-10-22 15:22 gezelter |
| 542 |
|
| 543 |
* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, |
| 544 |
charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, |
| 545 |
lj_interface.h, shapes.F90, simulation.F90: Added un-busticated |
| 546 |
fortran files and c/Fortran interfaces |
| 547 |
|
| 548 |
2004-10-22 15:21 gezelter |
| 549 |
|
| 550 |
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
| 551 |
DirectionalAtomType.hpp, Makefile: More on AtomType and |
| 552 |
DirectionalAtomType |
| 553 |
|
| 554 |
2004-10-22 09:47 gezelter |
| 555 |
|
| 556 |
* src/types/AtomType.hpp: Adding AtomType |
| 557 |
|
| 558 |
2004-10-21 16:31 tim |
| 559 |
|
| 560 |
* ChangeLog, src/brains/Snapshot.hpp, |
| 561 |
src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, |
| 562 |
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
| 563 |
src/math/Vector.hpp, src/math/Vector3.hpp, |
| 564 |
test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: |
| 565 |
Snapshot and SnapshotManager in progress |
| 566 |
|
| 567 |
2004-10-21 16:30 tim |
| 568 |
|
| 569 |
* test/brains/: BrainsTest.cpp, Makefile, |
| 570 |
SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, |
| 571 |
SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for |
| 572 |
Snapshot and snapshotManager. |
| 573 |
|
| 574 |
2004-10-21 15:15 gezelter |
| 575 |
|
| 576 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 577 |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 578 |
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
| 579 |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
| 580 |
UseTheForce/doForces_interface.h, UseTheForce/fForceField.h, |
| 581 |
UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h, |
| 582 |
brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. |
| 583 |
Fixey Fixey. |
| 584 |
|
| 585 |
2004-10-21 11:32 tim |
| 586 |
|
| 587 |
* src/utils/GenericData.cpp, src/utils/Makefile, |
| 588 |
test/utils/Makefile, test/utils/UtilTest: remove some junk files |
| 589 |
|
| 590 |
2004-10-21 11:24 tim |
| 591 |
|
| 592 |
* test/utils/GenericData.hpp: remove backup of GenericData.hpp |
| 593 |
|
| 594 |
2004-10-21 11:22 tim |
| 595 |
|
| 596 |
* ChangeLog, src/brains/SimSetup.cpp, |
| 597 |
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
| 598 |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 599 |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 600 |
src/integrators/NVT.cpp, src/io/DumpReader.cpp, |
| 601 |
src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp, |
| 602 |
src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp, |
| 603 |
src/utils/GenericData.cpp, src/utils/GenericData.hpp, |
| 604 |
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
| 605 |
src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 606 |
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
| 607 |
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
| 608 |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 609 |
src/visitors/ZconsVisitor.hpp: replace old GebericData with new |
| 610 |
GenericData |
| 611 |
|
| 612 |
2004-10-21 10:25 chuckv |
| 613 |
|
| 614 |
* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj |
| 615 |
module. |
| 616 |
|
| 617 |
2004-10-21 10:24 chuckv |
| 618 |
|
| 619 |
* src/UseTheForce/DarkSide/lj_interface.h: Added interface for |
| 620 |
fortran lj module. |
| 621 |
|
| 622 |
2004-10-20 17:54 tim |
| 623 |
|
| 624 |
* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, |
| 625 |
test/utils/GenericDataTestCase.cpp, test/utils/Makefile, |
| 626 |
test/utils/PropertyMapTestCase.cpp, |
| 627 |
test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: |
| 628 |
GenericData and PropertyMap pass unit test. |
| 629 |
|
| 630 |
2004-10-20 16:52 gezelter |
| 631 |
|
| 632 |
* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, |
| 633 |
DarkSide/sticky_interface.h: fixed a fortran name problem |
| 634 |
|
| 635 |
2004-10-20 16:38 tim |
| 636 |
|
| 637 |
* test/utils/: GenericData.hpp, GenericDataTestCase.cpp, |
| 638 |
GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, |
| 639 |
UtilTest, UtilTest.cpp: adding generic data test case |
| 640 |
|
| 641 |
2004-10-20 16:16 chuckv |
| 642 |
|
| 643 |
* configure, ac-tools/aclocal.m4, |
| 644 |
src/UseTheForce/DarkSide/Makefile, |
| 645 |
src/UseTheForce/DarkSide/mpiSimulation.F90, |
| 646 |
src/UseTheForce/DarkSide/mpiSimulation_interface.h, |
| 647 |
src/UseTheForce/DarkSide/simParallel.F90, |
| 648 |
src/UseTheForce/DarkSide/simParallel_interface.h, |
| 649 |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: |
| 650 |
Fortran/C++ interface de-obfuscation project appears to be |
| 651 |
complete! Woo hoo! |
| 652 |
|
| 653 |
2004-10-20 15:47 chuckv |
| 654 |
|
| 655 |
* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, |
| 656 |
fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project |
| 657 |
continues |
| 658 |
|
| 659 |
2004-10-20 15:46 chuckv |
| 660 |
|
| 661 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 662 |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 663 |
UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, |
| 664 |
UseTheForce/doForces_interface.h, |
| 665 |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, |
| 666 |
UseTheForce/DarkSide/atype_interface.h, |
| 667 |
UseTheForce/DarkSide/eam_interface.h, |
| 668 |
UseTheForce/DarkSide/gb_interface.h, |
| 669 |
UseTheForce/DarkSide/mpiSimulation_interface.h, |
| 670 |
UseTheForce/DarkSide/shapes_interface.h, |
| 671 |
UseTheForce/DarkSide/simulation_interface.h, |
| 672 |
UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, |
| 673 |
brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface |
| 674 |
de-obfuscation project (It is a very long story) |
| 675 |
|
| 676 |
2004-10-20 13:07 tim |
| 677 |
|
| 678 |
* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
| 679 |
test/math/SquareMatrix3TestCase.cpp, |
| 680 |
test/math/SquareMatrixTestCase.cpp, |
| 681 |
test/math/SquareMatrixTestCase.hpp: Math library pass the unit test |
| 682 |
|
| 683 |
2004-10-20 00:52 tim |
| 684 |
|
| 685 |
* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
| 686 |
SnapshotManager in design phase |
| 687 |
|
| 688 |
2004-10-19 23:54 gezelter |
| 689 |
|
| 690 |
* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
| 691 |
problem prevented linking |
| 692 |
|
| 693 |
2004-10-19 23:54 gezelter |
| 694 |
|
| 695 |
* src/UseTheForce/Shapes_FF.cpp: fixed include |
| 696 |
|
| 697 |
2004-10-19 23:26 gezelter |
| 698 |
|
| 699 |
* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
| 700 |
oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
| 701 |
more fortran name mangling |
| 702 |
|
| 703 |
2004-10-19 23:23 gezelter |
| 704 |
|
| 705 |
* src/profiling/timing.F90: yet more fortran renaming |
