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Comparing trunk/OOPSE-3.0/ChangeLog (file contents):
Revision 2229 by chrisfen, Tue May 17 22:35:01 2005 UTC vs.
Revision 2568 by gezelter, Mon Jan 16 23:10:15 2006 UTC

#	Line 1 | Line 1
1	<	2005-05-16 23:20  chuckv
2	<
3	<	* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp:
4	<	Fixed merge issues between Kyle and Chris so OOPSE will actually
5	<	build.
6	<
7	<	2005-05-16 22:46  kdaily
8	<
9	<	* src/io/: GayBerneAtomTypesSectionParser.cpp,
10	<	GayBerneAtomTypesSectionParser.hpp, Makefile: help
11	<
12	<	2005-05-16 21:08  kdaily
13	<
14	<	* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90,
15	<	src/UseTheForce/DarkSide/gb.F90, src/io/Makefile,
16	<	src/types/DirectionalAtomType.cpp,
17	<	src/types/DirectionalAtomType.hpp: added gb
18	<
19	<	2005-05-13 15:36  chrisfen
20	<
21	<	* forceFields/DUFF2.frc: Better tap
22	<
23	<	2005-05-12 14:43  chrisfen
24	<
25	<	* forceFields/DUFF2.frc, samples/water/dimer/ssd.in,
26	<	samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90,
27	<	src/applications/dump2Xyz/Dump2XYZ.cpp,
28	<	src/visitors/AtomVisitor.hpp: Couple of changes for TAP water.
29	<	Need to parametrize.
30	<
31	<	2005-05-11 18:15  chuckv
32	<
33	<	* src/: io/ShapeAtomTypesSectionParser.cpp,
34	<	math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed
35	<	build issues under ifc7.
36	<
37	<	2005-05-09 17:07  chuckv
38	<
39	<	* src/applications/nanoRodBuilder/Geometry.hpp: More geometry
40	<	builder changes.
41	<
42	<	2005-05-05 10:06  chrisfen
43	<
44	<	* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED
45	<	to TAP
46	<
47	<	2005-05-05 09:47  chrisfen
48	<
49	<	* forceFields/DUFF2.frc, samples/water/ssde/ssde.md,
50	<	samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp,
51	<	src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile,
52	<	src/UseTheForce/DarkSide/atype.F90,
53	<	src/UseTheForce/DarkSide/atype_interface.F90,
54	<	src/UseTheForce/DarkSide/simulation.F90,
55	<	src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp,
56	<	src/brains/fSimulation.h, src/io/Makefile,
57	<	src/io/StickyAtomTypesSectionParser.cpp,
58	<	src/io/StickyPowerAtomTypesSectionParser.cpp,
59	<	src/io/StickyPowerAtomTypesSectionParser.hpp,
60	<	src/types/AtomType.cpp, src/types/AtomType.hpp,
61	<	src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp,
62	<	src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water.  It's
63	<	not parametrized, but OOPSE will now let me run it...
64	<
65	<	2005-05-03 17:55  chuckv
66	<
67	<	* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
68	<	GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp:
69	<	Adding support for generic geometry to nanorodbuilder.
70	<
71	<	2005-05-03 12:55  chuckv
72	<
73	<	* src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
74	<	nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c,
75	<	nanorodBuilderCmd.h: More changes to nanoRodBuilder....
76	<
77	<	2005-04-29 14:16  gezelter
78	<
79	<	* make/Makefile.in: [no log message]
80	<
81	<	2005-04-29 11:26  chrisfen
82	<
83	<	* forceFields/DUFF2.frc, samples/water/spce/water.md,
84	<	samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md,
85	<	samples/water/ssd-ion/water.md, samples/water/ssde/water.md,
86	<	samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md,
87	<	samples/water/tip4p/water.md: Added TIP4P-Ew
88	<
89	<	2005-04-27 19:24  chuckv
90	<
91	<	* src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
92	<	GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo,
93	<	nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with
94	<	nanoRodBuilder....
95	<
96	<	2005-04-27 15:13  chrisfen
97	<
98	<	* samples/shape/Shapes.frc, samples/shape/linear.shape,
99	<	src/UseTheForce/DarkSide/atype.F90,
100	<	src/UseTheForce/DarkSide/shapes.F90,
101	<	src/UseTheForce/DarkSide/shapes_interface.F90,
102	<	src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of
103	<	write statements and am closer to a working shapes
104	<
105	<	2005-04-22 16:57  chuckv
106	<
107	<	* src/utils/Predicate.hpp: Fixed gcc4 bug...
108	<
109	<	2005-04-22 16:52  tim
110	<
111	<	* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp,
112	<	Trim.hpp: adding CharClassificationFunctor to fix the locale
113	<	problem  of c++
114	<
115	<	2005-04-21 09:12  chrisfen
116	<
117	<	* samples/shape/Shapes.frc, samples/shape/linear.in,
118	<	samples/shape/linear.md, src/UseTheForce/ForceField.hpp,
119	<	src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile,
120	<	src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp,
121	<	src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90,
122	<	src/UseTheForce/DarkSide/shapes.F90,
123	<	src/UseTheForce/DarkSide/shapes_interface.F90,
124	<	src/UseTheForce/DarkSide/shapes_interface.h,
125	<	src/brains/Register.cpp, src/brains/SimCreator.cpp,
126	<	src/io/Makefile, src/io/SectionParser.cpp,
127	<	src/io/SectionParser.hpp, src/io/SectionParserManager.cpp,
128	<	src/io/ShapeAtomTypesSectionParser.cpp,
129	<	src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile,
130	<	src/types/AtomType.cpp, src/types/ShapeAtomType.cpp,
131	<	src/types/ShapeAtomType.hpp: Shapes is limping along with a array
132	<	bounds overwrite (I think...). At least the parser loads the
133	<	forcefield fine...
134	<
135	<	2005-04-18 10:44  chrisfen
136	<
137	<	* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on
138	<	Mac (capitalization confusion of filenames)
139	<
140	<	2005-04-17 22:50  chrisfen
141	<
142	<	* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp,
143	<	UseTheForce/Shapes_FF.cpp,
144	<	io/DirectionalAtomTypesSectionParser.cpp,
145	<	io/ShapeAtomTypesSectionParser.cpp,
146	<	io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser...
147	<
148	<	2005-04-15 17:43  gezelter
149	<
150	<	* README: gmake in case people forget
151	<
152	<	2005-04-15 17:40  gezelter
153	<
154	<	* src/applications/oopse/oopse.cpp: fixed the spacing on the
155	<	banner.  Vanity.
156	<
157	<	2005-04-15 17:22  gezelter
158	<
159	<	* src/: config.h.in, applications/oopse/oopse.cpp: Version string
160	<	in banner (and version numbers in config.h)
161	<
162	<	2005-04-15 17:22  gezelter
163	<
164	<	* ChangeLog, LICENSE, README: Documentation changes
165	<
166	<	2005-04-15 17:03  gezelter
167	<
168	<	* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
169	<	UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp,
170	<	UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
171	<	UseTheForce/ForceFieldCreator.hpp,
172	<	UseTheForce/ForceFieldFactory.cpp,
173	<	UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp,
174	<	UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90,
175	<	UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h,
176	<	UseTheForce/notifyCutoffs.F90,
177	<	UseTheForce/notifyCutoffs_interface.F90,
178	<	UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90,
179	<	UseTheForce/DarkSide/atype.F90,
180	<	UseTheForce/DarkSide/atype_interface.F90,
181	<	UseTheForce/DarkSide/eam.F90,
182	<	UseTheForce/DarkSide/eam_interface.F90,
183	<	UseTheForce/DarkSide/eam_interface.h,
184	<	UseTheForce/DarkSide/electrostatic.F90,
185	<	UseTheForce/DarkSide/electrostatic_interface.F90,
186	<	UseTheForce/DarkSide/electrostatic_interface.h,
187	<	UseTheForce/DarkSide/force_globals.F90,
188	<	UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h,
189	<	UseTheForce/DarkSide/lj_interface.F90,
190	<	UseTheForce/DarkSide/lj_interface.h,
191	<	UseTheForce/DarkSide/neighborLists.F90,
192	<	UseTheForce/DarkSide/reactionField.F90,
193	<	UseTheForce/DarkSide/shapes.F90,
194	<	UseTheForce/DarkSide/shapes_interface.F90,
195	<	UseTheForce/DarkSide/shapes_interface.h,
196	<	UseTheForce/DarkSide/simParallel.F90,
197	<	UseTheForce/DarkSide/simParallel_interface.F90,
198	<	UseTheForce/DarkSide/simParallel_interface.h,
199	<	UseTheForce/DarkSide/simulation.F90,
200	<	UseTheForce/DarkSide/simulation_interface.F90,
201	<	UseTheForce/DarkSide/simulation_interface.h,
202	<	UseTheForce/DarkSide/sticky.F90,
203	<	UseTheForce/DarkSide/sticky_interface.F90,
204	<	UseTheForce/DarkSide/sticky_interface.h,
205	<	UseTheForce/DarkSide/switcheroo.F90,
206	<	applications/dump2Xyz/Dump2XYZ.cpp,
207	<	applications/dump2Xyz/Dump2XYZCmd.c,
208	<	applications/dump2Xyz/Dump2XYZCmd.h,
209	<	applications/dynamicProps/CrossTimeCorrFunc.cpp,
210	<	applications/dynamicProps/CrossTimeCorrFunc.hpp,
211	<	applications/dynamicProps/DipoleCorrFunc.cpp,
212	<	applications/dynamicProps/DipoleCorrFunc.hpp,
213	<	applications/dynamicProps/DynamicProps.cpp,
214	<	applications/dynamicProps/DynamicPropsCmd.c,
215	<	applications/dynamicProps/DynamicPropsCmd.h,
216	<	applications/dynamicProps/FrameTimeCorrFunc.hpp,
217	<	applications/dynamicProps/ParticleTimeCorrFunc.cpp,
218	<	applications/dynamicProps/ParticleTimeCorrFunc.hpp,
219	<	applications/dynamicProps/RCorrFunc.cpp,
220	<	applications/dynamicProps/RCorrFunc.hpp,
221	<	applications/dynamicProps/TimeCorrFunc.cpp,
222	<	applications/dynamicProps/TimeCorrFunc.hpp,
223	<	applications/dynamicProps/VCorrFunc.cpp,
224	<	applications/dynamicProps/VCorrFunc.hpp,
225	<	applications/nanoRodBuilder/GeometryBuilder.cpp,
226	<	applications/nanoRodBuilder/GeometryBuilder.hpp,
227	<	applications/nanoRodBuilder/nanorodBuilder.cpp,
228	<	applications/nanoRodBuilder/nanorodBuilderCmd.c,
229	<	applications/nanoRodBuilder/nanorodBuilderCmd.h,
230	<	applications/oopse/oopse.cpp,
231	<	applications/simpleBuilder/simpleBuilder.cpp,
232	<	applications/simpleBuilder/simpleBuilderCmd.c,
233	<	applications/simpleBuilder/simpleBuilderCmd.h,
234	<	applications/staticProps/GofAngle2.cpp,
235	<	applications/staticProps/GofAngle2.hpp,
236	<	applications/staticProps/GofR.cpp,
237	<	applications/staticProps/GofR.hpp,
238	<	applications/staticProps/GofRAngle.cpp,
239	<	applications/staticProps/GofRAngle.hpp,
240	<	applications/staticProps/GofXyz.cpp,
241	<	applications/staticProps/GofXyz.hpp,
242	<	applications/staticProps/RadialDistrFunc.cpp,
243	<	applications/staticProps/RadialDistrFunc.hpp,
244	<	applications/staticProps/StaticProps.cpp,
245	<	applications/staticProps/StaticPropsCmd.c,
246	<	applications/staticProps/StaticPropsCmd.h,
247	<	brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
248	<	brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp,
249	<	brains/Exclude.hpp, brains/ForceManager.cpp,
250	<	brains/ForceManager.hpp, brains/MoleculeCreator.cpp,
251	<	brains/MoleculeCreator.hpp, brains/Register.cpp,
252	<	brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
253	<	brains/SimInfo.hpp, brains/SimSnapshotManager.cpp,
254	<	brains/SimSnapshotManager.hpp, brains/Snapshot.cpp,
255	<	brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp,
256	<	brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp,
257	<	brains/fSimulation.h, constraints/ConstraintElem.hpp,
258	<	constraints/ConstraintPair.hpp, constraints/Rattle.cpp,
259	<	constraints/Rattle.hpp, constraints/ZconsStruct.hpp,
260	<	constraints/ZconstraintForceManager.cpp,
261	<	constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp,
262	<	integrators/DLM.hpp, integrators/Integrator.cpp,
263	<	integrators/Integrator.hpp, integrators/IntegratorCreator.hpp,
264	<	integrators/IntegratorFactory.cpp,
265	<	integrators/IntegratorFactory.hpp, integrators/NPT.cpp,
266	<	integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp,
267	<	integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp,
268	<	integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp,
269	<	integrators/NVT.cpp, integrators/NVT.hpp,
270	<	integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp,
271	<	integrators/Velocitizer.hpp,
272	<	integrators/VelocityVerletIntegrator.cpp,
273	<	integrators/VelocityVerletIntegrator.hpp,
274	<	io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp,
275	<	io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c,
276	<	io/BASS_parse.h, io/BendTypesSectionParser.cpp,
277	<	io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
278	<	io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
279	<	io/ChargeAtomTypesSectionParser.hpp,
280	<	io/DirectionalAtomTypesSectionParser.cpp,
281	<	io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
282	<	io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp,
283	<	io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
284	<	io/Globals.cpp, io/Globals.hpp,
285	<	io/LennardJonesAtomTypesSectionParser.cpp,
286	<	io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp,
287	<	io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp,
288	<	io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp,
289	<	io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp,
290	<	io/SectionParser.cpp, io/SectionParser.hpp,
291	<	io/SectionParserManager.cpp, io/SectionParserManager.hpp,
292	<	io/StatWriter.cpp, io/StatWriter.hpp,
293	<	io/StickyAtomTypesSectionParser.cpp,
294	<	io/StickyAtomTypesSectionParser.hpp,
295	<	io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
296	<	io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
297	<	io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp,
298	<	io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c,
299	<	io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h,
300	<	io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp,
