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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 2205 by gezelter, Fri Apr 15 22:22:10 2005 UTC

# Line 1 | Line 1
1 + 2005-04-15 17:03  gezelter
2 +
3 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
4 +        UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp,
5 +        UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
6 +        UseTheForce/ForceFieldCreator.hpp,
7 +        UseTheForce/ForceFieldFactory.cpp,
8 +        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp,
9 +        UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90,
10 +        UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h,
11 +        UseTheForce/notifyCutoffs.F90,
12 +        UseTheForce/notifyCutoffs_interface.F90,
13 +        UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90,
14 +        UseTheForce/DarkSide/atype.F90,
15 +        UseTheForce/DarkSide/atype_interface.F90,
16 +        UseTheForce/DarkSide/eam.F90,
17 +        UseTheForce/DarkSide/eam_interface.F90,
18 +        UseTheForce/DarkSide/eam_interface.h,
19 +        UseTheForce/DarkSide/electrostatic.F90,
20 +        UseTheForce/DarkSide/electrostatic_interface.F90,
21 +        UseTheForce/DarkSide/electrostatic_interface.h,
22 +        UseTheForce/DarkSide/force_globals.F90,
23 +        UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h,
24 +        UseTheForce/DarkSide/lj_interface.F90,
25 +        UseTheForce/DarkSide/lj_interface.h,
26 +        UseTheForce/DarkSide/neighborLists.F90,
27 +        UseTheForce/DarkSide/reactionField.F90,
28 +        UseTheForce/DarkSide/shapes.F90,
29 +        UseTheForce/DarkSide/shapes_interface.F90,
30 +        UseTheForce/DarkSide/shapes_interface.h,
31 +        UseTheForce/DarkSide/simParallel.F90,
32 +        UseTheForce/DarkSide/simParallel_interface.F90,
33 +        UseTheForce/DarkSide/simParallel_interface.h,
34 +        UseTheForce/DarkSide/simulation.F90,
35 +        UseTheForce/DarkSide/simulation_interface.F90,
36 +        UseTheForce/DarkSide/simulation_interface.h,
37 +        UseTheForce/DarkSide/sticky.F90,
38 +        UseTheForce/DarkSide/sticky_interface.F90,
39 +        UseTheForce/DarkSide/sticky_interface.h,
40 +        UseTheForce/DarkSide/switcheroo.F90,
41 +        applications/dump2Xyz/Dump2XYZ.cpp,
42 +        applications/dump2Xyz/Dump2XYZCmd.c,
43 +        applications/dump2Xyz/Dump2XYZCmd.h,
44 +        applications/dynamicProps/CrossTimeCorrFunc.cpp,
45 +        applications/dynamicProps/CrossTimeCorrFunc.hpp,
46 +        applications/dynamicProps/DipoleCorrFunc.cpp,
47 +        applications/dynamicProps/DipoleCorrFunc.hpp,
48 +        applications/dynamicProps/DynamicProps.cpp,
49 +        applications/dynamicProps/DynamicPropsCmd.c,
50 +        applications/dynamicProps/DynamicPropsCmd.h,
51 +        applications/dynamicProps/FrameTimeCorrFunc.hpp,
52 +        applications/dynamicProps/ParticleTimeCorrFunc.cpp,
53 +        applications/dynamicProps/ParticleTimeCorrFunc.hpp,
54 +        applications/dynamicProps/RCorrFunc.cpp,
55 +        applications/dynamicProps/RCorrFunc.hpp,
56 +        applications/dynamicProps/TimeCorrFunc.cpp,
57 +        applications/dynamicProps/TimeCorrFunc.hpp,
58 +        applications/dynamicProps/VCorrFunc.cpp,
59 +        applications/dynamicProps/VCorrFunc.hpp,
60 +        applications/nanoRodBuilder/GeometryBuilder.cpp,
61 +        applications/nanoRodBuilder/GeometryBuilder.hpp,
62 +        applications/nanoRodBuilder/nanorodBuilder.cpp,
63 +        applications/nanoRodBuilder/nanorodBuilderCmd.c,
64 +        applications/nanoRodBuilder/nanorodBuilderCmd.h,
65 +        applications/oopse/oopse.cpp,
66 +        applications/simpleBuilder/simpleBuilder.cpp,
67 +        applications/simpleBuilder/simpleBuilderCmd.c,
68 +        applications/simpleBuilder/simpleBuilderCmd.h,
69 +        applications/staticProps/GofAngle2.cpp,
70 +        applications/staticProps/GofAngle2.hpp,
71 +        applications/staticProps/GofR.cpp,
72 +        applications/staticProps/GofR.hpp,
73 +        applications/staticProps/GofRAngle.cpp,
74 +        applications/staticProps/GofRAngle.hpp,
75 +        applications/staticProps/GofXyz.cpp,
76 +        applications/staticProps/GofXyz.hpp,
77 +        applications/staticProps/RadialDistrFunc.cpp,
78 +        applications/staticProps/RadialDistrFunc.hpp,
79 +        applications/staticProps/StaticProps.cpp,
80 +        applications/staticProps/StaticPropsCmd.c,
81 +        applications/staticProps/StaticPropsCmd.h,
82 +        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
83 +        brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp,
84 +        brains/Exclude.hpp, brains/ForceManager.cpp,
85 +        brains/ForceManager.hpp, brains/MoleculeCreator.cpp,
86 +        brains/MoleculeCreator.hpp, brains/Register.cpp,
87 +        brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
88 +        brains/SimInfo.hpp, brains/SimSnapshotManager.cpp,
89 +        brains/SimSnapshotManager.hpp, brains/Snapshot.cpp,
90 +        brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp,
91 +        brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp,
92 +        brains/fSimulation.h, constraints/ConstraintElem.hpp,
93 +        constraints/ConstraintPair.hpp, constraints/Rattle.cpp,
94 +        constraints/Rattle.hpp, constraints/ZconsStruct.hpp,
95 +        constraints/ZconstraintForceManager.cpp,
96 +        constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp,
97 +        integrators/DLM.hpp, integrators/Integrator.cpp,
98 +        integrators/Integrator.hpp, integrators/IntegratorCreator.hpp,
99 +        integrators/IntegratorFactory.cpp,
100 +        integrators/IntegratorFactory.hpp, integrators/NPT.cpp,
101 +        integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp,
102 +        integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp,
103 +        integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp,
104 +        integrators/NVT.cpp, integrators/NVT.hpp,
105 +        integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp,
106 +        integrators/Velocitizer.hpp,
107 +        integrators/VelocityVerletIntegrator.cpp,
108 +        integrators/VelocityVerletIntegrator.hpp,
109 +        io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp,
110 +        io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c,
111 +        io/BASS_parse.h, io/BendTypesSectionParser.cpp,
112 +        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
113 +        io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
114 +        io/ChargeAtomTypesSectionParser.hpp,
115 +        io/DirectionalAtomTypesSectionParser.cpp,
116 +        io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
117 +        io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp,
118 +        io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
119 +        io/Globals.cpp, io/Globals.hpp,
120 +        io/LennardJonesAtomTypesSectionParser.cpp,
121 +        io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp,
122 +        io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp,
123 +        io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp,
124 +        io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp,
125 +        io/SectionParser.cpp, io/SectionParser.hpp,
126 +        io/SectionParserManager.cpp, io/SectionParserManager.hpp,
127 +        io/StatWriter.cpp, io/StatWriter.hpp,
128 +        io/StickyAtomTypesSectionParser.cpp,
129 +        io/StickyAtomTypesSectionParser.hpp,
130 +        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
131 +        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
132 +        io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp,
133 +        io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c,
134 +        io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h,
135 +        io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp,
136 +        lattice/CubicLattice.hpp, lattice/FCCLattice.cpp,
137 +        lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
138 +        lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp,
139 +        lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp,
140 +        math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h,
141 +        math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp,
142 +        math/ParallelRandNumGen.hpp, math/Polynomial.hpp,
143 +        math/Quaternion.hpp, math/RandNumGen.hpp,
144 +        math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp,
145 +        math/RectMatrix.hpp, math/SeqRandNumGen.cpp,
146 +        math/SeqRandNumGen.hpp, math/SquareMatrix.hpp,
147 +        math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp,
148 +        minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp,
149 +        minimizers/Minimizer.cpp, minimizers/Minimizer.hpp,
150 +        minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp,
151 +        minimizers/MinimizerFactory.hpp,
152 +        minimizers/MinimizerParameterSet.cpp,
153 +        minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp,
154 +        minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp,
155 +        minimizers/SDMinimizer.hpp, primitives/Atom.cpp,
156 +        primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp,
157 +        primitives/Bond.hpp, primitives/CutoffGroup.hpp,
158 +        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
159 +        primitives/GhostBend.cpp, primitives/GhostBend.hpp,
160 +        primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp,
161 +        primitives/Molecule.cpp, primitives/Molecule.hpp,
162 +        primitives/RigidBody.cpp, primitives/RigidBody.hpp,
163 +        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
164 +        primitives/Torsion.cpp, primitives/Torsion.hpp,
165 +        primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp,
166 +        profiling/mdProfile.cpp, profiling/mdProfile.hpp,
167 +        profiling/timing.F90, restraints/Restraints.cpp,
168 +        restraints/Restraints.hpp,
169 +        restraints/ThermoIntegrationForceManager.cpp,
170 +        restraints/ThermoIntegrationForceManager.hpp,
171 +        selection/DistanceFinder.cpp, selection/DistanceFinder.hpp,
172 +        selection/IndexFinder.cpp, selection/IndexFinder.hpp,
173 +        selection/NameFinder.cpp, selection/NameFinder.hpp,
174 +        selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp,