| 706 |
|
| 707 |
2004-10-19 23:19 gezelter |
| 708 |
|
| 709 |
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
| 710 |
do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
| 711 |
notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
| 712 |
wrappers.F90: Fortran name cleanup continues |
| 713 |
|
| 714 |
2004-10-19 23:12 gezelter |
| 715 |
|
| 716 |
* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
| 717 |
broken fortran stuff |
| 718 |
|
| 719 |
2004-10-19 23:02 gezelter |
| 720 |
|
| 721 |
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
| 722 |
atype_interface.h, atype_module.F90, atype_module_interface.h, |
| 723 |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
| 724 |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
| 725 |
calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, |
| 726 |
eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, |
| 727 |
gb_interface.h, gb_module_interface.h, mpiSimulation.F90, |
| 728 |
mpiSimulation_interface.h, mpiSimulation_module.F90, |
| 729 |
mpisimulation_module_interface.h, reactionField.F90, shapes.F90, |
| 730 |
shapes_interface.h, shapes_module.h, simulation.F90, |
| 731 |
simulation_interface.h, simulation_module.F90, |
| 732 |
simulation_module_interface.h, sticky.F90, sticky_interface.h, |
| 733 |
sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
| 734 |
name sanity on the fortran side |
| 735 |
|
| 736 |
2004-10-19 19:18 tim |
| 737 |
|
| 738 |
* test/math/SquareMatrix3TestCase.hpp: [no log message] |
| 739 |
|
| 740 |
2004-10-19 18:01 tim |
| 741 |
|
| 742 |
* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
| 743 |
src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
| 744 |
except diagonalize(), all of functions in math library pass the |
| 745 |
test |
| 746 |
|
| 747 |
2004-10-19 17:43 chuckv |
| 748 |
|
| 749 |
* src/UseTheForce/do_Forces.h: Added correct prototypes for |
| 750 |
C-fortran interface functions. |
| 751 |
|
| 752 |
2004-10-19 17:37 chuckv |
| 753 |
|
| 754 |
* src/UseTheForce/DarkSide/: atype_module_interface.h, |
| 755 |
eam_module_inteface.h, gb_module_interface.h, |
| 756 |
mpisimulation_module_interface.h, simulation_module_interface.h, |
| 757 |
sticky_pair_module_interface.h: Added correct prototypes for |
| 758 |
C-fortran interface functions. |
| 759 |
|
| 760 |
2004-10-19 16:28 tim |
| 761 |
|
| 762 |
* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
| 763 |
src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
| 764 |
test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, |
| 765 |
test/math/RectMatrixTestCase.cpp, |
| 766 |
test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, |
| 767 |
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
| 768 |
bugs get fixed at math library |
| 769 |
|
| 770 |
2004-10-19 15:43 chuckv |
| 771 |
|
| 772 |
* src/UseTheForce/: DarkSide/atype_module_interface.h, |
| 773 |
DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
| 774 |
DarkSide/mpisimulation_module_interface.h, |
| 775 |
DarkSide/simulation_module_interface.h, |
| 776 |
DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, |
| 777 |
DarkSide/atype_module.F90, DarkSide/calc_gb.F90, |
| 778 |
DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, |
| 779 |
DarkSide/simulation_module.F90, do_Forces.F90, |
| 780 |
fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, |
| 781 |
notifycutoffs_module_interface.h: Added new files for fortran |
| 782 |
interface. |
| 783 |
|
| 784 |
2004-10-19 15:43 gezelter |
| 785 |
|
| 786 |
* src/UseTheForce/Makefile: regressing |
| 787 |
|
| 788 |
2004-10-19 15:40 gezelter |
| 789 |
|
| 790 |
* src/: UseTheForce/DarkSide/calc_shapes.F90, |
| 791 |
UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
| 792 |
working on shapes for portability |
| 793 |
|
| 794 |
2004-10-19 15:40 gezelter |
| 795 |
|
| 796 |
* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
| 797 |
|
| 798 |
2004-10-19 13:21 chrisfen |
| 799 |
|
| 800 |
* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
| 801 |
findBegin |
| 802 |
|
| 803 |
2004-10-18 23:34 tim |
| 804 |
|
| 805 |
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
| 806 |
are fixed in Vector class |
| 807 |
|
| 808 |
2004-10-18 23:28 tim |
| 809 |
|
| 810 |
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
| 811 |
some bugs in RectMatrixTestCase |
| 812 |
|
| 813 |
2004-10-18 23:21 tim |
| 814 |
|
| 815 |
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
| 816 |
test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
| 817 |
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
| 818 |
test/math/VectorTestCase.hpp: implement more test cases |
| 819 |
|
| 820 |
2004-10-18 18:13 tim |
| 821 |
|
| 822 |
* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
| 823 |
src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
| 824 |
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
| 825 |
src/utils/StringTokenizer.hpp, test/math/Makefile, |
| 826 |
test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
| 827 |
tests on math library |
| 828 |
|
| 829 |
2004-10-18 16:03 tim |
| 830 |
|
| 831 |
* test/math/: Makefile, QuaternionTestCase.cpp, |
| 832 |
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
| 833 |
SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
| 834 |
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
| 835 |
more testing units |
| 836 |
|
| 837 |
2004-10-18 12:07 tim |
| 838 |
|
| 839 |
* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
| 840 |
math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
| 841 |
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
| 842 |
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
| 843 |
|
| 844 |
2004-10-18 11:30 gezelter |
| 845 |
|
| 846 |
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
| 847 |
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
| 848 |
\phi) |
| 849 |
|
| 850 |
2004-10-18 11:29 gezelter |
| 851 |
|
| 852 |
* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
| 853 |
types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
| 854 |
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
| 855 |
Shapes into OOPSE |
| 856 |
|
| 857 |
2004-10-18 10:21 gezelter |
| 858 |
|
| 859 |
* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
| 860 |
|
| 861 |
2004-10-18 00:23 tim |
| 862 |
|
| 863 |
* test/math/VectorTestCase.hpp: adding vector test case |
| 864 |
|
| 865 |
2004-10-18 00:23 tim |
| 866 |
|
| 867 |
* src/utils/GenericFactory.hpp: adding generic factory and vector |
| 868 |
test case |
| 869 |
|
| 870 |
2004-10-16 20:19 tim |
| 871 |
|
| 872 |
* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
| 873 |
SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
| 874 |
progress |
| 875 |
|
| 876 |
2004-10-15 20:31 tim |
