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Comparing trunk/OOPSE-3.0/ChangeLog (file contents):
Revision 2116 by tim, Fri Mar 11 15:00:20 2005 UTC vs.
Revision 2229 by chrisfen, Tue May 17 22:35:01 2005 UTC

# Line 1 | Line 1
1 < 2005-03-11 00:43  chrisfen
1 > 2005-05-16 23:20  chuckv
2  
3 +        * src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp:
4 +        Fixed merge issues between Kyle and Chris so OOPSE will actually
5 +        build.
6 +
7 + 2005-05-16 22:46  kdaily
8 +
9 +        * src/io/: GayBerneAtomTypesSectionParser.cpp,
10 +        GayBerneAtomTypesSectionParser.hpp, Makefile: help
11 +
12 + 2005-05-16 21:08  kdaily
13 +
14 +        * forceFields/DUFF2.frc, src/UseTheForce/doForces.F90,
15 +        src/UseTheForce/DarkSide/gb.F90, src/io/Makefile,
16 +        src/types/DirectionalAtomType.cpp,
17 +        src/types/DirectionalAtomType.hpp: added gb
18 +
19 + 2005-05-13 15:36  chrisfen
20 +
21 +        * forceFields/DUFF2.frc: Better tap
22 +
23 + 2005-05-12 14:43  chrisfen
24 +
25 +        * forceFields/DUFF2.frc, samples/water/dimer/ssd.in,
26 +        samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90,
27 +        src/applications/dump2Xyz/Dump2XYZ.cpp,
28 +        src/visitors/AtomVisitor.hpp: Couple of changes for TAP water.
29 +        Need to parametrize.
30 +
31 + 2005-05-11 18:15  chuckv
32 +
33 +        * src/: io/ShapeAtomTypesSectionParser.cpp,
34 +        math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed
35 +        build issues under ifc7.
36 +
37 + 2005-05-09 17:07  chuckv
38 +
39 +        * src/applications/nanoRodBuilder/Geometry.hpp: More geometry
40 +        builder changes.
41 +
42 + 2005-05-05 10:06  chrisfen
43 +
44 +        * forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED
45 +        to TAP
46 +
47 + 2005-05-05 09:47  chrisfen
48 +
49 +        * forceFields/DUFF2.frc, samples/water/ssde/ssde.md,
50 +        samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp,
51 +        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile,
52 +        src/UseTheForce/DarkSide/atype.F90,
53 +        src/UseTheForce/DarkSide/atype_interface.F90,
54 +        src/UseTheForce/DarkSide/simulation.F90,
55 +        src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp,
56 +        src/brains/fSimulation.h, src/io/Makefile,
57 +        src/io/StickyAtomTypesSectionParser.cpp,
58 +        src/io/StickyPowerAtomTypesSectionParser.cpp,
59 +        src/io/StickyPowerAtomTypesSectionParser.hpp,
60 +        src/types/AtomType.cpp, src/types/AtomType.hpp,
61 +        src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp,
62 +        src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water.  It's
63 +        not parametrized, but OOPSE will now let me run it...
64 +
65 + 2005-05-03 17:55  chuckv
66 +
67 +        * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
68 +        GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp:
69 +        Adding support for generic geometry to nanorodbuilder.
70 +
71 + 2005-05-03 12:55  chuckv
72 +
73 +        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
74 +        nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c,
75 +        nanorodBuilderCmd.h: More changes to nanoRodBuilder....
76 +
77 + 2005-04-29 14:16  gezelter
78 +
79 +        * make/Makefile.in: [no log message]
80 +
81 + 2005-04-29 11:26  chrisfen
82 +
83 +        * forceFields/DUFF2.frc, samples/water/spce/water.md,
84 +        samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md,
85 +        samples/water/ssd-ion/water.md, samples/water/ssde/water.md,
86 +        samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md,
87 +        samples/water/tip4p/water.md: Added TIP4P-Ew
88 +
89 + 2005-04-27 19:24  chuckv
90 +
91 +        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
92 +        GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo,
93 +        nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with
94 +        nanoRodBuilder....
95 +
96 + 2005-04-27 15:13  chrisfen
97 +
98 +        * samples/shape/Shapes.frc, samples/shape/linear.shape,
99 +        src/UseTheForce/DarkSide/atype.F90,
100 +        src/UseTheForce/DarkSide/shapes.F90,
101 +        src/UseTheForce/DarkSide/shapes_interface.F90,
102 +        src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of
103 +        write statements and am closer to a working shapes
104 +
105 + 2005-04-22 16:57  chuckv
106 +
107 +        * src/utils/Predicate.hpp: Fixed gcc4 bug...
108 +
109 + 2005-04-22 16:52  tim
110 +
111 +        * src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp,
112 +        Trim.hpp: adding CharClassificationFunctor to fix the locale
113 +        problem  of c++
114 +
115 + 2005-04-21 09:12  chrisfen
116 +
117 +        * samples/shape/Shapes.frc, samples/shape/linear.in,
118 +        samples/shape/linear.md, src/UseTheForce/ForceField.hpp,
119 +        src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile,
120 +        src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp,
121 +        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90,
122 +        src/UseTheForce/DarkSide/shapes.F90,
123 +        src/UseTheForce/DarkSide/shapes_interface.F90,
124 +        src/UseTheForce/DarkSide/shapes_interface.h,
125 +        src/brains/Register.cpp, src/brains/SimCreator.cpp,
126 +        src/io/Makefile, src/io/SectionParser.cpp,
127 +        src/io/SectionParser.hpp, src/io/SectionParserManager.cpp,
128 +        src/io/ShapeAtomTypesSectionParser.cpp,
129 +        src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile,
130 +        src/types/AtomType.cpp, src/types/ShapeAtomType.cpp,
131 +        src/types/ShapeAtomType.hpp: Shapes is limping along with a array
132 +        bounds overwrite (I think...). At least the parser loads the
133 +        forcefield fine...
134 +
135 + 2005-04-18 10:44  chrisfen
136 +
137 +        * src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on
138 +        Mac (capitalization confusion of filenames)
139 +
140 + 2005-04-17 22:50  chrisfen
141 +
142 +        * src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp,
143 +        UseTheForce/Shapes_FF.cpp,
144 +        io/DirectionalAtomTypesSectionParser.cpp,
145 +        io/ShapeAtomTypesSectionParser.cpp,
146 +        io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser...
147 +
148 + 2005-04-15 17:43  gezelter
149 +
150 +        * README: gmake in case people forget
151 +
152 + 2005-04-15 17:40  gezelter
153 +
154 +        * src/applications/oopse/oopse.cpp: fixed the spacing on the
155 +        banner.  Vanity.
156 +
157 + 2005-04-15 17:22  gezelter
158 +
159 +        * src/: config.h.in, applications/oopse/oopse.cpp: Version string
160 +        in banner (and version numbers in config.h)
161 +
162 + 2005-04-15 17:22  gezelter
163 +
164 +        * ChangeLog, LICENSE, README: Documentation changes
165 +
166 + 2005-04-15 17:03  gezelter
167 +
168 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
169 +        UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp,
170 +        UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
171 +        UseTheForce/ForceFieldCreator.hpp,
172 +        UseTheForce/ForceFieldFactory.cpp,
173 +        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp,
174 +        UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90,
175 +        UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h,
176 +        UseTheForce/notifyCutoffs.F90,
177 +        UseTheForce/notifyCutoffs_interface.F90,
178 +        UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90,
179 +        UseTheForce/DarkSide/atype.F90,
180 +        UseTheForce/DarkSide/atype_interface.F90,
181 +        UseTheForce/DarkSide/eam.F90,
182 +        UseTheForce/DarkSide/eam_interface.F90,
183 +        UseTheForce/DarkSide/eam_interface.h,
184 +        UseTheForce/DarkSide/electrostatic.F90,
185 +        UseTheForce/DarkSide/electrostatic_interface.F90,
186 +        UseTheForce/DarkSide/electrostatic_interface.h,
187 +        UseTheForce/DarkSide/force_globals.F90,
188 +        UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h,
189 +        UseTheForce/DarkSide/lj_interface.F90,
190 +        UseTheForce/DarkSide/lj_interface.h,
191 +        UseTheForce/DarkSide/neighborLists.F90,
192 +        UseTheForce/DarkSide/reactionField.F90,
193 +        UseTheForce/DarkSide/shapes.F90,
194 +        UseTheForce/DarkSide/shapes_interface.F90,
195 +        UseTheForce/DarkSide/shapes_interface.h,
196 +        UseTheForce/DarkSide/simParallel.F90,
197 +        UseTheForce/DarkSide/simParallel_interface.F90,
198 +        UseTheForce/DarkSide/simParallel_interface.h,
199 +        UseTheForce/DarkSide/simulation.F90,
200 +        UseTheForce/DarkSide/simulation_interface.F90,
201 +        UseTheForce/DarkSide/simulation_interface.h,
202 +        UseTheForce/DarkSide/sticky.F90,
203 +        UseTheForce/DarkSide/sticky_interface.F90,
204 +        UseTheForce/DarkSide/sticky_interface.h,
205 +        UseTheForce/DarkSide/switcheroo.F90,
206 +        applications/dump2Xyz/Dump2XYZ.cpp,
207 +        applications/dump2Xyz/Dump2XYZCmd.c,
208 +        applications/dump2Xyz/Dump2XYZCmd.h,
209 +        applications/dynamicProps/CrossTimeCorrFunc.cpp,
210 +        applications/dynamicProps/CrossTimeCorrFunc.hpp,
211 +        applications/dynamicProps/DipoleCorrFunc.cpp,
212 +        applications/dynamicProps/DipoleCorrFunc.hpp,
213 +        applications/dynamicProps/DynamicProps.cpp,
214 +        applications/dynamicProps/DynamicPropsCmd.c,
215 +        applications/dynamicProps/DynamicPropsCmd.h,
216 +        applications/dynamicProps/FrameTimeCorrFunc.hpp,
217 +        applications/dynamicProps/ParticleTimeCorrFunc.cpp,
218 +        applications/dynamicProps/ParticleTimeCorrFunc.hpp,
219 +        applications/dynamicProps/RCorrFunc.cpp,
220 +        applications/dynamicProps/RCorrFunc.hpp,
221 +        applications/dynamicProps/TimeCorrFunc.cpp,
222 +        applications/dynamicProps/TimeCorrFunc.hpp,
223 +        applications/dynamicProps/VCorrFunc.cpp,
224 +        applications/dynamicProps/VCorrFunc.hpp,
225 +        applications/nanoRodBuilder/GeometryBuilder.cpp,
226 +        applications/nanoRodBuilder/GeometryBuilder.hpp,
227 +        applications/nanoRodBuilder/nanorodBuilder.cpp,
228 +        applications/nanoRodBuilder/nanorodBuilderCmd.c,
229 +        applications/nanoRodBuilder/nanorodBuilderCmd.h,
230 +        applications/oopse/oopse.cpp,
231 +        applications/simpleBuilder/simpleBuilder.cpp,
232 +        applications/simpleBuilder/simpleBuilderCmd.c,
233 +        applications/simpleBuilder/simpleBuilderCmd.h,
234 +        applications/staticProps/GofAngle2.cpp,
235 +        applications/staticProps/GofAngle2.hpp,
236 +        applications/staticProps/GofR.cpp,
237 +        applications/staticProps/GofR.hpp,
238 +        applications/staticProps/GofRAngle.cpp,
239 +        applications/staticProps/GofRAngle.hpp,
240 +        applications/staticProps/GofXyz.cpp,
241 +        applications/staticProps/GofXyz.hpp,
242 +        applications/staticProps/RadialDistrFunc.cpp,
243 +        applications/staticProps/RadialDistrFunc.hpp,
244 +        applications/staticProps/StaticProps.cpp,
245 +        applications/staticProps/StaticPropsCmd.c,
246 +        applications/staticProps/StaticPropsCmd.h,
247 +        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
248 +        brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp,
249 +        brains/Exclude.hpp, brains/ForceManager.cpp,
250 +        brains/ForceManager.hpp, brains/MoleculeCreator.cpp,
251 +        brains/MoleculeCreator.hpp, brains/Register.cpp,
252 +        brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
253 +        brains/SimInfo.hpp, brains/SimSnapshotManager.cpp,
254 +        brains/SimSnapshotManager.hpp, brains/Snapshot.cpp,
255 +        brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp,
256 +        brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp,
257 +        brains/fSimulation.h, constraints/ConstraintElem.hpp,
258 +        constraints/ConstraintPair.hpp, constraints/Rattle.cpp,
259 +        constraints/Rattle.hpp, constraints/ZconsStruct.hpp,
260 +        constraints/ZconstraintForceManager.cpp,
261 +        constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp,
262 +        integrators/DLM.hpp, integrators/Integrator.cpp,
263 +        integrators/Integrator.hpp, integrators/IntegratorCreator.hpp,
264 +        integrators/IntegratorFactory.cpp,
265 +        integrators/IntegratorFactory.hpp, integrators/NPT.cpp,
266 +        integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp,
267 +        integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp,
268 +        integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp,
269 +        integrators/NVT.cpp, integrators/NVT.hpp,
270 +        integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp,
271 +        integrators/Velocitizer.hpp,
272 +        integrators/VelocityVerletIntegrator.cpp,
273 +        integrators/VelocityVerletIntegrator.hpp,
274 +        io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp,
275 +        io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c,
276 +        io/BASS_parse.h, io/BendTypesSectionParser.cpp,
277 +        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
278 +        io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
279 +        io/ChargeAtomTypesSectionParser.hpp,
280 +        io/DirectionalAtomTypesSectionParser.cpp,
281 +        io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
282 +        io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp,
283 +        io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
284 +        io/Globals.cpp, io/Globals.hpp,
285 +        io/LennardJonesAtomTypesSectionParser.cpp,
286 +        io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp,
287 +        io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp,
288 +        io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp,
289 +        io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp,
290 +        io/SectionParser.cpp, io/SectionParser.hpp,
291 +        io/SectionParserManager.cpp, io/SectionParserManager.hpp,
292 +        io/StatWriter.cpp, io/StatWriter.hpp,
293 +        io/StickyAtomTypesSectionParser.cpp,
294 +        io/StickyAtomTypesSectionParser.hpp,
295 +        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
296 +        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
297 +        io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp,
298 +        io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c,
299 +        io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h,
300 +        io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp,
301 +        lattice/CubicLattice.hpp, lattice/FCCLattice.cpp,
302 +        lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
303 +        lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp,
304 +        lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp,
305 +        math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h,
306 +        math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp,
307 +        math/ParallelRandNumGen.hpp, math/Polynomial.hpp,
308 +        math/Quaternion.hpp, math/RandNumGen.hpp,
309 +        math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp,
310 +        math/RectMatrix.hpp, math/SeqRandNumGen.cpp,
311 +        math/SeqRandNumGen.hpp, math/SquareMatrix.hpp,
312 +        math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp,
313 +        minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp,
314 +        minimizers/Minimizer.cpp, minimizers/Minimizer.hpp,
315 +        minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp,
316 +        minimizers/MinimizerFactory.hpp,
317 +        minimizers/MinimizerParameterSet.cpp,
318 +        minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp,
319 +        minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp,
320 +        minimizers/SDMinimizer.hpp, primitives/Atom.cpp,
321 +        primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp,
322 +        primitives/Bond.hpp, primitives/CutoffGroup.hpp,
323 +        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
324 +        primitives/GhostBend.cpp, primitives/GhostBend.hpp,
325 +        primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp,
326 +        primitives/Molecule.cpp, primitives/Molecule.hpp,
327 +        primitives/RigidBody.cpp, primitives/RigidBody.hpp,
328 +        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
329 +        primitives/Torsion.cpp, primitives/Torsion.hpp,
330 +        primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp,
331 +        profiling/mdProfile.cpp, profiling/mdProfile.hpp,
332 +        profiling/timing.F90, restraints/Restraints.cpp,
333 +        restraints/Restraints.hpp,
334 +        restraints/ThermoIntegrationForceManager.cpp,
335 +        restraints/ThermoIntegrationForceManager.hpp,
336 +        selection/DistanceFinder.cpp, selection/DistanceFinder.hpp,
337 +        selection/IndexFinder.cpp, selection/IndexFinder.hpp,
338 +        selection/NameFinder.cpp, selection/NameFinder.hpp,
339 +        selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp,
340 +        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
341 +        selection/SelectionManager.cpp, selection/SelectionManager.hpp,
342 +        selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp,
343 +        selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp,
344 +        types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h,
345 +        types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp,
346 +        types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp,
347 +        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
348 +        types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp,
349 +        types/CubicBondType.hpp, types/CubicTorsionType.hpp,
350 +        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
351 +        types/DirectionalAtomType.hpp, types/FixedBondType.hpp,
352 +        types/HarmonicBendType.hpp, types/HarmonicBondType.hpp,
353 +        types/MakeStamps.cpp, types/MakeStamps.hpp,
354 +        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
355 +        types/MorseBondType.hpp, types/OplsTorsionType.hpp,
356 +        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
357 +        types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp,
358 +        types/QuarticBondType.hpp, types/QuarticTorsionType.hpp,
359 +        types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
360 +        types/ShapeAtomType.cpp, types/ShapeAtomType.hpp,
361 +        types/TorsionStamp.cpp, types/TorsionStamp.hpp,
362 +        types/TorsionType.hpp, types/UreyBradleyBendType.hpp,
363 +        types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp,
364 +        utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp,
365 +        utils/GenericFactory.hpp, utils/LocalIndexManager.hpp,
366 +        utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp,
367 +        utils/NumericConstant.hpp, utils/OOPSEConstant.hpp,
368 +        utils/PropertyMap.cpp, utils/PropertyMap.hpp,
369 +        utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
370 +        utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp,
371 +        utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp,
372 +        utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp,
373 +        utils/any.hpp, utils/definitions.F90, utils/fError.c,
374 +        utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h,
375 +        utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h,
376 +        utils/residentMem.h, utils/simError.c, utils/simError.h,
377 +        utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp,
378 +        visitors/AtomData.hpp, visitors/AtomVisitor.cpp,
379 +        visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp,
380 +        visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp,
381 +        visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
382 +        visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp,
383 +        visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp,
384 +        visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has
385 +        been drafted to perform our indentation services
386 +
387 + 2005-04-15 17:03  gezelter
388 +
389 +        * configure, ac-tools/configure.in: Jedi mind-trick warning
390 +        messages have been added to make users ignore CGAL.
391 +
392 + 2005-04-15 13:41  tim
393 +
394 +        * make/Makefile.in: fix make install
395 +
396 + 2005-04-15 13:41  tim
397 +
398 +        * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile:
399 +        add  Makefile of samples
400 +
401 + 2005-04-15 13:33  tim
402 +
403 +        * samples/: lipid/Makefile, water/dimer/Makefile,
404 +        water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not
405 +        installed correctly
406 +
407 + 2005-04-14 16:41  gezelter
408 +
409 +        * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in,
410 +        make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl,
411 +        scripts/filepp, scripts/filepp.in: configure now searches for perl
412 +        to use with filepp
413 +
414 + 2005-04-14 16:20  gezelter
415 +
416 +        * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of
417 +        MoLocator
418 +
419 + 2005-04-14 14:12  gezelter
420 +
421 +        * LICENSE: [no log message]
422 +
423 + 2005-04-14 11:10  chuckv
424 +
425 +        * src/applications/nanoRodBuilder/nanorodBuilder.cpp:
426 +        nanorodbuilder now exit's when libCGAL is not present.
427 +
428 + 2005-04-14 10:20  tim
429 +
430 +        * src/io/make_nodes.h: fix one more warning message in make_nodes
431 +
432 + 2005-04-13 18:36  chuckv
433 +
434 +        * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed
435 +        interface name for SGI Compiler
436 +
437 + 2005-04-13 18:29  chrisfen
438 +
439 +        * samples/water/ssde/ssde.md: oops...  bad sample
440 +
441 + 2005-04-13 18:00  chuckv
442 +
443 +        * src/config.h.in: Change typo in CGAL.
444 +
445 + 2005-04-13 17:43  tim
446 +
447 +        * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp,
448 +        selection/SelectionCompiler.hpp: fix some warning messages
449 +
450 + 2005-04-13 17:30  gezelter
451 +
452 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
453 +        make/Makefile.in, src/config.h.in,
454 +        src/applications/nanoRodBuilder/Makefile,
455 +        src/applications/nanoRodBuilder/Makefile.in,
456 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL
457 +        checks
458 +
459 + 2005-04-13 15:36  chuckv
460 +
461 +        * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp,
462 +        DarkSide/LJ.F90, DarkSide/electrostatic.F90,
463 +        DarkSide/electrostatic_interface.F90,
464 +        DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90,
465 +        DarkSide/lj_interface.h, DarkSide/sticky.F90,
466 +        DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added
467 +        destroy methods for Fortran modules.
468 +
469 + 2005-04-13 15:17  chuckv
470 +
471 +        * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90,
472 +        shapes_interface.h: Added destroy method to clean up memory
473 +
474 + 2005-04-13 13:41  tim
475 +
476 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
477 +        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
478 +        io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp,
479 +        primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp,
480 +        types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are
481 +        fixed
482 +
483 + 2005-04-12 17:44  chuckv
484 +
485 +        * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed
486 +        for nanoRodBuilder.
487 +
488 + 2005-04-12 17:42  tim
489 +
490 +        * src/applications/: nanoRodBuilder/nanorodBuilder.cpp,
491 +        simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder
492 +        and simpleBuilder(forget to delete lattice)
493 +
494 + 2005-04-12 17:33  tim
495 +
496 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
497 +        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp:
498 +        refactory lattice
499 +
500 + 2005-04-12 17:07  tim
501 +
502 +        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp,
503 +        CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp,
504 +        Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory
505 +        LatticeFactory and LatticeCreator
506 +
507 + 2005-04-12 16:58  tim
508 +
509 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
510 +        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp,
511 +        brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
512 +        lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp,
513 +        lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp,
514 +        lattice/Makefile: refactory LatticeFactory and LatticeCreator
515 +
516 + 2005-04-12 16:28  gezelter
517 +
518 +        * src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp,
519 +        vector_class.F90: cleaned up vector_class memory leak fix by
520 +        deallocating in reverse order of how we allocated.  Also migrated
521 +        MoLocator into utils directory
522 +
523 + 2005-04-12 16:27  gezelter
524 +
525 +        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp,
526 +        Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
527 +        LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice
528 +        directory
529 +
530 + 2005-04-12 16:27  gezelter
531 +
532 +        * src/applications/: nanoRodBuilder/BaseLattice.cpp,
533 +        nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp,
534 +        nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp,
535 +        nanoRodBuilder/LatticeCreator.hpp,
536 +        nanoRodBuilder/LatticeFactory.cpp,
537 +        nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile,
538 +        nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp,
539 +        nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp,
540 +        simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
541 +        simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
542 +        simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
543 +        simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile,
544 +        simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp,
545 +        simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of
546 +        these files are now redundant
547 +
548 + 2005-04-12 16:27  gezelter
549 +
550 +        * src/UseTheForce/DarkSide/: atype_interface.F90,
551 +        atype_interface.h: cleaned up memory leak fix
552 +
553 + 2005-04-12 16:26  gezelter
554 +
555 +        * make/Makefile.in: added lattice subdirectory
556 +
557 + 2005-04-12 15:57  chrisfen
558 +
559 +        * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added
560 +        a space by accident
561 +
562 + 2005-04-12 15:56  chrisfen
563 +
564 +        * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added
565 +        quadrupole sample
566 +
567 + 2005-04-12 15:56  chrisfen
568 +
569 +        * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating
570 +        samples
571 +
572 + 2005-04-12 13:30  tim
573 +
574 +        * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom
575 +        type in fortran side
576 +
577 + 2005-04-12 12:45  chuckv
578 +
579 +        * src/utils/vector_class.F90: Further changes to vector_class
580 +        destroy function.
581 +
582 + 2005-04-12 12:39  chuckv
583 +
584 +        * src/utils/vector_class.F90: Fixed pointer memory leak in
585 +        vector_class.
586 +
587 + 2005-04-12 12:12  chuckv
588 +
589 +        * src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp,
590 +        DarkSide/atype_interface.F90, DarkSide/atype_interface.h,
591 +        DarkSide/eam.F90, DarkSide/eam_interface.F90,
592 +        DarkSide/eam_interface.h: Updates to deallocate object in fortran.
593 +
594 + 2005-04-12 09:24  chrisfen
595 +
596 +        * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI
597 +        output
598 +
599 + 2005-04-11 19:29  chuckv
600 +
601 +        * src/: UseTheForce/DarkSide/atype.F90,
602 +        applications/nanoRodBuilder/Makefile: Changes to delete atypes...
