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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 2246 by chrisfen, Sun May 29 21:13:23 2005 UTC

# Line 1 | Line 1
1 + 2005-05-28 19:16  tim
2 +
3 +        * src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding
4 +        AtomNameVisitor
5 +
6 + 2005-05-28 19:09  tim
7 +
8 +        * src/integrators/Integrator.cpp: dding resetIntegrator
9 +
10 + 2005-05-28 19:06  tim
11 +
12 +        * src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp,
13 +        NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp,
14 +        VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding
15 +        resetIntegrator
16 +
17 + 2005-05-27 16:11  tim
18 +
19 +        * src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp,
20 +        Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp,
21 +        SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo,
22 +        StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into
23 +        StaticProps
24 +
25 + 2005-05-26 23:41  tim
26 +
27 +        * src/: applications/staticProps/Makefile,
28 +        applications/staticProps/P2OrderParameter.cpp,
29 +        applications/staticProps/P2OrderParameter.hpp,
30 +        applications/staticProps/StaticProps.cpp,
31 +        applications/staticProps/StaticProps.ggo,
32 +        applications/staticProps/StaticPropsCmd.c,
33 +        applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp,
34 +        utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps
35 +
36 + 2005-05-26 17:45  tim
37 +
38 +        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
39 +        applications/dump2Xyz/Dump2XYZCmd.c,
40 +        applications/dump2Xyz/Dump2XYZCmd.h,
41 +        applications/staticProps/Makefile,
42 +        applications/staticProps/P2OrderParameter.cpp,
43 +        applications/staticProps/P2OrderParameter.hpp,
44 +        applications/staticProps/RadialDistrFunc.cpp,
45 +        applications/staticProps/RadialDistrFunc.hpp,
46 +        applications/staticProps/StaticAnalyser.hpp,
47 +        applications/staticProps/StaticProps.cpp,
48 +        applications/staticProps/StaticProps.ggo,
49 +        applications/staticProps/StaticPropsCmd.c,
50 +        applications/staticProps/StaticPropsCmd.h, visitors/Makefile,
51 +        visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding
52 +        AtomNameVisitor to convert atom name to its base name;
53 +        wrappingvisitor now wrap back to the center of the mass; adding
54 +        P2OrderParameter into StaticProps
55 +
56 + 2005-05-22 16:36  chuckv
57 +
58 +        * samples/metals/nanorod/Au_nanoparticle_FCC.md,
59 +        src/applications/nanoRodBuilder/Geometry.cpp,
60 +        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
61 +        src/applications/nanoRodBuilder/GeometryFactory.cpp,
62 +        src/applications/nanoRodBuilder/GeometryFactory.hpp,
63 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
64 +        src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure
65 +        tensor.
66 +
67 + 2005-05-22 16:05  tim
68 +
69 +        * src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
70 +        integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp,
71 +        io/Globals.hpp, io/SectionParserManager.cpp: adding keyword
72 +        printPressureTensor
73 +
74 + 2005-05-20 14:27  tim
75 +
76 +        * src/integrators/NPrT.cpp: NPrT in progress
77 +
78 + 2005-05-20 11:01  tim
79 +
80 +        * src/: integrators/NPrT.cpp, io/Globals.cpp,
81 +        utils/OOPSEConstant.hpp: NPrT in progress
82 +
83 + 2005-05-19 16:31  tim
84 +
85 +        * src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp,
86 +        integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp,
87 +        io/Globals.hpp: NPAT is working
88 +
89 + 2005-05-19 10:49  tim
90 +
91 +        * src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile,
92 +        integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT
93 +
94 + 2005-05-18 23:28  tim
95 +
96 +        * src/: brains/Register.cpp, integrators/NPAT.cpp,
97 +        integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp,
98 +        io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators
99 +
100 + 2005-05-18 14:06  chrisfen
101 +
102 +        * forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just
103 +        some tap changes
104 +
105 + 2005-05-18 13:31  chrisfen
106 +
107 +        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
108 +        DarkSide/sticky.F90: Modifications to temper the dipolar strength
109 +        in the first solvation shell for tap
110 +
111 + 2005-05-18 07:35  chrisfen
112 +
113 +        * samples/water/tap/: tap.in, tap.md, water.md: added a tap example
114 +        for testing purposes
115 +
116 + 2005-05-17 17:35  chrisfen
117 +
118 +        * ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md,
119 +        samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp,
120 +        src/UseTheForce/doForces.F90,
121 +        src/UseTheForce/DarkSide/electrostatic.F90,
122 +        src/UseTheForce/DarkSide/electrostatic_interface.F90,
123 +        src/UseTheForce/DarkSide/sticky.F90: Modifications to tap.  Also
124 +        correcting changes to the previous merge that were not caught
125 +
126 + 2005-05-16 23:20  chuckv
127 +
128 +        * src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp:
129 +        Fixed merge issues between Kyle and Chris so OOPSE will actually
130 +        build.
131 +
132 + 2005-05-16 22:46  kdaily
133 +
134 +        * src/io/: GayBerneAtomTypesSectionParser.cpp,
135 +        GayBerneAtomTypesSectionParser.hpp, Makefile: help
136 +
137 + 2005-05-16 21:08  kdaily
138 +
139 +        * forceFields/DUFF2.frc, src/UseTheForce/doForces.F90,
140 +        src/UseTheForce/DarkSide/gb.F90, src/io/Makefile,
141 +        src/types/DirectionalAtomType.cpp,
142 +        src/types/DirectionalAtomType.hpp: added gb
143 +
144 + 2005-05-13 15:36  chrisfen
145 +
146 +        * forceFields/DUFF2.frc: Better tap
147 +
148 + 2005-05-12 14:43  chrisfen
149 +
150 +        * forceFields/DUFF2.frc, samples/water/dimer/ssd.in,
151 +        samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90,
152 +        src/applications/dump2Xyz/Dump2XYZ.cpp,
153 +        src/visitors/AtomVisitor.hpp: Couple of changes for TAP water.
154 +        Need to parametrize.
155 +
156 + 2005-05-11 18:15  chuckv
157 +
158 +        * src/: io/ShapeAtomTypesSectionParser.cpp,
159 +        math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed
160 +        build issues under ifc7.
161 +
162 + 2005-05-09 17:07  chuckv
163 +
164 +        * src/applications/nanoRodBuilder/Geometry.hpp: More geometry
165 +        builder changes.
166 +
167 + 2005-05-05 10:06  chrisfen
168 +
169 +        * forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED
170 +        to TAP
171 +
172 + 2005-05-05 09:47  chrisfen
173 +
174 +        * forceFields/DUFF2.frc, samples/water/ssde/ssde.md,
175 +        samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp,
176 +        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile,
177 +        src/UseTheForce/DarkSide/atype.F90,
178 +        src/UseTheForce/DarkSide/atype_interface.F90,
179 +        src/UseTheForce/DarkSide/simulation.F90,
180 +        src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp,
181 +        src/brains/fSimulation.h, src/io/Makefile,
182 +        src/io/StickyAtomTypesSectionParser.cpp,
183 +        src/io/StickyPowerAtomTypesSectionParser.cpp,
184 +        src/io/StickyPowerAtomTypesSectionParser.hpp,
185 +        src/types/AtomType.cpp, src/types/AtomType.hpp,
186 +        src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp,
187 +        src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water.  It's
188 +        not parametrized, but OOPSE will now let me run it...
189 +
190 + 2005-05-03 17:55  chuckv
191 +
192 +        * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
193 +        GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp:
194 +        Adding support for generic geometry to nanorodbuilder.
195 +
196 + 2005-05-03 12:55  chuckv
197 +
198 +        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
199 +        nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c,
200 +        nanorodBuilderCmd.h: More changes to nanoRodBuilder....
201 +
202 + 2005-04-29 14:16  gezelter
203 +
204 +        * make/Makefile.in: [no log message]
205 +
206 + 2005-04-29 11:26  chrisfen
207 +
208 +        * forceFields/DUFF2.frc, samples/water/spce/water.md,
209 +        samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md,
210 +        samples/water/ssd-ion/water.md, samples/water/ssde/water.md,
211 +        samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md,
212 +        samples/water/tip4p/water.md: Added TIP4P-Ew
213 +
214 + 2005-04-27 19:24  chuckv
215 +
216 +        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
217 +        GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo,
218 +        nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with
219 +        nanoRodBuilder....
220 +
221 + 2005-04-27 15:13  chrisfen
222 +
223 +        * samples/shape/Shapes.frc, samples/shape/linear.shape,
224 +        src/UseTheForce/DarkSide/atype.F90,
225 +        src/UseTheForce/DarkSide/shapes.F90,
226 +        src/UseTheForce/DarkSide/shapes_interface.F90,
227 +        src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of
228 +        write statements and am closer to a working shapes
229 +
230 + 2005-04-22 16:57  chuckv
231 +
232 +        * src/utils/Predicate.hpp: Fixed gcc4 bug...
233 +
234 + 2005-04-22 16:52  tim
235 +
236 +        * src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp,
237 +        Trim.hpp: adding CharClassificationFunctor to fix the locale
238 +        problem  of c++
239 +
240 + 2005-04-21 09:12  chrisfen
241 +
242 +        * samples/shape/Shapes.frc, samples/shape/linear.in,
243 +        samples/shape/linear.md, src/UseTheForce/ForceField.hpp,
244 +        src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile,
245 +        src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp,
246 +        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90,
247 +        src/UseTheForce/DarkSide/shapes.F90,
248 +        src/UseTheForce/DarkSide/shapes_interface.F90,
249 +        src/UseTheForce/DarkSide/shapes_interface.h,
250 +        src/brains/Register.cpp, src/brains/SimCreator.cpp,
251 +        src/io/Makefile, src/io/SectionParser.cpp,
252 +        src/io/SectionParser.hpp, src/io/SectionParserManager.cpp,
253 +        src/io/ShapeAtomTypesSectionParser.cpp,
254 +        src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile,
255 +        src/types/AtomType.cpp, src/types/ShapeAtomType.cpp,
256 +        src/types/ShapeAtomType.hpp: Shapes is limping along with a array
257 +        bounds overwrite (I think...). At least the parser loads the
258 +        forcefield fine...