175 +        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
176 +        selection/SelectionManager.cpp, selection/SelectionManager.hpp,
177 +        selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp,
178 +        selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp,
179 +        types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h,
180 +        types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp,
181 +        types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp,
182 +        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
183 +        types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp,
184 +        types/CubicBondType.hpp, types/CubicTorsionType.hpp,
185 +        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
186 +        types/DirectionalAtomType.hpp, types/FixedBondType.hpp,
187 +        types/HarmonicBendType.hpp, types/HarmonicBondType.hpp,
188 +        types/MakeStamps.cpp, types/MakeStamps.hpp,
189 +        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
190 +        types/MorseBondType.hpp, types/OplsTorsionType.hpp,
191 +        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
192 +        types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp,
193 +        types/QuarticBondType.hpp, types/QuarticTorsionType.hpp,
194 +        types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
195 +        types/ShapeAtomType.cpp, types/ShapeAtomType.hpp,
196 +        types/TorsionStamp.cpp, types/TorsionStamp.hpp,
197 +        types/TorsionType.hpp, types/UreyBradleyBendType.hpp,
198 +        types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp,
199 +        utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp,
200 +        utils/GenericFactory.hpp, utils/LocalIndexManager.hpp,
201 +        utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp,
202 +        utils/NumericConstant.hpp, utils/OOPSEConstant.hpp,
203 +        utils/PropertyMap.cpp, utils/PropertyMap.hpp,
204 +        utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
205 +        utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp,
206 +        utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp,
207 +        utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp,
208 +        utils/any.hpp, utils/definitions.F90, utils/fError.c,
209 +        utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h,
210 +        utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h,
211 +        utils/residentMem.h, utils/simError.c, utils/simError.h,
212 +        utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp,
213 +        visitors/AtomData.hpp, visitors/AtomVisitor.cpp,
214 +        visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp,
215 +        visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp,
216 +        visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
217 +        visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp,
218 +        visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp,
219 +        visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has
220 +        been drafted to perform our indentation services
221 +
222 + 2005-04-15 17:03  gezelter
223 +
224 +        * configure, ac-tools/configure.in: Jedi mind-trick warning
225 +        messages have been added to make users ignore CGAL.
226 +
227 + 2005-04-15 13:41  tim
228 +
229 +        * make/Makefile.in: fix make install
230 +
231 + 2005-04-15 13:41  tim
232 +
233 +        * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile:
234 +        add  Makefile of samples
235 +
236 + 2005-04-15 13:33  tim
237 +
238 +        * samples/: lipid/Makefile, water/dimer/Makefile,
239 +        water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not
240 +        installed correctly
241 +
242 + 2005-04-14 16:41  gezelter
243 +
244 +        * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in,
245 +        make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl,
246 +        scripts/filepp, scripts/filepp.in: configure now searches for perl
247 +        to use with filepp
248 +
249 + 2005-04-14 16:20  gezelter
250 +
251 +        * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of
252 +        MoLocator
253 +
254 + 2005-04-14 14:12  gezelter
255 +
256 +        * LICENSE: [no log message]
257 +
258 + 2005-04-14 11:10  chuckv
259 +
260 +        * src/applications/nanoRodBuilder/nanorodBuilder.cpp:
261 +        nanorodbuilder now exit's when libCGAL is not present.
262 +
263 + 2005-04-14 10:20  tim
264 +
265 +        * src/io/make_nodes.h: fix one more warning message in make_nodes
266 +
267 + 2005-04-13 18:36  chuckv
268 +
269 +        * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed
270 +        interface name for SGI Compiler
271 +
272 + 2005-04-13 18:29  chrisfen
273 +
274 +        * samples/water/ssde/ssde.md: oops...  bad sample
275 +
276 + 2005-04-13 18:00  chuckv
277 +
278 +        * src/config.h.in: Change typo in CGAL.
279 +
280 + 2005-04-13 17:43  tim
281 +
282 +        * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp,
283 +        selection/SelectionCompiler.hpp: fix some warning messages
284 +
285 + 2005-04-13 17:30  gezelter
286 +
287 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
288 +        make/Makefile.in, src/config.h.in,
289 +        src/applications/nanoRodBuilder/Makefile,
290 +        src/applications/nanoRodBuilder/Makefile.in,
291 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL
292 +        checks
293 +
294 + 2005-04-13 15:36  chuckv
295 +
296 +        * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp,
297 +        DarkSide/LJ.F90, DarkSide/electrostatic.F90,
298 +        DarkSide/electrostatic_interface.F90,
299 +        DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90,
300 +        DarkSide/lj_interface.h, DarkSide/sticky.F90,
301 +        DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added
302 +        destroy methods for Fortran modules.
303 +
304 + 2005-04-13 15:17  chuckv
305 +
306 +        * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90,
307 +        shapes_interface.h: Added destroy method to clean up memory
308 +
309 + 2005-04-13 13:41  tim
310 +
311 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
312 +        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
313 +        io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp,
314 +        primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp,
315 +        types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are
316 +        fixed
317 +
318 + 2005-04-12 17:44  chuckv
319 +
320 +        * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed
321 +        for nanoRodBuilder.
322 +
323 + 2005-04-12 17:42  tim
324 +
325 +        * src/applications/: nanoRodBuilder/nanorodBuilder.cpp,
326 +        simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder
327 +        and simpleBuilder(forget to delete lattice)
328 +
329 + 2005-04-12 17:33  tim
330 +
331 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
332 +        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp:
333 +        refactory lattice
334 +
335 + 2005-04-12 17:07  tim
336 +
337 +        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp,
338 +        CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp,
339 +        Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory
340 +        LatticeFactory and LatticeCreator
341 +
342 + 2005-04-12 16:58  tim
343 +
344 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
345 +        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp,
346 +        brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
347 +        lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp,
348 +        lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp,
349 +        lattice/Makefile: refactory LatticeFactory and LatticeCreator
350 +
351 + 2005-04-12 16:28  gezelter
352 +
353 +        * src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp,
354 +        vector_class.F90: cleaned up vector_class memory leak fix by
355 +        deallocating in reverse order of how we allocated.  Also migrated
356 +        MoLocator into utils directory
357 +
358 + 2005-04-12 16:27  gezelter
359 +
360 +        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp,
361 +        Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
362 +        LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice
363 +        directory
364 +
365 + 2005-04-12 16:27  gezelter
366 +
367 +        * src/applications/: nanoRodBuilder/BaseLattice.cpp,
368 +        nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp,
369 +        nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp,
370 +        nanoRodBuilder/LatticeCreator.hpp,
371 +        nanoRodBuilder/LatticeFactory.cpp,
372 +        nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile,
373 +        nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp,
374 +        nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp,
375 +        simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
376 +        simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
377 +        simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
378 +        simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile,
379 +        simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp,
380 +        simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of
381 +        these files are now redundant
382 +
383 + 2005-04-12 16:27  gezelter
384 +
385 +        * src/UseTheForce/DarkSide/: atype_interface.F90,
386 +        atype_interface.h: cleaned up memory leak fix
387 +
388 + 2005-04-12 16:26  gezelter
389 +
390 +        * make/Makefile.in: added lattice subdirectory
391 +
392 + 2005-04-12 15:57  chrisfen
393 +
394 +        * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added
395 +        a space by accident
396 +
397 + 2005-04-12 15:56  chrisfen
398 +
399 +        * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added
400 +        quadrupole sample
401 +
402 + 2005-04-12 15:56  chrisfen
403 +
404 +        * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating
405 +        samples
406 +
407 + 2005-04-12 13:30  tim
408 +
409 +        * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom
410 +        type in fortran side
411 +
412 + 2005-04-12 12:45  chuckv
413 +
414 +        * src/utils/vector_class.F90: Further changes to vector_class
415 +        destroy function.