301	<	lattice/CubicLattice.hpp, lattice/FCCLattice.cpp,
302	<	lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
303	<	lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp,
304	<	lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp,
305	<	math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h,
306	<	math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp,
307	<	math/ParallelRandNumGen.hpp, math/Polynomial.hpp,
308	<	math/Quaternion.hpp, math/RandNumGen.hpp,
309	<	math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp,
310	<	math/RectMatrix.hpp, math/SeqRandNumGen.cpp,
311	<	math/SeqRandNumGen.hpp, math/SquareMatrix.hpp,
312	<	math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp,
313	<	minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp,
314	<	minimizers/Minimizer.cpp, minimizers/Minimizer.hpp,
315	<	minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp,
316	<	minimizers/MinimizerFactory.hpp,
317	<	minimizers/MinimizerParameterSet.cpp,
318	<	minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp,
319	<	minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp,
320	<	minimizers/SDMinimizer.hpp, primitives/Atom.cpp,
321	<	primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp,
322	<	primitives/Bond.hpp, primitives/CutoffGroup.hpp,
323	<	primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
324	<	primitives/GhostBend.cpp, primitives/GhostBend.hpp,
325	<	primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp,
326	<	primitives/Molecule.cpp, primitives/Molecule.hpp,
327	<	primitives/RigidBody.cpp, primitives/RigidBody.hpp,
328	<	primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
329	<	primitives/Torsion.cpp, primitives/Torsion.hpp,
330	<	primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp,
331	<	profiling/mdProfile.cpp, profiling/mdProfile.hpp,
332	<	profiling/timing.F90, restraints/Restraints.cpp,
333	<	restraints/Restraints.hpp,
334	<	restraints/ThermoIntegrationForceManager.cpp,
335	<	restraints/ThermoIntegrationForceManager.hpp,
336	<	selection/DistanceFinder.cpp, selection/DistanceFinder.hpp,
337	<	selection/IndexFinder.cpp, selection/IndexFinder.hpp,
338	<	selection/NameFinder.cpp, selection/NameFinder.hpp,
339	<	selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp,
340	<	selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
341	<	selection/SelectionManager.cpp, selection/SelectionManager.hpp,
342	<	selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp,
343	<	selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp,
344	<	types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h,
345	<	types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp,
346	<	types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp,
347	<	types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
348	<	types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp,
349	<	types/CubicBondType.hpp, types/CubicTorsionType.hpp,
350	<	types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
351	<	types/DirectionalAtomType.hpp, types/FixedBondType.hpp,
352	<	types/HarmonicBendType.hpp, types/HarmonicBondType.hpp,
353	<	types/MakeStamps.cpp, types/MakeStamps.hpp,
354	<	types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
355	<	types/MorseBondType.hpp, types/OplsTorsionType.hpp,
356	<	types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
357	<	types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp,
358	<	types/QuarticBondType.hpp, types/QuarticTorsionType.hpp,
359	<	types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
360	<	types/ShapeAtomType.cpp, types/ShapeAtomType.hpp,
361	<	types/TorsionStamp.cpp, types/TorsionStamp.hpp,
362	<	types/TorsionType.hpp, types/UreyBradleyBendType.hpp,
363	<	types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp,
364	<	utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp,
365	<	utils/GenericFactory.hpp, utils/LocalIndexManager.hpp,
366	<	utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp,
367	<	utils/NumericConstant.hpp, utils/OOPSEConstant.hpp,
368	<	utils/PropertyMap.cpp, utils/PropertyMap.hpp,
369	<	utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
370	<	utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp,
371	<	utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp,
372	<	utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp,
373	<	utils/any.hpp, utils/definitions.F90, utils/fError.c,
374	<	utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h,
375	<	utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h,
376	<	utils/residentMem.h, utils/simError.c, utils/simError.h,
377	<	utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp,
378	<	visitors/AtomData.hpp, visitors/AtomVisitor.cpp,
379	<	visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp,
380	<	visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp,
381	<	visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
382	<	visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp,
383	<	visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp,
384	<	visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has
385	<	been drafted to perform our indentation services
386	<
387	<	2005-04-15 17:03  gezelter
388	<
389	<	* configure, ac-tools/configure.in: Jedi mind-trick warning
390	<	messages have been added to make users ignore CGAL.
391	<
392	<	2005-04-15 13:41  tim
393	<
394	<	* make/Makefile.in: fix make install
395	<
396	<	2005-04-15 13:41  tim
397	<
398	<	* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile:
399	<	add  Makefile of samples
400	<
401	<	2005-04-15 13:33  tim
402	<
403	<	* samples/: lipid/Makefile, water/dimer/Makefile,
404	<	water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not
405	<	installed correctly
406	<
407	<	2005-04-14 16:41  gezelter
408	<
409	<	* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in,
410	<	make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl,
411	<	scripts/filepp, scripts/filepp.in: configure now searches for perl
412	<	to use with filepp
413	<
414	<	2005-04-14 16:20  gezelter
415	<
416	<	* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of
417	<	MoLocator
418	<
419	<	2005-04-14 14:12  gezelter
420	<
421	<	* LICENSE: [no log message]
422	<
423	<	2005-04-14 11:10  chuckv
424	<
425	<	* src/applications/nanoRodBuilder/nanorodBuilder.cpp:
426	<	nanorodbuilder now exit's when libCGAL is not present.
427	<
428	<	2005-04-14 10:20  tim
429	<
430	<	* src/io/make_nodes.h: fix one more warning message in make_nodes
431	<
432	<	2005-04-13 18:36  chuckv
433	<
434	<	* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed
435	<	interface name for SGI Compiler
436	<
437	<	2005-04-13 18:29  chrisfen
438	<
439	<	* samples/water/ssde/ssde.md: oops...  bad sample
440	<
441	<	2005-04-13 18:00  chuckv
442	<
443	<	* src/config.h.in: Change typo in CGAL.
444	<
445	<	2005-04-13 17:43  tim
446	<
447	<	* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp,
448	<	selection/SelectionCompiler.hpp: fix some warning messages
449	<
450	<	2005-04-13 17:30  gezelter
451	<
452	<	* configure, ac-tools/aclocal.m4, ac-tools/configure.in,
453	<	make/Makefile.in, src/config.h.in,
454	<	src/applications/nanoRodBuilder/Makefile,
455	<	src/applications/nanoRodBuilder/Makefile.in,
456	<	src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL
457	<	checks
458	<
459	<	2005-04-13 15:36  chuckv
460	<
461	<	* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp,
462	<	DarkSide/LJ.F90, DarkSide/electrostatic.F90,
463	<	DarkSide/electrostatic_interface.F90,
464	<	DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90,
465	<	DarkSide/lj_interface.h, DarkSide/sticky.F90,
466	<	DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added
467	<	destroy methods for Fortran modules.
468	<
469	<	2005-04-13 15:17  chuckv
470	<
471	<	* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90,
472	<	shapes_interface.h: Added destroy method to clean up memory
473	<
474	<	2005-04-13 13:41  tim
475	<
476	<	* src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
477	<	brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
478	<	io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp,
479	<	primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp,
480	<	types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are
481	<	fixed
482	<
483	<	2005-04-12 17:44  chuckv
484	<
485	<	* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed
486	<	for nanoRodBuilder.
487	<
488	<	2005-04-12 17:42  tim
489	<
490	<	* src/applications/: nanoRodBuilder/nanorodBuilder.cpp,
491	<	simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder
492	<	and simpleBuilder(forget to delete lattice)
493	<
494	<	2005-04-12 17:33  tim
495	<
496	<	* src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
497	<	applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp:
498	<	refactory lattice
499	<
500	<	2005-04-12 17:07  tim
501	<
502	<	* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp,
503	<	CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp,
504	<	Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory
505	<	LatticeFactory and LatticeCreator
506	<
507	<	2005-04-12 16:58  tim
508	<
509	<	* src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
510	<	applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp,
511	<	brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
512	<	lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp,
513	<	lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp,
514	<	lattice/Makefile: refactory LatticeFactory and LatticeCreator
515	<
516	<	2005-04-12 16:28  gezelter
517	<
518	<	* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp,
519	<	vector_class.F90: cleaned up vector_class memory leak fix by
520	<	deallocating in reverse order of how we allocated.  Also migrated
521	<	MoLocator into utils directory
522	<
523	<	2005-04-12 16:27  gezelter
524	<
525	<	* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp,
526	<	Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
527	<	LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice
528	<	directory
529	<
530	<	2005-04-12 16:27  gezelter
531	<
532	<	* src/applications/: nanoRodBuilder/BaseLattice.cpp,
533	<	nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp,
534	<	nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp,
535	<	nanoRodBuilder/LatticeCreator.hpp,
536	<	nanoRodBuilder/LatticeFactory.cpp,
537	<	nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile,
538	<	nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp,
539	<	nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp,
540	<	simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
541	<	simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
542	<	simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
543	<	simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile,
544	<	simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp,
545	<	simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of
546	<	these files are now redundant
547	<
548	<	2005-04-12 16:27  gezelter
549	<
550	<	* src/UseTheForce/DarkSide/: atype_interface.F90,
551	<	atype_interface.h: cleaned up memory leak fix
552	<
553	<	2005-04-12 16:26  gezelter
554	<
555	<	* make/Makefile.in: added lattice subdirectory
556	<
557	<	2005-04-12 15:57  chrisfen
558	<
559	<	* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added
560	<	a space by accident
561	<
562	<	2005-04-12 15:56  chrisfen
563	<
564	<	* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added
565	<	quadrupole sample
566	<
567	<	2005-04-12 15:56  chrisfen
568	<
569	<	* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating
570	<	samples
571	<
572	<	2005-04-12 13:30  tim
573	<
574	<	* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom
575	<	type in fortran side
576	<
577	<	2005-04-12 12:45  chuckv
578	<
579	<	* src/utils/vector_class.F90: Further changes to vector_class
580	<	destroy function.
581	<
582	<	2005-04-12 12:39  chuckv
583	<
584	<	* src/utils/vector_class.F90: Fixed pointer memory leak in
585	<	vector_class.
586	<
587	<	2005-04-12 12:12  chuckv
588	<
589	<	* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp,
590	<	DarkSide/atype_interface.F90, DarkSide/atype_interface.h,
591	<	DarkSide/eam.F90, DarkSide/eam_interface.F90,
592	<	DarkSide/eam_interface.h: Updates to deallocate object in fortran.
593	<
594	<	2005-04-12 09:24  chrisfen
595	<
596	<	* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI
597	<	output
598	<
599	<	2005-04-11 19:29  chuckv
600	<
601	<	* src/: UseTheForce/DarkSide/atype.F90,
602	<	applications/nanoRodBuilder/Makefile: Changes to delete atypes...
603	<
604	<	2005-04-11 19:28  chuckv
605	<
606	<	* src/utils/vector_class.F90: Added code to delete vector.
607	<
608	<	2005-04-11 17:03  chuckv
609	<
610	<	* samples/metals/nanorod/: Au_nanoparticle.md,
611	<	Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why
612	<	aren't these here?
1	>	2006-01-16 10:26  gezelter
2	>
3	>	* configure: Testing commit
4	>
5	>	2006-01-13 16:57  chuckv
6	>
7	>	* src/: UseTheForce/SC_FF.cpp,
8	>	applications/nanoparticleBuilder/sphericalNanoparticle.cpp,
9	>	io/Globals.cpp, io/Globals.hpp: Removed MixingRule from Globals.
10	>	Handled by forceField now.
11	>
12	>	2006-01-13 14:17  chuckv
13	>
14	>	* src/io/Globals.cpp: Added NPAT to Globals integrators.