| 877 |
|
| 878 |
* src/math/Quaternion.hpp: add quaternion class |
| 879 |
|
| 880 |
2004-10-15 16:11 tim |
| 881 |
|
| 882 |
* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
| 883 |
IfstrstreamTestCase.hpp: adding test file |
| 884 |
|
| 885 |
2004-10-15 16:10 tim |
| 886 |
|
| 887 |
* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
| 888 |
|
| 889 |
2004-10-15 15:42 tim |
| 890 |
|
| 891 |
* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
| 892 |
|
| 893 |
2004-10-15 15:35 tim |
| 894 |
|
| 895 |
* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
| 896 |
|
| 897 |
2004-10-15 15:34 tim |
| 898 |
|
| 899 |
* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
| 900 |
namespace oopse |
| 901 |
|
| 902 |
2004-10-15 14:38 chuckv |
| 903 |
|
| 904 |
* configure, ac-tools/aclocal.m4: Changed optimization flags for |
| 905 |
XLF and XLC. |
| 906 |
|
| 907 |
2004-10-15 13:28 tim |
| 908 |
|
| 909 |
* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
| 910 |
adding ifstrstream test case |
| 911 |
|
| 912 |
2004-10-15 13:20 tim |
| 913 |
|
| 914 |
* src/io/basic_ifstrstream.hpp: fix include |
| 915 |
|
| 916 |
2004-10-15 13:18 tim |
| 917 |
|
| 918 |
* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
| 919 |
|
| 920 |
2004-10-15 13:17 tim |
| 921 |
|
| 922 |
* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
| 923 |
|
| 924 |
2004-10-15 13:16 tim |
| 925 |
|
| 926 |
* test/io/: Makefile, ifstrstreamTestCase.cpp, |
| 927 |
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
| 928 |
|
| 929 |
2004-10-15 10:37 tim |
| 930 |
|
| 931 |
* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
| 932 |
ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
| 933 |
|
| 934 |
2004-10-15 10:20 tim |
| 935 |
|
| 936 |
* src/io/basic_ifstrstream.hpp: add checkFilename Option |
| 937 |
|
| 938 |
2004-10-15 10:19 tim |
| 939 |
|
| 940 |
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
| 941 |
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
| 942 |
SquareMatrixTestCase class |
| 943 |
|
| 944 |
2004-10-15 02:52 tim |
| 945 |
|
| 946 |
* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
| 947 |
|
| 948 |
2004-10-14 18:28 tim |
| 949 |
|
| 950 |
* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
| 951 |
Vector.hpp: math library in progress |
| 952 |
|
| 953 |
2004-10-14 18:27 tim |
| 954 |
|
| 955 |
* src/io/FileReader.hpp: FileReader in progress |
| 956 |
|
| 957 |
2004-10-13 18:53 tim |
| 958 |
|
| 959 |
* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
| 960 |
test in isOrthogonal of SquareMatrix is failed by some reasons |
| 961 |
|
| 962 |
2004-10-13 17:28 tim |
| 963 |
|
| 964 |
* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
| 965 |
class |
| 966 |
|
| 967 |
2004-10-13 17:27 tim |
| 968 |
|
| 969 |
* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
| 970 |
RectMatrixTestCase.hpp: adding testing unit |
| 971 |
|
| 972 |
2004-10-13 17:24 tim |
| 973 |
|
| 974 |
* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
| 975 |
|
| 976 |
2004-10-13 01:51 tim |
| 977 |
|
| 978 |
* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
| 979 |
Vector3.hpp: refactory vector and matrix classes |
| 980 |
|
| 981 |
2004-10-13 01:50 tim |
| 982 |
|
| 983 |
* src/math/Vector3d.hpp: Remove some Makefile.in |
| 984 |
|
| 985 |
2004-10-12 18:57 tim |
| 986 |
|
| 987 |
* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
| 988 |
Matrix3x3d.hpp |
| 989 |
|
| 990 |
2004-10-12 14:08 tim |
| 991 |
|
| 992 |
* doc/: cppstyle.html, style.css: adding c++ coding style |
| 993 |
|
| 994 |
2004-10-11 17:15 tim |
| 995 |
|
| 996 |
* src/: constraints/AbstractClasses.hpp, |
| 997 |
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
| 998 |
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
| 999 |
|
| 1000 |
2004-10-11 16:54 tim |
| 1001 |
|
| 1002 |
* scripts/filepp: fix a bug in filepp |
| 1003 |
|
| 1004 |
2004-10-11 16:13 tim |
| 1005 |
|
| 1006 |
* make/Makefile.in: using filepp to generate dependencies instead |
| 1007 |
of compilers |
| 1008 |
|
| 1009 |
2004-10-11 16:10 tim |
| 1010 |
|
| 1011 |
* scripts/filepp: filepp can be used to generate dependencies for |
| 1012 |
c/c++ now |
| 1013 |
|
| 1014 |
2004-10-11 13:40 tim |
| 1015 |
|
| 1016 |
* make/Makefile.in: remove -module from F90Options |
| 1017 |
|
| 1018 |
2004-10-11 13:01 tim |
| 1019 |
|
| 1020 |
* make/Makefile.in: adding rules to move fortran 90 module to |
| 1021 |
target directory |
| 1022 |
|
| 1023 |
2004-10-11 10:43 gezelter |
| 1024 |
|
| 1025 |
* make/Makefile.in: fixed makefile.in |
| 1026 |
|
| 1027 |
2004-10-11 09:51 tim |
| 1028 |
|
| 1029 |
* scripts/filepp: remove "use bytes" which causes problem in sgi |
| 1030 |
machine |
| 1031 |
|
| 1032 |
2004-10-11 09:26 tim |
| 1033 |
|
| 1034 |
* forceFields/Makefile: add Makefile |
| 1035 |
|
| 1036 |
2004-10-11 09:23 tim |
| 1037 |
|
| 1038 |
* samples/: water/dimer/Makefile, water/spce/Makefile, |
| 1039 |
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
| 1040 |
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
| 1041 |
directory |
| 1042 |
|
| 1043 |
2004-10-11 09:23 tim |
| 1044 |
|
| 1045 |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
| 1046 |
Makefile |
| 1047 |
|
| 1048 |
2004-10-09 01:01 tim |
| 1049 |
|
| 1050 |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
| 1051 |
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
| 1052 |
Remove some Makefile.in |
| 1053 |
|
| 1054 |
2004-10-08 18:15 tim |
| 1055 |
|
| 1056 |
* make/Makefile.in: [no log message] |
| 1057 |
|
| 1058 |
2004-10-08 17:51 tim |
| 1059 |
|
| 1060 |
* make/Makefile.in: fix make install |
| 1061 |
|
| 1062 |
2004-10-08 17:10 tim |
| 1063 |
|
| 1064 |
* make/Makefile.in: adding make install |
| 1065 |
|
| 1066 |
2004-10-08 17:04 tim |
| 1067 |
|
| 1068 |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
| 1069 |
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
| 1070 |
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
| 1071 |
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
| 1072 |
water/ssde/Makefile, water/ssde/Makefile.in, |
| 1073 |
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
| 1074 |
water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
| 1075 |
zcons/Makefile.in: add Makefile to sample directory |
| 1076 |
|
| 1077 |
2004-10-06 18:03 gezelter |
| 1078 |
|
| 1079 |
* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
| 1080 |
stuff |
| 1081 |
|
| 1082 |
2004-10-06 18:03 gezelter |
| 1083 |
|
| 1084 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1085 |
make/Doxyfile, src/applications/getopt.c, |
| 1086 |
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
| 1087 |
build fixes |
| 1088 |
|
| 1089 |
2004-10-06 17:20 tim |
| 1090 |
|
| 1091 |
* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
| 1092 |
|
| 1093 |
2004-10-06 17:19 tim |
| 1094 |
|
| 1095 |
* scripts/filepp: filepp can handle different fortran module case |
| 1096 |
and suffix |
| 1097 |
|
| 1098 |
2004-10-06 16:27 gezelter |
| 1099 |
|
| 1100 |
* src/restraints/Restraints.cpp: Chris doesn't know about the |
| 1101 |
OOPSE-2.0 directory structure yet |
| 1102 |
|
| 1103 |
2004-10-06 16:27 gezelter |
| 1104 |
|
| 1105 |
* ChangeLog: Yeah yeah, we'lll get around to it later |
| 1106 |
|
| 1107 |
2004-10-06 16:22 gezelter |
| 1108 |
|
| 1109 |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 1110 |
make/Makefile.in: cleaning up build process |
| 1111 |
|
| 1112 |
2004-10-06 15:01 chrisfen |
| 1113 |
|
| 1114 |
* src/restraints/Restraints.cpp: made the file reading in |
| 1115 |
restraints more intelligent - no longer gives uninformative seg |
| 1116 |
faults |
| 1117 |
|
| 1118 |
2004-10-06 14:55 gezelter |
| 1119 |
|
| 1120 |
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
| 1121 |
|
| 1122 |
2004-10-06 14:51 gezelter |
| 1123 |
|
| 1124 |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
| 1125 |
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
| 1126 |
|
| 1127 |
2004-10-06 13:53 tim |
| 1128 |
|
| 1129 |
* make/: Makefile, Makefile.in: fix make statistics |
| 1130 |
|
| 1131 |
2004-10-06 13:18 tim |
| 1132 |
|
| 1133 |
* make/: Makefile, Makefile.in: adding GNU make functions to |
| 1134 |
combine all of the static libraries to a big library |
| 1135 |
|
| 1136 |
2004-10-05 17:57 tim |
| 1137 |
|
| 1138 |
* make/: Makefile, Makefile.in: adding shared library flag |
| 1139 |
|
| 1140 |
2004-10-05 14:37 tim |
| 1141 |
|
| 1142 |
* src/: Makefile, UseTheForce/Makefile, |
| 1143 |
UseTheForce/mpiSimulation_module.F90, |
| 1144 |
UseTheForce/DarkSide/Makefile, |
| 1145 |
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
| 1146 |
mpiSimulation_module to DarkSide |
| 1147 |
|
| 1148 |
2004-10-05 14:35 tim |
| 1149 |
|
| 1150 |
* make/: Makefile, Makefile.in: building MPI version;using static |
| 1151 |
library instead of shared library |
| 1152 |
|
| 1153 |
2004-10-05 09:14 tim |
| 1154 |
|
| 1155 |
* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
| 1156 |
to filepp |
| 1157 |
|
| 1158 |
2004-10-04 15:56 tim |
| 1159 |
|
| 1160 |
* make/: Makefile, Makefile.in: add make cvslog |
| 1161 |
|
| 1162 |
2004-10-04 11:24 gezelter |
| 1163 |
|
| 1164 |
* make/: Makefile, Makefile.in: more work on the parallel build |
| 1165 |
|
| 1166 |
2004-10-04 11:06 gezelter |
| 1167 |
|
| 1168 |
* make/: Makefile, Makefile.in: changes to backport declare flags |
| 1169 |
|
| 1170 |
2004-10-04 10:27 gezelter |
| 1171 |
|
| 1172 |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
| 1173 |
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
| 1174 |
shapes |
| 1175 |
|
| 1176 |
2004-10-01 23:40 tim |
| 1177 |
|
| 1178 |
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
| 1179 |
|
| 1180 |
2004-10-01 23:22 tim |
| 1181 |
|
| 1182 |
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
| 1183 |
|
| 1184 |
2004-10-01 16:59 tim |
| 1185 |
|
| 1186 |
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
| 1187 |
|
| 1188 |
2004-10-01 16:22 gezelter |
| 1189 |
|
| 1190 |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
| 1191 |
few minor build changes |
| 1192 |
|
| 1193 |
2004-10-01 16:11 tim |
| 1194 |
|
| 1195 |
* scripts/filepp: adding fortran90 make dependency tool |
| 1196 |
|
| 1197 |
2004-09-30 10:41 tim |
| 1198 |
|
| 1199 |
* make/: Makefile, Makefile.in: make clean is smart enough to only |
| 1200 |
remove object files belong to current package. turn off silent |
| 1201 |
mode |
| 1202 |
|
| 1203 |
2004-09-29 16:55 tim |
| 1204 |
|
| 1205 |
* src/: Makefile, UseTheForce/Makefile, |
| 1206 |
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
| 1207 |
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
| 1208 |
brains/Makedepend, brains/Makefile, constraints/Makefile, |
| 1209 |
integrators/Makefile, io/Makefile, math/Makefile, |
| 1210 |
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
| 1211 |
restraints/Makefile, types/Makefile, utils/Makefile, |
| 1212 |
visitors/Makefile: define DEV_ROOT as relative path |
| 1213 |
|
| 1214 |
2004-09-29 16:54 tim |
| 1215 |
|
| 1216 |
* make/: Makefile, Makefile.in: get the relative path by shell |
| 1217 |
script |
| 1218 |
|
| 1219 |
2004-09-29 16:32 tim |
| 1220 |
|
| 1221 |
* make/Makefile: eliminate DEV_ROOT by relative path |
| 1222 |
|
| 1223 |
2004-09-29 13:37 tim |
| 1224 |
|
| 1225 |
* make/Makefile.in: add PackageLibs; fix dependency rule |
| 1226 |
|
| 1227 |
2004-09-29 12:57 gezelter |
| 1228 |
|
| 1229 |
* configure, ac-tools/configure.in: updates |
| 1230 |
|
| 1231 |
2004-09-29 12:56 gezelter |
| 1232 |
|
| 1233 |
* make/: Make.conf.in, Makefile.in, _files/style.css: Working on |
| 1234 |
make stuff |
| 1235 |
|
| 1236 |
2004-09-29 12:46 tim |
| 1237 |
|
| 1238 |
* Makefile: If makefile does not exist, print error message |
| 1239 |
|
| 1240 |
2004-09-29 12:12 tim |
| 1241 |
|
| 1242 |
* make/: Make.conf.in, Makefile: fix dependencies rule |
| 1243 |
|
| 1244 |
2004-09-29 10:58 gezelter |
| 1245 |
|
| 1246 |
* Makefile, make/Makefile: still working on build process |
| 1247 |
|
| 1248 |
2004-09-29 10:00 tim |
| 1249 |
|
| 1250 |
* make/Makefile: add print statment to rules |
| 1251 |
|
| 1252 |
2004-09-29 09:59 tim |
| 1253 |
|
| 1254 |
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
| 1255 |
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
| 1256 |
applications/simpleBuilder/Makefile, brains/Makefile, |
| 1257 |
constraints/Makefile, integrators/Makefile, io/Makefile, |
| 1258 |
math/Makefile, minimizers/Makefile, primitives/Makefile, |
| 1259 |
profiling/Makefile, restraints/Makefile, types/Makefile, |
| 1260 |
utils/Makefile, visitors/Makefile: change Makefile to relative path |
| 1261 |
|
| 1262 |
2004-09-28 21:55 tim |
| 1263 |
|
| 1264 |
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
| 1265 |
which cause headache in bulding libutils |
| 1266 |
|
| 1267 |
2004-09-28 18:24 tim |
| 1268 |
|
| 1269 |
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
| 1270 |
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
| 1271 |
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
| 1272 |
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
| 1273 |
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
| 1274 |
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
| 1275 |
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
| 1276 |
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
| 1277 |
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
| 1278 |
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
| 1279 |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