259 +
260 + 2005-04-18 10:44  chrisfen
261 +
262 +        * src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on
263 +        Mac (capitalization confusion of filenames)
264 +
265 + 2005-04-17 22:50  chrisfen
266 +
267 +        * src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp,
268 +        UseTheForce/Shapes_FF.cpp,
269 +        io/DirectionalAtomTypesSectionParser.cpp,
270 +        io/ShapeAtomTypesSectionParser.cpp,
271 +        io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser...
272 +
273 + 2005-04-15 17:43  gezelter
274 +
275 +        * README: gmake in case people forget
276 +
277 + 2005-04-15 17:40  gezelter
278 +
279 +        * src/applications/oopse/oopse.cpp: fixed the spacing on the
280 +        banner.  Vanity.
281 +
282 + 2005-04-15 17:22  gezelter
283 +
284 +        * src/: config.h.in, applications/oopse/oopse.cpp: Version string
285 +        in banner (and version numbers in config.h)
286 +
287 + 2005-04-15 17:22  gezelter
288 +
289 +        * ChangeLog, LICENSE, README: Documentation changes
290 +
291 + 2005-04-15 17:03  gezelter
292 +
293 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
294 +        UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp,
295 +        UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
296 +        UseTheForce/ForceFieldCreator.hpp,
297 +        UseTheForce/ForceFieldFactory.cpp,
298 +        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp,
299 +        UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90,
300 +        UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h,
301 +        UseTheForce/notifyCutoffs.F90,
302 +        UseTheForce/notifyCutoffs_interface.F90,
303 +        UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90,
304 +        UseTheForce/DarkSide/atype.F90,
305 +        UseTheForce/DarkSide/atype_interface.F90,
306 +        UseTheForce/DarkSide/eam.F90,
307 +        UseTheForce/DarkSide/eam_interface.F90,
308 +        UseTheForce/DarkSide/eam_interface.h,
309 +        UseTheForce/DarkSide/electrostatic.F90,
310 +        UseTheForce/DarkSide/electrostatic_interface.F90,
311 +        UseTheForce/DarkSide/electrostatic_interface.h,
312 +        UseTheForce/DarkSide/force_globals.F90,
313 +        UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h,
314 +        UseTheForce/DarkSide/lj_interface.F90,
315 +        UseTheForce/DarkSide/lj_interface.h,
316 +        UseTheForce/DarkSide/neighborLists.F90,
317 +        UseTheForce/DarkSide/reactionField.F90,
318 +        UseTheForce/DarkSide/shapes.F90,
319 +        UseTheForce/DarkSide/shapes_interface.F90,
320 +        UseTheForce/DarkSide/shapes_interface.h,
321 +        UseTheForce/DarkSide/simParallel.F90,
322 +        UseTheForce/DarkSide/simParallel_interface.F90,
323 +        UseTheForce/DarkSide/simParallel_interface.h,
324 +        UseTheForce/DarkSide/simulation.F90,
325 +        UseTheForce/DarkSide/simulation_interface.F90,
326 +        UseTheForce/DarkSide/simulation_interface.h,
327 +        UseTheForce/DarkSide/sticky.F90,
328 +        UseTheForce/DarkSide/sticky_interface.F90,
329 +        UseTheForce/DarkSide/sticky_interface.h,
330 +        UseTheForce/DarkSide/switcheroo.F90,
331 +        applications/dump2Xyz/Dump2XYZ.cpp,
332 +        applications/dump2Xyz/Dump2XYZCmd.c,
333 +        applications/dump2Xyz/Dump2XYZCmd.h,
334 +        applications/dynamicProps/CrossTimeCorrFunc.cpp,
335 +        applications/dynamicProps/CrossTimeCorrFunc.hpp,
336 +        applications/dynamicProps/DipoleCorrFunc.cpp,
337 +        applications/dynamicProps/DipoleCorrFunc.hpp,
338 +        applications/dynamicProps/DynamicProps.cpp,
339 +        applications/dynamicProps/DynamicPropsCmd.c,
340 +        applications/dynamicProps/DynamicPropsCmd.h,
341 +        applications/dynamicProps/FrameTimeCorrFunc.hpp,
342 +        applications/dynamicProps/ParticleTimeCorrFunc.cpp,
343 +        applications/dynamicProps/ParticleTimeCorrFunc.hpp,
344 +        applications/dynamicProps/RCorrFunc.cpp,
345 +        applications/dynamicProps/RCorrFunc.hpp,
346 +        applications/dynamicProps/TimeCorrFunc.cpp,
347 +        applications/dynamicProps/TimeCorrFunc.hpp,
348 +        applications/dynamicProps/VCorrFunc.cpp,
349 +        applications/dynamicProps/VCorrFunc.hpp,
350 +        applications/nanoRodBuilder/GeometryBuilder.cpp,
351 +        applications/nanoRodBuilder/GeometryBuilder.hpp,
352 +        applications/nanoRodBuilder/nanorodBuilder.cpp,
353 +        applications/nanoRodBuilder/nanorodBuilderCmd.c,
354 +        applications/nanoRodBuilder/nanorodBuilderCmd.h,
355 +        applications/oopse/oopse.cpp,
356 +        applications/simpleBuilder/simpleBuilder.cpp,
357 +        applications/simpleBuilder/simpleBuilderCmd.c,
358 +        applications/simpleBuilder/simpleBuilderCmd.h,
359 +        applications/staticProps/GofAngle2.cpp,
360 +        applications/staticProps/GofAngle2.hpp,
361 +        applications/staticProps/GofR.cpp,
362 +        applications/staticProps/GofR.hpp,
363 +        applications/staticProps/GofRAngle.cpp,
364 +        applications/staticProps/GofRAngle.hpp,
365 +        applications/staticProps/GofXyz.cpp,
366 +        applications/staticProps/GofXyz.hpp,
367 +        applications/staticProps/RadialDistrFunc.cpp,
368 +        applications/staticProps/RadialDistrFunc.hpp,
369 +        applications/staticProps/StaticProps.cpp,
370 +        applications/staticProps/StaticPropsCmd.c,
371 +        applications/staticProps/StaticPropsCmd.h,
372 +        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
373 +        brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp,
374 +        brains/Exclude.hpp, brains/ForceManager.cpp,
375 +        brains/ForceManager.hpp, brains/MoleculeCreator.cpp,
376 +        brains/MoleculeCreator.hpp, brains/Register.cpp,
377 +        brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
378 +        brains/SimInfo.hpp, brains/SimSnapshotManager.cpp,
379 +        brains/SimSnapshotManager.hpp, brains/Snapshot.cpp,
380 +        brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp,
381 +        brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp,
382 +        brains/fSimulation.h, constraints/ConstraintElem.hpp,
383 +        constraints/ConstraintPair.hpp, constraints/Rattle.cpp,
384 +        constraints/Rattle.hpp, constraints/ZconsStruct.hpp,
385 +        constraints/ZconstraintForceManager.cpp,
386 +        constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp,
387 +        integrators/DLM.hpp, integrators/Integrator.cpp,
388 +        integrators/Integrator.hpp, integrators/IntegratorCreator.hpp,
389 +        integrators/IntegratorFactory.cpp,
390 +        integrators/IntegratorFactory.hpp, integrators/NPT.cpp,
391 +        integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp,
392 +        integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp,
393 +        integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp,
394 +        integrators/NVT.cpp, integrators/NVT.hpp,
395 +        integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp,
396 +        integrators/Velocitizer.hpp,
397 +        integrators/VelocityVerletIntegrator.cpp,
398 +        integrators/VelocityVerletIntegrator.hpp,
399 +        io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp,
400 +        io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c,
401 +        io/BASS_parse.h, io/BendTypesSectionParser.cpp,
402 +        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
403 +        io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
404 +        io/ChargeAtomTypesSectionParser.hpp,
405 +        io/DirectionalAtomTypesSectionParser.cpp,
406 +        io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
407 +        io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp,
408 +        io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
409 +        io/Globals.cpp, io/Globals.hpp,
410 +        io/LennardJonesAtomTypesSectionParser.cpp,
411 +        io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp,
412 +        io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp,
413 +        io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp,
414 +        io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp,
415 +        io/SectionParser.cpp, io/SectionParser.hpp,
416 +        io/SectionParserManager.cpp, io/SectionParserManager.hpp,
417 +        io/StatWriter.cpp, io/StatWriter.hpp,
418 +        io/StickyAtomTypesSectionParser.cpp,
419 +        io/StickyAtomTypesSectionParser.hpp,
420 +        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
421 +        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
422 +        io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp,
423 +        io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c,
424 +        io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h,
425 +        io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp,
426 +        lattice/CubicLattice.hpp, lattice/FCCLattice.cpp,
427 +        lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
428 +        lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp,
429 +        lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp,
430 +        math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h,
431 +        math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp,
432 +        math/ParallelRandNumGen.hpp, math/Polynomial.hpp,
433 +        math/Quaternion.hpp, math/RandNumGen.hpp,
434 +        math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp,
435 +        math/RectMatrix.hpp, math/SeqRandNumGen.cpp,
436 +        math/SeqRandNumGen.hpp, math/SquareMatrix.hpp,
437 +        math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp,
438 +        minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp,
439 +        minimizers/Minimizer.cpp, minimizers/Minimizer.hpp,
440 +        minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp,
441 +        minimizers/MinimizerFactory.hpp,
442 +        minimizers/MinimizerParameterSet.cpp,
443 +        minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp,
444 +        minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp,
445 +        minimizers/SDMinimizer.hpp, primitives/Atom.cpp,
446 +        primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp,
447 +        primitives/Bond.hpp, primitives/CutoffGroup.hpp,
448 +        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
449 +        primitives/GhostBend.cpp, primitives/GhostBend.hpp,
450 +        primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp,
451 +        primitives/Molecule.cpp, primitives/Molecule.hpp,
452 +        primitives/RigidBody.cpp, primitives/RigidBody.hpp,
453 +        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
454 +        primitives/Torsion.cpp, primitives/Torsion.hpp,
455 +        primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp,
456 +        profiling/mdProfile.cpp, profiling/mdProfile.hpp,
457 +        profiling/timing.F90, restraints/Restraints.cpp,