603 +
604 + 2005-04-11 19:28  chuckv
605 +
606 +        * src/utils/vector_class.F90: Added code to delete vector.
607 +
608 + 2005-04-11 17:03  chuckv
609 +
610 +        * samples/metals/nanorod/: Au_nanoparticle.md,
611 +        Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why
612 +        aren't these here?
613 +
614 + 2005-04-11 16:58  tim
615 +
616 +        * src/io/basic_ifstrstream.hpp: avoid multiple inherit in
617 +        basic_ifstrstream
618 +
619 + 2005-04-11 16:37  chuckv
620 +
621 +        * make/Makefile.in,
622 +        src/applications/nanoRodBuilder/BaseLattice.cpp,
623 +        src/applications/nanoRodBuilder/BaseLattice.hpp,
624 +        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
625 +        src/applications/nanoRodBuilder/GeometryBuilder.hpp,
626 +        src/applications/nanoRodBuilder/Lattice.cpp,
627 +        src/applications/nanoRodBuilder/Lattice.hpp,
628 +        src/applications/nanoRodBuilder/LatticeCreator.cpp,
629 +        src/applications/nanoRodBuilder/LatticeCreator.hpp,
630 +        src/applications/nanoRodBuilder/LatticeFactory.cpp,
631 +        src/applications/nanoRodBuilder/LatticeFactory.hpp,
632 +        src/applications/nanoRodBuilder/Makefile,
633 +        src/applications/nanoRodBuilder/MoLocator.cpp,
634 +        src/applications/nanoRodBuilder/MoLocator.hpp,
635 +        src/applications/nanoRodBuilder/nanoBuilder.ggo,
636 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
637 +        src/applications/nanoRodBuilder/nanorodBuilder.ggo,
638 +        src/applications/nanoRodBuilder/nanorodBuilderCmd.c,
639 +        src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing
640 +        nanoRodBuilder application (may not work yet).  ((Doesn't work
641 +        yet.)) (((May never work....)))
642 +
643 + 2005-04-11 15:54  tim
644 +
645 +        * src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete
646 +        prepareVisitor in Dump2XYZ
647 +
648 + 2005-04-11 15:19  chrisfen
649 +
650 +        * src/UseTheForce/DarkSide/electrostatic.F90: fixing of the
651 +        quadrupoles.  look!  it's divide by 3 like stone says!
652 +
653 + 2005-04-11 15:18  chrisfen
654 +
655 +        * forceFields/DUFF2.frc: fixing of the quadrupoles
656 +
657 + 2005-04-11 15:16  tim
658 +
659 +        * src/selection/Token.hpp: change the parameter name in
660 +        constructors
661 +
662 + 2005-04-11 14:49  gezelter
663 +
664 +        * make/Makefile.in: One more bug fix for GNU make versions < 3.80
665 +
666 + 2005-04-11 14:06  gezelter
667 +
668 +        * make/Makefile.in: Fixed the uc and lc functions for GNU make
669 +        versions < 3.80
670 +
671 + 2005-04-11 11:13  gezelter
672 +
673 +        * make/Makefile.in, src/UseTheForce/Makefile,
674 +        src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added
675 +        some stuff to clean out module files during "make clean"
676 +
677 + 2005-04-08 17:13  chrisfen
678 +
679 +        * src/UseTheForce/DarkSide/electrostatic.F90: quadrupole
680 +        interactions should be working with a remaining question of
681 +        interaction magnitude
682 +
683 + 2005-04-08 17:12  chrisfen
684 +
685 +        * samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with
686 +        samples
687 +
688 + 2005-04-08 13:48  chrisfen
689 +
690 +        * samples/water/ssd/ssd.md: oops...  messed up a sample
691 +
692 + 2005-04-08 09:43  chrisfen
693 +
694 +        * src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix
695 +        charge-dipole interactions
696 +
697 + 2005-04-08 09:42  chrisfen
698 +
699 +        * samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md,
700 +        ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole
701 +
702 + 2005-04-08 09:41  chrisfen
703 +
704 +        * forceFields/DUFF2.frc: added Cl- and Na+
705 +
706 + 2005-04-06 18:59  tim
707 +
708 +        * src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser
709 +
710 + 2005-04-05 18:09  tim
711 +
712 +        * src/selection/: NameFinder.cpp, SelectionCompiler.cpp,
713 +        SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-'
714 +        in atom type name;clean the code a little bit
715 +
716 + 2005-03-29 16:00  tim
717 +
718 +        * src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug
719 +        in converting rotation matrix to quaternion
720 +
721 + 2005-03-28 17:41  tim
722 +
723 +        * src/visitors/LipidTransVisitor.cpp: fixed the wrapping
724 +
725 + 2005-03-28 17:30  tim
726 +
727 +        * src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do
728 +        the wrapping
729 +
730 + 2005-03-28 10:54  tim
731 +
732 +        * src/applications/staticProps/GofXyz.cpp: fix a bug in getting the
733 +        dimension of histogram
734 +
735 + 2005-03-22 11:38  tim
736 +
737 +        * make/Makefile.in, src/applications/dump2Xyz/Makefile,
738 +        src/applications/dynamicProps/Makefile,
739 +        src/applications/oopse/Makefile,
740 +        src/applications/simpleBuilder/Makefile,
741 +        src/applications/staticProps/Makefile: avoid building parallel
742 +        executable for dump2XYZ, simpleBuilder, staticProps and
743 +        dynamicProps
744 +
745 + 2005-03-21 17:34  chrisfen
746 +
747 +        * forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the
748 +        forcefield files
749 +
750 + 2005-03-21 15:51  chrisfen
751 +
752 +        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
753 +        DarkSide/reactionField.F90: Make sure electrostatic_module provides
754 +        data for reaction_field
755 +
756 + 2005-03-21 15:50  chrisfen
757 +
758 +        * forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff.  HE
759 +        WILL CHANGE THIS BACK, RIGHT?
760 +
761 + 2005-03-21 14:23  gezelter
762 +
763 +        * src/UseTheForce/DarkSide/electrostatic.F90: constant back to
764 +        correct value
765 +
766 + 2005-03-21 14:22  gezelter
767 +
768 +        * make/Makefile.in: fixed an install-related bug.
769 +        $(InstallCommand) had been set to $(InstallData)
770 +
771 + 2005-03-15 09:21  gezelter
772 +
773 +        * src/integrators/Integrator.cpp: VelocityVerletIntegrator already
774 +        deletes and Nullifies restWriter, so Integrator shouldn't do it.
775 +
776 + 2005-03-15 09:20  gezelter
777 +
778 +        * src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos
779 +
780 + 2005-03-13 02:39  gezelter
781 +
782 +        * src/UseTheForce/DarkSide/electrostatic.F90: first run at
783 +        charge-quadrupole interactions
784 +
785 + 2005-03-12 14:12  chrisfen
786 +
787 +        * samples/: Makefile.in, thermoIntegration/liquid/Makefile,
788 +        thermoIntegration/solid/Makefile: forgot a couple of makefiles
789 +
790 + 2005-03-12 14:05  chrisfen
791 +
792 +        * samples/thermoIntegration/liquid/ssde.in,
793 +        samples/thermoIntegration/liquid/ssde.md,
794 +        samples/thermoIntegration/liquid/water.md,
795 +        samples/thermoIntegration/solid/idealCrystal.in,
796 +        samples/thermoIntegration/solid/ssde.in,
797 +        samples/thermoIntegration/solid/ssde.md,
798 +        samples/thermoIntegration/solid/ssde.zang0,
799 +        samples/thermoIntegration/solid/water.md,
800 +        samples/water/tip3p_ice/tp3.md,
801 +        src/UseTheForce/DarkSide/sticky.F90,
802 +        src/restraints/ThermoIntegrationForceManager.cpp: added some
803 +        samples
804 +
805 + 2005-03-11 12:50  tim
806 +
807 +        * src/: brains/SimCreator.cpp,
808 +        io/MultipoleAtomTypesSectionParser.cpp: fix a typo in
809 +        MultipoleAtomTypesSectionParser
810 +
811 + 2005-03-11 10:55  tim
812 +
813 +        * src/brains/SimInfo.cpp: pairs inside cutoff group should not be
814 +        excluded
815 +
816 + 2005-03-11 10:53  gezelter
817 +
818 +        * src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for
819 +        quadrupoles
820 +
821 + 2005-03-11 10:52  gezelter
822 +
823 +        * forceFields/DUFF2.frc: quadrupoles for SSD models
824 +
825 + 2005-03-11 10:00  tim
826 +
827 +        * ChangeLog, doc/SelectionExpression.html,
828 +        doc/classoopse_1_1StuntDouble.png, doc/definition.jpg,
829 +        doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png,
830 +        src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp,
831 +        src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp,
832 +        src/selection/TokenMap.cpp: clean up SimInfo; modify the images of
833 +        SelectionExpression.html
834 +
835 + 2005-03-10 19:43  chrisfen
836 +
837          * samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md,
838          src/io/RestReader.cpp, src/restraints/Restraints.cpp,
839          src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in
840          MPI restraints
841  
842 < 2005-03-10 23:56  tim
842 > 2005-03-10 18:56  tim
843  
844          * doc/SelectionExpression.html, src/brains/SimInfo.cpp,
845          src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody
846          and cutoff group
847  
848 < 2005-03-10 22:06  gezelter
848 > 2005-03-10 17:06  gezelter
849  
850          * src/types/MorseBondType.hpp: fixed a doxygen problem
851  
852 < 2005-03-10 21:51  gezelter
852 > 2005-03-10 16:51  gezelter
853  
854          * samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with
855          the split dipole test cases
856  
857 < 2005-03-10 21:51  gezelter
857 > 2005-03-10 16:51  gezelter
858  
859          * doc/SelectionExpression.html: updated some documentation
860  
861 < 2005-03-10 20:40  gezelter
861 > 2005-03-10 15:40  gezelter
862  
863          * src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp,
864          Makefile: LinkedList removal project starts now
865  
866 < 2005-03-10 20:28  tim
866 > 2005-03-10 15:28  tim
867  
868          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
869          io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp:
870          using map to replace link list
871  
872 < 2005-03-10 19:11  tim
872 > 2005-03-10 14:11  tim
873  
874          * samples/dipole/: splitInWater.in, splitInWater.md: adding test
875          case  of split dipole
876  
877 < 2005-03-10 19:10  chrisfen
877 > 2005-03-10 14:10  chrisfen
878  
879          * samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp,
880          src/io/RestWriter.cpp,
881          src/restraints/ThermoIntegrationForceManager.cpp: Oops...  MPI now
882          builds...
883  
884 < 2005-03-10 18:44  tim
884 > 2005-03-10 13:44  tim
885  
886          * samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in,
887          split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md:
888          adding test case for split dipole
889  
890 < 2005-03-10 17:54  gezelter
890 > 2005-03-10 12:54  gezelter
891  
892          * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side
893          support for split dipoles
894  
895 < 2005-03-10 16:27  chrisfen
895 > 2005-03-10 11:27  chrisfen
896  
897          * samples/water/tip3p_ice/tp3.md,
898          src/restraints/ThermoIntegrationForceManager.cpp: fixes to
899          restraints
900  
901 < 2005-03-10 16:15  chrisfen
901 > 2005-03-10 11:15  chrisfen
902  
903          * samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp,
904          src/UseTheForce/ForceFields.hpp,
905          src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints
906  
907 < 2005-03-10 16:14  tim
907 > 2005-03-10 11:14  tim
908  
909          * ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc,
910          src/io/MultipoleAtomTypesSectionParser.cpp,
911          src/selection/SelectionEvaluator.cpp: minor change
912  
913 < 2005-03-10 15:10  chrisfen
913 > 2005-03-10 10:10  chrisfen
914  
915          * make/Makefile.in, samples/water/tip3p_ice/tp3.md,
916          src/brains/SimCreator.cpp, src/brains/SimInfo.hpp,
# Line 93 | Line 927
927          src/restraints/ThermoIntegrationForceManager.hpp: First commit of
928          the new restraints code
929  
930 < 2005-03-09 18:48  tim
930 > 2005-03-09 13:48  tim
931  
932          * src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding
933          IndexFinder
934  
935 < 2005-03-09 18:46  tim
935 > 2005-03-09 13:46  tim
936  
937          * src/: applications/dump2Xyz/Dump2XYZ.ggo,
938          applications/dump2Xyz/Dump2XYZCmd.c,
# Line 106 | Line 940
940          selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp:
941          fix compilation issue
942  
943 < 2005-03-09 17:58  tim
943 > 2005-03-09 12:58  tim
944  
945          * forceFields/DUFF2.frc, scripts/filepp,
946          src/UseTheForce/EAM_FF.cpp,
# Line 114 | Line 948
948          src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug
949          in SectionParser (lineNo is not updated)
950  
951 < 2005-03-09 17:30  tim
951 > 2005-03-09 12:30  tim
952  
953          * src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp,
954          applications/dump2Xyz/Dump2XYZ.ggo,
# Line 136 | Line 970
970          MultipoleAtomTypesSectionParser;remove print dipole option from
971          Dump2XYZ;
972  
973 < 2005-03-09 17:28  tim
973 > 2005-03-09 12:28  tim
974  
975          * forceFields/DUFF2.frc: change the format of DUFF2
976  
977 < 2005-03-09 15:44  gezelter
977 > 2005-03-09 10:44  gezelter
978  
979          * src/UseTheForce/DarkSide/: electrostatic.F90,
980          electrostatic_interface.F90, electrostatic_interface.h: new
981          electrostatic module
982  
983 < 2005-03-09 14:26  gezelter
983 > 2005-03-09 09:26  gezelter
984  
985          * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
986          DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole
987          and fixed quadrupole stuff
988  
989 < 2005-03-09 14:25  gezelter
989 > 2005-03-09 09:25  gezelter
990  
991          * src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines
992          for outdated charge and dipole interfaces
993  
994 < 2005-03-08 21:08  gezelter
994 > 2005-03-08 16:08  gezelter
995  
996          * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in,
997          mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun
998          charge-dipole test cases
999  
1000 < 2005-03-08 21:07  gezelter
1000 > 2005-03-08 16:07  gezelter
1001  
1002          * src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp,
1003          OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a
1004          strange icc8 bug (we think).
1005  
1006 < 2005-03-08 21:07  gezelter
1006 > 2005-03-08 16:07  gezelter
1007  
1008          * src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa!
1009  
1010 < 2005-03-08 21:07  gezelter
1010 > 2005-03-08 16:07  gezelter
1011  
1012          * src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic
1013          Unification Project
1014  
1015 < 2005-03-08 21:07  gezelter
1015 > 2005-03-08 16:07  gezelter
1016  
1017          * src/io/Globals.cpp: Dunno
1018  
1019 < 2005-03-08 21:06  gezelter
1019 > 2005-03-08 16:06  gezelter
1020  
1021          * src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using
1022          OOPSE_itoa and checking a NULL left over from the LinkedList days
1023  
1024 < 2005-03-08 21:06  gezelter
1024 > 2005-03-08 16:06  gezelter
1025  
1026          * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
1027          atype_interface.F90, atype_interface.h, charge.F90,
# Line 195 | Line 1029
1029          dipole_interface.F90, dipole_interface.h: electrostatic unification
1030          project fixed an uninitialized variable in Lennard Jones mixing map
1031  
1032 < 2005-03-08 21:05  gezelter
1032 > 2005-03-08 16:05  gezelter
1033  
1034          * src/UseTheForce/doForces.F90: electrostatic unification project
1035  
1036 < 2005-03-08 21:05  gezelter
1036 > 2005-03-08 16:05  gezelter
1037  
1038          * samples/water/dimer/: two.md, water.md: making some cool test
1039          cases
1040  
1041 < 2005-03-08 21:05  gezelter
1041 > 2005-03-08 16:05  gezelter
1042  
1043          * forceFields/DUFF2.frc: Added a charge for Chlorine
1044  
1045 < 2005-03-07 22:39  tim
1045 > 2005-03-07 17:39  tim
1046  
1047          * src/: brains/SimInfo.cpp, io/DumpReader.cpp,
1048          math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp,
1049          primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp:
1050          Fixing a bug in BitSet.cpp
1051  
1052 < 2005-03-04 15:28  gezelter
1052 > 2005-03-04 10:28  gezelter
1053  
1054          * src/config.h.in: Cleaning up config.h.in by adding comments
1055  
1056 < 2005-03-04 15:28  gezelter
1056 > 2005-03-04 10:28  gezelter
1057  
1058          * configure, ac-tools/configure.in, make/Makefile.in,
1059          src/brains/SimCreator.cpp: SPRNG eradication project
1060  
1061 < 2005-03-03 14:40  tim
1061 > 2005-03-03 09:40  tim
1062  
1063          * src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the
1064          missing atom type problem)
1065  
1066 < 2005-03-02 16:29  tim
1066 > 2005-03-02 11:29  tim
1067  
1068          * src/math/RandNumGen.hpp: adding base class of Random Number
1069          generator
1070  
1071 < 2005-03-02 16:28  tim
1071 > 2005-03-02 11:28  tim
1072  
1073          * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
1074          math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in
1075          Velocitizer is not initialized which causes a seg fault
1076  
1077 < 2005-03-02 15:36  tim
1077 > 2005-03-02 10:36  tim
1078  
1079          * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
1080          integrators/Velocitizer.hpp, math/Makefile,
# Line 250 | Line 1084
1084          MersenneTwister.hpp which causes all kinds of trouble.  Refactory
1085          random number generator
1086  
1087 < 2005-03-02 07:32  tim
1087 > 2005-03-02 02:32  tim
1088  
1089          * test/math/testRandNumGen.cpp: Adding unit test for random number
1090          generator
1091  
1092 < 2005-03-01 23:17  tim
1092 > 2005-03-01 18:17  tim
1093  
1094          * src/brains/Thermo.hpp: fixed a file inclusion problem
1095  
1096 < 2005-03-01 23:17  tim
1096 > 2005-03-01 18:17  tim
1097  
1098          * test/math/: Makefile, OOPSERandNumGenTestCase.cpp,
1099          OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp,
1100          ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp,
1101          RandNumGenTestCase.hpp: fixed compilation problem
1102  
1103 < 2005-03-01 23:02  tim
1103 > 2005-03-01 18:02  tim
1104  
1105          * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
1106          integrators/Velocitizer.hpp, math/Makefile,
# Line 274 | Line 1108
1108          math/ParallelRandNumGen.hpp, math/mt19937ar.c,
1109          math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand
1110  
1111 < 2005-03-01 23:00  tim
1111 > 2005-03-01 18:00  tim
1112  
1113          * test/math/: Makefile, ParallelandNumGenTestCase.cpp,
1114          ParallelandNumGenTestCase.hpp: Change the name of test case
1115  
1116 < 2005-03-01 21:00  tim
1116 > 2005-03-01 16:00  tim
1117  
1118          * test/math/: Makefile, OOPSERandNumGenTestCase.cpp,
1119          OOPSERandNumGenTestCase.hpp: adding testcase for random number
1120          generator
1121  
1122 < 2005-03-01 20:10  tim
1122 > 2005-03-01 15:10  tim
1123  
1124          * src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp,
1125          integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp,
# Line 296 | Line 1130
1130          utils/TypeContainer.hpp, visitors/AtomVisitor.cpp,
1131          visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4
1132  
1133 < 2005-03-01 19:11  tim
1133 > 2005-03-01 14:11  tim
1134  
1135          * src/: brains/SimCreator.cpp, brains/SimInfo.hpp,
1136          integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
1137          math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding
1138          OOPSERandNumGen
1139  
1140 < 2005-03-01 15:44  gezelter
1140 > 2005-03-01 10:44  gezelter
1141  
1142          * make/Makefile.in: Fixed the damned build problem with the
1143          libraries not being removed in make clean and make distclean (at
1144          least we think it is fixed).
1145  
1146 < 2005-03-01 15:26  gezelter
1146 > 2005-03-01 10:26  gezelter
1147  
1148          * src/math/MersenneTwister.hpp: Making small modifications to allow
1149          for use on MPI machines
1150  
1151 < 2005-03-01 14:45  tim
1151 > 2005-03-01 09:45  tim
1152  
1153          * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp,
1154          integrators/Velocitizer.cpp, io/DumpReader.cpp,
1155          math/MersenneTwister.hpp: adding MersenneTwister random number
1156          generator
1157  
1158 < 2005-03-01 03:55  tim
1158 > 2005-02-28 22:55  tim
1159  
1160          * src/math/MersenneTwister.hpp: Adding a modified version of
1161          MersenneTwister.hpp
1162  
1163 < 2005-02-28 17:24  tim
1163 > 2005-02-28 12:24  tim
1164  
1165          * doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png,
1166          definition.jpg: selection expression
1167  
1168 < 2005-02-25 21:22  tim
1168 > 2005-02-25 16:22  tim
1169  
1170          * src/: UseTheForce/DarkSide/LJ.F90,
1171          UseTheForce/DarkSide/lj_interface.F90,
# Line 339 | Line 1173
1173          io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp,
1174          types/AtomType.hpp: adding soft potential to LJ Module
1175  
1176 < 2005-02-25 16:38  tim
1176 > 2005-02-25 11:38  tim
1177  
1178          * doc/SelectionExpression.html: adding documentation for selection
1179          expression
1180  
1181 < 2005-02-24 20:55  tim
1181 > 2005-02-24 15:55  tim
1182  
1183          * src/: applications/simpleBuilder/simpleBuilder.cpp,
1184          integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp,
# Line 352 | Line 1186
1186          adding basic_teebuf which can operate on multiple stream
1187          simutaneously.