416 +
417 + 2005-04-12 12:39  chuckv
418 +
419 +        * src/utils/vector_class.F90: Fixed pointer memory leak in
420 +        vector_class.
421 +
422 + 2005-04-12 12:12  chuckv
423 +
424 +        * src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp,
425 +        DarkSide/atype_interface.F90, DarkSide/atype_interface.h,
426 +        DarkSide/eam.F90, DarkSide/eam_interface.F90,
427 +        DarkSide/eam_interface.h: Updates to deallocate object in fortran.
428 +
429 + 2005-04-12 09:24  chrisfen
430 +
431 +        * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI
432 +        output
433 +
434 + 2005-04-11 19:29  chuckv
435 +
436 +        * src/: UseTheForce/DarkSide/atype.F90,
437 +        applications/nanoRodBuilder/Makefile: Changes to delete atypes...
438 +
439 + 2005-04-11 19:28  chuckv
440 +
441 +        * src/utils/vector_class.F90: Added code to delete vector.
442 +
443 + 2005-04-11 17:03  chuckv
444 +
445 +        * samples/metals/nanorod/: Au_nanoparticle.md,
446 +        Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why
447 +        aren't these here?
448 +
449 + 2005-04-11 16:58  tim
450 +
451 +        * src/io/basic_ifstrstream.hpp: avoid multiple inherit in
452 +        basic_ifstrstream
453 +
454 + 2005-04-11 16:37  chuckv
455 +
456 +        * make/Makefile.in,
457 +        src/applications/nanoRodBuilder/BaseLattice.cpp,
458 +        src/applications/nanoRodBuilder/BaseLattice.hpp,
459 +        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
460 +        src/applications/nanoRodBuilder/GeometryBuilder.hpp,
461 +        src/applications/nanoRodBuilder/Lattice.cpp,
462 +        src/applications/nanoRodBuilder/Lattice.hpp,
463 +        src/applications/nanoRodBuilder/LatticeCreator.cpp,
464 +        src/applications/nanoRodBuilder/LatticeCreator.hpp,
465 +        src/applications/nanoRodBuilder/LatticeFactory.cpp,
466 +        src/applications/nanoRodBuilder/LatticeFactory.hpp,
467 +        src/applications/nanoRodBuilder/Makefile,
468 +        src/applications/nanoRodBuilder/MoLocator.cpp,
469 +        src/applications/nanoRodBuilder/MoLocator.hpp,
470 +        src/applications/nanoRodBuilder/nanoBuilder.ggo,
471 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
472 +        src/applications/nanoRodBuilder/nanorodBuilder.ggo,
473 +        src/applications/nanoRodBuilder/nanorodBuilderCmd.c,
474 +        src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing
475 +        nanoRodBuilder application (may not work yet).  ((Doesn't work
476 +        yet.)) (((May never work....)))
477 +
478 + 2005-04-11 15:54  tim
479 +
480 +        * src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete
481 +        prepareVisitor in Dump2XYZ
482 +
483 + 2005-04-11 15:19  chrisfen
484 +
485 +        * src/UseTheForce/DarkSide/electrostatic.F90: fixing of the
486 +        quadrupoles.  look!  it's divide by 3 like stone says!
487 +
488 + 2005-04-11 15:18  chrisfen
489 +
490 +        * forceFields/DUFF2.frc: fixing of the quadrupoles
491 +
492 + 2005-04-11 15:16  tim
493 +
494 +        * src/selection/Token.hpp: change the parameter name in
495 +        constructors
496 +
497 + 2005-04-11 14:49  gezelter
498 +
499 +        * make/Makefile.in: One more bug fix for GNU make versions < 3.80
500 +
501 + 2005-04-11 14:06  gezelter
502 +
503 +        * make/Makefile.in: Fixed the uc and lc functions for GNU make
504 +        versions < 3.80
505 +
506 + 2005-04-11 11:13  gezelter
507 +
508 +        * make/Makefile.in, src/UseTheForce/Makefile,
509 +        src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added
510 +        some stuff to clean out module files during "make clean"
511 +
512 + 2005-04-08 17:13  chrisfen
513 +
514 +        * src/UseTheForce/DarkSide/electrostatic.F90: quadrupole
515 +        interactions should be working with a remaining question of
516 +        interaction magnitude
517 +
518 + 2005-04-08 17:12  chrisfen
519 +
520 +        * samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with
521 +        samples
522 +
523 + 2005-04-08 13:48  chrisfen
524 +
525 +        * samples/water/ssd/ssd.md: oops...  messed up a sample
526 +
527 + 2005-04-08 09:43  chrisfen
528 +
529 +        * src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix
530 +        charge-dipole interactions
531 +
532 + 2005-04-08 09:42  chrisfen
533 +
534 +        * samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md,
535 +        ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole
536 +
537 + 2005-04-08 09:41  chrisfen
538 +
539 +        * forceFields/DUFF2.frc: added Cl- and Na+
540 +
541 + 2005-04-06 18:59  tim
542 +
543 +        * src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser
544 +
545 + 2005-04-05 18:09  tim
546 +
547 +        * src/selection/: NameFinder.cpp, SelectionCompiler.cpp,
548 +        SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-'
549 +        in atom type name;clean the code a little bit
550 +
551 + 2005-03-29 16:00  tim
552 +
553 +        * src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug
554 +        in converting rotation matrix to quaternion
555 +
556 + 2005-03-28 17:41  tim
557 +
558 +        * src/visitors/LipidTransVisitor.cpp: fixed the wrapping
559 +
560 + 2005-03-28 17:30  tim
561 +
562 +        * src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do
563 +        the wrapping
564 +
565 + 2005-03-28 10:54  tim
566 +
567 +        * src/applications/staticProps/GofXyz.cpp: fix a bug in getting the
568 +        dimension of histogram
569 +
570 + 2005-03-22 11:38  tim
571 +
572 +        * make/Makefile.in, src/applications/dump2Xyz/Makefile,
573 +        src/applications/dynamicProps/Makefile,
574 +        src/applications/oopse/Makefile,
575 +        src/applications/simpleBuilder/Makefile,
576 +        src/applications/staticProps/Makefile: avoid building parallel
577 +        executable for dump2XYZ, simpleBuilder, staticProps and
578 +        dynamicProps
579 +
580 + 2005-03-21 17:34  chrisfen
581 +
582 +        * forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the
583 +        forcefield files
584 +
585 + 2005-03-21 15:51  chrisfen
586 +
587 +        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
588 +        DarkSide/reactionField.F90: Make sure electrostatic_module provides
589 +        data for reaction_field
590 +
591 + 2005-03-21 15:50  chrisfen
592 +
593 +        * forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff.  HE
594 +        WILL CHANGE THIS BACK, RIGHT?
595 +
596 + 2005-03-21 14:23  gezelter
597 +
598 +        * src/UseTheForce/DarkSide/electrostatic.F90: constant back to
599 +        correct value
600 +
601 + 2005-03-21 14:22  gezelter
602 +
603 +        * make/Makefile.in: fixed an install-related bug.
604 +        $(InstallCommand) had been set to $(InstallData)
605 +
606 + 2005-03-15 09:21  gezelter
607 +
608 +        * src/integrators/Integrator.cpp: VelocityVerletIntegrator already
609 +        deletes and Nullifies restWriter, so Integrator shouldn't do it.