15	>
16	>	2006-01-13 11:33  gezelter
17	>
18	>	* Makefile: [no log message]
19	>
20	>	2006-01-13 11:26  gezelter
21	>
22	>	* Makefile: testing to make sure GNU make is the make that was used
23	>	to build OOPSE
24	>
25	>	2006-01-13 10:48  gezelter
26	>
27	>	* configure, ac-tools/configure.in: changed compiler search order
28	>
29	>	2006-01-12 19:09  chuckv
30	>
31	>	* forceFields/SuttonChen.QSC.frc, forceFields/SuttonChen.frc,
32	>	samples/metals/Sutton-Chen/Au_bulk.in,
33	>	samples/metals/Sutton-Chen/Au_bulk_QSC.md,
34	>	samples/metals/Sutton-Chen/Au_bulk_SC.md: Changes in Sutton-Chen
35	>	units
36	>
37	>	2006-01-12 16:16  gezelter
38	>
39	>	* LICENSE, configure, src/applications/oopse/oopse.cpp: fixed some
40	>	version info and the copyright date
41	>
42	>	2006-01-12 15:52  gezelter
43	>
44	>	* src/config.h.in: added some missing checks for header files
45	>	(particularly zlib.h), used autoheader to help generate config.h.in
46	>
47	>	2006-01-12 15:51  gezelter
48	>
49	>	* configure, ac-tools/configure.in: added some missing checks for
50	>	header files (particularly zlib.h)
51	>
52	>	2006-01-12 15:19  gezelter
53	>
54	>	* make/Makefile.in: fixed a dependency problem for the Executable
55	>	builds
56	>
57	>	2006-01-12 15:02  gezelter
58	>
59	>	* samples/gbljtest/Makefile: Missing Makefile in this sample
60	>	directory
61	>
62	>	2006-01-12 15:01  gezelter
63	>
64	>	* make/Makefile.in, samples/Makefile.in, samples/cutoff/Makefile:
65	>	Old makefile.in no longer required
66	>
67	>	2006-01-12 15:01  gezelter
68	>
69	>	* forceFields/: Makefile, Makefile.in: All of the OpenBabel stuff
70	>	needs to be installed
71	>
72	>	2006-01-12 14:56  chuckv
73	>
74	>	* src/io/DumpWriter.cpp: Changed formating.
75	>
76	>	2006-01-12 11:47  chrisfen
77	>
78	>	* samples/water/tip4p/tp4.md,
79	>	src/UseTheForce/DarkSide/electrostatic.F90,
80	>	src/UseTheForce/DarkSide/electrostatic_interface.F90,
81	>	src/UseTheForce/DarkSide/electrostatic_interface.h,
82	>	src/brains/SimInfo.cpp: unifying function name in electrostatics
83	>
84	>	2006-01-12 11:04  tim
85	>
86	>	* samples/metals/: EAM/nanoparticle/Makefile,
87	>	EAM/nanorod/Au_nanoparticle.in, EAM/nanorod/Makefile,
88	>	Sutton-Chen/Makefile: fix make install problem for metals samples
89	>
90	>	2006-01-12 10:22  tim
91	>
92	>	* make/Makefile.in: remove samples/metals from install list.
93	>
94	>	2006-01-12 09:31  tim
95	>
96	>	* src/io/: ForceFieldOptions.cpp, Globals.cpp: filepp can not
97	>	handle multiple line macro, just convert multiple line macro into
98	>	single line macro.
99	>
100	>	2006-01-11 23:13  chrisfen
101	>
102	>	* src/: UseTheForce/DarkSide/electrostatic.F90,
103	>	UseTheForce/DarkSide/neighborLists.F90, io/Globals.cpp: Made some
104	>	changes to electrostatics for shifted-potential and shifted-force
105	>	with mono and multipoles
106	>
107	>	2006-01-11 18:04  gezelter
108	>
109	>	* src/config.h.in, src/UseTheForce/doForces_interface.h,
110	>	src/UseTheForce/DarkSide/atype_interface.h,
111	>	src/UseTheForce/DarkSide/eam_interface.h,
112	>	src/UseTheForce/DarkSide/electrostatic_interface.h,
113	>	src/UseTheForce/DarkSide/fForceOptions_interface.h,
114	>	src/UseTheForce/DarkSide/gb_interface.h,
115	>	src/UseTheForce/DarkSide/lj_interface.h,
116	>	src/UseTheForce/DarkSide/shapes_interface.h,
117	>	src/UseTheForce/DarkSide/simParallel_interface.h,
118	>	src/UseTheForce/DarkSide/simulation_interface.h,
119	>	src/UseTheForce/DarkSide/sticky_interface.h,
120	>	src/UseTheForce/DarkSide/suttonchen_interface.h,
121	>	src/UseTheForce/DarkSide/switcheroo_interface.h,
122	>	src/mdParser/MDParser.g, src/profiling/mdProfile.cpp,
123	>	src/utils/fError.c, configure, make/Makefile.in: autoconf
124	>	modernization and cruft removal
125	>
126	>	2006-01-11 18:04  gezelter
127	>
128	>	* ac-tools/: aclocal.m4, configure.in, fortran90.m4: autoconf
129	>	modernization and cruft-removal
130	>
131	>	2006-01-11 17:50  tim
132	>
133	>	* src/types/: BendStamp.hpp, BondStamp.hpp, TorsionStamp.hpp: fix
134	>	some error messages
135	>
136	>	2006-01-11 14:01  tim
137	>
138	>	* src/: applications/staticProps/RhoZ.cpp, brains/SimCreator.cpp,
139	>	io/Globals.cpp, types/AtomStamp.cpp, types/BendStamp.hpp,
140	>	types/BondStamp.hpp, types/DataHolder.hpp, types/MoleculeStamp.cpp,
141	>	types/TorsionStamp.hpp, utils/OOPSEException.hpp,
142	>	utils/StringUtils.hpp: instead of printing to std::cout, throwing
143	>	an exception when error is found.
144	>
145	>	2006-01-11 13:41  gezelter
146	>
147	>	* src/types/: AtomStamp.hpp, MoleculeStamp.cpp: Fixed a spelling
148	>	error
149	>
150	>	2006-01-10 17:55  chuckv
151	>
152	>	* forceFields/SuttonChen.frc: Changed conversion factor.
153	>
154	>	2006-01-10 16:14  chuckv
155	>
156	>	* samples/metals/Sutton-Chen/Au_bulk_SC.md,
157	>	src/UseTheForce/DarkSide/suttonchen.F90: Sutton and Chen should be
158	>	working now.
159	>
160	>	2006-01-09 17:22  chuckv
161	>
162	>	* src/UseTheForce/doForces.F90: Fixed SC bug with SIM_uses_SC
163	>
164	>	2006-01-09 17:14  tim
165	>
166	>	* src/applications/staticProps/: Makefile, RhoZ.cpp, RhoZ.hpp,
167	>	StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
168	>	StaticPropsCmd.h: fixing RhoZ
169	>
170	>	2006-01-09 14:26  chuckv
171	>
172	>	* forceFields/SuttonChen.frc,
173	>	samples/metals/Sutton-Chen/Au_bulk_SC.md,
174	>	src/io/LennardJonesAtomTypesSectionParser.cpp,
175	>	src/io/SCAtomTypesSectionParser.cpp: Added energy scaling to
176	>	section parsers.
177	>
178	>	2006-01-09 14:11  tim
179	>
180	>	* src/: io/ForceFieldOptions.hpp, utils/StringUtils.cpp,
181	>	utils/StringUtils.hpp: replace isType<int> with isInteger
182	>
183	>	2006-01-06 16:15  tim
184	>
185	>	* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: remove extra
186	>	forceFieldOptions from SC_FF
187	>
188	>	2006-01-06 15:27  chuckv
189	>
190	>	* forceFields/SuttonChen.frc: Add force file.
191	>
192	>	2005-12-31 17:42  chuckv
193	>
194	>	* src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen no longer
195	>	segfaults or produces 0 potential, but rather produces Inf for the
196	>	potential. Progress....
197	>
198	>	2005-12-30 18:15  chuckv
199	>
200	>	* samples/metals/Sutton-Chen/Au_bulk_SC.md,
201	>	src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90,
202	>	src/UseTheForce/DarkSide/suttonchen.F90, src/brains/SimInfo.cpp,
203	>	src/io/ForceFieldOptions.cpp, src/io/ForceFieldOptions.hpp: More
204	>	Sutton-Chen bug fixes.
205	>
206	>	2005-12-30 16:25  tim
207	>
208	>	* src/: UseTheForce/doForces.F90, brains/Thermo.cpp: Long range
209	>	potential return from fortran is already accumulated, it should not
210	>	be accumulated again; nGroupTypesCol is not initialized;
211	>	GroupMaxCutoffCol is not allocated;
212	>
213	>	2005-12-30 10:32  tim
214	>
215	>	* make/Makefile.in, src/brains/SimCreator.cpp: In order to compile
216	>	MPI version, we need to cast const char* to void* for
217	>	stringstream.str(); Previous Makefile use bjects of single version
218	>	to make the MPI library;
219	>
220	>	2005-12-29 19:18  chuckv
221	>
222	>	* make/Makefile.in, samples/metals/Makefile,
223	>	src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90,
224	>	src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen bug fixes.
225	>	Almost there...
226	>
227	>	2005-12-29 15:19  chuckv
228	>
229	>	* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Changes in
230	>	forcefield.
231	>
232	>	2005-12-29 15:07  chuckv
233	>
234	>	* samples/metals/Sutton-Chen/: Au_bulk.in, Au_bulk_SC.md, Makefile,
235	>	metals.md: added files for sutton-chen
236	>
237	>	2005-12-29 11:37  chuckv
238	>
239	>	* samples/metals/EAM/nanorod/: Au_nanoparticle_FCC.md, Makefile,
240	>	metals.md: More cvs changing.
241	>
242	>	2005-12-29 11:34  chuckv
243	>
244	>	* samples/metals/Au_nanoparticle.in: More moving...
245	>
246	>	2005-12-29 11:33  chuckv
247	>
248	>	* samples/metals/EAM/nanoparticle/:
249	>	Au-Core-Ag-Shell_Nanoparticle.in, Au-Core-Ag-Shell_Nanoparticle.md,
250	>	Au_nanoparticle.in, Au_nanoparticle.md, Makefile, metals.md: More
251	>	changes to directory structure.
252	>
253	>	2005-12-29 11:21  chuckv
254	>
255	>	* samples/metals/EAM/: Au_bulk.in, Au_bulk_FBD.md,
256	>	Au_bulk_voter.md, Makefile, metals.md: More Directory changes...
257	>
258	>	2005-12-29 11:17  chuckv
259	>
260	>	* samples/metals/: Au-Core-Ag-Shell_Nanoparticle.in,
261	>	Au-Core-Ag-Shell_Nanoparticle.md, Au_bulk.in, Au_bulk_FBD.md,
262	>	Au_bulk_voter.md, Au_nanoparticle.md, metals.md: More changing of
263	>	directory structure
264	>
265	>	2005-12-29 11:03  chuckv
266	>
267	>	* src/: UseTheForce/DarkSide/fForceOptions_interface.F90,
268	>	brains/SimCreator.cpp: Fixed issue with symbol naming and added
269	>	call to set force options in SimCreator.
270	>
271	>	2005-12-28 16:44  chuckv
272	>
273	>	* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp: More
274	>	changes to forcefield options.
275	>
276	>	2005-12-28 16:42  chuckv
277	>
278	>	* src/UseTheForce/: ForceField.cpp, ForceField.hpp: Force options
279	>	passed to fortran.
280	>
281	>	2005-12-23 18:04  chuckv
282	>
283	>	* src/: UseTheForce/DarkSide/fForceOptions_interface.h,
284	>	io/ForceFieldOptions.cpp, io/ForceFieldOptions.hpp: Force option
285	>	changes.
286	>
287	>	2005-12-16 16:52  tim
288	>
289	>	* configure, ac-tools/aclocal.m4, ac-tools/configure.in,
290	>	src/config.h.in, src/UseTheForce/DarkSide/gb.F90,
291	>	src/openbabel/bitvec.cpp, src/openbabel/bondtyper.cpp,
292	>	src/openbabel/chains.cpp, src/openbabel/chiral.cpp,
293	>	src/openbabel/data.cpp, src/openbabel/fingerprint.cpp,
294	>	src/openbabel/fingerprintformat.cpp, src/openbabel/generic.cpp,
295	>	src/openbabel/gromos96format.hpp, src/openbabel/kekulize.cpp,
296	>	src/openbabel/matrix3x3.cpp, src/openbabel/mol.cpp,
297	>	src/openbabel/molchrg.cpp, src/openbabel/obatom.cpp,
298	>	src/openbabel/obbond.cpp, src/openbabel/oberror.cpp,
299	>	src/openbabel/oberror.hpp, src/openbabel/obmolecformat.hpp,
300	>	src/openbabel/obutil.cpp, src/openbabel/patty.cpp,
301	>	src/openbabel/pdbformat.cpp, src/openbabel/phmodel.cpp,
302	>	src/openbabel/povrayformat.hpp, src/openbabel/residue.cpp,
303	>	src/openbabel/ring.cpp, src/openbabel/rotor.cpp,
304	>	src/openbabel/smilesformat.cpp, src/openbabel/tinkerformat.hpp,
305	>	src/openbabel/typer.cpp, src/openbabel/xyzformat.cpp: changed
306	>	__FUNCTION__ to __func__ to match C99 standard, and then added an
307	>	autoconf test to check for __func__ usability.  Changed some
308	>	default compile flags for the Sun architecture
309	>
310	>	2005-12-16 14:01  gezelter
311	>
312	>	* ac-tools/AC_CXX_HAVE_STL.m4: added the STL check
313	>
314	>	2005-12-16 13:55  tim
315	>
316	>	* src/utils/: CaseConversion.hpp, ParameterManager.hpp: make minor
317	>	change to build oopse under solaris
318	>
319	>	2005-12-16 13:26  tim
320	>
321	>	* src/: brains/SimCreator.cpp, io/Globals.cpp,
322	>	types/MoleculeStamp.cpp, utils/Predicate.hpp: the standard library
323	>	came with SUN compiler does not have a conforming std::use_facet,
324	>	define a macro to handle it. Adding exception handling to
325	>	SimCreator.
