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Comparing trunk/OOPSE-2.0/ChangeLog (file contents):
Revision 2102 by tim, Thu Mar 10 16:14:07 2005 UTC vs.
Revision 2229 by chrisfen, Tue May 17 22:35:01 2005 UTC

# Line 1 | Line 1
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 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 17:06  gezelter
849 +
850 +        * src/types/MorseBondType.hpp: fixed a doxygen problem
851 +
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 16:51  gezelter
858 +
859 +        * doc/SelectionExpression.html: updated some documentation
860 +
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 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 14:11  tim
873 +
874 +        * samples/dipole/: splitInWater.in, splitInWater.md: adding test
875 +        case  of split dipole
876 +
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 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 12:54  gezelter
891 +
892 +        * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side
893 +        support for split dipoles
894 +
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 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 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 10:10  chrisfen
914  
915          * make/Makefile.in, samples/water/tip3p_ice/tp3.md,
# Line 273 | Line 1185
1185          io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp:
1186          adding basic_teebuf which can operate on multiple stream
1187          simutaneously.
1188 +
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  
# Line 1479 | Line 2396
2396  
2397   2005-01-11 10:52  tim
2398  
2399 <        * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
2399 >        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
2400          on branch new_design.
2401  
2402   2005-01-11 10:52  tim
2403  
2404 <        * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
2404 >        * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
2405 >        on branch new_design.
2406  
2407   2005-01-11 10:52  tim
2408  
2409 <        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
1492 <        on branch new_design.
2409 >        * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
2410  
2411   2005-01-11 10:47  tim
2412  
# Line 1557 | Line 2474
2474  
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 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 16:50  tim
2488 +
2489          * src/: applications/simpleBuilder/BaseLattice.hpp,
2490          applications/simpleBuilder/Lattice.hpp,
2491          applications/simpleBuilder/LatticeCreator.hpp,
# Line 1574 | Line 2503
2503          * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was
2504          initially added on branch new_design.
2505  
1577 – 2005-01-07 16:50  tim
1578 –
1579 –        * src/constraints/ZconstraintForceManager.cpp: file
1580 –        ZconstraintForceManager.cpp was initially added on branch
1581 –        new_design.
1582 –
1583 – 2005-01-07 16:50  tim
1584 –
1585 –        * src/constraints/ZconstraintForceManager.hpp: file
1586 –        ZconstraintForceManager.hpp was initially added on branch
1587 –        new_design.
1588 –
2506   2005-01-06 17:31  tim
2507  
2508          * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
# Line 1622 | Line 2539
2539  
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 12:35  tim
2546 +
2547          * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
2548          Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp,
2549          MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp,
# Line 1630 | Line 2552
2552  
2553   2005-01-05 12:35  tim
2554  
2555 <        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
2556 <        added on branch new_design.
2555 >        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
2556 >        was initially added on branch new_design.
2557  
2558   2005-01-05 12:35  tim
2559  
2560 <        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
2560 >        * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
2561          was initially added on branch new_design.
2562  
2563   2005-01-05 12:35  tim
2564  
2565 <        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
2565 >        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
2566          was initially added on branch new_design.
2567  
2568   2005-01-05 12:35  tim
# Line 1648 | Line 2570
2570          * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially
2571          added on branch new_design.
2572  
1651 – 2005-01-05 12:35  tim
1652 –
1653 –        * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
1654 –        was initially added on branch new_design.
1655 –
2573   2005-01-04 17:18  tim
2574  
1658 –        * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was
1659 –        initially added on branch new_design.
1660 –
1661 – 2005-01-04 17:18  tim
1662 –
2575          * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
2576          brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp,
2577          brains/Thermo.cpp, constraints/ConstraintPair.hpp,
# Line 1671 | Line 2583
2583  
2584   2005-01-04 17:18  tim
2585  
2586 <        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
2587 <        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
1676 <        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
1677 <        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
2586 >        * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was
2587 >        initially added on branch new_design.
2588  
2589   2005-01-04 17:18  tim
2590  
1681 –        * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
1682 –        was initially added on branch new_design.