610 +
611 + 2005-03-15 09:20  gezelter
612 +
613 +        * src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos
614 +
615 + 2005-03-13 02:39  gezelter
616 +
617 +        * src/UseTheForce/DarkSide/electrostatic.F90: first run at
618 +        charge-quadrupole interactions
619 +
620 + 2005-03-12 14:12  chrisfen
621 +
622 +        * samples/: Makefile.in, thermoIntegration/liquid/Makefile,
623 +        thermoIntegration/solid/Makefile: forgot a couple of makefiles
624 +
625 + 2005-03-12 14:05  chrisfen
626 +
627 +        * samples/thermoIntegration/liquid/ssde.in,
628 +        samples/thermoIntegration/liquid/ssde.md,
629 +        samples/thermoIntegration/liquid/water.md,
630 +        samples/thermoIntegration/solid/idealCrystal.in,
631 +        samples/thermoIntegration/solid/ssde.in,
632 +        samples/thermoIntegration/solid/ssde.md,
633 +        samples/thermoIntegration/solid/ssde.zang0,
634 +        samples/thermoIntegration/solid/water.md,
635 +        samples/water/tip3p_ice/tp3.md,
636 +        src/UseTheForce/DarkSide/sticky.F90,
637 +        src/restraints/ThermoIntegrationForceManager.cpp: added some
638 +        samples
639 +
640 + 2005-03-11 12:50  tim
641 +
642 +        * src/: brains/SimCreator.cpp,
643 +        io/MultipoleAtomTypesSectionParser.cpp: fix a typo in
644 +        MultipoleAtomTypesSectionParser
645 +
646 + 2005-03-11 10:55  tim
647 +
648 +        * src/brains/SimInfo.cpp: pairs inside cutoff group should not be
649 +        excluded
650 +
651 + 2005-03-11 10:53  gezelter
652 +
653 +        * src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for
654 +        quadrupoles
655 +
656 + 2005-03-11 10:52  gezelter
657 +
658 +        * forceFields/DUFF2.frc: quadrupoles for SSD models
659 +
660 + 2005-03-11 10:00  tim
661 +
662 +        * ChangeLog, doc/SelectionExpression.html,
663 +        doc/classoopse_1_1StuntDouble.png, doc/definition.jpg,
664 +        doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png,
665 +        src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp,
666 +        src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp,
667 +        src/selection/TokenMap.cpp: clean up SimInfo; modify the images of
668 +        SelectionExpression.html
669 +
670 + 2005-03-10 19:43  chrisfen
671 +
672 +        * samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md,
673 +        src/io/RestReader.cpp, src/restraints/Restraints.cpp,
674 +        src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in
675 +        MPI restraints
676 +
677 + 2005-03-10 18:56  tim
678 +
679 +        * doc/SelectionExpression.html, src/brains/SimInfo.cpp,
680 +        src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody
681 +        and cutoff group
682 +
683 + 2005-03-10 17:06  gezelter
684 +
685 +        * src/types/MorseBondType.hpp: fixed a doxygen problem
686 +
687 + 2005-03-10 16:51  gezelter
688 +
689 +        * samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with
690 +        the split dipole test cases
691 +
692 + 2005-03-10 16:51  gezelter
693 +
694 +        * doc/SelectionExpression.html: updated some documentation
695 +
696 + 2005-03-10 15:40  gezelter
697 +
698 +        * src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp,
699 +        Makefile: LinkedList removal project starts now
700 +
701 + 2005-03-10 15:28  tim
702 +
703 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
704 +        io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp:
705 +        using map to replace link list
706 +
707 + 2005-03-10 14:11  tim
708 +
709 +        * samples/dipole/: splitInWater.in, splitInWater.md: adding test
710 +        case  of split dipole
711 +
712 + 2005-03-10 14:10  chrisfen
713 +
714 +        * samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp,
715 +        src/io/RestWriter.cpp,
716 +        src/restraints/ThermoIntegrationForceManager.cpp: Oops...  MPI now
717 +        builds...
718 +
719 + 2005-03-10 13:44  tim
720 +
721 +        * samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in,
722 +        split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md:
723 +        adding test case for split dipole
724 +
725 + 2005-03-10 12:54  gezelter
726 +
727 +        * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side
728 +        support for split dipoles
729 +
730 + 2005-03-10 11:27  chrisfen
731 +
732 +        * samples/water/tip3p_ice/tp3.md,
733 +        src/restraints/ThermoIntegrationForceManager.cpp: fixes to
734 +        restraints
735 +
736 + 2005-03-10 11:15  chrisfen
737 +
738 +        * samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp,
739 +        src/UseTheForce/ForceFields.hpp,
740 +        src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints
741 +
742 + 2005-03-10 11:14  tim
743 +
744 +        * ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc,
745 +        src/io/MultipoleAtomTypesSectionParser.cpp,
746 +        src/selection/SelectionEvaluator.cpp: minor change
747 +
748   2005-03-10 10:10  chrisfen
749  
750          * make/Makefile.in, samples/water/tip3p_ice/tp3.md,
# Line 274 | Line 1021
1021          adding basic_teebuf which can operate on multiple stream
1022          simutaneously.
1023  
1024 + 2005-02-22 14:26  chrisfen
1025 +
1026 +        * samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf
1027 +        sample
1028 +
1029   2005-02-22 13:56  tim
1030  
1031          * src/: UseTheForce/DarkSide/reactionField.F90,
# Line 1479 | Line 2231
2231  
2232   2005-01-11 10:52  tim
2233  
2234 <        * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
2234 >        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
2235          on branch new_design.
2236  
2237   2005-01-11 10:52  tim
2238  
2239 <        * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
2239 >        * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
2240 >        on branch new_design.
2241  
2242   2005-01-11 10:52  tim
2243  
2244 <        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
1492 <        on branch new_design.
2244 >        * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
2245  
2246   2005-01-11 10:47  tim
2247  
# Line 1554 | Line 2306
2306  
2307          * src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was
2308          initially added on branch new_design.
2309 +
2310 + 2005-01-07 16:50  tim
2311 +
2312 +        * src/constraints/ZconstraintForceManager.cpp: file
2313 +        ZconstraintForceManager.cpp was initially added on branch
2314 +        new_design.
2315 +
2316 + 2005-01-07 16:50  tim
2317 +
2318 +        * src/constraints/ZconstraintForceManager.hpp: file
2319 +        ZconstraintForceManager.hpp was initially added on branch
2320 +        new_design.
2321  
2322   2005-01-07 16:50  tim
2323  
# Line 1574 | Line 2338
2338          * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was
2339          initially added on branch new_design.
2340  
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 –
2341   2005-01-06 17:31  tim
2342  
2343          * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
# Line 1622 | Line 2374
2374  
2375   2005-01-05 12:35  tim
2376  
2377 +        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
2378 +        added on branch new_design.
2379 +
2380 + 2005-01-05 12:35  tim
2381 +
2382          * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
2383          Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp,
2384          MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp,
# Line 1630 | Line 2387
2387  
2388   2005-01-05 12:35  tim
2389  
2390 <        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
2391 <        added on branch new_design.
2390 >        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
2391 >        was initially added on branch new_design.
2392  
2393   2005-01-05 12:35  tim
2394  
2395 <        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
2395 >        * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
2396          was initially added on branch new_design.
2397  
2398   2005-01-05 12:35  tim
2399  
2400 <        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
2400 >        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
2401          was initially added on branch new_design.
2402  
2403   2005-01-05 12:35  tim
# Line 1648 | Line 2405
2405          * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially
2406          added on branch new_design.
2407  
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 –
2408   2005-01-04 17:18  tim
2409  
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 –
2410          * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
2411          brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp,
2412          brains/Thermo.cpp, constraints/ConstraintPair.hpp,
# Line 1671 | Line 2418
2418  
2419   2005-01-04 17:18  tim
2420  
2421 <        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
2422 <        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
1676 <        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
1677 <        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
1678 <
1679 < 2005-01-04 17:18  tim
1680 <
1681 <        * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
1682 <        was initially added on branch new_design.
2421 >        * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was
2422 >        initially added on branch new_design.
2423  
2424   2005-01-04 17:18  tim
2425  
# Line 1693 | Line 2433
2433  
2434   2005-01-04 17:18  tim
2435  
2436 +        * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
2437 +        was initially added on branch new_design.
2438 +
2439 + 2005-01-04 17:18  tim
2440 +
2441 +        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
2442 +        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
2443 +        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
2444 +        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
2445 +
2446 + 2005-01-04 17:18  tim
2447 +
2448          * src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on
2449          branch new_design.