326	>
327	>	2005-12-16 10:53  gezelter
328	>
329	>	* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md,
330	>	GB-Ar-traditional.md, gb-ar.in: Removed one parasitic argon atom
331	>	which was living inside the GB particle.  No alien-like ripping out
332	>	of the stomach was required.
333	>
334	>	2005-12-15 21:57  tim
335	>
336	>	* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp,
337	>	MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp,
338	>	MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp:
339	>	replace grammar for numerical parsing
340	>
341	>	2005-12-15 16:43  gezelter
342	>
343	>	* src/UseTheForce/doForces.F90: fixed a cutoff bug
344	>
345	>	2005-12-15 09:48  gezelter
346	>
347	>	* src/antlr/: CharScanner.hpp, config.hpp: Removing compiler
348	>	dependencies and replacing them with real autoconf checks
349	>
350	>	2005-12-15 09:47  gezelter
351	>
352	>	* configure, ac-tools/AC_CXX_NAMESPACES.m4, ac-tools/AC_CXX_STD.m4,
353	>	ac-tools/configure.in, src/config.h.in: Adding checks for various
354	>	features used by ANTLR
355	>
356	>	2005-12-14 13:02  tim
357	>
358	>	* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp,
359	>	MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp,
360	>	MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: fix a
361	>	nasty negative integer parsing problem by refining the grammar
362	>
363	>	2005-12-12 14:32  gezelter
364	>
365	>	* src/: UseTheForce/doForces_interface.F90,
366	>	UseTheForce/doForces_interface.h,
367	>	UseTheForce/DarkSide/electrostatic.F90,
368	>	UseTheForce/DarkSide/electrostatic_interface.F90,
369	>	UseTheForce/DarkSide/electrostatic_interface.h,
370	>	brains/MoleculeCreator.cpp, brains/SimInfo.cpp,
371	>	math/ChebyshevPolynomials.hpp, openbabel/obconversion.hpp: made
372	>	some minor changes to allow compilation with the portland group
373	>	compilers
374	>
375	>	2005-12-10 11:54  tim
376	>
377	>	* src/: types/MoleculeStamp.cpp, utils/Tuple.hpp: fixed compilation
378	>	problem for icc7
379	>
380	>	2005-12-09 16:18  gezelter
381	>
382	>	* src/utils/CaseConversion.hpp: added missing include
383	>
384	>	2005-12-09 12:11  gezelter
385	>
386	>	* configure, ac-tools/aclocal.m4: added some checks for pathscale
387	>	compiler
388	>
389	>	2005-12-08 17:05  gezelter
390	>
391	>	* src/io/ForceFieldOptions.cpp: added copyright
392	>
393	>	2005-12-08 17:04  gezelter
394	>
395	>	* src/UseTheForce/doForces.F90: added info printout
396	>
397	>	2005-12-08 17:04  gezelter
398	>
399	>	* configure, ac-tools/configure.in: added pathscale
400	>
401	>	2005-12-08 10:38  chuckv
402	>
403	>	* src/: UseTheForce/CLAYFF.cpp, UseTheForce/DUFF.cpp,
404	>	UseTheForce/EAM_FF.cpp, UseTheForce/SC_FF.cpp,
405	>	UseTheForce/SHAPES_FF.cpp, io/BendTypesSectionParser.cpp,
406	>	io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
407	>	io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
408	>	io/ChargeAtomTypesSectionParser.hpp,
409	>	io/DirectionalAtomTypesSectionParser.cpp,
410	>	io/DirectionalAtomTypesSectionParser.hpp,
411	>	io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
412	>	io/GayBerneAtomTypesSectionParser.cpp,
413	>	io/GayBerneAtomTypesSectionParser.hpp,
414	>	io/MultipoleAtomTypesSectionParser.cpp,
415	>	io/MultipoleAtomTypesSectionParser.hpp,
416	>	io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp,
417	>	io/ShapeAtomTypesSectionParser.cpp,
418	>	io/ShapeAtomTypesSectionParser.hpp,
419	>	io/StickyAtomTypesSectionParser.cpp,
420	>	io/StickyAtomTypesSectionParser.hpp,
421	>	io/StickyPowerAtomTypesSectionParser.cpp,
422	>	io/StickyPowerAtomTypesSectionParser.hpp,
423	>	io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp:
424	>	Wow thats alot o' files. Now passing forceFieldOptions to all of
425	>	the parsers.
426	>
427	>	2005-12-07 18:10  chuckv
428	>
429	>	* src/UseTheForce/: CLAYFF.cpp, DUFF.cpp, EAM_FF.cpp, EAM_FF.hpp,
430	>	SHAPES_FF.cpp, SHAPES_FF.hpp: This should really break things....
431	>	Started adding support for ForceOptions to section parsers.
432	>
433	>	2005-12-07 18:01  gezelter
434	>
435	>	* src/UseTheForce/DarkSide/gb_interface.h: [no log message]
436	>
437	>	2005-12-07 18:00  chuckv
438	>
439	>	* src/io/: LennardJonesAtomTypesSectionParser.cpp,
440	>	LennardJonesAtomTypesSectionParser.hpp: Added forceOptions to
441	>	section parser
442	>
443	>	2005-12-07 14:58  chuckv
444	>
445	>	* src/UseTheForce/DarkSide/: LJ.F90, lj_interface.F90,
446	>	lj_interface.h, suttonchen.F90, suttonchen_interface.F90,
447	>	suttonchen_interface.h: Removed geometric distance mixing from
448	>	individual modules and now use force options to detemine what the
449	>	deal is.
450	>
451	>	2005-12-07 14:46  chuckv
452	>
453	>	* src/UseTheForce/: fForceOptions.h, DarkSide/fForceOptions.F90:
454	>	Further fixes for compiler issues.
455	>
456	>	2005-12-07 14:44  chuckv
457	>
458	>	* src/UseTheForce/fForceOptions.h: Fixed ifc public-private issue.
459	>
460	>	2005-12-07 14:38  chuckv
461	>
462	>	* src/UseTheForce/DarkSide/: Makefile, fForceOptions.F90,
463	>	fForceOptions_interface.F90, fForceOptions_interface.h: Added
464	>	support for fortran force options.
465	>
466	>	2005-12-06 16:01  tim
467	>
468	>	* src/types/MoleculeStamp.cpp: Fixed a bug in checkTorsion
469	>
470	>	2005-12-06 14:26  chuckv
471	>
472	>	* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: Changes to SC.
473	>
474	>	2005-12-06 12:53  chuckv
475	>
476	>	* src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
477	>	GeometryBuilder.hpp, nanorodBuilder.cpp: Changes to build twinned
478	>	crystal
479	>
480	>	2005-12-06 12:52  chuckv
481	>
482	>	* src/io/: DumpWriter.cpp, DumpWriter.hpp: Overloaded interface for
483	>	dumpwriter.
484	>
485	>	2005-12-06 11:49  tim
486	>
487	>	* samples/: alkane/alkanes.md, alkane/butane.md, argon/500.md,
488	>	argon/ar864.md, argon/argonNVT.md, argon/lj.md,
489	>	dipole/splitDipole.md, dipole/splitInWater.md, dipole/split_SSD.md,
490	>	dipole/twoSplitDipole.md, dipole/water.md, gbljtest/2gb.md,
491	>	gbljtest/gb.md, gbljtest/gb2lj1.md, gbljtest/gbRotRoundX.md,
492	>	gbljtest/gbRotRoundY.md, gbljtest/gbRotRoundZ.md, gbljtest/lj.md,
493	>	lipid/5x5.md, lipid/lipid.md, lipid/water.md,
494	>	metals/Au-Core-Ag-Shell_Nanoparticle.md, metals/Au_bulk_FBD.md,
495	>	metals/Au_bulk_voter.md, metals/Au_nanoparticle.md,
496	>	metals/metals.md, minimizer/ssdEM.md, minimizer/tip4p_two.md,
497	>	minimizer/water.md, shape/linear.md,
498	>	thermoIntegration/liquid/ssde.md,
499	>	thermoIntegration/liquid/water.md, thermoIntegration/solid/ssde.md,
500	>	thermoIntegration/solid/water.md, water/dimer/cl.md,
501	>	water/dimer/mix.md, water/dimer/mix2.md, water/dimer/ssd.md,
502	>	water/dimer/tap.md, water/dimer/two.md, water/dimer/water.md,
503	>	water/spce/spce.md, water/spce/water.md, water/ssd/ssd.md,
504	>	water/ssd/water.md, water/ssd-ion/ssdCl.md, water/ssd-ion/water.md,
505	>	water/ssde/ssde.md, water/ssde/water.md, water/ssdrf/ssdrf.md,
506	>	water/ssdrf/water.md, water/tap/tap.md, water/tap/water.md,
507	>	water/tip3p_ice/tp3.md, water/tip3p_ice/water.md,
508	>	water/tip4p/tp4.md, water/tip4p/water.md, zcons/water.md,
509	>	zcons/zconsFixed.md, zcons/zconsMoving.md: remove deprecated
510	>	keywords from samples
511	>
512	>	2005-12-05 18:37  tim
513	>
514	>	* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp,
515	>	Globals.cpp, Makefile: Fix parsing error in OptionSectionParser
516	>
517	>	2005-12-05 17:23  gezelter
518	>
519	>	* src/: UseTheForce/CLAYFF.cpp, UseTheForce/CLAYFF.hpp,
520	>	UseTheForce/Makefile, brains/Register.cpp,
521	>	io/ForceFieldOptions.hpp, io/OptionSectionParser.cpp: Adding
522	>	handler for CLAY force field
523	>
524	>	2005-12-05 16:45  chuckv
525	>
526	>	* src/openbabel/: zipstream.hpp, zipstreamimpl.hpp: Fixed build bug
527	>	in openbabel.
528	>
529	>	2005-12-05 14:10  tim
530	>
531	>	* src/types/MoleculeStamp.cpp: reformat error message
532	>
533	>	2005-12-05 14:07  gezelter
534	>
535	>	* forceFields/CLAYFF.frc: Adding .frc file for CLAYFF
536	>
537	>	2005-12-05 13:23  tim
538	>
539	>	* src/: types/AtomStamp.cpp, types/AtomStamp.hpp,
540	>	types/BendStamp.hpp, types/MoleculeStamp.cpp,
541	>	types/MoleculeStamp.hpp, types/TorsionStamp.hpp, utils/Tuple.hpp:
542	>	adding more checking for topology
543	>
544	>	2005-12-02 17:37  gezelter
545	>
546	>	* src/antlr/TokenStreamRewriteEngine.cpp: Spurious semicolon
547	>	removal
548	>
549	>	2005-12-02 17:37  gezelter
550	>
551	>	* src/config.h.in: We've made big changes.  This isn't 2.0 anymore.
552	>
553	>	2005-12-02 17:37  gezelter
554	>
555	>	* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md,
556	>	GB-Ar-traditional.md, cutoff_test.md, gb.md, lj.md, max.md, mix.md,
557	>	traditional.md: removing deprecated nAtoms and nComponents lines
558	>
559	>	2005-12-02 15:34  tim
560	>
561	>	* src/selection/SelectionToken.cpp: adding SelectionToken.cpp
562	>
563	>	2005-12-02 15:18  tim
564	>
565	>	* src/types/: FragmentStamp.cpp, FragmentStamp.hpp: Adding
566	>	FragmentStamp
567	>
568	>	2005-12-02 15:11  gezelter
569	>
570	>	* src/openbabel/: matrix3x3.cpp, matrix3x3.hpp: Errors are no
571	>	longer thrown with consts (fixes compilation bug on the Mac).