| 1280 |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
| 1281 |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
| 1282 |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
| 1283 |
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
| 1284 |
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
| 1285 |
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
| 1286 |
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
| 1287 |
change directory structure of application. Every executable file is |
| 1288 |
replaced in seperate directory |
| 1289 |
|
| 1290 |
2004-09-28 17:15 gezelter |
| 1291 |
|
| 1292 |
* lib/dummy: Keep that lib around, please. |
| 1293 |
|
| 1294 |
2004-09-28 17:14 gezelter |
| 1295 |
|
| 1296 |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
| 1297 |
starting a configure version |
| 1298 |
|
| 1299 |
2004-09-28 16:08 tim |
| 1300 |
|
| 1301 |
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
| 1302 |
UseTheForce/DarkSide/Makefile, |
| 1303 |
UseTheForce/DarkSide/notifyCutoffs.F90, |
| 1304 |
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
| 1305 |
brains/Makefile, brains/simulation_module.F90: move fortran files |
| 1306 |
around to solve dependency problem |
| 1307 |
|
| 1308 |
2004-09-28 15:43 tim |
| 1309 |
|
| 1310 |
* Makefile, src/UseTheForce/ForceFields.hpp, |
| 1311 |
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
| 1312 |
src/applications/Makedepend, src/applications/Makefile, |
| 1313 |
src/brains/Makedepend, src/brains/simulation_module.F90, |
| 1314 |
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
| 1315 |
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
| 1316 |
src/utils/Makefile: [no log message] |
| 1317 |
|
| 1318 |
2004-09-28 15:41 tim |
| 1319 |
|
| 1320 |
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
| 1321 |
problem |
| 1322 |
|
| 1323 |
2004-09-28 11:13 tim |
| 1324 |
|
| 1325 |
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
| 1326 |
src/io/Makefile: add yacc and lex rules |
| 1327 |
|
| 1328 |
2004-09-27 15:24 tim |
| 1329 |
|
| 1330 |
* make/Makefile: adding include path to F90Options |
| 1331 |
|
| 1332 |
2004-09-27 15:13 tim |
| 1333 |
|
| 1334 |
* make/Makefile: change suffix from .cc to .cpp |
| 1335 |
|
| 1336 |
2004-09-24 11:27 tim |
| 1337 |
|
| 1338 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 1339 |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 1340 |
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
| 1341 |
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
| 1342 |
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
| 1343 |
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
| 1344 |
UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 1345 |
UseTheForce/DarkSide/notifyCutoffs.F90, |
| 1346 |
UseTheForce/DarkSide/switch_module.F90, |
| 1347 |
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
| 1348 |
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
| 1349 |
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
| 1350 |
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
| 1351 |
applications/MoLocator.cpp, applications/MoLocator.hpp, |
| 1352 |
applications/cmdline.c, applications/nanoBuilder.cpp, |
| 1353 |
applications/oopse.cpp, applications/simpleBuilder.cpp, |
| 1354 |
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
| 1355 |
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 1356 |
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
| 1357 |
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 1358 |
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
| 1359 |
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
| 1360 |
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
| 1361 |
integrators/Integrator.hpp, integrators/NPT.cpp, |
| 1362 |
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
| 1363 |
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
| 1364 |
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
| 1365 |
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
| 1366 |
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
| 1367 |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
| 1368 |
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
| 1369 |
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
| 1370 |
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
| 1371 |
math/MatVec3.h, math/randomSPRNG.cpp, |
| 1372 |
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
| 1373 |
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
| 1374 |
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
| 1375 |
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
| 1376 |
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
| 1377 |
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
| 1378 |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 1379 |
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
| 1380 |
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
| 1381 |
primitives/RigidBody.hpp, primitives/SRI.hpp, |
| 1382 |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
| 1383 |
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
| 1384 |
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
| 1385 |
restraints/Restraints.hpp, types/AtomStamp.cpp, |
| 1386 |
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
| 1387 |
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
| 1388 |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 1389 |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
| 1390 |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 1391 |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
| 1392 |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
| 1393 |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
| 1394 |
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
| 1395 |
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
| 1396 |
utils/simError.c, visitors/AtomVisitor.cpp, |
| 1397 |
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
| 1398 |
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
| 1399 |
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 1400 |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
| 1401 |
visitors/ZconsVisitor.hpp: change the #include in source files |
| 1402 |
|
| 1403 |
2004-09-23 23:16 gezelter |
| 1404 |
|
| 1405 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 1406 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
| 1407 |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
| 1408 |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
| 1409 |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
| 1410 |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
| 1411 |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
| 1412 |