1188  
1189 < 2005-02-22 18:56  tim
1189 > 2005-02-22 14:26  chrisfen
1190  
1191 +        * samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf
1192 +        sample
1193 +
1194 + 2005-02-22 13:56  tim
1195 +
1196          * src/: UseTheForce/DarkSide/reactionField.F90,
1197          primitives/RigidBody.cpp: reactionfield get fixed
1198  
1199 < 2005-02-21 16:57  tim
1199 > 2005-02-21 11:57  tim
1200  
1201          * src/: applications/staticProps/GofRAngle.cpp,
1202          visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix
1203          a bug in GofRAngle
1204  
1205 < 2005-02-21 15:28  tim
1205 > 2005-02-21 10:28  tim
1206  
1207          * src/primitives/Molecule.cpp: Fix for compilation on the Sun
1208  
1209 < 2005-02-21 15:22  tim
1209 > 2005-02-21 10:22  tim
1210  
1211          * src/utils/next_combination.hpp: fix for compilation on the Sun
1212  
1213 < 2005-02-21 15:21  tim
1213 > 2005-02-21 10:21  tim
1214  
1215          * src/utils/GenericData.hpp: fix problem in sun
1216  
1217 < 2005-02-18 23:07  tim
1217 > 2005-02-18 18:07  tim
1218  
1219          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
1220          applications/dump2Xyz/Dump2XYZ.ggo,
# Line 392 | Line 1231
1231          visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
1232          visitors/Makefile: adding LipidTransVisitor, GofXyz is working now
1233  
1234 < 2005-02-18 15:58  gezelter
1234 > 2005-02-18 10:58  gezelter
1235  
1236          * src/brains/Register.cpp: Corrected filename collision for EAM on
1237          Mac OS X
1238  
1239 < 2005-02-18 15:58  gezelter
1239 > 2005-02-18 10:58  gezelter
1240  
1241          * src/applications/oopse/oopse.cpp: Updated copyright information
1242  
1243 < 2005-02-18 15:58  gezelter
1243 > 2005-02-18 10:58  gezelter
1244  
1245          * src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp,
1246          Makefile: corrected filename collision for EAM on operating systems
1247          which are not case sensitive (aka Mac OS X)
1248  
1249 < 2005-02-17 20:15  tim
1249 > 2005-02-17 15:15  tim
1250  
1251          * src/applications/staticProps/GofXyz.cpp: more bug get fixed
1252  
1253 < 2005-02-17 19:50  tim
1253 > 2005-02-17 14:50  tim
1254  
1255          * src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug
1256          in GofXyz
1257  
1258 < 2005-02-17 19:09  tim
1258 > 2005-02-17 14:09  tim
1259  
1260          * src/applications/staticProps/RadialDistrFunc.hpp: make
1261          processHistogram non-abstrct function
1262  
1263 < 2005-02-17 18:41  tim
1263 > 2005-02-17 13:41  tim
1264  
1265          * src/applications/staticProps/GofXyz.cpp: [no log message]
1266  
1267 < 2005-02-17 18:30  tim
1267 > 2005-02-17 13:30  tim
1268  
1269          * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp,
1270          GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp:
1271          finish GofXyz
1272  
1273 < 2005-02-17 16:21  tim
1273 > 2005-02-17 11:21  tim
1274  
1275          * src/applications/staticProps/: GofAngle2.cpp, GofR.cpp,
1276          GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial
1277          distribution function
1278  
1279 < 2005-02-17 15:23  tim
1279 > 2005-02-17 10:23  tim
1280  
1281          * src/utils/BitSet.hpp: forget the const correctness for BitSet
1282  
1283 < 2005-02-17 15:18  tim
1283 > 2005-02-17 10:18  tim
1284  
1285          * src/: brains/BlockSnapshotManager.cpp,
1286          selection/DistanceFinder.cpp: The change of interface of BitSet
1287          cause a bug in SelectionEvaluation
1288  
1289 < 2005-02-16 21:13  tim
1289 > 2005-02-16 16:13  tim
1290  
1291          * src/utils/residentMem.c: return residentMem in byte
1292  
1293 < 2005-02-16 21:00  tim
1293 > 2005-02-16 16:00  tim
1294  
1295          * src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix
1296          a bug in writing out the value of cosang
1297  
1298 < 2005-02-16 20:43  tim
1298 > 2005-02-16 15:43  tim
1299  
1300          * src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to
1301          estimate avaliable memory
1302  
1303 < 2005-02-16 20:30  tim
1303 > 2005-02-16 15:30  tim
1304  
1305          * src/: applications/staticProps/GofAngle2.cpp,
1306          applications/staticProps/GofAngle2.hpp,
# Line 477 | Line 1316
1316          applications/staticProps/StaticPropsCmd.h,
1317          brains/BlockSnapshotManager.cpp: change the default bin number
1318  
1319 < 2005-02-16 19:36  tim
1319 > 2005-02-16 14:36  tim
1320  
1321          * src/: applications/dynamicProps/DipoleCorrFunc.cpp,
1322          applications/dynamicProps/RCorrFunc.cpp,
# Line 494 | Line 1333
1333          utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output
1334          files;fix the problem of counting in staticProps
1335  
1336 < 2005-02-15 19:39  tim
1336 > 2005-02-15 14:39  tim
1337  
1338          * src/brains/BlockSnapshotManager.cpp: fix a bug in
1339          BlockSnapshotManager
1340  
1341 < 2005-02-15 19:36  tim
1341 > 2005-02-15 14:36  tim
1342  
1343          * src/: applications/dynamicProps/TimeCorrFunc.cpp,
1344          applications/staticProps/RadialDistrFunc.cpp,
# Line 507 | Line 1346
1346          selection/SelectionEvaluator.cpp: BlockSnapshotManager is using
1347          reference counting now
1348  
1349 < 2005-02-15 17:49  tim
1349 > 2005-02-15 12:49  tim
1350  
1351          * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
1352          replace std::make_pair by VariablesType::value_type to make Sun
1353          Compiler happy
1354  
1355 < 2005-02-15 17:35  tim
1355 > 2005-02-15 12:35  tim
1356  
1357          * src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to
1358          TokenMap, using TokenMapType::value_type instead of std::make_pair
1359          to make Sun compiler happy
1360  
1361 < 2005-02-15 17:24  tim
1361 > 2005-02-15 12:24  tim
1362  
1363          * src/applications/staticProps/: GofRAngle.cpp,
1364          RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps
1365  
1366 < 2005-02-15 17:11  tim
1366 > 2005-02-15 12:11  tim
1367  
1368          * src/: applications/staticProps/GofR.cpp,
1369          applications/staticProps/RadialDistrFunc.cpp,
# Line 533 | Line 1372
1372          #ifdef __RWSTD to make sun compiler happy (2) fix pair density
1373          calculation problem when two selections intersect with each other
1374  
1375 < 2005-02-15 15:24  gezelter
1375 > 2005-02-15 10:24  gezelter
1376  
1377          * src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy
1378          xlc++
1379  
1380 < 2005-02-15 15:17  gezelter
1380 > 2005-02-15 10:17  gezelter
1381  
1382          * configure, ac-tools/configure.in, src/config.h.in,
1383          src/utils/residentMem.c: [no log message]
1384  
1385 < 2005-02-15 06:17  gezelter
1385 > 2005-02-15 01:17  gezelter
1386  
1387          * src/utils/residentMem.c: bug fix for null termination
1388  
1389 < 2005-02-15 06:11  gezelter
1389 > 2005-02-15 01:11  gezelter
1390  
1391          * configure, ac-tools/configure.in, src/utils/residentMem.c:
1392          bugfixing residentMem
1393  
1394 < 2005-02-15 05:59  gezelter
1394 > 2005-02-15 00:59  gezelter
1395  
1396          * configure, ac-tools/configure.in, src/config.h.in,
1397          src/utils/residentMem.c: bugfixes for residentMem on LINUX
1398  
1399 < 2005-02-15 05:08  gezelter
1399 > 2005-02-15 00:08  gezelter
1400  
1401          * src/utils/Makefile.in: added residentMem
1402  
1403 < 2005-02-15 05:05  gezelter
1403 > 2005-02-15 00:05  gezelter
1404  
1405          * configure, ac-tools/configure.in, make/Makefile.in,
1406          src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c,
# Line 569 | Line 1408
1408          other processes autoconf fixes ps syntax checking config.h file
1409          cleaning
1410  
1411 < 2005-02-14 23:26  gezelter
1411 > 2005-02-14 18:26  gezelter
1412  
1413          * configure, ac-tools/configure.in, make/Makefile.in: ps niceness
1414  
1415 < 2005-02-14 23:16  gezelter
1415 > 2005-02-14 18:16  gezelter
1416  
1417          * configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps
1418          strangeness
1419  
1420 < 2005-02-14 19:42  tim
1420 > 2005-02-14 14:42  tim
1421  
1422          * src/brains/BlockSnapshotManager.cpp: fix a bug in
1423          BlockSnapshotManager.hpp
1424  
1425 < 2005-02-14 18:51  tim
1425 > 2005-02-14 13:51  tim
1426  
1427          * src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo,
1428          StaticPropsCmd.c: default length for staticProps is 1/2 smallest
1429          length of first frame
1430  
1431 < 2005-02-14 18:12  tim
1431 > 2005-02-14 13:12  tim
1432  
1433          * src/integrators/VelocityVerletIntegrator.cpp: fix a bug in
1434          VelocityVerletIntegrator : last frame is written twice
1435  
1436 < 2005-02-14 17:57  tim
1436 > 2005-02-14 12:57  tim
1437  
1438          * src/: applications/dynamicProps/TimeCorrFunc.cpp,
1439          brains/SimInfo.cpp, primitives/RigidBody.cpp,
1440          primitives/StuntDouble.hpp: begin bug fix
1441  
1442 < 2005-02-14 17:35  tim
1442 > 2005-02-14 12:35  tim
1443  
1444          * src/applications/dynamicProps/: CorrelationFunction.cpp,
1445          CorrelationFunction.hpp, CrossTimeCorrFunc.cpp,
# Line 610 | Line 1449
1449          RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp,
1450          VCorrFunc.hpp: refactory CorrelationFunction
1451  
1452 < 2005-02-14 15:18  gezelter
1452 > 2005-02-14 10:18  gezelter
1453  
1454          * src/applications/dynamicProps/CorrelationFunction.cpp: bug fix
1455          and start of switch for type of correlation function
1456  
1457 < 2005-02-13 21:18  tim
1457 > 2005-02-13 16:18  tim
1458  
1459          * src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in
1460          calculating  bytes per stuntdouble
1461  
1462 < 2005-02-13 21:03  tim
1462 > 2005-02-13 16:03  tim
1463  
1464          * src/applications/dynamicProps/CorrelationFunction.cpp: more fix
1465  
1466 < 2005-02-13 20:57  tim
1466 > 2005-02-13 15:57  tim
1467  
1468          * src/applications/dynamicProps/CorrelationFunction.cpp: fixed a
1469          bug in CorrelationFunction
1470  
1471 < 2005-02-13 20:36  tim
1471 > 2005-02-13 15:36  tim
1472  
1473          * src/: applications/staticProps/GofR.cpp,
1474          applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a
1475          bug in SimInfo::getCutoff()
1476  
1477 < 2005-02-13 20:08  tim
1477 > 2005-02-13 15:08  tim
1478  
1479          * make/Makefile.in: adding staticProps and dynamicProps into
1480          Makefile.in
1481  
1482 < 2005-02-13 20:05  tim
1482 > 2005-02-13 15:05  tim
1483  
1484          * src/: applications/dynamicProps/CorrelationFunction.cpp,
1485          applications/dynamicProps/CorrelationFunction.hpp,
# Line 651 | Line 1490
1490          brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length
1491          defaults to the cutoff radius
1492  
1493 < 2005-02-13 19:14  tim
1493 > 2005-02-13 14:14  tim
1494  
1495          * src/utils/Algorithm.hpp: adding Algorithm.hpp
1496  
1497 < 2005-02-13 19:10  tim
1497 > 2005-02-13 14:10  tim
1498  
1499          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
1500          applications/dynamicProps/CorrelationFunction.cpp,
# Line 669 | Line 1508
1508          utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h,
1509          visitors/OtherVisitor.cpp: dynamicProps get built
1510  
1511 < 2005-02-13 15:56  tim
1511 > 2005-02-13 10:56  tim
1512  
1513          * src/: applications/dynamicProps/CorrelationFunction.cpp,
1514          brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
1515          brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in
1516          progress
1517  
1518 < 2005-02-13 08:04  tim
1518 > 2005-02-13 03:04  tim
1519  
1520          * src/: applications/dynamicProps/CorrelationFunction.hpp,
1521          brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
# Line 684 | Line 1523
1523          brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more
1524          work in dynamicProps
1525  
1526 < 2005-02-13 07:25  tim
1526 > 2005-02-13 02:25  tim
1527  
1528          * src/applications/dynamicProps/DynamicProps.cpp: adding
1529          dynamicProps
1530  
1531 < 2005-02-13 07:14  tim
1531 > 2005-02-13 02:14  tim
1532  
1533          * src/applications/dynamicProps/: DynamicPropsCmd.c,
1534          DynamicPropsCmd.h: adding command line option to DynamicProps
1535  
1536 < 2005-02-13 07:13  tim
1536 > 2005-02-13 02:13  tim
1537  
1538          * src/applications/dynamicProps/: DynamicProps.ggo, Makefile:
1539          adding command line option for DynamicProps
1540  
1541 < 2005-02-13 06:57  tim
1541 > 2005-02-13 01:57  tim
1542  
1543          * src/: applications/dynamicProps/CorrelationFunction.cpp,
1544          applications/dynamicProps/CorrelationFunction.hpp,
# Line 716 | Line 1555
1555          primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding
1556          dynamicProps
1557  
1558 < 2005-02-12 20:09  tim
1558 > 2005-02-12 15:09  tim
1559  
1560          * src/selection/SelectionManager.cpp: adding SelectionManager.cpp
1561  
1562 < 2005-02-11 22:41  tim
1562 > 2005-02-11 17:41  tim
1563  
1564          * src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one
1565          more constructor to Snapshot to create customized DataStorage
1566  
1567 < 2005-02-11 22:39  tim
1567 > 2005-02-11 17:39  tim
1568  
1569          * src/selection/: DistanceFinder.hpp, Makefile,
1570          SelectionManager.hpp: adding beginSelected, nextSelected method to
1571          SelectionManager
1572  
1573 < 2005-02-11 22:36  tim
1573 > 2005-02-11 17:36  tim
1574  
1575          * src/config.h.in, configure: adding support for physmem
1576  
1577 < 2005-02-11 22:35  tim
1577 > 2005-02-11 17:35  tim
1578  
1579          * ac-tools/configure.in: adding supprot for physmem
1580  
1581 < 2005-02-11 22:35  tim
1581 > 2005-02-11 17:35  tim
1582  
1583          * src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding
1584          physmem
1585  
1586 < 2005-02-10 22:37  tim
1586 > 2005-02-10 17:37  tim
1587  
1588          * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp,
1589          GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp,
# Line 752 | Line 1591
1591          StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
1592          StaticPropsCmd.h: more work in StaticProps
1593  
1594 < 2005-02-10 18:14  tim
1594 > 2005-02-10 13:14  tim
1595  
1596          * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp,
1597          GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp,
# Line 761 | Line 1600
1600          StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
1601          StaticPropsCmd.h: change the filenames
1602  
1603 < 2005-02-10 14:15  tim
1603 > 2005-02-10 09:15  tim
1604  
1605          * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp,
1606          GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp,
1607          RadialDistrFunc.hpp: adding GofRAngle
1608  
1609 < 2005-02-09 18:21  tim
1609 > 2005-02-09 13:21  tim
1610  
1611          * src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some
1612          useless files
1613  
1614 < 2005-02-09 18:12  tim
1614 > 2005-02-09 13:12  tim
1615  
1616          * src/applications/staticProps/: GofR.cpp, Makefile,
1617          RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress
1618  
1619 < 2005-02-09 17:08  tim
1619 > 2005-02-09 12:08  tim
1620  
1621          * src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp,
1622          GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h,
1623          RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR
1624  
1625 < 2005-02-07 22:39  tim
1625 > 2005-02-07 17:39  tim
1626  
1627          * src/primitives/Molecule.hpp: add getRigidBodyAt  function into
1628          Molecule class
1629  
1630 < 2005-02-07 22:38  tim
1630 > 2005-02-07 17:38  tim
1631  
1632          * src/applications/dump2Xyz/Dump2XYZCmd.c: update help info
1633  
1634 < 2005-02-07 22:36  tim
1634 > 2005-02-07 17:36  tim
1635  
1636          * src/selection/: NameFinder.cpp, NameFinder.hpp,
1637          SelectionCompiler.cpp: support select internal index selection, for
1638          example, select DMPC.3
1639  
1640 < 2005-02-07 21:11  tim
1640 > 2005-02-07 16:11  tim
1641  
1642          * src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update
1643          help info for Dump2XYZ
1644  
1645 < 2005-02-07 20:39  chrisfen
1645 > 2005-02-07 15:39  chrisfen
1646  
1647          * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
1648          selection librarys added
1649  
1650 < 2005-02-07 20:31  tim
1650 > 2005-02-07 15:31  tim
1651  
1652          * src/selection/Makefile, make/Makefile.in: adding Makefile
1653  
1654 < 2005-02-07 20:20  chrisfen
1654 > 2005-02-07 15:20  chrisfen
1655  
1656          * src/utils/wildcards.hpp: issue commented out in wildcards
1657  
1658 < 2005-02-07 20:06  tim
1658 > 2005-02-07 15:06  tim
1659  
1660          * src/selection/SelectionEvaluator.cpp: forget to reset the pc
1661          which cause reevaluate return NULL
1662  
1663 < 2005-02-07 19:14  tim
1663 > 2005-02-07 14:14  tim
1664  
1665          * src/brains/: SimCreator.cpp, SimSnapshotManager.cpp,
1666          SimSnapshotManager.hpp: fix a bug in determing the global index for
1667          rigidbodies
1668  
1669 < 2005-02-07 19:13  tim
1669 > 2005-02-07 14:13  tim
1670  
1671          * src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change
1672          in Bitset
1673  
1674 < 2005-02-07 19:13  tim
1674 > 2005-02-07 14:13  tim
1675  
1676          * src/selection/: DistanceFinder.cpp, DistanceFinder.hpp,
1677          SelectionCompiler.cpp, SelectionCompiler.hpp,
1678          SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp,
1679          TokenMap.cpp: selection library is working
1680  
1681 < 2005-02-04 22:46  tim
1681 > 2005-02-04 17:46  tim
1682  
1683          * src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor
1684  
1685 < 2005-02-04 22:45  tim
1685 > 2005-02-04 17:45  tim
1686  
1687          * src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor
1688          and XYZVisitor now use selection library
1689  
1690 < 2005-02-04 22:44  tim
1690 > 2005-02-04 17:44  tim
1691  
1692          * src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp:
1693          adding SelectionManager into SimInfo
1694  
1695 < 2005-02-04 22:43  tim
1695 > 2005-02-04 17:43  tim
1696  
1697          * src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo,
1698          Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of
1699          selection library
1700  
1701 < 2005-02-04 22:42  tim
1701 > 2005-02-04 17:42  tim
1702  
1703          * src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change
1704          in BitSet
1705  
1706 < 2005-02-04 22:41  tim
1706 > 2005-02-04 17:41  tim
1707  
1708          * src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing
1709          implementation
1710  
1711 < 2005-02-04 22:39  tim
1711 > 2005-02-04 17:39  tim
1712  
1713          * src/selection/: NameFinder.cpp, NameFinder.hpp,
1714          SelectionCompiler.cpp, SelectionCompiler.hpp,
# Line 877 | Line 1716
1716          SelectionManager.hpp, Token.hpp: half of the selection utility is
1717          working need to debug within keyword and atomproperty keyword
1718  
1719 < 2005-02-04 05:42  tim
1719 > 2005-02-04 00:42  tim
1720  
1721          * src/selection/: NameFinder.cpp, NameFinder.hpp: selection library
1722          get built
1723  
1724 < 2005-02-04 05:42  tim
1724 > 2005-02-04 00:42  tim
1725  
1726          * src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet
1727  
1728 < 2005-02-04 05:26  tim
1728 > 2005-02-04 00:26  tim
1729  
1730          * src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp:
1731          remove some useless files
1732  
1733 < 2005-02-04 04:57  tim
1733 > 2005-02-03 23:57  tim
1734  
1735          * src/: primitives/RigidBody.hpp, selection/NameFinder.cpp,
1736          selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp:
1737          adding wildcard class; NameFinder is finished
1738  
1739 < 2005-02-03 23:14  tim
1739 > 2005-02-03 18:14  tim
1740  
1741          * src/selection/: NameFinder.cpp, NameFinder.hpp,
1742          SelectionCompiler.cpp, SelectionCompiler.hpp,
# Line 905 | Line 1744
1744          SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in
1745          selection library
1746  
1747 < 2005-02-03 14:04  tim
1747 > 2005-02-03 09:04  tim
1748  
1749          * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
1750          selection in progress
1751  
1752 < 2005-02-02 23:13  tim
1752 > 2005-02-02 18:13  tim
1753  
1754          * src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp,
1755          SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp,
1756          Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in
1757          progress, except SelectionEvaluator, other files are compiled
1758  
1759 < 2005-02-02 23:12  tim
1759 > 2005-02-02 18:12  tim
1760  
1761          * src/utils/: Makefile.in, any.hpp: adding boost::any
1762  
1763 < 2005-02-02 12:51  tim
1763 > 2005-02-02 07:51  tim
1764  
1765          * src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp
1766  
1767 < 2005-02-01 22:49  tim
1767 > 2005-02-01 17:49  tim
1768  
1769          * src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp,
1770          selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp,
1771          selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp,
1772          selection/Token.hpp: Selection in progress
1773  
1774 < 2005-02-01 06:55  tim
1774 > 2005-02-01 01:55  tim
1775  
1776          * src/: selection/SelectionCompiler.hpp,
1777          selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
1778          selection/SelectionManager.hpp, selection/Token.hpp,
1779          utils/BitSet.cpp, utils/BitSet.hpp: adding selection library
1780  
1781 < 2005-01-26 15:26  tim
1781 > 2005-01-26 10:26  tim
1782  
1783          * src/integrators/: Integrator.cpp, Integrator.hpp,
1784          VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget
1785          to add eorWriter
1786  
1787 < 2005-01-26 15:15  tim
1787 > 2005-01-26 10:15  tim
1788  
1789          * src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp:
1790          (1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the
1791          wrong column of electroframe
1792  
1793 < 2005-01-25 21:59  tim
1793 > 2005-01-25 16:59  tim
1794  
1795          * src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in
1796          SimInfo, use number of cutoff stamp as counter to loop over
1797          rigidbody stamp
1798  
1799 < 2005-01-25 17:45  tim
1799 > 2005-01-25 12:45  tim
1800  
1801          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
1802          brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
# Line 977 | Line 1816
1816          inertial tensor from the directional atoms before calculate
1817          rigidbody's inertial tensor
1818  
1819 < 2005-01-17 22:17  tim
1819 > 2005-01-17 17:17  tim
1820  
1821          * forceFields/DUFF2.frc: forget to set dipole for lipid head group
1822  
1823 < 2005-01-17 16:58  tim
1823 > 2005-01-17 11:58  tim
1824  
1825          * src/integrators/NVT.cpp: fix a bug in loading initial extended
1826          system parameters
1827  
1828 < 2005-01-17 16:05  tim
1828 > 2005-01-17 11:05  tim
1829  
1830          * src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT
1831  
1832 < 2005-01-14 22:02  tim
1832 > 2005-01-14 17:02  tim
1833  
1834          * src/UseTheForce/WATER.cpp: remove WATER.cpp
1835  
1836 < 2005-01-14 21:37  tim
1836 > 2005-01-14 16:37  tim
1837  
1838          * forceFields/Makefile: sync Makefile
1839  
1840 < 2005-01-14 21:13  gezelter
1840 > 2005-01-14 16:13  gezelter
1841  
1842          * make/Makefile.in, src/Makefile, src/UseTheForce/Makefile,
1843          src/UseTheForce/DarkSide/Makefile, src/applications/Makefile,
# Line 1012 | Line 1851
1851          src/visitors/Makefile: moved Package variable into subdirectory
1852          makefiles to speed up the building process
1853  
1854 < 2005-01-14 20:48  gezelter
1854 > 2005-01-14 15:48  gezelter
1855  
1856          * src/applications/oopse/oopse.cpp: Fixed publication details in
1857          banner
1858  
1859 < 2005-01-14 20:48  gezelter
1859 > 2005-01-14 15:48  gezelter
1860  
1861          * src/UseTheForce/DarkSide/: simParallel_interface.F90,
1862          simParallel_interface.h: added dummy subroutine to avoid empty
1863          unit, synchronized this dummy routine between C and fortran
1864  
1865 < 2005-01-14 20:31  gezelter
1865 > 2005-01-14 15:31  gezelter
1866  
1867          * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90,
1868          notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90,
# Line 1039 | Line 1878
1878          DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating
1879          modules and C/Fortran interface subroutines
1880  
1881 < 2005-01-14 20:15  gezelter
1881 > 2005-01-14 15:15  gezelter
1882  
1883          * configure, ac-tools/aclocal.m4: more fixes for gnugetopt
1884  
1885 < 2005-01-14 20:09  gezelter
1885 > 2005-01-14 15:09  gezelter
1886  
1887          * configure, ac-tools/configure.in, src/config.h.in,
1888          src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt
1889  
1890 < 2005-01-14 16:49  tim
1890 > 2005-01-14 11:49  tim
1891  
1892          * src/: io/EAMAtomTypesSectionParser.cpp,
1893          utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
1894          utils/StringUtils.hpp: using c library to do conversion instead of
1895          using iostream due to a bug in libstdc++(GCC 3.2)
1896  
1897 < 2005-01-14 02:40  tim
1897 > 2005-01-13 21:40  tim
1898  
1899          * src/brains/SimSetup.cpp: no message
1900  
1901 < 2005-01-14 01:56  tim
1901 > 2005-01-13 20:56  tim
1902  
1903          * src/primitives/Molecule.hpp: fix a bug in global index
1904  
1905 < 2005-01-14 01:04  tim
1905 > 2005-01-13 20:04  tim
1906  
1907          * src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include
1908          Integrator.hpp in Minimizer
1909  
1910 < 2005-01-13 22:14  gezelter
1910 > 2005-01-13 17:14  gezelter
1911  
1912          * src/utils/Makefile: compile getopt and getopt1 if we need to
1913  
1914 < 2005-01-13 21:56  gezelter
1914 > 2005-01-13 16:56  gezelter
1915  
1916          * make/Makefile.in: template flags
1917  
1918 < 2005-01-13 21:48  gezelter
1918 > 2005-01-13 16:48  gezelter
1919  
1920          * src/applications/oopse/Makefile: formatting
1921  
1922 < 2005-01-13 21:48  gezelter
1922 > 2005-01-13 16:48  gezelter
1923  
1924          * make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir
1925          target
1926  
1927 < 2005-01-13 19:40  tim
1927 > 2005-01-13 14:40  tim
1928  
1929          * src/: UseTheForce/fSwitchingFunction.h,
1930          UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile,
# Line 1093 | Line 1932
1932          primitives/RigidBody.cpp, types/AtomTypeProperties.h,
1933          types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform
1934  
1935 < 2005-01-13 18:26  tim
1935 > 2005-01-13 13:26  tim
1936  
1937          * make/Makefile.in: change the order of linking (object file comes
1938          first and then follow by user built library)
1939  
1940 < 2005-01-12 23:24  tim
1940 > 2005-01-12 18:24  tim
1941  
1942          * src/io/DumpWriter.cpp: remove useless debug info
1943  
1944 < 2005-01-12 23:21  tim
1944 > 2005-01-12 18:21  tim
1945  
1946          * src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix
1947  
1948 < 2005-01-12 23:17  tim
1948 > 2005-01-12 18:17  tim
1949  
1950          * make/: Makefile.in, Makefile.in: missing tab
1951  
1952 < 2005-01-12 23:15  tim
1952 > 2005-01-12 18:15  tim
1953  
1954          * src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor
1955          get fixed
1956  
1957 < 2005-01-12 22:40  gezelter
1957 > 2005-01-12 17:40  gezelter
1958  
1959          * make/Makefile.in, src/UseTheForce/DUFF.cpp,
1960          src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp,
# Line 1325 | Line 2164
2164          src/visitors/ZconsVisitor.hpp: merging new_design branch into
2165          OOPSE-2.0
2166  
2167 < 2005-01-12 18:13  tim
2167 > 2005-01-12 13:13  tim
2168  
2169          * src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp,
2170          utils/TypeContainer.hpp: forget to include <algorithm>
2171  
2172 < 2005-01-12 17:25  tim
2172 > 2005-01-12 12:25  tim
2173  
2174          * forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc,
2175          newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force
2176          fields
2177  
2178 < 2005-01-12 17:14  tim
2178 > 2005-01-12 12:14  tim
2179  
2180          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2181          UseTheForce/EAM.cpp, UseTheForce/EAM.hpp,
# Line 1498 | Line 2337
2337          visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
2338          visitors/ZconsVisitor.hpp: change license
2339  
2340 < 2005-01-12 17:14  tim
2340 > 2005-01-12 12:14  tim
2341  
2342          * src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on
2343          branch new_design.