1683 –
1684 – 2005-01-04 17:18  tim
1685 –
2591          * src/minimizers/MinimizerParameterSet.cpp: file
2592          MinimizerParameterSet.cpp was initially added on branch new_design.
2593  
# Line 1693 | Line 2598
2598  
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 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 17:18  tim
2612 +
2613          * src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on
2614          branch new_design.
2615  
# Line 2008 | Line 2925
2925          io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp,
2926          io/SectionParserManager.cpp, utils/LocalIndexManager.hpp,
2927          utils/TypeContainer.hpp: begin to fix bugs
2928 +
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   2004-12-02 19:26  tim
2935  
2936          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
# Line 2020 | Line 2942
2942          utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a
2943          bug in countTokens in StringTokenizer
2944  
2023 – 2004-12-02 19:26  tim
2024 –
2025 –        * src/utils/Trim.cpp: file Trim.cpp was initially added on branch
2026 –        new_design.
2027 –
2945   2004-12-02 19:06  tim
2946  
2947          * forceFields/newDUFF.frc: minor fix
# Line 2035 | Line 2952
2952  
2953   2004-12-02 17:15  tim
2954  
2038 –        * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp
2039 –        was initially added on branch new_design.
2040 –
2041 – 2004-12-02 17:15  tim
2042 –
2043 –        * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp
2044 –        was initially added on branch new_design.
2045 –
2046 – 2004-12-02 17:15  tim
2047 –
2048 –        * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp
2049 –        was initially added on branch new_design.
2050 –
2051 – 2004-12-02 17:15  tim
2052 –
2955          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2956          UseTheForce/ForceFieldCreator.cpp,
2957          UseTheForce/ForceFieldCreator.hpp,
# Line 2070 | Line 2972
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 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 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 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 11:53  tim
# Line 2230 | Line 3147
3147  
3148   2004-12-01 19:09  tim
3149  
3150 <        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
3151 <        was initially added on branch new_design.
3150 >        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
3151 >        branch new_design.
3152  
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 + 2004-12-01 19:09  tim
3159 +
3160          * src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp,
3161          brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
3162          brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp,
# Line 2244 | Line 3166
3166          integrators/VelocityVerletIntegrator.cpp,
3167          integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE
3168          get built
2247 –
2248 – 2004-12-01 19:09  tim
2249 –
2250 –        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
2251 –        branch new_design.
3169  
3170   2004-12-01 19:09  tim
3171  
3172 <        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
3173 <        branch new_design.
3172 >        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
3173 >        was initially added on branch new_design.
3174  
3175   2004-12-01 17:45  tim
3176  
# Line 2350 | Line 3267
3267          brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
3268          primitives/RigidBody.cpp, primitives/RigidBody.hpp,
3269          utils/StringUtils.hpp: brains get built, io is next
2353 –
2354 – 2004-11-30 14:58  tim
2355 –
2356 –        * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially
2357 –        added on branch new_design.
3270  
3271   2004-11-30 14:58  tim
3272  
# Line 2367 | 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 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 12:54  tim
3288  
3289          * src/: primitives/Bend.hpp, primitives/Bond.hpp,
# Line 2375 | Line 3292
3292  
3293   2004-11-30 00:03  tim
3294  
3295 <        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
3296 <        LocalndexManager.hpp to LocalIndexManager.hpp
3295 >        * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
3296 >        initially added on branch new_design.
3297  
3298   2004-11-30 00:03  tim
3299  
3300 <        * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
3301 <        initially added on branch new_design.
3300 >        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
3301 >        LocalndexManager.hpp to LocalIndexManager.hpp
3302  
3303   2004-11-29 23:43  tim
3304  
# Line 2509 | Line 3426
3426  
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 15:18  tim
3433 +
3434          * src/: io/AtomTypesSectionParser.cpp,
3435          io/BondTypesSectionParser.cpp,
3436          io/DirectionalAtomTypesSectionParser.cpp,
# Line 2521 | Line 3443
3443          * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was
3444          initially added on branch new_design.
3445  
2524 – 2004-11-25 15:18  tim
2525 –
2526 –        * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was
2527 –        initially added on branch new_design.