572	>
573	>	2005-12-02 15:10  gezelter
574	>
575	>	* src/integrators/VelocityVerletIntegrator.cpp: Got rid of spurious
576	>	printing out of timestep
577	>
578	>	2005-12-02 15:10  gezelter
579	>
580	>	* src/brains/ForceManager.cpp: Got rid of spurious printing out of
581	>	junk
582	>
583	>	2005-12-02 15:10  gezelter
584	>
585	>	* make/Makefile.in: Change build process for libOOPSE.a so that the
586	>	libraries aren't unpacked.  libOOPSE.a is now made directly from
587	>	the object files
588	>
589	>	2005-12-02 15:09  gezelter
590	>
591	>	* configure, ac-tools/configure.in: added check for egrep (grep -E)
592	>	needed for new build of libOOPSE.a
593	>
594	>	2005-12-02 13:43  tim
595	>
596	>	* src/types/DataHolder.hpp: adding DataHolder
597	>
598	>	2005-12-02 12:01  gezelter
599	>
600	>	* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md,
601	>	GB-Ar-traditional.md, gb-ar.in, gb.md: Added Gay-Berne / Argon test
602	>	case for the cutoff policies
603	>
604	>	2005-12-02 10:38  tim
605	>
606	>	* make/Makefile.in: update Makefile
607	>
608	>	2005-12-02 10:38  tim
609	>
610	>	* src/: antlr/ANTLRException.hpp, antlr/ANTLRUtil.cpp,
611	>	antlr/ANTLRUtil.hpp, antlr/AST.hpp, antlr/ASTArray.hpp,
612	>	antlr/ASTFactory.cpp, antlr/ASTFactory.hpp, antlr/ASTNULLType.cpp,
613	>	antlr/ASTNULLType.hpp, antlr/ASTPair.hpp, antlr/ASTRefCount.cpp,
614	>	antlr/ASTRefCount.hpp, antlr/BaseAST.cpp, antlr/BaseAST.hpp,
615	>	antlr/BitSet.cpp, antlr/BitSet.hpp, antlr/CharBuffer.cpp,
616	>	antlr/CharBuffer.hpp, antlr/CharInputBuffer.hpp,
617	>	antlr/CharScanner.cpp, antlr/CharScanner.hpp,
618	>	antlr/CharStreamException.hpp, antlr/CharStreamIOException.hpp,
619	>	antlr/CircularQueue.hpp, antlr/CommonAST.cpp, antlr/CommonAST.hpp,
620	>	antlr/CommonASTWithHiddenTokens.cpp,
621	>	antlr/CommonASTWithHiddenTokens.hpp,
622	>	antlr/CommonHiddenStreamToken.cpp,
623	>	antlr/CommonHiddenStreamToken.hpp, antlr/CommonToken.cpp,
624	>	antlr/CommonToken.hpp, antlr/IOException.hpp,
625	>	antlr/InputBuffer.cpp, antlr/InputBuffer.hpp, antlr/LLkParser.cpp,
626	>	antlr/LLkParser.hpp, antlr/LexerSharedInputState.hpp,
627	>	antlr/Makefile, antlr/MismatchedCharException.cpp,
628	>	antlr/MismatchedCharException.hpp,
629	>	antlr/MismatchedTokenException.cpp,
630	>	antlr/MismatchedTokenException.hpp, antlr/NoViableAltException.cpp,
631	>	antlr/NoViableAltException.hpp,
632	>	antlr/NoViableAltForCharException.cpp,
633	>	antlr/NoViableAltForCharException.hpp, antlr/Parser.cpp,
634	>	antlr/Parser.hpp, antlr/ParserSharedInputState.hpp,
635	>	antlr/RecognitionException.cpp, antlr/RecognitionException.hpp,
636	>	antlr/RefCount.hpp, antlr/SemanticException.hpp, antlr/String.cpp,
637	>	antlr/String.hpp, antlr/Token.cpp, antlr/Token.hpp,
638	>	antlr/TokenBuffer.cpp, antlr/TokenBuffer.hpp,
639	>	antlr/TokenRefCount.cpp, antlr/TokenRefCount.hpp,
640	>	antlr/TokenStream.hpp, antlr/TokenStreamBasicFilter.cpp,
641	>	antlr/TokenStreamBasicFilter.hpp, antlr/TokenStreamException.hpp,
642	>	antlr/TokenStreamHiddenTokenFilter.cpp,
643	>	antlr/TokenStreamHiddenTokenFilter.hpp,
644	>	antlr/TokenStreamIOException.hpp,
645	>	antlr/TokenStreamRecognitionException.hpp,
646	>	antlr/TokenStreamRetryException.hpp,
647	>	antlr/TokenStreamRewriteEngine.cpp,
648	>	antlr/TokenStreamRewriteEngine.hpp, antlr/TokenStreamSelector.cpp,
649	>	antlr/TokenStreamSelector.hpp, antlr/TokenWithIndex.hpp,
650	>	antlr/TreeParser.cpp, antlr/TreeParser.hpp,
651	>	antlr/TreeParserSharedInputState.hpp, antlr/config.hpp,
652	>	applications/oopse/oopse.cpp, brains/ForceManager.cpp,
653	>	brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
654	>	brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
655	>	constraints/ZconstraintForceManager.cpp,
656	>	integrators/VelocityVerletIntegrator.cpp, io/BASS_interface.cpp,
657	>	io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h,
658	>	io/BASSlex.l, io/BASSyacc.y, io/Globals.cpp, io/Globals.hpp,
659	>	io/LinkedAssign.cpp, io/LinkedAssign.hpp, io/Makefile,
660	>	io/ZConsReader.cpp, io/interface.c, io/make_nodes.c,
661	>	io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/node_list.h,
662	>	io/parse_interface.h, io/parse_me.h, io/parse_tree.c,
663	>	io/parse_tree.h, mdParser/FilenameObserver.cpp,
664	>	mdParser/FilenameObserver.hpp, mdParser/MDLexer.cpp,
665	>	mdParser/MDLexer.hpp, mdParser/MDParser.cpp, mdParser/MDParser.g,
666	>	mdParser/MDParser.hpp, mdParser/MDTokenTypes.hpp,
667	>	mdParser/MDTreeParser.cpp, mdParser/MDTreeParser.g,
668	>	mdParser/MDTreeParser.hpp, mdParser/MDTreeParserTokenTypes.hpp,
669	>	mdParser/Makefile, mdParser/SimplePreprocessor.hpp,
670	>	openbabel/obconversion.cpp, openbabel/oopseformat.cpp,
671	>	openbabel/xyzformat.cpp, primitives/RigidBody.cpp,
672	>	selection/DistanceFinder.cpp, selection/DistanceFinder.hpp,
673	>	selection/IndexFinder.cpp, selection/IndexFinder.hpp,
674	>	selection/Makefile, selection/NameFinder.cpp,
675	>	selection/NameFinder.hpp, selection/SelectionCompiler.hpp,
676	>	selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
677	>	selection/SelectionManager.hpp, selection/SelectionToken.hpp,
678	>	selection/Token.cpp, selection/Token.hpp, selection/TokenMap.hpp,
679	>	types/AtomStamp.cpp, types/AtomStamp.hpp, types/BendStamp.cpp,
680	>	types/BendStamp.hpp, types/BondStamp.cpp, types/BondStamp.hpp,
681	>	types/Component.cpp, types/Component.hpp,
682	>	types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
683	>	types/MakeStamps.cpp, types/MakeStamps.hpp, types/Makefile,
684	>	types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
685	>	types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
686	>	types/TorsionStamp.cpp, types/TorsionStamp.hpp,
687	>	types/ZconStamp.cpp, types/ZconStamp.hpp, types/ZconsStamp.cpp,
688	>	types/ZconsStamp.hpp, utils/BitSet.cpp, utils/BitSet.hpp,
689	>	utils/Makefile.in, utils/MoLocator.cpp, utils/OOPSEBitSet.cpp,
690	>	utils/OOPSEBitSet.hpp, utils/StringTokenizer.cpp,
691	>	utils/StringTokenizer.hpp, visitors/ZconsVisitor.cpp: End of the
692	>	Link --> List Return of the Oject-Oriented replace yacc/lex parser
693	>	with antlr parser
694	>
695	>	2005-11-30 16:00  chuckv
696	>
697	>	* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Code to
698	>	calculate rho(Z) to calculate density profiles for water slabs.
699	>
700	>	2005-11-29 17:54  chuckv
701	>
702	>	* configure, ac-tools/configure.in: added checks for some functions
703	>	to configure script
704	>
705	>	2005-11-22 20:05  chuckv
706	>
707	>	* src/openbabel/: Makefile, atom.cpp, bond.cpp, obatom.cpp,
708	>	obbond.cpp: Changed file names that conflict w/ oopse file name
709	>	object files.
710	>
711	>	2005-11-21 17:59  gezelter
712	>
713	>	* src/utils/residentMem.c: compilation bug
714	>
715	>	2005-11-21 17:59  gezelter
716	>
717	>	* src/io/: ForceFieldOptions.hpp, Globals.cpp: parsing by filepp
718	>
719	>	2005-11-21 17:59  gezelter
720	>
721	>	* src/brains/: SimInfo.cpp, SimInfo.hpp: Cutoff Mixing fixes
722	>
723	>	2005-11-21 17:59  gezelter
724	>
725	>	* src/applications/atom2mdin/: Makefile, atom2mdin.cpp: compilation
726	>	issue
727	>
728	>	2005-11-21 17:58  gezelter
729	>
730	>	* src/UseTheForce/: ForceField.hpp, Makefile, doForces.F90,
731	>	doForces_interface.F90, doForces_interface.h, fForceOptions.h,
732	>	notifyCutoffs.F90, notifyCutoffs_interface.F90,
733	>	notifyCutoffs_interface.h, DarkSide/LJ.F90,
734	>	DarkSide/electrostatic.F90, DarkSide/gb.F90,
735	>	DarkSide/suttonchen.F90: Cutoff mixing fixes have been made.
736	>
737	>	2005-11-21 11:22  tim
738	>
739	>	* src/io/ParamConstraint.cpp: Adding  ParamConstraint.cpp
740	>
741	>	2005-11-21 09:59  tim
742	>
743	>	* forceFields/: SMARTS_InteLigand_051110.txt, aromatic.txt,
744	>	atomtyp.txt, bondtyp.txt, element.txt, extable.txt,
745	>	isotope-small.txt, isotope.txt, patterns.txt, phmodel.txt,
746	>	resdata.txt, torlib.txt, types.txt: adding openbabel data files
747	>
748	>	2005-11-18 15:17  tim
749	>
750	>	* src/: applications/atom2mdin/Makefile, openbabel/oopseformat.cpp:
751	>	adding support for soft linking
752	>
753	>	2005-11-18 15:17  tim
754	>
755	>	* make/Makefile.in: Adding support for soft linking
756	>
757	>	2005-11-18 12:50  gezelter
758	>
759	>	* make/Makefile.in: Adding linking stuff
760	>
761	>	2005-11-18 11:38  tim
762	>
763	>	* make/Makefile.in, src/applications/atom2mdin/Makefile,
764	>	src/applications/atom2mdin/atom2mdin.cpp,
765	>	src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp:
766	>	rename mdinConverter to atom2mdin
767	>
768	>	2005-11-17 15:44  gezelter
769	>
770	>	* src/openbabel/obconversion.cpp: fixed a bug
771	>
772	>	2005-11-17 15:39  gezelter
773	>
774	>	* configure: Adding some config checks for OpenBabel codes we are
775	>	using
776	>
777	>	2005-11-17 15:39  gezelter
778	>
779	>	* ac-tools/configure.in: Adding some checks for OpenBabel code
780	>
781	>	2005-11-17 15:39  gezelter
782	>
783	>	* src/config.h.in: Unifying config.h stuff from OOPSE and OpenBabel
784	>
785	>	2005-11-17 15:38  gezelter
786	>
787	>	* src/openbabel/: babelconfig.hpp, base.cpp, base.hpp, bitvec.hpp,
788	>	bondtyper.cpp, config.h.in, config.hpp, data.cpp, data.hpp,
789	>	fingerprint.cpp, generic.hpp, grid.hpp, matrix.hpp, mol.hpp,
790	>	obconversion.hpp, oberror.cpp, oberror.hpp, obutil.cpp, obutil.hpp,
791	>	patty.cpp, pdbformat.hpp, phmodel.cpp, povrayformat.hpp,
792	>	residue.cpp, rotor.cpp, smilesformat.cpp, tokenst.cpp, typer.cpp:
793	>	Unifying config.h stuff and making sure the OpenBabel codes can
794	>	find our default (and environment variable) Force Field
795	>	directories.
796	>
797	>	2005-11-17 13:35  tim
798	>
799	>	* src/io/ForceFieldOptions.hpp: adding ForceFieldOptions
800	>
801	>	2005-11-16 18:10  tim
802	>
803	>	* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
804	>	brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp,
805	>	brains/ForceManager.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp,
806	>	integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp,
807	>	io/Globals.hpp, io/Makefile, io/OptionSectionParser.cpp,
808	>	io/OptionSectionParser.hpp, io/ParamConstraint.hpp,
809	>	io/SectionParser.hpp, io/SectionParserManager.cpp,
810	>	io/TorsionTypesSectionParser.cpp, math/ChebyshevPolynomials.hpp,
811	>	math/Makefile, math/Polynomial.hpp, primitives/Bend.cpp,
812	>	primitives/Bend.hpp, primitives/GhostBend.cpp,
813	>	primitives/GhostBend.hpp, primitives/GhostTorsion.cpp,
814	>	primitives/GhostTorsion.hpp, primitives/Torsion.cpp,
815	>	primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp,
816	>	primitives/UreyBradleyBend.hpp, types/CharmmTorsionType.cpp,
817	>	types/CharmmTorsionType.hpp, types/CubicTorsionType.hpp,
818	>	types/PolynomialTorsionType.hpp, types/QuarticTorsionType.hpp,
819	>	types/TorsionType.hpp, utils/StringUtils.hpp: OptionSectionParser
820	>	get compiled
821	>
822	>	2005-11-16 16:37  chuckv
823	>
824	>	* src/: io/Globals.cpp, io/Globals.hpp, io/OptionSectionParser.cpp,
825	>	io/OptionSectionParser.hpp, io/SCAtomTypesSectionParser.cpp,
826	>	UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField
827	>	optional parameters....