2344  
2345 < 2005-01-11 21:03  tim
2345 > 2005-01-11 16:03  tim
2346  
2347          * src/: constraints/ZconstraintForceManager.cpp,
2348          constraints/ZconstraintForceManager.hpp,
# Line 1511 | Line 2350
2350          minimizers/MinimizerParameterSet.hpp: change const static double
2351          data member to const double
2352  
2353 < 2005-01-11 20:50  tim
2353 > 2005-01-11 15:50  tim
2354  
2355          * src/io/basic_ifstrstream.hpp: forget namespace qualifier std::
2356  
2357 < 2005-01-11 20:39  tim
2357 > 2005-01-11 15:39  tim
2358  
2359          * src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h:
2360          change data type from logical to integer in AtomTypeProperties.h
2361  
2362 < 2005-01-11 16:36  tim
2362 > 2005-01-11 11:36  tim
2363  
2364          * forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding
2365          new format of EAM force field
2366  
2367 < 2005-01-11 16:24  tim
2367 > 2005-01-11 11:24  tim
2368  
2369          * src/UseTheForce/DUFF.cpp: change default name of DUFF force field
2370          to DUFF2.frc
2371  
2372 < 2005-01-11 16:23  tim
2372 > 2005-01-11 11:23  tim
2373  
2374          * forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to
2375          DUFF2.frc
2376  
2377 < 2005-01-11 16:09  tim
2377 > 2005-01-11 11:09  tim
2378  
2379          * make/Makefile.in: adding constraints and minimizers into
2380          Makefile.in
2381  
2382 < 2005-01-11 16:03  tim
2382 > 2005-01-11 11:03  tim
2383  
2384          * src/io/: ChargeAtomTypesSectionParser.cpp,
2385          ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp,
2386          DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless
2387          files
2388  
2389 < 2005-01-11 15:59  tim
2389 > 2005-01-11 10:59  tim
2390  
2391          * src/io/ZConsWriter.cpp: [no log message]
2392  
2393 < 2005-01-11 15:53  tim
2393 > 2005-01-11 10:53  tim
2394  
2395          * src/UseTheForce/EAM.cpp: minor fix
2396  
2397 < 2005-01-11 15:52  tim
2397 > 2005-01-11 10:52  tim
2398  
2399          * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
2400          on branch new_design.
2401  
2402 < 2005-01-11 15:52  tim
2402 > 2005-01-11 10:52  tim
2403  
2404          * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
2405          on branch new_design.
2406  
2407 < 2005-01-11 15:52  tim
2407 > 2005-01-11 10:52  tim
2408  
2409          * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
2410  
2411 < 2005-01-11 15:47  tim
2411 > 2005-01-11 10:47  tim
2412  
2413          * make/Makefile.in: forget a '$' sign
2414  
2415 < 2005-01-11 15:46  tim
2415 > 2005-01-11 10:46  tim
2416  
2417          * make/Makefile.in: missing tab in rules
2418  
2419 < 2005-01-10 22:04  tim
2419 > 2005-01-10 17:04  tim
2420  
2421          * src/: UseTheForce/ForceFieldCreator.cpp,
2422          UseTheForce/ForceFieldCreator.hpp,
# Line 1596 | Line 2435
2435          minimizers/MinimizerFactory.hpp: create a register module to
2436          register force fields, integrators and minimizers
2437  
2438 < 2005-01-10 22:04  tim
2438 > 2005-01-10 17:04  tim
2439  
2440          * src/brains/Register.cpp: file Register.cpp was initially added on
2441          branch new_design.
2442  
2443 < 2005-01-10 22:04  tim
2443 > 2005-01-10 17:04  tim
2444  
2445          * src/brains/Register.hpp: file Register.hpp was initially added on
2446          branch new_design.
2447  
2448 < 2005-01-10 20:52  tim
2448 > 2005-01-10 15:52  tim
2449  
2450          * src/: UseTheForce/ForceFieldFactory.cpp,
2451          applications/oopse/oopse.cpp, brains/ForceManager.hpp,
# Line 1618 | Line 2457
2457          visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint
2458          method is working now
2459  
2460 < 2005-01-10 18:05  tim
2460 > 2005-01-10 13:05  tim
2461  
2462          * src/: constraints/ConstraintElem.hpp,
2463          constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp,
# Line 1628 | Line 2467
2467          visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in
2468          zconstraint
2469  
2470 < 2005-01-10 18:05  tim
2470 > 2005-01-10 13:05  tim
2471  
2472          * src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was
2473          initially added on branch new_design.
2474  
2475 < 2005-01-07 21:50  tim
2475 > 2005-01-07 16:50  tim
2476  
2477          * src/constraints/ZconstraintForceManager.cpp: file
2478          ZconstraintForceManager.cpp was initially added on branch
2479          new_design.
2480  
2481 < 2005-01-07 21:50  tim
2481 > 2005-01-07 16:50  tim
2482  
2483          * src/constraints/ZconstraintForceManager.hpp: file
2484          ZconstraintForceManager.hpp was initially added on branch
2485          new_design.
2486  
2487 < 2005-01-07 21:50  tim
2487 > 2005-01-07 16:50  tim
2488  
2489          * src/: applications/simpleBuilder/BaseLattice.hpp,
2490          applications/simpleBuilder/Lattice.hpp,
# Line 1659 | Line 2498
2498          integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp,
2499          utils/NumericConstant.hpp: ZConstraintForceManager in progress
2500  
2501 < 2005-01-07 21:50  tim
2501 > 2005-01-07 16:50  tim
2502  
2503          * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was
2504          initially added on branch new_design.
2505  
2506 < 2005-01-06 22:31  tim
2506 > 2005-01-06 17:31  tim
2507  
2508          * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
2509          brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
# Line 1673 | Line 2512
2512          io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp:
2513          constraint is almost working
2514  
2515 < 2005-01-06 00:36  tim
2515 > 2005-01-05 19:36  tim
2516  
2517          * src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is
2518          working
2519  
2520 < 2005-01-06 00:16  tim
2520 > 2005-01-05 19:16  tim
2521  
2522          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
2523          applications/oopse/oopse.cpp,
# Line 1693 | Line 2532
2532          minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder
2533          in progress
2534  
2535 < 2005-01-05 17:35  tim
2535 > 2005-01-05 12:35  tim
2536  
2537          * src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp
2538          was initially added on branch new_design.
2539  
2540 < 2005-01-05 17:35  tim
2540 > 2005-01-05 12:35  tim
2541  
2542          * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
2543          added on branch new_design.
2544  
2545 < 2005-01-05 17:35  tim
2545 > 2005-01-05 12:35  tim
2546  
2547          * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
2548          Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp,
# Line 1711 | Line 2550
2550          OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp,
2551          SDMinimizer.hpp: minimizer in progress
2552  
2553 < 2005-01-05 17:35  tim
2553 > 2005-01-05 12:35  tim
2554  
2555          * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
2556          was initially added on branch new_design.
2557  
2558 < 2005-01-05 17:35  tim
2558 > 2005-01-05 12:35  tim
2559  
2560          * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
2561          was initially added on branch new_design.
2562  
2563 < 2005-01-05 17:35  tim
2563 > 2005-01-05 12:35  tim
2564  
2565          * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
2566          was initially added on branch new_design.
2567  
2568 < 2005-01-05 17:35  tim
2568 > 2005-01-05 12:35  tim
2569  
2570          * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially
2571          added on branch new_design.
2572  
2573 < 2005-01-04 22:18  tim
2573 > 2005-01-04 17:18  tim
2574  
2575          * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
2576          brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp,
# Line 1742 | Line 2581
2581          primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in
2582          progress
2583  
2584 < 2005-01-04 22:18  tim
2584 > 2005-01-04 17:18  tim
2585  
2586          * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was
2587          initially added on branch new_design.
2588  
2589 < 2005-01-04 22:18  tim
2589 > 2005-01-04 17:18  tim
2590  
2591          * src/minimizers/MinimizerParameterSet.cpp: file
2592          MinimizerParameterSet.cpp was initially added on branch new_design.
2593  
2594 < 2005-01-04 22:18  tim
2594 > 2005-01-04 17:18  tim
2595  
2596          * src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was
2597          initially added on branch new_design.
2598  
2599 < 2005-01-04 22:18  tim
2599 > 2005-01-04 17:18  tim
2600  
2601          * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
2602          was initially added on branch new_design.
2603  
2604 < 2005-01-04 22:18  tim
2604 > 2005-01-04 17:18  tim
2605  
2606          * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
2607          Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
2608          OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
2609          SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
2610  
2611 < 2005-01-04 22:18  tim
2611 > 2005-01-04 17:18  tim
2612  
2613          * src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on
2614          branch new_design.
2615  
2616 < 2004-12-20 20:50  chuckv
2616 > 2004-12-20 15:50  chuckv
2617  
2618          * make/Makefile.in: Fixed Makefile test bug under OSX and possibly
2619          other BSD's, replaced test -f *.mod with ls function since BSD test
2620          apparently doesn't support wildcards.
2621  
2622 < 2004-12-20 20:36  tim
2622 > 2004-12-20 15:36  tim
2623  
2624          * make/Makefile.in: fix a test command incompatiable problem
2625  
2626 < 2004-12-20 19:49  tim
2626 > 2004-12-20 14:49  tim
2627  
2628          * src/integrators/NPTi.cpp: NPT is working now
2629  
2630 < 2004-12-16 19:20  tim
2630 > 2004-12-16 14:20  tim
2631  
2632          * src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the
2633          invalid stamp id
2634  
2635 < 2004-12-16 19:00  tim
2635 > 2004-12-16 14:00  tim
2636  
2637          * forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc,
2638          newEAM.u6.frc: adding new EAM force field files
2639  
2640 < 2004-12-16 18:55  tim
2640 > 2004-12-16 13:55  tim
2641  
2642          * src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays
2643          in  EAM parameter file is incorrect
2644  
2645 < 2004-12-16 17:27  tim
2645 > 2004-12-16 12:27  tim
2646  
2647          * src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp,
2648          brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp,
2649          utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM
2650  
2651 < 2004-12-15 22:34  tim
2651 > 2004-12-15 17:34  tim
2652  
2653          * src/: applications/simpleBuilder/BaseLattice.cpp,
2654          applications/simpleBuilder/BaseLattice.hpp,
# Line 1822 | Line 2661
2661          applications/simpleBuilder/simpleBuilder.cpp,
2662          io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream
2663  
2664 < 2004-12-15 21:07  tim
2664 > 2004-12-15 16:07  tim
2665  
2666          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2667          UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile,
2668          applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp:
2669          add EAM Force Field
2670  
2671 < 2004-12-15 19:40  tim
2671 > 2004-12-15 14:40  tim
2672  
2673          * src/applications/oopse/oopse.cpp: add more force fields
2674  
2675 < 2004-12-15 16:44  tim
2675 > 2004-12-15 11:44  tim
2676  
2677          * src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget
2678          to call All_reduce in MPI version)
2679  
2680 < 2004-12-15 16:13  tim
2680 > 2004-12-15 11:13  tim
2681  
2682          * src/: brains/SimCreator.cpp, brains/SimInfo.cpp,
2683          io/DumpReader.cpp: MPI in NVE is working
2684  
2685 < 2004-12-14 21:57  tim
2685 > 2004-12-14 16:57  tim
2686  
2687          * src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader.
2688          Master nodes does not brocast the total number of frames
2689  
2690 < 2004-12-14 19:08  tim
2690 > 2004-12-14 14:08  tim
2691  
2692          * src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp,
2693          integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
# Line 1857 | Line 2696
2696          minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp,
2697          minimizers/SDMinimizer.cpp: more fix in MPI version
2698  
2699 < 2004-12-13 22:30  tim
2699 > 2004-12-13 17:30  tim
2700  
2701          * src/: UseTheForce/DarkSide/simParallel.F90,
2702          applications/oopse/oopse.cpp, brains/SimCreator.cpp,
# Line 1875 | Line 2714
2714          utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version
2715          is built
2716  
2717 < 2004-12-10 18:41  tim
2717 > 2004-12-10 13:41  tim
2718  
2719          * src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp
2720  
2721 < 2004-12-10 16:14  tim
2721 > 2004-12-10 11:14  tim
2722  
2723          * src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp,
2724          primitives/StuntDouble.hpp: forget to zero out the torque. Sticky
2725          and Dipole is working now
2726  
2727 < 2004-12-09 23:15  tim
2727 > 2004-12-09 18:15  tim
2728  
2729          * src/: UseTheForce/DarkSide/dipole.F90,
2730          UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp:
2731          fix an index problem in eFrame matrix
2732  
2733 < 2004-12-09 23:09  tim
2733 > 2004-12-09 18:09  tim
2734  
2735          * src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when
2736          initializing the new Charge AtomType
2737  
2738 < 2004-12-09 21:15  tim
2738 > 2004-12-09 16:15  tim
2739  
2740          * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90,
2741          types/DirectionalAtomType.cpp: sticky module get compiled
2742  
2743 < 2004-12-09 20:43  gezelter
2743 > 2004-12-09 15:43  gezelter
2744  
2745          * src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90,
2746          reactionField.F90: u_l -> eFrame  for electrostatics u_l -> A for
2747          GB
2748  
2749 < 2004-12-09 20:42  gezelter
2749 > 2004-12-09 15:42  gezelter
2750  
2751          * src/UseTheForce/doForces.F90: u_l -> eFrame
2752  
2753 < 2004-12-09 20:27  gezelter
2753 > 2004-12-09 15:27  gezelter
2754  
2755          * src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky
2756          module now has the option for multiple sticky types
2757  
2758 < 2004-12-09 20:27  gezelter
2758 > 2004-12-09 15:27  gezelter
2759  
2760          * src/UseTheForce/doForces.F90: sticky
2761  
2762 < 2004-12-09 16:22  tim
2762 > 2004-12-09 11:22  tim
2763  
2764          * src/integrators/: NPT.cpp, NVT.cpp: fix an interface
2765          inconsistency in lab2Bidy
2766  
2767 < 2004-12-09 15:45  tim
2767 > 2004-12-09 10:45  tim
2768  
2769          * src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug
2770          in calculating torque in rigid body
2771  
2772 < 2004-12-08 20:37  tim
2772 > 2004-12-08 15:37  tim
2773  
2774          * src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h,
2775          brains/SnapShot.cpp, brains/Snapshot.hpp,
# Line 1938 | Line 2777
2777          io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp:
2778          fix a parsing bug in ElectroStaticAtomTypesSectionParser
2779  
2780 < 2004-12-08 17:03  tim
2780 > 2004-12-08 12:03  tim
2781  
2782          * src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane
2783          in  NVT is working
2784  
2785 < 2004-12-07 23:08  tim
2785 > 2004-12-07 18:08  tim
2786  
2787          * src/: UseTheForce/Makefile, brains/SimInfo.hpp,
2788          integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp,
2789          integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp,
2790          io/DumpWriter.cpp: NPT in progress
2791  
2792 < 2004-12-07 14:43  tim
2792 > 2004-12-07 09:43  tim
2793  
2794          * test/utils/: Makefile, NextCombinationTestCase.hpp: [no log
2795          message]
2796  
2797 < 2004-12-07 05:12  tim
2797 > 2004-12-07 00:12  tim
2798  
2799          * src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in
2800          UseInitXSstate
2801  
2802 < 2004-12-07 05:00  tim
2802 > 2004-12-07 00:00  tim
2803  
2804          * src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message
2805  
2806 < 2004-12-07 04:47  tim
2806 > 2004-12-06 23:47  tim
2807  
2808          * src/types/DirectionalAtomType.cpp: [no log message]
2809  
2810 < 2004-12-07 02:18  tim
2810 > 2004-12-06 21:18  tim
2811  
2812          * forceFields/newDUFF.frc: merge WATER force field into DUFF
2813  
2814 < 2004-12-07 01:33  tim
2814 > 2004-12-06 20:33  tim
2815  
2816          * forceFields/newDUFF.frc: change the force constant of bonds
2817  
2818 < 2004-12-06 23:29  tim
2818 > 2004-12-06 18:29  tim
2819  
2820          * src/: UseTheForce/DarkSide/charge.F90,
2821          UseTheForce/DarkSide/charge_interface.h,
# Line 1984 | Line 2823
2823          UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp:
2824          fix atom type ident in Charge and Dipole Module
2825  
2826 < 2004-12-06 22:56  tim
2826 > 2004-12-06 17:56  tim
2827  
2828          * src/primitives/Torsion.cpp: butane is working now
2829  
2830 < 2004-12-06 20:15  tim
2830 > 2004-12-06 15:15  tim
2831  
2832          * src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp,
2833          primitives/Bond.hpp, primitives/Torsion.cpp: short range
2834          interaction for butane is correct.Still something wrong with long
2835          range one
2836  
2837 < 2004-12-06 04:49  tim
2837 > 2004-12-05 23:49  tim
2838  
2839          * src/: brains/Exclude.cpp, brains/Exclude.hpp,
2840          brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
# Line 2003 | Line 2842
2842          primitives/Atom.hpp, utils/NumericConstant.hpp,
2843          utils/TypeContainer.hpp: fix a bug in Exclude List
2844  
2845 < 2004-12-05 22:21  tim
2845 > 2004-12-05 17:21  tim
2846  
2847          * forceFields/newDUFF.frc: minor fix in DUFF
2848  
2849 < 2004-12-05 22:02  tim
2849 > 2004-12-05 17:02  tim
2850  
2851          * src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp,
2852          utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp:
2853          fix a bug in filling MolMembership
2854  
2855 < 2004-12-05 17:12  tim
2855 > 2004-12-05 12:12  tim
2856  
2857          * forceFields/newDUFF.frc: minor fix in force field file
2858  
2859 < 2004-12-05 17:09  tim
2859 > 2004-12-05 12:09  tim
2860  
2861          * src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp,
2862          integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp
2863  
2864 < 2004-12-04 20:09  tim
2864 > 2004-12-04 15:09  tim
2865  
2866          * src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp,
2867          math/Vector3.hpp: NVE is working now, get the same result as
2868          OOPSE-1.0
2869  
2870 < 2004-12-04 19:29  tim
2870 > 2004-12-04 14:29  tim
2871  
2872          * src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy
2873  
2874 < 2004-12-04 19:24  gezelter
2874 > 2004-12-04 14:24  gezelter
2875  
2876          * src/primitives/: Bend.cpp, Torsion.cpp: What?
2877  
2878 < 2004-12-04 19:24  gezelter
2878 > 2004-12-04 14:24  gezelter
2879  
2880          * src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion
2881  
2882 < 2004-12-04 05:24  tim
2882 > 2004-12-04 00:24  tim
2883  
2884          * src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp,
2885          integrators/Integrator.hpp,
# Line 2051 | Line 2890
2890          dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step
2891          4 EAM Step 5 Shape Step 6 Constraint & Restraint
2892  
2893 < 2004-12-04 00:01  tim
2893 > 2004-12-03 19:01  tim
2894  
2895          * src/: UseTheForce/DarkSide/LJ.F90,
2896          applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp,
# Line 2060 | Line 2899
2899          io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working,
2900          energy of NVE is not conserved
2901  
2902 < 2004-12-03 22:36  tim
2902 > 2004-12-03 17:36  tim
2903  
2904          * src/: brains/DataStorage.hpp, brains/Snapshot.hpp,
2905          primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running
2906  
2907 < 2004-12-03 21:30  tim
2907 > 2004-12-03 16:30  tim
2908  
2909          * src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp,
2910          brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile,
# Line 2073 | Line 2912
2912          primitives/Molecule.hpp, primitives/StuntDouble.hpp,
2913          primitives/Torsion.hpp: more missing function get implemented
2914  
2915 < 2004-12-03 20:30  tim
2915 > 2004-12-03 15:30  tim
2916  
2917          * src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp,
2918          SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo
2919  
2920 < 2004-12-03 17:59  tim
2920 > 2004-12-03 12:59  tim
2921  
2922          * src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp,
2923          brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
# Line 2087 | Line 2926
2926          io/SectionParserManager.cpp, utils/LocalIndexManager.hpp,
2927          utils/TypeContainer.hpp: begin to fix bugs
2928  
2929 < 2004-12-03 00:26  tim
2929 > 2004-12-02 19:26  tim
2930  
2931          * src/utils/Trim.cpp: file Trim.cpp was initially added on branch
2932          new_design.
2933  
2934 < 2004-12-03 00:26  tim
2934 > 2004-12-02 19:26  tim
2935  
2936          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2937          UseTheForce/ForceFieldCreator.cpp,
# Line 2103 | Line 2942
2942          utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a
2943          bug in countTokens in StringTokenizer
2944  
2945 < 2004-12-03 00:06  tim
2945 > 2004-12-02 19:06  tim
2946  
2947          * forceFields/newDUFF.frc: minor fix
2948  
2949 < 2004-12-02 23:15  tim
2949 > 2004-12-02 18:15  tim
2950  
2951          * forceFields/newDUFF.frc: new ForceField format
2952  
2953 < 2004-12-02 22:15  tim
2953 > 2004-12-02 17:15  tim
2954  
2955          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2956          UseTheForce/ForceFieldCreator.cpp,
# Line 2130 | Line 2969
2969          types/Makefile: refine factory pattern to make it initialized
2970          correctly
2971  
2972 < 2004-12-02 22:15  tim
2972 > 2004-12-02 17:15  tim
2973  
2974          * src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp
2975          was initially added on branch new_design.
2976  
2977 < 2004-12-02 22:15  tim
2977 > 2004-12-02 17:15  tim
2978  
2979          * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp
2980          was initially added on branch new_design.
2981  
2982 < 2004-12-02 22:15  tim
2982 > 2004-12-02 17:15  tim
2983  
2984          * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp
2985          was initially added on branch new_design.
2986  
2987 < 2004-12-02 22:15  tim
2987 > 2004-12-02 17:15  tim
2988  
2989          * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp
2990          was initially added on branch new_design.