2528 –
3446   2004-11-24 17:12  tim
3447  
3448          * src/: io/AtomTypesSectionParser.cpp,
# Line 2635 | Line 3552
3552  
3553          * samples/water/tip3p_ice/tp3.md: just some testing changes, I'll
3554          return to the original on next commit
2638 –
2639 – 2004-11-23 12:53  tim
3555  
2641 –        * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
2642 –        ElectrostaticAtomTypesSectionParser.cpp was initially added on
2643 –        branch new_design.
2644 –
3556   2004-11-23 12:53  tim
3557  
3558          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
# Line 2661 | Line 3572
3572          ElectrostaticAtomTypesSectionParser.hpp was initially added on
3573          branch new_design.
3574  
3575 < 2004-11-23 01:03  tim
3575 > 2004-11-23 12:53  tim
3576  
3577 <        * src/io/EAMAtomTypesSectionParser.cpp: file
3578 <        EAMAtomTypesSectionParser.cpp was initially added on branch
3579 <        new_design.
3577 >        * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
3578 >        ElectrostaticAtomTypesSectionParser.cpp was initially added on
3579 >        branch new_design.
3580  
3581   2004-11-23 01:03  tim
3582  
# Line 2676 | Line 3587
3587  
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 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 01:03  tim
3600  
3601 <        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
3602 <        was initially added on branch new_design.
3601 >        * src/io/EAMAtomTypesSectionParser.cpp: file
3602 >        EAMAtomTypesSectionParser.cpp was initially added on branch
3603 >        new_design.
3604  
3605   2004-11-22 23:35  tim
3606  
3607 <        * src/io/TorsionTypesSectionParser.cpp: file
3608 <        TorsionTypesSectionParser.cpp was initially added on branch
3607 >        * src/io/TorsionTypesSectionParser.hpp: file
3608 >        TorsionTypesSectionParser.hpp was initially added on branch
3609          new_design.
3610  
3611   2004-11-22 23:35  tim
# Line 2699 | Line 3616
3616  
3617   2004-11-22 23:35  tim
3618  
2702 –        * src/io/BondTypesSectionParser.cpp: file
2703 –        BondTypesSectionParser.cpp was initially added on branch
2704 –        new_design.
2705 –
2706 – 2004-11-22 23:35  tim
2707 –
3619          * src/io/BondTypesSectionParser.hpp: file
3620          BondTypesSectionParser.hpp was initially added on branch
3621          new_design.
3622  
3623   2004-11-22 23:35  tim
3624  
3625 <        * src/io/TorsionTypesSectionParser.hpp: file
3626 <        TorsionTypesSectionParser.hpp was initially added on branch
3625 >        * src/io/BondTypesSectionParser.cpp: file
3626 >        BondTypesSectionParser.cpp was initially added on branch
3627          new_design.
3628  
3629   2004-11-22 23:35  tim
3630  
3631 <        * src/io/BendTypesSectionParser.cpp: file
3632 <        BendTypesSectionParser.cpp was initially added on branch
3631 >        * src/io/TorsionTypesSectionParser.cpp: file
3632 >        TorsionTypesSectionParser.cpp was initially added on branch
3633          new_design.
3634  
3635   2004-11-22 23:35  tim
# Line 2729 | Line 3640
3640          BondTypesSectionParser, BendTypesSectionParser and
3641          TorsionTypeSectionParser
3642  
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 18:04  tim
3650  
3651          * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in
# Line 2736 | Line 3653
3653  
3654   2004-11-22 18:02  tim
3655  
3656 +        * src/io/: DirectionalAtomTypesParser.hpp,
3657 +        DirectionalAtomTypesSectionParser.hpp: adding section parsers
3658 +
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 18:02  tim
3665 > 2004-11-22 15:55  tim
3666  
3667 <        * src/io/: DirectionalAtomTypesParser.hpp,
3668 <        DirectionalAtomTypesSectionParser.hpp: adding section parsers
3667 >        * src/io/DipoleAtomTypesSectionParser.hpp: file
3668 >        DipoleAtomTypesSectionParser.hpp was initially added on branch
3669 >        new_design.
3670  
3671   2004-11-22 15:55  tim
3672  
3673 <        * src/io/DirectionalAtomTypesParser.hpp: file
3674 <        DirectionalAtomTypesParser.hpp was initially added on branch
3673 >        * src/io/AtomTypesSectionParser.hpp: file
3674 >        AtomTypesSectionParser.hpp was initially added on branch
3675          new_design.
