[ViewVC] Diff of: group/trunk/OOPSE-2.0/ChangeLog

Comparing trunk/OOPSE-2.0/ChangeLog (file contents):
Revision 2116 by tim, Fri Mar 11 15:00:20 2005 UTC vs.
Revision 2246 by chrisfen, Sun May 29 21:13:23 2005 UTC

#	Line 1 \| Line 1
1	<	2005-03-11 00:43 chrisfen
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 23:56 tim
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 22:06 gezelter
973	>	2005-03-10 17:06 gezelter
974
975		* src/types/MorseBondType.hpp: fixed a doxygen problem
976
977	<	2005-03-10 21:51 gezelter
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 21:51 gezelter
982	>	2005-03-10 16:51 gezelter
983
984		* doc/SelectionExpression.html: updated some documentation
985
986	<	2005-03-10 20:40 gezelter
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 20:28 tim
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 19:11 tim
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 19:10 chrisfen
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 18:44 tim
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 17:54 gezelter
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 16:27 chrisfen
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 16:15 chrisfen
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 16:14 tim
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 15:10 chrisfen
1038	>	2005-03-10 10:10 chrisfen
1039
1040		* make/Makefile.in, samples/water/tip3p_ice/tp3.md,
1041		src/brains/SimCreator.cpp, src/brains/SimInfo.hpp,
#	Line 93 \| Line 1052
1052		src/restraints/ThermoIntegrationForceManager.hpp: First commit of
1053		the new restraints code
1054
1055	<	2005-03-09 18:48 tim
1055	>	2005-03-09 13:48 tim
1056
1057		* src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding
1058		IndexFinder
1059
1060	<	2005-03-09 18:46 tim
1060	>	2005-03-09 13:46 tim
1061
1062		* src/: applications/dump2Xyz/Dump2XYZ.ggo,
1063		applications/dump2Xyz/Dump2XYZCmd.c,
#	Line 106 \| Line 1065
1065		selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp:
1066		fix compilation issue
1067
1068	<	2005-03-09 17:58 tim
1068	>	2005-03-09 12:58 tim
1069
1070		* forceFields/DUFF2.frc, scripts/filepp,
1071		src/UseTheForce/EAM_FF.cpp,
#	Line 114 \| Line 1073
1073		src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug
1074		in SectionParser (lineNo is not updated)
1075
1076	<	2005-03-09 17:30 tim
1076	>	2005-03-09 12:30 tim
1077
1078		* src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp,
1079		applications/dump2Xyz/Dump2XYZ.ggo,
#	Line 136 \| Line 1095
1095		MultipoleAtomTypesSectionParser;remove print dipole option from
1096		Dump2XYZ;
1097
1098	<	2005-03-09 17:28 tim
1098	>	2005-03-09 12:28 tim
1099
1100		* forceFields/DUFF2.frc: change the format of DUFF2
1101
1102	<	2005-03-09 15:44 gezelter
1102	>	2005-03-09 10:44 gezelter
1103
1104		* src/UseTheForce/DarkSide/: electrostatic.F90,
1105		electrostatic_interface.F90, electrostatic_interface.h: new
1106		electrostatic module
1107
1108	<	2005-03-09 14:26 gezelter
1108	>	2005-03-09 09:26 gezelter
1109
1110		* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
1111		DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole
1112		and fixed quadrupole stuff
1113
1114	<	2005-03-09 14:25 gezelter
1114	>	2005-03-09 09:25 gezelter
1115
1116		* src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines
1117		for outdated charge and dipole interfaces
1118
1119	<	2005-03-08 21:08 gezelter
1119	>	2005-03-08 16:08 gezelter
1120
1121		* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in,
1122		mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun
1123		charge-dipole test cases
1124
1125	<	2005-03-08 21:07 gezelter
1125	>	2005-03-08 16:07 gezelter
1126
1127		* src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp,
1128		OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a
1129		strange icc8 bug (we think).
1130
1131	<	2005-03-08 21:07 gezelter
1131	>	2005-03-08 16:07 gezelter
1132
1133		* src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa!
1134
1135	<	2005-03-08 21:07 gezelter
1135	>	2005-03-08 16:07 gezelter
1136
1137		* src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic
1138		Unification Project
1139
1140	<	2005-03-08 21:07 gezelter
1140	>	2005-03-08 16:07 gezelter
1141
1142		* src/io/Globals.cpp: Dunno
1143
1144	<	2005-03-08 21:06 gezelter
1144	>	2005-03-08 16:06 gezelter
1145
1146		* src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using
1147		OOPSE_itoa and checking a NULL left over from the LinkedList days
1148
1149	<	2005-03-08 21:06 gezelter
1149	>	2005-03-08 16:06 gezelter
1150
1151		* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
1152		atype_interface.F90, atype_interface.h, charge.F90,
#	Line 195 \| Line 1154
1154		dipole_interface.F90, dipole_interface.h: electrostatic unification
1155		project fixed an uninitialized variable in Lennard Jones mixing map
1156
1157	<	2005-03-08 21:05 gezelter
1157	>	2005-03-08 16:05 gezelter
1158
1159		* src/UseTheForce/doForces.F90: electrostatic unification project
1160
1161	<	2005-03-08 21:05 gezelter
1161	>	2005-03-08 16:05 gezelter
1162
1163		* samples/water/dimer/: two.md, water.md: making some cool test
1164		cases
1165
1166	<	2005-03-08 21:05 gezelter
1166	>	2005-03-08 16:05 gezelter
1167
1168		* forceFields/DUFF2.frc: Added a charge for Chlorine
1169
1170	<	2005-03-07 22:39 tim
1170	>	2005-03-07 17:39 tim
1171
1172		* src/: brains/SimInfo.cpp, io/DumpReader.cpp,
1173		math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp,
1174		primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp:
1175		Fixing a bug in BitSet.cpp
1176
1177	<	2005-03-04 15:28 gezelter
1177	>	2005-03-04 10:28 gezelter
1178
1179		* src/config.h.in: Cleaning up config.h.in by adding comments
1180
1181	<	2005-03-04 15:28 gezelter
1181	>	2005-03-04 10:28 gezelter
1182
1183		* configure, ac-tools/configure.in, make/Makefile.in,
1184		src/brains/SimCreator.cpp: SPRNG eradication project
1185
1186	<	2005-03-03 14:40 tim
1186	>	2005-03-03 09:40 tim
1187
1188		* src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the
1189		missing atom type problem)
1190
1191	<	2005-03-02 16:29 tim
1191	>	2005-03-02 11:29 tim
1192
1193		* src/math/RandNumGen.hpp: adding base class of Random Number
1194		generator
1195
1196	<	2005-03-02 16:28 tim
1196	>	2005-03-02 11:28 tim
1197
1198		* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
1199		math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in
1200		Velocitizer is not initialized which causes a seg fault
1201
1202	<	2005-03-02 15:36 tim
1202	>	2005-03-02 10:36 tim
1203
1204		* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
1205		integrators/Velocitizer.hpp, math/Makefile,
#	Line 250 \| Line 1209
1209		MersenneTwister.hpp which causes all kinds of trouble. Refactory
1210		random number generator
1211
1212	<	2005-03-02 07:32 tim
1212	>	2005-03-02 02:32 tim
1213
1214		* test/math/testRandNumGen.cpp: Adding unit test for random number
1215		generator
1216
1217	<	2005-03-01 23:17 tim
1217	>	2005-03-01 18:17 tim
1218
1219		* src/brains/Thermo.hpp: fixed a file inclusion problem
1220
1221	<	2005-03-01 23:17 tim
1221	>	2005-03-01 18:17 tim
1222
1223		* test/math/: Makefile, OOPSERandNumGenTestCase.cpp,
1224		OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp,
1225		ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp,
1226		RandNumGenTestCase.hpp: fixed compilation problem
1227
1228	<	2005-03-01 23:02 tim
1228	>	2005-03-01 18:02 tim
1229
1230		* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
1231		integrators/Velocitizer.hpp, math/Makefile,
#	Line 274 \| Line 1233
1233		math/ParallelRandNumGen.hpp, math/mt19937ar.c,
1234		math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand
1235
1236	<	2005-03-01 23:00 tim
1236	>	2005-03-01 18:00 tim
1237
1238		* test/math/: Makefile, ParallelandNumGenTestCase.cpp,
1239		ParallelandNumGenTestCase.hpp: Change the name of test case
1240
1241	<	2005-03-01 21:00 tim
1241	>	2005-03-01 16:00 tim
1242
1243		* test/math/: Makefile, OOPSERandNumGenTestCase.cpp,
1244		OOPSERandNumGenTestCase.hpp: adding testcase for random number
1245		generator
1246
1247	<	2005-03-01 20:10 tim
1247	>	2005-03-01 15:10 tim
1248
1249		* src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp,
1250		integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp,
#	Line 296 \| Line 1255
1255		utils/TypeContainer.hpp, visitors/AtomVisitor.cpp,
1256		visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4
1257
1258	<	2005-03-01 19:11 tim
1258	>	2005-03-01 14:11 tim
1259
1260		* src/: brains/SimCreator.cpp, brains/SimInfo.hpp,
1261		integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
1262		math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding
1263		OOPSERandNumGen
1264
1265	<	2005-03-01 15:44 gezelter
1265	>	2005-03-01 10:44 gezelter
1266
1267		* make/Makefile.in: Fixed the damned build problem with the
1268		libraries not being removed in make clean and make distclean (at
1269		least we think it is fixed).
1270
1271	<	2005-03-01 15:26 gezelter
1271	>	2005-03-01 10:26 gezelter
1272
1273		* src/math/MersenneTwister.hpp: Making small modifications to allow
1274		for use on MPI machines
1275
1276	<	2005-03-01 14:45 tim
1276	>	2005-03-01 09:45 tim
1277
1278		* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp,
1279		integrators/Velocitizer.cpp, io/DumpReader.cpp,
1280		math/MersenneTwister.hpp: adding MersenneTwister random number
1281		generator
1282
1283	<	2005-03-01 03:55 tim
1283	>	2005-02-28 22:55 tim
1284
1285		* src/math/MersenneTwister.hpp: Adding a modified version of
1286		MersenneTwister.hpp
1287
1288	<	2005-02-28 17:24 tim
1288	>	2005-02-28 12:24 tim
1289
1290		* doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png,
1291		definition.jpg: selection expression
1292
1293	<	2005-02-25 21:22 tim
1293	>	2005-02-25 16:22 tim
1294
1295		* src/: UseTheForce/DarkSide/LJ.F90,
1296		UseTheForce/DarkSide/lj_interface.F90,
#	Line 339 \| Line 1298
1298		io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp,
1299		types/AtomType.hpp: adding soft potential to LJ Module
1300
1301	<	2005-02-25 16:38 tim
1301	>	2005-02-25 11:38 tim
1302
1303		* doc/SelectionExpression.html: adding documentation for selection
1304		expression
1305
1306	<	2005-02-24 20:55 tim
1306	>	2005-02-24 15:55 tim
1307
1308		* src/: applications/simpleBuilder/simpleBuilder.cpp,
1309		integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp,
#	Line 352 \| Line 1311
1311		adding basic_teebuf which can operate on multiple stream
1312		simutaneously.
1313
1314	<	2005-02-22 18:56 tim
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,
1322		primitives/RigidBody.cpp: reactionfield get fixed
1323
1324	<	2005-02-21 16:57 tim
1324	>	2005-02-21 11:57 tim
1325
1326		* src/: applications/staticProps/GofRAngle.cpp,
1327		visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix
1328		a bug in GofRAngle
1329
1330	<	2005-02-21 15:28 tim
1330	>	2005-02-21 10:28 tim
1331
1332		* src/primitives/Molecule.cpp: Fix for compilation on the Sun
1333
1334	<	2005-02-21 15:22 tim
1334	>	2005-02-21 10:22 tim
1335
1336		* src/utils/next_combination.hpp: fix for compilation on the Sun
1337
1338	<	2005-02-21 15:21 tim
1338	>	2005-02-21 10:21 tim
1339
1340		* src/utils/GenericData.hpp: fix problem in sun
1341
1342	<	2005-02-18 23:07 tim
1342	>	2005-02-18 18:07 tim
1343
1344		* src/: applications/dump2Xyz/Dump2XYZ.cpp,
1345		applications/dump2Xyz/Dump2XYZ.ggo,
#	Line 392 \| Line 1356
1356		visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
1357		visitors/Makefile: adding LipidTransVisitor, GofXyz is working now
1358
1359	<	2005-02-18 15:58 gezelter
1359	>	2005-02-18 10:58 gezelter
1360
1361		* src/brains/Register.cpp: Corrected filename collision for EAM on
1362		Mac OS X
1363
1364	<	2005-02-18 15:58 gezelter
1364	>	2005-02-18 10:58 gezelter
1365
1366		* src/applications/oopse/oopse.cpp: Updated copyright information
1367
1368	<	2005-02-18 15:58 gezelter
1368	>	2005-02-18 10:58 gezelter
1369
1370		* src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp,
1371		Makefile: corrected filename collision for EAM on operating systems
1372		which are not case sensitive (aka Mac OS X)
1373
1374	<	2005-02-17 20:15 tim
1374	>	2005-02-17 15:15 tim
1375
1376		* src/applications/staticProps/GofXyz.cpp: more bug get fixed
1377
1378	<	2005-02-17 19:50 tim
1378	>	2005-02-17 14:50 tim
1379
1380		* src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug
1381		in GofXyz
1382
1383	<	2005-02-17 19:09 tim
1383	>	2005-02-17 14:09 tim
1384
1385		* src/applications/staticProps/RadialDistrFunc.hpp: make
1386		processHistogram non-abstrct function
1387
1388	<	2005-02-17 18:41 tim
1388	>	2005-02-17 13:41 tim
1389
1390		* src/applications/staticProps/GofXyz.cpp: [no log message]
1391
1392	<	2005-02-17 18:30 tim
1392	>	2005-02-17 13:30 tim
1393
1394		* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp,
1395		GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp:
1396		finish GofXyz
1397
1398	<	2005-02-17 16:21 tim
1398	>	2005-02-17 11:21 tim
1399
1400		* src/applications/staticProps/: GofAngle2.cpp, GofR.cpp,
1401		GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial
1402		distribution function
1403
1404	<	2005-02-17 15:23 tim
1404	>	2005-02-17 10:23 tim
1405
1406		* src/utils/BitSet.hpp: forget the const correctness for BitSet
1407
1408	<	2005-02-17 15:18 tim
1408	>	2005-02-17 10:18 tim
1409
1410		* src/: brains/BlockSnapshotManager.cpp,
1411		selection/DistanceFinder.cpp: The change of interface of BitSet
1412		cause a bug in SelectionEvaluation
1413
1414	<	2005-02-16 21:13 tim
1414	>	2005-02-16 16:13 tim
1415
1416		* src/utils/residentMem.c: return residentMem in byte
1417
1418	<	2005-02-16 21:00 tim
1418	>	2005-02-16 16:00 tim
1419
1420		* src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix
1421		a bug in writing out the value of cosang
1422
1423	<	2005-02-16 20:43 tim
1423	>	2005-02-16 15:43 tim
1424
1425		* src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to
1426		estimate avaliable memory
1427
1428	<	2005-02-16 20:30 tim
1428	>	2005-02-16 15:30 tim
1429
1430		* src/: applications/staticProps/GofAngle2.cpp,
1431		applications/staticProps/GofAngle2.hpp,
#	Line 477 \| Line 1441
1441		applications/staticProps/StaticPropsCmd.h,
1442		brains/BlockSnapshotManager.cpp: change the default bin number
1443
1444	<	2005-02-16 19:36 tim
1444	>	2005-02-16 14:36 tim
1445
1446		* src/: applications/dynamicProps/DipoleCorrFunc.cpp,
1447		applications/dynamicProps/RCorrFunc.cpp,
#	Line 494 \| Line 1458
1458		utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output
1459		files;fix the problem of counting in staticProps
1460
1461	<	2005-02-15 19:39 tim
1461	>	2005-02-15 14:39 tim
1462
1463		* src/brains/BlockSnapshotManager.cpp: fix a bug in
1464		BlockSnapshotManager
1465
1466	<	2005-02-15 19:36 tim
1466	>	2005-02-15 14:36 tim
1467
1468		* src/: applications/dynamicProps/TimeCorrFunc.cpp,
1469		applications/staticProps/RadialDistrFunc.cpp,
#	Line 507 \| Line 1471
1471		selection/SelectionEvaluator.cpp: BlockSnapshotManager is using
1472		reference counting now
1473
1474	<	2005-02-15 17:49 tim
1474	>	2005-02-15 12:49 tim
1475
1476		* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
1477		replace std::make_pair by VariablesType::value_type to make Sun
1478		Compiler happy
1479
1480	<	2005-02-15 17:35 tim
1480	>	2005-02-15 12:35 tim
1481
1482		* src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to
1483		TokenMap, using TokenMapType::value_type instead of std::make_pair
1484		to make Sun compiler happy
1485
1486	<	2005-02-15 17:24 tim
1486	>	2005-02-15 12:24 tim
1487
1488		* src/applications/staticProps/: GofRAngle.cpp,
1489		RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps
1490
1491	<	2005-02-15 17:11 tim
1491	>	2005-02-15 12:11 tim
1492
1493		* src/: applications/staticProps/GofR.cpp,
1494		applications/staticProps/RadialDistrFunc.cpp,
#	Line 533 \| Line 1497
1497		#ifdef __RWSTD to make sun compiler happy (2) fix pair density
1498		calculation problem when two selections intersect with each other
1499
1500	<	2005-02-15 15:24 gezelter
1500	>	2005-02-15 10:24 gezelter
1501
1502		* src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy
1503		xlc++
1504
1505	<	2005-02-15 15:17 gezelter
1505	>	2005-02-15 10:17 gezelter
1506
1507		* configure, ac-tools/configure.in, src/config.h.in,
1508		src/utils/residentMem.c: [no log message]
1509
1510	<	2005-02-15 06:17 gezelter
1510	>	2005-02-15 01:17 gezelter
1511
1512		* src/utils/residentMem.c: bug fix for null termination
1513
1514	<	2005-02-15 06:11 gezelter
1514	>	2005-02-15 01:11 gezelter
1515
1516		* configure, ac-tools/configure.in, src/utils/residentMem.c:
1517		bugfixing residentMem
1518
1519	<	2005-02-15 05:59 gezelter
1519	>	2005-02-15 00:59 gezelter
1520
1521		* configure, ac-tools/configure.in, src/config.h.in,
1522		src/utils/residentMem.c: bugfixes for residentMem on LINUX
1523
1524	<	2005-02-15 05:08 gezelter
1524	>	2005-02-15 00:08 gezelter
1525
1526		* src/utils/Makefile.in: added residentMem
1527
1528	<	2005-02-15 05:05 gezelter
1528	>	2005-02-15 00:05 gezelter
1529
1530		* configure, ac-tools/configure.in, make/Makefile.in,
1531		src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c,
#	Line 569 \| Line 1533
1533		other processes autoconf fixes ps syntax checking config.h file
1534		cleaning
1535
1536	<	2005-02-14 23:26 gezelter
1536	>	2005-02-14 18:26 gezelter
1537
1538		* configure, ac-tools/configure.in, make/Makefile.in: ps niceness
1539
1540	<	2005-02-14 23:16 gezelter
1540	>	2005-02-14 18:16 gezelter
1541
1542		* configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps
1543		strangeness
1544
1545	<	2005-02-14 19:42 tim
1545	>	2005-02-14 14:42 tim
1546
1547		* src/brains/BlockSnapshotManager.cpp: fix a bug in
1548		BlockSnapshotManager.hpp
1549
1550	<	2005-02-14 18:51 tim
1550	>	2005-02-14 13:51 tim
1551
1552		* src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo,
1553		StaticPropsCmd.c: default length for staticProps is 1/2 smallest
1554		length of first frame
1555
1556	<	2005-02-14 18:12 tim
1556	>	2005-02-14 13:12 tim
1557
1558		* src/integrators/VelocityVerletIntegrator.cpp: fix a bug in
1559		VelocityVerletIntegrator : last frame is written twice
1560
1561	<	2005-02-14 17:57 tim
1561	>	2005-02-14 12:57 tim
1562
1563		* src/: applications/dynamicProps/TimeCorrFunc.cpp,