828	>
829	>	2005-11-16 16:22  tim
830	>
831	>	* src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp,
832	>	fingerprint.hpp, fingerprintformat.cpp, fingerprintformat.hpp,
833	>	gromos96format.cpp, gromos96format.hpp, oopseformat.cpp,
834	>	oopseformat.hpp, pdbformat.cpp, pdbformat.hpp, povrayformat.cpp,
835	>	povrayformat.hpp, smilesformat.cpp, smilesformat.hpp,
836	>	tinkerformat.cpp, tinkerformat.hpp, xyzformat.cpp, xyzformat.hpp:
837	>	adding more readers/writers
838	>
839	>	2005-11-16 16:20  tim
840	>
841	>	* make/Makefile.in: adding openbabel
842	>
843	>	2005-11-16 16:20  tim
844	>
845	>	* src/brains/: Register.cpp, Register.hpp: register openbabel
846	>	readers/writers
847	>
848	>	2005-11-16 14:57  chrisfen
849	>
850	>	* src/UseTheForce/DarkSide/electrostatic.F90: included shifted
851	>	potential self term
852	>
853	>	2005-11-16 14:57  chrisfen
854	>
855	>	* samples/water/spce/spce.md: just some parameters
856	>
857	>	2005-11-16 14:42  tim
858	>
859	>	* src/openbabel/: Makefile, aromatic.hpp, atom.cpp, atomtyp.hpp,
860	>	babelconfig.hpp, base.cpp, base.hpp, bitvec.cpp, bitvec.hpp,
861	>	bond.cpp, bondtyp.hpp, bondtyper.cpp, bondtyper.hpp, chains.cpp,
862	>	chains.hpp, chiral.cpp, chiral.hpp, config.h.in, config.hpp,
863	>	data.cpp, data.hpp, element.hpp, extable.hpp, fingerprint.cpp,
864	>	fingerprint.hpp, generic.cpp, generic.hpp, grid.cpp, grid.hpp,
865	>	isotope.hpp, kekulize.cpp, matrix.cpp, matrix.hpp, matrix3x3.cpp,
866	>	matrix3x3.hpp, mol.cpp, mol.hpp, molchrg.cpp, molchrg.hpp,
867	>	obconversion.cpp, obconversion.hpp, obconversion.lo, oberror.cpp,
868	>	oberror.hpp, obiter.cpp, obiter.hpp, obmolecformat.hpp, obutil.cpp,
869	>	obutil.hpp, oopseformat.cpp, parsmart.cpp, parsmart.hpp, patty.cpp,
870	>	patty.hpp, pdbformat.cpp, phmodel.cpp, phmodel.hpp,
871	>	phmodeldata.hpp, rand.cpp, reaction.hpp, resdata.hpp, residue.cpp,
872	>	ring.cpp, ring.hpp, rotamer.cpp, rotamer.hpp, rotor.cpp, rotor.hpp,
873	>	snprintf.c, snprintf.h, strncasecmp.c, tinkerformat.cpp,
874	>	tokenst.cpp, torlib.hpp, transform.cpp, typer.cpp, typer.hpp,
875	>	types.hpp, vector3.cpp, vector3.hpp, xyzformat.cpp, zipstream.hpp,
876	>	zipstreamimpl.hpp: adding openbabel
877	>
878	>	2005-11-15 14:42  chrisfen
879	>
880	>	* src/UseTheForce/DarkSide/electrostatic.F90: removed unnecessary
881	>	commented code
882	>
883	>	2005-11-15 14:04  chrisfen
884	>
885	>	* src/UseTheForce/DarkSide/electrostatic.F90: cleaned up the
886	>	charge-charge interactions a bit...
887	>
888	>	2005-11-15 14:03  chrisfen
889	>
890	>	* samples/water/spce/: spce.md, water.md: just playing
891	>
892	>	2005-11-15 11:38  chrisfen
893	>
894	>	* src/UseTheForce/DarkSide/electrostatic.F90: fixed a bug in the
895	>	shifted_potential case
896	>
897	>	2005-11-15 11:37  chrisfen
898	>
899	>	* samples/: argon/500.md, water/spce/spce.md, water/spce/water.md:
900	>	just playing around - we need to refresh all the samples sometime
901	>	soon...
902	>
903	>	2005-11-15 11:18  chuckv
904	>
905	>	* src/UseTheForce/: SC_FF.cpp, DarkSide/suttonchen.F90: Made
906	>	preforce calc public in suttonchen.
907	>
908	>	2005-11-15 11:05  chuckv
909	>
910	>	* src/brains/: SimInfo.cpp, fSimulation.h: Sutton-Chen added to
911	>	SimInfo
912	>
913	>	2005-11-15 11:01  chuckv
914	>
915	>	* src/UseTheForce/: doForces.F90, DarkSide/fInteractionMap.h,
916	>	DarkSide/simulation.F90: Added Sutton-Chen to force loop...
917	>
918	>	2005-11-15 10:34  chuckv
919	>
920	>	* forceFields/Makefile: Added sutton-chen to makefile.
921	>
922	>	2005-11-14 17:20  chuckv
923	>
924	>	* src/UseTheForce/DarkSide/: suttonchen.F90,
925	>	suttonchen_interface.h: Build Fixes for sutton-chen.
926	>
927	>	2005-11-14 17:03  chuckv
928	>
929	>	* src/io/Makefile: Missed makefile for sutton-chen.
930	>
931	>	2005-11-14 17:03  chuckv
932	>
933	>	* src/UseTheForce/: Makefile, DarkSide/Makefile,
934	>	DarkSide/atype.F90, DarkSide/atype_interface.F90: Sutton-chen stuff
935	>
936	>	2005-11-14 16:29  chuckv
937	>
938	>	* src/: UseTheForce/SC_FF.cpp, UseTheForce/SC_FF.hpp,
939	>	io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp,
940	>	UseTheForce/DarkSide/suttonchen.F90,
941	>	UseTheForce/DarkSide/suttonchen_interface.F90,
942	>	UseTheForce/DarkSide/suttonchen_interface.h, brains/Register.cpp,
943	>	brains/fSimulation.h, types/AtomType.cpp, types/AtomType.hpp,
944	>	types/AtomTypeProperties.h: Sutton-Chen almost done. Just need to
945	>	fix do_forces to use Sutton-Chen.
946	>
947	>	2005-11-11 12:21  chrisfen
948	>
949	>	* src/UseTheForce/DarkSide/: fSwitchingFunctionType.h,
950	>	switcheroo_interface.F90, switcheroo_interface.h: Forgot to add
951	>	some files
952	>
953	>	2005-11-11 10:22  chrisfen
954	>
955	>	* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/DumpWriter.cpp,
956	>	io/Globals.cpp, io/Globals.hpp: added in a 5th order polynomial
957	>	switching function option
958	>
959	>	2005-11-11 10:21  chrisfen
960	>
961	>	* src/UseTheForce/DarkSide/: Makefile, switcheroo.F90: added in a
962	>	5th order polynomial switching function
963	>
964	>	2005-11-11 10:21  chrisfen
965	>
966	>	* samples/water/ssd/ssd.md: playing with switching functions again
967	>
968	>	2005-11-11 10:21  chrisfen
969	>
970	>	* samples/argon/500.md: playing with switching functions
971	>
972	>	2005-11-08 19:11  chuckv
973	>
974	>	* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Added force
975	>	files for Sutton-Chen and Quantum Sutton-Chen
976	>
977	>	2005-11-08 08:32  chrisfen
978	>
979	>	* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp,
980	>	DumpWriter.hpp, Globals.cpp, Globals.hpp: Added a keyword and
981	>	ability to output forces and torques
982	>
983	>	2005-11-08 08:32  chrisfen
984	>
985	>	* src/brains/: SimInfo.cpp, fSimulation.h: Added a keyword for
986	>	output of forces and torques
987	>
988	>	2005-11-08 08:31  chrisfen
989	>
990	>	* src/UseTheForce/DarkSide/: electrostatic.F90, simulation.F90:
991	>	Working on shifted_force...
992	>
993	>	2005-11-08 08:31  chrisfen
994	>
995	>	* samples/water/: spce/spce.md, ssde/ssde.md: Just testing...
996	>
997	>	2005-11-03 18:22  chrisfen
998	>
999	>	* src/UseTheForce/DarkSide/electrostatic.F90: removed a poorly
1000	>	commented section
1001	>
1002	>	2005-11-03 18:12  chrisfen
1003	>
1004	>	* src/: UseTheForce/DarkSide/electrostatic.F90,
1005	>	UseTheForce/DarkSide/fElectrostaticScreeningMethod.h,
1006	>	UseTheForce/DarkSide/fScreeningMethod.h, brains/SimInfo.cpp,
1007	>	io/Globals.cpp, io/Globals.hpp: improvements in shifted-force
1008	>
1009	>	2005-11-03 18:11  chrisfen
1010	>
1011	>	* samples/water/spce/spce.md: mmm...  damped shifted force...
1012	>
1013	>	2005-11-03 18:06  chuckv
1014	>
1015	>	* src/UseTheForce/DarkSide/suttonchen.F90: More work on SC.
1016	>
1017	>	2005-11-02 18:50  chuckv
1018	>
1019	>	* src/UseTheForce/DarkSide/suttonchen.F90: More work on suttonchen.
1020	>
1021	>	2005-11-02 16:01  chrisfen
1022	>
1023	>	* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90:
1024	>	removed some test code
1025	>
1026	>	2005-11-02 15:45  chrisfen
1027	>
1028	>	* src/UseTheForce/DarkSide/fScreeningMethod.h: forgot to add the
1029	>	screening method header
1030	>
1031	>	2005-11-02 15:36  chrisfen
1032	>
1033	>	* src/brains/SimInfo.cpp: again, changing how we deal with
1034	>	summation and screening methods
1035	>
1036	>	2005-11-02 15:36  chrisfen
1037	>
1038	>	* src/: UseTheForce/DarkSide/electrostatic.F90,
1039	>	UseTheForce/DarkSide/electrostatic_interface.F90,
1040	>	UseTheForce/DarkSide/electrostatic_interface.h,
1041	>	UseTheForce/DarkSide/fElectrostaticSummationMethod.h,
1042	>	io/Globals.cpp, io/Globals.hpp: changing how we deal with summation
1043	>	and screening methods
1044	>
1045	>	2005-11-02 15:35  chrisfen
1046	>
1047	>	* src/UseTheForce/doForces.F90: debug stuff for rf removed
1048	>
1049	>	2005-11-01 18:32  chuckv
1050	>
1051	>	* src/: UseTheForce/DarkSide/atype.F90,
1052	>	UseTheForce/DarkSide/atype_interface.F90,
1053	>	UseTheForce/DarkSide/suttonchen.F90, types/AtomType.cpp,
1054	>	types/AtomTypeProperties.h: Added suppport to atypes for MEAM and
1055	>	sutton-chen
1056	>
1057	>	2005-11-01 14:24  chrisfen
1058	>
1059	>	* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90:
1060	>	removed some testing code...
1061	>
1062	>	2005-11-01 14:14  chrisfen
1063	>
1064	>	* src/: brains/Register.cpp, brains/SimInfo.cpp,
1065	>	brains/fSimulation.h, integrators/IntegratorFactory.hpp,
1066	>	io/Globals.cpp: fixed a capitalization problem with NPT integrator
1067	>	initialization
1068	>
1069	>	2005-11-01 14:13  chrisfen
1070	>
1071	>	* src/applications/oopse/oopse.cpp: nothing
1072	>
1073	>	2005-11-01 14:09  chrisfen
1074	>
1075	>	* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
1076	>	DarkSide/simulation.F90: still fixing up wolf...
1077	>
1078	>	2005-11-01 13:29  chuckv
1079	>
1080	>	* src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In
1081	>	process of adding sutton-chen forcefield.
1082	>
1083	>	2005-10-26 18:32  chrisfen
1084	>
1085	>	* src/brains/SimInfo.cpp: changed the default switching radius to
1086	>	85% of rcut
1087	>
1088	>	2005-10-26 18:31  chrisfen
1089	>
1090	>	* src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks
1091	>	to be working now - for charges and dipoles alike
1092	>
1093	>	2005-10-26 18:31  chrisfen
1094	>
1095	>	* src/UseTheForce/doForces.F90: reaction field looks to be working
1096	>	now
1097	>
1098	>	2005-10-26 18:30  chrisfen
1099	>
1100	>	* samples/water/ssdrf/water.md: added a test molecule
1101	>
1102	>	2005-10-26 18:30  chrisfen
1103	>
1104	>	* forceFields/DUFF2.frc: added a test atom type
1105	>
1106	>	2005-10-24 09:06  chrisfen
1107	>
1108	>	* src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole
1109	>	reaction field - don't know if it works...
1110	>
1111	>	2005-10-23 16:08  chrisfen
1112	>
1113	>	* src/: UseTheForce/doForces.F90,
1114	>	UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp:
1115	>	streamlined reaction field for dipoles (now a good bit faster) and
1116	>	added reaction field for charges - still need to do charge-dipole
1117	>	RF
1118	>
1119	>	2005-10-23 16:07  chrisfen
1120	>
1121	>	* samples/water/ssdrf/ssdrf.md: minor changes when testing reaction
1122	>	field
1123	>
1124	>	2005-10-23 16:06  chrisfen
1125	>
1126	>	* samples/water/spce/spce.md: reaction field now works for charges
1127	>
1128	>	2005-10-20 15:27  tim
1129	>
1130	>	* src/primitives/Torsion.cpp: Fix the other branch of force
1131	>	calculation in Torision.cpp
1132	>
1133	>	2005-10-19 14:24  chrisfen
1134	>
1135	>	* src/: UseTheForce/doForces.F90,
1136	>	UseTheForce/DarkSide/electrostatic.F90,
1137	>	UseTheForce/DarkSide/simulation.F90, applications/oopse/oopse.cpp,
1138	>	brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals
1139	>	toUpper problems - these changes should fix those...