src/UseTheForce/fForceField.h, |
| 1413 |
src/UseTheForce/fSwitchingFunction.h, |
| 1414 |
src/UseTheForce/fortranWrapDefines.hpp, |
| 1415 |
src/UseTheForce/fortranWrappers.cpp, |
| 1416 |
src/UseTheForce/fortranWrappers.hpp, |
| 1417 |
src/UseTheForce/mpiComponentPlan.h, |
| 1418 |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 1419 |
src/UseTheForce/mpiSimulation_module.F90, |
| 1420 |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
| 1421 |
src/UseTheForce/DarkSide/atype_module.F90, |
| 1422 |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 1423 |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
| 1424 |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
| 1425 |
src/UseTheForce/DarkSide/calc_eam.F90, |
| 1426 |
src/UseTheForce/DarkSide/calc_gb.F90, |
| 1427 |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
| 1428 |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
| 1429 |
src/UseTheForce/DarkSide/force_globals.F90, |
| 1430 |
src/UseTheForce/DarkSide/neighborLists.F90, |
| 1431 |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
| 1432 |
src/UseTheForce/DarkSide/switch_module.F90, |
| 1433 |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 1434 |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
| 1435 |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
| 1436 |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
| 1437 |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 1438 |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
| 1439 |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 1440 |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
| 1441 |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
| 1442 |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
| 1443 |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
| 1444 |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
| 1445 |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
| 1446 |
src/types/BondStamp.hpp, src/types/Component.cpp, |
| 1447 |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
| 1448 |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
| 1449 |
src/types/MakeStamps.hpp, src/types/Makefile, |
| 1450 |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
| 1451 |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 1452 |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 1453 |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 1454 |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
| 1455 |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
| 1456 |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
| 1457 |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
| 1458 |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
| 1459 |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 1460 |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
| 1461 |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 1462 |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 1463 |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
| 1464 |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
| 1465 |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
| 1466 |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
| 1467 |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
| 1468 |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
| 1469 |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
| 1470 |
src/minimizers/OOPSEMinimizer.cpp, |
| 1471 |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 1472 |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
| 1473 |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 1474 |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
| 1475 |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
| 1476 |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 1477 |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 1478 |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
| 1479 |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
| 1480 |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
| 1481 |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
| 1482 |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
| 1483 |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
| 1484 |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
| 1485 |
src/utils/GenericData.hpp, src/utils/Makefile, |
| 1486 |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
| 1487 |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
| 1488 |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
| 1489 |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
| 1490 |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
| 1491 |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
| 1492 |
src/utils/simError.c, src/utils/simError.h, |
| 1493 |
src/utils/status_module.F90, src/utils/vector_class.F90, |
| 1494 |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 1495 |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 1496 |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
| 1497 |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 1498 |
src/visitors/RigidBodyVisitor.cpp, |
| 1499 |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 1500 |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
| 1501 |
make/_files/style.css, samples/Makefile.in, |
| 1502 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 1503 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 1504 |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 1505 |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
| 1506 |
samples/zcons/Makefile.in, samples/zcons/water.md, |
| 1507 |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
| 1508 |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
| 1509 |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
| 1510 |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
| 1511 |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
| 1512 |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
| 1513 |
src/applications/LatticeCreator.cpp, |
| 1514 |
src/applications/LatticeCreator.hpp, |
| 1515 |
src/applications/LatticeFactory.cpp, |
| 1516 |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
| 1517 |
src/applications/Makefile, src/applications/MoLocator.cpp, |
| 1518 |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
| 1519 |
src/applications/cmdline.c, src/applications/cmdline.h, |
| 1520 |
src/applications/getopt.c, src/applications/getopt1.c, |
| 1521 |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
| 1522 |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
| 1523 |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
| 1524 |
src/applications/simpleBuilder.ggo, |
| 1525 |
src/applications/simpleBuilderCmd.c, |
| 1526 |
src/integrators/AbstractClasses.hpp, |