1564		brains/SimInfo.cpp, primitives/RigidBody.cpp,
1565		primitives/StuntDouble.hpp: begin bug fix
1566
1567	<	2005-02-14 17:35 tim
1567	>	2005-02-14 12:35 tim
1568
1569		* src/applications/dynamicProps/: CorrelationFunction.cpp,
1570		CorrelationFunction.hpp, CrossTimeCorrFunc.cpp,
#	Line 610 \| Line 1574
1574		RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp,
1575		VCorrFunc.hpp: refactory CorrelationFunction
1576
1577	<	2005-02-14 15:18 gezelter
1577	>	2005-02-14 10:18 gezelter
1578
1579		* src/applications/dynamicProps/CorrelationFunction.cpp: bug fix
1580		and start of switch for type of correlation function
1581
1582	<	2005-02-13 21:18 tim
1582	>	2005-02-13 16:18 tim
1583
1584		* src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in
1585		calculating bytes per stuntdouble
1586
1587	<	2005-02-13 21:03 tim
1587	>	2005-02-13 16:03 tim
1588
1589		* src/applications/dynamicProps/CorrelationFunction.cpp: more fix
1590
1591	<	2005-02-13 20:57 tim
1591	>	2005-02-13 15:57 tim
1592
1593		* src/applications/dynamicProps/CorrelationFunction.cpp: fixed a
1594		bug in CorrelationFunction
1595
1596	<	2005-02-13 20:36 tim
1596	>	2005-02-13 15:36 tim
1597
1598		* src/: applications/staticProps/GofR.cpp,
1599		applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a
1600		bug in SimInfo::getCutoff()
1601
1602	<	2005-02-13 20:08 tim
1602	>	2005-02-13 15:08 tim
1603
1604		* make/Makefile.in: adding staticProps and dynamicProps into
1605		Makefile.in
1606
1607	<	2005-02-13 20:05 tim
1607	>	2005-02-13 15:05 tim
1608
1609		* src/: applications/dynamicProps/CorrelationFunction.cpp,
1610		applications/dynamicProps/CorrelationFunction.hpp,
#	Line 651 \| Line 1615
1615		brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length
1616		defaults to the cutoff radius
1617
1618	<	2005-02-13 19:14 tim
1618	>	2005-02-13 14:14 tim
1619
1620		* src/utils/Algorithm.hpp: adding Algorithm.hpp
1621
1622	<	2005-02-13 19:10 tim
1622	>	2005-02-13 14:10 tim
1623
1624		* src/: applications/dump2Xyz/Dump2XYZ.cpp,
1625		applications/dynamicProps/CorrelationFunction.cpp,
#	Line 669 \| Line 1633
1633		utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h,
1634		visitors/OtherVisitor.cpp: dynamicProps get built
1635
1636	<	2005-02-13 15:56 tim
1636	>	2005-02-13 10:56 tim
1637
1638		* src/: applications/dynamicProps/CorrelationFunction.cpp,
1639		brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
1640		brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in
1641		progress
1642
1643	<	2005-02-13 08:04 tim
1643	>	2005-02-13 03:04 tim
1644
1645		* src/: applications/dynamicProps/CorrelationFunction.hpp,
1646		brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
#	Line 684 \| Line 1648
1648		brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more
1649		work in dynamicProps
1650
1651	<	2005-02-13 07:25 tim
1651	>	2005-02-13 02:25 tim
1652
1653		* src/applications/dynamicProps/DynamicProps.cpp: adding
1654		dynamicProps
1655
1656	<	2005-02-13 07:14 tim
1656	>	2005-02-13 02:14 tim
1657
1658		* src/applications/dynamicProps/: DynamicPropsCmd.c,
1659		DynamicPropsCmd.h: adding command line option to DynamicProps
1660
1661	<	2005-02-13 07:13 tim
1661	>	2005-02-13 02:13 tim
1662
1663		* src/applications/dynamicProps/: DynamicProps.ggo, Makefile:
1664		adding command line option for DynamicProps
1665
1666	<	2005-02-13 06:57 tim
1666	>	2005-02-13 01:57 tim
1667
1668		* src/: applications/dynamicProps/CorrelationFunction.cpp,
1669		applications/dynamicProps/CorrelationFunction.hpp,
#	Line 716 \| Line 1680
1680		primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding
1681		dynamicProps
1682
1683	<	2005-02-12 20:09 tim
1683	>	2005-02-12 15:09 tim
1684
1685		* src/selection/SelectionManager.cpp: adding SelectionManager.cpp
1686
1687	<	2005-02-11 22:41 tim
1687	>	2005-02-11 17:41 tim
1688
1689		* src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one
1690		more constructor to Snapshot to create customized DataStorage
1691
1692	<	2005-02-11 22:39 tim
1692	>	2005-02-11 17:39 tim
1693
1694		* src/selection/: DistanceFinder.hpp, Makefile,
1695		SelectionManager.hpp: adding beginSelected, nextSelected method to
1696		SelectionManager
1697
1698	<	2005-02-11 22:36 tim
1698	>	2005-02-11 17:36 tim
1699
1700		* src/config.h.in, configure: adding support for physmem
1701
1702	<	2005-02-11 22:35 tim
1702	>	2005-02-11 17:35 tim
1703
1704		* ac-tools/configure.in: adding supprot for physmem
1705
1706	<	2005-02-11 22:35 tim
1706	>	2005-02-11 17:35 tim
1707
1708		* src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding
1709		physmem
1710
1711	<	2005-02-10 22:37 tim
1711	>	2005-02-10 17:37 tim
1712
1713		* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp,
1714		GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp,
#	Line 752 \| Line 1716
1716		StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
1717		StaticPropsCmd.h: more work in StaticProps
1718
1719	<	2005-02-10 18:14 tim
1719	>	2005-02-10 13:14 tim
1720
1721		* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp,
1722		GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp,
#	Line 761 \| Line 1725
1725		StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
1726		StaticPropsCmd.h: change the filenames
1727
1728	<	2005-02-10 14:15 tim
1728	>	2005-02-10 09:15 tim
1729
1730		* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp,
1731		GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp,
1732		RadialDistrFunc.hpp: adding GofRAngle
1733
1734	<	2005-02-09 18:21 tim
1734	>	2005-02-09 13:21 tim
1735
1736		* src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some
1737		useless files
1738
1739	<	2005-02-09 18:12 tim
1739	>	2005-02-09 13:12 tim
1740
1741		* src/applications/staticProps/: GofR.cpp, Makefile,
1742		RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress
1743
1744	<	2005-02-09 17:08 tim
1744	>	2005-02-09 12:08 tim
1745
1746		* src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp,
1747		GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h,
1748		RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR
1749
1750	<	2005-02-07 22:39 tim
1750	>	2005-02-07 17:39 tim
1751
1752		* src/primitives/Molecule.hpp: add getRigidBodyAt function into
1753		Molecule class
1754
1755	<	2005-02-07 22:38 tim
1755	>	2005-02-07 17:38 tim
1756
1757		* src/applications/dump2Xyz/Dump2XYZCmd.c: update help info
1758
1759	<	2005-02-07 22:36 tim
1759	>	2005-02-07 17:36 tim
1760
1761		* src/selection/: NameFinder.cpp, NameFinder.hpp,
1762		SelectionCompiler.cpp: support select internal index selection, for
1763		example, select DMPC.3
1764
1765	<	2005-02-07 21:11 tim
1765	>	2005-02-07 16:11 tim
1766
1767		* src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update
1768		help info for Dump2XYZ
1769
1770	<	2005-02-07 20:39 chrisfen
1770	>	2005-02-07 15:39 chrisfen
1771
1772		* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
1773		selection librarys added
1774
1775	<	2005-02-07 20:31 tim
1775	>	2005-02-07 15:31 tim
1776
1777		* src/selection/Makefile, make/Makefile.in: adding Makefile
1778
1779	<	2005-02-07 20:20 chrisfen
1779	>	2005-02-07 15:20 chrisfen
1780
1781		* src/utils/wildcards.hpp: issue commented out in wildcards
1782
1783	<	2005-02-07 20:06 tim
1783	>	2005-02-07 15:06 tim
1784
1785		* src/selection/SelectionEvaluator.cpp: forget to reset the pc
1786		which cause reevaluate return NULL
1787
1788	<	2005-02-07 19:14 tim
1788	>	2005-02-07 14:14 tim
1789
1790		* src/brains/: SimCreator.cpp, SimSnapshotManager.cpp,
1791		SimSnapshotManager.hpp: fix a bug in determing the global index for
1792		rigidbodies
1793
1794	<	2005-02-07 19:13 tim
1794	>	2005-02-07 14:13 tim
1795
1796		* src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change
1797		in Bitset
1798
1799	<	2005-02-07 19:13 tim
1799	>	2005-02-07 14:13 tim
1800
1801		* src/selection/: DistanceFinder.cpp, DistanceFinder.hpp,
1802		SelectionCompiler.cpp, SelectionCompiler.hpp,
1803		SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp,
1804		TokenMap.cpp: selection library is working
1805
1806	<	2005-02-04 22:46 tim
1806	>	2005-02-04 17:46 tim
1807
1808		* src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor
1809
1810	<	2005-02-04 22:45 tim
1810	>	2005-02-04 17:45 tim
1811
1812		* src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor
1813		and XYZVisitor now use selection library
1814
1815	<	2005-02-04 22:44 tim
1815	>	2005-02-04 17:44 tim
1816
1817		* src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp:
1818		adding SelectionManager into SimInfo
1819
1820	<	2005-02-04 22:43 tim
1820	>	2005-02-04 17:43 tim
1821
1822		* src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo,
1823		Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of
1824		selection library
1825
1826	<	2005-02-04 22:42 tim
1826	>	2005-02-04 17:42 tim
1827
1828		* src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change
1829		in BitSet
1830
1831	<	2005-02-04 22:41 tim
1831	>	2005-02-04 17:41 tim
1832
1833		* src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing
1834		implementation
1835
1836	<	2005-02-04 22:39 tim
1836	>	2005-02-04 17:39 tim
1837
1838		* src/selection/: NameFinder.cpp, NameFinder.hpp,
1839		SelectionCompiler.cpp, SelectionCompiler.hpp,
#	Line 877 \| Line 1841
1841		SelectionManager.hpp, Token.hpp: half of the selection utility is
1842		working need to debug within keyword and atomproperty keyword
1843
1844	<	2005-02-04 05:42 tim
1844	>	2005-02-04 00:42 tim
1845
1846		* src/selection/: NameFinder.cpp, NameFinder.hpp: selection library
1847		get built
1848
1849	<	2005-02-04 05:42 tim
1849	>	2005-02-04 00:42 tim
1850
1851		* src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet
1852
1853	<	2005-02-04 05:26 tim
1853	>	2005-02-04 00:26 tim
1854
1855		* src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp:
1856		remove some useless files
1857
1858	<	2005-02-04 04:57 tim
1858	>	2005-02-03 23:57 tim
1859
1860		* src/: primitives/RigidBody.hpp, selection/NameFinder.cpp,
1861		selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp:
1862		adding wildcard class; NameFinder is finished
1863
1864	<	2005-02-03 23:14 tim
1864	>	2005-02-03 18:14 tim
1865
1866		* src/selection/: NameFinder.cpp, NameFinder.hpp,
1867		SelectionCompiler.cpp, SelectionCompiler.hpp,
#	Line 905 \| Line 1869
1869		SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in
1870		selection library
1871
1872	<	2005-02-03 14:04 tim
1872	>	2005-02-03 09:04 tim
1873
1874		* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
1875		selection in progress
1876
1877	<	2005-02-02 23:13 tim
1877	>	2005-02-02 18:13 tim
1878
1879		* src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp,
1880		SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp,
1881		Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in
1882		progress, except SelectionEvaluator, other files are compiled
1883
1884	<	2005-02-02 23:12 tim
1884	>	2005-02-02 18:12 tim
1885
1886		* src/utils/: Makefile.in, any.hpp: adding boost::any
1887
1888	<	2005-02-02 12:51 tim
1888	>	2005-02-02 07:51 tim
1889
1890		* src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp
1891
1892	<	2005-02-01 22:49 tim
1892	>	2005-02-01 17:49 tim
1893
1894		* src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp,
1895		selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp,
1896		selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp,
1897		selection/Token.hpp: Selection in progress
1898
1899	<	2005-02-01 06:55 tim
1899	>	2005-02-01 01:55 tim
1900
1901		* src/: selection/SelectionCompiler.hpp,
1902		selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
1903		selection/SelectionManager.hpp, selection/Token.hpp,
1904		utils/BitSet.cpp, utils/BitSet.hpp: adding selection library
1905
1906	<	2005-01-26 15:26 tim
1906	>	2005-01-26 10:26 tim
1907
1908		* src/integrators/: Integrator.cpp, Integrator.hpp,
1909		VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget
1910		to add eorWriter
1911
1912	<	2005-01-26 15:15 tim
1912	>	2005-01-26 10:15 tim
1913
1914		* src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp:
1915		(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the
1916		wrong column of electroframe
1917
1918	<	2005-01-25 21:59 tim
1918	>	2005-01-25 16:59 tim
1919
1920		* src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in
1921		SimInfo, use number of cutoff stamp as counter to loop over
1922		rigidbody stamp
1923
1924	<	2005-01-25 17:45 tim
1924	>	2005-01-25 12:45 tim
1925
1926		* src/: applications/dump2Xyz/Dump2XYZ.cpp,
1927		brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
#	Line 977 \| Line 1941
1941		inertial tensor from the directional atoms before calculate
1942		rigidbody's inertial tensor
1943
1944	<	2005-01-17 22:17 tim
1944	>	2005-01-17 17:17 tim
1945
1946		* forceFields/DUFF2.frc: forget to set dipole for lipid head group
1947
1948	<	2005-01-17 16:58 tim
1948	>	2005-01-17 11:58 tim
1949
1950		* src/integrators/NVT.cpp: fix a bug in loading initial extended
1951		system parameters
1952
1953	<	2005-01-17 16:05 tim
1953	>	2005-01-17 11:05 tim
1954
1955		* src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT
1956
1957	<	2005-01-14 22:02 tim
1957	>	2005-01-14 17:02 tim
1958
1959		* src/UseTheForce/WATER.cpp: remove WATER.cpp
1960
1961	<	2005-01-14 21:37 tim
1961	>	2005-01-14 16:37 tim
1962
1963		* forceFields/Makefile: sync Makefile
1964
1965	<	2005-01-14 21:13 gezelter
1965	>	2005-01-14 16:13 gezelter
1966
1967		* make/Makefile.in, src/Makefile, src/UseTheForce/Makefile,
1968		src/UseTheForce/DarkSide/Makefile, src/applications/Makefile,
#	Line 1012 \| Line 1976
1976		src/visitors/Makefile: moved Package variable into subdirectory
1977		makefiles to speed up the building process
1978
1979	<	2005-01-14 20:48 gezelter
1979	>	2005-01-14 15:48 gezelter
1980
1981		* src/applications/oopse/oopse.cpp: Fixed publication details in
1982		banner
1983
1984	<	2005-01-14 20:48 gezelter
1984	>	2005-01-14 15:48 gezelter
1985
1986		* src/UseTheForce/DarkSide/: simParallel_interface.F90,
1987		simParallel_interface.h: added dummy subroutine to avoid empty
1988		unit, synchronized this dummy routine between C and fortran
1989
1990	<	2005-01-14 20:31 gezelter
1990	>	2005-01-14 15:31 gezelter
1991
1992		* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90,
1993		notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90,
#	Line 1039 \| Line 2003
2003		DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating
2004		modules and C/Fortran interface subroutines
2005
2006	<	2005-01-14 20:15 gezelter
2006	>	2005-01-14 15:15 gezelter
2007
2008		* configure, ac-tools/aclocal.m4: more fixes for gnugetopt
2009
2010	<	2005-01-14 20:09 gezelter
2010	>	2005-01-14 15:09 gezelter
2011
2012		* configure, ac-tools/configure.in, src/config.h.in,
2013		src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt
2014
2015	<	2005-01-14 16:49 tim
2015	>	2005-01-14 11:49 tim
2016
2017		* src/: io/EAMAtomTypesSectionParser.cpp,
2018		utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
2019		utils/StringUtils.hpp: using c library to do conversion instead of
2020		using iostream due to a bug in libstdc++(GCC 3.2)
2021
2022	<	2005-01-14 02:40 tim
2022	>	2005-01-13 21:40 tim
2023
2024		* src/brains/SimSetup.cpp: no message
2025
2026	<	2005-01-14 01:56 tim
2026	>	2005-01-13 20:56 tim
2027
2028		* src/primitives/Molecule.hpp: fix a bug in global index
2029
2030	<	2005-01-14 01:04 tim
2030	>	2005-01-13 20:04 tim
2031
2032		* src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include
2033		Integrator.hpp in Minimizer
2034
2035	<	2005-01-13 22:14 gezelter
2035	>	2005-01-13 17:14 gezelter
2036
2037		* src/utils/Makefile: compile getopt and getopt1 if we need to
2038
2039	<	2005-01-13 21:56 gezelter
2039	>	2005-01-13 16:56 gezelter
2040
2041		* make/Makefile.in: template flags
2042
2043	<	2005-01-13 21:48 gezelter
2043	>	2005-01-13 16:48 gezelter
2044
2045		* src/applications/oopse/Makefile: formatting
2046
2047	<	2005-01-13 21:48 gezelter
2047	>	2005-01-13 16:48 gezelter
2048
2049		* make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir
2050		target
2051
2052	<	2005-01-13 19:40 tim
2052	>	2005-01-13 14:40 tim
2053
2054		* src/: UseTheForce/fSwitchingFunction.h,
2055		UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile,
#	Line 1093 \| Line 2057
2057		primitives/RigidBody.cpp, types/AtomTypeProperties.h,
2058		types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform
2059
2060	<	2005-01-13 18:26 tim
2060	>	2005-01-13 13:26 tim
2061
2062		* make/Makefile.in: change the order of linking (object file comes
2063		first and then follow by user built library)
2064
2065	<	2005-01-12 23:24 tim
2065	>	2005-01-12 18:24 tim
2066
2067		* src/io/DumpWriter.cpp: remove useless debug info
2068
2069	<	2005-01-12 23:21 tim
2069	>	2005-01-12 18:21 tim
2070
2071		* src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix
2072
2073	<	2005-01-12 23:17 tim
2073	>	2005-01-12 18:17 tim
2074
2075		* make/: Makefile.in, Makefile.in: missing tab
2076
2077	<	2005-01-12 23:15 tim
2077	>	2005-01-12 18:15 tim
2078
2079		* src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor
2080		get fixed
2081
2082	<	2005-01-12 22:40 gezelter
2082	>	2005-01-12 17:40 gezelter
2083
2084		* make/Makefile.in, src/UseTheForce/DUFF.cpp,
2085		src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp,
#	Line 1325 \| Line 2289
2289		src/visitors/ZconsVisitor.hpp: merging new_design branch into
2290		OOPSE-2.0
2291
2292	<	2005-01-12 18:13 tim
2292	>	2005-01-12 13:13 tim
2293
2294		* src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp,
2295		utils/TypeContainer.hpp: forget to include <algorithm>
2296
2297	<	2005-01-12 17:25 tim
2297	>	2005-01-12 12:25 tim
2298
2299		* forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc,
2300		newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force
2301		fields
2302
2303	<	2005-01-12 17:14 tim
2303	>	2005-01-12 12:14 tim
2304
2305		* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2306		UseTheForce/EAM.cpp, UseTheForce/EAM.hpp,
#	Line 1498 \| Line 2462
2462		visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
2463		visitors/ZconsVisitor.hpp: change license
2464
2465	<	2005-01-12 17:14 tim
2465	>	2005-01-12 12:14 tim
2466
2467		* src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on
2468		branch new_design.