458 +        restraints/Restraints.hpp,
459 +        restraints/ThermoIntegrationForceManager.cpp,
460 +        restraints/ThermoIntegrationForceManager.hpp,
461 +        selection/DistanceFinder.cpp, selection/DistanceFinder.hpp,
462 +        selection/IndexFinder.cpp, selection/IndexFinder.hpp,
463 +        selection/NameFinder.cpp, selection/NameFinder.hpp,
464 +        selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp,
465 +        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
466 +        selection/SelectionManager.cpp, selection/SelectionManager.hpp,
467 +        selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp,
468 +        selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp,
469 +        types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h,
470 +        types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp,
471 +        types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp,
472 +        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
473 +        types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp,
474 +        types/CubicBondType.hpp, types/CubicTorsionType.hpp,
475 +        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
476 +        types/DirectionalAtomType.hpp, types/FixedBondType.hpp,
477 +        types/HarmonicBendType.hpp, types/HarmonicBondType.hpp,
478 +        types/MakeStamps.cpp, types/MakeStamps.hpp,
479 +        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
480 +        types/MorseBondType.hpp, types/OplsTorsionType.hpp,
481 +        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
482 +        types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp,
483 +        types/QuarticBondType.hpp, types/QuarticTorsionType.hpp,
484 +        types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
485 +        types/ShapeAtomType.cpp, types/ShapeAtomType.hpp,
486 +        types/TorsionStamp.cpp, types/TorsionStamp.hpp,
487 +        types/TorsionType.hpp, types/UreyBradleyBendType.hpp,
488 +        types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp,
489 +        utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp,
490 +        utils/GenericFactory.hpp, utils/LocalIndexManager.hpp,
491 +        utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp,
492 +        utils/NumericConstant.hpp, utils/OOPSEConstant.hpp,
493 +        utils/PropertyMap.cpp, utils/PropertyMap.hpp,
494 +        utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
495 +        utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp,
496 +        utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp,
497 +        utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp,
498 +        utils/any.hpp, utils/definitions.F90, utils/fError.c,
499 +        utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h,
500 +        utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h,
501 +        utils/residentMem.h, utils/simError.c, utils/simError.h,
502 +        utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp,
503 +        visitors/AtomData.hpp, visitors/AtomVisitor.cpp,
504 +        visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp,
505 +        visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp,
506 +        visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
507 +        visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp,
508 +        visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp,
509 +        visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has
510 +        been drafted to perform our indentation services
511 +
512 + 2005-04-15 17:03  gezelter
513 +
514 +        * configure, ac-tools/configure.in: Jedi mind-trick warning
515 +        messages have been added to make users ignore CGAL.
516 +
517 + 2005-04-15 13:41  tim
518 +
519 +        * make/Makefile.in: fix make install
520 +
521 + 2005-04-15 13:41  tim
522 +
523 +        * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile:
524 +        add  Makefile of samples
525 +
526 + 2005-04-15 13:33  tim
527 +
528 +        * samples/: lipid/Makefile, water/dimer/Makefile,
529 +        water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not
530 +        installed correctly
531 +
532 + 2005-04-14 16:41  gezelter
533 +
534 +        * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in,
535 +        make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl,
536 +        scripts/filepp, scripts/filepp.in: configure now searches for perl
537 +        to use with filepp
538 +
539 + 2005-04-14 16:20  gezelter
540 +
541 +        * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of
542 +        MoLocator
543 +
544 + 2005-04-14 14:12  gezelter
545 +
546 +        * LICENSE: [no log message]
547 +
548 + 2005-04-14 11:10  chuckv
549 +
550 +        * src/applications/nanoRodBuilder/nanorodBuilder.cpp:
551 +        nanorodbuilder now exit's when libCGAL is not present.
552 +
553 + 2005-04-14 10:20  tim
554 +
555 +        * src/io/make_nodes.h: fix one more warning message in make_nodes
556 +
557 + 2005-04-13 18:36  chuckv
558 +
559 +        * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed
560 +        interface name for SGI Compiler
561 +
562 + 2005-04-13 18:29  chrisfen
563 +
564 +        * samples/water/ssde/ssde.md: oops...  bad sample
565 +
566 + 2005-04-13 18:00  chuckv
567 +
568 +        * src/config.h.in: Change typo in CGAL.
569 +
570 + 2005-04-13 17:43  tim
571 +
572 +        * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp,
573 +        selection/SelectionCompiler.hpp: fix some warning messages
574 +
575 + 2005-04-13 17:30  gezelter
576 +
577 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
578 +        make/Makefile.in, src/config.h.in,
579 +        src/applications/nanoRodBuilder/Makefile,
580 +        src/applications/nanoRodBuilder/Makefile.in,
581 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL
582 +        checks
583 +
584 + 2005-04-13 15:36  chuckv
585 +
586 +        * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp,
587 +        DarkSide/LJ.F90, DarkSide/electrostatic.F90,
588 +        DarkSide/electrostatic_interface.F90,
589 +        DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90,
590 +        DarkSide/lj_interface.h, DarkSide/sticky.F90,
591 +        DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added
592 +        destroy methods for Fortran modules.
593 +
594 + 2005-04-13 15:17  chuckv
595 +
596 +        * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90,
597 +        shapes_interface.h: Added destroy method to clean up memory
598 +
599 + 2005-04-13 13:41  tim
600 +
601 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
602 +        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
603 +        io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp,
604 +        primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp,
605 +        types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are
606 +        fixed
607 +
608 + 2005-04-12 17:44  chuckv
609 +
610 +        * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed
611 +        for nanoRodBuilder.
612 +
613 + 2005-04-12 17:42  tim
614 +
615 +        * src/applications/: nanoRodBuilder/nanorodBuilder.cpp,
616 +        simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder
617 +        and simpleBuilder(forget to delete lattice)
618 +
619 + 2005-04-12 17:33  tim
620 +
621 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
622 +        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp:
623 +        refactory lattice
624 +
625 + 2005-04-12 17:07  tim
626 +
627 +        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp,
628 +        CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp,
629 +        Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory
630 +        LatticeFactory and LatticeCreator
631 +
632 + 2005-04-12 16:58  tim
633 +
634 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
635 +        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp,
636 +        brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
637 +        lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp,
638 +        lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp,
639 +        lattice/Makefile: refactory LatticeFactory and LatticeCreator
640 +
641 + 2005-04-12 16:28  gezelter
642 +
643 +        * src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp,
644 +        vector_class.F90: cleaned up vector_class memory leak fix by
645 +        deallocating in reverse order of how we allocated.  Also migrated
646 +        MoLocator into utils directory
647 +
648 + 2005-04-12 16:27  gezelter
649 +
650 +        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp,
651 +        Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
652 +        LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice
653 +        directory
654 +
655 + 2005-04-12 16:27  gezelter
656 +
657 +        * src/applications/: nanoRodBuilder/BaseLattice.cpp,
658 +        nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp,
659 +        nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp,
660 +        nanoRodBuilder/LatticeCreator.hpp,
661 +        nanoRodBuilder/LatticeFactory.cpp,
662 +        nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile,
663 +        nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp,
664 +        nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp,
665 +        simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
666 +        simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
667 +        simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
668 +        simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile,
669 +        simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp,
670 +        simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of
671 +        these files are now redundant
672 +
673 + 2005-04-12 16:27  gezelter
674 +
675 +        * src/UseTheForce/DarkSide/: atype_interface.F90,
676 +        atype_interface.h: cleaned up memory leak fix
677 +
678 + 2005-04-12 16:26  gezelter
679 +
680 +        * make/Makefile.in: added lattice subdirectory
681 +
682 + 2005-04-12 15:57  chrisfen
683 +
684 +        * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added
685 +        a space by accident
686 +
687 + 2005-04-12 15:56  chrisfen
688 +
689 +        * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added
690 +        quadrupole sample
691 +
692 + 2005-04-12 15:56  chrisfen
693 +
694 +        * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating
695 +        samples
696 +
697 + 2005-04-12 13:30  tim
698 +
699 +        * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom
700 +        type in fortran side
701 +
702 + 2005-04-12 12:45  chuckv
703 +
704 +        * src/utils/vector_class.F90: Further changes to vector_class
705 +        destroy function.
706 +
707 + 2005-04-12 12:39  chuckv
708 +
709 +        * src/utils/vector_class.F90: Fixed pointer memory leak in
710 +        vector_class.