3676  
3677   2004-11-22 15:55  tim
# Line 2759 | Line 3682
3682  
3683   2004-11-22 15:55  tim
3684  
3685 <        * src/io/ChargeAtomTypesSectionParser.hpp: file
3686 <        ChargeAtomTypesSectionParser.hpp was initially added on branch
3685 >        * src/io/StickyAtomTypesSectionParser.cpp: file
3686 >        StickyAtomTypesSectionParser.cpp was initially added on branch
3687          new_design.
3688  
3689   2004-11-22 15:55  tim
3690  
3691 <        * src/io/DirectionalAtomTypesSectionParser.cpp: file
3692 <        DirectionalAtomTypesSectionParser.cpp was initially added on branch
2770 <        new_design.
2771 <
2772 < 2004-11-22 15:55  tim
2773 <
2774 <        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
2775 <        LennardJonesAtomTypesSectionParser.cpp was initially added on
3691 >        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
3692 >        LennardJonesAtomTypesSectionParser.hpp was initially added on
3693          branch new_design.
3694  
3695   2004-11-22 15:55  tim
3696  
3697 <        * src/io/DipoleAtomTypesSectionParser.cpp: file
3698 <        DipoleAtomTypesSectionParser.cpp was initially added on branch
3697 >        * src/io/HarmonicBondTypesSectionParser.cpp: file
3698 >        HarmonicBondTypesSectionParser.cpp was initially added on branch
3699          new_design.
3700  
3701   2004-11-22 15:55  tim
3702  
3703 <        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
3704 <        brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
2788 <        brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp,
2789 <        integrators/NVT.hpp, io/AtomTypesSectionParser.cpp,
2790 <        io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
2791 <        io/ChargeAtomTypesSectionParser.hpp,
2792 <        io/DipoleAtomTypesSectionParser.cpp,
2793 <        io/DipoleAtomTypesSectionParser.hpp,
2794 <        io/DirectionalAtomTypesParser.hpp,
2795 <        io/DirectionalAtomTypesSectionParser.cpp,
2796 <        io/HarmonicBondTypesSectionParser.cpp,
2797 <        io/HarmonicBondTypesSectionParser.hpp,
2798 <        io/LennardJonesAtomTypesSectionParser.cpp,
2799 <        io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp,
2800 <        io/SectionParser.hpp, io/SectionParserManager.cpp,
2801 <        io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp,
2802 <        io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp,
2803 <        types/AtomType.hpp, types/DirectionalAtomType.hpp,
2804 <        utils/GenericData.hpp: adding section parsers
2805 <
2806 < 2004-11-22 15:55  tim
2807 <
2808 <        * src/io/DipoleAtomTypesSectionParser.hpp: file
2809 <        DipoleAtomTypesSectionParser.hpp was initially added on branch
3703 >        * src/io/DirectionalAtomTypesSectionParser.cpp: file
3704 >        DirectionalAtomTypesSectionParser.cpp was initially added on branch
3705          new_design.
3706  
3707   2004-11-22 15:55  tim
3708  
3709 <        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
2815 <        added on branch new_design.
2816 <
2817 < 2004-11-22 15:55  tim
2818 <
2819 <        * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
3709 >        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
3710          was initially added on branch new_design.
3711  
3712   2004-11-22 15:55  tim
# Line 2827 | Line 3717
3717  
3718   2004-11-22 15:55  tim
3719  
3720 <        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
3721 <        LennardJonesAtomTypesSectionParser.hpp was initially added on
3722 <        branch new_design.
3720 >        * src/io/ChargeAtomTypesSectionParser.cpp: file
3721 >        ChargeAtomTypesSectionParser.cpp was initially added on branch
3722 >        new_design.
3723  
3724   2004-11-22 15:55  tim
3725  
3726 <        * src/io/HarmonicBondTypesSectionParser.cpp: file
3727 <        HarmonicBondTypesSectionParser.cpp was initially added on branch
3726 >        * src/io/DipoleAtomTypesSectionParser.cpp: file
3727 >        DipoleAtomTypesSectionParser.cpp was initially added on branch
3728          new_design.