2469
2470	<	2005-01-11 21:03 tim
2470	>	2005-01-11 16:03 tim
2471
2472		* src/: constraints/ZconstraintForceManager.cpp,
2473		constraints/ZconstraintForceManager.hpp,
#	Line 1511 \| Line 2475
2475		minimizers/MinimizerParameterSet.hpp: change const static double
2476		data member to const double
2477
2478	<	2005-01-11 20:50 tim
2478	>	2005-01-11 15:50 tim
2479
2480		* src/io/basic_ifstrstream.hpp: forget namespace qualifier std::
2481
2482	<	2005-01-11 20:39 tim
2482	>	2005-01-11 15:39 tim
2483
2484		* src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h:
2485		change data type from logical to integer in AtomTypeProperties.h
2486
2487	<	2005-01-11 16:36 tim
2487	>	2005-01-11 11:36 tim
2488
2489		* forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding
2490		new format of EAM force field
2491
2492	<	2005-01-11 16:24 tim
2492	>	2005-01-11 11:24 tim
2493
2494		* src/UseTheForce/DUFF.cpp: change default name of DUFF force field
2495		to DUFF2.frc
2496
2497	<	2005-01-11 16:23 tim
2497	>	2005-01-11 11:23 tim
2498
2499		* forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to
2500		DUFF2.frc
2501
2502	<	2005-01-11 16:09 tim
2502	>	2005-01-11 11:09 tim
2503
2504		* make/Makefile.in: adding constraints and minimizers into
2505		Makefile.in
2506
2507	<	2005-01-11 16:03 tim
2507	>	2005-01-11 11:03 tim
2508
2509		* src/io/: ChargeAtomTypesSectionParser.cpp,
2510		ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp,
2511		DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless
2512		files
2513
2514	<	2005-01-11 15:59 tim
2514	>	2005-01-11 10:59 tim
2515
2516		* src/io/ZConsWriter.cpp: [no log message]
2517
2518	<	2005-01-11 15:53 tim
2518	>	2005-01-11 10:53 tim
2519
2520		* src/UseTheForce/EAM.cpp: minor fix
2521
2522	<	2005-01-11 15:52 tim
2522	>	2005-01-11 10:52 tim
2523
2524		* src/constraints/Rattle.hpp: file Rattle.hpp was initially added
2525		on branch new_design.
2526
2527	<	2005-01-11 15:52 tim
2527	>	2005-01-11 10:52 tim
2528
2529		* src/constraints/Rattle.cpp: file Rattle.cpp was initially added
2530		on branch new_design.
2531
2532	<	2005-01-11 15:52 tim
2532	>	2005-01-11 10:52 tim
2533
2534		* src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
2535
2536	<	2005-01-11 15:47 tim
2536	>	2005-01-11 10:47 tim
2537
2538		* make/Makefile.in: forget a '$' sign
2539
2540	<	2005-01-11 15:46 tim
2540	>	2005-01-11 10:46 tim
2541
2542		* make/Makefile.in: missing tab in rules
2543
2544	<	2005-01-10 22:04 tim
2544	>	2005-01-10 17:04 tim
2545
2546		* src/: UseTheForce/ForceFieldCreator.cpp,
2547		UseTheForce/ForceFieldCreator.hpp,
#	Line 1596 \| Line 2560
2560		minimizers/MinimizerFactory.hpp: create a register module to
2561		register force fields, integrators and minimizers
2562
2563	<	2005-01-10 22:04 tim
2563	>	2005-01-10 17:04 tim
2564
2565		* src/brains/Register.cpp: file Register.cpp was initially added on
2566		branch new_design.
2567
2568	<	2005-01-10 22:04 tim
2568	>	2005-01-10 17:04 tim
2569
2570		* src/brains/Register.hpp: file Register.hpp was initially added on
2571		branch new_design.
2572
2573	<	2005-01-10 20:52 tim
2573	>	2005-01-10 15:52 tim
2574
2575		* src/: UseTheForce/ForceFieldFactory.cpp,
2576		applications/oopse/oopse.cpp, brains/ForceManager.hpp,
#	Line 1618 \| Line 2582
2582		visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint
2583		method is working now
2584
2585	<	2005-01-10 18:05 tim
2585	>	2005-01-10 13:05 tim
2586
2587		* src/: constraints/ConstraintElem.hpp,
2588		constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp,
#	Line 1628 \| Line 2592
2592		visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in
2593		zconstraint
2594
2595	<	2005-01-10 18:05 tim
2595	>	2005-01-10 13:05 tim
2596
2597		* src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was
2598		initially added on branch new_design.
2599
2600	<	2005-01-07 21:50 tim
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 21:50 tim
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 21:50 tim
2612	>	2005-01-07 16:50 tim
2613
2614		* src/: applications/simpleBuilder/BaseLattice.hpp,
2615		applications/simpleBuilder/Lattice.hpp,
#	Line 1659 \| Line 2623
2623		integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp,
2624		utils/NumericConstant.hpp: ZConstraintForceManager in progress
2625
2626	<	2005-01-07 21:50 tim
2626	>	2005-01-07 16:50 tim
2627
2628		* src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was
2629		initially added on branch new_design.
2630
2631	<	2005-01-06 22:31 tim
2631	>	2005-01-06 17:31 tim
2632
2633		* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
2634		brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
#	Line 1673 \| Line 2637
2637		io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp:
2638		constraint is almost working
2639
2640	<	2005-01-06 00:36 tim
2640	>	2005-01-05 19:36 tim
2641
2642		* src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is
2643		working
2644
2645	<	2005-01-06 00:16 tim
2645	>	2005-01-05 19:16 tim
2646
2647		* src/: applications/dump2Xyz/Dump2XYZ.cpp,
2648		applications/oopse/oopse.cpp,
#	Line 1693 \| Line 2657
2657		minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder
2658		in progress
2659
2660	<	2005-01-05 17:35 tim
2660	>	2005-01-05 12:35 tim
2661
2662		* src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp
2663		was initially added on branch new_design.
2664
2665	<	2005-01-05 17:35 tim
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 17:35 tim
2670	>	2005-01-05 12:35 tim
2671
2672		* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
2673		Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp,
#	Line 1711 \| Line 2675
2675		OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp,
2676		SDMinimizer.hpp: minimizer in progress
2677
2678	<	2005-01-05 17:35 tim
2678	>	2005-01-05 12:35 tim
2679
2680		* src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
2681		was initially added on branch new_design.
2682
2683	<	2005-01-05 17:35 tim
2683	>	2005-01-05 12:35 tim
2684
2685		* src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
2686		was initially added on branch new_design.
2687
2688	<	2005-01-05 17:35 tim
2688	>	2005-01-05 12:35 tim
2689
2690		* src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
2691		was initially added on branch new_design.
2692
2693	<	2005-01-05 17:35 tim
2693	>	2005-01-05 12:35 tim
2694
2695		* src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially
2696		added on branch new_design.
2697
2698	<	2005-01-04 22:18 tim
2698	>	2005-01-04 17:18 tim
2699
2700		* src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
2701		brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp,
#	Line 1742 \| Line 2706
2706		primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in
2707		progress
2708
2709	<	2005-01-04 22:18 tim
2709	>	2005-01-04 17:18 tim
2710
2711		* src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was
2712		initially added on branch new_design.
2713
2714	<	2005-01-04 22:18 tim
2714	>	2005-01-04 17:18 tim
2715
2716		* src/minimizers/MinimizerParameterSet.cpp: file
2717		MinimizerParameterSet.cpp was initially added on branch new_design.
2718
2719	<	2005-01-04 22:18 tim
2719	>	2005-01-04 17:18 tim
2720
2721		* src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was
2722		initially added on branch new_design.
2723
2724	<	2005-01-04 22:18 tim
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 22:18 tim
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 22:18 tim
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
2741	<	2004-12-20 20:50 chuckv
2741	>	2004-12-20 15:50 chuckv
2742
2743		* make/Makefile.in: Fixed Makefile test bug under OSX and possibly
2744		other BSD's, replaced test -f *.mod with ls function since BSD test
2745		apparently doesn't support wildcards.
2746
2747	<	2004-12-20 20:36 tim
2747	>	2004-12-20 15:36 tim
2748
2749		* make/Makefile.in: fix a test command incompatiable problem
2750
2751	<	2004-12-20 19:49 tim
2751	>	2004-12-20 14:49 tim
2752
2753		* src/integrators/NPTi.cpp: NPT is working now
2754
2755	<	2004-12-16 19:20 tim
2755	>	2004-12-16 14:20 tim
2756
2757		* src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the
2758		invalid stamp id
2759
2760	<	2004-12-16 19:00 tim
2760	>	2004-12-16 14:00 tim
2761
2762		* forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc,
2763		newEAM.u6.frc: adding new EAM force field files
2764
2765	<	2004-12-16 18:55 tim
2765	>	2004-12-16 13:55 tim
2766
2767		* src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays
2768		in EAM parameter file is incorrect
2769
2770	<	2004-12-16 17:27 tim
2770	>	2004-12-16 12:27 tim
2771
2772		* src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp,
2773		brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp,
2774		utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM
2775
2776	<	2004-12-15 22:34 tim
2776	>	2004-12-15 17:34 tim
2777
2778		* src/: applications/simpleBuilder/BaseLattice.cpp,
2779		applications/simpleBuilder/BaseLattice.hpp,
#	Line 1822 \| Line 2786
2786		applications/simpleBuilder/simpleBuilder.cpp,
2787		io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream
2788
2789	<	2004-12-15 21:07 tim
2789	>	2004-12-15 16:07 tim
2790
2791		* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2792		UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile,
2793		applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp:
2794		add EAM Force Field
2795
2796	<	2004-12-15 19:40 tim
2796	>	2004-12-15 14:40 tim
2797
2798		* src/applications/oopse/oopse.cpp: add more force fields
2799
2800	<	2004-12-15 16:44 tim
2800	>	2004-12-15 11:44 tim
2801
2802		* src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget
2803		to call All_reduce in MPI version)
2804
2805	<	2004-12-15 16:13 tim
2805	>	2004-12-15 11:13 tim
2806
2807		* src/: brains/SimCreator.cpp, brains/SimInfo.cpp,
2808		io/DumpReader.cpp: MPI in NVE is working
2809
2810	<	2004-12-14 21:57 tim
2810	>	2004-12-14 16:57 tim
2811
2812		* src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader.
2813		Master nodes does not brocast the total number of frames
2814
2815	<	2004-12-14 19:08 tim
2815	>	2004-12-14 14:08 tim
2816
2817		* src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp,
2818		integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
#	Line 1857 \| Line 2821
2821		minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp,
2822		minimizers/SDMinimizer.cpp: more fix in MPI version
2823
2824	<	2004-12-13 22:30 tim
2824	>	2004-12-13 17:30 tim
2825
2826		* src/: UseTheForce/DarkSide/simParallel.F90,
2827		applications/oopse/oopse.cpp, brains/SimCreator.cpp,
#	Line 1875 \| Line 2839
2839		utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version
2840		is built
2841
2842	<	2004-12-10 18:41 tim
2842	>	2004-12-10 13:41 tim
2843
2844		* src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp
2845
2846	<	2004-12-10 16:14 tim
2846	>	2004-12-10 11:14 tim
2847
2848		* src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp,
2849		primitives/StuntDouble.hpp: forget to zero out the torque. Sticky
2850		and Dipole is working now
2851
2852	<	2004-12-09 23:15 tim
2852	>	2004-12-09 18:15 tim
2853
2854		* src/: UseTheForce/DarkSide/dipole.F90,
2855		UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp:
2856		fix an index problem in eFrame matrix
2857
2858	<	2004-12-09 23:09 tim
2858	>	2004-12-09 18:09 tim
2859
2860		* src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when
2861		initializing the new Charge AtomType
2862
2863	<	2004-12-09 21:15 tim
2863	>	2004-12-09 16:15 tim
2864
2865		* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90,
2866		types/DirectionalAtomType.cpp: sticky module get compiled
2867
2868	<	2004-12-09 20:43 gezelter
2868	>	2004-12-09 15:43 gezelter
2869
2870		* src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90,
2871		reactionField.F90: u_l -> eFrame for electrostatics u_l -> A for
2872		GB
2873
2874	<	2004-12-09 20:42 gezelter
2874	>	2004-12-09 15:42 gezelter
2875
2876		* src/UseTheForce/doForces.F90: u_l -> eFrame
2877
2878	<	2004-12-09 20:27 gezelter
2878	>	2004-12-09 15:27 gezelter
2879
2880		* src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky
2881		module now has the option for multiple sticky types
2882
2883	<	2004-12-09 20:27 gezelter
2883	>	2004-12-09 15:27 gezelter
2884
2885		* src/UseTheForce/doForces.F90: sticky
2886
2887	<	2004-12-09 16:22 tim
2887	>	2004-12-09 11:22 tim
2888
2889		* src/integrators/: NPT.cpp, NVT.cpp: fix an interface
2890		inconsistency in lab2Bidy
2891
2892	<	2004-12-09 15:45 tim
2892	>	2004-12-09 10:45 tim
2893
2894		* src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug
2895		in calculating torque in rigid body
2896
2897	<	2004-12-08 20:37 tim
2897	>	2004-12-08 15:37 tim
2898
2899		* src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h,
2900		brains/SnapShot.cpp, brains/Snapshot.hpp,
#	Line 1938 \| Line 2902
2902		io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp:
2903		fix a parsing bug in ElectroStaticAtomTypesSectionParser
2904
2905	<	2004-12-08 17:03 tim
2905	>	2004-12-08 12:03 tim
2906
2907		* src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane
2908		in NVT is working
2909
2910	<	2004-12-07 23:08 tim
2910	>	2004-12-07 18:08 tim
2911
2912		* src/: UseTheForce/Makefile, brains/SimInfo.hpp,
2913		integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp,
2914		integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp,
2915		io/DumpWriter.cpp: NPT in progress
2916
2917	<	2004-12-07 14:43 tim
2917	>	2004-12-07 09:43 tim
2918
2919		* test/utils/: Makefile, NextCombinationTestCase.hpp: [no log
2920		message]
2921
2922	<	2004-12-07 05:12 tim
2922	>	2004-12-07 00:12 tim
2923
2924		* src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in
2925		UseInitXSstate
2926
2927	<	2004-12-07 05:00 tim
2927	>	2004-12-07 00:00 tim
2928
2929		* src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message
2930
2931	<	2004-12-07 04:47 tim
2931	>	2004-12-06 23:47 tim
2932
2933		* src/types/DirectionalAtomType.cpp: [no log message]
2934
2935	<	2004-12-07 02:18 tim
2935	>	2004-12-06 21:18 tim
2936
2937		* forceFields/newDUFF.frc: merge WATER force field into DUFF
2938
2939	<	2004-12-07 01:33 tim
2939	>	2004-12-06 20:33 tim
2940
2941		* forceFields/newDUFF.frc: change the force constant of bonds
2942
2943	<	2004-12-06 23:29 tim
2943	>	2004-12-06 18:29 tim
2944
2945		* src/: UseTheForce/DarkSide/charge.F90,
2946		UseTheForce/DarkSide/charge_interface.h,
#	Line 1984 \| Line 2948
2948		UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp:
2949		fix atom type ident in Charge and Dipole Module
2950
2951	<	2004-12-06 22:56 tim
2951	>	2004-12-06 17:56 tim
2952
2953		* src/primitives/Torsion.cpp: butane is working now
2954
2955	<	2004-12-06 20:15 tim
2955	>	2004-12-06 15:15 tim
2956
2957		* src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp,
2958		primitives/Bond.hpp, primitives/Torsion.cpp: short range
2959		interaction for butane is correct.Still something wrong with long
2960		range one
2961
2962	<	2004-12-06 04:49 tim
2962	>	2004-12-05 23:49 tim
2963
2964		* src/: brains/Exclude.cpp, brains/Exclude.hpp,
2965		brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
#	Line 2003 \| Line 2967
2967		primitives/Atom.hpp, utils/NumericConstant.hpp,
2968		utils/TypeContainer.hpp: fix a bug in Exclude List
2969
2970	<	2004-12-05 22:21 tim
2970	>	2004-12-05 17:21 tim
2971
2972		* forceFields/newDUFF.frc: minor fix in DUFF
2973
2974	<	2004-12-05 22:02 tim
2974	>	2004-12-05 17:02 tim
2975
2976		* src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp,
2977		utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp:
2978		fix a bug in filling MolMembership
2979
2980	<	2004-12-05 17:12 tim
2980	>	2004-12-05 12:12 tim
2981
2982		* forceFields/newDUFF.frc: minor fix in force field file
2983
2984	<	2004-12-05 17:09 tim
2984	>	2004-12-05 12:09 tim
2985
2986		* src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp,
2987		integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp
2988
2989	<	2004-12-04 20:09 tim
2989	>	2004-12-04 15:09 tim
2990
2991		* src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp,
2992		math/Vector3.hpp: NVE is working now, get the same result as
2993		OOPSE-1.0
2994
2995	<	2004-12-04 19:29 tim
2995	>	2004-12-04 14:29 tim
2996
2997		* src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy
2998
2999	<	2004-12-04 19:24 gezelter
2999	>	2004-12-04 14:24 gezelter
3000
3001		* src/primitives/: Bend.cpp, Torsion.cpp: What?