2450  
# Line 2008 | Line 2760
2760          io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp,
2761          io/SectionParserManager.cpp, utils/LocalIndexManager.hpp,
2762          utils/TypeContainer.hpp: begin to fix bugs
2763 +
2764 + 2004-12-02 19:26  tim
2765 +
2766 +        * src/utils/Trim.cpp: file Trim.cpp was initially added on branch
2767 +        new_design.
2768  
2769   2004-12-02 19:26  tim
2770  
# Line 2019 | Line 2776
2776          io/SectionParserManager.hpp, utils/Makefile,
2777          utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a
2778          bug in countTokens in StringTokenizer
2022 –
2023 – 2004-12-02 19:26  tim
2024 –
2025 –        * src/utils/Trim.cpp: file Trim.cpp was initially added on branch
2026 –        new_design.
2779  
2780   2004-12-02 19:06  tim
2781  
# Line 2035 | Line 2787
2787  
2788   2004-12-02 17:15  tim
2789  
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 –
2790          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2791          UseTheForce/ForceFieldCreator.cpp,
2792          UseTheForce/ForceFieldCreator.hpp,
# Line 2072 | Line 2809
2809          * src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp
2810          was initially added on branch new_design.
2811  
2812 + 2004-12-02 17:15  tim
2813 +
2814 +        * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp
2815 +        was initially added on branch new_design.
2816 +
2817 + 2004-12-02 17:15  tim
2818 +
2819 +        * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp
2820 +        was initially added on branch new_design.
2821 +
2822 + 2004-12-02 17:15  tim
2823 +
2824 +        * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp
2825 +        was initially added on branch new_design.
2826 +
2827   2004-12-02 11:53  tim
2828  
2829          * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp,
# Line 2230 | Line 2982
2982  
2983   2004-12-01 19:09  tim
2984  
2985 <        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
2986 <        was initially added on branch new_design.
2985 >        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
2986 >        branch new_design.
2987  
2988   2004-12-01 19:09  tim
2989  
2990 +        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
2991 +        branch new_design.
2992 +
2993 + 2004-12-01 19:09  tim
2994 +
2995          * src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp,
2996          brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
2997          brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp,
# Line 2247 | Line 3004
3004  
3005   2004-12-01 19:09  tim
3006  
3007 <        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
3008 <        branch new_design.
2252 <
2253 < 2004-12-01 19:09  tim
3007 >        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
3008 >        was initially added on branch new_design.
3009  
2255 –        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
2256 –        branch new_design.
2257 –
3010   2004-12-01 17:45  tim
3011  
3012          * src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp,
# Line 2353 | Line 3105
3105  
3106   2004-11-30 14:58  tim
3107  
2356 –        * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially
2357 –        added on branch new_design.
2358 –
2359 – 2004-11-30 14:58  tim
2360 –
3108          * src/: brains/Exclude.cpp, brains/Exclude.hpp,
3109          brains/ForceManager.cpp, brains/ForceManager.hpp,
3110          brains/MoleculeCreator.cpp, brains/SimCreator.hpp,
# Line 2367 | Line 3114
3114          brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile,
3115          math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo
3116  
3117 + 2004-11-30 14:58  tim
3118 +
3119 +        * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially
3120 +        added on branch new_design.
3121 +
3122   2004-11-30 12:54  tim
3123  
3124          * src/: primitives/Bend.hpp, primitives/Bond.hpp,
# Line 2375 | Line 3127
3127  
3128   2004-11-30 00:03  tim
3129  
3130 <        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
3131 <        LocalndexManager.hpp to LocalIndexManager.hpp
3130 >        * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
3131 >        initially added on branch new_design.
3132  
3133   2004-11-30 00:03  tim
3134  
3135 <        * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
3136 <        initially added on branch new_design.
3135 >        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
3136 >        LocalndexManager.hpp to LocalIndexManager.hpp
3137  
3138   2004-11-29 23:43  tim
3139  
# Line 2509 | Line 3261
3261  
3262   2004-11-25 15:18  tim
3263  
3264 +        * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was
3265 +        initially added on branch new_design.
3266 +
3267 + 2004-11-25 15:18  tim
3268 +
3269          * src/: io/AtomTypesSectionParser.cpp,
3270          io/BondTypesSectionParser.cpp,
3271          io/DirectionalAtomTypesSectionParser.cpp,
# Line 2521 | Line 3278
3278          * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was
3279          initially added on branch new_design.
3280  
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 –
3281   2004-11-24 17:12  tim
3282  
3283          * src/: io/AtomTypesSectionParser.cpp,
# Line 2638 | Line 3390
3390  
3391   2004-11-23 12:53  tim
3392  
2641 –        * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
2642 –        ElectrostaticAtomTypesSectionParser.cpp was initially added on
2643 –        branch new_design.
2644 –
2645 – 2004-11-23 12:53  tim
2646 –
3393          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3394          UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
3395          applications/simpleBuilder/simpleBuilder.cpp,
# Line 2661 | Line 3407
3407          ElectrostaticAtomTypesSectionParser.hpp was initially added on
3408          branch new_design.
3409  
3410 < 2004-11-23 01:03  tim
3410 > 2004-11-23 12:53  tim
3411  
3412 <        * src/io/EAMAtomTypesSectionParser.cpp: file
3413 <        EAMAtomTypesSectionParser.cpp was initially added on branch
3414 <        new_design.
3412 >        * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
3413 >        ElectrostaticAtomTypesSectionParser.cpp was initially added on
3414 >        branch new_design.
3415  
3416   2004-11-23 01:03  tim
3417  
# Line 2676 | Line 3422
3422  
3423   2004-11-23 01:03  tim
3424  
3425 +        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
3426 +        was initially added on branch new_design.
3427 +
3428 + 2004-11-23 01:03  tim
3429 +
3430          * src/io/EAMAtomTypesSectionParser.hpp: file
3431          EAMAtomTypesSectionParser.hpp was initially added on branch
3432          new_design.
3433  
3434   2004-11-23 01:03  tim
3435  
3436 <        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
3437 <        was initially added on branch new_design.
3436 >        * src/io/EAMAtomTypesSectionParser.cpp: file
3437 >        EAMAtomTypesSectionParser.cpp was initially added on branch
3438 >        new_design.
3439  
3440   2004-11-22 23:35  tim
3441  
3442 <        * src/io/TorsionTypesSectionParser.cpp: file
3443 <        TorsionTypesSectionParser.cpp was initially added on branch
3442 >        * src/io/TorsionTypesSectionParser.hpp: file
3443 >        TorsionTypesSectionParser.hpp was initially added on branch
3444          new_design.
3445  
3446   2004-11-22 23:35  tim
# Line 2699 | Line 3451
3451  
3452   2004-11-22 23:35  tim
3453  
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 –
3454          * src/io/BondTypesSectionParser.hpp: file
3455          BondTypesSectionParser.hpp was initially added on branch
3456          new_design.
3457  
3458   2004-11-22 23:35  tim
3459  
3460 <        * src/io/TorsionTypesSectionParser.hpp: file
3461 <        TorsionTypesSectionParser.hpp was initially added on branch
3460 >        * src/io/BondTypesSectionParser.cpp: file
3461 >        BondTypesSectionParser.cpp was initially added on branch
3462          new_design.
3463  
3464   2004-11-22 23:35  tim
3465  
3466 <        * src/io/BendTypesSectionParser.cpp: file
3467 <        BendTypesSectionParser.cpp was initially added on branch
3466 >        * src/io/TorsionTypesSectionParser.cpp: file
3467 >        TorsionTypesSectionParser.cpp was initially added on branch
3468          new_design.
3469  
3470   2004-11-22 23:35  tim
# Line 2729 | Line 3475
3475          BondTypesSectionParser, BendTypesSectionParser and
3476          TorsionTypeSectionParser
3477  
3478 + 2004-11-22 23:35  tim
3479 +
3480 +        * src/io/BendTypesSectionParser.cpp: file
3481 +        BendTypesSectionParser.cpp was initially added on branch
3482 +        new_design.
3483 +
3484   2004-11-22 18:04  tim
3485  
3486          * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in
# Line 2736 | Line 3488
3488  
3489   2004-11-22 18:02  tim
3490  
3491 <        * src/io/DirectionalAtomTypesSectionParser.hpp: file
3492 <        DirectionalAtomTypesSectionParser.hpp was initially added on branch
2741 <        new_design.