2991  
2992 < 2004-12-02 16:53  tim
2992 > 2004-12-02 11:53  tim
2993  
2994          * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp,
2995          types/DirectionalAtomType.cpp, types/Makefile: oopse get built
2996  
2997 < 2004-12-02 16:04  tim
2997 > 2004-12-02 11:04  tim
2998  
2999          * src/: applications/simpleBuilder/LatticeCreator.cpp,
3000          applications/simpleBuilder/LatticeCreator.hpp,
# Line 2179 | Line 3018
3018          visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still
3019          have two linking problem
3020  
3021 < 2004-12-02 05:17  tim
3021 > 2004-12-02 00:17  tim
3022  
3023          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
3024          applications/simpleBuilder/Lattice.cpp,
# Line 2191 | Line 3030
3030          visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp,
3031          visitors/ZconsVisitor.cpp: change endl to std::endl
3032  
3033 < 2004-12-02 05:14  tim
3033 > 2004-12-02 00:14  tim
3034  
3035          * src/: UseTheForce/Shapes_FF.cpp,
3036          applications/dump2Xyz/Dump2XYZ.cpp,
# Line 2207 | Line 3046
3046          visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
3047          visitors/RigidBodyVisitor.hpp: minor fix
3048  
3049 < 2004-12-02 05:09  tim
3049 > 2004-12-02 00:09  tim
3050  
3051          * src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp:
3052          remove StreamTokenizer
3053  
3054 < 2004-12-02 05:06  tim
3054 > 2004-12-02 00:06  tim
3055  
3056          * src/: UseTheForce/Shapes_FF.cpp,
3057          applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp,
# Line 2221 | Line 3060
3060          restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using
3061          namespace std in .cpp file
3062  
3063 < 2004-12-02 05:04  tim
3063 > 2004-12-02 00:04  tim
3064  
3065          * src/: UseTheForce/Shapes_FF.cpp,
3066          applications/dump2Xyz/Dump2XYZ.cpp,
# Line 2245 | Line 3084
3084          visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding
3085          qulified name prefix std
3086  
3087 < 2004-12-02 04:55  tim
3087 > 2004-12-01 23:55  tim
3088  
3089          * src/: UseTheForce/Shapes_FF.cpp,
3090          applications/dump2Xyz/Dump2XYZ.cpp,
# Line 2261 | Line 3100
3100          visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
3101          visitors/RigidBodyVisitor.hpp: replace string by std::string
3102  
3103 < 2004-12-02 03:12  tim
3103 > 2004-12-01 22:12  tim
3104  
3105          * make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp,
3106          src/applications/simpleBuilder/BaseLattice.hpp,
# Line 2282 | Line 3121
3121          test/brains/RigidBody.cpp: replace misuse of using namespace std in
3122          header files
3123  
3124 < 2004-12-02 02:23  tim
3124 > 2004-12-01 21:23  tim
3125  
3126          * src/: primitives/Atom.hpp, primitives/RigidBody.hpp,
3127          primitives/StuntDouble.hpp, utils/TypeContainer.hpp,
3128          utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp:
3129          begin to fix linking problem
3130  
3131 < 2004-12-02 02:08  tim
3131 > 2004-12-01 21:08  tim
3132  
3133          * src/: applications/oopse/oopse.cpp, brains/Stats.cpp,
3134          brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile,
# Line 2301 | Line 3140
3140          utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled,
3141          still has some linking problem
3142  
3143 < 2004-12-02 00:26  tim
3143 > 2004-12-01 19:26  tim
3144  
3145          * src/: integrators/NVT.cpp, integrators/NVT.hpp,
3146          utils/OOPSEConstant.hpp: NVT get built
3147  
3148 < 2004-12-02 00:09  tim
3148 > 2004-12-01 19:09  tim
3149  
3150          * src/integrators/DLM.cpp: file DLM.cpp was initially added on
3151          branch new_design.
3152  
3153 < 2004-12-02 00:09  tim
3153 > 2004-12-01 19:09  tim
3154  
3155          * src/integrators/DLM.hpp: file DLM.hpp was initially added on
3156          branch new_design.
3157  
3158 < 2004-12-02 00:09  tim
3158 > 2004-12-01 19:09  tim
3159  
3160          * src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp,
3161          brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
# Line 2328 | Line 3167
3167          integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE
3168          get built
3169  
3170 < 2004-12-02 00:09  tim
3170 > 2004-12-01 19:09  tim
3171  
3172          * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
3173          was initially added on branch new_design.
3174  
3175 < 2004-12-01 22:45  tim
3175 > 2004-12-01 17:45  tim
3176  
3177          * src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp,
3178          integrators/IntegratorFactory.cpp,
# Line 2344 | Line 3183
3183          io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp,
3184          io/StatWriter.hpp: rename DumpWrite to DumpWriter
3185  
3186 < 2004-12-01 22:45  tim
3186 > 2004-12-01 17:45  tim
3187  
3188          * src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on
3189          branch new_design.
3190  
3191 < 2004-12-01 20:05  tim
3191 > 2004-12-01 15:05  tim
3192  
3193          * src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp,
3194          io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile,
# Line 2358 | Line 3197
3197          visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp,
3198          visitors/ZconsVisitor.hpp: visitors get built
3199  
3200 < 2004-12-01 19:32  chrisfen
3200 > 2004-12-01 14:32  chrisfen
3201  
3202          * samples/water/tip3p_ice/tp3.md: fixed a sample
3203  
3204 < 2004-12-01 19:10  tim
3204 > 2004-12-01 14:10  tim
3205  
3206          * src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp,
3207          src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
# Line 2371 | Line 3210
3210          src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp:
3211          spell check
3212  
3213 < 2004-12-01 18:42  tim
3213 > 2004-12-01 13:42  tim
3214  
3215          * src/: UseTheForce/DarkSide/atype.F90,
3216          io/ElectrostaticAtomTypesSectionParser.cpp,
# Line 2380 | Line 3219
3219          primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator
3220          and constraint, other directories get built
3221  
3222 < 2004-12-01 17:38  tim
3222 > 2004-12-01 12:38  tim
3223  
3224          * src/: brains/DataStorage.cpp, brains/DataStorage.hpp,
3225          brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
# Line 2393 | Line 3232
3232          types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp:
3233          refactory AtomType
3234  
3235 < 2004-12-01 03:11  tim
3235 > 2004-11-30 22:11  tim
3236  
3237          * src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change
3238  
3239 < 2004-12-01 02:30  tim
3239 > 2004-11-30 21:30  tim
3240  
3241          * src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change
3242          NumericConstant
3243  
3244 < 2004-12-01 02:24  tim
3244 > 2004-11-30 21:24  tim
3245  
3246          * src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp,
3247          primitives/RigidBody.cpp: minor fix
3248  
3249 < 2004-11-30 23:14  tim
3249 > 2004-11-30 18:14  tim
3250  
3251          * src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp,
3252          io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile,
3253          io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io
3254          get built, next is integrator
3255  
3256 < 2004-11-30 22:43  tim
3256 > 2004-11-30 17:43  tim
3257  
3258          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3259          UseTheForce/ForceField.hpp, brains/SimCreator.cpp,
# Line 2422 | Line 3261
3261          io/BASS_interface.cpp, primitives/StuntDouble.hpp,
3262          utils/StringUtils.hpp: brains get built
3263  
3264 < 2004-11-30 20:50  tim
3264 > 2004-11-30 15:50  tim
3265  
3266          * src/: brains/ForceManager.cpp, brains/Makefile,
3267          brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
3268          primitives/RigidBody.cpp, primitives/RigidBody.hpp,
3269          utils/StringUtils.hpp: brains get built, io is next
3270  
3271 < 2004-11-30 19:58  tim
3271 > 2004-11-30 14:58  tim
3272  
3273          * src/: brains/Exclude.cpp, brains/Exclude.hpp,
3274          brains/ForceManager.cpp, brains/ForceManager.hpp,
# Line 2440 | Line 3279
3279          brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile,
3280          math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo
3281  
3282 < 2004-11-30 19:58  tim
3282 > 2004-11-30 14:58  tim
3283  
3284          * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially
3285          added on branch new_design.
3286  
3287 < 2004-11-30 17:54  tim
3287 > 2004-11-30 12:54  tim
3288  
3289          * src/: primitives/Bend.hpp, primitives/Bond.hpp,
3290          primitives/StuntDouble.hpp, primitives/Torsion.hpp,
3291          utils/LocalIndexManager.hpp: more get fixed
3292  
3293 < 2004-11-30 05:03  tim
3293 > 2004-11-30 00:03  tim
3294  
3295          * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
3296          initially added on branch new_design.
3297  
3298 < 2004-11-30 05:03  tim
3298 > 2004-11-30 00:03  tim
3299  
3300          * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
3301          LocalndexManager.hpp to LocalIndexManager.hpp
3302  
3303 < 2004-11-30 04:43  tim
3303 > 2004-11-29 23:43  tim
3304  
3305          * src/: io/BendTypesSectionParser.cpp,
3306          io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
# Line 2470 | Line 3309
3309          types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
3310          types/PolynomialTorsionType.hpp: Section Parsers get compiled
3311  
3312 < 2004-11-30 04:14  tim
3312 > 2004-11-29 23:14  tim
3313  
3314          * src/: io/BendTypesSectionParser.cpp,
3315          io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
# Line 2478 | Line 3317
3317          types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor
3318          fixed
3319  
3320 < 2004-11-30 03:49  tim
3320 > 2004-11-29 22:49  tim
3321  
3322          * src/: io/TorsionTypesSectionParser.cpp,
3323          io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp,
# Line 2486 | Line 3325
3325          types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp,
3326          types/QuarticTorsionType.hpp: minor fixed
3327  
3328 < 2004-11-30 03:32  tim
3328 > 2004-11-29 22:32  tim
3329  
3330          * src/: io/TorsionTypesSectionParser.cpp,
3331          types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
3332          types/PolynomialTorsionType.hpp: #inlcude statement can not be
3333          embedded
3334  
3335 < 2004-11-29 21:42  tim
3335 > 2004-11-29 16:42  tim
3336  
3337          * test/math/: Makefile, PolynomialTestCase.cpp,
3338          PolynomialTestCase.hpp: add PolynomialTestCase
3339  
3340 < 2004-11-29 21:42  tim
3340 > 2004-11-29 16:42  tim
3341  
3342          * src/math/Polynomial.hpp: Polynomial passes unit test
3343  
3344 < 2004-11-29 20:03  tim
3344 > 2004-11-29 15:03  tim
3345  
3346          * src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename
3347          QuarticTorsion.hpp to QuarticTorsionType.hpp
3348  
3349 < 2004-11-29 20:03  tim
3349 > 2004-11-29 15:03  tim
3350  
3351          * src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was
3352          initially added on branch new_design.
3353  
3354 < 2004-11-29 19:56  tim
3354 > 2004-11-29 14:56  tim
3355  
3356          * src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was
3357          initially added on branch new_design.
3358  
3359 < 2004-11-29 19:56  tim
3359 > 2004-11-29 14:56  tim
3360  
3361          * src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add
3362          CubicTorsionType and QuarticTorsionType
3363  
3364 < 2004-11-29 19:56  tim
3364 > 2004-11-29 14:56  tim
3365  
3366          * src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was
3367          initially added on branch new_design.
3368  
3369 < 2004-11-29 18:00  tim
3369 > 2004-11-29 13:00  tim
3370  
3371          * src/: brains/DataStorage.hpp, brains/Snapshot.hpp,
3372          types/CubicBendType.hpp, types/CubicBondType.hpp,
3373          types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get
3374          fixed
3375  
3376 < 2004-11-29 17:59  tim
3376 > 2004-11-29 12:59  tim
3377  
3378          * src/utils/Trim.hpp: file Trim.hpp was initially added on branch
3379          new_design.
3380  
3381 < 2004-11-29 17:59  tim
3381 > 2004-11-29 12:59  tim
3382  
3383          * src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim
3384          Algorithm for std::string
3385  
3386 < 2004-11-29 15:52  tim
3386 > 2004-11-29 10:52  tim
3387  
3388          * src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove
3389          some useless files
3390  
3391 < 2004-11-29 15:50  tim
3391 > 2004-11-29 10:50  tim
3392  
3393          * src/io/: BondTypesSectionParser.cpp,
3394          ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp,
# Line 2560 | Line 3399
3399          SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp,
3400          StickyAtomTypesSectionParser.hpp: more files get fixed
3401  
3402 < 2004-11-29 15:27  tim
3402 > 2004-11-29 10:27  tim
3403  
3404          * src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp,
3405          DirectionalAtomTypesSectionParser.cpp,
# Line 2569 | Line 3408
3408          SectionParserManager.cpp, SectionParserManager.hpp: part of io get
3409          built
3410  
3411 < 2004-11-29 14:49  tim
3411 > 2004-11-29 09:49  tim
3412  
3413          * src/types/UreyBradleyBendType.hpp: types get built
3414  
3415 < 2004-11-29 14:40  tim
3415 > 2004-11-29 09:40  tim
3416  
3417          * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp:
3418          types  get built
3419  
3420 < 2004-11-26 02:13  tim
3420 > 2004-11-25 21:13  tim
3421  
3422          * src/: UseTheForce/ForceField.hpp,
3423          io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp,
3424          types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some
3425          files
3426  
3427 < 2004-11-25 20:18  tim
3427 > 2004-11-25 15:18  tim
3428  
3429          * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was
3430          initially added on branch new_design.
3431  
3432 < 2004-11-25 20:18  tim
3432 > 2004-11-25 15:18  tim
3433  
3434          * src/: io/AtomTypesSectionParser.cpp,
3435          io/BondTypesSectionParser.cpp,
# Line 2599 | Line 3438
3438          types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some
3439          files
3440  
3441 < 2004-11-25 20:18  tim
3441 > 2004-11-25 15:18  tim
3442  
3443          * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was
3444          initially added on branch new_design.
3445  
3446 < 2004-11-24 22:12  tim
3446 > 2004-11-24 17:12  tim
3447  
3448          * src/: io/AtomTypesSectionParser.cpp,
3449          io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp,
# Line 2627 | Line 3466
3466          io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
3467          utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built
3468  
3469 < 2004-11-24 21:33  tim
3469 > 2004-11-24 16:33  tim
3470  
3471          * src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp,
3472          ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp,
3473          LJFF.cpp, Makefile: UseTheForce get built
3474  
3475 < 2004-11-24 20:55  tim
3475 > 2004-11-24 15:55  tim
3476  
3477          * src/: math/RectMatrix.hpp, primitives/Bend.cpp,
3478          primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp,
# Line 2643 | Line 3482
3482          primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp,
3483          primitives/UreyBradleyBend.hpp: types and primitives get built
3484  
3485 < 2004-11-24 19:49  tim
3485 > 2004-11-24 14:49  tim
3486  
3487          * test/utils/: Makefile, NextCombinationTestCase.cpp,
3488          StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint
3489          StringTokenizerTestCase
3490  
3491 < 2004-11-24 19:49  tim
3491 > 2004-11-24 14:49  tim
3492  
3493          * src/utils/: GenericData.hpp, StringTokenizer.cpp,
3494          StringTokenizer.hpp: StringTokenizer passes unit test
3495  
3496 < 2004-11-24 18:20  tim
3496 > 2004-11-24 13:20  tim
3497  
3498          * ChangeLog, make/Makefile.in, src/UseTheForce/Makefile,
3499          src/io/Makefile, src/primitives/Makefile, src/utils/Makefile:
3500          change Makefile
3501  
3502 < 2004-11-24 18:06  chrisfen
3502 > 2004-11-24 13:06  chrisfen
3503  
3504          * src/io/RestraintReader.cpp: improved restraints - mpi should work
3505          fine
3506  
3507 < 2004-11-24 18:06  chrisfen
3507 > 2004-11-24 13:06  chrisfen
3508  
3509          * src/integrators/Integrator.cpp: improved restraints
3510  
3511 < 2004-11-24 18:05  chrisfen
3511 > 2004-11-24 13:05  chrisfen
3512  
3513          * samples/water/tip3p_ice/tp3.md: oops...
3514  
3515 < 2004-11-24 17:42  tim
3515 > 2004-11-24 12:42  tim
3516  
3517          * src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp,
3518          brains/DataStorage.hpp, brains/SimCreator.cpp,
# Line 2682 | Line 3521
3521          primitives/DirectionalAtom.cpp: add SetForceManager method to
3522          integrator
3523  
3524 < 2004-11-23 23:12  tim
3524 > 2004-11-23 18:12  tim
3525  
3526          * src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp,
3527          integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp,
# Line 2694 | Line 3533
3533          integrators/VelocityVerletIntegrator.hpp,
3534          types/UreyBradleyBendType.hpp: refactory NPT integrator
3535  
3536 < 2004-11-23 22:50  chrisfen
3536 > 2004-11-23 17:50  chrisfen
3537  
3538          * samples/water/tip3p_ice/tp3.md: Back to normal... Oh...
3539          Restraints should work in parallel now
3540  
3541 < 2004-11-23 22:48  chrisfen
3541 > 2004-11-23 17:48  chrisfen
3542  
3543          * src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
3544          brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
# Line 2709 | Line 3548
3548          restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements
3549          to restraints
3550  
3551 < 2004-11-23 22:47  chrisfen
3551 > 2004-11-23 17:47  chrisfen
3552  
3553          * samples/water/tip3p_ice/tp3.md: just some testing changes, I'll
3554          return to the original on next commit
3555  
3556 < 2004-11-23 17:53  tim
3556 > 2004-11-23 12:53  tim
3557  
3558          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3559          UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
# Line 2727 | Line 3566
3566          io/SectionParser.hpp, types/DirectionalAtomType.cpp,
3567          utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser
3568  
3569 < 2004-11-23 17:53  tim
3569 > 2004-11-23 12:53  tim
3570  
3571          * src/io/ElectrostaticAtomTypesSectionParser.hpp: file
3572          ElectrostaticAtomTypesSectionParser.hpp was initially added on
3573          branch new_design.
3574  
3575 < 2004-11-23 17:53  tim
3575 > 2004-11-23 12:53  tim
3576  
3577          * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
3578          ElectrostaticAtomTypesSectionParser.cpp was initially added on
3579          branch new_design.
3580  
3581 < 2004-11-23 06:03  tim
3581 > 2004-11-23 01:03  tim
3582  
3583          * src/: io/EAMAtomTypesSectionParser.cpp,
3584          io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp,
3585          types/AtomType.hpp, types/DirectionalAtomType.cpp,
3586          types/DirectionalAtomType.hpp: add EAM AtomType Section Parser
3587  
3588 < 2004-11-23 06:03  tim
3588 > 2004-11-23 01:03  tim
3589  
3590          * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
3591          was initially added on branch new_design.
3592  
3593 < 2004-11-23 06:03  tim
3593 > 2004-11-23 01:03  tim
3594  
3595          * src/io/EAMAtomTypesSectionParser.hpp: file
3596          EAMAtomTypesSectionParser.hpp was initially added on branch
3597          new_design.
3598  
3599 < 2004-11-23 06:03  tim
3599 > 2004-11-23 01:03  tim
3600  
3601          * src/io/EAMAtomTypesSectionParser.cpp: file
3602          EAMAtomTypesSectionParser.cpp was initially added on branch
3603          new_design.
3604  
3605 < 2004-11-23 04:35  tim
3605 > 2004-11-22 23:35  tim
3606  
3607          * src/io/TorsionTypesSectionParser.hpp: file
3608          TorsionTypesSectionParser.hpp was initially added on branch
3609          new_design.
3610  
3611 < 2004-11-23 04:35  tim
3611 > 2004-11-22 23:35  tim
3612  
3613          * src/io/BendTypesSectionParser.hpp: file
3614          BendTypesSectionParser.hpp was initially added on branch
3615          new_design.
3616  
3617 < 2004-11-23 04:35  tim
3617 > 2004-11-22 23:35  tim
3618  
3619          * src/io/BondTypesSectionParser.hpp: file
3620          BondTypesSectionParser.hpp was initially added on branch
3621          new_design.
3622  
3623 < 2004-11-23 04:35  tim
3623 > 2004-11-22 23:35  tim
3624  
3625          * src/io/BondTypesSectionParser.cpp: file
3626          BondTypesSectionParser.cpp was initially added on branch
3627          new_design.
3628  
3629 < 2004-11-23 04:35  tim
3629 > 2004-11-22 23:35  tim
3630  
3631          * src/io/TorsionTypesSectionParser.cpp: file
3632          TorsionTypesSectionParser.cpp was initially added on branch
3633          new_design.
3634  
3635 < 2004-11-23 04:35  tim
3635 > 2004-11-22 23:35  tim
3636  
3637          * src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp,
3638          BondTypesSectionParser.cpp, BondTypesSectionParser.hpp,
# Line 2801 | Line 3640
3640          BondTypesSectionParser, BendTypesSectionParser and
3641          TorsionTypeSectionParser
3642  
3643 < 2004-11-23 04:35  tim
3643 > 2004-11-22 23:35  tim
3644  
3645          * src/io/BendTypesSectionParser.cpp: file
3646          BendTypesSectionParser.cpp was initially added on branch
3647          new_design.
3648  
3649 < 2004-11-22 23:04  tim
3649 > 2004-11-22 18:04  tim
3650  
3651          * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in
3652          DUFF and EAM
3653  
3654 < 2004-11-22 23:02  tim
3654 > 2004-11-22 18:02  tim
3655  
3656          * src/io/: DirectionalAtomTypesParser.hpp,
3657          DirectionalAtomTypesSectionParser.hpp: adding section parsers
3658  
3659 < 2004-11-22 23:02  tim
3659 > 2004-11-22 18:02  tim
3660  
3661          * src/io/DirectionalAtomTypesSectionParser.hpp: file
3662          DirectionalAtomTypesSectionParser.hpp was initially added on branch
3663          new_design.
3664  
3665 < 2004-11-22 20:55  tim
3665 > 2004-11-22 15:55  tim
3666  
3667          * src/io/DipoleAtomTypesSectionParser.hpp: file
3668          DipoleAtomTypesSectionParser.hpp was initially added on branch
3669          new_design.
3670  
3671 < 2004-11-22 20:55  tim
3671 > 2004-11-22 15:55  tim
3672  
3673          * src/io/AtomTypesSectionParser.hpp: file
3674          AtomTypesSectionParser.hpp was initially added on branch
3675          new_design.
3676  
3677 < 2004-11-22 20:55  tim
3677 > 2004-11-22 15:55  tim
3678  
3679          * src/io/HarmonicBondTypesSectionParser.hpp: file
3680          HarmonicBondTypesSectionParser.hpp was initially added on branch
3681          new_design.
3682  
3683 < 2004-11-22 20:55  tim
3683 > 2004-11-22 15:55  tim
3684  
3685          * src/io/StickyAtomTypesSectionParser.cpp: file
3686          StickyAtomTypesSectionParser.cpp was initially added on branch
3687          new_design.
3688  
3689 < 2004-11-22 20:55  tim
3689 > 2004-11-22 15:55  tim
3690  
3691          * src/io/LennardJonesAtomTypesSectionParser.hpp: file
3692          LennardJonesAtomTypesSectionParser.hpp was initially added on
3693          branch new_design.
3694  
3695 < 2004-11-22 20:55  tim
3695 > 2004-11-22 15:55  tim
3696  
3697          * src/io/HarmonicBondTypesSectionParser.cpp: file
3698          HarmonicBondTypesSectionParser.cpp was initially added on branch
3699          new_design.
3700  
3701 < 2004-11-22 20:55  tim
3701 > 2004-11-22 15:55  tim
3702  
3703          * src/io/DirectionalAtomTypesSectionParser.cpp: file
3704          DirectionalAtomTypesSectionParser.cpp was initially added on branch
3705          new_design.
3706  
3707 < 2004-11-22 20:55  tim
3707 > 2004-11-22 15:55  tim
3708  
3709          * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
3710          was initially added on branch new_design.
3711  
3712 < 2004-11-22 20:55  tim
3712 > 2004-11-22 15:55  tim
3713  
3714          * src/io/AtomTypesSectionParser.cpp: file
3715          AtomTypesSectionParser.cpp was initially added on branch
3716          new_design.
3717  
3718 < 2004-11-22 20:55  tim
3718 > 2004-11-22 15:55  tim
3719  
3720          * src/io/ChargeAtomTypesSectionParser.cpp: file
3721          ChargeAtomTypesSectionParser.cpp was initially added on branch
3722          new_design.
3723  
3724 < 2004-11-22 20:55  tim
3724 > 2004-11-22 15:55  tim
3725  
3726          * src/io/DipoleAtomTypesSectionParser.cpp: file
3727          DipoleAtomTypesSectionParser.cpp was initially added on branch
3728          new_design.
3729  
3730 < 2004-11-22 20:55  tim
3730 > 2004-11-22 15:55  tim
3731  
3732          * src/io/LennardJonesAtomTypesSectionParser.cpp: file
3733          LennardJonesAtomTypesSectionParser.cpp was initially added on
3734          branch new_design.
3735  
3736 < 2004-11-22 20:55  tim
3736 > 2004-11-22 15:55  tim
3737  
3738          * src/io/ChargeAtomTypesSectionParser.hpp: file
3739          ChargeAtomTypesSectionParser.hpp was initially added on branch
3740          new_design.
3741  
3742 < 2004-11-22 20:55  tim
3742 > 2004-11-22 15:55  tim
3743  
3744          * src/io/StickyAtomTypesSectionParser.hpp: file
3745          StickyAtomTypesSectionParser.hpp was initially added on branch
3746          new_design.
3747  
3748 < 2004-11-22 20:55  tim
3748 > 2004-11-22 15:55  tim
3749  
3750          * src/io/SectionParser.hpp: file SectionParser.hpp was initially
3751          added on branch new_design.
3752  
3753 < 2004-11-22 20:55  tim
3753 > 2004-11-22 15:55  tim
3754  
3755          * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
3756          brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
# Line 2933 | Line 3772
3772          types/AtomType.hpp, types/DirectionalAtomType.hpp,
3773          utils/GenericData.hpp: adding section parsers
3774  
3775 < 2004-11-22 20:55  tim
3775 > 2004-11-22 15:55  tim
3776  
3777          * src/io/DirectionalAtomTypesParser.hpp: file
3778          DirectionalAtomTypesParser.hpp was initially added on branch
3779          new_design.