3729  
3730   2004-11-22 15:55  tim
3731  
3732 <        * src/io/AtomTypesSectionParser.hpp: file
3733 <        AtomTypesSectionParser.hpp was initially added on branch
3732 >        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
3733 >        LennardJonesAtomTypesSectionParser.cpp was initially added on
3734 >        branch new_design.
3735 >
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 15:55  tim
3743  
3744 <        * src/io/StickyAtomTypesSectionParser.cpp: file
3745 <        StickyAtomTypesSectionParser.cpp was initially added on branch
3744 >        * src/io/StickyAtomTypesSectionParser.hpp: file
3745 >        StickyAtomTypesSectionParser.hpp was initially added on branch
3746          new_design.
3747  
3748   2004-11-22 15:55  tim
# Line 2856 | Line 3752
3752  
3753   2004-11-22 15:55  tim
3754  
3755 <        * src/io/ChargeAtomTypesSectionParser.cpp: file
3756 <        ChargeAtomTypesSectionParser.cpp was initially added on branch
3755 >        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
3756 >        brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
3757 >        brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp,
3758 >        integrators/NVT.hpp, io/AtomTypesSectionParser.cpp,
3759 >        io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
3760 >        io/ChargeAtomTypesSectionParser.hpp,
3761 >        io/DipoleAtomTypesSectionParser.cpp,
3762 >        io/DipoleAtomTypesSectionParser.hpp,
3763 >        io/DirectionalAtomTypesParser.hpp,
3764 >        io/DirectionalAtomTypesSectionParser.cpp,
3765 >        io/HarmonicBondTypesSectionParser.cpp,
3766 >        io/HarmonicBondTypesSectionParser.hpp,
3767 >        io/LennardJonesAtomTypesSectionParser.cpp,
3768 >        io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp,
3769 >        io/SectionParser.hpp, io/SectionParserManager.cpp,
3770 >        io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp,
3771 >        io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp,
3772 >        types/AtomType.hpp, types/DirectionalAtomType.hpp,
3773 >        utils/GenericData.hpp: adding section parsers
3774 >
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 15:55  tim
3782  
3783 <        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
3783 >        * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
3784          was initially added on branch new_design.
3785  
3786   2004-11-22 15:55  tim
3787  
3788 <        * src/io/StickyAtomTypesSectionParser.hpp: file
3789 <        StickyAtomTypesSectionParser.hpp was initially added on branch
2872 <        new_design.
3788 >        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
3789 >        added on branch new_design.
3790  
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 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  
2880 – 2004-11-19 17:12  tim
2881 –
2882 –        * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
2883 –        added on branch new_design.
2884 –
3802   2004-11-19 16:47  tim
3803  
3804          * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp,
# Line 2890 | Line 3807
3807  
3808   2004-11-19 16:38  tim
3809  
3810 <        * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on
3811 <        branch new_design.
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 16:38  tim
3816  
3817 <        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
3818 <        on branch new_design.
3817 >        * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on
3818 >        branch new_design.
3819  
3820   2004-11-19 16:38  tim
3821  
3822 <        * src/integrators/NPT.hpp: file NPT.hpp was initially added on
3822 >        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
3823          branch new_design.
3824  
3825   2004-11-19 16:38  tim
3826  
3827 <        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
3827 >        * src/integrators/NPT.hpp: file NPT.hpp was initially added on
3828          branch new_design.
3829  
3830   2004-11-19 16:38  tim
3831  
3832 <        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
3833 <        branch new_design.
3832 >        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
3833 >        on branch new_design.
3834  
3835   2004-11-19 16:38  tim
3836  
3837 <        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3838 <        UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp,
2920 <        integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp,
2921 <        integrators/NVT.hpp: refactory integrator
3837 >        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
3838 >        branch new_design.
3839  
3840   2004-11-19 15:37  tim
3841  
# Line 2926 | Line 3843
3843  
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 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
# Line 2935 | Line 3857
3857          * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on
3858          branch new_design.
3859  
2938 – 2004-11-19 15:23  tim
2939 –
2940 –        * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
2941 –        branch new_design.