3002
3003	<	2004-12-04 19:24 gezelter
3003	>	2004-12-04 14:24 gezelter
3004
3005		* src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion
3006
3007	<	2004-12-04 05:24 tim
3007	>	2004-12-04 00:24 tim
3008
3009		* src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp,
3010		integrators/Integrator.hpp,
#	Line 2051 \| Line 3015
3015		dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step
3016		4 EAM Step 5 Shape Step 6 Constraint & Restraint
3017
3018	<	2004-12-04 00:01 tim
3018	>	2004-12-03 19:01 tim
3019
3020		* src/: UseTheForce/DarkSide/LJ.F90,
3021		applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp,
#	Line 2060 \| Line 3024
3024		io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working,
3025		energy of NVE is not conserved
3026
3027	<	2004-12-03 22:36 tim
3027	>	2004-12-03 17:36 tim
3028
3029		* src/: brains/DataStorage.hpp, brains/Snapshot.hpp,
3030		primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running
3031
3032	<	2004-12-03 21:30 tim
3032	>	2004-12-03 16:30 tim
3033
3034		* src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp,
3035		brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile,
#	Line 2073 \| Line 3037
3037		primitives/Molecule.hpp, primitives/StuntDouble.hpp,
3038		primitives/Torsion.hpp: more missing function get implemented
3039
3040	<	2004-12-03 20:30 tim
3040	>	2004-12-03 15:30 tim
3041
3042		* src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp,
3043		SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo
3044
3045	<	2004-12-03 17:59 tim
3045	>	2004-12-03 12:59 tim
3046
3047		* src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp,
3048		brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
#	Line 2087 \| Line 3051
3051		io/SectionParserManager.cpp, utils/LocalIndexManager.hpp,
3052		utils/TypeContainer.hpp: begin to fix bugs
3053
3054	<	2004-12-03 00:26 tim
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	<	2004-12-03 00:26 tim
3059	>	2004-12-02 19:26 tim
3060
3061		* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3062		UseTheForce/ForceFieldCreator.cpp,
#	Line 2103 \| Line 3067
3067		utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a
3068		bug in countTokens in StringTokenizer
3069
3070	<	2004-12-03 00:06 tim
3070	>	2004-12-02 19:06 tim
3071
3072		* forceFields/newDUFF.frc: minor fix
3073
3074	<	2004-12-02 23:15 tim
3074	>	2004-12-02 18:15 tim
3075
3076		* forceFields/newDUFF.frc: new ForceField format
3077
3078	<	2004-12-02 22:15 tim
3078	>	2004-12-02 17:15 tim
3079
3080		* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3081		UseTheForce/ForceFieldCreator.cpp,
#	Line 2130 \| Line 3094
3094		types/Makefile: refine factory pattern to make it initialized
3095		correctly
3096
3097	<	2004-12-02 22:15 tim
3097	>	2004-12-02 17:15 tim
3098
3099		* src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp
3100		was initially added on branch new_design.
3101
3102	<	2004-12-02 22:15 tim
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 22:15 tim
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 22:15 tim
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 16:53 tim
3117	>	2004-12-02 11:53 tim
3118
3119		* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp,
3120		types/DirectionalAtomType.cpp, types/Makefile: oopse get built
3121
3122	<	2004-12-02 16:04 tim
3122	>	2004-12-02 11:04 tim
3123
3124		* src/: applications/simpleBuilder/LatticeCreator.cpp,
3125		applications/simpleBuilder/LatticeCreator.hpp,
#	Line 2179 \| Line 3143
3143		visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still
3144		have two linking problem
3145
3146	<	2004-12-02 05:17 tim
3146	>	2004-12-02 00:17 tim
3147
3148		* src/: applications/dump2Xyz/Dump2XYZ.cpp,
3149		applications/simpleBuilder/Lattice.cpp,
#	Line 2191 \| Line 3155
3155		visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp,
3156		visitors/ZconsVisitor.cpp: change endl to std::endl
3157
3158	<	2004-12-02 05:14 tim
3158	>	2004-12-02 00:14 tim
3159
3160		* src/: UseTheForce/Shapes_FF.cpp,
3161		applications/dump2Xyz/Dump2XYZ.cpp,
#	Line 2207 \| Line 3171
3171		visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
3172		visitors/RigidBodyVisitor.hpp: minor fix
3173
3174	<	2004-12-02 05:09 tim
3174	>	2004-12-02 00:09 tim
3175
3176		* src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp:
3177		remove StreamTokenizer
3178
3179	<	2004-12-02 05:06 tim
3179	>	2004-12-02 00:06 tim
3180
3181		* src/: UseTheForce/Shapes_FF.cpp,
3182		applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp,
#	Line 2221 \| Line 3185
3185		restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using
3186		namespace std in .cpp file
3187
3188	<	2004-12-02 05:04 tim
3188	>	2004-12-02 00:04 tim
3189
3190		* src/: UseTheForce/Shapes_FF.cpp,
3191		applications/dump2Xyz/Dump2XYZ.cpp,
#	Line 2245 \| Line 3209
3209		visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding
3210		qulified name prefix std
3211
3212	<	2004-12-02 04:55 tim
3212	>	2004-12-01 23:55 tim
3213
3214		* src/: UseTheForce/Shapes_FF.cpp,
3215		applications/dump2Xyz/Dump2XYZ.cpp,
#	Line 2261 \| Line 3225
3225		visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
3226		visitors/RigidBodyVisitor.hpp: replace string by std::string
3227
3228	<	2004-12-02 03:12 tim
3228	>	2004-12-01 22:12 tim
3229
3230		* make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp,
3231		src/applications/simpleBuilder/BaseLattice.hpp,
#	Line 2282 \| Line 3246
3246		test/brains/RigidBody.cpp: replace misuse of using namespace std in
3247		header files
3248
3249	<	2004-12-02 02:23 tim
3249	>	2004-12-01 21:23 tim
3250
3251		* src/: primitives/Atom.hpp, primitives/RigidBody.hpp,
3252		primitives/StuntDouble.hpp, utils/TypeContainer.hpp,
3253		utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp:
3254		begin to fix linking problem
3255
3256	<	2004-12-02 02:08 tim
3256	>	2004-12-01 21:08 tim
3257
3258		* src/: applications/oopse/oopse.cpp, brains/Stats.cpp,
3259		brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile,
#	Line 2301 \| Line 3265
3265		utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled,
3266		still has some linking problem
3267
3268	<	2004-12-02 00:26 tim
3268	>	2004-12-01 19:26 tim
3269
3270		* src/: integrators/NVT.cpp, integrators/NVT.hpp,
3271		utils/OOPSEConstant.hpp: NVT get built
3272
3273	<	2004-12-02 00:09 tim
3273	>	2004-12-01 19:09 tim
3274
3275		* src/integrators/DLM.cpp: file DLM.cpp was initially added on
3276		branch new_design.
3277
3278	<	2004-12-02 00:09 tim
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	<	2004-12-02 00:09 tim
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,
#	Line 2328 \| Line 3292
3292		integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE
3293		get built
3294
3295	<	2004-12-02 00:09 tim
3295	>	2004-12-01 19:09 tim
3296
3297		* src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
3298		was initially added on branch new_design.
3299
3300	<	2004-12-01 22:45 tim
3300	>	2004-12-01 17:45 tim
3301
3302		* src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp,
3303		integrators/IntegratorFactory.cpp,
#	Line 2344 \| Line 3308
3308		io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp,
3309		io/StatWriter.hpp: rename DumpWrite to DumpWriter
3310
3311	<	2004-12-01 22:45 tim
3311	>	2004-12-01 17:45 tim
3312
3313		* src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on
3314		branch new_design.
3315
3316	<	2004-12-01 20:05 tim
3316	>	2004-12-01 15:05 tim
3317
3318		* src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp,
3319		io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile,
#	Line 2358 \| Line 3322
3322		visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp,
3323		visitors/ZconsVisitor.hpp: visitors get built
3324
3325	<	2004-12-01 19:32 chrisfen
3325	>	2004-12-01 14:32 chrisfen
3326
3327		* samples/water/tip3p_ice/tp3.md: fixed a sample
3328
3329	<	2004-12-01 19:10 tim
3329	>	2004-12-01 14:10 tim
3330
3331		* src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp,
3332		src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
#	Line 2371 \| Line 3335
3335		src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp:
3336		spell check
3337
3338	<	2004-12-01 18:42 tim
3338	>	2004-12-01 13:42 tim
3339
3340		* src/: UseTheForce/DarkSide/atype.F90,
3341		io/ElectrostaticAtomTypesSectionParser.cpp,
#	Line 2380 \| Line 3344
3344		primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator
3345		and constraint, other directories get built
3346
3347	<	2004-12-01 17:38 tim
3347	>	2004-12-01 12:38 tim
3348
3349		* src/: brains/DataStorage.cpp, brains/DataStorage.hpp,
3350		brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
#	Line 2393 \| Line 3357
3357		types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp:
3358		refactory AtomType
3359
3360	<	2004-12-01 03:11 tim
3360	>	2004-11-30 22:11 tim
3361
3362		* src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change
3363
3364	<	2004-12-01 02:30 tim
3364	>	2004-11-30 21:30 tim
3365
3366		* src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change
3367		NumericConstant
3368
3369	<	2004-12-01 02:24 tim
3369	>	2004-11-30 21:24 tim
3370
3371		* src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp,
3372		primitives/RigidBody.cpp: minor fix
3373
3374	<	2004-11-30 23:14 tim
3374	>	2004-11-30 18:14 tim
3375
3376		* src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp,
3377		io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile,
3378		io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io
3379		get built, next is integrator
3380
3381	<	2004-11-30 22:43 tim
3381	>	2004-11-30 17:43 tim
3382
3383		* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3384		UseTheForce/ForceField.hpp, brains/SimCreator.cpp,
#	Line 2422 \| Line 3386
3386		io/BASS_interface.cpp, primitives/StuntDouble.hpp,
3387		utils/StringUtils.hpp: brains get built
3388
3389	<	2004-11-30 20:50 tim
3389	>	2004-11-30 15:50 tim
3390
3391		* src/: brains/ForceManager.cpp, brains/Makefile,
3392		brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
3393		primitives/RigidBody.cpp, primitives/RigidBody.hpp,
3394		utils/StringUtils.hpp: brains get built, io is next
3395
3396	<	2004-11-30 19:58 tim
3396	>	2004-11-30 14:58 tim
3397
3398		* src/: brains/Exclude.cpp, brains/Exclude.hpp,
3399		brains/ForceManager.cpp, brains/ForceManager.hpp,
#	Line 2440 \| 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 19:58 tim
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 17:54 tim
3412	>	2004-11-30 12:54 tim
3413
3414		* src/: primitives/Bend.hpp, primitives/Bond.hpp,
3415		primitives/StuntDouble.hpp, primitives/Torsion.hpp,
3416		utils/LocalIndexManager.hpp: more get fixed
3417
3418	<	2004-11-30 05:03 tim
3418	>	2004-11-30 00:03 tim
3419
3420		* src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
3421		initially added on branch new_design.
3422
3423	<	2004-11-30 05:03 tim
3423	>	2004-11-30 00:03 tim
3424
3425		* src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
3426		LocalndexManager.hpp to LocalIndexManager.hpp
3427
3428	<	2004-11-30 04:43 tim
3428	>	2004-11-29 23:43 tim
3429
3430		* src/: io/BendTypesSectionParser.cpp,
3431		io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
#	Line 2470 \| Line 3434
3434		types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
3435		types/PolynomialTorsionType.hpp: Section Parsers get compiled
3436
3437	<	2004-11-30 04:14 tim
3437	>	2004-11-29 23:14 tim
3438
3439		* src/: io/BendTypesSectionParser.cpp,
3440		io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
#	Line 2478 \| Line 3442
3442		types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor
3443		fixed
3444
3445	<	2004-11-30 03:49 tim
3445	>	2004-11-29 22:49 tim
3446
3447		* src/: io/TorsionTypesSectionParser.cpp,
3448		io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp,
#	Line 2486 \| Line 3450
3450		types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp,
3451		types/QuarticTorsionType.hpp: minor fixed
3452
3453	<	2004-11-30 03:32 tim
3453	>	2004-11-29 22:32 tim
3454
3455		* src/: io/TorsionTypesSectionParser.cpp,
3456		types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
3457		types/PolynomialTorsionType.hpp: #inlcude statement can not be
3458		embedded
3459
3460	<	2004-11-29 21:42 tim
3460	>	2004-11-29 16:42 tim
3461
3462		* test/math/: Makefile, PolynomialTestCase.cpp,
3463		PolynomialTestCase.hpp: add PolynomialTestCase
3464
3465	<	2004-11-29 21:42 tim
3465	>	2004-11-29 16:42 tim
3466
3467		* src/math/Polynomial.hpp: Polynomial passes unit test
3468
3469	<	2004-11-29 20:03 tim
3469	>	2004-11-29 15:03 tim
3470
3471		* src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename
3472		QuarticTorsion.hpp to QuarticTorsionType.hpp
3473
3474	<	2004-11-29 20:03 tim
3474	>	2004-11-29 15:03 tim
3475
3476		* src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was
3477		initially added on branch new_design.
3478
3479	<	2004-11-29 19:56 tim
3479	>	2004-11-29 14:56 tim
3480
3481		* src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was
3482		initially added on branch new_design.
3483
3484	<	2004-11-29 19:56 tim
3484	>	2004-11-29 14:56 tim
3485
3486		* src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add
3487		CubicTorsionType and QuarticTorsionType
3488
3489	<	2004-11-29 19:56 tim
3489	>	2004-11-29 14:56 tim
3490
3491		* src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was
3492		initially added on branch new_design.
3493
3494	<	2004-11-29 18:00 tim
3494	>	2004-11-29 13:00 tim
3495
3496		* src/: brains/DataStorage.hpp, brains/Snapshot.hpp,
3497		types/CubicBendType.hpp, types/CubicBondType.hpp,
3498		types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get
3499		fixed
3500
3501	<	2004-11-29 17:59 tim
3501	>	2004-11-29 12:59 tim
3502
3503		* src/utils/Trim.hpp: file Trim.hpp was initially added on branch
3504		new_design.
3505
3506	<	2004-11-29 17:59 tim
3506	>	2004-11-29 12:59 tim
3507
3508		* src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim
3509		Algorithm for std::string
3510
3511	<	2004-11-29 15:52 tim
3511	>	2004-11-29 10:52 tim
3512
3513		* src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove
3514		some useless files
3515
3516	<	2004-11-29 15:50 tim
3516	>	2004-11-29 10:50 tim
3517
3518		* src/io/: BondTypesSectionParser.cpp,
3519		ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp,
#	Line 2560 \| Line 3524
3524		SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp,
3525		StickyAtomTypesSectionParser.hpp: more files get fixed
3526
3527	<	2004-11-29 15:27 tim
3527	>	2004-11-29 10:27 tim
3528
3529		* src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp,
3530		DirectionalAtomTypesSectionParser.cpp,
#	Line 2569 \| Line 3533
3533		SectionParserManager.cpp, SectionParserManager.hpp: part of io get
3534		built
3535
3536	<	2004-11-29 14:49 tim
3536	>	2004-11-29 09:49 tim
3537
3538		* src/types/UreyBradleyBendType.hpp: types get built
3539
3540	<	2004-11-29 14:40 tim
3540	>	2004-11-29 09:40 tim
3541
3542		* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp:
3543		types get built
3544
3545	<	2004-11-26 02:13 tim
3545	>	2004-11-25 21:13 tim
3546
3547		* src/: UseTheForce/ForceField.hpp,
3548		io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp,
3549		types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some
3550		files
3551
3552	<	2004-11-25 20:18 tim
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 20:18 tim
3557	>	2004-11-25 15:18 tim
3558
3559		* src/: io/AtomTypesSectionParser.cpp,
3560		io/BondTypesSectionParser.cpp,
#	Line 2599 \| Line 3563
3563		types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some
3564		files
3565
3566	<	2004-11-25 20:18 tim
3566	>	2004-11-25 15:18 tim
3567
3568		* src/types/QuarticBendType.hpp: file QuarticBendType.hpp was
3569		initially added on branch new_design.
3570
3571	<	2004-11-24 22:12 tim
3571	>	2004-11-24 17:12 tim
3572
3573		* src/: io/AtomTypesSectionParser.cpp,
3574		io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp,
#	Line 2627 \| Line 3591
3591		io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
3592		utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built
3593
3594	<	2004-11-24 21:33 tim
3594	>	2004-11-24 16:33 tim
3595
3596		* src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp,
3597		ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp,
3598		LJFF.cpp, Makefile: UseTheForce get built
3599
3600	<	2004-11-24 20:55 tim
3600	>	2004-11-24 15:55 tim
3601
3602		* src/: math/RectMatrix.hpp, primitives/Bend.cpp,
3603		primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp,
#	Line 2643 \| Line 3607
3607		primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp,
3608		primitives/UreyBradleyBend.hpp: types and primitives get built
3609
3610	<	2004-11-24 19:49 tim
3610	>	2004-11-24 14:49 tim
3611
3612		* test/utils/: Makefile, NextCombinationTestCase.cpp,
3613		StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint
3614		StringTokenizerTestCase
3615
3616	<	2004-11-24 19:49 tim
3616	>	2004-11-24 14:49 tim
3617
3618		* src/utils/: GenericData.hpp, StringTokenizer.cpp,
3619		StringTokenizer.hpp: StringTokenizer passes unit test
3620
3621	<	2004-11-24 18:20 tim
3621	>	2004-11-24 13:20 tim
3622
3623		* ChangeLog, make/Makefile.in, src/UseTheForce/Makefile,
3624		src/io/Makefile, src/primitives/Makefile, src/utils/Makefile:
3625		change Makefile
3626
3627	<	2004-11-24 18:06 chrisfen
3627	>	2004-11-24 13:06 chrisfen
3628
3629		* src/io/RestraintReader.cpp: improved restraints - mpi should work
3630		fine
3631
3632	<	2004-11-24 18:06 chrisfen
3632	>	2004-11-24 13:06 chrisfen
3633
3634		* src/integrators/Integrator.cpp: improved restraints
3635
3636	<	2004-11-24 18:05 chrisfen
3636	>	2004-11-24 13:05 chrisfen
3637
3638		* samples/water/tip3p_ice/tp3.md: oops...