3491 >        * src/io/: DirectionalAtomTypesParser.hpp,
3492 >        DirectionalAtomTypesSectionParser.hpp: adding section parsers
3493  
3494   2004-11-22 18:02  tim
3495  
3496 <        * src/io/: DirectionalAtomTypesParser.hpp,
3497 <        DirectionalAtomTypesSectionParser.hpp: adding section parsers
3496 >        * src/io/DirectionalAtomTypesSectionParser.hpp: file
3497 >        DirectionalAtomTypesSectionParser.hpp was initially added on branch
3498 >        new_design.
3499  
3500   2004-11-22 15:55  tim
3501  
3502 <        * src/io/DirectionalAtomTypesParser.hpp: file
3503 <        DirectionalAtomTypesParser.hpp was initially added on branch
3502 >        * src/io/DipoleAtomTypesSectionParser.hpp: file
3503 >        DipoleAtomTypesSectionParser.hpp was initially added on branch
3504          new_design.
3505  
3506   2004-11-22 15:55  tim
3507  
3508 <        * src/io/HarmonicBondTypesSectionParser.hpp: file
3509 <        HarmonicBondTypesSectionParser.hpp was initially added on branch
3508 >        * src/io/AtomTypesSectionParser.hpp: file
3509 >        AtomTypesSectionParser.hpp was initially added on branch
3510          new_design.
3511  
3512   2004-11-22 15:55  tim
3513  
3514 <        * src/io/ChargeAtomTypesSectionParser.hpp: file
3515 <        ChargeAtomTypesSectionParser.hpp was initially added on branch
3514 >        * src/io/HarmonicBondTypesSectionParser.hpp: file
3515 >        HarmonicBondTypesSectionParser.hpp was initially added on branch
3516          new_design.
3517  
3518   2004-11-22 15:55  tim
3519  
3520 <        * src/io/DirectionalAtomTypesSectionParser.cpp: file
3521 <        DirectionalAtomTypesSectionParser.cpp was initially added on branch
3520 >        * src/io/StickyAtomTypesSectionParser.cpp: file
3521 >        StickyAtomTypesSectionParser.cpp was initially added on branch
3522          new_design.
3523  
3524   2004-11-22 15:55  tim
3525  
3526 <        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
3527 <        LennardJonesAtomTypesSectionParser.cpp was initially added on
3526 >        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
3527 >        LennardJonesAtomTypesSectionParser.hpp was initially added on
3528          branch new_design.
3529  
3530   2004-11-22 15:55  tim
3531  
3532 <        * src/io/DipoleAtomTypesSectionParser.cpp: file
3533 <        DipoleAtomTypesSectionParser.cpp was initially added on branch
3532 >        * src/io/HarmonicBondTypesSectionParser.cpp: file
3533 >        HarmonicBondTypesSectionParser.cpp was initially added on branch
3534          new_design.
3535  
3536   2004-11-22 15:55  tim
3537  
3538 <        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
3539 <        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
3538 >        * src/io/DirectionalAtomTypesSectionParser.cpp: file
3539 >        DirectionalAtomTypesSectionParser.cpp was initially added on branch
3540          new_design.
3541  
3542   2004-11-22 15:55  tim
3543  
3544 <        * 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
3544 >        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
3545          was initially added on branch new_design.
3546  
3547   2004-11-22 15:55  tim
# Line 2827 | Line 3552
3552  
3553   2004-11-22 15:55  tim
3554  
3555 <        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
3556 <        LennardJonesAtomTypesSectionParser.hpp was initially added on
3557 <        branch new_design.
3555 >        * src/io/ChargeAtomTypesSectionParser.cpp: file
3556 >        ChargeAtomTypesSectionParser.cpp was initially added on branch
3557 >        new_design.
3558  
3559   2004-11-22 15:55  tim
3560  
3561 <        * src/io/HarmonicBondTypesSectionParser.cpp: file
3562 <        HarmonicBondTypesSectionParser.cpp was initially added on branch
3561 >        * src/io/DipoleAtomTypesSectionParser.cpp: file
3562 >        DipoleAtomTypesSectionParser.cpp was initially added on branch
3563          new_design.
3564  
3565   2004-11-22 15:55  tim
3566  
3567 <        * src/io/AtomTypesSectionParser.hpp: file
3568 <        AtomTypesSectionParser.hpp was initially added on branch
3567 >        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
3568 >        LennardJonesAtomTypesSectionParser.cpp was initially added on
3569 >        branch new_design.
3570 >
3571 > 2004-11-22 15:55  tim
3572 >
3573 >        * src/io/ChargeAtomTypesSectionParser.hpp: file
3574 >        ChargeAtomTypesSectionParser.hpp was initially added on branch
3575          new_design.
3576  
3577   2004-11-22 15:55  tim
3578  
3579 <        * src/io/StickyAtomTypesSectionParser.cpp: file
3580 <        StickyAtomTypesSectionParser.cpp was initially added on branch
3579 >        * src/io/StickyAtomTypesSectionParser.hpp: file
3580 >        StickyAtomTypesSectionParser.hpp was initially added on branch
3581          new_design.
3582  
3583   2004-11-22 15:55  tim
# Line 2856 | Line 3587
3587  
3588   2004-11-22 15:55  tim
3589  
3590 <        * src/io/ChargeAtomTypesSectionParser.cpp: file
3591 <        ChargeAtomTypesSectionParser.cpp was initially added on branch
3590 >        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
3591 >        brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
3592 >        brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp,
3593 >        integrators/NVT.hpp, io/AtomTypesSectionParser.cpp,
3594 >        io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
3595 >        io/ChargeAtomTypesSectionParser.hpp,
3596 >        io/DipoleAtomTypesSectionParser.cpp,
3597 >        io/DipoleAtomTypesSectionParser.hpp,
3598 >        io/DirectionalAtomTypesParser.hpp,
3599 >        io/DirectionalAtomTypesSectionParser.cpp,
3600 >        io/HarmonicBondTypesSectionParser.cpp,
3601 >        io/HarmonicBondTypesSectionParser.hpp,
3602 >        io/LennardJonesAtomTypesSectionParser.cpp,
3603 >        io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp,
3604 >        io/SectionParser.hpp, io/SectionParserManager.cpp,
3605 >        io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp,
3606 >        io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp,
3607 >        types/AtomType.hpp, types/DirectionalAtomType.hpp,
3608 >        utils/GenericData.hpp: adding section parsers
3609 >
3610 > 2004-11-22 15:55  tim
3611 >
3612 >        * src/io/DirectionalAtomTypesParser.hpp: file
3613 >        DirectionalAtomTypesParser.hpp was initially added on branch
3614          new_design.
3615  
3616   2004-11-22 15:55  tim
3617  
3618 <        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
3618 >        * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
3619          was initially added on branch new_design.
3620  
3621   2004-11-22 15:55  tim
3622  
3623 <        * src/io/StickyAtomTypesSectionParser.hpp: file
3624 <        StickyAtomTypesSectionParser.hpp was initially added on branch
2872 <        new_design.
3623 >        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
3624 >        added on branch new_design.
3625  
3626   2004-11-19 17:12  tim
3627  
3628 +        * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
3629 +        added on branch new_design.
3630 +
3631 + 2004-11-19 17:12  tim
3632 +
3633          * src/: brains/SimState.cpp, brains/SimState.hpp,
3634          io/InitializeFromFile.cpp, types/FixBondType.hpp,
3635          types/FixedBondType.hpp: remove more useless files
3636  
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 –
3637   2004-11-19 16:47  tim
3638  
3639          * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp,
# Line 2890 | Line 3642
3642  
3643   2004-11-19 16:38  tim
3644  
3645 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3646 +        UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp,
3647 +        integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp,
3648 +        integrators/NVT.hpp: refactory integrator
3649 +
3650 + 2004-11-19 16:38  tim
3651 +
3652          * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on
3653          branch new_design.
3654  
3655   2004-11-19 16:38  tim
3656  
3657 <        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
3658 <        on branch new_design.
3657 >        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
3658 >        branch new_design.
3659  
3660   2004-11-19 16:38  tim
3661  
# Line 2905 | Line 3664
3664  
3665   2004-11-19 16:38  tim
3666  
3667 <        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
3668 <        branch new_design.
3667 >        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
3668 >        on branch new_design.
3669  
3670   2004-11-19 16:38  tim
3671  
3672 <        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
3672 >        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
3673          branch new_design.