2942 –
3860   2004-11-19 13:02  tim
3861  
3862          * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except
# Line 2947 | Line 3864
3864  
3865   2004-11-19 12:56  tim
3866  
3867 <        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
3867 >        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
3868          was initially added on branch new_design.
3869  
3870   2004-11-19 12:56  tim
3871  
3872 <        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
3872 >        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
3873          was initially added on branch new_design.
3874  
3875   2004-11-19 12:56  tim
# Line 2977 | Line 3894
3894  
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 18:26  tim
3901 +
3902          * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp,
3903          integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
3904          integrators/VelocityVerletIntegrator.cpp,
# Line 2987 | Line 3909
3909          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding
3910          DUFF parser
3911  
2990 – 2004-11-18 18:26  tim
2991 –
2992 –        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
2993 –        initially added on branch new_design.
2994 –
3912   2004-11-18 16:42  tim
3913  
3914          * forceFields/newDUFF.frc: adding new format DUFF force field
# Line 3003 | Line 3920
3920  
3921   2004-11-18 00:42  tim
3922  
3923 <        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
3923 >        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
3924          initially added on branch new_design.
3925  
3926   2004-11-18 00:42  tim
3927  
3928 <        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
3928 >        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
3929          initially added on branch new_design.
3930  
3931   2004-11-18 00:42  tim
# Line 3051 | Line 3968
3968  
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 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 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 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 16:47  tim
3990  
3991 <        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
3991 >        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
3992          initially added on branch new_design.
3993  
3994   2004-11-17 16:47  tim
3995  
3996 <        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
3996 >        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
3997          initially added on branch new_design.
3998  
3999   2004-11-17 16:47  tim
# Line 3086 | Line 4013
4013          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp:
4014          UreyBradleyBend and GhostBend
4015  
3089 – 2004-11-17 16:47  tim
3090 –
3091 –        * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially
3092 –        added on branch new_design.
3093 –
3094 – 2004-11-17 16:47  tim
3095 –
3096 –        * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp
3097 –        was initially added on branch new_design.
3098 –
4016   2004-11-17 13:58  tim
4017  
4018          * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp
# Line 3103 | Line 4020
4020  
4021   2004-11-17 13:58  tim
4022  
3106 –        * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
3107 –        initially added on branch new_design.
3108 –
3109 – 2004-11-17 13:58  tim
3110 –
4023          * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp
4024          was initially added on branch new_design.
4025  
# Line 3120 | Line 4032
4032          types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types
4033          stuff and Chebyshev Polynomial
4034  
4035 < 2004-11-17 01:37  tim
4035 > 2004-11-17 13:58  tim
4036  
4037 <        * src/types/PolynomialTorsionType.hpp: file
3126 <        PolynomialTorsionType.hpp was initially added on branch new_design.
3127 <
3128 < 2004-11-17 01:37  tim
3129 <
3130 <        * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
4037 >        * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
4038          initially added on branch new_design.
4039  
4040   2004-11-17 01:37  tim
4041  
4042 <        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
4043 <        initially added on branch new_design.
4042 >        * src/types/PolynomialTorsionType.hpp: file
4043 >        PolynomialTorsionType.hpp was initially added on branch new_design.
4044  
4045   2004-11-17 01:37  tim
4046  
# Line 3142 | Line 4049
4049  
4050   2004-11-17 01:37  tim
4051  
3145 –        * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was
3146 –        initially added on branch new_design.
3147 –
3148 – 2004-11-17 01:37  tim
3149 –
4052          * src/: math/Polynomial.hpp, primitives/Bend.cpp,
4053          primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp,
4054          types/BondType.hpp, types/CharmmTorsionType.cpp,
# Line 3159 | Line 4061
4061          CharmmTorsionType. Need to refine the design and add document for
4062          them
4063  
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 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 01:37  tim
4075 +
4076 +        * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
4077 +        initially added on branch new_design.
4078 +
4079   2004-11-16 20:11  tim
4080  
4081          * src/types/: BendType.hpp, PolynomialBondType.hpp,
# Line 3171 | Line 4088
4088  
4089   2004-11-16 18:20  tim
4090  
3174 –        * src/math/Polynomial.hpp: Adding Polynomial class
3175 –
3176 – 2004-11-16 18:20  tim
3177 –
4091          * src/math/Polynomial.hpp: file Polynomial.hpp was initially added
4092          on branch new_design.