| 1527 |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
| 1528 |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
| 1529 |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 1530 |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 1531 |
src/integrators/NVT.cpp, src/profiling/Makefile, |
| 1532 |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
| 1533 |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
| 1534 |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
| 1535 |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
| 1536 |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
| 1537 |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
| 1538 |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
| 1539 |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
| 1540 |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
| 1541 |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
| 1542 |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
| 1543 |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
| 1544 |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
| 1545 |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
| 1546 |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 1547 |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 1548 |
samples/alkane/butane.in, samples/alkane/butane.md, |
| 1549 |
samples/argon/500.in, samples/argon/500.md, |
| 1550 |
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 1551 |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 1552 |
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 1553 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 1554 |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 1555 |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
| 1556 |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
| 1557 |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
| 1558 |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
| 1559 |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
| 1560 |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
| 1561 |
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
| 1562 |
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
| 1563 |
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
| 1564 |
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
| 1565 |
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
| 1566 |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
| 1567 |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
| 1568 |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
| 1569 |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
| 1570 |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
| 1571 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 1572 |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 1573 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
| 1574 |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
| 1575 |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
| 1576 |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 1577 |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
| 1578 |
|
| 1579 |
2004-09-23 23:16 gezelter |
| 1580 |
|
| 1581 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 1582 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
| 1583 |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
| 1584 |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
| 1585 |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
| 1586 |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
| 1587 |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
| 1588 |
src/UseTheForce/fForceField.h, |
| 1589 |
src/UseTheForce/fSwitchingFunction.h, |
| 1590 |
src/UseTheForce/fortranWrapDefines.hpp, |
| 1591 |
src/UseTheForce/fortranWrappers.cpp, |
| 1592 |
src/UseTheForce/fortranWrappers.hpp, |
| 1593 |
src/UseTheForce/mpiComponentPlan.h, |
| 1594 |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 1595 |
src/UseTheForce/mpiSimulation_module.F90, |
| 1596 |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
| 1597 |
src/UseTheForce/DarkSide/atype_module.F90, |
| 1598 |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 1599 |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
| 1600 |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
| 1601 |
src/UseTheForce/DarkSide/calc_eam.F90, |
| 1602 |
src/UseTheForce/DarkSide/calc_gb.F90, |
| 1603 |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
| 1604 |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
| 1605 |
src/UseTheForce/DarkSide/force_globals.F90, |
| 1606 |
src/UseTheForce/DarkSide/neighborLists.F90, |
| 1607 |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
| 1608 |
src/UseTheForce/DarkSide/switch_module.F90, |
| 1609 |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 1610 |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
| 1611 |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
| 1612 |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
| 1613 |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 1614 |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
| 1615 |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 1616 |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
| 1617 |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
| 1618 |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
| 1619 |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
| 1620 |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
| 1621 |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
| 1622 |
src/types/BondStamp.hpp, src/types/Component.cpp, |
| 1623 |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
| 1624 |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
| 1625 |
src/types/MakeStamps.hpp, src/types/Makefile, |
| 1626 |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
| 1627 |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 1628 |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 1629 |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 1630 |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
| 1631 |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
| 1632 |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
| 1633 |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
| 1634 |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
| 1635 |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 1636 |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
| 1637 |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 1638 |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 1639 |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
| 1640 |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
| 1641 |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