1140	>
1141	>	2005-10-19 14:23  chrisfen
1142	>
1143	>	* samples/water/ssdrf/ssdrf.md: nothing
1144	>
1145	>	2005-10-19 12:03  gezelter
1146	>
1147	>	* src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in
1148	>	GayBerne
1149	>
1150	>	2005-10-19 11:49  tim
1151	>
1152	>	* src/: UseTheForce/DarkSide/fInteractionMap.h,
1153	>	brains/ForceManager.cpp: fix an index mismathcing between c and
1154	>	fortran
1155	>
1156	>	2005-10-18 18:03  gezelter
1157	>
1158	>	* samples/cutoff/: lj.md, max.md, mix.md, traditional.md: added
1159	>	samples for the cutoff methods that Yang Zheng has been working on
1160	>
1161	>	2005-10-18 16:13  gezelter
1162	>
1163	>	* src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques
1164	>	and a rotation matrix bug
1165	>
1166	>	2005-10-18 16:13  gezelter
1167	>
1168	>	* samples/gbljtest/: 2gb.in, 2gb.md, gb.md, gb2lj1.in, gb2lj1.md,
1169	>	gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md:
1170	>	added a few GB test cases
1171	>
1172	>	2005-10-18 16:13  gezelter
1173	>
1174	>	* forceFields/DUFF2.frc: Fixing GB parameters
1175	>
1176	>	2005-10-18 13:36  kdaily
1177	>
1178	>	* forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne
1179	>	type
1180	>
1181	>	2005-10-18 10:01  chrisfen
1182	>
1183	>	* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90,
1184	>	UseTheForce/DarkSide/Makefile,
1185	>	UseTheForce/DarkSide/electrostatic.F90,
1186	>	UseTheForce/DarkSide/electrostatic_interface.F90,
1187	>	UseTheForce/DarkSide/electrostatic_interface.h,
1188	>	UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged
1189	>	reaction field with electrostatics.F90
1190	>
1191	>	2005-10-17 18:13  tim
1192	>
1193	>	* src/: brains/ForceManager.cpp, brains/Stats.cpp,
1194	>	brains/Stats.hpp, integrators/VelocityVerletIntegrator.cpp,
1195	>	io/BASS_interface.h, io/Globals.cpp, io/StatWriter.cpp,
1196	>	io/StatWriter.hpp: Customized StatWriter is working
1197	>
1198	>	2005-10-17 17:42  kdaily
1199	>
1200	>	* src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver
1201	>	paper
1202	>
1203	>	2005-10-17 16:47  gezelter
1204	>
1205	>	* src/UseTheForce/DarkSide/gb.F90: bugtracking gb
1206	>
1207	>	2005-10-17 14:24  tim
1208	>
1209	>	* src/io/ParamConstraint.hpp: Another bug fix
1210	>
1211	>	2005-10-17 14:22  tim
1212	>
1213	>	* src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace
1214	>	issues in Globals
1215	>
1216	>	2005-10-17 14:12  gezelter
1217	>
1218	>	* src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90,
1219	>	UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90,
1220	>	UseTheForce/DarkSide/gb_interface.F90,
1221	>	UseTheForce/DarkSide/gb_interface.h,
1222	>	io/GayBerneAtomTypesSectionParser.cpp,
1223	>	types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp:
1224	>	changing GB architecture
1225	>
1226	>	2005-10-17 14:12  gezelter
1227	>
1228	>	* samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in,
1229	>	gbRotRoundZ.in: Adding samples for gb tests
1230	>
1231	>	2005-10-16 22:06  tim
1232	>
1233	>	* src/io/: Globals.cpp, Globals.hpp: fix a seg fault when try copy
1234	>	a  string to event's err_msg, there are still tons of memory
1235	>	leaking problem in Globals
1236	>
1237	>	2005-10-16 19:51  tim
1238	>
1239	>	* src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change
1240	>	error message in Globals
1241	>
1242	>	2005-10-14 16:43  tim
1243	>
1244	>	* src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for
1245	>	parameters are working now
1246	>
1247	>	2005-10-14 11:43  gezelter
1248	>
1249	>	* samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests
1250	>
1251	>	2005-10-14 11:05  gezelter
1252	>
1253	>	* samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md,
1254	>	gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md:
1255	>	Adding some Gay Berne tests
1256	>
1257	>	2005-10-14 11:05  gezelter
1258	>
1259	>	* samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some
1260	>	cutoff tests
1261	>
1262	>	2005-10-14 10:44  kdaily
1263	>
1264	>	* forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp,
1265	>	src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90,
1266	>	src/UseTheForce/DarkSide/gb_interface.F90,
1267	>	src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne
1268	>	LJ
1269	>
1270	>	2005-10-14 09:48  tim
1271	>
1272	>	* src/io/ParamConstraint.hpp: Adding Parameter Constraint class
1273	>
1274	>	2005-10-14 09:18  chrisfen
1275	>
1276	>	* samples/thermoIntegration/liquid/ssde.md,
1277	>	samples/thermoIntegration/solid/ssde.md, src/io/Globals.cpp,
1278	>	src/restraints/Restraints.cpp: added default restraint spring
1279	>	constants into Globals
1280	>
1281	>	2005-10-13 17:26  tim
1282	>
1283	>	* src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp,
1284	>	brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp,
1285	>	constraints/ZconstraintForceManager.cpp,
1286	>	integrators/Integrator.cpp, integrators/NPT.cpp,
1287	>	integrators/NVT.cpp, integrators/Velocitizer.cpp, io/Globals.cpp,
1288	>	io/Globals.hpp, io/ZConsReader.cpp, minimizers/Minimizer.cpp,
1289	>	minimizers/MinimizerParameterSet.cpp, restraints/Restraints.cpp,
1290	>	restraints/ThermoIntegrationForceManager.cpp,
1291	>	visitors/ZconsVisitor.cpp: rewrite Globals
1292	>
1293	>	2005-10-12 16:57  chuckv
1294	>
1295	>	* src/brains/ForceManager.cpp: Fix to forceManager to pass
1296	>	potential array to fortran.
1297	>
1298	>	2005-10-12 16:00  gezelter
1299	>
1300	>	* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't
1301	>	remember what we did
1302	>
1303	>	2005-10-12 16:00  gezelter
1304	>
1305	>	* src/UseTheForce/: doForces.F90, doForces_interface.F90,
1306	>	DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/fInteractionMap.h,
1307	>	DarkSide/force_globals.F90, DarkSide/gb.F90, DarkSide/shapes.F90,
1308	>	DarkSide/sticky.F90: simplifying long range potential array
1309	>
1310	>	2005-10-12 16:00  gezelter
1311	>
1312	>	* samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new
1313	>	cutoff methods
1314	>
1315	>	2005-10-12 16:00  gezelter
1316	>
1317	>	* forceFields/DUFF2.frc: Messing with 2-point water models
1318	>
1319	>	2005-10-12 15:22  chuckv
1320	>
1321	>	* src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran
1322	>	interface now expects an array for pot.
1323	>
1324	>	2005-10-12 15:18  chuckv
1325	>
1326	>	* src/UseTheForce/: doForces.F90, DarkSide/gb.F90,
1327	>	DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for
1328	>	calculation of potential.
1329	>
1330	>	2005-10-12 14:55  chuckv
1331	>
1332	>	* src/UseTheForce/doForces.F90: More changes to MPI potential
1333	>	calculations.
1334	>
1335	>	2005-10-12 13:59  chuckv
1336	>
1337	>	* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90,
1338	>	DarkSide/eam.F90, DarkSide/electrostatic.F90,
1339	>	DarkSide/fInteractionMap.h, DarkSide/force_globals.F90,
1340	>	DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky
1341	>	Breaky: Add Support for seperating potential contributions.
1342	>
1343	>	2005-10-11 17:00  chuckv
1344	>
1345	>	* src/UseTheForce/doForces.F90: Free some variables that weren't
1346	>	freed before.
1347	>
1348	>	2005-10-11 16:59  chuckv
1349	>
1350	>	* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
1351	>	GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod
1352	>	builder --twinned.
1353	>
1354	>	2005-10-11 16:57  chuckv
1355	>
1356	>	* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp,
1357	>	nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c,
1358	>	nanoparticleBuilderCmd.h, sphericalNanoparticle.cpp,
1359	>	sphericalNanoparticle.hpp: Added code for nanoparticle builder to
1360	>	cvs.
1361	>
1362	>	2005-10-10 16:34  chuckv
1363	>
1364	>	* src/UseTheForce/doForces.F90: Bug fix, undeclared local variable
1365	>	in MPI.
1366	>
1367	>	2005-10-10 16:20  chuckv
1368	>
1369	>	* src/UseTheForce/doForces.F90: Fixed MPI bug with Row and Column
1370	>	indexing of groupToGtype. We now have two seperate maps
1371	>	groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer
1372	>	that is set to groupToGtypeRow in the single processor version.
1373	>
1374	>	2005-10-06 13:44  chrisfen
1375	>
1376	>	* samples/water/: dimer/water.md, spce/water.md, ssd/water.md,
1377	>	ssd-ion/water.md, ssde/water.md, ssdrf/water.md, tap/water.md,
1378	>	tip3p_ice/water.md, tip4p/water.md: fixing up the samples
1379	>
1380	>	2005-10-05 16:12  tim
1381	>
1382	>	* src/primitives/RigidBody.cpp: There is still something wrong with
1383	>	inertia tensor projection
1384	>
1385	>	2005-10-05 14:35  tim
1386	>
1387	>	* src/primitives/RigidBody.cpp: erase output of inertia tensor.
1388	>	There is still something wrong with current implementation.
1389	>
1390	>	2005-10-05 14:34  tim
1391	>
1392	>	* src/brains/MoleculeCreator.cpp: fix a bug in creating
1393	>	cutoffGroup. When cutoffGroup is turned off, there is a mismatch
1394	>	between group and center of mass array
1395	>
1396	>	2005-10-05 14:12  tim
1397	>
1398	>	* src/primitives/RigidBody.cpp: fix a bug in creating cutoffGroup.
1399	>	When cutoffGroup is turned off, there is a mismatch between group
1400	>	and center of mass array
1401	>
1402	>	2005-10-04 14:34  chrisfen
1403	>
1404	>	* src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying
1405	>	mass ratio bug that results in simulation failure with massless
1406	>	particles
1407	>
1408	>	2005-10-04 14:33  chrisfen
1409	>
1410	>	* src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on
1411	>	wolf
1412	>
1413	>	2005-10-04 14:32  chrisfen
1414	>
1415	>	* samples/water/dimer/two.md, samples/water/dimer/water.md,
1416	>	samples/water/tip3p_ice/tp3.md, samples/water/tip3p_ice/water.md,
1417	>	samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90: just some
1418	>	random changes when testing
1419	>
1420	>	2005-10-03 10:54  tim
1421	>
1422	>	* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: fix a bug in
1423	>	projecting the inertia tensor of directional atom in rigibody into
1424	>	rigidbody's body frame (previous commit is wrong)
1425	>
1426	>	2005-10-03 09:31  tim
1427	>
1428	>	* src/primitives/RigidBody.cpp: fix a bug in projecting the inertia
1429	>	tensor of directional atom in rigibody into rigidbody's body frame
1430	>
1431	>	2005-09-28 13:47  chrisfen
1432	>
1433	>	* src/UseTheForce/DarkSide/electrostatic.F90: working on wolf
1434	>
1435	>	2005-09-28 13:46  chrisfen
1436	>
1437	>	* samples/water/: dimer/cl.md, dimer/mix.md, dimer/mix2.md,
1438	>	dimer/ssd.md, dimer/tap.md, dimer/two.md, spce/spce.md, ssd/ssd.md,
1439	>	ssd-ion/ssdCl.md, ssde/ssde.md, tap/tap.md, tip3p_ice/tp3.md,
1440	>	tip4p/tp4.md: fixed some samples
1441	>
1442	>	2005-09-28 13:46  chrisfen
1443	>
1444	>	* ChangeLog: updated
1445	>
1446	>	2005-09-28 11:55  tim
1447	>
1448	>	* src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid
1449	>	divergence in rotation matrix to quaternion transformation
1450	>
1451	>	2005-09-28 11:32  gezelter
1452	>
1453	>	* src/primitives/RigidBody.cpp: Rotation matrix multiplication
1454	>	order error
1455	>
1456	>	2005-09-28 11:32  gezelter
1457	>
1458	>	* src/io/DumpReader.cpp: tracking down quaternion bug
1459	>
1460	>	2005-09-28 11:32  gezelter
1461	>
1462	>	* forceFields/DUFF2.frc: Added DIP atom types for 2-point water
1463	>	model
1464	>
1465	>	2005-09-27 15:02  tim
1466	>
1467	>	* src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix
1468	>	to quaternion
1469	>
1470	>	2005-09-26 13:38  chuckv
1471	>
1472	>	* src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc
1473	>	7 so derfc is external. Other compilers should treat erfc as
1474	>	intrinsic.
1475	>
1476	>	2005-09-26 12:07  chuckv
1477	>
1478	>	* src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc
1479	>	and declared it to be external to fix issure with ifc7. Hopefully
1480	>	this will not cause a problem with other compilers where derfc is
1481	>	an intrinsic function.