3639
3640	<	2004-11-24 17:42 tim
3640	>	2004-11-24 12:42 tim
3641
3642		* src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp,
3643		brains/DataStorage.hpp, brains/SimCreator.cpp,
#	Line 2682 \| Line 3646
3646		primitives/DirectionalAtom.cpp: add SetForceManager method to
3647		integrator
3648
3649	<	2004-11-23 23:12 tim
3649	>	2004-11-23 18:12 tim
3650
3651		* src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp,
3652		integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp,
#	Line 2694 \| Line 3658
3658		integrators/VelocityVerletIntegrator.hpp,
3659		types/UreyBradleyBendType.hpp: refactory NPT integrator
3660
3661	<	2004-11-23 22:50 chrisfen
3661	>	2004-11-23 17:50 chrisfen
3662
3663		* samples/water/tip3p_ice/tp3.md: Back to normal... Oh...
3664		Restraints should work in parallel now
3665
3666	<	2004-11-23 22:48 chrisfen
3666	>	2004-11-23 17:48 chrisfen
3667
3668		* src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
3669		brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
#	Line 2709 \| Line 3673
3673		restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements
3674		to restraints
3675
3676	<	2004-11-23 22:47 chrisfen
3676	>	2004-11-23 17:47 chrisfen
3677
3678		* samples/water/tip3p_ice/tp3.md: just some testing changes, I'll
3679		return to the original on next commit
3680
3681	<	2004-11-23 17:53 tim
3681	>	2004-11-23 12:53 tim
3682
3683		* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3684		UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
#	Line 2727 \| Line 3691
3691		io/SectionParser.hpp, types/DirectionalAtomType.cpp,
3692		utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser
3693
3694	<	2004-11-23 17:53 tim
3694	>	2004-11-23 12:53 tim
3695
3696		* src/io/ElectrostaticAtomTypesSectionParser.hpp: file
3697		ElectrostaticAtomTypesSectionParser.hpp was initially added on
3698		branch new_design.
3699
3700	<	2004-11-23 17:53 tim
3700	>	2004-11-23 12:53 tim
3701
3702		* src/io/ElectrostaticAtomTypesSectionParser.cpp: file
3703		ElectrostaticAtomTypesSectionParser.cpp was initially added on
3704		branch new_design.
3705
3706	<	2004-11-23 06:03 tim
3706	>	2004-11-23 01:03 tim
3707
3708		* src/: io/EAMAtomTypesSectionParser.cpp,
3709		io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp,
3710		types/AtomType.hpp, types/DirectionalAtomType.cpp,
3711		types/DirectionalAtomType.hpp: add EAM AtomType Section Parser
3712
3713	<	2004-11-23 06:03 tim
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 06:03 tim
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 06:03 tim
3724	>	2004-11-23 01:03 tim
3725
3726		* src/io/EAMAtomTypesSectionParser.cpp: file
3727		EAMAtomTypesSectionParser.cpp was initially added on branch
3728		new_design.
3729
3730	<	2004-11-23 04:35 tim
3730	>	2004-11-22 23:35 tim
3731
3732		* src/io/TorsionTypesSectionParser.hpp: file
3733		TorsionTypesSectionParser.hpp was initially added on branch
3734		new_design.
3735
3736	<	2004-11-23 04:35 tim
3736	>	2004-11-22 23:35 tim
3737
3738		* src/io/BendTypesSectionParser.hpp: file
3739		BendTypesSectionParser.hpp was initially added on branch
3740		new_design.
3741
3742	<	2004-11-23 04:35 tim
3742	>	2004-11-22 23:35 tim
3743
3744		* src/io/BondTypesSectionParser.hpp: file
3745		BondTypesSectionParser.hpp was initially added on branch
3746		new_design.
3747
3748	<	2004-11-23 04:35 tim
3748	>	2004-11-22 23:35 tim
3749
3750		* src/io/BondTypesSectionParser.cpp: file
3751		BondTypesSectionParser.cpp was initially added on branch
3752		new_design.
3753
3754	<	2004-11-23 04:35 tim
3754	>	2004-11-22 23:35 tim
3755
3756		* src/io/TorsionTypesSectionParser.cpp: file
3757		TorsionTypesSectionParser.cpp was initially added on branch
3758		new_design.
3759
3760	<	2004-11-23 04:35 tim
3760	>	2004-11-22 23:35 tim
3761
3762		* src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp,
3763		BondTypesSectionParser.cpp, BondTypesSectionParser.hpp,
#	Line 2801 \| Line 3765
3765		BondTypesSectionParser, BendTypesSectionParser and
3766		TorsionTypeSectionParser
3767
3768	<	2004-11-23 04:35 tim
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 23:04 tim
3774	>	2004-11-22 18:04 tim
3775
3776		* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in
3777		DUFF and EAM
3778
3779	<	2004-11-22 23:02 tim
3779	>	2004-11-22 18:02 tim
3780
3781		* src/io/: DirectionalAtomTypesParser.hpp,
3782		DirectionalAtomTypesSectionParser.hpp: adding section parsers
3783
3784	<	2004-11-22 23:02 tim
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
3790	<	2004-11-22 20:55 tim
3790	>	2004-11-22 15:55 tim
3791
3792		* src/io/DipoleAtomTypesSectionParser.hpp: file
3793		DipoleAtomTypesSectionParser.hpp was initially added on branch
3794		new_design.
3795
3796	<	2004-11-22 20:55 tim
3796	>	2004-11-22 15:55 tim
3797
3798		* src/io/AtomTypesSectionParser.hpp: file
3799		AtomTypesSectionParser.hpp was initially added on branch
3800		new_design.
3801
3802	<	2004-11-22 20:55 tim
3802	>	2004-11-22 15:55 tim
3803
3804		* src/io/HarmonicBondTypesSectionParser.hpp: file
3805		HarmonicBondTypesSectionParser.hpp was initially added on branch
3806		new_design.
3807
3808	<	2004-11-22 20:55 tim
3808	>	2004-11-22 15:55 tim
3809
3810		* src/io/StickyAtomTypesSectionParser.cpp: file
3811		StickyAtomTypesSectionParser.cpp was initially added on branch
3812		new_design.
3813
3814	<	2004-11-22 20:55 tim
3814	>	2004-11-22 15:55 tim
3815
3816		* src/io/LennardJonesAtomTypesSectionParser.hpp: file
3817		LennardJonesAtomTypesSectionParser.hpp was initially added on
3818		branch new_design.
3819
3820	<	2004-11-22 20:55 tim
3820	>	2004-11-22 15:55 tim
3821
3822		* src/io/HarmonicBondTypesSectionParser.cpp: file
3823		HarmonicBondTypesSectionParser.cpp was initially added on branch
3824		new_design.
3825
3826	<	2004-11-22 20:55 tim
3826	>	2004-11-22 15:55 tim
3827
3828		* src/io/DirectionalAtomTypesSectionParser.cpp: file
3829		DirectionalAtomTypesSectionParser.cpp was initially added on branch
3830		new_design.
3831
3832	<	2004-11-22 20:55 tim
3832	>	2004-11-22 15:55 tim
3833
3834		* src/io/SectionParserManager.cpp: file SectionParserManager.cpp
3835		was initially added on branch new_design.
3836
3837	<	2004-11-22 20:55 tim
3837	>	2004-11-22 15:55 tim
3838
3839		* src/io/AtomTypesSectionParser.cpp: file
3840		AtomTypesSectionParser.cpp was initially added on branch
3841		new_design.
3842
3843	<	2004-11-22 20:55 tim
3843	>	2004-11-22 15:55 tim
3844
3845		* src/io/ChargeAtomTypesSectionParser.cpp: file
3846		ChargeAtomTypesSectionParser.cpp was initially added on branch
3847		new_design.
3848
3849	<	2004-11-22 20:55 tim
3849	>	2004-11-22 15:55 tim
3850
3851		* src/io/DipoleAtomTypesSectionParser.cpp: file
3852		DipoleAtomTypesSectionParser.cpp was initially added on branch
3853		new_design.
3854
3855	<	2004-11-22 20:55 tim
3855	>	2004-11-22 15:55 tim
3856
3857		* src/io/LennardJonesAtomTypesSectionParser.cpp: file
3858		LennardJonesAtomTypesSectionParser.cpp was initially added on
3859		branch new_design.
3860
3861	<	2004-11-22 20:55 tim
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 20:55 tim
3867	>	2004-11-22 15:55 tim
3868
3869		* src/io/StickyAtomTypesSectionParser.hpp: file
3870		StickyAtomTypesSectionParser.hpp was initially added on branch
3871		new_design.
3872
3873	<	2004-11-22 20:55 tim
3873	>	2004-11-22 15:55 tim
3874
3875		* src/io/SectionParser.hpp: file SectionParser.hpp was initially
3876		added on branch new_design.
3877
3878	<	2004-11-22 20:55 tim
3878	>	2004-11-22 15:55 tim
3879
3880		* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
3881		brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
#	Line 2933 \| Line 3897
3897		types/AtomType.hpp, types/DirectionalAtomType.hpp,
3898		utils/GenericData.hpp: adding section parsers
3899
3900	<	2004-11-22 20:55 tim
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 20:55 tim
3906	>	2004-11-22 15:55 tim
3907
3908		* src/io/SectionParserManager.hpp: file SectionParserManager.hpp
3909		was initially added on branch new_design.
3910
3911	<	2004-11-22 20:55 tim
3911	>	2004-11-22 15:55 tim
3912
3913		* src/io/SectionParser.cpp: file SectionParser.cpp was initially
3914		added on branch new_design.
3915
3916	<	2004-11-19 22:12 tim
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 22:12 tim
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
3927	<	2004-11-19 21:47 tim
3927	>	2004-11-19 16:47 tim
3928
3929		* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp,
3930		integrators/Integrator.cpp, applications/Makedepend: remove more
3931		useless files
3932
3933	<	2004-11-19 21:38 tim
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 21:38 tim
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 21:38 tim
3945	>	2004-11-19 16:38 tim
3946
3947		* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
3948		branch new_design.
3949
3950	<	2004-11-19 21:38 tim
3950	>	2004-11-19 16:38 tim
3951
3952		* src/integrators/NPT.hpp: file NPT.hpp was initially added on
3953		branch new_design.
3954
3955	<	2004-11-19 21:38 tim
3955	>	2004-11-19 16:38 tim
3956
3957		* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
3958		on branch new_design.
3959
3960	<	2004-11-19 21:38 tim
3960	>	2004-11-19 16:38 tim
3961
3962		* src/integrators/NVT.hpp: file NVT.hpp was initially added on
3963		branch new_design.
3964
3965	<	2004-11-19 20:37 tim
3965	>	2004-11-19 15:37 tim
3966
3967		* forceFields/newDUFF.frc: new DUFF forcefield
3968
3969	<	2004-11-19 20:23 tim
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 20:23 tim
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
3979
3980	<	2004-11-19 20:23 tim
3980	>	2004-11-19 15:23 tim
3981
3982		* src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on
3983		branch new_design.
3984
3985	<	2004-11-19 18:02 tim
3985	>	2004-11-19 13:02 tim
3986
3987		* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except
3988		error checking
3989
3990	<	2004-11-19 17:56 tim
3990	>	2004-11-19 12:56 tim
3991
3992		* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
3993		was initially added on branch new_design.
3994
3995	<	2004-11-19 17:56 tim
3995	>	2004-11-19 12:56 tim
3996
3997		* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
3998		was initially added on branch new_design.
3999
4000	<	2004-11-19 17:56 tim
4000	>	2004-11-19 12:56 tim
4001
4002		* src/types/FixBondType.hpp: file FixBondType.hpp was initially
4003		added on branch new_design.
4004
4005	<	2004-11-19 17:56 tim
4005	>	2004-11-19 12:56 tim
4006
4007		* src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp,
4008		UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp,
#	Line 3049 \| Line 4013
4013		utils/StringTokenizer.cpp: DUFF is almost done except error
4014		checking
4015
4016	<	2004-11-19 00:11 tim
4016	>	2004-11-18 19:11 tim
4017
4018		* src/UseTheForce/DUFF.cpp: adding DUFF parser
4019
4020	<	2004-11-18 23:26 tim
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 23:26 tim
4025	>	2004-11-18 18:26 tim
4026
4027		* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp,
4028		integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
#	Line 3070 \| Line 4034
4034		types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding
4035		DUFF parser
4036
4037	<	2004-11-18 21:42 tim
4037	>	2004-11-18 16:42 tim
4038
4039		* forceFields/newDUFF.frc: adding new format DUFF force field
4040
4041	<	2004-11-18 15:57 chrisfen
4041	>	2004-11-18 10:57 chrisfen
4042
4043		* src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that
4044		slowed down the force loop
4045
4046	<	2004-11-18 05:42 tim
4046	>	2004-11-18 00:42 tim
4047
4048		* src/utils/NumericConstant.cpp: file NumericConstant.cpp was
4049		initially added on branch new_design.
4050
4051	<	2004-11-18 05:42 tim
4051	>	2004-11-18 00:42 tim
4052
4053		* src/utils/NumericConstant.hpp: file NumericConstant.hpp was
4054		initially added on branch new_design.
4055
4056	<	2004-11-18 05:42 tim
4056	>	2004-11-18 00:42 tim
4057
4058		* src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp,
4059		primitives/Bend.cpp, utils/NumericConstant.cpp,
4060		utils/NumericConstant.hpp: Adding NumericConstant class
4061
4062	<	2004-11-18 04:16 tim
4062	>	2004-11-17 23:16 tim
4063
4064		* src/: applications/quickLate.c, UseTheForce/ForceFields.cpp,
4065		UseTheForce/ForceFields.hpp: remove more junk files
4066
4067	<	2004-11-18 04:12 tim
4067	>	2004-11-17 23:12 tim
4068
4069		* src/: brains/ForceFields.cpp, brains/SimSetup.cpp,
4070		brains/SimSetup.hpp, constraints/AbstractClasses.hpp,
#	Line 3109 \| Line 4073
4073		primitives/BondExtensions.cpp, primitives/SRI.hpp,
4074		primitives/TorsionExtensions.cpp: remove some junk files
4075
4076	<	2004-11-18 04:07 tim
4076	>	2004-11-17 23:07 tim
4077
4078		* src/primitives/BendExtensions.cpp: remove some junk files
4079
4080	<	2004-11-18 04:04 tim
4080	>	2004-11-17 23:04 tim
4081
4082		* src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp,
4083		QuadraticBondType.hpp: refine QudraticBond
4084
4085	<	2004-11-18 03:57 tim
4085	>	2004-11-17 22:57 tim
4086
4087		* src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp
4088
4089	<	2004-11-18 03:57 tim
4089	>	2004-11-17 22:57 tim
4090
4091		* src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was
4092		initially added on branch new_design.
4093
4094	<	2004-11-17 21:47 tim
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 21:47 tim
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 21:47 tim
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 21:47 tim
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 21:47 tim
4114	>	2004-11-17 16:47 tim
4115
4116		* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
4117		initially added on branch new_design.
4118
4119	<	2004-11-17 21:47 tim
4119	>	2004-11-17 16:47 tim
4120
4121		* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
4122		initially added on branch new_design.
4123
4124	<	2004-11-17 21:47 tim
4124	>	2004-11-17 16:47 tim
4125
4126		* src/types/CubicBondType.hpp: file CubicBondType.hpp was initially
4127		added on branch new_design.
4128
4129	<	2004-11-17 21:47 tim
4129	>	2004-11-17 16:47 tim
4130
4131		* src/: math/ChebyshevPolynomials.cpp,
4132		math/ChebyshevPolynomials.hpp, primitives/Bend.cpp,
#	Line 3174 \| Line 4138
4138		types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp:
4139		UreyBradleyBend and GhostBend
4140
4141	<	2004-11-17 18:58 tim
4141	>	2004-11-17 13:58 tim
4142
4143		* src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp
4144		was initially added on branch new_design.
4145
4146	<	2004-11-17 18:58 tim
4146	>	2004-11-17 13:58 tim
4147
4148		* src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp
4149		was initially added on branch new_design.
4150
4151	<	2004-11-17 18:58 tim
4151	>	2004-11-17 13:58 tim
4152
4153		* src/: math/ChebyshevPolynomials.cpp,
4154		math/ChebyshevPolynomials.hpp, math/Polynomial.hpp,
#	Line 3193 \| Line 4157
4157		types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types
4158		stuff and Chebyshev Polynomial
4159
4160	<	2004-11-17 18:58 tim
4160	>	2004-11-17 13:58 tim
4161
4162		* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
4163		initially added on branch new_design.
4164
4165	<	2004-11-17 06:37 tim
4165	>	2004-11-17 01:37 tim
4166
4167		* src/types/PolynomialTorsionType.hpp: file
4168		PolynomialTorsionType.hpp was initially added on branch new_design.
4169
4170	<	2004-11-17 06:37 tim
4170	>	2004-11-17 01:37 tim
4171
4172		* src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was
4173		initially added on branch new_design.
4174
4175	<	2004-11-17 06:37 tim
4175	>	2004-11-17 01:37 tim
4176
4177		* src/: math/Polynomial.hpp, primitives/Bend.cpp,
4178		primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp,
#	Line 3222 \| Line 4186
4186		CharmmTorsionType. Need to refine the design and add document for
4187		them
4188
4189	<	2004-11-17 06:37 tim
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 06:37 tim
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 06:37 tim
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	<	2004-11-17 01:11 tim
4204	>	2004-11-16 20:11 tim
4205
4206		* src/types/: BendType.hpp, PolynomialBondType.hpp,
4207		TorsionType.hpp: add PolynomialBondType
4208
4209	<	2004-11-17 01:11 tim
4209	>	2004-11-16 20:11 tim
4210
4211		* src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was
4212		initially added on branch new_design.
4213
4214	<	2004-11-16 23:20 tim
4214	>	2004-11-16 18:20 tim
4215
4216		* src/math/Polynomial.hpp: file Polynomial.hpp was initially added
4217		on branch new_design.
4218
4219	<	2004-11-16 23:20 tim
4219	>	2004-11-16 18:20 tim
4220
4221		* src/math/Polynomial.hpp: Adding Polynomial class
4222
4223	<	2004-11-16 22:04 gezelter
4223	>	2004-11-16 17:04 gezelter
4224
4225		* src/types/MorseBondType.hpp: file MorseBondType.hpp was initially
4226		added on branch new_design.
4227
4228	<	2004-11-16 22:04 gezelter
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 22:04 gezelter
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
4238	<	2004-11-16 20:36 tim
4238	>	2004-11-16 15:36 tim
4239
4240		* src/: primitives/Bend.cpp, primitives/Bend.hpp,
4241		primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp,
4242		types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and
4243		TorsionType
4244
4245	<	2004-11-16 02:07 tim
4245	>	2004-11-15 21:07 tim
4246
4247		* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
4248		branch new_design.