3780  
3781 < 2004-11-22 20:55  tim
3781 > 2004-11-22 15:55  tim
3782  
3783          * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
3784          was initially added on branch new_design.
3785  
3786 < 2004-11-22 20:55  tim
3786 > 2004-11-22 15:55  tim
3787  
3788          * src/io/SectionParser.cpp: file SectionParser.cpp was initially
3789          added on branch new_design.
3790  
3791 < 2004-11-19 22:12  tim
3791 > 2004-11-19 17:12  tim
3792  
3793          * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
3794          added on branch new_design.
3795  
3796 < 2004-11-19 22:12  tim
3796 > 2004-11-19 17:12  tim
3797  
3798          * src/: brains/SimState.cpp, brains/SimState.hpp,
3799          io/InitializeFromFile.cpp, types/FixBondType.hpp,
3800          types/FixedBondType.hpp: remove more useless files
3801  
3802 < 2004-11-19 21:47  tim
3802 > 2004-11-19 16:47  tim
3803  
3804          * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp,
3805          integrators/Integrator.cpp, applications/Makedepend: remove more
3806          useless files
3807  
3808 < 2004-11-19 21:38  tim
3808 > 2004-11-19 16:38  tim
3809  
3810          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3811          UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp,
3812          integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp,
3813          integrators/NVT.hpp: refactory integrator
3814  
3815 < 2004-11-19 21:38  tim
3815 > 2004-11-19 16:38  tim
3816  
3817          * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on
3818          branch new_design.
3819  
3820 < 2004-11-19 21:38  tim
3820 > 2004-11-19 16:38  tim
3821  
3822          * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
3823          branch new_design.
3824  
3825 < 2004-11-19 21:38  tim
3825 > 2004-11-19 16:38  tim
3826  
3827          * src/integrators/NPT.hpp: file NPT.hpp was initially added on
3828          branch new_design.
3829  
3830 < 2004-11-19 21:38  tim
3830 > 2004-11-19 16:38  tim
3831  
3832          * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
3833          on branch new_design.
3834  
3835 < 2004-11-19 21:38  tim
3835 > 2004-11-19 16:38  tim
3836  
3837          * src/integrators/NVT.hpp: file NVT.hpp was initially added on
3838          branch new_design.
3839  
3840 < 2004-11-19 20:37  tim
3840 > 2004-11-19 15:37  tim
3841  
3842          * forceFields/newDUFF.frc: new DUFF forcefield
3843  
3844 < 2004-11-19 20:23  tim
3844 > 2004-11-19 15:23  tim
3845  
3846          * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
3847          branch new_design.
3848  
3849 < 2004-11-19 20:23  tim
3849 > 2004-11-19 15:23  tim
3850  
3851          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp,
3852          UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp,
3853          utils/TypeContainer.hpp: add EAM
3854  
3855 < 2004-11-19 20:23  tim
3855 > 2004-11-19 15:23  tim
3856  
3857          * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on
3858          branch new_design.
3859  
3860 < 2004-11-19 18:02  tim
3860 > 2004-11-19 13:02  tim
3861  
3862          * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except
3863          error checking
3864  
3865 < 2004-11-19 17:56  tim
3865 > 2004-11-19 12:56  tim
3866  
3867          * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
3868          was initially added on branch new_design.
3869  
3870 < 2004-11-19 17:56  tim
3870 > 2004-11-19 12:56  tim
3871  
3872          * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
3873          was initially added on branch new_design.
3874  
3875 < 2004-11-19 17:56  tim
3875 > 2004-11-19 12:56  tim
3876  
3877          * src/types/FixBondType.hpp: file FixBondType.hpp was initially
3878          added on branch new_design.
3879  
3880 < 2004-11-19 17:56  tim
3880 > 2004-11-19 12:56  tim
3881  
3882          * src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp,
3883          UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp,
# Line 3049 | Line 3888
3888          utils/StringTokenizer.cpp: DUFF is almost done except error
3889          checking
3890  
3891 < 2004-11-19 00:11  tim
3891 > 2004-11-18 19:11  tim
3892  
3893          * src/UseTheForce/DUFF.cpp: adding DUFF parser
3894  
3895 < 2004-11-18 23:26  tim
3895 > 2004-11-18 18:26  tim
3896  
3897          * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
3898          initially added on branch new_design.
3899  
3900 < 2004-11-18 23:26  tim
3900 > 2004-11-18 18:26  tim
3901  
3902          * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp,
3903          integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
# Line 3070 | Line 3909
3909          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding
3910          DUFF parser
3911  
3912 < 2004-11-18 21:42  tim
3912 > 2004-11-18 16:42  tim
3913  
3914          * forceFields/newDUFF.frc: adding new format DUFF force field
3915  
3916 < 2004-11-18 15:57  chrisfen
3916 > 2004-11-18 10:57  chrisfen
3917  
3918          * src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that
3919          slowed down the force loop
3920  
3921 < 2004-11-18 05:42  tim
3921 > 2004-11-18 00:42  tim
3922  
3923          * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
3924          initially added on branch new_design.
3925  
3926 < 2004-11-18 05:42  tim
3926 > 2004-11-18 00:42  tim
3927  
3928          * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
3929          initially added on branch new_design.
3930  
3931 < 2004-11-18 05:42  tim
3931 > 2004-11-18 00:42  tim
3932  
3933          * src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp,
3934          primitives/Bend.cpp, utils/NumericConstant.cpp,
3935          utils/NumericConstant.hpp: Adding NumericConstant class
3936  
3937 < 2004-11-18 04:16  tim
3937 > 2004-11-17 23:16  tim
3938  
3939          * src/: applications/quickLate.c, UseTheForce/ForceFields.cpp,
3940          UseTheForce/ForceFields.hpp: remove more junk files
3941  
3942 < 2004-11-18 04:12  tim
3942 > 2004-11-17 23:12  tim
3943  
3944          * src/: brains/ForceFields.cpp, brains/SimSetup.cpp,
3945          brains/SimSetup.hpp, constraints/AbstractClasses.hpp,
# Line 3109 | Line 3948
3948          primitives/BondExtensions.cpp, primitives/SRI.hpp,
3949          primitives/TorsionExtensions.cpp: remove some junk files
3950  
3951 < 2004-11-18 04:07  tim
3951 > 2004-11-17 23:07  tim
3952  
3953          * src/primitives/BendExtensions.cpp: remove some junk files
3954  
3955 < 2004-11-18 04:04  tim
3955 > 2004-11-17 23:04  tim
3956  
3957          * src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp,
3958          QuadraticBondType.hpp: refine QudraticBond
3959  
3960 < 2004-11-18 03:57  tim
3960 > 2004-11-17 22:57  tim
3961  
3962          * src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp
3963  
3964 < 2004-11-18 03:57  tim
3964 > 2004-11-17 22:57  tim
3965  
3966          * src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was
3967          initially added on branch new_design.
3968  
3969 < 2004-11-17 21:47  tim
3969 > 2004-11-17 16:47  tim
3970  
3971          * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp
3972          was initially added on branch new_design.
3973  
3974 < 2004-11-17 21:47  tim
3974 > 2004-11-17 16:47  tim
3975  
3976          * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially
3977          added on branch new_design.
3978  
3979 < 2004-11-17 21:47  tim
3979 > 2004-11-17 16:47  tim
3980  
3981          * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially
3982          added on branch new_design.
3983  
3984 < 2004-11-17 21:47  tim
3984 > 2004-11-17 16:47  tim
3985  
3986          * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was
3987          initially added on branch new_design.
3988  
3989 < 2004-11-17 21:47  tim
3989 > 2004-11-17 16:47  tim
3990  
3991          * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
3992          initially added on branch new_design.
3993  
3994 < 2004-11-17 21:47  tim
3994 > 2004-11-17 16:47  tim
3995  
3996          * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
3997          initially added on branch new_design.
3998  
3999 < 2004-11-17 21:47  tim
3999 > 2004-11-17 16:47  tim
4000  
4001          * src/types/CubicBondType.hpp: file CubicBondType.hpp was initially
4002          added on branch new_design.
4003  
4004 < 2004-11-17 21:47  tim
4004 > 2004-11-17 16:47  tim
4005  
4006          * src/: math/ChebyshevPolynomials.cpp,
4007          math/ChebyshevPolynomials.hpp, primitives/Bend.cpp,
# Line 3174 | Line 4013
4013          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp:
4014          UreyBradleyBend and GhostBend
4015  
4016 < 2004-11-17 18:58  tim
4016 > 2004-11-17 13:58  tim
4017  
4018          * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp
4019          was initially added on branch new_design.
4020  
4021 < 2004-11-17 18:58  tim
4021 > 2004-11-17 13:58  tim
4022  
4023          * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp
4024          was initially added on branch new_design.
4025  
4026 < 2004-11-17 18:58  tim
4026 > 2004-11-17 13:58  tim
4027  
4028          * src/: math/ChebyshevPolynomials.cpp,
4029          math/ChebyshevPolynomials.hpp, math/Polynomial.hpp,
# Line 3193 | Line 4032
4032          types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types
4033          stuff and Chebyshev Polynomial
4034  
4035 < 2004-11-17 18:58  tim
4035 > 2004-11-17 13:58  tim
4036  
4037          * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
4038          initially added on branch new_design.
4039  
4040 < 2004-11-17 06:37  tim
4040 > 2004-11-17 01:37  tim
4041  
4042          * src/types/PolynomialTorsionType.hpp: file
4043          PolynomialTorsionType.hpp was initially added on branch new_design.
4044  
4045 < 2004-11-17 06:37  tim
4045 > 2004-11-17 01:37  tim
4046  
4047          * src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was
4048          initially added on branch new_design.
4049  
4050 < 2004-11-17 06:37  tim
4050 > 2004-11-17 01:37  tim
4051  
4052          * src/: math/Polynomial.hpp, primitives/Bend.cpp,
4053          primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp,
# Line 3222 | Line 4061
4061          CharmmTorsionType. Need to refine the design and add document for
4062          them
4063  
4064 < 2004-11-17 06:37  tim
4064 > 2004-11-17 01:37  tim
4065  
4066          * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
4067          initially added on branch new_design.
4068  
4069 < 2004-11-17 06:37  tim
4069 > 2004-11-17 01:37  tim
4070  
4071          * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was
4072          initially added on branch new_design.
4073  
4074 < 2004-11-17 06:37  tim
4074 > 2004-11-17 01:37  tim
4075  
4076          * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
4077          initially added on branch new_design.
4078  
4079 < 2004-11-17 01:11  tim
4079 > 2004-11-16 20:11  tim
4080  
4081          * src/types/: BendType.hpp, PolynomialBondType.hpp,
4082          TorsionType.hpp: add PolynomialBondType
4083  
4084 < 2004-11-17 01:11  tim
4084 > 2004-11-16 20:11  tim
4085  
4086          * src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was
4087          initially added on branch new_design.
4088  
4089 < 2004-11-16 23:20  tim
4089 > 2004-11-16 18:20  tim
4090  
4091          * src/math/Polynomial.hpp: file Polynomial.hpp was initially added
4092          on branch new_design.
4093  
4094 < 2004-11-16 23:20  tim
4094 > 2004-11-16 18:20  tim
4095  
4096          * src/math/Polynomial.hpp: Adding Polynomial class
4097  
4098 < 2004-11-16 22:04  gezelter
4098 > 2004-11-16 17:04  gezelter
4099  
4100          * src/types/MorseBondType.hpp: file MorseBondType.hpp was initially
4101          added on branch new_design.
4102  
4103 < 2004-11-16 22:04  gezelter
4103 > 2004-11-16 17:04  gezelter
4104  
4105          * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
4106          initially added on branch new_design.
4107  
4108 < 2004-11-16 22:04  gezelter
4108 > 2004-11-16 17:04  gezelter
4109  
4110          * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp,
4111          MorseBondType.hpp, TorsionType.hpp: added some new stuff
4112  
4113 < 2004-11-16 20:36  tim
4113 > 2004-11-16 15:36  tim
4114  
4115          * src/: primitives/Bend.cpp, primitives/Bend.hpp,
4116          primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp,
4117          types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and
4118          TorsionType
4119  
4120 < 2004-11-16 02:07  tim
4120 > 2004-11-15 21:07  tim
4121  
4122          * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
4123          branch new_design.
4124  
4125 < 2004-11-16 02:07  tim
4125 > 2004-11-15 21:07  tim
4126  
4127          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
4128          UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp,
4129          utils/StringTokenizer.cpp: adding DUFF class; adding checking
4130          statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer
4131  
4132 < 2004-11-15 23:00  tim
4132 > 2004-11-15 18:00  tim
4133  
4134          * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
4135          UseTheForce/ForceFieldFactory.cpp,
# Line 3298 | Line 4137
4137          UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp,
4138          types/AtomType.hpp: adding ForceFieldFactory and LJFF classes
4139  
4140 < 2004-11-15 23:00  tim
4140 > 2004-11-15 18:00  tim
4141  
4142          * src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp
4143          was initially added on branch new_design.
4144  
4145 < 2004-11-15 23:00  tim
4145 > 2004-11-15 18:00  tim
4146  
4147          * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
4148          was initially added on branch new_design.
4149  
4150 < 2004-11-15 23:00  tim
4150 > 2004-11-15 18:00  tim
4151  
4152          * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
4153          branch new_design.
4154  
4155 < 2004-11-15 18:02  tim
4155 > 2004-11-15 13:02  tim
4156  
4157          * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was
4158          initially added on branch new_design.
4159  
4160 < 2004-11-15 18:02  tim
4160 > 2004-11-15 13:02  tim
4161  
4162          * src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on
4163          branch new_design.
4164  
4165 < 2004-11-15 18:02  tim
4165 > 2004-11-15 13:02  tim
4166  
4167          * src/io/DumpReader.hpp: file DumpReader.hpp was initially added on
4168          branch new_design.
4169  
4170 < 2004-11-15 18:02  tim
4170 > 2004-11-15 13:02  tim
4171  
4172          * src/: brains/SimInfo.cpp, brains/SimInfo.hpp,
4173          brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
# Line 3336 | Line 4175
4175          io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader,
4176          DumpWriter.Next Step is LJFF and integrators
4177  
4178 < 2004-11-13 05:08  tim
4178 > 2004-11-13 00:08  tim
4179  
4180          * src/: brains/ForceManager.cpp, brains/ForceManager.hpp,
4181          brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
# Line 3344 | Line 4183
4183          primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory,
4184          refactory, refactory
4185  
4186 < 2004-11-12 22:43  tim
4186 > 2004-11-12 17:43  tim
4187  
4188          * src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp,
4189          StringTokenizer.cpp: bug fix in hasMoreTokens
4190  
4191 < 2004-11-12 22:28  tim
4191 > 2004-11-12 17:28  tim
4192  
4193          * src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was
4194          initially added on branch new_design.
4195  
4196 < 2004-11-12 22:28  tim
4196 > 2004-11-12 17:28  tim
4197  
4198          * src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding
4199          StringUtils, a c-style strtok like class, need unit test
4200  
4201 < 2004-11-12 17:40  tim
4201 > 2004-11-12 12:40  tim
4202  
4203          * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
4204          brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
4205          brains/SimInfo.hpp: SimCreator and SimInfo are  ready for unit test
4206  
4207 < 2004-11-12 07:05  tim
4207 > 2004-11-12 02:05  tim
4208  
4209          * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
4210          primitives/CutoffGroup.hpp, primitives/Molecule.cpp:
4211          MoleculeCreator forget to create CutoffGroups for free atoms
4212  
4213 < 2004-11-12 06:19  tim
4213 > 2004-11-12 01:19  tim
4214  
4215          * src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
4216          brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
# Line 3379 | Line 4218
4218          io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp:
4219          OOPSE = Object-Obfuscated Parallel Simulation Engine
4220  
4221 < 2004-11-11 21:48  chrisfen
4221 > 2004-11-11 16:48  chrisfen
4222  
4223          * samples/water/tip3p_ice/tp3.md: working sample
4224  
4225 < 2004-11-11 21:47  chrisfen
4225 > 2004-11-11 16:47  chrisfen
4226  
4227          * src/restraints/Restraints.cpp: working towards parallel
4228          restraints
4229  
4230 < 2004-11-11 21:47  chrisfen
4230 > 2004-11-11 16:47  chrisfen
4231  
4232          * src/integrators/Integrator.cpp: Commented out some write
4233          statements
4234  
4235 < 2004-11-11 21:46  chrisfen
4235 > 2004-11-11 16:46  chrisfen
4236  
4237          * src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some
4238          write statements
4239  
4240 < 2004-11-11 21:46  chrisfen
4240 > 2004-11-11 16:46  chrisfen
4241  
4242          * samples/water/tip3p_ice/tp3.md: Fun with ice
4243  
4244 < 2004-11-11 16:41  tim
4244 > 2004-11-11 11:41  tim
4245  
4246          * src/: brains/Exclude.cpp, brains/Exclude.hpp,
4247          brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
# Line 3411 | Line 4250
4250          io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove
4251          useless mpiSimulation
4252  
4253 < 2004-11-11 16:41  tim
4253 > 2004-11-11 11:41  tim
4254  
4255          * src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on
4256          branch new_design.
4257  
4258 < 2004-11-10 22:50  tim
4258 > 2004-11-10 17:50  tim
4259  
4260          * src/: brains/ForceManager.cpp, brains/SimInfo.cpp,
4261          brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp,
4262          integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo
4263  
4264 < 2004-11-10 22:01  tim
4264 > 2004-11-10 17:01  tim
4265  
4266          * src/: brains/SimCreator.cpp, brains/SimCreator.hpp,
4267          brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
# Line 3436 | Line 4275
4275          BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors &
4276          Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint
4277  
4278 < 2004-11-10 14:52  tim
4278 > 2004-11-10 09:52  tim
4279  
4280          * src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a
4281          configurable StatWriter
4282  
4283 < 2004-11-10 14:52  tim
4283 > 2004-11-10 09:52  tim
4284  
4285          * src/io/StatWriter.hpp: file StatWriter.hpp was initially added on
4286          branch new_design.
4287  
4288 < 2004-11-10 02:58  tim
4288 > 2004-11-09 21:58  tim
4289  
4290          * src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation
4291          in progress
4292  
4293 < 2004-11-09 23:11  tim
4293 > 2004-11-09 18:11  tim
4294  
4295          * src/brains/ForceManager.cpp: file ForceManager.cpp was initially
4296          added on branch new_design.
4297  
4298 < 2004-11-09 23:11  tim
4298 > 2004-11-09 18:11  tim
4299  
4300          * src/integrators/VelocityVerletIntegrator.cpp: file
4301          VelocityVerletIntegrator.cpp was initially added on branch
4302          new_design.
4303  
4304 < 2004-11-09 23:11  tim
4304 > 2004-11-09 18:11  tim
4305  
4306          * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp,
4307          brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
# Line 3471 | Line 4310
4310          integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp,
4311          integrators/VelocityVerletIntegrator.hpp: adding ForceManager
4312  
4313 < 2004-11-09 23:11  tim
4313 > 2004-11-09 18:11  tim
4314  
4315          * src/brains/ForceManager.hpp: file ForceManager.hpp was initially
4316          added on branch new_design.
4317  
4318 < 2004-11-09 23:11  tim
4318 > 2004-11-09 18:11  tim
4319  
4320          * src/integrators/NVE.cpp: file NVE.cpp was initially added on
4321          branch new_design.
4322  
4323 < 2004-11-09 01:08  tim
4323 > 2004-11-08 20:08  tim
4324  
4325          * src/integrators/VelocityVerletIntegrator.hpp: file
4326          VelocityVerletIntegrator.hpp was initially added on branch
4327          new_design.
4328  
4329 < 2004-11-09 01:08  tim
4329 > 2004-11-08 20:08  tim
4330  
4331          * src/integrators/NVE.hpp: file NVE.hpp was initially added on
4332          branch new_design.
4333  
4334 < 2004-11-09 01:08  tim
4334 > 2004-11-08 20:08  tim
4335  
4336          * src/: brains/Exclude.hpp, brains/Stats.hpp,
4337          integrators/Integrator.hpp, integrators/NVE.hpp,
4338          integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
4339          utils/TypeContainer.hpp: More to break
4340  
4341 < 2004-11-06 05:21  tim
4341 > 2004-11-06 00:21  tim
4342  
4343          * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially
4344          added on branch new_design.
4345  
4346 < 2004-11-06 05:21  tim
4346 > 2004-11-06 00:21  tim
4347  
4348          * src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp,
4349          UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp,
4350          utils/TypeContainer.hpp, utils/next_combination.hpp: adding
4351          ForceField and TypeContainer classes
4352  
4353 < 2004-11-05 23:38  tim
4353 > 2004-11-05 18:38  tim
4354  
4355          * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
4356          initially added on branch new_design.
4357  
4358 < 2004-11-05 23:38  tim
4358 > 2004-11-05 18:38  tim
4359  
4360          * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was
4361          initially added on branch new_design.
4362  
4363 < 2004-11-05 23:38  tim
4363 > 2004-11-05 18:38  tim
4364  
4365          * src/: brains/Exclude.cpp, brains/Exclude.hpp,
4366          brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
# Line 3529 | Line 4368
4368          brains/SimInfo.hpp, primitives/Molecule.hpp,
4369          utils/LocalndexManager.hpp: Fix Exclude class etc.
4370  
4371 < 2004-11-05 21:45  chrisfen
4371 > 2004-11-05 16:45  chrisfen
4372  
4373          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
4374          visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the
4375          linear visitor
4376  
4377 < 2004-11-05 21:04  chrisfen
4377 > 2004-11-05 16:04  chrisfen
4378  
4379          * src/UseTheForce/DarkSide/shapes.F90: current status of the
4380          debugging process
4381  
4382 < 2004-11-05 21:04  chrisfen
4382 > 2004-11-05 16:04  chrisfen
4383  
4384          * make/Makefile.in: included visitors and minimizer
4385  
4386 < 2004-11-05 21:03  chrisfen
4386 > 2004-11-05 16:03  chrisfen
4387  
4388          * ChangeLog: new changes
4389  
4390 < 2004-11-05 02:56  tim
4390 > 2004-11-04 21:56  tim
4391  
4392          * src/: brains/SimCreator.cpp, brains/SimCreator.hpp,
4393          primitives/Molecule.hpp: Pain......
4394  
4395 < 2004-11-04 20:55  tim
4395 > 2004-11-04 15:55  tim
4396  
4397          * ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp,
4398          src/brains/SimCreator.hpp, src/brains/SimInfo.hpp,
4399          src/brains/Stats.hpp: time to break SimSetup
4400  
4401 < 2004-11-04 20:51  gezelter
4401 > 2004-11-04 15:51  gezelter
4402  
4403          * src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new
4404          classes in progress
4405  
4406 < 2004-11-04 19:48  tim
4406 > 2004-11-04 14:48  tim
4407  
4408          * src/brains/Stats.cpp: file Stats.cpp was initially added on
4409          branch new_design.
4410  
4411 < 2004-11-04 19:48  tim
4411 > 2004-11-04 14:48  tim
4412  
4413          * src/brains/Stats.hpp: file Stats.hpp was initially added on
4414          branch new_design.
4415  
4416 < 2004-11-04 19:48  tim
4416 > 2004-11-04 14:48  tim
4417  
4418          * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
4419          SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
4420          class
4421  
4422 < 2004-11-04 16:22  gezelter
4422 > 2004-11-04 11:22  gezelter
4423  
4424          * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp,
4425          RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and
# Line 3589 | Line 4428
4428          false and "-1" but there should be logic to figure them out in the
4429          other two classes
4430  
4431 < 2004-11-04 16:20  gezelter
4431 > 2004-11-04 11:20  gezelter
4432  
4433          * src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't
4434          remember what I did
4435  
4436 < 2004-11-04 16:20  gezelter
4436 > 2004-11-04 11:20  gezelter
4437  
4438          * src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky
4439  
4440 < 2004-11-04 16:20  gezelter
4440 > 2004-11-04 11:20  gezelter
4441  
4442          * src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX
4443          in the entry_plug so that it only is set if the atoms really are in
4444          the simulation
4445  
4446 < 2004-11-04 16:20  gezelter
4446 > 2004-11-04 11:20  gezelter
4447  
4448          * samples/water/ssd/ssd.md: testing force fields
4449  
4450 < 2004-11-04 16:19  gezelter
4450 > 2004-11-04 11:19  gezelter
4451  
4452          * samples/shape/linear.in: testing shapes
4453  
4454 < 2004-11-03 19:56  tim
4454 > 2004-11-03 14:56  tim
4455  
4456          * src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator
4457          class(similar as SimSetup)
4458  
4459 < 2004-11-03 19:56  tim
4459 > 2004-11-03 14:56  tim
4460  
4461          * src/brains/SimCreator.hpp: file SimCreator.hpp was initially
4462          added on branch new_design.