711 +
712 + 2005-04-12 12:12  chuckv
713 +
714 +        * src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp,
715 +        DarkSide/atype_interface.F90, DarkSide/atype_interface.h,
716 +        DarkSide/eam.F90, DarkSide/eam_interface.F90,
717 +        DarkSide/eam_interface.h: Updates to deallocate object in fortran.
718 +
719 + 2005-04-12 09:24  chrisfen
720 +
721 +        * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI
722 +        output
723 +
724 + 2005-04-11 19:29  chuckv
725 +
726 +        * src/: UseTheForce/DarkSide/atype.F90,
727 +        applications/nanoRodBuilder/Makefile: Changes to delete atypes...
728 +
729 + 2005-04-11 19:28  chuckv
730 +
731 +        * src/utils/vector_class.F90: Added code to delete vector.
732 +
733 + 2005-04-11 17:03  chuckv
734 +
735 +        * samples/metals/nanorod/: Au_nanoparticle.md,
736 +        Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why
737 +        aren't these here?
738 +
739 + 2005-04-11 16:58  tim
740 +
741 +        * src/io/basic_ifstrstream.hpp: avoid multiple inherit in
742 +        basic_ifstrstream
743 +
744 + 2005-04-11 16:37  chuckv
745 +
746 +        * make/Makefile.in,
747 +        src/applications/nanoRodBuilder/BaseLattice.cpp,
748 +        src/applications/nanoRodBuilder/BaseLattice.hpp,
749 +        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
750 +        src/applications/nanoRodBuilder/GeometryBuilder.hpp,
751 +        src/applications/nanoRodBuilder/Lattice.cpp,
752 +        src/applications/nanoRodBuilder/Lattice.hpp,
753 +        src/applications/nanoRodBuilder/LatticeCreator.cpp,
754 +        src/applications/nanoRodBuilder/LatticeCreator.hpp,
755 +        src/applications/nanoRodBuilder/LatticeFactory.cpp,
756 +        src/applications/nanoRodBuilder/LatticeFactory.hpp,
757 +        src/applications/nanoRodBuilder/Makefile,
758 +        src/applications/nanoRodBuilder/MoLocator.cpp,
759 +        src/applications/nanoRodBuilder/MoLocator.hpp,
760 +        src/applications/nanoRodBuilder/nanoBuilder.ggo,
761 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
762 +        src/applications/nanoRodBuilder/nanorodBuilder.ggo,
763 +        src/applications/nanoRodBuilder/nanorodBuilderCmd.c,
764 +        src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing
765 +        nanoRodBuilder application (may not work yet).  ((Doesn't work
766 +        yet.)) (((May never work....)))
767 +
768 + 2005-04-11 15:54  tim
769 +
770 +        * src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete
771 +        prepareVisitor in Dump2XYZ
772 +
773 + 2005-04-11 15:19  chrisfen
774 +
775 +        * src/UseTheForce/DarkSide/electrostatic.F90: fixing of the
776 +        quadrupoles.  look!  it's divide by 3 like stone says!
777 +
778 + 2005-04-11 15:18  chrisfen
779 +
780 +        * forceFields/DUFF2.frc: fixing of the quadrupoles
781 +
782 + 2005-04-11 15:16  tim
783 +
784 +        * src/selection/Token.hpp: change the parameter name in
785 +        constructors
786 +
787 + 2005-04-11 14:49  gezelter
788 +
789 +        * make/Makefile.in: One more bug fix for GNU make versions < 3.80
790 +
791 + 2005-04-11 14:06  gezelter
792 +
793 +        * make/Makefile.in: Fixed the uc and lc functions for GNU make
794 +        versions < 3.80
795 +
796 + 2005-04-11 11:13  gezelter
797 +
798 +        * make/Makefile.in, src/UseTheForce/Makefile,
799 +        src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added
800 +        some stuff to clean out module files during "make clean"
801 +
802 + 2005-04-08 17:13  chrisfen
803 +
804 +        * src/UseTheForce/DarkSide/electrostatic.F90: quadrupole
805 +        interactions should be working with a remaining question of
806 +        interaction magnitude
807 +
808 + 2005-04-08 17:12  chrisfen
809 +
810 +        * samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with
811 +        samples
812 +
813 + 2005-04-08 13:48  chrisfen
814 +
815 +        * samples/water/ssd/ssd.md: oops...  messed up a sample
816 +
817 + 2005-04-08 09:43  chrisfen
818 +
819 +        * src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix
820 +        charge-dipole interactions
821 +
822 + 2005-04-08 09:42  chrisfen
823 +
824 +        * samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md,
825 +        ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole
826 +
827 + 2005-04-08 09:41  chrisfen
828 +
829 +        * forceFields/DUFF2.frc: added Cl- and Na+
830 +
831 + 2005-04-06 18:59  tim
832 +
833 +        * src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser
834 +
835 + 2005-04-05 18:09  tim
836 +
837 +        * src/selection/: NameFinder.cpp, SelectionCompiler.cpp,
838 +        SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-'
839 +        in atom type name;clean the code a little bit
840 +
841 + 2005-03-29 16:00  tim
842 +
843 +        * src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug
844 +        in converting rotation matrix to quaternion
845 +
846 + 2005-03-28 17:41  tim
847 +
848 +        * src/visitors/LipidTransVisitor.cpp: fixed the wrapping
849 +
850 + 2005-03-28 17:30  tim
851 +
852 +        * src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do
853 +        the wrapping
854 +
855 + 2005-03-28 10:54  tim
856 +
857 +        * src/applications/staticProps/GofXyz.cpp: fix a bug in getting the
858 +        dimension of histogram
859 +
860 + 2005-03-22 11:38  tim
861 +
862 +        * make/Makefile.in, src/applications/dump2Xyz/Makefile,
863 +        src/applications/dynamicProps/Makefile,
864 +        src/applications/oopse/Makefile,
865 +        src/applications/simpleBuilder/Makefile,
866 +        src/applications/staticProps/Makefile: avoid building parallel
867 +        executable for dump2XYZ, simpleBuilder, staticProps and
868 +        dynamicProps
869 +
870 + 2005-03-21 17:34  chrisfen
871 +
872 +        * forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the
873 +        forcefield files
874 +
875 + 2005-03-21 15:51  chrisfen
876 +
877 +        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
878 +        DarkSide/reactionField.F90: Make sure electrostatic_module provides
879 +        data for reaction_field
880 +
881 + 2005-03-21 15:50  chrisfen
882 +
883 +        * forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff.  HE
884 +        WILL CHANGE THIS BACK, RIGHT?
885 +
886 + 2005-03-21 14:23  gezelter
887 +
888 +        * src/UseTheForce/DarkSide/electrostatic.F90: constant back to
889 +        correct value
890 +
891 + 2005-03-21 14:22  gezelter
892 +
893 +        * make/Makefile.in: fixed an install-related bug.
894 +        $(InstallCommand) had been set to $(InstallData)
895 +
896 + 2005-03-15 09:21  gezelter
897 +
898 +        * src/integrators/Integrator.cpp: VelocityVerletIntegrator already
899 +        deletes and Nullifies restWriter, so Integrator shouldn't do it.
900 +
901 + 2005-03-15 09:20  gezelter
902 +
903 +        * src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos
904 +
905 + 2005-03-13 02:39  gezelter
906 +
907 +        * src/UseTheForce/DarkSide/electrostatic.F90: first run at
908 +        charge-quadrupole interactions
909 +
910 + 2005-03-12 14:12  chrisfen
911 +
912 +        * samples/: Makefile.in, thermoIntegration/liquid/Makefile,
913 +        thermoIntegration/solid/Makefile: forgot a couple of makefiles
914 +
915 + 2005-03-12 14:05  chrisfen
916 +
917 +        * samples/thermoIntegration/liquid/ssde.in,
918 +        samples/thermoIntegration/liquid/ssde.md,
919 +        samples/thermoIntegration/liquid/water.md,
920 +        samples/thermoIntegration/solid/idealCrystal.in,
921 +        samples/thermoIntegration/solid/ssde.in,
922 +        samples/thermoIntegration/solid/ssde.md,
923 +        samples/thermoIntegration/solid/ssde.zang0,
924 +        samples/thermoIntegration/solid/water.md,
925 +        samples/water/tip3p_ice/tp3.md,
926 +        src/UseTheForce/DarkSide/sticky.F90,
927 +        src/restraints/ThermoIntegrationForceManager.cpp: added some
928 +        samples
929 +
930 + 2005-03-11 12:50  tim
931 +
932 +        * src/: brains/SimCreator.cpp,
933 +        io/MultipoleAtomTypesSectionParser.cpp: fix a typo in
934 +        MultipoleAtomTypesSectionParser
935 +
936 + 2005-03-11 10:55  tim
937 +
938 +        * src/brains/SimInfo.cpp: pairs inside cutoff group should not be
939 +        excluded
940 +
941 + 2005-03-11 10:53  gezelter
942 +
943 +        * src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for
944 +        quadrupoles
945 +
946 + 2005-03-11 10:52  gezelter
947 +
948 +        * forceFields/DUFF2.frc: quadrupoles for SSD models
949 +
950 + 2005-03-11 10:00  tim
951 +
952 +        * ChangeLog, doc/SelectionExpression.html,
953 +        doc/classoopse_1_1StuntDouble.png, doc/definition.jpg,
954 +        doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png,
955 +        src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp,
956 +        src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp,
957 +        src/selection/TokenMap.cpp: clean up SimInfo; modify the images of
958 +        SelectionExpression.html
959 +
960 + 2005-03-10 19:43  chrisfen
961 +
962 +        * samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md,
963 +        src/io/RestReader.cpp, src/restraints/Restraints.cpp,
964 +        src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in
965 +        MPI restraints
966 +
967 + 2005-03-10 18:56  tim
968 +
969 +        * doc/SelectionExpression.html, src/brains/SimInfo.cpp,
970 +        src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody
971 +        and cutoff group
972 +
973 + 2005-03-10 17:06  gezelter
974 +
975 +        * src/types/MorseBondType.hpp: fixed a doxygen problem
976 +
977 + 2005-03-10 16:51  gezelter
978 +
979 +        * samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with
980 +        the split dipole test cases
981 +
982 + 2005-03-10 16:51  gezelter
983 +
984 +        * doc/SelectionExpression.html: updated some documentation
985 +
986 + 2005-03-10 15:40  gezelter
987 +
988 +        * src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp,
989 +        Makefile: LinkedList removal project starts now
990 +
991 + 2005-03-10 15:28  tim
992 +
993 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
994 +        io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp:
995 +        using map to replace link list
996 +
997 + 2005-03-10 14:11  tim
998 +
999 +        * samples/dipole/: splitInWater.in, splitInWater.md: adding test
1000 +        case  of split dipole
1001 +
1002 + 2005-03-10 14:10  chrisfen
1003 +
1004 +        * samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp,
1005 +        src/io/RestWriter.cpp,
1006 +        src/restraints/ThermoIntegrationForceManager.cpp: Oops...  MPI now
1007 +        builds...