4093  
4094 < 2004-11-16 17:04  gezelter
4094 > 2004-11-16 18:20  tim
4095  
4096 <        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
3184 <        initially added on branch new_design.
4096 >        * src/math/Polynomial.hpp: Adding Polynomial class
4097  
4098   2004-11-16 17:04  gezelter
4099  
# Line 3190 | Line 4102
4102  
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 17:04  gezelter
4109 +
4110          * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp,
4111          MorseBondType.hpp, TorsionType.hpp: added some new stuff
4112  
# Line 3202 | Line 4119
4119  
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 + 2004-11-15 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 21:07  tim
4132 > 2004-11-15 18:00  tim
4133  
4134 <        * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
4135 <        branch new_design.
4134 >        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
4135 >        UseTheForce/ForceFieldFactory.cpp,
4136 >        UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp,
4137 >        UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp,
4138 >        types/AtomType.hpp: adding ForceFieldFactory and LJFF classes
4139  
4140   2004-11-15 18:00  tim
4141  
# Line 3219 | Line 4144
4144  
4145   2004-11-15 18:00  tim
4146  
4147 <        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
4148 <        branch new_design.
4147 >        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
4148 >        was initially added on branch new_design.
4149  
4150   2004-11-15 18:00  tim
4151  
4152 <        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
4153 <        UseTheForce/ForceFieldFactory.cpp,
3229 <        UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp,
3230 <        UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp,
3231 <        types/AtomType.hpp: adding ForceFieldFactory and LJFF classes
4152 >        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
4153 >        branch new_design.
4154  
4155 < 2004-11-15 18:00  tim
4155 > 2004-11-15 13:02  tim
4156  
4157 <        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
4158 <        was initially added on branch new_design.
4157 >        * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was
4158 >        initially added on branch new_design.
4159  
4160   2004-11-15 13:02  tim
4161  
# Line 3247 | Line 4169
4169  
4170   2004-11-15 13:02  tim
4171  
3250 –        * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was
3251 –        initially added on branch new_design.
3252 –
3253 – 2004-11-15 13:02  tim
3254 –
4172          * src/: brains/SimInfo.cpp, brains/SimInfo.hpp,
4173          brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
4174          integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp,
# Line 3375 | Line 4292
4292  
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 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 18:11  tim
4305 +
4306          * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp,
4307          brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
4308          brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp,
# Line 3389 | Line 4317
4317  
4318   2004-11-09 18:11  tim
4319  
3392 –        * src/integrators/VelocityVerletIntegrator.cpp: file
3393 –        VelocityVerletIntegrator.cpp was initially added on branch
3394 –        new_design.
3395 –
3396 – 2004-11-09 18:11  tim
3397 –
4320          * src/integrators/NVE.cpp: file NVE.cpp was initially added on
4321          branch new_design.
4322  
3401 – 2004-11-09 18:11  tim
3402 –
3403 –        * src/brains/ForceManager.cpp: file ForceManager.cpp was initially
3404 –        added on branch new_design.
3405 –
4323   2004-11-08 20:08  tim
4324  
4325          * src/integrators/VelocityVerletIntegrator.hpp: file
# Line 3411 | Line 4328
4328  
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 + 2004-11-08 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  
3419 – 2004-11-08 20:08  tim
3420 –
3421 –        * src/integrators/NVE.hpp: file NVE.hpp was initially added on
3422 –        branch new_design.
3423 –
4341   2004-11-06 00:21  tim
4342  
4343          * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially
# Line 3435 | Line 4352
4352  
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 18:38  tim
4359 +
4360          * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was
4361          initially added on branch new_design.
4362  
# Line 3445 | Line 4367
4367          brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
4368          brains/SimInfo.hpp, primitives/Molecule.hpp,
4369          utils/LocalndexManager.hpp: Fix Exclude class etc.
3448 –
3449 – 2004-11-05 18:38  tim
3450 –
3451 –        * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
3452 –        initially added on branch new_design.