| 1642 |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
| 1643 |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
| 1644 |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
| 1645 |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
| 1646 |
src/minimizers/OOPSEMinimizer.cpp, |
| 1647 |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 1648 |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
| 1649 |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 1650 |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
| 1651 |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
| 1652 |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 1653 |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 1654 |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
| 1655 |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
| 1656 |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
| 1657 |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
| 1658 |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
| 1659 |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
| 1660 |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
| 1661 |
src/utils/GenericData.hpp, src/utils/Makefile, |
| 1662 |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
| 1663 |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
| 1664 |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
| 1665 |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
| 1666 |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
| 1667 |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
| 1668 |
src/utils/simError.c, src/utils/simError.h, |
| 1669 |
src/utils/status_module.F90, src/utils/vector_class.F90, |
| 1670 |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 1671 |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 1672 |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
| 1673 |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 1674 |
src/visitors/RigidBodyVisitor.cpp, |
| 1675 |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 1676 |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
| 1677 |
make/_files/style.css, samples/Makefile.in, |
| 1678 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 1679 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 1680 |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 1681 |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
| 1682 |
samples/zcons/Makefile.in, samples/zcons/water.md, |
| 1683 |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
| 1684 |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
| 1685 |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
| 1686 |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
| 1687 |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
| 1688 |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
| 1689 |
src/applications/LatticeCreator.cpp, |
| 1690 |
src/applications/LatticeCreator.hpp, |
| 1691 |
src/applications/LatticeFactory.cpp, |
| 1692 |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
| 1693 |
src/applications/Makefile, src/applications/MoLocator.cpp, |
| 1694 |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
| 1695 |
src/applications/cmdline.c, src/applications/cmdline.h, |
| 1696 |
src/applications/getopt.c, src/applications/getopt1.c, |
| 1697 |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
| 1698 |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
| 1699 |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
| 1700 |
src/applications/simpleBuilder.ggo, |
| 1701 |
src/applications/simpleBuilderCmd.c, |
| 1702 |
src/integrators/AbstractClasses.hpp, |
| 1703 |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
| 1704 |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
| 1705 |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 1706 |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 1707 |
src/integrators/NVT.cpp, src/profiling/Makefile, |
| 1708 |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
| 1709 |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
| 1710 |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
| 1711 |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
| 1712 |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
| 1713 |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
| 1714 |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
| 1715 |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
| 1716 |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
| 1717 |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
| 1718 |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
| 1719 |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
| 1720 |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
| 1721 |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
| 1722 |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 1723 |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 1724 |
samples/alkane/butane.in, samples/alkane/butane.md, |
| 1725 |
samples/argon/500.in, samples/argon/500.md, |
| 1726 |
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 1727 |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 1728 |
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 1729 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 1730 |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 1731 |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
| 1732 |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
| 1733 |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
| 1734 |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
| 1735 |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
| 1736 |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
| 1737 |
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
| 1738 |
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
| 1739 |
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
| 1740 |
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
| 1741 |
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
| 1742 |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
| 1743 |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
| 1744 |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
| 1745 |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
| 1746 |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
| 1747 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 1748 |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 1749 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
| 1750 |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
| 1751 |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
| 1752 |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 1753 |
forceFields/Pt.VC.funcfl: Initial revision |
| 1754 |
|