1008 +
1009 + 2005-03-10 13:44  tim
1010 +
1011 +        * samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in,
1012 +        split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md:
1013 +        adding test case for split dipole
1014 +
1015 + 2005-03-10 12:54  gezelter
1016 +
1017 +        * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side
1018 +        support for split dipoles
1019 +
1020 + 2005-03-10 11:27  chrisfen
1021 +
1022 +        * samples/water/tip3p_ice/tp3.md,
1023 +        src/restraints/ThermoIntegrationForceManager.cpp: fixes to
1024 +        restraints
1025 +
1026 + 2005-03-10 11:15  chrisfen
1027 +
1028 +        * samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp,
1029 +        src/UseTheForce/ForceFields.hpp,
1030 +        src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints
1031 +
1032 + 2005-03-10 11:14  tim
1033 +
1034 +        * ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc,
1035 +        src/io/MultipoleAtomTypesSectionParser.cpp,
1036 +        src/selection/SelectionEvaluator.cpp: minor change
1037 +
1038   2005-03-10 10:10  chrisfen
1039  
1040          * make/Makefile.in, samples/water/tip3p_ice/tp3.md,
# Line 274 | Line 1311
1311          adding basic_teebuf which can operate on multiple stream
1312          simutaneously.
1313  
1314 + 2005-02-22 14:26  chrisfen
1315 +
1316 +        * samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf
1317 +        sample
1318 +
1319   2005-02-22 13:56  tim
1320  
1321          * src/: UseTheForce/DarkSide/reactionField.F90,
# Line 1479 | Line 2521
2521  
2522   2005-01-11 10:52  tim
2523  
2524 <        * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
2524 >        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
2525          on branch new_design.
2526  
2527   2005-01-11 10:52  tim
2528  
2529 <        * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
2529 >        * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
2530 >        on branch new_design.
2531  
2532   2005-01-11 10:52  tim
2533  
2534 <        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
1492 <        on branch new_design.
2534 >        * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
2535  
2536   2005-01-11 10:47  tim
2537  
# Line 1554 | Line 2596
2596  
2597          * src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was
2598          initially added on branch new_design.
2599 +
2600 + 2005-01-07 16:50  tim
2601 +
2602 +        * src/constraints/ZconstraintForceManager.cpp: file
2603 +        ZconstraintForceManager.cpp was initially added on branch
2604 +        new_design.
2605 +
2606 + 2005-01-07 16:50  tim
2607  
2608 +        * src/constraints/ZconstraintForceManager.hpp: file
2609 +        ZconstraintForceManager.hpp was initially added on branch
2610 +        new_design.
2611 +
2612   2005-01-07 16:50  tim
2613  
2614          * src/: applications/simpleBuilder/BaseLattice.hpp,
# Line 1574 | Line 2628
2628          * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was
2629          initially added on branch new_design.
2630  
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 –
2631   2005-01-06 17:31  tim
2632  
2633          * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
# Line 1622 | Line 2664
2664  
2665   2005-01-05 12:35  tim
2666  
2667 +        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
2668 +        added on branch new_design.
2669 +
2670 + 2005-01-05 12:35  tim
2671 +
2672          * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
2673          Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp,
2674          MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp,
# Line 1630 | Line 2677
2677  
2678   2005-01-05 12:35  tim
2679  
2680 <        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
2681 <        added on branch new_design.
2680 >        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
2681 >        was initially added on branch new_design.
2682  
2683   2005-01-05 12:35  tim
2684  
2685 <        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
2685 >        * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
2686          was initially added on branch new_design.
2687  
2688   2005-01-05 12:35  tim
2689  
2690 <        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
2690 >        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
2691          was initially added on branch new_design.
2692  
2693   2005-01-05 12:35  tim
# Line 1648 | Line 2695
2695          * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially
2696          added on branch new_design.
2697  
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 –
2698   2005-01-04 17:18  tim
2699  
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 –
2700          * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
2701          brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp,
2702          brains/Thermo.cpp, constraints/ConstraintPair.hpp,
# Line 1671 | Line 2708
2708  
2709   2005-01-04 17:18  tim
2710  
2711 <        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
2712 <        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
1676 <        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
1677 <        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
2711 >        * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was
2712 >        initially added on branch new_design.
2713  
2714   2005-01-04 17:18  tim
2715  
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 –
2716          * src/minimizers/MinimizerParameterSet.cpp: file
2717          MinimizerParameterSet.cpp was initially added on branch new_design.
2718  
# Line 1693 | Line 2723
2723  
2724   2005-01-04 17:18  tim
2725  
2726 +        * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
2727 +        was initially added on branch new_design.
2728 +
2729 + 2005-01-04 17:18  tim
2730 +
2731 +        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
2732 +        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
2733 +        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
2734 +        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
2735 +
2736 + 2005-01-04 17:18  tim
2737 +
2738          * src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on
2739          branch new_design.
2740  
# Line 2008 | Line 3050
3050          io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp,
3051          io/SectionParserManager.cpp, utils/LocalIndexManager.hpp,
3052          utils/TypeContainer.hpp: begin to fix bugs
3053 +
3054 + 2004-12-02 19:26  tim
3055 +
3056 +        * src/utils/Trim.cpp: file Trim.cpp was initially added on branch
3057 +        new_design.
3058  
3059   2004-12-02 19:26  tim
3060  
# Line 2020 | Line 3067
3067          utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a
3068          bug in countTokens in StringTokenizer
3069  
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 –
3070   2004-12-02 19:06  tim
3071  
3072          * forceFields/newDUFF.frc: minor fix
# Line 2032 | Line 3074
3074   2004-12-02 18:15  tim
3075  
3076          * forceFields/newDUFF.frc: new ForceField format
2035 –
2036 – 2004-12-02 17:15  tim
2037 –
2038 –        * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp
2039 –        was initially added on branch new_design.
2040 –
2041 – 2004-12-02 17:15  tim
3077  
2043 –        * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp
2044 –        was initially added on branch new_design.
2045 –
3078   2004-12-02 17:15  tim
3079  
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 –
3080          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3081          UseTheForce/ForceFieldCreator.cpp,
3082          UseTheForce/ForceFieldCreator.hpp,
# Line 2072 | Line 3099
3099          * src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp
3100          was initially added on branch new_design.
3101  
3102 + 2004-12-02 17:15  tim
3103 +
3104 +        * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp
3105 +        was initially added on branch new_design.
3106 +
3107 + 2004-12-02 17:15  tim
3108 +
3109 +        * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp
3110 +        was initially added on branch new_design.
3111 +
3112 + 2004-12-02 17:15  tim
3113 +
3114 +        * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp
3115 +        was initially added on branch new_design.
3116 +
3117   2004-12-02 11:53  tim
3118  
3119          * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp,
# Line 2230 | Line 3272
3272  
3273   2004-12-01 19:09  tim
3274  
3275 <        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
3276 <        was initially added on branch new_design.
3275 >        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
3276 >        branch new_design.
3277  
3278   2004-12-01 19:09  tim
3279  
3280 +        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
3281 +        branch new_design.
3282 +
3283 + 2004-12-01 19:09  tim
3284 +
3285          * src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp,
3286          brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
3287          brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp,
# Line 2247 | Line 3294
3294  
3295   2004-12-01 19:09  tim
3296  
3297 <        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
3298 <        branch new_design.
3297 >        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
3298 >        was initially added on branch new_design.
3299  
2253 – 2004-12-01 19:09  tim
2254 –
2255 –        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
2256 –        branch new_design.
2257 –
3300   2004-12-01 17:45  tim
3301  
3302          * src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp,
# Line 2353 | Line 3395
3395  
3396   2004-11-30 14:58  tim
3397  
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 –
3398          * src/: brains/Exclude.cpp, brains/Exclude.hpp,
3399          brains/ForceManager.cpp, brains/ForceManager.hpp,
3400          brains/MoleculeCreator.cpp, brains/SimCreator.hpp,
# Line 2367 | Line 3404
3404          brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile,
3405          math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo
3406  
3407 + 2004-11-30 14:58  tim
3408 +
3409 +        * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially
3410 +        added on branch new_design.