4249
4250	<	2004-11-16 02:07 tim
4250	>	2004-11-15 21:07 tim
4251
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 23:00 tim
4257	>	2004-11-15 18:00 tim
4258
4259		* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
4260		UseTheForce/ForceFieldFactory.cpp,
#	Line 3298 \| Line 4262
4262		UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp,
4263		types/AtomType.hpp: adding ForceFieldFactory and LJFF classes
4264
4265	<	2004-11-15 23:00 tim
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 23:00 tim
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 23:00 tim
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 18:02 tim
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 18:02 tim
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
4290	<	2004-11-15 18:02 tim
4290	>	2004-11-15 13:02 tim
4291
4292		* src/io/DumpReader.hpp: file DumpReader.hpp was initially added on
4293		branch new_design.
4294
4295	<	2004-11-15 18:02 tim
4295	>	2004-11-15 13:02 tim
4296
4297		* src/: brains/SimInfo.cpp, brains/SimInfo.hpp,
4298		brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
#	Line 3336 \| Line 4300
4300		io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader,
4301		DumpWriter.Next Step is LJFF and integrators
4302
4303	<	2004-11-13 05:08 tim
4303	>	2004-11-13 00:08 tim
4304
4305		* src/: brains/ForceManager.cpp, brains/ForceManager.hpp,
4306		brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
#	Line 3344 \| Line 4308
4308		primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory,
4309		refactory, refactory
4310
4311	<	2004-11-12 22:43 tim
4311	>	2004-11-12 17:43 tim
4312
4313		* src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp,
4314		StringTokenizer.cpp: bug fix in hasMoreTokens
4315
4316	<	2004-11-12 22:28 tim
4316	>	2004-11-12 17:28 tim
4317
4318		* src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was
4319		initially added on branch new_design.
4320
4321	<	2004-11-12 22:28 tim
4321	>	2004-11-12 17:28 tim
4322
4323		* src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding
4324		StringUtils, a c-style strtok like class, need unit test
4325
4326	<	2004-11-12 17:40 tim
4326	>	2004-11-12 12:40 tim
4327
4328		* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
4329		brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
4330		brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test
4331
4332	<	2004-11-12 07:05 tim
4332	>	2004-11-12 02:05 tim
4333
4334		* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
4335		primitives/CutoffGroup.hpp, primitives/Molecule.cpp:
4336		MoleculeCreator forget to create CutoffGroups for free atoms
4337
4338	<	2004-11-12 06:19 tim
4338	>	2004-11-12 01:19 tim
4339
4340		* src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
4341		brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
#	Line 3379 \| Line 4343
4343		io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp:
4344		OOPSE = Object-Obfuscated Parallel Simulation Engine
4345
4346	<	2004-11-11 21:48 chrisfen
4346	>	2004-11-11 16:48 chrisfen
4347
4348		* samples/water/tip3p_ice/tp3.md: working sample
4349
4350	<	2004-11-11 21:47 chrisfen
4350	>	2004-11-11 16:47 chrisfen
4351
4352		* src/restraints/Restraints.cpp: working towards parallel
4353		restraints
4354
4355	<	2004-11-11 21:47 chrisfen
4355	>	2004-11-11 16:47 chrisfen
4356
4357		* src/integrators/Integrator.cpp: Commented out some write
4358		statements
4359
4360	<	2004-11-11 21:46 chrisfen
4360	>	2004-11-11 16:46 chrisfen
4361
4362		* src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some
4363		write statements
4364
4365	<	2004-11-11 21:46 chrisfen
4365	>	2004-11-11 16:46 chrisfen
4366
4367		* samples/water/tip3p_ice/tp3.md: Fun with ice
4368
4369	<	2004-11-11 16:41 tim
4369	>	2004-11-11 11:41 tim
4370
4371		* src/: brains/Exclude.cpp, brains/Exclude.hpp,
4372		brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
#	Line 3411 \| Line 4375
4375		io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove
4376		useless mpiSimulation
4377
4378	<	2004-11-11 16:41 tim
4378	>	2004-11-11 11:41 tim
4379
4380		* src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on
4381		branch new_design.
4382
4383	<	2004-11-10 22:50 tim
4383	>	2004-11-10 17:50 tim
4384
4385		* src/: brains/ForceManager.cpp, brains/SimInfo.cpp,
4386		brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp,
4387		integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo
4388
4389	<	2004-11-10 22:01 tim
4389	>	2004-11-10 17:01 tim
4390
4391		* src/: brains/SimCreator.cpp, brains/SimCreator.hpp,
4392		brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
#	Line 3436 \| Line 4400
4400		BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors &
4401		Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint
4402
4403	<	2004-11-10 14:52 tim
4403	>	2004-11-10 09:52 tim
4404
4405		* src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a
4406		configurable StatWriter
4407
4408	<	2004-11-10 14:52 tim
4408	>	2004-11-10 09:52 tim
4409
4410		* src/io/StatWriter.hpp: file StatWriter.hpp was initially added on
4411		branch new_design.
4412
4413	<	2004-11-10 02:58 tim
4413	>	2004-11-09 21:58 tim
4414
4415		* src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation
4416		in progress
4417
4418	<	2004-11-09 23:11 tim
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 23:11 tim
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 23:11 tim
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,
#	Line 3471 \| Line 4435
4435		integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp,
4436		integrators/VelocityVerletIntegrator.hpp: adding ForceManager
4437
4438	<	2004-11-09 23:11 tim
4438	>	2004-11-09 18:11 tim
4439
4440		* src/brains/ForceManager.hpp: file ForceManager.hpp was initially
4441		added on branch new_design.
4442
4443	<	2004-11-09 23:11 tim
4443	>	2004-11-09 18:11 tim
4444
4445		* src/integrators/NVE.cpp: file NVE.cpp was initially added on
4446		branch new_design.
4447
4448	<	2004-11-09 01:08 tim
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	<	2004-11-09 01:08 tim
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	<	2004-11-09 01:08 tim
4459	>	2004-11-08 20:08 tim
4460
4461		* src/: brains/Exclude.hpp, brains/Stats.hpp,
4462		integrators/Integrator.hpp, integrators/NVE.hpp,
4463		integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
4464		utils/TypeContainer.hpp: More to break
4465
4466	<	2004-11-06 05:21 tim
4466	>	2004-11-06 00:21 tim
4467
4468		* src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially
4469		added on branch new_design.
4470
4471	<	2004-11-06 05:21 tim
4471	>	2004-11-06 00:21 tim
4472
4473		* src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp,
4474		UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp,
4475		utils/TypeContainer.hpp, utils/next_combination.hpp: adding
4476		ForceField and TypeContainer classes
4477
4478	<	2004-11-05 23:38 tim
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 23:38 tim
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
4488	<	2004-11-05 23:38 tim
4488	>	2004-11-05 18:38 tim
4489
4490		* src/: brains/Exclude.cpp, brains/Exclude.hpp,
4491		brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
#	Line 3529 \| Line 4493
4493		brains/SimInfo.hpp, primitives/Molecule.hpp,
4494		utils/LocalndexManager.hpp: Fix Exclude class etc.
4495
4496	<	2004-11-05 21:45 chrisfen
4496	>	2004-11-05 16:45 chrisfen
4497
4498		* src/: applications/dump2Xyz/Dump2XYZ.cpp,
4499		visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the
4500		linear visitor
4501
4502	<	2004-11-05 21:04 chrisfen
4502	>	2004-11-05 16:04 chrisfen
4503
4504		* src/UseTheForce/DarkSide/shapes.F90: current status of the
4505		debugging process
4506
4507	<	2004-11-05 21:04 chrisfen
4507	>	2004-11-05 16:04 chrisfen
4508
4509		* make/Makefile.in: included visitors and minimizer
4510
4511	<	2004-11-05 21:03 chrisfen
4511	>	2004-11-05 16:03 chrisfen
4512
4513		* ChangeLog: new changes
4514
4515	<	2004-11-05 02:56 tim
4515	>	2004-11-04 21:56 tim
4516
4517		* src/: brains/SimCreator.cpp, brains/SimCreator.hpp,
4518		primitives/Molecule.hpp: Pain......
4519
4520	<	2004-11-04 20:55 tim
4520	>	2004-11-04 15:55 tim
4521
4522		* ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp,
4523		src/brains/SimCreator.hpp, src/brains/SimInfo.hpp,
4524		src/brains/Stats.hpp: time to break SimSetup
4525
4526	<	2004-11-04 20:51 gezelter
4526	>	2004-11-04 15:51 gezelter
4527
4528		* src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new
4529		classes in progress
4530
4531	<	2004-11-04 19:48 tim
4531	>	2004-11-04 14:48 tim
4532
4533		* src/brains/Stats.cpp: file Stats.cpp was initially added on
4534		branch new_design.
4535
4536	<	2004-11-04 19:48 tim
4536	>	2004-11-04 14:48 tim
4537
4538		* src/brains/Stats.hpp: file Stats.hpp was initially added on
4539		branch new_design.
4540
4541	<	2004-11-04 19:48 tim
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 16:22 gezelter
4547	>	2004-11-04 11:22 gezelter
4548
4549		* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp,
4550		RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and
#	Line 3589 \| Line 4553
4553		false and "-1" but there should be logic to figure them out in the
4554		other two classes
4555
4556	<	2004-11-04 16:20 gezelter
4556	>	2004-11-04 11:20 gezelter
4557
4558		* src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't
4559		remember what I did
4560
4561	<	2004-11-04 16:20 gezelter
4561	>	2004-11-04 11:20 gezelter
4562
4563		* src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky
4564
4565	<	2004-11-04 16:20 gezelter
4565	>	2004-11-04 11:20 gezelter
4566
4567		* src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX
4568		in the entry_plug so that it only is set if the atoms really are in
4569		the simulation
4570
4571	<	2004-11-04 16:20 gezelter
4571	>	2004-11-04 11:20 gezelter
4572
4573		* samples/water/ssd/ssd.md: testing force fields
4574
4575	<	2004-11-04 16:19 gezelter
4575	>	2004-11-04 11:19 gezelter
4576
4577		* samples/shape/linear.in: testing shapes
4578
4579	<	2004-11-03 19:56 tim
4579	>	2004-11-03 14:56 tim
4580
4581		* src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator
4582		class(similar as SimSetup)
4583
4584	<	2004-11-03 19:56 tim
4584	>	2004-11-03 14:56 tim
4585
4586		* src/brains/SimCreator.hpp: file SimCreator.hpp was initially
4587		added on branch new_design.
4588
4589	<	2004-11-03 19:56 tim
4589	>	2004-11-03 14:56 tim
4590
4591		* src/brains/SimCreator.cpp: file SimCreator.cpp was initially
4592		added on branch new_design.
4593
4594	<	2004-11-03 18:00 tim
4594	>	2004-11-03 13:00 tim
4595
4596		* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4597		UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp,
#	Line 3637 \| Line 4601
4601		visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get
4602		compiled. Still a long way to go ......
4603
4604	<	2004-11-03 16:08 tim
4604	>	2004-11-03 11:08 tim
4605
4606		* ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp,
4607		src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp,
#	Line 3652 \| Line 4616
4616		src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp,
4617		src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ......
4618
4619	<	2004-11-02 22:41 tim
4619	>	2004-11-02 17:41 tim
4620
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 22:41 tim
4625	>	2004-11-02 17:41 tim
4626
4627		* src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was
4628		initially added on branch new_design.
4629
4630	<	2004-11-02 22:41 tim
4630	>	2004-11-02 17:41 tim
4631
4632		* src/brains/Migrator.hpp: file Migrator.hpp was initially added on
4633		branch new_design.
4634
4635	<	2004-11-02 16:59 tim
4635	>	2004-11-02 11:59 tim
4636
4637		* src/brains/SimModel.cpp: file SimModel.cpp was initially added on
4638		branch new_design.
4639
4640	<	2004-11-02 16:59 tim
4640	>	2004-11-02 11:59 tim
4641
4642		* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
4643		SimSnapshotManager.hpp: SimModel in progress
4644
4645	<	2004-11-02 15:28 chrisfen
4645	>	2004-11-02 10:28 chrisfen
4646
4647		* src/: UseTheForce/DarkSide/shapes.F90,
4648		primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes
4649		looks like it's working
4650
4651	<	2004-11-02 15:27 tim
4651	>	2004-11-02 10:27 tim
4652
4653		* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
4654		functions for dealing with memory issue
4655
4656	<	2004-11-02 15:27 tim
4656	>	2004-11-02 10:27 tim
4657
4658		* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
4659		added on branch new_design.
4660
4661	<	2004-11-02 15:23 tim
4661	>	2004-11-02 10:23 tim
4662
4663		* src/: brains/SimModel.hpp, brains/Snapshot.hpp,
4664		brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding
4665		SimModel(something similar as SimInfo)
4666
4667	<	2004-11-01 22:52 tim
4667	>	2004-11-01 17:52 tim
4668
4669		* src/: applications/simpleBuilder/MoLocator.hpp,
4670		applications/simpleBuilder/simpleBuilder.cpp,
#	Line 3719 \| Line 4683
4683		visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom,
4684		RigidBody and StuntDouble classes get compiled
4685
4686	<	2004-11-01 21:40 tim
4686	>	2004-11-01 16:40 tim
4687
4688		* src/primitives/Torsion.hpp: file Torsion.hpp was initially added
4689		on branch new_design.
4690
4691	<	2004-11-01 21:40 tim
4691	>	2004-11-01 16:40 tim
4692
4693		* src/primitives/Bend.hpp: file Bend.hpp was initially added on
4694		branch new_design.
4695
4696	<	2004-11-01 21:40 tim
4696	>	2004-11-01 16:40 tim
4697
4698		* src/primitives/Bond.hpp: file Bond.hpp was initially added on
4699		branch new_design.
4700
4701	<	2004-11-01 21:40 tim
4701	>	2004-11-01 16:40 tim
4702
4703		* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
4704		version of Bond, Bend and Torsion.
4705
4706	<	2004-11-01 21:37 tim
4706	>	2004-11-01 16:37 tim
4707
4708		* src/types/BendType.hpp: file BendType.hpp was initially added on
4709		branch new_design.
4710
4711	<	2004-11-01 21:37 tim
4711	>	2004-11-01 16:37 tim
4712
4713		* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
4714		BondType, BendType, TorsionType
4715
4716	<	2004-11-01 21:37 tim
4716	>	2004-11-01 16:37 tim
4717
4718		* src/types/TorsionType.hpp: file TorsionType.hpp was initially
4719		added on branch new_design.
4720
4721	<	2004-11-01 21:37 tim
4721	>	2004-11-01 16:37 tim
4722
4723		* src/types/BondType.hpp: file BondType.hpp was initially added on
4724		branch new_design.
4725
4726	<	2004-11-01 20:15 tim
4726	>	2004-11-01 15:15 tim
4727
4728		* src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp,
4729		CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp,
#	Line 3767 \| Line 4731
4731		RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp:
4732		break, break and break.....
4733
4734	<	2004-11-01 19:57 tim
4734	>	2004-11-01 14:57 tim
4735
4736		* test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp,
4737		DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp,
4738		StuntDouble.hpp: these core classes get compiled
4739
4740	<	2004-10-29 22:37 tim
4740	>	2004-10-29 17:37 tim
4741
4742		* test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule
4743		class
4744
4745	<	2004-10-29 22:28 chrisfen
4745	>	2004-10-29 17:28 chrisfen
4746
4747		* src/: UseTheForce/DarkSide/atype.F90,
4748		UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp,
4749		types/ShapeAtomType.cpp: still debugging
4750
4751	<	2004-10-29 22:28 chrisfen
4751	>	2004-10-29 17:28 chrisfen
4752
4753		* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90:
4754		shapes rcut calculator added
4755
4756	<	2004-10-29 22:27 chrisfen
4756	>	2004-10-29 17:27 chrisfen
4757
4758		* samples/shape/linear.md: shorter run
4759
4760	<	2004-10-29 20:54 tim
4760	>	2004-10-29 15:54 tim
4761
4762		* test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class.
4763
4764	<	2004-10-29 16:22 tim
4764	>	2004-10-29 11:22 tim
4765
4766		* test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp,
4767		ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove
4768		some deprecated files
4769
4770	<	2004-10-29 16:20 tim
4770	>	2004-10-29 11:20 tim
4771
4772		* test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp,
4773		DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp:
4774		More painful reconstruction is coming !!!
4775
4776	<	2004-10-28 22:34 tim
4776	>	2004-10-28 17:34 tim
4777
4778		* src/brains/DataStorage.hpp, src/utils/next_combination.hpp,
4779		test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp,
#	Line 3817 \| Line 4781
4781		test/brains/StuntDouble.hpp: More work on StuntDouble, Atom,
4782		DirectionalAtom and RigidBody
4783
4784	<	2004-10-28 22:26 tim
4784	>	2004-10-28 17:26 tim
4785
4786		* ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp,
4787		src/applications/simpleBuilder/MoLocator.cpp,
#	Line 3825 \| Line 4789
4789		src/utils/GenericFactory.hpp, src/utils/next_combination.hpp:
4790		remove old Vector3d.hpp from application/simpleBuilder
4791
4792	<	2004-10-28 21:42 tim
4792	>	2004-10-28 16:42 tim
4793
4794		* src/utils/next_combination.hpp: Minor change in next_combination
4795
4796	<	2004-10-28 21:28 tim
4796	>	2004-10-28 16:28 tim
4797
4798		* src/utils/next_combination.hpp,
4799		test/utils/NextCombinationTestCase.cpp,
4800		test/utils/ReplaceWildCardTestCase.cpp: Done with combination
4801
4802	<	2004-10-28 21:11 tim
4802	>	2004-10-28 16:11 tim
4803
4804		* src/utils/next_combination.hpp: change documentation of
4805		next_combination.hpp
4806
4807	<	2004-10-28 20:41 tim
4807	>	2004-10-28 15:41 tim
4808
4809		* ChangeLog, src/utils/next_combination.hpp,
4810		test/utils/NextCombinationTestCase.cpp,
4811		test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working
4812
4813	<	2004-10-28 20:01 tim
4813	>	2004-10-28 15:01 tim
4814
4815		* src/utils/next_combination.hpp: adding replace wildcard function
4816
4817	<	2004-10-28 19:33 tim
4817	>	2004-10-28 14:33 tim
4818
4819		* src/utils/next_combination.hpp: Minor change
4820
4821	<	2004-10-28 19:06 tim
4821	>	2004-10-28 14:06 tim
4822
4823		* ChangeLog, src/applications/simpleBuilder/MoLocator.hpp,
4824		src/applications/simpleBuilder/simpleBuilder.cpp,
#	Line 3864 \| Line 4828
4828		test/utils/next_combination.hpp: STL next_permutation like
4829		next_combination is working
4830
4831	<	2004-10-28 17:22 chrisfen
4831	>	2004-10-28 12:22 chrisfen
4832
4833		* src/UseTheForce/WATER.cpp: fix of setDipoles
4834
4835	<	2004-10-28 17:20 gezelter
4835	>	2004-10-28 12:20 gezelter
4836
4837		* src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the
4838		shapeFile
4839
4840	<	2004-10-28 17:20 gezelter
4840	>	2004-10-28 12:20 gezelter
4841
4842		* samples/shape/linear.md: forgot the orientation line
4843
4844	<	2004-10-28 16:56 gezelter
4844	>	2004-10-28 11:56 gezelter
4845
4846		* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4847		UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
4848		UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate
4849		declaration foo
4850
4851	<	2004-10-28 16:55 gezelter
4851	>	2004-10-28 11:55 gezelter
4852
4853		* samples/lipid/5x5.md: uncommented .in line
4854
4855	<	2004-10-28 15:42 tim
4855	>	2004-10-28 10:42 tim
4856
4857		* test/utils/: Makefile, NextCombinationTestCase.cpp,
4858		NextCombinationTestCase.hpp, next_combination.hpp: next_combination
4859		in progress
4860
4861	<	2004-10-28 15:15 tim
4861	>	2004-10-28 10:15 tim
4862
4863		* test/utils/: NextCombinationTestCase.cpp,
4864		NextCombinationTestCase.hpp: adding next_combination test case
4865
4866	<	2004-10-28 15:02 tim
4866	>	2004-10-28 10:02 tim
4867
4868		* test/utils/next_combination.hpp: STL Compatible combination
4869		sequence generator
4870
4871	<	2004-10-28 06:23 tim
4871	>	2004-10-28 01:23 tim
4872
4873		* test/utils/: GenerateCombination.hpp,
4874		ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp
4875
4876	<	2004-10-28 06:16 tim
4876	>	2004-10-28 01:16 tim
4877
4878		* test/utils/GenerateCombination.hpp: a STL next_permutaion like
4879		next_combination function.