4370  
4371   2004-11-05 16:45  chrisfen
4372  
# Line 3488 | Line 4405
4405  
4406   2004-11-04 14:48  tim
4407  
3491 –        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
3492 –        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
3493 –        class
3494 –
3495 – 2004-11-04 14:48  tim
3496 –
4408          * src/brains/Stats.cpp: file Stats.cpp was initially added on
4409          branch new_design.
4410  
# Line 3502 | Line 4413
4413          * src/brains/Stats.hpp: file Stats.hpp was initially added on
4414          branch new_design.
4415  
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 11:22  gezelter
4423  
4424          * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp,
# Line 3576 | Line 4493
4493  
4494   2004-11-02 17:41  tim
4495  
4496 <        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
4497 <        branch new_design.
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 17:41  tim
4501  
# Line 3586 | Line 4504
4504  
4505   2004-11-02 17:41  tim
4506  
4507 <        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
4508 <        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
3591 <        Need unit test
4507 >        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
4508 >        branch new_design.
4509  
4510   2004-11-02 11:59  tim
4511  
4512 <        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
4513 <        SimSnapshotManager.hpp: SimModel in progress
4512 >        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
4513 >        branch new_design.
4514  
4515   2004-11-02 11:59  tim
4516  
4517 <        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
4518 <        branch new_design.
4517 >        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
4518 >        SimSnapshotManager.hpp: SimModel in progress
4519  
4520   2004-11-02 10:28  chrisfen
4521  
# Line 3608 | Line 4525
4525  
4526   2004-11-02 10:27  tim
4527  
4528 <        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
4529 <        added on branch new_design.
4528 >        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
4529 >        functions for dealing with memory issue
4530  
4531   2004-11-02 10:27  tim
4532  
4533 <        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
4534 <        functions for dealing with memory issue
4533 >        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
4534 >        added on branch new_design.
4535  
4536   2004-11-02 10:23  tim
4537  
# Line 3643 | Line 4560
4560  
4561   2004-11-01 16:40  tim
4562  
4563 <        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
4564 <        branch new_design.
4563 >        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
4564 >        on branch new_design.
4565  
4566   2004-11-01 16:40  tim
4567  
4568 <        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
4569 <        version of Bond, Bend and Torsion.
4568 >        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
4569 >        branch new_design.
4570  
4571   2004-11-01 16:40  tim
4572  
# Line 3658 | Line 4575
4575  
4576   2004-11-01 16:40  tim
4577  
4578 <        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
4579 <        on branch new_design.
4578 >        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
4579 >        version of Bond, Bend and Torsion.
4580  
4581   2004-11-01 16:37  tim
4582  
# Line 3668 | Line 4585
4585  
4586   2004-11-01 16:37  tim
4587  
4588 <        * src/types/BondType.hpp: file BondType.hpp was initially added on
4589 <        branch new_design.
4588 >        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
4589 >        BondType, BendType, TorsionType
4590  
4591   2004-11-01 16:37  tim
4592  
# Line 3678 | Line 4595
4595  
4596   2004-11-01 16:37  tim
4597  
4598 <        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
4599 <        BondType, BendType, TorsionType
4598 >        * src/types/BondType.hpp: file BondType.hpp was initially added on
4599 >        branch new_design.
4600  
4601   2004-11-01 15:15  tim
4602  
# Line 4511 | Line 5428
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 + 2004-10-11 09:23  tim
5433 +
5434 +        * samples/argon/Makefile: remove argon.dump and argon.eor from
5435 +        Makefile
5436  
5437   2004-10-09 01:01  tim
5438  
5439 <        * samples/: alkane/Makefile.in, lipid/Makefile.in,
5440 <        metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in
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  
# Line 4531 | Line 5454
5454  
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,
# Line 4696 | Line 5619
5619  
5620   2004-09-29 12:56  gezelter
5621  
5622 <        * make/: Make.conf.in, Makefile.in, _files/style.css: Working on
4700 <        make stuff
5622 >        * make/: Make.conf.in, Makefile.in: Working on make stuff
5623  
5624   2004-09-29 12:46  tim
5625  
# Line 4963 | 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,
4967 <        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 5012 | 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 5135 | 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,
5139 <        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 5184 | 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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