3411 +
3412   2004-11-30 12:54  tim
3413  
3414          * src/: primitives/Bend.hpp, primitives/Bond.hpp,
# Line 2375 | Line 3417
3417  
3418   2004-11-30 00:03  tim
3419  
3420 <        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
3421 <        LocalndexManager.hpp to LocalIndexManager.hpp
3420 >        * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
3421 >        initially added on branch new_design.
3422  
3423   2004-11-30 00:03  tim
3424  
3425 <        * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
3426 <        initially added on branch new_design.
3425 >        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
3426 >        LocalndexManager.hpp to LocalIndexManager.hpp
3427  
3428   2004-11-29 23:43  tim
3429  
# Line 2509 | Line 3551
3551  
3552   2004-11-25 15:18  tim
3553  
3554 +        * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was
3555 +        initially added on branch new_design.
3556 +
3557 + 2004-11-25 15:18  tim
3558 +
3559          * src/: io/AtomTypesSectionParser.cpp,
3560          io/BondTypesSectionParser.cpp,
3561          io/DirectionalAtomTypesSectionParser.cpp,
# Line 2521 | Line 3568
3568          * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was
3569          initially added on branch new_design.
3570  
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 –
3571   2004-11-24 17:12  tim
3572  
3573          * src/: io/AtomTypesSectionParser.cpp,
# Line 2638 | Line 3680
3680  
3681   2004-11-23 12:53  tim
3682  
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 –
3683          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3684          UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
3685          applications/simpleBuilder/simpleBuilder.cpp,
# Line 2661 | Line 3697
3697          ElectrostaticAtomTypesSectionParser.hpp was initially added on
3698          branch new_design.
3699  
3700 < 2004-11-23 01:03  tim
3700 > 2004-11-23 12:53  tim
3701  
3702 <        * src/io/EAMAtomTypesSectionParser.cpp: file
3703 <        EAMAtomTypesSectionParser.cpp was initially added on branch
3704 <        new_design.
3702 >        * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
3703 >        ElectrostaticAtomTypesSectionParser.cpp was initially added on
3704 >        branch new_design.
3705  
3706   2004-11-23 01:03  tim
3707  
# Line 2676 | Line 3712
3712  
3713   2004-11-23 01:03  tim
3714  
3715 +        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
3716 +        was initially added on branch new_design.
3717 +
3718 + 2004-11-23 01:03  tim
3719 +
3720          * src/io/EAMAtomTypesSectionParser.hpp: file
3721          EAMAtomTypesSectionParser.hpp was initially added on branch
3722          new_design.
3723  
3724   2004-11-23 01:03  tim
3725  
3726 <        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
3727 <        was initially added on branch new_design.
3726 >        * src/io/EAMAtomTypesSectionParser.cpp: file
3727 >        EAMAtomTypesSectionParser.cpp was initially added on branch
3728 >        new_design.
3729  
3730   2004-11-22 23:35  tim
3731  
3732 <        * src/io/TorsionTypesSectionParser.cpp: file
3733 <        TorsionTypesSectionParser.cpp was initially added on branch
3732 >        * src/io/TorsionTypesSectionParser.hpp: file
3733 >        TorsionTypesSectionParser.hpp was initially added on branch
3734          new_design.
3735  
3736   2004-11-22 23:35  tim
# Line 2699 | Line 3741
3741  
3742   2004-11-22 23:35  tim
3743  
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 –
3744          * src/io/BondTypesSectionParser.hpp: file
3745          BondTypesSectionParser.hpp was initially added on branch
3746          new_design.
3747  
3748   2004-11-22 23:35  tim
3749  
3750 <        * src/io/TorsionTypesSectionParser.hpp: file
3751 <        TorsionTypesSectionParser.hpp was initially added on branch
3750 >        * src/io/BondTypesSectionParser.cpp: file
3751 >        BondTypesSectionParser.cpp was initially added on branch
3752          new_design.
3753  
3754   2004-11-22 23:35  tim
3755  
3756 <        * src/io/BendTypesSectionParser.cpp: file
3757 <        BendTypesSectionParser.cpp was initially added on branch
3756 >        * src/io/TorsionTypesSectionParser.cpp: file
3757 >        TorsionTypesSectionParser.cpp was initially added on branch
3758          new_design.
3759  
3760   2004-11-22 23:35  tim
# Line 2729 | Line 3765
3765          BondTypesSectionParser, BendTypesSectionParser and
3766          TorsionTypeSectionParser
3767  
3768 + 2004-11-22 23:35  tim
3769 +
3770 +        * src/io/BendTypesSectionParser.cpp: file
3771 +        BendTypesSectionParser.cpp was initially added on branch
3772 +        new_design.
3773 +
3774   2004-11-22 18:04  tim
3775  
3776          * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in
# Line 2736 | Line 3778
3778  
3779   2004-11-22 18:02  tim
3780  
3781 +        * src/io/: DirectionalAtomTypesParser.hpp,
3782 +        DirectionalAtomTypesSectionParser.hpp: adding section parsers
3783 +
3784 + 2004-11-22 18:02  tim
3785 +
3786          * src/io/DirectionalAtomTypesSectionParser.hpp: file
3787          DirectionalAtomTypesSectionParser.hpp was initially added on branch
3788          new_design.
3789  
2743 – 2004-11-22 18:02  tim
2744 –
2745 –        * src/io/: DirectionalAtomTypesParser.hpp,
2746 –        DirectionalAtomTypesSectionParser.hpp: adding section parsers
2747 –
3790   2004-11-22 15:55  tim
3791  
3792 <        * src/io/DirectionalAtomTypesParser.hpp: file
3793 <        DirectionalAtomTypesParser.hpp was initially added on branch
3792 >        * src/io/DipoleAtomTypesSectionParser.hpp: file
3793 >        DipoleAtomTypesSectionParser.hpp was initially added on branch
3794          new_design.
3795  
3796   2004-11-22 15:55  tim
3797  
3798 <        * src/io/HarmonicBondTypesSectionParser.hpp: file
3799 <        HarmonicBondTypesSectionParser.hpp was initially added on branch
3798 >        * src/io/AtomTypesSectionParser.hpp: file
3799 >        AtomTypesSectionParser.hpp was initially added on branch
3800          new_design.
3801  
3802   2004-11-22 15:55  tim
3803  
3804 <        * src/io/ChargeAtomTypesSectionParser.hpp: file
3805 <        ChargeAtomTypesSectionParser.hpp was initially added on branch
3804 >        * src/io/HarmonicBondTypesSectionParser.hpp: file
3805 >        HarmonicBondTypesSectionParser.hpp was initially added on branch
3806          new_design.
3807  
3808   2004-11-22 15:55  tim
3809  
3810 <        * src/io/DirectionalAtomTypesSectionParser.cpp: file
3811 <        DirectionalAtomTypesSectionParser.cpp was initially added on branch
3810 >        * src/io/StickyAtomTypesSectionParser.cpp: file
3811 >        StickyAtomTypesSectionParser.cpp was initially added on branch
3812          new_design.
3813  
3814   2004-11-22 15:55  tim
3815  
3816 <        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
3817 <        LennardJonesAtomTypesSectionParser.cpp was initially added on
3816 >        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
3817 >        LennardJonesAtomTypesSectionParser.hpp was initially added on
3818          branch new_design.
3819  
3820   2004-11-22 15:55  tim
3821  
3822 <        * src/io/DipoleAtomTypesSectionParser.cpp: file
3823 <        DipoleAtomTypesSectionParser.cpp was initially added on branch
3822 >        * src/io/HarmonicBondTypesSectionParser.cpp: file
3823 >        HarmonicBondTypesSectionParser.cpp was initially added on branch
3824          new_design.
3825  
3826   2004-11-22 15:55  tim
3827  
3828 <        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
3829 <        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
3828 >        * src/io/DirectionalAtomTypesSectionParser.cpp: file
3829 >        DirectionalAtomTypesSectionParser.cpp was initially added on branch
3830          new_design.
3831  
3832   2004-11-22 15:55  tim
3833  
3834 <        * 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
3834 >        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
3835          was initially added on branch new_design.
3836  
3837   2004-11-22 15:55  tim
# Line 2827 | Line 3842
3842  
3843   2004-11-22 15:55  tim
3844  
3845 <        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
3846 <        LennardJonesAtomTypesSectionParser.hpp was initially added on
3847 <        branch new_design.
3845 >        * src/io/ChargeAtomTypesSectionParser.cpp: file
3846 >        ChargeAtomTypesSectionParser.cpp was initially added on branch
3847 >        new_design.
3848  
3849   2004-11-22 15:55  tim
3850  
3851 <        * src/io/HarmonicBondTypesSectionParser.cpp: file
3852 <        HarmonicBondTypesSectionParser.cpp was initially added on branch
3851 >        * src/io/DipoleAtomTypesSectionParser.cpp: file
3852 >        DipoleAtomTypesSectionParser.cpp was initially added on branch
3853          new_design.
3854  
3855   2004-11-22 15:55  tim
3856  
3857 <        * src/io/AtomTypesSectionParser.hpp: file
3858 <        AtomTypesSectionParser.hpp was initially added on branch
3857 >        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
3858 >        LennardJonesAtomTypesSectionParser.cpp was initially added on
3859 >        branch new_design.
3860 >
3861 > 2004-11-22 15:55  tim
3862 >
3863 >        * src/io/ChargeAtomTypesSectionParser.hpp: file
3864 >        ChargeAtomTypesSectionParser.hpp was initially added on branch
3865          new_design.