4880
4881	<	2004-10-28 03:27 tim
4881	>	2004-10-27 22:27 tim
4882
4883		* test/utils/ReplaceWildCard.hpp: no message
4884
4885	<	2004-10-28 03:14 tim
4885	>	2004-10-27 22:14 tim
4886
4887		* test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp:
4888		ReplaceWildCard(recursive version) is working, need refactoring. An
4889		iterative version is on the way
4890
4891	<	2004-10-28 02:28 tim
4891	>	2004-10-27 21:28 tim
4892
4893		* test/utils/: Makefile, ReplaceWildCard.hpp,
4894		ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress
4895
4896	<	2004-10-28 02:08 tim
4896	>	2004-10-27 21:08 tim
4897
4898		* test/utils/: ReplaceWildCardTestCase.cpp,
4899		ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard
4900
4901	<	2004-10-27 23:17 tim
4901	>	2004-10-27 18:17 tim
4902
4903		* test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need
4904		test
4905
4906	<	2004-10-27 06:25 tim
4906	>	2004-10-27 01:25 tim
4907
4908		* src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild
4909		char matching is on the way
4910
4911	<	2004-10-27 06:07 tim
4911	>	2004-10-27 01:07 tim
4912
4913		* src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4
4914
4915	<	2004-10-27 03:00 gezelter
4915	>	2004-10-26 22:00 gezelter
4916
4917		* src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix
4918
4919	<	2004-10-27 02:20 gezelter
4919	>	2004-10-26 21:20 gezelter
4920
4921		* src/UseTheForce/ForceFields.hpp: subclass foo
4922
4923	<	2004-10-27 02:16 gezelter
4923	>	2004-10-26 21:16 gezelter
4924
4925		* src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* ->
4926		string conversion
4927
4928	<	2004-10-27 00:01 gezelter
4928	>	2004-10-26 19:01 gezelter
4929
4930		* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4931		UseTheForce/ForceFields.hpp, brains/SimSetup.cpp,
4932		brains/SimSetup.hpp: char* -> string
4933
4934	<	2004-10-26 22:25 gezelter
4934	>	2004-10-26 17:25 gezelter
4935
4936		* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp,
4937		Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp,
4938		ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some
4939		isXXX
4940
4941	<	2004-10-26 22:25 gezelter
4941	>	2004-10-26 17:25 gezelter
4942
4943		* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
4944		define name collision
4945
4946	<	2004-10-26 22:24 gezelter
4946	>	2004-10-26 17:24 gezelter
4947
4948		* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4949		UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
#	Line 3988 \| Line 4952
4952		UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp:
4953		forcefield refactoring for shapes
4954
4955	<	2004-10-26 22:24 gezelter
4955	>	2004-10-26 17:24 gezelter
4956
4957		* samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape,
4958		Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in,
4959		linear.md, linear.shape, toluene.shape: adding sample shape
4960		directory
4961
4962	<	2004-10-26 22:19 tim
4962	>	2004-10-26 17:19 tim
4963
4964		* ChangeLog, src/brains/DataStorage.cpp,
4965		src/brains/DataStorage.hpp, src/brains/Snapshot.hpp,
#	Line 4003 \| Line 4967
4967		test/brains/DataStorageTestCase.hpp, test/brains/Makefile:
4968		DataStorage passes unit test
4969
4970	<	2004-10-26 18:03 chrisfen
4970	>	2004-10-26 13:03 chrisfen
4971
4972		* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h:
4973		Changes to help advance shapes
4974
4975	<	2004-10-26 18:02 chrisfen
4975	>	2004-10-26 13:02 chrisfen
4976
4977		* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to
4978		Shapes force field reader
4979
4980	<	2004-10-26 17:28 tim
4980	>	2004-10-26 12:28 tim
4981
4982		* src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and
4983		SnapshotTestCase in progress
4984
4985	<	2004-10-25 22:46 tim
4985	>	2004-10-25 17:46 tim
4986
4987		* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
4988		src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
#	Line 4027 \| Line 4991
4991		test/math/VectorTestCase.cpp: add getArray function to RectMatrix
4992		and Vector classes
4993
4994	<	2004-10-25 17:03 tim
4994	>	2004-10-25 12:03 tim
4995
4996		* ChangeLog, src/utils/GenericFactory.hpp,
4997		test/utils/GenericFactoryTestCase.cpp,
#	Line 4035 \| Line 4999
4999		GenericFactory Test Case. GenericFactory now can bed used to creat
5000		ForcefieldFactory and IntegratorFactory etc.
5001
5002	<	2004-10-25 04:08 tim
5002	>	2004-10-24 23:08 tim
5003
5004		* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp,
5005		brains/SimSnapshotManager.hpp, brains/Snapshot.hpp,
5006		brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes
5007		get reconstructed
5008
5009	<	2004-10-24 07:55 tim
5009	>	2004-10-24 02:55 tim
5010
5011		* src/utils/GenericFactory.hpp: GenericFactory pass unit test
5012
5013	<	2004-10-23 23:09 tim
5013	>	2004-10-23 18:09 tim
5014
5015		* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp,
5016		StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp,
5017		RigidBody.cpp: Refactoring in progress
5018
5019	<	2004-10-22 23:09 tim
5019	>	2004-10-22 18:09 tim
5020
5021		* ChangeLog, src/brains/Snapshot.hpp,
5022		src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp,
5023		test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp,
5024		test/brains/StuntDouble.hpp: more work in Snapshot
5025
5026	<	2004-10-22 22:59 chrisfen
5026	>	2004-10-22 17:59 chrisfen
5027
5028		* src/: UseTheForce/LJFF.cpp,
5029		UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear
5030		god! It runs and conserves energy!
5031
5032	<	2004-10-22 22:54 chrisfen
5032	>	2004-10-22 17:54 chrisfen
5033
5034		* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY
5035
5036	<	2004-10-22 22:53 chrisfen
5036	>	2004-10-22 17:53 chrisfen
5037
5038		* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
5039		UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
#	Line 4077 \| Line 5041
5041		brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey
5042		breakey
5043
5044	<	2004-10-22 22:53 chrisfen
5044	>	2004-10-22 17:53 chrisfen
5045
5046		* make/Makefile.in: compiler flags
5047
5048	<	2004-10-22 21:20 gezelter
5048	>	2004-10-22 16:20 gezelter
5049
5050		* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
5051		UseTheForce/LJFF.cpp, UseTheForce/doForces.F90,
5052		brains/fSimulation.h, types/AtomType.hpp,
5053		types/DirectionalAtomType.hpp: fixey fixey
5054
5055	<	2004-10-22 20:22 gezelter
5055	>	2004-10-22 15:22 gezelter
5056
5057		* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h,
5058		charge.F90, charge_interface.h, dipole.F90, dipole_interface.h,
5059		lj_interface.h, shapes.F90, simulation.F90: Added un-busticated
5060		fortran files and c/Fortran interfaces
5061
5062	<	2004-10-22 20:21 gezelter
5062	>	2004-10-22 15:21 gezelter
5063
5064		* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
5065		DirectionalAtomType.hpp, Makefile: More on AtomType and
5066		DirectionalAtomType
5067
5068	<	2004-10-22 14:47 gezelter
5068	>	2004-10-22 09:47 gezelter
5069
5070		* src/types/AtomType.hpp: Adding AtomType
5071
5072	<	2004-10-21 21:31 tim
5072	>	2004-10-21 16:31 tim
5073
5074		* ChangeLog, src/brains/Snapshot.hpp,
5075		src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp,
#	Line 4114 \| Line 5078
5078		test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp:
5079		Snapshot and SnapshotManager in progress
5080
5081	<	2004-10-21 21:30 tim
5081	>	2004-10-21 16:30 tim
5082
5083		* test/brains/: BrainsTest.cpp, Makefile,
5084		SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp,
5085		SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for
5086		Snapshot and snapshotManager.
5087
5088	<	2004-10-21 20:15 gezelter
5088	>	2004-10-21 15:15 gezelter
5089
5090		* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
5091		UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
#	Line 4132 \| Line 5096
5096		brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky.
5097		Fixey Fixey.
5098
5099	<	2004-10-21 16:32 tim
5099	>	2004-10-21 11:32 tim
5100
5101		* src/utils/GenericData.cpp, src/utils/Makefile,
5102		test/utils/Makefile, test/utils/UtilTest: remove some junk files
5103
5104	<	2004-10-21 16:24 tim
5104	>	2004-10-21 11:24 tim
5105
5106		* test/utils/GenericData.hpp: remove backup of GenericData.hpp
5107
5108	<	2004-10-21 16:22 tim
5108	>	2004-10-21 11:22 tim
5109
5110		* ChangeLog, src/brains/SimSetup.cpp,
5111		src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp,
#	Line 4159 \| Line 5123
5123		src/visitors/ZconsVisitor.hpp: replace old GebericData with new
5124		GenericData
5125
5126	<	2004-10-21 15:25 chuckv
5126	>	2004-10-21 10:25 chuckv
5127
5128		* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj
5129		module.
5130
5131	<	2004-10-21 15:24 chuckv
5131	>	2004-10-21 10:24 chuckv
5132
5133		* src/UseTheForce/DarkSide/lj_interface.h: Added interface for
5134		fortran lj module.
5135
5136	<	2004-10-20 22:54 tim
5136	>	2004-10-20 17:54 tim
5137
5138		* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp,
5139		test/utils/GenericDataTestCase.cpp, test/utils/Makefile,
#	Line 4177 \| Line 5141
5141		test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest:
5142		GenericData and PropertyMap pass unit test.
5143
5144	<	2004-10-20 21:52 gezelter
5144	>	2004-10-20 16:52 gezelter
5145
5146		* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90,
5147		DarkSide/sticky_interface.h: fixed a fortran name problem
5148
5149	<	2004-10-20 21:38 tim
5149	>	2004-10-20 16:38 tim
5150
5151		* test/utils/: GenericData.hpp, GenericDataTestCase.cpp,
5152		GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp,
5153		UtilTest, UtilTest.cpp: adding generic data test case
5154
5155	<	2004-10-20 21:16 chuckv
5155	>	2004-10-20 16:16 chuckv
5156
5157		* configure, ac-tools/aclocal.m4,
5158		src/UseTheForce/DarkSide/Makefile,
#	Line 4200 \| Line 5164
5164		Fortran/C++ interface de-obfuscation project appears to be
5165		complete! Woo hoo!
5166
5167	<	2004-10-20 20:47 chuckv
5167	>	2004-10-20 15:47 chuckv
5168
5169		* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp,
5170		fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project
5171		continues
5172
5173	<	2004-10-20 20:46 chuckv
5173	>	2004-10-20 15:46 chuckv
5174
5175		* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
5176		UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
#	Line 4223 \| Line 5187
5187		brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface
5188		de-obfuscation project (It is a very long story)
5189
5190	<	2004-10-20 18:07 tim
5190	>	2004-10-20 13:07 tim
5191
5192		* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
5193		test/math/SquareMatrix3TestCase.cpp,
5194		test/math/SquareMatrixTestCase.cpp,
5195		test/math/SquareMatrixTestCase.hpp: Math library pass the unit test
5196
5197	<	2004-10-20 05:52 tim
5197	>	2004-10-20 00:52 tim
5198
5199		* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and
5200		SnapshotManager in design phase
5201
5202	<	2004-10-20 04:54 gezelter
5202	>	2004-10-19 23:54 gezelter
5203
5204		* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace
5205		problem prevented linking
5206
5207	<	2004-10-20 04:54 gezelter
5207	>	2004-10-19 23:54 gezelter
5208
5209		* src/UseTheForce/Shapes_FF.cpp: fixed include
5210
5211	<	2004-10-20 04:26 gezelter
5211	>	2004-10-19 23:26 gezelter
5212
5213		* src/utils/: Makefile, definitions.F90, definitions_module.F90,
5214		oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90:
5215		more fortran name mangling
5216
5217	<	2004-10-20 04:23 gezelter
5217	>	2004-10-19 23:23 gezelter
5218
5219		* src/profiling/timing.F90: yet more fortran renaming
5220
5221	<	2004-10-20 04:19 gezelter
5221	>	2004-10-19 23:19 gezelter
5222
5223		* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h,
5224		do_Forces.F90, do_Forces.h, notifyCutoffs.F90,
5225		notifyCutoffs_interface.h, notifycutoffs_module_interface.h,
5226		wrappers.F90: Fortran name cleanup continues
5227
5228	<	2004-10-20 04:12 gezelter
5228	>	2004-10-19 23:12 gezelter
5229
5230		* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some
5231		broken fortran stuff
5232
5233	<	2004-10-20 04:02 gezelter
5233	>	2004-10-19 23:02 gezelter
5234
5235		* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
5236		atype_interface.h, atype_module.F90, atype_module_interface.h,
#	Line 4283 \| Line 5247
5247		sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90:
5248		name sanity on the fortran side
5249
5250	<	2004-10-20 00:18 tim
5250	>	2004-10-19 19:18 tim
5251
5252		* test/math/SquareMatrix3TestCase.hpp: [no log message]
5253
5254	<	2004-10-19 23:01 tim
5254	>	2004-10-19 18:01 tim
5255
5256		* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
5257		src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp:
5258		except diagonalize(), all of functions in math library pass the
5259		test
5260
5261	<	2004-10-19 22:43 chuckv
5261	>	2004-10-19 17:43 chuckv
5262
5263		* src/UseTheForce/do_Forces.h: Added correct prototypes for
5264		C-fortran interface functions.
5265
5266	<	2004-10-19 22:37 chuckv
5266	>	2004-10-19 17:37 chuckv
5267
5268		* src/UseTheForce/DarkSide/: atype_module_interface.h,
5269		eam_module_inteface.h, gb_module_interface.h,
#	Line 4307 \| Line 5271
5271		sticky_pair_module_interface.h: Added correct prototypes for
5272		C-fortran interface functions.
5273
5274	<	2004-10-19 21:28 tim
5274	>	2004-10-19 16:28 tim
5275
5276		* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp,
5277		src/math/SquareMatrix.hpp, src/math/Vector.hpp,
#	Line 4317 \| Line 5281
5281		test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more
5282		bugs get fixed at math library
5283
5284	<	2004-10-19 20:43 chuckv
5284	>	2004-10-19 15:43 chuckv
5285
5286		* src/UseTheForce/: DarkSide/atype_module_interface.h,
5287		DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h,
#	Line 4331 \| Line 5295
5295		notifycutoffs_module_interface.h: Added new files for fortran
5296		interface.