3674  
2916 – 2004-11-19 16:38  tim
2917 –
2918 –        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2919 –        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
2922 –
3675   2004-11-19 15:37  tim
3676  
3677          * forceFields/newDUFF.frc: new DUFF forcefield
3678  
3679   2004-11-19 15:23  tim
3680  
3681 +        * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
3682 +        branch new_design.
3683 +
3684 + 2004-11-19 15:23  tim
3685 +
3686          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp,
3687          UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp,
3688          utils/TypeContainer.hpp: add EAM
# Line 2935 | Line 3692
3692          * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on
3693          branch new_design.
3694  
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 –
3695   2004-11-19 13:02  tim
3696  
3697          * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except
# Line 2947 | Line 3699
3699  
3700   2004-11-19 12:56  tim
3701  
3702 <        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
3702 >        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
3703          was initially added on branch new_design.
3704  
3705   2004-11-19 12:56  tim
3706  
3707 <        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
3707 >        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
3708          was initially added on branch new_design.
3709  
3710   2004-11-19 12:56  tim
# Line 2977 | Line 3729
3729  
3730   2004-11-18 18:26  tim
3731  
3732 +        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
3733 +        initially added on branch new_design.
3734 +
3735 + 2004-11-18 18:26  tim
3736 +
3737          * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp,
3738          integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
3739          integrators/VelocityVerletIntegrator.cpp,
# Line 2987 | Line 3744
3744          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding
3745          DUFF parser
3746  
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 –
3747   2004-11-18 16:42  tim
3748  
3749          * forceFields/newDUFF.frc: adding new format DUFF force field
# Line 3003 | Line 3755
3755  
3756   2004-11-18 00:42  tim
3757  
3758 <        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
3758 >        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
3759          initially added on branch new_design.
3760  
3761   2004-11-18 00:42  tim
3762  
3763 <        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
3763 >        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
3764          initially added on branch new_design.
3765  
3766   2004-11-18 00:42  tim
# Line 3051 | Line 3803
3803  
3804   2004-11-17 16:47  tim
3805  
3806 +        * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp
3807 +        was initially added on branch new_design.
3808 +
3809 + 2004-11-17 16:47  tim
3810 +
3811          * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially
3812          added on branch new_design.
3813  
3814   2004-11-17 16:47  tim
3815  
3816 +        * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially
3817 +        added on branch new_design.
3818 +
3819 + 2004-11-17 16:47  tim
3820 +
3821          * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was
3822          initially added on branch new_design.
3823  
3824   2004-11-17 16:47  tim
3825  
3826 <        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
3826 >        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
3827          initially added on branch new_design.
3828  
3829   2004-11-17 16:47  tim
3830  
3831 <        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
3831 >        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
3832          initially added on branch new_design.
3833  
3834   2004-11-17 16:47  tim
# Line 3086 | Line 3848
3848          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp:
3849          UreyBradleyBend and GhostBend
3850  
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 –
3851   2004-11-17 13:58  tim
3852  
3853          * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp
# Line 3103 | Line 3855
3855  
3856   2004-11-17 13:58  tim
3857  
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 –
3858          * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp
3859          was initially added on branch new_design.
3860  
# Line 3120 | Line 3867
3867          types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types
3868          stuff and Chebyshev Polynomial
3869  
3870 < 2004-11-17 01:37  tim
3870 > 2004-11-17 13:58  tim
3871  
3872 <        * 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
3872 >        * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
3873          initially added on branch new_design.
3874  
3875   2004-11-17 01:37  tim
3876  
3877 <        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
3878 <        initially added on branch new_design.
3877 >        * src/types/PolynomialTorsionType.hpp: file
3878 >        PolynomialTorsionType.hpp was initially added on branch new_design.
3879  
3880   2004-11-17 01:37  tim
3881  
# Line 3142 | Line 3884
3884  
3885   2004-11-17 01:37  tim
3886  
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 –
3887          * src/: math/Polynomial.hpp, primitives/Bend.cpp,
3888          primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp,
3889          types/BondType.hpp, types/CharmmTorsionType.cpp,
# Line 3159 | Line 3896
3896          CharmmTorsionType. Need to refine the design and add document for
3897          them
3898  
3899 + 2004-11-17 01:37  tim
3900 +
3901 +        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
3902 +        initially added on branch new_design.
3903 +
3904 + 2004-11-17 01:37  tim
3905 +
3906 +        * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was
3907 +        initially added on branch new_design.
3908 +
3909 + 2004-11-17 01:37  tim
3910 +
3911 +        * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
3912 +        initially added on branch new_design.
3913 +
3914   2004-11-16 20:11  tim
3915  
3916          * src/types/: BendType.hpp, PolynomialBondType.hpp,
# Line 3171 | Line 3923
3923  
3924   2004-11-16 18:20  tim
3925  
3174 –        * src/math/Polynomial.hpp: Adding Polynomial class
3175 –
3176 – 2004-11-16 18:20  tim
3177 –
3926          * src/math/Polynomial.hpp: file Polynomial.hpp was initially added
3927          on branch new_design.
3928  
3929 < 2004-11-16 17:04  gezelter
3929 > 2004-11-16 18:20  tim
3930  
3931 <        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
3184 <        initially added on branch new_design.
3931 >        * src/math/Polynomial.hpp: Adding Polynomial class
3932  
3933   2004-11-16 17:04  gezelter
3934  
# Line 3190 | Line 3937
3937  
3938   2004-11-16 17:04  gezelter
3939  
3940 +        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
3941 +        initially added on branch new_design.
3942 +
3943 + 2004-11-16 17:04  gezelter
3944 +
3945          * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp,
3946          MorseBondType.hpp, TorsionType.hpp: added some new stuff
3947  
# Line 3199 | Line 3951
3951          primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp,
3952          types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and
3953          TorsionType
3954 +
3955 + 2004-11-15 21:07  tim
3956 +
3957 +        * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
3958 +        branch new_design.
3959  
3960   2004-11-15 21:07  tim
3961  
# Line 3207 | Line 3964
3964          utils/StringTokenizer.cpp: adding DUFF class; adding checking
3965          statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer
3966  
3967 < 2004-11-15 21:07  tim
3967 > 2004-11-15 18:00  tim
3968  
3969 <        * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
3970 <        branch new_design.
3969 >        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
3970 >        UseTheForce/ForceFieldFactory.cpp,
3971 >        UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp,
3972 >        UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp,
3973 >        types/AtomType.hpp: adding ForceFieldFactory and LJFF classes
3974  
3975   2004-11-15 18:00  tim
3976  
# Line 3219 | Line 3979
3979  
3980   2004-11-15 18:00  tim
3981  
3982 <        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
3983 <        branch new_design.
3982 >        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
3983 >        was initially added on branch new_design.
3984  
3985   2004-11-15 18:00  tim
3986  
3987 <        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
3988 <        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
3987 >        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
3988 >        branch new_design.
3989  
3990 < 2004-11-15 18:00  tim
3990 > 2004-11-15 13:02  tim
3991  
3992 <        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
3993 <        was initially added on branch new_design.
3992 >        * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was
3993 >        initially added on branch new_design.
3994  
3995   2004-11-15 13:02  tim
3996  
# Line 3247 | Line 4004
4004  
4005   2004-11-15 13:02  tim
4006  
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 –
4007          * src/: brains/SimInfo.cpp, brains/SimInfo.hpp,
4008          brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
4009          integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp,
# Line 3372 | Line 4124
4124  
4125          * src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation
4126          in progress
4127 +
4128 + 2004-11-09 18:11  tim
4129 +
4130 +        * src/brains/ForceManager.cpp: file ForceManager.cpp was initially
4131 +        added on branch new_design.
4132 +
4133 + 2004-11-09 18:11  tim
4134 +
4135 +        * src/integrators/VelocityVerletIntegrator.cpp: file
4136 +        VelocityVerletIntegrator.cpp was initially added on branch
4137 +        new_design.
4138  
4139   2004-11-09 18:11  tim
4140  
# Line 3389 | Line 4152
4152  
4153   2004-11-09 18:11  tim
4154  
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 –
4155          * src/integrators/NVE.cpp: file NVE.cpp was initially added on
4156          branch new_design.