3866  
3867   2004-11-22 15:55  tim
3868  
3869 <        * src/io/StickyAtomTypesSectionParser.cpp: file
3870 <        StickyAtomTypesSectionParser.cpp was initially added on branch
3869 >        * src/io/StickyAtomTypesSectionParser.hpp: file
3870 >        StickyAtomTypesSectionParser.hpp was initially added on branch
3871          new_design.
3872  
3873   2004-11-22 15:55  tim
# Line 2856 | Line 3877
3877  
3878   2004-11-22 15:55  tim
3879  
3880 <        * src/io/ChargeAtomTypesSectionParser.cpp: file
3881 <        ChargeAtomTypesSectionParser.cpp was initially added on branch
3880 >        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
3881 >        brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
3882 >        brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp,
3883 >        integrators/NVT.hpp, io/AtomTypesSectionParser.cpp,
3884 >        io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
3885 >        io/ChargeAtomTypesSectionParser.hpp,
3886 >        io/DipoleAtomTypesSectionParser.cpp,
3887 >        io/DipoleAtomTypesSectionParser.hpp,
3888 >        io/DirectionalAtomTypesParser.hpp,
3889 >        io/DirectionalAtomTypesSectionParser.cpp,
3890 >        io/HarmonicBondTypesSectionParser.cpp,
3891 >        io/HarmonicBondTypesSectionParser.hpp,
3892 >        io/LennardJonesAtomTypesSectionParser.cpp,
3893 >        io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp,
3894 >        io/SectionParser.hpp, io/SectionParserManager.cpp,
3895 >        io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp,
3896 >        io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp,
3897 >        types/AtomType.hpp, types/DirectionalAtomType.hpp,
3898 >        utils/GenericData.hpp: adding section parsers
3899 >
3900 > 2004-11-22 15:55  tim
3901 >
3902 >        * src/io/DirectionalAtomTypesParser.hpp: file
3903 >        DirectionalAtomTypesParser.hpp was initially added on branch
3904          new_design.
3905  
3906   2004-11-22 15:55  tim
3907  
3908 <        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
3908 >        * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
3909          was initially added on branch new_design.
3910  
3911   2004-11-22 15:55  tim
3912  
3913 <        * src/io/StickyAtomTypesSectionParser.hpp: file
3914 <        StickyAtomTypesSectionParser.hpp was initially added on branch
2872 <        new_design.
3913 >        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
3914 >        added on branch new_design.
3915  
3916   2004-11-19 17:12  tim
3917  
3918 +        * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
3919 +        added on branch new_design.
3920 +
3921 + 2004-11-19 17:12  tim
3922 +
3923          * src/: brains/SimState.cpp, brains/SimState.hpp,
3924          io/InitializeFromFile.cpp, types/FixBondType.hpp,
3925          types/FixedBondType.hpp: remove more useless files
3926  
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 –
3927   2004-11-19 16:47  tim
3928  
3929          * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp,
# Line 2890 | Line 3932
3932  
3933   2004-11-19 16:38  tim
3934  
3935 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3936 +        UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp,
3937 +        integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp,
3938 +        integrators/NVT.hpp: refactory integrator
3939 +
3940 + 2004-11-19 16:38  tim
3941 +
3942          * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on
3943          branch new_design.
3944  
3945   2004-11-19 16:38  tim
3946  
3947 <        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
3948 <        on branch new_design.
3947 >        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
3948 >        branch new_design.
3949  
3950   2004-11-19 16:38  tim
3951  
# Line 2905 | Line 3954
3954  
3955   2004-11-19 16:38  tim
3956  
3957 <        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
3958 <        branch new_design.
3957 >        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
3958 >        on branch new_design.
3959  
3960   2004-11-19 16:38  tim
3961  
3962 <        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
3962 >        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
3963          branch new_design.
3964  
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 –
3965   2004-11-19 15:37  tim
3966  
3967          * forceFields/newDUFF.frc: new DUFF forcefield
3968  
3969   2004-11-19 15:23  tim
3970  
3971 +        * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
3972 +        branch new_design.
3973 +
3974 + 2004-11-19 15:23  tim
3975 +
3976          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp,
3977          UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp,
3978          utils/TypeContainer.hpp: add EAM
# Line 2935 | Line 3982
3982          * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on
3983          branch new_design.
3984  
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 –
3985   2004-11-19 13:02  tim
3986  
3987          * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except
# Line 2947 | Line 3989
3989  
3990   2004-11-19 12:56  tim
3991  
3992 <        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
3992 >        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
3993          was initially added on branch new_design.
3994  
3995   2004-11-19 12:56  tim
3996  
3997 <        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
3997 >        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
3998          was initially added on branch new_design.
3999  
4000   2004-11-19 12:56  tim
# Line 2977 | Line 4019
4019  
4020   2004-11-18 18:26  tim
4021  
4022 +        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
4023 +        initially added on branch new_design.
4024 +
4025 + 2004-11-18 18:26  tim
4026 +
4027          * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp,
4028          integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
4029          integrators/VelocityVerletIntegrator.cpp,
# Line 2987 | Line 4034
4034          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding
4035          DUFF parser
4036  
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 –
4037   2004-11-18 16:42  tim
4038  
4039          * forceFields/newDUFF.frc: adding new format DUFF force field
# Line 3003 | Line 4045
4045  
4046   2004-11-18 00:42  tim
4047  
4048 <        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
4048 >        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
4049          initially added on branch new_design.
4050  
4051   2004-11-18 00:42  tim
4052  
4053 <        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
4053 >        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
4054          initially added on branch new_design.
4055  
4056   2004-11-18 00:42  tim
# Line 3051 | Line 4093
4093  
4094   2004-11-17 16:47  tim
4095  
4096 +        * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp
4097 +        was initially added on branch new_design.
4098 +
4099 + 2004-11-17 16:47  tim
4100 +
4101          * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially
4102          added on branch new_design.
4103  
4104   2004-11-17 16:47  tim
4105  
4106 +        * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially
4107 +        added on branch new_design.
4108 +
4109 + 2004-11-17 16:47  tim
4110 +
4111          * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was
4112          initially added on branch new_design.
4113  
4114   2004-11-17 16:47  tim
4115  
4116 <        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
4116 >        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
4117          initially added on branch new_design.
4118  
4119   2004-11-17 16:47  tim
4120  
4121 <        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
4121 >        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
4122          initially added on branch new_design.
4123  
4124   2004-11-17 16:47  tim
# Line 3086 | Line 4138
4138          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp:
4139          UreyBradleyBend and GhostBend
4140  
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 –
4141   2004-11-17 13:58  tim
4142  
4143          * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp
# Line 3103 | Line 4145
4145  
4146   2004-11-17 13:58  tim
4147  
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 –
4148          * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp
4149          was initially added on branch new_design.
4150  
# Line 3120 | Line 4157
4157          types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types
4158          stuff and Chebyshev Polynomial
4159  
4160 < 2004-11-17 01:37  tim
3124 <
3125 <        * src/types/PolynomialTorsionType.hpp: file
3126 <        PolynomialTorsionType.hpp was initially added on branch new_design.
3127 <
3128 < 2004-11-17 01:37  tim
4160 > 2004-11-17 13:58  tim
4161  
4162 <        * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
4162 >        * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
4163          initially added on branch new_design.
4164  
4165   2004-11-17 01:37  tim
4166  
4167 <        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
4168 <        initially added on branch new_design.
4167 >        * src/types/PolynomialTorsionType.hpp: file
4168 >        PolynomialTorsionType.hpp was initially added on branch new_design.
4169  
4170   2004-11-17 01:37  tim
4171  
# Line 3142 | Line 4174
4174  
4175   2004-11-17 01:37  tim
4176  
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 –
4177          * src/: math/Polynomial.hpp, primitives/Bend.cpp,
4178          primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp,
4179          types/BondType.hpp, types/CharmmTorsionType.cpp,
# Line 3159 | Line 4186
4186          CharmmTorsionType. Need to refine the design and add document for
4187          them
4188  
4189 + 2004-11-17 01:37  tim
4190 +
4191 +        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
4192 +        initially added on branch new_design.
4193 +
4194 + 2004-11-17 01:37  tim
4195 +
4196 +        * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was
4197 +        initially added on branch new_design.
4198 +
4199 + 2004-11-17 01:37  tim
4200 +
4201 +        * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
4202 +        initially added on branch new_design.
4203 +
4204   2004-11-16 20:11  tim
4205  
4206          * src/types/: BendType.hpp, PolynomialBondType.hpp,
# Line 3171 | Line 4213
4213  
4214   2004-11-16 18:20  tim
4215  
3174 –        * src/math/Polynomial.hpp: Adding Polynomial class
3175 –
3176 – 2004-11-16 18:20  tim
3177 –
4216          * src/math/Polynomial.hpp: file Polynomial.hpp was initially added
4217          on branch new_design.
4218  
4219 < 2004-11-16 17:04  gezelter
4219 > 2004-11-16 18:20  tim
4220  
4221 <        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
3184 <        initially added on branch new_design.
4221 >        * src/math/Polynomial.hpp: Adding Polynomial class
4222  
4223   2004-11-16 17:04  gezelter
4224  
# Line 3190 | Line 4227
4227  
4228   2004-11-16 17:04  gezelter
4229  
4230 +        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
4231 +        initially added on branch new_design.
4232 +
4233 + 2004-11-16 17:04  gezelter
4234 +
4235          * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp,
4236          MorseBondType.hpp, TorsionType.hpp: added some new stuff
4237  
# Line 3202 | Line 4244
4244  
4245   2004-11-15 21:07  tim
4246  
3205 –        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3206 –        UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp,
3207 –        utils/StringTokenizer.cpp: adding DUFF class; adding checking
3208 –        statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer
3209 –
3210 – 2004-11-15 21:07  tim
3211 –
4247          * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
4248          branch new_design.