5297
5298	<	2004-10-19 20:43 gezelter
5298	>	2004-10-19 15:43 gezelter
5299
5300		* src/UseTheForce/Makefile: regressing
5301
5302	<	2004-10-19 20:40 gezelter
5302	>	2004-10-19 15:40 gezelter
5303
5304		* src/: UseTheForce/DarkSide/calc_shapes.F90,
5305		UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp:
5306		working on shapes for portability
5307
5308	<	2004-10-19 20:40 gezelter
5308	>	2004-10-19 15:40 gezelter
5309
5310		* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes
5311
5312	<	2004-10-19 18:21 chrisfen
5312	>	2004-10-19 13:21 chrisfen
5313
5314		* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around
5315		findBegin
5316
5317	<	2004-10-19 04:34 tim
5317	>	2004-10-18 23:34 tim
5318
5319		* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs
5320		are fixed in Vector class
5321
5322	<	2004-10-19 04:28 tim
5322	>	2004-10-18 23:28 tim
5323
5324		* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix
5325		some bugs in RectMatrixTestCase
5326
5327	<	2004-10-19 04:21 tim
5327	>	2004-10-18 23:21 tim
5328
5329		* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp,
5330		test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp,
5331		test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp,
5332		test/math/VectorTestCase.hpp: implement more test cases
5333
5334	<	2004-10-18 23:13 tim
5334	>	2004-10-18 18:13 tim
5335
5336		* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp,
5337		src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
#	Line 4376 \| Line 5340
5340		test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more
5341		tests on math library
5342
5343	<	2004-10-18 21:03 tim
5343	>	2004-10-18 16:03 tim
5344
5345		* test/math/: Makefile, QuaternionTestCase.cpp,
5346		QuaternionTestCase.hpp, RectMatrixTestCase.cpp,
#	Line 4384 \| Line 5348
5348		Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding
5349		more testing units
5350
5351	<	2004-10-18 17:07 tim
5351	>	2004-10-18 12:07 tim
5352
5353		* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp,
5354		math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp,
5355		math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp,
5356		utils/GenericFactory.hpp: fix some bugs in Quaternion class
5357
5358	<	2004-10-18 16:30 gezelter
5358	>	2004-10-18 11:30 gezelter
5359
5360		* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
5361		Your basic run of the mill real-valued versions of Y_l^m(\theta,
5362		\phi)
5363
5364	<	2004-10-18 16:29 gezelter
5364	>	2004-10-18 11:29 gezelter
5365
5366		* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp,
5367		types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp,
5368		utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting
5369		Shapes into OOPSE
5370
5371	<	2004-10-18 15:21 gezelter
5371	>	2004-10-18 10:21 gezelter
5372
5373		* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType
5374
5375	<	2004-10-18 05:23 tim
5375	>	2004-10-18 00:23 tim
5376
5377		* test/math/VectorTestCase.hpp: adding vector test case
5378
5379	<	2004-10-18 05:23 tim
5379	>	2004-10-18 00:23 tim
5380
5381		* src/utils/GenericFactory.hpp: adding generic factory and vector
5382		test case
5383
5384	<	2004-10-17 01:19 tim
5384	>	2004-10-16 20:19 tim
5385
5386		* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp,
5387		SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in
5388		progress
5389
5390	<	2004-10-16 01:31 tim
5390	>	2004-10-15 20:31 tim
5391
5392		* src/math/Quaternion.hpp: add quaternion class
5393
5394	<	2004-10-15 21:11 tim
5394	>	2004-10-15 16:11 tim
5395
5396		* test/io/: DUFF.frc, IfstrstreamTestCase.cpp,
5397		IfstrstreamTestCase.hpp: adding test file
5398
5399	<	2004-10-15 21:10 tim
5399	>	2004-10-15 16:10 tim
5400
5401		* src/io/basic_ifstrstream.hpp: fix a bunch of bugs
5402
5403	<	2004-10-15 20:42 tim
5403	>	2004-10-15 15:42 tim
5404
5405		* src/io/basic_ifstrstream.hpp: change const_cast to statc_const
5406
5407	<	2004-10-15 20:35 tim
5407	>	2004-10-15 15:35 tim
5408
5409		* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp
5410
5411	<	2004-10-15 20:34 tim
5411	>	2004-10-15 15:34 tim
5412
5413		* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use
5414		namespace oopse
5415
5416	<	2004-10-15 19:38 chuckv
5416	>	2004-10-15 14:38 chuckv
5417
5418		* configure, ac-tools/aclocal.m4: Changed optimization flags for
5419		XLF and XLC.
5420
5421	<	2004-10-15 18:28 tim
5421	>	2004-10-15 13:28 tim
5422
5423		* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp:
5424		adding ifstrstream test case
5425
5426	<	2004-10-15 18:20 tim
5426	>	2004-10-15 13:20 tim
5427
5428		* src/io/basic_ifstrstream.hpp: fix include
5429
5430	<	2004-10-15 18:18 tim
5430	>	2004-10-15 13:18 tim
5431
5432		* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi
5433
5434	<	2004-10-15 18:17 tim
5434	>	2004-10-15 13:17 tim
5435
5436		* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile
5437
5438	<	2004-10-15 18:16 tim
5438	>	2004-10-15 13:16 tim
5439
5440		* test/io/: Makefile, ifstrstreamTestCase.cpp,
5441		ifstrstreamTestCase.hpp: adding test case for ifstrstream
5442
5443	<	2004-10-15 15:37 tim
5443	>	2004-10-15 10:37 tim
5444
5445		* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp,
5446		ifstrstreamTestCase.hpp: add ifstrstreamTestCase
5447
5448	<	2004-10-15 15:20 tim
5448	>	2004-10-15 10:20 tim
5449
5450		* src/io/basic_ifstrstream.hpp: add checkFilename Option
5451
5452	<	2004-10-15 15:19 tim
5452	>	2004-10-15 10:19 tim
5453
5454		* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp,
5455		SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add
5456		SquareMatrixTestCase class
5457
5458	<	2004-10-15 07:52 tim
5458	>	2004-10-15 02:52 tim
5459
5460		* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream
5461
5462	<	2004-10-14 23:28 tim
5462	>	2004-10-14 18:28 tim
5463
5464		* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp,
5465		Vector.hpp: math library in progress
5466
5467	<	2004-10-14 23:27 tim
5467	>	2004-10-14 18:27 tim
5468
5469		* src/io/FileReader.hpp: FileReader in progress
5470
5471	<	2004-10-13 23:53 tim
5471	>	2004-10-13 18:53 tim
5472
5473		* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress,
5474		test in isOrthogonal of SquareMatrix is failed by some reasons
5475
5476	<	2004-10-13 22:28 tim
5476	>	2004-10-13 17:28 tim
5477
5478		* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap
5479		class
5480
5481	<	2004-10-13 22:27 tim
5481	>	2004-10-13 17:27 tim
5482
5483		* test/math/: MainTest.cpp, RectMatrixTestCase.cpp,
5484		RectMatrixTestCase.hpp: adding testing unit
5485
5486	<	2004-10-13 22:24 tim
5486	>	2004-10-13 17:24 tim
5487
5488		* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix
5489
5490	<	2004-10-13 06:51 tim
5490	>	2004-10-13 01:51 tim
5491
5492		* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp,
5493		Vector3.hpp: refactory vector and matrix classes
5494
5495	<	2004-10-13 06:50 tim
5495	>	2004-10-13 01:50 tim
5496
5497		* src/math/Vector3d.hpp: Remove some Makefile.in
5498
5499	<	2004-10-12 23:57 tim
5499	>	2004-10-12 18:57 tim
5500
5501		* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and
5502		Matrix3x3d.hpp
5503
5504	<	2004-10-12 19:08 tim
5504	>	2004-10-12 14:08 tim
5505
5506		* doc/: cppstyle.html, style.css: adding c++ coding style
5507
5508	<	2004-10-11 22:15 tim
5508	>	2004-10-11 17:15 tim
5509
5510		* src/: constraints/AbstractClasses.hpp,
5511		integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp:
5512		change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
5513
5514	<	2004-10-11 21:54 tim
5514	>	2004-10-11 16:54 tim
5515
5516		* scripts/filepp: fix a bug in filepp
5517
5518	<	2004-10-11 21:13 tim
5518	>	2004-10-11 16:13 tim
5519
5520		* make/Makefile.in: using filepp to generate dependencies instead
5521		of compilers
5522
5523	<	2004-10-11 21:10 tim
5523	>	2004-10-11 16:10 tim
5524
5525		* scripts/filepp: filepp can be used to generate dependencies for
5526		c/c++ now
5527
5528	<	2004-10-11 18:40 tim
5528	>	2004-10-11 13:40 tim
5529
5530		* make/Makefile.in: remove -module from F90Options
5531
5532	<	2004-10-11 18:01 tim
5532	>	2004-10-11 13:01 tim
5533
5534		* make/Makefile.in: adding rules to move fortran 90 module to
5535		target directory
5536
5537	<	2004-10-11 15:43 gezelter
5537	>	2004-10-11 10:43 gezelter
5538
5539		* make/Makefile.in: fixed makefile.in
5540
5541	<	2004-10-11 14:51 tim
5541	>	2004-10-11 09:51 tim
5542
5543		* scripts/filepp: remove "use bytes" which causes problem in sgi
5544		machine
5545
5546	<	2004-10-11 14:26 tim
5546	>	2004-10-11 09:26 tim
5547
5548		* forceFields/Makefile: add Makefile
5549
5550	<	2004-10-11 14:23 tim
5550	>	2004-10-11 09:23 tim
5551
5552		* samples/: water/dimer/Makefile, water/spce/Makefile,
5553		water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile,
5554		water/tip4p/Makefile, zcons/Makefile: fix Makefile under water
5555		directory
5556
5557	<	2004-10-09 06:01 tim
5557	>	2004-10-11 09:23 tim
5558
5559	<	* samples/: alkane/Makefile.in, lipid/Makefile.in,
5560	<	metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in
5559	>	* samples/argon/Makefile: remove argon.dump and argon.eor from
5560	>	Makefile
5561
5562	<	2004-10-08 23:15 tim
5562	>	2004-10-09 01:01 tim
5563	>
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	+
5570		* make/Makefile.in: [no log message]
5571
5572	<	2004-10-08 22:51 tim
5572	>	2004-10-08 17:51 tim
5573
5574		* make/Makefile.in: fix make install
5575
5576	<	2004-10-08 22:10 tim
5576	>	2004-10-08 17:10 tim
5577
5578		* make/Makefile.in: adding make install
5579
5580	<	2004-10-08 22:04 tim
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,
5588		water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile,
5589		zcons/Makefile.in: add Makefile to sample directory
5590
5591	<	2004-10-06 23:03 gezelter
5591	>	2004-10-06 18:03 gezelter
5592
5593		* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt
5594		stuff
5595
5596	<	2004-10-06 23:03 gezelter
5596	>	2004-10-06 18:03 gezelter
5597
5598		* configure, ac-tools/aclocal.m4, ac-tools/configure.in,
5599		make/Doxyfile, src/applications/getopt.c,
5600		src/applications/getopt1.c, src/applications/gnugetopt.h: more
5601		build fixes
5602
5603	<	2004-10-06 22:20 tim
5603	>	2004-10-06 17:20 tim
5604
5605		* make/: Doxyfile, Makefile.in: adding doxygen configuration file
5606
5607	<	2004-10-06 22:19 tim
5607	>	2004-10-06 17:19 tim
5608
5609		* scripts/filepp: filepp can handle different fortran module case
5610		and suffix
5611
5612	<	2004-10-06 21:27 gezelter
5612	>	2004-10-06 16:27 gezelter
5613
5614		* src/restraints/Restraints.cpp: Chris doesn't know about the
5615		OOPSE-2.0 directory structure yet
5616
5617	<	2004-10-06 21:27 gezelter
5617	>	2004-10-06 16:27 gezelter
5618
5619		* ChangeLog: Yeah yeah, we'lll get around to it later
5620
5621	<	2004-10-06 21:22 gezelter
5621	>	2004-10-06 16:22 gezelter
5622
5623		* configure, ac-tools/configure.in, ac-tools/fortran90.m4,
5624		make/Makefile.in: cleaning up build process
5625
5626	<	2004-10-06 20:01 chrisfen
5626	>	2004-10-06 15:01 chrisfen
5627
5628		* src/restraints/Restraints.cpp: made the file reading in
5629		restraints more intelligent - no longer gives uninformative seg
5630		faults
5631
5632	<	2004-10-06 19:55 gezelter
5632	>	2004-10-06 14:55 gezelter
5633
5634		* src/applications/simpleBuilder/Make.ftemp.old: cleaning up
5635
5636	<	2004-10-06 19:51 gezelter
5636	>	2004-10-06 14:51 gezelter
5637
5638		* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy,
5639		scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit
5640
5641	<	2004-10-06 18:53 tim
5641	>	2004-10-06 13:53 tim
5642
5643		* make/: Makefile, Makefile.in: fix make statistics
5644
5645	<	2004-10-06 18:18 tim
5645	>	2004-10-06 13:18 tim
5646
5647		* make/: Makefile, Makefile.in: adding GNU make functions to
5648		combine all of the static libraries to a big library
5649
5650	<	2004-10-05 22:57 tim
5650	>	2004-10-05 17:57 tim
5651
5652		* make/: Makefile, Makefile.in: adding shared library flag
5653
5654	<	2004-10-05 19:37 tim
5654	>	2004-10-05 14:37 tim
5655
5656		* src/: Makefile, UseTheForce/Makefile,
5657		UseTheForce/mpiSimulation_module.F90,
#	Line 4689 \| Line 5659
5659		UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move
5660		mpiSimulation_module to DarkSide
5661
5662	<	2004-10-05 19:35 tim
5662	>	2004-10-05 14:35 tim
5663
5664		* make/: Makefile, Makefile.in: building MPI version;using static
5665		library instead of shared library
5666
5667	<	2004-10-05 14:14 tim
5667	>	2004-10-05 09:14 tim
5668
5669		* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90
5670		to filepp
5671
5672	<	2004-10-04 20:56 tim
5672	>	2004-10-04 15:56 tim
5673
5674		* make/: Makefile, Makefile.in: add make cvslog
5675
5676	<	2004-10-04 16:24 gezelter
5676	>	2004-10-04 11:24 gezelter
5677
5678		* make/: Makefile, Makefile.in: more work on the parallel build
5679
5680	<	2004-10-04 16:06 gezelter
5680	>	2004-10-04 11:06 gezelter
5681
5682		* make/: Makefile, Makefile.in: changes to backport declare flags
5683
5684	<	2004-10-04 15:27 gezelter
5684	>	2004-10-04 10:27 gezelter
5685
5686		* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp,
5687		DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging
5688		shapes
5689
5690	<	2004-10-02 04:40 tim
5690	>	2004-10-01 23:40 tim
5691
5692		* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree
5693
5694	<	2004-10-02 04:22 tim
5694	>	2004-10-01 23:22 tim
5695
5696		* make/: Makefile, Makefile.in: add oopse_ as library prefix
5697
5698	<	2004-10-01 21:59 tim
5698	>	2004-10-01 16:59 tim
5699
5700		* make/: Makefile, Makefile.in: fix a space trimming bug in filepp
5701
5702	<	2004-10-01 21:22 gezelter
5702	>	2004-10-01 16:22 gezelter
5703
5704		* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A
5705		few minor build changes
5706
5707	<	2004-10-01 21:11 tim
5707	>	2004-10-01 16:11 tim
5708
5709		* scripts/filepp: adding fortran90 make dependency tool
5710
5711	<	2004-09-30 15:41 tim
5711	>	2004-09-30 10:41 tim
5712
5713		* make/: Makefile, Makefile.in: make clean is smart enough to only
5714		remove object files belong to current package. turn off silent
5715		mode
5716
5717	<	2004-09-29 21:55 tim
5717	>	2004-09-29 16:55 tim
5718
5719		* src/: Makefile, UseTheForce/Makefile,
5720		UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile,
#	Line 4755 \| Line 5725
5725		restraints/Makefile, types/Makefile, utils/Makefile,
5726		visitors/Makefile: define DEV_ROOT as relative path
5727
5728	<	2004-09-29 21:54 tim
5728	>	2004-09-29 16:54 tim
5729
5730		* make/: Makefile, Makefile.in: get the relative path by shell
5731		script
5732
5733	<	2004-09-29 21:32 tim
5733	>	2004-09-29 16:32 tim
5734
5735		* make/Makefile: eliminate DEV_ROOT by relative path
5736
5737	<	2004-09-29 18:37 tim
5737	>	2004-09-29 13:37 tim
5738
5739		* make/Makefile.in: add PackageLibs; fix dependency rule
5740
5741	<	2004-09-29 17:57 gezelter
5741	>	2004-09-29 12:57 gezelter
5742
5743		* configure, ac-tools/configure.in: updates
5744
5745	<	2004-09-29 17:56 gezelter
5745	>	2004-09-29 12:56 gezelter
5746
5747		* make/: Make.conf.in, Makefile.in, _files/style.css: Working on
5748		make stuff
5749
5750	<	2004-09-29 17:46 tim
5750	>	2004-09-29 12:46 tim
5751
5752		* Makefile: If makefile does not exist, print error message
5753
5754	<	2004-09-29 17:12 tim
5754	>	2004-09-29 12:12 tim
5755
5756		* make/: Make.conf.in, Makefile: fix dependencies rule
5757
5758	<	2004-09-29 15:58 gezelter
5758	>	2004-09-29 10:58 gezelter
5759
5760		* Makefile, make/Makefile: still working on build process
5761
5762	<	2004-09-29 15:00 tim
5762	>	2004-09-29 10:00 tim
5763
5764		* make/Makefile: add print statment to rules
5765
5766	<	2004-09-29 14:59 tim
5766	>	2004-09-29 09:59 tim
5767
5768		* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile,
5769		applications/dump2Xyz/Makefile, applications/oopse/Makefile,
#	Line 4803 \| Line 5773
5773		profiling/Makefile, restraints/Makefile, types/Makefile,
5774		utils/Makefile, visitors/Makefile: change Makefile to relative path
5775
5776	<	2004-09-29 02:55 tim
5776	>	2004-09-28 21:55 tim
5777
5778		* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c
5779		which cause headache in bulding libutils
5780
5781	<	2004-09-28 23:24 tim
5781	>	2004-09-28 18:24 tim
5782
5783		* src/applications/: BaseLattice.cpp, BaseLattice.hpp,
5784		Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h,
#	Line 4831 \| Line 5801
5801		change directory structure of application. Every executable file is
5802		replaced in seperate directory
5803
5804	<	2004-09-28 22:15 gezelter
5804	>	2004-09-28 17:15 gezelter
5805
5806		* lib/dummy: Keep that lib around, please.
5807
5808	<	2004-09-28 22:14 gezelter
5808	>	2004-09-28 17:14 gezelter
5809
5810		* Makefile, configure, ac-tools/configure.in, make/Make.conf.in:
5811		starting a configure version
5812
5813	<	2004-09-28 21:08 tim
5813	>	2004-09-28 16:08 tim
5814
5815		* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90,
5816		UseTheForce/DarkSide/Makefile,
#	Line 4849 \| Line 5819
5819		brains/Makefile, brains/simulation_module.F90: move fortran files
5820		around to solve dependency problem
5821
5822	<	2004-09-28 20:43 tim
5822	>	2004-09-28 15:43 tim
5823
5824		* Makefile, src/UseTheForce/ForceFields.hpp,
5825		src/UseTheForce/Makefile, src/applications/BaseLattice.hpp,
#	Line 4859 \| Line 5829
5829		src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp,
5830		src/utils/Makefile: [no log message]
5831
5832	<	2004-09-28 20:41 tim
5832	>	2004-09-28 15:41 tim
5833
5834		* make/Makefile, scripts/sfmakedepend: fix fortran dependency
5835		problem
5836
5837	<	2004-09-28 16:13 tim
5837	>	2004-09-28 11:13 tim
5838
5839		* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y,
5840		src/io/Makefile: add yacc and lex rules
5841
5842	<	2004-09-27 20:24 tim
5842	>	2004-09-27 15:24 tim
5843
5844		* make/Makefile: adding include path to F90Options
5845
5846	<	2004-09-27 20:13 tim
5846	>	2004-09-27 15:13 tim
5847
5848		* make/Makefile: change suffix from .cc to .cpp
5849
5850	<	2004-09-24 16:27 tim
5850	>	2004-09-24 11:27 tim
5851
5852		* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
5853		UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
#	Line 4944 \| Line 5914
5914		visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
5915		visitors/ZconsVisitor.hpp: change the #include in source files
5916
5917	<	2004-09-24 04:16 gezelter
5917	>	2004-09-23 23:16 gezelter
5918
5919		* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
5920		src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
#	Line 5090 \| 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 5116 \| Line 6090
6090		forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
6091		forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0
6092
6093	<	2004-09-24 04:16 gezelter
6093	>	2004-09-23 23:16 gezelter
6094
6095		* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
6096		src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
#	Line 5262 \| 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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Comparing trunk/OOPSE-2.0/ChangeLog (file contents): Revision 2116 by tim, Fri Mar 11 15:00:20 2005 UTC vs. Revision 2246 by chrisfen, Sun May 29 21:13:23 2005 UTC

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Comparing trunk/OOPSE-2.0/ChangeLog (file contents):
Revision 2116 by tim, Fri Mar 11 15:00:20 2005 UTC vs.
Revision 2246 by chrisfen, Sun May 29 21:13:23 2005 UTC