4463  
4464 < 2004-11-03 19:56  tim
4464 > 2004-11-03 14:56  tim
4465  
4466          * src/brains/SimCreator.cpp: file SimCreator.cpp was initially
4467          added on branch new_design.
4468  
4469 < 2004-11-03 18:00  tim
4469 > 2004-11-03 13:00  tim
4470  
4471          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4472          UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp,
# Line 3637 | Line 4476
4476          visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get
4477          compiled. Still a long way to go ......
4478  
4479 < 2004-11-03 16:08  tim
4479 > 2004-11-03 11:08  tim
4480  
4481          * ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp,
4482          src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp,
# Line 3652 | Line 4491
4491          src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp,
4492          src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ......
4493  
4494 < 2004-11-02 22:41  tim
4494 > 2004-11-02 17:41  tim
4495  
4496          * src/: brains/Migrator.hpp, brains/SimModel.cpp,
4497          utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
4498          Need unit test
4499  
4500 < 2004-11-02 22:41  tim
4500 > 2004-11-02 17:41  tim
4501  
4502          * src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was
4503          initially added on branch new_design.
4504  
4505 < 2004-11-02 22:41  tim
4505 > 2004-11-02 17:41  tim
4506  
4507          * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
4508          branch new_design.
4509  
4510 < 2004-11-02 16:59  tim
4510 > 2004-11-02 11:59  tim
4511  
4512          * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
4513          branch new_design.
4514  
4515 < 2004-11-02 16:59  tim
4515 > 2004-11-02 11:59  tim
4516  
4517          * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
4518          SimSnapshotManager.hpp: SimModel in progress
4519  
4520 < 2004-11-02 15:28  chrisfen
4520 > 2004-11-02 10:28  chrisfen
4521  
4522          * src/: UseTheForce/DarkSide/shapes.F90,
4523          primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes
4524          looks like it's working
4525  
4526 < 2004-11-02 15:27  tim
4526 > 2004-11-02 10:27  tim
4527  
4528          * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
4529          functions for dealing with memory issue
4530  
4531 < 2004-11-02 15:27  tim
4531 > 2004-11-02 10:27  tim
4532  
4533          * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
4534          added on branch new_design.
4535  
4536 < 2004-11-02 15:23  tim
4536 > 2004-11-02 10:23  tim
4537  
4538          * src/: brains/SimModel.hpp, brains/Snapshot.hpp,
4539          brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding
4540          SimModel(something similar as SimInfo)
4541  
4542 < 2004-11-01 22:52  tim
4542 > 2004-11-01 17:52  tim
4543  
4544          * src/: applications/simpleBuilder/MoLocator.hpp,
4545          applications/simpleBuilder/simpleBuilder.cpp,
# Line 3719 | Line 4558
4558          visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom,
4559          RigidBody and StuntDouble classes get compiled
4560  
4561 < 2004-11-01 21:40  tim
4561 > 2004-11-01 16:40  tim
4562  
4563          * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
4564          on branch new_design.
4565  
4566 < 2004-11-01 21:40  tim
4566 > 2004-11-01 16:40  tim
4567  
4568          * src/primitives/Bend.hpp: file Bend.hpp was initially added on
4569          branch new_design.
4570  
4571 < 2004-11-01 21:40  tim
4571 > 2004-11-01 16:40  tim
4572  
4573          * src/primitives/Bond.hpp: file Bond.hpp was initially added on
4574          branch new_design.
4575  
4576 < 2004-11-01 21:40  tim
4576 > 2004-11-01 16:40  tim
4577  
4578          * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
4579          version of Bond, Bend and Torsion.
4580  
4581 < 2004-11-01 21:37  tim
4581 > 2004-11-01 16:37  tim
4582  
4583          * src/types/BendType.hpp: file BendType.hpp was initially added on
4584          branch new_design.
4585  
4586 < 2004-11-01 21:37  tim
4586 > 2004-11-01 16:37  tim
4587  
4588          * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
4589          BondType, BendType, TorsionType
4590  
4591 < 2004-11-01 21:37  tim
4591 > 2004-11-01 16:37  tim
4592  
4593          * src/types/TorsionType.hpp: file TorsionType.hpp was initially
4594          added on branch new_design.
4595  
4596 < 2004-11-01 21:37  tim
4596 > 2004-11-01 16:37  tim
4597  
4598          * src/types/BondType.hpp: file BondType.hpp was initially added on
4599          branch new_design.
4600  
4601 < 2004-11-01 20:15  tim
4601 > 2004-11-01 15:15  tim
4602  
4603          * src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp,
4604          CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp,
# Line 3767 | Line 4606
4606          RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp:
4607          break, break and break.....
4608  
4609 < 2004-11-01 19:57  tim
4609 > 2004-11-01 14:57  tim
4610  
4611          * test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp,
4612          DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp,
4613          StuntDouble.hpp: these core classes get compiled
4614  
4615 < 2004-10-29 22:37  tim
4615 > 2004-10-29 17:37  tim
4616  
4617          * test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule
4618          class
4619  
4620 < 2004-10-29 22:28  chrisfen
4620 > 2004-10-29 17:28  chrisfen
4621  
4622          * src/: UseTheForce/DarkSide/atype.F90,
4623          UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp,
4624          types/ShapeAtomType.cpp: still debugging
4625  
4626 < 2004-10-29 22:28  chrisfen
4626 > 2004-10-29 17:28  chrisfen
4627  
4628          * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90:
4629          shapes rcut calculator added
4630  
4631 < 2004-10-29 22:27  chrisfen
4631 > 2004-10-29 17:27  chrisfen
4632  
4633          * samples/shape/linear.md: shorter run
4634  
4635 < 2004-10-29 20:54  tim
4635 > 2004-10-29 15:54  tim
4636  
4637          * test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class.
4638  
4639 < 2004-10-29 16:22  tim
4639 > 2004-10-29 11:22  tim
4640  
4641          * test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp,
4642          ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove
4643          some deprecated files
4644  
4645 < 2004-10-29 16:20  tim
4645 > 2004-10-29 11:20  tim
4646  
4647          * test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp,
4648          DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp:
4649          More painful reconstruction is coming !!!
4650  
4651 < 2004-10-28 22:34  tim
4651 > 2004-10-28 17:34  tim
4652  
4653          * src/brains/DataStorage.hpp, src/utils/next_combination.hpp,
4654          test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp,
# Line 3817 | Line 4656
4656          test/brains/StuntDouble.hpp: More work on StuntDouble, Atom,
4657          DirectionalAtom and RigidBody
4658  
4659 < 2004-10-28 22:26  tim
4659 > 2004-10-28 17:26  tim
4660  
4661          * ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp,
4662          src/applications/simpleBuilder/MoLocator.cpp,
# Line 3825 | Line 4664
4664          src/utils/GenericFactory.hpp, src/utils/next_combination.hpp:
4665          remove old Vector3d.hpp from application/simpleBuilder
4666  
4667 < 2004-10-28 21:42  tim
4667 > 2004-10-28 16:42  tim
4668  
4669          * src/utils/next_combination.hpp: Minor change in next_combination
4670  
4671 < 2004-10-28 21:28  tim
4671 > 2004-10-28 16:28  tim
4672  
4673          * src/utils/next_combination.hpp,
4674          test/utils/NextCombinationTestCase.cpp,
4675          test/utils/ReplaceWildCardTestCase.cpp: Done with combination
4676  
4677 < 2004-10-28 21:11  tim
4677 > 2004-10-28 16:11  tim
4678  
4679          * src/utils/next_combination.hpp: change documentation of
4680          next_combination.hpp
4681  
4682 < 2004-10-28 20:41  tim
4682 > 2004-10-28 15:41  tim
4683  
4684          * ChangeLog, src/utils/next_combination.hpp,
4685          test/utils/NextCombinationTestCase.cpp,
4686          test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working
4687  
4688 < 2004-10-28 20:01  tim
4688 > 2004-10-28 15:01  tim
4689  
4690          * src/utils/next_combination.hpp: adding replace wildcard function
4691  
4692 < 2004-10-28 19:33  tim
4692 > 2004-10-28 14:33  tim
4693  
4694          * src/utils/next_combination.hpp: Minor change
4695  
4696 < 2004-10-28 19:06  tim
4696 > 2004-10-28 14:06  tim
4697  
4698          * ChangeLog, src/applications/simpleBuilder/MoLocator.hpp,
4699          src/applications/simpleBuilder/simpleBuilder.cpp,
# Line 3864 | Line 4703
4703          test/utils/next_combination.hpp: STL next_permutation like
4704          next_combination is working
4705  
4706 < 2004-10-28 17:22  chrisfen
4706 > 2004-10-28 12:22  chrisfen
4707  
4708          * src/UseTheForce/WATER.cpp: fix of setDipoles
4709  
4710 < 2004-10-28 17:20  gezelter
4710 > 2004-10-28 12:20  gezelter
4711  
4712          * src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the
4713          shapeFile
4714  
4715 < 2004-10-28 17:20  gezelter
4715 > 2004-10-28 12:20  gezelter
4716  
4717          * samples/shape/linear.md: forgot the orientation line
4718  
4719 < 2004-10-28 16:56  gezelter
4719 > 2004-10-28 11:56  gezelter
4720  
4721          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4722          UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
4723          UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate
4724          declaration foo
4725  
4726 < 2004-10-28 16:55  gezelter
4726 > 2004-10-28 11:55  gezelter
4727  
4728          * samples/lipid/5x5.md: uncommented .in line
4729  
4730 < 2004-10-28 15:42  tim
4730 > 2004-10-28 10:42  tim
4731  
4732          * test/utils/: Makefile, NextCombinationTestCase.cpp,
4733          NextCombinationTestCase.hpp, next_combination.hpp: next_combination
4734          in progress
4735  
4736 < 2004-10-28 15:15  tim
4736 > 2004-10-28 10:15  tim
4737  
4738          * test/utils/: NextCombinationTestCase.cpp,
4739          NextCombinationTestCase.hpp: adding next_combination test case
4740  
4741 < 2004-10-28 15:02  tim
4741 > 2004-10-28 10:02  tim
4742  
4743          * test/utils/next_combination.hpp: STL Compatible combination
4744          sequence generator
4745  
4746 < 2004-10-28 06:23  tim
4746 > 2004-10-28 01:23  tim
4747  
4748          * test/utils/: GenerateCombination.hpp,
4749          ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp
4750  
4751 < 2004-10-28 06:16  tim
4751 > 2004-10-28 01:16  tim
4752  
4753          * test/utils/GenerateCombination.hpp: a STL next_permutaion like
4754          next_combination function.
4755  
4756 < 2004-10-28 03:27  tim
4756 > 2004-10-27 22:27  tim
4757  
4758          * test/utils/ReplaceWildCard.hpp: no message
4759  
4760 < 2004-10-28 03:14  tim
4760 > 2004-10-27 22:14  tim
4761  
4762          * test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp:
4763          ReplaceWildCard(recursive version) is working, need refactoring. An
4764          iterative version is on the way
4765  
4766 < 2004-10-28 02:28  tim
4766 > 2004-10-27 21:28  tim
4767  
4768          * test/utils/: Makefile, ReplaceWildCard.hpp,
4769          ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress
4770  
4771 < 2004-10-28 02:08  tim
4771 > 2004-10-27 21:08  tim
4772  
4773          * test/utils/: ReplaceWildCardTestCase.cpp,
4774          ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard
4775  
4776 < 2004-10-27 23:17  tim
4776 > 2004-10-27 18:17  tim
4777  
4778          * test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need
4779          test
4780  
4781 < 2004-10-27 06:25  tim
4781 > 2004-10-27 01:25  tim
4782  
4783          * src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild
4784          char matching is on the way
4785  
4786 < 2004-10-27 06:07  tim
4786 > 2004-10-27 01:07  tim
4787  
4788          * src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4
4789  
4790 < 2004-10-27 03:00  gezelter
4790 > 2004-10-26 22:00  gezelter
4791  
4792          * src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix
4793  
4794 < 2004-10-27 02:20  gezelter
4794 > 2004-10-26 21:20  gezelter
4795  
4796          * src/UseTheForce/ForceFields.hpp: subclass foo
4797  
4798 < 2004-10-27 02:16  gezelter
4798 > 2004-10-26 21:16  gezelter
4799  
4800          * src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* ->
4801          string conversion
4802  
4803 < 2004-10-27 00:01  gezelter
4803 > 2004-10-26 19:01  gezelter
4804  
4805          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4806          UseTheForce/ForceFields.hpp, brains/SimSetup.cpp,
4807          brains/SimSetup.hpp: char* -> string
4808  
4809 < 2004-10-26 22:25  gezelter
4809 > 2004-10-26 17:25  gezelter
4810  
4811          * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp,
4812          Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp,
4813          ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some
4814          isXXX
4815  
4816 < 2004-10-26 22:25  gezelter
4816 > 2004-10-26 17:25  gezelter
4817  
4818          * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
4819          define name collision
4820  
4821 < 2004-10-26 22:24  gezelter
4821 > 2004-10-26 17:24  gezelter
4822  
4823          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4824          UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
# Line 3988 | Line 4827
4827          UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp:
4828          forcefield refactoring for shapes
4829  
4830 < 2004-10-26 22:24  gezelter
4830 > 2004-10-26 17:24  gezelter
4831  
4832          * samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape,
4833          Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in,
4834          linear.md, linear.shape, toluene.shape: adding sample shape
4835          directory
4836  
4837 < 2004-10-26 22:19  tim
4837 > 2004-10-26 17:19  tim
4838  
4839          * ChangeLog, src/brains/DataStorage.cpp,
4840          src/brains/DataStorage.hpp, src/brains/Snapshot.hpp,
# Line 4003 | Line 4842
4842          test/brains/DataStorageTestCase.hpp, test/brains/Makefile:
4843          DataStorage passes unit test
4844  
4845 < 2004-10-26 18:03  chrisfen
4845 > 2004-10-26 13:03  chrisfen
4846  
4847          * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h:
4848          Changes to help advance shapes
4849  
4850 < 2004-10-26 18:02  chrisfen
4850 > 2004-10-26 13:02  chrisfen
4851  
4852          * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to
4853          Shapes force field reader
4854  
4855 < 2004-10-26 17:28  tim
4855 > 2004-10-26 12:28  tim
4856  
4857          * src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and
4858          SnapshotTestCase in progress
4859  
4860 < 2004-10-25 22:46  tim
4860 > 2004-10-25 17:46  tim
4861  
4862          * ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
4863          src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
# Line 4027 | Line 4866
4866          test/math/VectorTestCase.cpp: add getArray function to  RectMatrix
4867          and Vector classes
4868  
4869 < 2004-10-25 17:03  tim
4869 > 2004-10-25 12:03  tim
4870  
4871          * ChangeLog, src/utils/GenericFactory.hpp,
4872          test/utils/GenericFactoryTestCase.cpp,
# Line 4035 | Line 4874
4874          GenericFactory Test Case. GenericFactory now can bed used to creat
4875          ForcefieldFactory and IntegratorFactory etc.
4876  
4877 < 2004-10-25 04:08  tim
4877 > 2004-10-24 23:08  tim
4878  
4879          * src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp,
4880          brains/SimSnapshotManager.hpp, brains/Snapshot.hpp,
4881          brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes
4882          get reconstructed
4883  
4884 < 2004-10-24 07:55  tim
4884 > 2004-10-24 02:55  tim
4885  
4886          * src/utils/GenericFactory.hpp: GenericFactory pass unit test
4887  
4888 < 2004-10-23 23:09  tim
4888 > 2004-10-23 18:09  tim
4889  
4890          * test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp,
4891          StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp,
4892          RigidBody.cpp: Refactoring in progress
4893  
4894 < 2004-10-22 23:09  tim
4894 > 2004-10-22 18:09  tim
4895  
4896          * ChangeLog, src/brains/Snapshot.hpp,
4897          src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp,
4898          test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp,
4899          test/brains/StuntDouble.hpp: more work in Snapshot
4900  
4901 < 2004-10-22 22:59  chrisfen
4901 > 2004-10-22 17:59  chrisfen
4902  
4903          * src/: UseTheForce/LJFF.cpp,
4904          UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear
4905          god!  It runs and conserves energy!
4906  
4907 < 2004-10-22 22:54  chrisfen
4907 > 2004-10-22 17:54  chrisfen
4908  
4909          * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY
4910  
4911 < 2004-10-22 22:53  chrisfen
4911 > 2004-10-22 17:53  chrisfen
4912  
4913          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4914          UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
# Line 4077 | Line 4916
4916          brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey
4917          breakey
4918  
4919 < 2004-10-22 22:53  chrisfen
4919 > 2004-10-22 17:53  chrisfen
4920  
4921          * make/Makefile.in: compiler flags
4922  
4923 < 2004-10-22 21:20  gezelter
4923 > 2004-10-22 16:20  gezelter
4924  
4925          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4926          UseTheForce/LJFF.cpp, UseTheForce/doForces.F90,
4927          brains/fSimulation.h, types/AtomType.hpp,
4928          types/DirectionalAtomType.hpp: fixey fixey
4929  
4930 < 2004-10-22 20:22  gezelter
4930 > 2004-10-22 15:22  gezelter
4931  
4932          * src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h,
4933          charge.F90, charge_interface.h, dipole.F90, dipole_interface.h,
4934          lj_interface.h, shapes.F90, simulation.F90: Added un-busticated
4935          fortran files and c/Fortran interfaces
4936  
4937 < 2004-10-22 20:21  gezelter
4937 > 2004-10-22 15:21  gezelter
4938  
4939          * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
4940          DirectionalAtomType.hpp, Makefile: More on AtomType and
4941          DirectionalAtomType
4942  
4943 < 2004-10-22 14:47  gezelter
4943 > 2004-10-22 09:47  gezelter
4944  
4945          * src/types/AtomType.hpp: Adding AtomType
4946  
4947 < 2004-10-21 21:31  tim
4947 > 2004-10-21 16:31  tim
4948  
4949          * ChangeLog, src/brains/Snapshot.hpp,
4950          src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp,
# Line 4114 | Line 4953
4953          test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp:
4954          Snapshot and SnapshotManager in progress
4955  
4956 < 2004-10-21 21:30  tim
4956 > 2004-10-21 16:30  tim
4957  
4958          * test/brains/: BrainsTest.cpp, Makefile,
4959          SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp,
4960          SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for
4961          Snapshot and snapshotManager.
4962  
4963 < 2004-10-21 20:15  gezelter
4963 > 2004-10-21 15:15  gezelter
4964  
4965          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4966          UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
# Line 4132 | Line 4971
4971          brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky.  
4972          Fixey Fixey.
4973  
4974 < 2004-10-21 16:32  tim
4974 > 2004-10-21 11:32  tim
4975  
4976          * src/utils/GenericData.cpp, src/utils/Makefile,
4977          test/utils/Makefile, test/utils/UtilTest: remove some junk files
4978  
4979 < 2004-10-21 16:24  tim
4979 > 2004-10-21 11:24  tim
4980  
4981          * test/utils/GenericData.hpp: remove backup of  GenericData.hpp
4982  
4983 < 2004-10-21 16:22  tim
4983 > 2004-10-21 11:22  tim
4984  
4985          * ChangeLog, src/brains/SimSetup.cpp,
4986          src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp,
# Line 4159 | Line 4998
4998          src/visitors/ZconsVisitor.hpp: replace old GebericData with  new
4999          GenericData
5000  
5001 < 2004-10-21 15:25  chuckv
5001 > 2004-10-21 10:25  chuckv
5002  
5003          * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj
5004          module.
5005  
5006 < 2004-10-21 15:24  chuckv
5006 > 2004-10-21 10:24  chuckv
5007  
5008          * src/UseTheForce/DarkSide/lj_interface.h: Added interface for
5009          fortran lj module.
5010  
5011 < 2004-10-20 22:54  tim
5011 > 2004-10-20 17:54  tim
5012  
5013          * ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp,
5014          test/utils/GenericDataTestCase.cpp, test/utils/Makefile,
# Line 4177 | Line 5016
5016          test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest:
5017          GenericData and PropertyMap  pass unit test.
5018  
5019 < 2004-10-20 21:52  gezelter
5019 > 2004-10-20 16:52  gezelter
5020  
5021          * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90,
5022          DarkSide/sticky_interface.h: fixed a fortran name problem
5023  
5024 < 2004-10-20 21:38  tim
5024 > 2004-10-20 16:38  tim
5025  
5026          * test/utils/: GenericData.hpp, GenericDataTestCase.cpp,
5027          GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp,
5028          UtilTest, UtilTest.cpp: adding generic data test case
5029  
5030 < 2004-10-20 21:16  chuckv
5030 > 2004-10-20 16:16  chuckv
5031  
5032          * configure, ac-tools/aclocal.m4,
5033          src/UseTheForce/DarkSide/Makefile,
# Line 4200 | Line 5039
5039          Fortran/C++ interface de-obfuscation project appears to be
5040          complete!  Woo hoo!
5041  
5042 < 2004-10-20 20:47  chuckv
5042 > 2004-10-20 15:47  chuckv
5043  
5044          * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp,
5045          fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project
5046          continues
5047  
5048 < 2004-10-20 20:46  chuckv
5048 > 2004-10-20 15:46  chuckv
5049  
5050          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
5051          UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
# Line 4223 | Line 5062
5062          brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface
5063          de-obfuscation project (It is a very long story)
5064  
5065 < 2004-10-20 18:07  tim
5065 > 2004-10-20 13:07  tim
5066  
5067          * ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
5068          test/math/SquareMatrix3TestCase.cpp,
5069          test/math/SquareMatrixTestCase.cpp,
5070          test/math/SquareMatrixTestCase.hpp: Math library pass the unit test
5071  
5072 < 2004-10-20 05:52  tim
5072 > 2004-10-20 00:52  tim
5073  
5074          * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and
5075          SnapshotManager in design phase
5076  
5077 < 2004-10-20 04:54  gezelter
5077 > 2004-10-19 23:54  gezelter
5078  
5079          * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace
5080          problem prevented linking
5081  
5082 < 2004-10-20 04:54  gezelter
5082 > 2004-10-19 23:54  gezelter
5083  
5084          * src/UseTheForce/Shapes_FF.cpp: fixed include
5085  
5086 < 2004-10-20 04:26  gezelter
5086 > 2004-10-19 23:26  gezelter
5087  
5088          * src/utils/: Makefile, definitions.F90, definitions_module.F90,
5089          oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90:
5090          more fortran name mangling
5091  
5092 < 2004-10-20 04:23  gezelter
5092 > 2004-10-19 23:23  gezelter
5093  
5094          * src/profiling/timing.F90: yet more fortran renaming
5095  
5096 < 2004-10-20 04:19  gezelter
5096 > 2004-10-19 23:19  gezelter
5097  
5098          * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h,
5099          do_Forces.F90, do_Forces.h, notifyCutoffs.F90,
5100          notifyCutoffs_interface.h, notifycutoffs_module_interface.h,
5101          wrappers.F90: Fortran name cleanup continues
5102  
5103 < 2004-10-20 04:12  gezelter
5103 > 2004-10-19 23:12  gezelter
5104  
5105          * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some
5106          broken fortran stuff
5107  
5108 < 2004-10-20 04:02  gezelter
5108 > 2004-10-19 23:02  gezelter
5109  
5110          * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
5111          atype_interface.h, atype_module.F90, atype_module_interface.h,
# Line 4283 | Line 5122
5122          sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90:
5123          name sanity on the fortran side
5124  
5125 < 2004-10-20 00:18  tim
5125 > 2004-10-19 19:18  tim
5126  
5127          * test/math/SquareMatrix3TestCase.hpp: [no log message]
5128  
5129 < 2004-10-19 23:01  tim
5129 > 2004-10-19 18:01  tim
5130  
5131          * src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
5132          src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp:
5133          except diagonalize(), all of functions in math library pass the
5134          test
5135  
5136 < 2004-10-19 22:43  chuckv
5136 > 2004-10-19 17:43  chuckv
5137  
5138          * src/UseTheForce/do_Forces.h: Added correct prototypes for
5139          C-fortran interface functions.
5140  
5141 < 2004-10-19 22:37  chuckv
5141 > 2004-10-19 17:37  chuckv
5142  
5143          * src/UseTheForce/DarkSide/: atype_module_interface.h,
5144          eam_module_inteface.h, gb_module_interface.h,
# Line 4307 | Line 5146
5146          sticky_pair_module_interface.h: Added correct prototypes for
5147          C-fortran interface functions.
5148  
5149 < 2004-10-19 21:28  tim
5149 > 2004-10-19 16:28  tim
5150  
5151          * ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp,
5152          src/math/SquareMatrix.hpp, src/math/Vector.hpp,
# Line 4317 | Line 5156
5156          test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more
5157          bugs get fixed at math library
5158  
5159 < 2004-10-19 20:43  chuckv
5159 > 2004-10-19 15:43  chuckv
5160  
5161          * src/UseTheForce/: DarkSide/atype_module_interface.h,
5162          DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h,
# Line 4331 | Line 5170
5170          notifycutoffs_module_interface.h: Added new files for fortran
5171          interface.