4157  
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 –
4158   2004-11-08 20:08  tim
4159  
4160          * src/integrators/VelocityVerletIntegrator.hpp: file
# Line 3411 | Line 4163
4163  
4164   2004-11-08 20:08  tim
4165  
4166 +        * src/integrators/NVE.hpp: file NVE.hpp was initially added on
4167 +        branch new_design.
4168 +
4169 + 2004-11-08 20:08  tim
4170 +
4171          * src/: brains/Exclude.hpp, brains/Stats.hpp,
4172          integrators/Integrator.hpp, integrators/NVE.hpp,
4173          integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
4174          utils/TypeContainer.hpp: More to break
4175  
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 –
4176   2004-11-06 00:21  tim
4177  
4178          * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially
# Line 3435 | Line 4187
4187  
4188   2004-11-05 18:38  tim
4189  
4190 +        * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
4191 +        initially added on branch new_design.
4192 +
4193 + 2004-11-05 18:38  tim
4194 +
4195          * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was
4196          initially added on branch new_design.
4197  
# Line 3446 | Line 4203
4203          brains/SimInfo.hpp, primitives/Molecule.hpp,
4204          utils/LocalndexManager.hpp: Fix Exclude class etc.
4205  
3449 – 2004-11-05 18:38  tim
3450 –
3451 –        * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
3452 –        initially added on branch new_design.
3453 –
4206   2004-11-05 16:45  chrisfen
4207  
4208          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
# Line 3488 | Line 4240
4240  
4241   2004-11-04 14:48  tim
4242  
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 –
4243          * src/brains/Stats.cpp: file Stats.cpp was initially added on
4244          branch new_design.
4245  
# Line 3501 | Line 4247
4247  
4248          * src/brains/Stats.hpp: file Stats.hpp was initially added on
4249          branch new_design.
4250 +
4251 + 2004-11-04 14:48  tim
4252 +
4253 +        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
4254 +        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
4255 +        class
4256  
4257   2004-11-04 11:22  gezelter
4258  
# Line 3576 | Line 4328
4328  
4329   2004-11-02 17:41  tim
4330  
4331 <        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
4332 <        branch new_design.
4331 >        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
4332 >        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
4333 >        Need unit test
4334  
4335   2004-11-02 17:41  tim
4336  
# Line 3586 | Line 4339
4339  
4340   2004-11-02 17:41  tim
4341  
4342 <        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
4343 <        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
3591 <        Need unit test
4342 >        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
4343 >        branch new_design.
4344  
4345   2004-11-02 11:59  tim
4346  
4347 <        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
4348 <        SimSnapshotManager.hpp: SimModel in progress
4347 >        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
4348 >        branch new_design.
4349  
4350   2004-11-02 11:59  tim
4351  
4352 <        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
4353 <        branch new_design.
4352 >        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
4353 >        SimSnapshotManager.hpp: SimModel in progress
4354  
4355   2004-11-02 10:28  chrisfen
4356  
# Line 3608 | Line 4360
4360  
4361   2004-11-02 10:27  tim
4362  
4363 <        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
4364 <        added on branch new_design.
4363 >        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
4364 >        functions for dealing with memory issue
4365  
4366   2004-11-02 10:27  tim
4367  
4368 <        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
4369 <        functions for dealing with memory issue
4368 >        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
4369 >        added on branch new_design.
4370  
4371   2004-11-02 10:23  tim
4372  
# Line 3643 | Line 4395
4395  
4396   2004-11-01 16:40  tim
4397  
4398 <        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
4399 <        branch new_design.
4398 >        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
4399 >        on branch new_design.
4400  
4401   2004-11-01 16:40  tim
4402  
4403 <        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
4404 <        version of Bond, Bend and Torsion.
4403 >        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
4404 >        branch new_design.
4405  
4406   2004-11-01 16:40  tim
4407  
# Line 3658 | Line 4410
4410  
4411   2004-11-01 16:40  tim
4412  
4413 <        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
4414 <        on branch new_design.
4413 >        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
4414 >        version of Bond, Bend and Torsion.
4415  
4416   2004-11-01 16:37  tim
4417  
# Line 3668 | Line 4420
4420  
4421   2004-11-01 16:37  tim
4422  
4423 <        * src/types/BondType.hpp: file BondType.hpp was initially added on
4424 <        branch new_design.
4423 >        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
4424 >        BondType, BendType, TorsionType
4425  
4426   2004-11-01 16:37  tim
4427  
# Line 3678 | Line 4430
4430  
4431   2004-11-01 16:37  tim
4432  
4433 <        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
4434 <        BondType, BendType, TorsionType
4433 >        * src/types/BondType.hpp: file BondType.hpp was initially added on
4434 >        branch new_design.
4435  
4436   2004-11-01 15:15  tim
4437  
# Line 4511 | Line 5263
5263          water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile,
5264          water/tip4p/Makefile, zcons/Makefile: fix Makefile under water
5265          directory
5266 +
5267 + 2004-10-11 09:23  tim
5268 +
5269 +        * samples/argon/Makefile: remove argon.dump and argon.eor from
5270 +        Makefile
5271  
5272   2004-10-09 01:01  tim
5273  
5274 <        * samples/: alkane/Makefile.in, lipid/Makefile.in,
5275 <        metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in
5274 >        * samples/: alkane/Makefile.in, argon/Makefile.in,
5275 >        lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in:
5276 >        Remove some Makefile.in
5277  
5278   2004-10-08 18:15  tim
5279  
# Line 4531 | Line 5289
5289  
5290   2004-10-08 17:04  tim
5291  
5292 <        * samples/: alkane/Makefile, lipid/Makefile, metals/Makefile,
5293 <        minimizer/Makefile, water/Makefile.in, water/dimer/Makefile,
5294 <        water/dimer/Makefile.in, water/spce/Makefile,
5292 >        * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile,
5293 >        metals/Makefile, minimizer/Makefile, water/Makefile.in,
5294 >        water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile,
5295          water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in,
5296          water/ssde/Makefile, water/ssde/Makefile.in,
5297          water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in,
# Line 4696 | Line 5454
5454  
5455   2004-09-29 12:56  gezelter
5456  
5457 <        * make/: Make.conf.in, Makefile.in, _files/style.css: Working on
4700 <        make stuff
5457 >        * make/: Make.conf.in, Makefile.in: Working on make stuff
5458  
5459   2004-09-29 12:46  tim
5460  
# Line 4963 | Line 5720
5720          src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
5721          src/visitors/RigidBodyVisitor.cpp,
5722          src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
5723 <        src/visitors/ZconsVisitor.hpp, make/Makefile,
4967 <        make/_files/style.css, samples/Makefile.in,
5723 >        src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
5724          samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
5725          samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
5726          samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
# Line 5012 | Line 5768
5768          samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
5769          samples/alkane/Makefile.in, samples/alkane/alkanes.md,
5770          samples/alkane/butane.in, samples/alkane/butane.md,
5771 +        samples/argon/500.in, samples/argon/500.md,
5772 +        samples/argon/Makefile.in, samples/argon/ar864.in,
5773 +        samples/argon/ar864.md, samples/argon/argonNVT.in,
5774 +        samples/argon/argonNVT.md, samples/argon/lj.md,
5775          samples/lipid/5x5.in, samples/lipid/5x5.md,
5776          samples/lipid/Makefile.in, samples/lipid/lipid.md,
5777          samples/lipid/water.md, samples/minimizer/Makefile.in,
# Line 5135 | Line 5895
5895          src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
5896          src/visitors/RigidBodyVisitor.cpp,
5897          src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
5898 <        src/visitors/ZconsVisitor.hpp, make/Makefile,
5139 <        make/_files/style.css, samples/Makefile.in,
5898 >        src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
5899          samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
5900          samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
5901          samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
# Line 5184 | Line 5943
5943          samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
5944          samples/alkane/Makefile.in, samples/alkane/alkanes.md,
5945          samples/alkane/butane.in, samples/alkane/butane.md,
5946 +        samples/argon/500.in, samples/argon/500.md,
5947 +        samples/argon/Makefile.in, samples/argon/ar864.in,
5948 +        samples/argon/ar864.md, samples/argon/argonNVT.in,
5949 +        samples/argon/argonNVT.md, samples/argon/lj.md,
5950          samples/lipid/5x5.in, samples/lipid/5x5.md,
5951          samples/lipid/Makefile.in, samples/lipid/lipid.md,
5952          samples/lipid/water.md, samples/minimizer/Makefile.in,

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