4249  
4250 < 2004-11-15 18:00  tim
3216 <
3217 <        * src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp
3218 <        was initially added on branch new_design.
3219 <
3220 < 2004-11-15 18:00  tim
4250 > 2004-11-15 21:07  tim
4251  
4252 <        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
4253 <        branch new_design.
4252 >        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
4253 >        UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp,
4254 >        utils/StringTokenizer.cpp: adding DUFF class; adding checking
4255 >        statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer
4256  
4257   2004-11-15 18:00  tim
4258  
# Line 3232 | Line 4264
4264  
4265   2004-11-15 18:00  tim
4266  
4267 +        * src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp
4268 +        was initially added on branch new_design.
4269 +
4270 + 2004-11-15 18:00  tim
4271 +
4272          * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
4273          was initially added on branch new_design.
4274  
4275 + 2004-11-15 18:00  tim
4276 +
4277 +        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
4278 +        branch new_design.
4279 +
4280   2004-11-15 13:02  tim
4281  
4282 +        * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was
4283 +        initially added on branch new_design.
4284 +
4285 + 2004-11-15 13:02  tim
4286 +
4287          * src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on
4288          branch new_design.
4289  
# Line 3247 | Line 4294
4294  
4295   2004-11-15 13:02  tim
4296  
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 –
4297          * src/: brains/SimInfo.cpp, brains/SimInfo.hpp,
4298          brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
4299          integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp,
# Line 3375 | Line 4417
4417  
4418   2004-11-09 18:11  tim
4419  
4420 +        * src/brains/ForceManager.cpp: file ForceManager.cpp was initially
4421 +        added on branch new_design.
4422 +
4423 + 2004-11-09 18:11  tim
4424 +
4425 +        * src/integrators/VelocityVerletIntegrator.cpp: file
4426 +        VelocityVerletIntegrator.cpp was initially added on branch
4427 +        new_design.
4428 +
4429 + 2004-11-09 18:11  tim
4430 +
4431          * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp,
4432          brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
4433          brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp,
# Line 3389 | Line 4442
4442  
4443   2004-11-09 18:11  tim
4444  
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 –
4445          * src/integrators/NVE.cpp: file NVE.cpp was initially added on
4446          branch new_design.
4447  
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 –
4448   2004-11-08 20:08  tim
4449  
4450          * src/integrators/VelocityVerletIntegrator.hpp: file
4451          VelocityVerletIntegrator.hpp was initially added on branch
4452          new_design.
4453 +
4454 + 2004-11-08 20:08  tim
4455 +
4456 +        * src/integrators/NVE.hpp: file NVE.hpp was initially added on
4457 +        branch new_design.
4458  
4459   2004-11-08 20:08  tim
4460  
# Line 3416 | Line 4463
4463          integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
4464          utils/TypeContainer.hpp: More to break
4465  
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 –
4466   2004-11-06 00:21  tim
4467  
4468          * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially
# Line 3435 | Line 4477
4477  
4478   2004-11-05 18:38  tim
4479  
4480 +        * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
4481 +        initially added on branch new_design.
4482 +
4483 + 2004-11-05 18:38  tim
4484 +
4485          * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was
4486          initially added on branch new_design.
4487  
# Line 3446 | Line 4493
4493          brains/SimInfo.hpp, primitives/Molecule.hpp,
4494          utils/LocalndexManager.hpp: Fix Exclude class etc.
4495  
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 –
4496   2004-11-05 16:45  chrisfen
4497  
4498          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
# Line 3488 | Line 4530
4530  
4531   2004-11-04 14:48  tim
4532  
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 –
4533          * src/brains/Stats.cpp: file Stats.cpp was initially added on
4534          branch new_design.
4535  
# Line 3502 | Line 4538
4538          * src/brains/Stats.hpp: file Stats.hpp was initially added on
4539          branch new_design.
4540  
4541 + 2004-11-04 14:48  tim
4542 +
4543 +        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
4544 +        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
4545 +        class
4546 +
4547   2004-11-04 11:22  gezelter
4548  
4549          * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp,
# Line 3576 | Line 4618
4618  
4619   2004-11-02 17:41  tim
4620  
4621 <        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
4622 <        branch new_design.
4621 >        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
4622 >        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
4623 >        Need unit test
4624  
4625   2004-11-02 17:41  tim
4626  
# Line 3586 | Line 4629
4629  
4630   2004-11-02 17:41  tim
4631  
4632 <        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
4633 <        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
3591 <        Need unit test
4632 >        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
4633 >        branch new_design.
4634  
4635   2004-11-02 11:59  tim
4636  
4637 <        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
4638 <        SimSnapshotManager.hpp: SimModel in progress
4637 >        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
4638 >        branch new_design.
4639  
4640   2004-11-02 11:59  tim
4641  
4642 <        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
4643 <        branch new_design.
4642 >        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
4643 >        SimSnapshotManager.hpp: SimModel in progress
4644  
4645   2004-11-02 10:28  chrisfen
4646  
# Line 3608 | Line 4650
4650  
4651   2004-11-02 10:27  tim
4652  
4653 <        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
4654 <        added on branch new_design.
4653 >        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
4654 >        functions for dealing with memory issue
4655  
4656   2004-11-02 10:27  tim
4657  
4658 <        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
4659 <        functions for dealing with memory issue
4658 >        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
4659 >        added on branch new_design.
4660  
4661   2004-11-02 10:23  tim
4662  
# Line 3643 | Line 4685
4685  
4686   2004-11-01 16:40  tim
4687  
4688 <        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
4689 <        branch new_design.
4688 >        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
4689 >        on branch new_design.
4690  
4691   2004-11-01 16:40  tim
4692  
4693 <        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
4694 <        version of Bond, Bend and Torsion.
4693 >        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
4694 >        branch new_design.
4695  
4696   2004-11-01 16:40  tim
4697  
# Line 3658 | Line 4700
4700  
4701   2004-11-01 16:40  tim
4702  
4703 <        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
4704 <        on branch new_design.
4703 >        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
4704 >        version of Bond, Bend and Torsion.
4705  
4706   2004-11-01 16:37  tim
4707  
# Line 3668 | Line 4710
4710  
4711   2004-11-01 16:37  tim
4712  
4713 <        * src/types/BondType.hpp: file BondType.hpp was initially added on
4714 <        branch new_design.
4713 >        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
4714 >        BondType, BendType, TorsionType
4715  
4716   2004-11-01 16:37  tim
4717  
# Line 3678 | Line 4720
4720  
4721   2004-11-01 16:37  tim
4722  
4723 <        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
4724 <        BondType, BendType, TorsionType
4723 >        * src/types/BondType.hpp: file BondType.hpp was initially added on
4724 >        branch new_design.
4725  
4726   2004-11-01 15:15  tim
4727  
# Line 4512 | Line 5554
5554          water/tip4p/Makefile, zcons/Makefile: fix Makefile under water
5555          directory
5556  
5557 + 2004-10-11 09:23  tim
5558 +
5559 +        * samples/argon/Makefile: remove argon.dump and argon.eor from
5560 +        Makefile
5561 +
5562   2004-10-09 01:01  tim
5563  
5564 <        * samples/: alkane/Makefile.in, lipid/Makefile.in,
5565 <        metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in
5564 >        * samples/: alkane/Makefile.in, argon/Makefile.in,
5565 >        lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in:
5566 >        Remove some Makefile.in
5567  
5568   2004-10-08 18:15  tim
5569  
# Line 4531 | Line 5579
5579  
5580   2004-10-08 17:04  tim
5581  
5582 <        * samples/: alkane/Makefile, lipid/Makefile, metals/Makefile,
5583 <        minimizer/Makefile, water/Makefile.in, water/dimer/Makefile,
5584 <        water/dimer/Makefile.in, water/spce/Makefile,
5582 >        * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile,
5583 >        metals/Makefile, minimizer/Makefile, water/Makefile.in,
5584 >        water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile,
5585          water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in,
5586          water/ssde/Makefile, water/ssde/Makefile.in,
5587          water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in,
# Line 5012 | Line 6060
6060          samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
6061          samples/alkane/Makefile.in, samples/alkane/alkanes.md,
6062          samples/alkane/butane.in, samples/alkane/butane.md,
6063 +        samples/argon/500.in, samples/argon/500.md,
6064 +        samples/argon/Makefile.in, samples/argon/ar864.in,
6065 +        samples/argon/ar864.md, samples/argon/argonNVT.in,
6066 +        samples/argon/argonNVT.md, samples/argon/lj.md,
6067          samples/lipid/5x5.in, samples/lipid/5x5.md,
6068          samples/lipid/Makefile.in, samples/lipid/lipid.md,
6069          samples/lipid/water.md, samples/minimizer/Makefile.in,
# Line 5184 | Line 6236
6236          samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
6237          samples/alkane/Makefile.in, samples/alkane/alkanes.md,
6238          samples/alkane/butane.in, samples/alkane/butane.md,
6239 +        samples/argon/500.in, samples/argon/500.md,
6240 +        samples/argon/Makefile.in, samples/argon/ar864.in,
6241 +        samples/argon/ar864.md, samples/argon/argonNVT.in,
6242 +        samples/argon/argonNVT.md, samples/argon/lj.md,
6243          samples/lipid/5x5.in, samples/lipid/5x5.md,
6244          samples/lipid/Makefile.in, samples/lipid/lipid.md,
6245          samples/lipid/water.md, samples/minimizer/Makefile.in,

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