5172  
5173 < 2004-10-19 20:43  gezelter
5173 > 2004-10-19 15:43  gezelter
5174  
5175          * src/UseTheForce/Makefile: regressing
5176  
5177 < 2004-10-19 20:40  gezelter
5177 > 2004-10-19 15:40  gezelter
5178  
5179          * src/: UseTheForce/DarkSide/calc_shapes.F90,
5180          UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp:
5181          working on shapes for portability
5182  
5183 < 2004-10-19 20:40  gezelter
5183 > 2004-10-19 15:40  gezelter
5184  
5185          * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes
5186  
5187 < 2004-10-19 18:21  chrisfen
5187 > 2004-10-19 13:21  chrisfen
5188  
5189          * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around
5190          findBegin
5191  
5192 < 2004-10-19 04:34  tim
5192 > 2004-10-18 23:34  tim
5193  
5194          * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs
5195          are fixed in Vector class
5196  
5197 < 2004-10-19 04:28  tim
5197 > 2004-10-18 23:28  tim
5198  
5199          * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix
5200          some bugs in RectMatrixTestCase
5201  
5202 < 2004-10-19 04:21  tim
5202 > 2004-10-18 23:21  tim
5203  
5204          * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp,
5205          test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp,
5206          test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp,
5207          test/math/VectorTestCase.hpp: implement more test cases
5208  
5209 < 2004-10-18 23:13  tim
5209 > 2004-10-18 18:13  tim
5210  
5211          * ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp,
5212          src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
# Line 4376 | Line 5215
5215          test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more
5216          tests on math library
5217  
5218 < 2004-10-18 21:03  tim
5218 > 2004-10-18 16:03  tim
5219  
5220          * test/math/: Makefile, QuaternionTestCase.cpp,
5221          QuaternionTestCase.hpp, RectMatrixTestCase.cpp,
# Line 4384 | Line 5223
5223          Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding
5224          more testing units
5225  
5226 < 2004-10-18 17:07  tim
5226 > 2004-10-18 12:07  tim
5227  
5228          * src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp,
5229          math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp,
5230          math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp,
5231          utils/GenericFactory.hpp: fix some bugs in Quaternion class
5232  
5233 < 2004-10-18 16:30  gezelter
5233 > 2004-10-18 11:30  gezelter
5234  
5235          * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
5236          Your basic run of the mill real-valued versions of Y_l^m(\theta,
5237          \phi)
5238  
5239 < 2004-10-18 16:29  gezelter
5239 > 2004-10-18 11:29  gezelter
5240  
5241          * src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp,
5242          types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp,
5243          utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting
5244          Shapes into OOPSE
5245  
5246 < 2004-10-18 15:21  gezelter
5246 > 2004-10-18 10:21  gezelter
5247  
5248          * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType
5249  
5250 < 2004-10-18 05:23  tim
5250 > 2004-10-18 00:23  tim
5251  
5252          * test/math/VectorTestCase.hpp: adding  vector test case
5253  
5254 < 2004-10-18 05:23  tim
5254 > 2004-10-18 00:23  tim
5255  
5256          * src/utils/GenericFactory.hpp: adding generic factory and vector
5257          test case
5258  
5259 < 2004-10-17 01:19  tim
5259 > 2004-10-16 20:19  tim
5260  
5261          * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp,
5262          SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in
5263          progress
5264  
5265 < 2004-10-16 01:31  tim
5265 > 2004-10-15 20:31  tim
5266  
5267          * src/math/Quaternion.hpp: add quaternion class
5268  
5269 < 2004-10-15 21:11  tim
5269 > 2004-10-15 16:11  tim
5270  
5271          * test/io/: DUFF.frc, IfstrstreamTestCase.cpp,
5272          IfstrstreamTestCase.hpp: adding test file
5273  
5274 < 2004-10-15 21:10  tim
5274 > 2004-10-15 16:10  tim
5275  
5276          * src/io/basic_ifstrstream.hpp: fix a bunch of bugs
5277  
5278 < 2004-10-15 20:42  tim
5278 > 2004-10-15 15:42  tim
5279  
5280          * src/io/basic_ifstrstream.hpp: change const_cast to statc_const
5281  
5282 < 2004-10-15 20:35  tim
5282 > 2004-10-15 15:35  tim
5283  
5284          * src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp
5285  
5286 < 2004-10-15 20:34  tim
5286 > 2004-10-15 15:34  tim
5287  
5288          * test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use
5289          namespace oopse
5290  
5291 < 2004-10-15 19:38  chuckv
5291 > 2004-10-15 14:38  chuckv
5292  
5293          * configure, ac-tools/aclocal.m4: Changed optimization flags for
5294          XLF and XLC.
5295  
5296 < 2004-10-15 18:28  tim
5296 > 2004-10-15 13:28  tim
5297  
5298          * test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp:
5299          adding ifstrstream test case
5300  
5301 < 2004-10-15 18:20  tim
5301 > 2004-10-15 13:20  tim
5302  
5303          * src/io/basic_ifstrstream.hpp: fix include
5304  
5305 < 2004-10-15 18:18  tim
5305 > 2004-10-15 13:18  tim
5306  
5307          * src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi
5308  
5309 < 2004-10-15 18:17  tim
5309 > 2004-10-15 13:17  tim
5310  
5311          * test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile
5312  
5313 < 2004-10-15 18:16  tim
5313 > 2004-10-15 13:16  tim
5314  
5315          * test/io/: Makefile, ifstrstreamTestCase.cpp,
5316          ifstrstreamTestCase.hpp: adding test case for ifstrstream
5317  
5318 < 2004-10-15 15:37  tim
5318 > 2004-10-15 10:37  tim
5319  
5320          * test/io/: IOTest.cpp, ifstrstreamTestCase.cpp,
5321          ifstrstreamTestCase.hpp: add ifstrstreamTestCase
5322  
5323 < 2004-10-15 15:20  tim
5323 > 2004-10-15 10:20  tim
5324  
5325          * src/io/basic_ifstrstream.hpp: add checkFilename Option
5326  
5327 < 2004-10-15 15:19  tim
5327 > 2004-10-15 10:19  tim
5328  
5329          * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp,
5330          SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add
5331          SquareMatrixTestCase class
5332  
5333 < 2004-10-15 07:52  tim
5333 > 2004-10-15 02:52  tim
5334  
5335          * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream
5336  
5337 < 2004-10-14 23:28  tim
5337 > 2004-10-14 18:28  tim
5338  
5339          * src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp,
5340          Vector.hpp: math library in progress
5341  
5342 < 2004-10-14 23:27  tim
5342 > 2004-10-14 18:27  tim
5343  
5344          * src/io/FileReader.hpp: FileReader in progress
5345  
5346 < 2004-10-13 23:53  tim
5346 > 2004-10-13 18:53  tim
5347  
5348          * src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress,
5349          test in isOrthogonal of SquareMatrix is failed by some reasons
5350  
5351 < 2004-10-13 22:28  tim
5351 > 2004-10-13 17:28  tim
5352  
5353          * src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap
5354          class
5355  
5356 < 2004-10-13 22:27  tim
5356 > 2004-10-13 17:27  tim
5357  
5358          * test/math/: MainTest.cpp, RectMatrixTestCase.cpp,
5359          RectMatrixTestCase.hpp: adding testing unit
5360  
5361 < 2004-10-13 22:24  tim
5361 > 2004-10-13 17:24  tim
5362  
5363          * src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix
5364  
5365 < 2004-10-13 06:51  tim
5365 > 2004-10-13 01:51  tim
5366  
5367          * src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp,
5368          Vector3.hpp: refactory vector and matrix classes
5369  
5370 < 2004-10-13 06:50  tim
5370 > 2004-10-13 01:50  tim
5371  
5372          * src/math/Vector3d.hpp: Remove some Makefile.in
5373  
5374 < 2004-10-12 23:57  tim
5374 > 2004-10-12 18:57  tim
5375  
5376          * src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and
5377          Matrix3x3d.hpp
5378  
5379 < 2004-10-12 19:08  tim
5379 > 2004-10-12 14:08  tim
5380  
5381          * doc/: cppstyle.html, style.css: adding c++ coding style
5382  
5383 < 2004-10-11 22:15  tim
5383 > 2004-10-11 17:15  tim
5384  
5385          * src/: constraints/AbstractClasses.hpp,
5386          integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp:
5387          change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
5388  
5389 < 2004-10-11 21:54  tim
5389 > 2004-10-11 16:54  tim
5390  
5391          * scripts/filepp: fix a bug in filepp
5392  
5393 < 2004-10-11 21:13  tim
5393 > 2004-10-11 16:13  tim
5394  
5395          * make/Makefile.in: using filepp to generate dependencies instead
5396          of compilers
5397  
5398 < 2004-10-11 21:10  tim
5398 > 2004-10-11 16:10  tim
5399  
5400          * scripts/filepp: filepp can be used to generate dependencies for
5401          c/c++ now
5402  
5403 < 2004-10-11 18:40  tim
5403 > 2004-10-11 13:40  tim
5404  
5405          * make/Makefile.in: remove -module from F90Options
5406  
5407 < 2004-10-11 18:01  tim
5407 > 2004-10-11 13:01  tim
5408  
5409          * make/Makefile.in: adding rules to move fortran 90 module to
5410          target directory
5411  
5412 < 2004-10-11 15:43  gezelter
5412 > 2004-10-11 10:43  gezelter
5413  
5414          * make/Makefile.in: fixed makefile.in
5415  
5416 < 2004-10-11 14:51  tim
5416 > 2004-10-11 09:51  tim
5417  
5418          * scripts/filepp: remove "use bytes" which causes problem in sgi
5419          machine
5420  
5421 < 2004-10-11 14:26  tim
5421 > 2004-10-11 09:26  tim
5422  
5423          * forceFields/Makefile: add Makefile
5424  
5425 < 2004-10-11 14:23  tim
5425 > 2004-10-11 09:23  tim
5426  
5427          * samples/: water/dimer/Makefile, water/spce/Makefile,
5428          water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile,
5429          water/tip4p/Makefile, zcons/Makefile: fix Makefile under water
5430          directory
5431  
5432 < 2004-10-09 06:01  tim
5432 > 2004-10-11 09:23  tim
5433  
5434 <        * samples/: alkane/Makefile.in, lipid/Makefile.in,
5435 <        metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in
5434 >        * samples/argon/Makefile: remove argon.dump and argon.eor from
5435 >        Makefile
5436  
5437 < 2004-10-08 23:15  tim
5437 > 2004-10-09 01:01  tim
5438  
5439 +        * samples/: alkane/Makefile.in, argon/Makefile.in,
5440 +        lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in:
5441 +        Remove some Makefile.in
5442 +
5443 + 2004-10-08 18:15  tim
5444 +
5445          * make/Makefile.in: [no log message]
5446  
5447 < 2004-10-08 22:51  tim
5447 > 2004-10-08 17:51  tim
5448  
5449          * make/Makefile.in: fix make install
5450  
5451 < 2004-10-08 22:10  tim
5451 > 2004-10-08 17:10  tim
5452  
5453          * make/Makefile.in: adding make install
5454  
5455 < 2004-10-08 22:04  tim
5455 > 2004-10-08 17:04  tim
5456  
5457 <        * samples/: alkane/Makefile, lipid/Makefile, metals/Makefile,
5458 <        minimizer/Makefile, water/Makefile.in, water/dimer/Makefile,
5459 <        water/dimer/Makefile.in, water/spce/Makefile,
5457 >        * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile,
5458 >        metals/Makefile, minimizer/Makefile, water/Makefile.in,
5459 >        water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile,
5460          water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in,
5461          water/ssde/Makefile, water/ssde/Makefile.in,
5462          water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in,
5463          water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile,
5464          zcons/Makefile.in: add Makefile to sample directory
5465  
5466 < 2004-10-06 23:03  gezelter
5466 > 2004-10-06 18:03  gezelter
5467  
5468          * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt
5469          stuff
5470  
5471 < 2004-10-06 23:03  gezelter
5471 > 2004-10-06 18:03  gezelter
5472  
5473          * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
5474          make/Doxyfile, src/applications/getopt.c,
5475          src/applications/getopt1.c, src/applications/gnugetopt.h: more
5476          build fixes
5477  
5478 < 2004-10-06 22:20  tim
5478 > 2004-10-06 17:20  tim
5479  
5480          * make/: Doxyfile, Makefile.in: adding doxygen configuration file
5481  
5482 < 2004-10-06 22:19  tim
5482 > 2004-10-06 17:19  tim
5483  
5484          * scripts/filepp: filepp can handle different fortran module case
5485          and suffix
5486  
5487 < 2004-10-06 21:27  gezelter
5487 > 2004-10-06 16:27  gezelter
5488  
5489          * src/restraints/Restraints.cpp: Chris doesn't know about the
5490          OOPSE-2.0 directory structure yet
5491  
5492 < 2004-10-06 21:27  gezelter
5492 > 2004-10-06 16:27  gezelter
5493  
5494          * ChangeLog: Yeah yeah, we'lll get around to it later
5495  
5496 < 2004-10-06 21:22  gezelter
5496 > 2004-10-06 16:22  gezelter
5497  
5498          * configure, ac-tools/configure.in, ac-tools/fortran90.m4,
5499          make/Makefile.in: cleaning up build process
5500  
5501 < 2004-10-06 20:01  chrisfen
5501 > 2004-10-06 15:01  chrisfen
5502  
5503          * src/restraints/Restraints.cpp: made the file reading in
5504          restraints more intelligent - no longer gives uninformative seg
5505          faults
5506  
5507 < 2004-10-06 19:55  gezelter
5507 > 2004-10-06 14:55  gezelter
5508  
5509          * src/applications/simpleBuilder/Make.ftemp.old: cleaning up
5510  
5511 < 2004-10-06 19:51  gezelter
5511 > 2004-10-06 14:51  gezelter
5512  
5513          * LICENSE, MPIobj/dummy, make/Makefile, obj/dummy,
5514          scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit
5515  
5516 < 2004-10-06 18:53  tim
5516 > 2004-10-06 13:53  tim
5517  
5518          * make/: Makefile, Makefile.in: fix make statistics
5519  
5520 < 2004-10-06 18:18  tim
5520 > 2004-10-06 13:18  tim
5521  
5522          * make/: Makefile, Makefile.in: adding GNU make functions to
5523          combine all of the static libraries to a big library
5524  
5525 < 2004-10-05 22:57  tim
5525 > 2004-10-05 17:57  tim
5526  
5527          * make/: Makefile, Makefile.in:  adding shared library flag
5528  
5529 < 2004-10-05 19:37  tim
5529 > 2004-10-05 14:37  tim
5530  
5531          * src/: Makefile, UseTheForce/Makefile,
5532          UseTheForce/mpiSimulation_module.F90,
# Line 4689 | Line 5534
5534          UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move
5535          mpiSimulation_module to DarkSide
5536  
5537 < 2004-10-05 19:35  tim
5537 > 2004-10-05 14:35  tim
5538  
5539          * make/: Makefile, Makefile.in: building MPI version;using static
5540          library instead of shared library
5541  
5542 < 2004-10-05 14:14  tim
5542 > 2004-10-05 09:14  tim
5543  
5544          * make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90
5545          to filepp
5546  
5547 < 2004-10-04 20:56  tim
5547 > 2004-10-04 15:56  tim
5548  
5549          * make/: Makefile, Makefile.in: add make cvslog
5550  
5551 < 2004-10-04 16:24  gezelter
5551 > 2004-10-04 11:24  gezelter
5552  
5553          * make/: Makefile, Makefile.in: more work on the parallel build
5554  
5555 < 2004-10-04 16:06  gezelter
5555 > 2004-10-04 11:06  gezelter
5556  
5557          * make/: Makefile, Makefile.in: changes to backport declare flags
5558  
5559 < 2004-10-04 15:27  gezelter
5559 > 2004-10-04 10:27  gezelter
5560  
5561          * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp,
5562          DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging
5563          shapes
5564  
5565 < 2004-10-02 04:40  tim
5565 > 2004-10-01 23:40  tim
5566  
5567          * scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree
5568  
5569 < 2004-10-02 04:22  tim
5569 > 2004-10-01 23:22  tim
5570  
5571          * make/: Makefile, Makefile.in: add oopse_ as library prefix
5572  
5573 < 2004-10-01 21:59  tim
5573 > 2004-10-01 16:59  tim
5574  
5575          * make/: Makefile, Makefile.in: fix a space trimming bug in filepp
5576  
5577 < 2004-10-01 21:22  gezelter
5577 > 2004-10-01 16:22  gezelter
5578  
5579          * Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A
5580          few minor build changes
5581  
5582 < 2004-10-01 21:11  tim
5582 > 2004-10-01 16:11  tim
5583  
5584          * scripts/filepp: adding fortran90 make dependency tool
5585  
5586 < 2004-09-30 15:41  tim
5586 > 2004-09-30 10:41  tim
5587  
5588          * make/: Makefile, Makefile.in: make clean is smart enough to only
5589          remove object files belong to current package.  turn off silent
5590          mode
5591  
5592 < 2004-09-29 21:55  tim
5592 > 2004-09-29 16:55  tim
5593  
5594          * src/: Makefile, UseTheForce/Makefile,
5595          UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile,
# Line 4755 | Line 5600
5600          restraints/Makefile, types/Makefile, utils/Makefile,
5601          visitors/Makefile: define DEV_ROOT as relative path
5602  
5603 < 2004-09-29 21:54  tim
5603 > 2004-09-29 16:54  tim
5604  
5605          * make/: Makefile, Makefile.in: get the relative path by shell
5606          script
5607  
5608 < 2004-09-29 21:32  tim
5608 > 2004-09-29 16:32  tim
5609  
5610          * make/Makefile: eliminate DEV_ROOT by relative path
5611  
5612 < 2004-09-29 18:37  tim
5612 > 2004-09-29 13:37  tim
5613  
5614          * make/Makefile.in: add PackageLibs;  fix dependency rule
5615  
5616 < 2004-09-29 17:57  gezelter
5616 > 2004-09-29 12:57  gezelter
5617  
5618          * configure, ac-tools/configure.in: updates
5619  
5620 < 2004-09-29 17:56  gezelter
5620 > 2004-09-29 12:56  gezelter
5621  
5622 <        * make/: Make.conf.in, Makefile.in, _files/style.css: Working on
4778 <        make stuff
5622 >        * make/: Make.conf.in, Makefile.in: Working on make stuff
5623  
5624 < 2004-09-29 17:46  tim
5624 > 2004-09-29 12:46  tim
5625  
5626          * Makefile: If makefile does not exist, print error message
5627  
5628 < 2004-09-29 17:12  tim
5628 > 2004-09-29 12:12  tim
5629  
5630          * make/: Make.conf.in, Makefile: fix dependencies rule
5631  
5632 < 2004-09-29 15:58  gezelter
5632 > 2004-09-29 10:58  gezelter
5633  
5634          * Makefile, make/Makefile: still working on build process
5635  
5636 < 2004-09-29 15:00  tim
5636 > 2004-09-29 10:00  tim
5637  
5638          * make/Makefile: add print statment to rules
5639  
5640 < 2004-09-29 14:59  tim
5640 > 2004-09-29 09:59  tim
5641  
5642          * src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile,
5643          applications/dump2Xyz/Makefile, applications/oopse/Makefile,
# Line 4803 | Line 5647
5647          profiling/Makefile, restraints/Makefile, types/Makefile,
5648          utils/Makefile, visitors/Makefile: change Makefile to relative path
5649  
5650 < 2004-09-29 02:55  tim
5650 > 2004-09-28 21:55  tim
5651  
5652          * src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c
5653          which cause headache in bulding libutils
5654  
5655 < 2004-09-28 23:24  tim
5655 > 2004-09-28 18:24  tim
5656  
5657          * src/applications/: BaseLattice.cpp, BaseLattice.hpp,
5658          Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h,
# Line 4831 | Line 5675
5675          change directory structure of application. Every executable file is
5676          replaced in seperate directory
5677  
5678 < 2004-09-28 22:15  gezelter
5678 > 2004-09-28 17:15  gezelter
5679  
5680          * lib/dummy: Keep that lib around, please.
5681  
5682 < 2004-09-28 22:14  gezelter
5682 > 2004-09-28 17:14  gezelter
5683  
5684          * Makefile, configure, ac-tools/configure.in, make/Make.conf.in:
5685          starting a configure version
5686  
5687 < 2004-09-28 21:08  tim
5687 > 2004-09-28 16:08  tim
5688  
5689          * src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90,
5690          UseTheForce/DarkSide/Makefile,
# Line 4849 | Line 5693
5693          brains/Makefile, brains/simulation_module.F90: move fortran files
5694          around to solve dependency problem
5695  
5696 < 2004-09-28 20:43  tim
5696 > 2004-09-28 15:43  tim
5697  
5698          * Makefile, src/UseTheForce/ForceFields.hpp,
5699          src/UseTheForce/Makefile, src/applications/BaseLattice.hpp,
# Line 4859 | Line 5703
5703          src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp,
5704          src/utils/Makefile: [no log message]
5705  
5706 < 2004-09-28 20:41  tim
5706 > 2004-09-28 15:41  tim
5707  
5708          * make/Makefile, scripts/sfmakedepend: fix fortran dependency
5709          problem
5710  
5711 < 2004-09-28 16:13  tim
5711 > 2004-09-28 11:13  tim
5712  
5713          * make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y,
5714          src/io/Makefile: add yacc and lex rules
5715  
5716 < 2004-09-27 20:24  tim
5716 > 2004-09-27 15:24  tim
5717  
5718          * make/Makefile: adding include path to F90Options
5719  
5720 < 2004-09-27 20:13  tim
5720 > 2004-09-27 15:13  tim
5721  
5722          * make/Makefile: change suffix from .cc to .cpp
5723  
5724 < 2004-09-24 16:27  tim
5724 > 2004-09-24 11:27  tim
5725  
5726          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
5727          UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
# Line 4944 | Line 5788
5788          visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
5789          visitors/ZconsVisitor.hpp: change the #include in source files
5790  
5791 < 2004-09-24 04:16  gezelter
5791 > 2004-09-23 23:16  gezelter
5792  
5793          * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
5794          src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
# Line 5041 | Line 5885
5885          src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
5886          src/visitors/RigidBodyVisitor.cpp,
5887          src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
5888 <        src/visitors/ZconsVisitor.hpp, make/Makefile,
5045 <        make/_files/style.css, samples/Makefile.in,
5888 >        src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
5889          samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
5890          samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
5891          samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
# Line 5090 | Line 5933
5933          samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
5934          samples/alkane/Makefile.in, samples/alkane/alkanes.md,
5935          samples/alkane/butane.in, samples/alkane/butane.md,
5936 +        samples/argon/500.in, samples/argon/500.md,
5937 +        samples/argon/Makefile.in, samples/argon/ar864.in,
5938 +        samples/argon/ar864.md, samples/argon/argonNVT.in,
5939 +        samples/argon/argonNVT.md, samples/argon/lj.md,
5940          samples/lipid/5x5.in, samples/lipid/5x5.md,
5941          samples/lipid/Makefile.in, samples/lipid/lipid.md,
5942          samples/lipid/water.md, samples/minimizer/Makefile.in,
# Line 5116 | Line 5963
5963          forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
5964          forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0
5965  
5966 < 2004-09-24 04:16  gezelter
5966 > 2004-09-23 23:16  gezelter
5967  
5968          * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
5969          src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
# Line 5213 | Line 6060
6060          src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
6061          src/visitors/RigidBodyVisitor.cpp,
6062          src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
6063 <        src/visitors/ZconsVisitor.hpp, make/Makefile,
5217 <        make/_files/style.css, samples/Makefile.in,
6063 >        src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
6064          samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
6065          samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
6066          samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
# Line 5262 | Line 6108
6108          samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
6109          samples/alkane/Makefile.in, samples/alkane/alkanes.md,
6110          samples/alkane/butane.in, samples/alkane/butane.md,
6111 +        samples/argon/500.in, samples/argon/500.md,
6112 +        samples/argon/Makefile.in, samples/argon/ar864.in,
6113 +        samples/argon/ar864.md, samples/argon/argonNVT.in,
6114 +        samples/argon/argonNVT.md, samples/argon/lj.md,
6115          samples/lipid/5x5.in, samples/lipid/5x5.md,
6116          samples/lipid/Makefile.in, samples/lipid/lipid.md,
6117          samples/lipid/water.md, samples/minimizer/Makefile.in,

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