1482	>
1483	>	2005-09-26 11:42  chuckv
1484	>
1485	>	* src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype
1486	>	in simulation module. We needed a seperate receive buffer.
1487	>
1488	>	2005-09-26 10:58  chuckv
1489	>
1490	>	* src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added
1491	>	support for skinThickness keyword to Globals.
1492	>
1493	>	2005-09-26 10:56  tim
1494	>
1495	>	* src/io/DumpReader.cpp: fix a typo in DumpReader
1496	>
1497	>	2005-09-26 09:27  chrisfen
1498	>
1499	>	* samples/: minimizer/tip4p_two.md,
1500	>	thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md,
1501	>	water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md,
1502	>	water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md,
1503	>	water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md,
1504	>	water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md,
1505	>	water/tip4p/tp4.md: fixing up some samples
1506	>
1507	>	2005-09-24 12:39  chrisfen
1508	>
1509	>	* src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now
1510	>	roughly the same speed as the old version when using dipoles
1511	>
1512	>	energies are now exactly the same between the old version of OOPSE
1513	>	and this version
1514	>
1515	>	2005-09-24 12:38  chrisfen
1516	>
1517	>	* samples/water/ssdrf/ssdrf.md: turned rf on
1518	>
1519	>	2005-09-23 15:31  chuckv
1520	>
1521	>	* src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the
1522	>	skin thickness and hardcode listSkin to be 1.0. We now get listskin
1523	>	from skin. This will get fixed to where we can manually set skin
1524	>	thickness.
1525	>
1526	>	2005-09-22 13:50  gezelter
1527	>
1528	>	* src/math/derfc.F90: added error function
1529	>
1530	>	2005-09-21 19:08  chuckv
1531	>
1532	>	* src/integrators/Velocitizer.cpp: Removed print statement for
1533	>	angular momentum and inertia tensor from velocitizer.
1534	>
1535	>	2005-09-21 19:04  chuckv
1536	>
1537	>	* src/integrators/Velocitizer.cpp: Removed print statements for
1538	>	remove angular momentum.
1539	>
1540	>	2005-09-21 18:45  chuckv
1541	>
1542	>	* src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ
1543	>	(say we are using EAM), we probably shouldn't rebuild the LJ mixing
1544	>	map.
1545	>
1546	>	2005-09-21 15:59  tim
1547	>
1548	>	* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp:
1549	>	DumpReader using pure c++ io
1550	>
1551	>	2005-09-21 12:20  chrisfen
1552	>
1553	>	* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a
1554	>	defaultCutoff bug (HEMES!)
1555	>
1556	>	2005-09-20 17:13  gezelter
1557	>
1558	>	* make/Makefile.in: libz additions
1559	>
1560	>	2005-09-20 17:03  gezelter
1561	>
1562	>	* configure, ac-tools/aclocal.m4, ac-tools/configure.in,
1563	>	src/config.h.in: added check for zlib in configure
1564	>
1565	>	2005-09-20 16:22  tim
1566	>
1567	>	* src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp,
1568	>	gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter
1569	>
1570	>	2005-09-20 11:22  tim
1571	>
1572	>	* test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding
1573	>	testcase for zipstream
1574	>
1575	>	2005-09-20 10:41  tim
1576	>
1577	>	* src/io/zipstream.hpp: adding zipstream.hpp
1578	>
1579	>	2005-09-20 10:34  chrisfen
1580	>
1581	>	* samples/: dipole/splitInWater.md, dipole/split_SSD.md,
1582	>	dipole/twoSplitDipole.md, minimizer/ssdEM.md,
1583	>	minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md,
1584	>	zcons/zconsMoving.md: fixed up some sample md files
1585	>
1586	>	2005-09-19 18:21  chrisfen
1587	>
1588	>	* ChangeLog, samples/water/ssdrf/ssdrf.md,
1589	>	src/UseTheForce/doForces.F90,
1590	>	src/UseTheForce/DarkSide/electrostatic.F90,
1591	>	src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp,
1592	>	src/brains/fSimulation.h: Fixed bugs in reaction field, now it
1593	>	appears as though it really is working...
1594	>
1595	>	2005-09-18 15:45  chrisfen
1596	>
1597	>	* ChangeLog, samples/water/ssdrf/ssdrf.md,
1598	>	src/UseTheForce/doForces.F90,
1599	>	src/UseTheForce/doForces_interface.F90,
1600	>	src/UseTheForce/doForces_interface.h,
1601	>	src/UseTheForce/DarkSide/electrostatic.F90,
1602	>	src/UseTheForce/DarkSide/electrostatic_interface.h,
1603	>	src/brains/SimInfo.cpp: reaction field seems to work now, still
1604	>	need to do some testing...
1605	>
1606	>	2005-09-16 18:04  chuckv
1607	>
1608	>	* src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed
1609	>	dump files.
1610	>
1611	>	2005-09-16 16:07  chrisfen
1612	>
1613	>	* src/: UseTheForce/doForces_interface.F90,
1614	>	UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a
1615	>	bug that ifc missed...
1616	>
1617	>	2005-09-16 15:36  chrisfen
1618	>
1619	>	* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90:
1620	>	fixing some summation method issues
1621	>
1622	>	2005-09-16 14:35  chrisfen
1623	>
1624	>	* src/brains/SimInfo.cpp: fixed a capitalization error
1625	>
1626	>	2005-09-16 14:34  chrisfen
1627	>
1628	>	* src/UseTheForce/: fElectrostaticSummationMethod.h,
1629	>	DarkSide/fElectrostaticSummationMethod.h: moved a header file
1630	>	around
1631	>
1632	>	2005-09-16 14:00  chrisfen
1633	>
1634	>	* src/: UseTheForce/DarkSide/electrostatic_interface.F90,
1635	>	brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there
1636	>	are known issues - particularly with reaction field...
1637	>
1638	>	2005-09-16 11:07  chrisfen
1639	>
1640	>	* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp,
1641	>	io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking
1642	>	(cutting out the old way to do reaction field)
1643	>
1644	>	2005-09-15 17:05  gezelter
1645	>
1646	>	* src/UseTheForce/: doForces.F90, fCoulombicCorrection.h,
1647	>	fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90,
1648	>	DarkSide/electrostatic_interface.F90,
1649	>	DarkSide/electrostatic_interface.h: Working on adding WOLF
1650	>
1651	>	2005-09-15 14:17  tim
1652	>
1653	>	* src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame
1654	>	is called without calling getNFrames
1655	>
1656	>	2005-09-15 08:47  chrisfen
1657	>
1658	>	* src/UseTheForce/fCoulombicCorrection.h: forgot to add a header
1659	>
1660	>	2005-09-14 21:48  chuckv
1661	>
1662	>	* src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was
1663	>	not initialized after creation. When maxval(gtypeMaxCutoff) was
1664	>	called, the largest random garbage value was returned from the
1665	>	array.
1666	>
1667	>	2005-09-14 19:14  chrisfen
1668	>
1669	>	* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp,
1670	>	io/Globals.hpp: changes to include the coulombicCorrection selector
1671	>
1672	>	2005-09-14 19:13  chrisfen
1673	>
1674	>	* src/UseTheForce/DarkSide/: Makefile, electrostatic.F90,
1675	>	reactionField.F90: added in the undamped wolf, in the process of
1676	>	doing the damped wolf
1677	>
1678	>	2005-09-14 19:13  chrisfen
1679	>
1680	>	* src/UseTheForce/: doForces.F90, doForces_interface.F90,
1681	>	doForces_interface.h, notifyCutoffs.F90: some changes to activate
1682	>	the coulombicCorrection selector
1683	>
1684	>	2005-09-14 19:11  chrisfen
1685	>
1686	>	* samples/water/dimer/: cl.in, cl.md, water.md: just some testing
1687	>
1688	>	2005-09-14 19:11  chrisfen
1689	>
1690	>	* samples/argon/: 500.in, 500.md: Equilibrated the sample
1691	>
1692	>	2005-09-14 19:10  chrisfen
1693	>
1694	>	* forceFields/DUFF2.frc: re-added Cl- and Na+
1695	>
1696	>	2005-09-14 15:31  chuckv
1697	>
1698	>	* src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup
1699	>	eamAtypes instead of assuming a 1-1 correspondence to atypes.
1700	>
1701	>	2005-09-14 15:28  gezelter
1702	>
1703	>	* src/UseTheForce/doForces.F90: fix to put back calculation of r in
1704	>	do_prepair
1705	>
1706	>	2005-09-14 14:02  gezelter
1707	>
1708	>	* src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the
1709	>	createMixingMap routine.  It should now set doShift correctly
1710	>
1711	>	2005-09-07 17:44  chuckv
1712	>
1713	>	* src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build.
1714	>
1715	>	2005-09-07 17:23  chuckv
1716	>
1717	>	* src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi
1718	>	logical variables
1719	>
1720	>	2005-09-07 17:08  gezelter
1721	>
1722	>	* src/UseTheForce/doForces.F90: bugfix on the grouptype finding
1723	>	algorithm
1724	>
1725	>	2005-09-07 15:46  gezelter
1726	>
1727	>	* src/: UseTheForce/doForces.F90,
1728	>	UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90,
1729	>	UseTheForce/notifyCutoffs_interface.F90,
1730	>	UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp,
1731	>	io/Globals.cpp, io/Globals.hpp: adding c-side interface to change
1732	>	cutoff Policy
1733	>
1734	>	2005-09-07 14:18  gezelter
1735	>
1736	>	* src/UseTheForce/doForces.F90: Some bug hunting
1737	>
1738	>	2005-09-07 14:18  gezelter
1739	>
1740	>	* samples/argon/argonNVT.md: Just a longer test
1741	>
1742	>	2005-09-06 12:32  chuckv
1743	>
1744	>	* src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap
1745	>	etc..
1746	>
1747	>	2005-09-01 17:56  gezelter
1748	>
1749	>	* src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to
1750	>	zero
1751	>
1752	>	2005-09-01 15:17  gezelter
1753	>
1754	>	* src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote
1755	>	createGtypeCutoffMap
1756	>
1757	>	2005-08-30 13:23  chrisfen
1758	>
1759	>	* src/: UseTheForce/doForces.F90,
1760	>	UseTheForce/doForces_interface.F90,
1761	>	UseTheForce/doForces_interface.h,
1762	>	UseTheForce/DarkSide/electrostatic.F90,
1763	>	UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp,
1764	>	brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some
1765	>	changes for implementing the wolf potential
1766	>
1767	>	2005-08-26 17:39  chrisfen
1768	>
1769	>	* src/UseTheForce/DarkSide/eam.F90: updated getEAMCut
1770	>
1771	>	2005-08-26 16:30  chrisfen
1772	>
1773	>	* src/UseTheForce/: doForces.F90, DarkSide/eam.F90,
1774	>	DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added
1775	>	some probably nonfunctional get*cut routines
1776	>
1777	>	2005-08-26 15:34  chuckv
1778	>
1779	>	* src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map.
1780	>
1781	>	2005-08-26 11:36  gezelter
1782	>
1783	>	* src/UseTheForce/doForces.F90: fixing some of the problems in the
1784	>	interactionHash and gtypeCutoff routines
1785	>
1786	>	2005-08-17 10:26  gezelter
1787	>
1788	>	* src/UseTheForce/: doForces.F90, fCutoffPolicy.h,
1789	>	DarkSide/simulation.F90: added fCutoffPolicy.h
1790	>
1791	>	2005-08-11 16:04  gezelter
1792	>
1793	>	* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in
1794	>	progress
1795	>
1796	>	2005-08-10 14:17  gezelter
1797	>
1798	>	* src/primitives/StuntDouble.hpp: putting spaceballs back where
1799	>	they belong
1800	>
1801	>	2005-08-09 17:33  gezelter
1802	>
1803	>	* src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard
1804	>	Jones module
1805	>
1806	>	2005-08-09 17:33  gezelter
1807	>
1808	>	* src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky
1809	>
1810	>	2005-08-09 14:40  chuckv
1811	>
1812	>	* src/UseTheForce/doForces.F90: In process of re-write for group
1813	>	based cutoff....
1814	>
1815	>	2005-07-29 14:38  gezelter
1816	>
1817	>	* src/UseTheForce/doForces.F90: fixes in progress
1818	>
1819	>	2005-07-29 12:34  tim
1820	>
1821	>	* src/UseTheForce/doForces.F90: fix a bug which does not update
1822	>	me_i and me_j correctly
1823	>
1824	>	2005-07-28 17:12  chuckv
1825	>
1826	>	* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed
1827	>	cutoffs... Segfaults nicely now...
1828	>
1829	>	2005-07-20 12:04  gezelter
1830	>
1831	>	* configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text
1832	>	error messages from pathscale compiler
1833	>
1834	>	2005-07-13 11:48  tim
1835	>
1836	>	* src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in
1837	>	<functional>
1838	>
1839	>	2005-07-13 10:54  tim
1840	>
1841	>	* src/: UseTheForce/fSwitchingFunction.h,
1842	>	UseTheForce/mpiComponentPlan.h,
1843	>	UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h,
1844	>	io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h,
1845	>	io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c,
1846	>	io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c,
1847	>	io/parse_tree.h, math/MatVec3.c, utils/residentMem.c,
1848	>	utils/simError.c, utils/simError.h: replace c++ style comment in c
1849	>	files
1850	>
1851	>	2005-07-03 15:53  chuckv
1852	>
1853	>	* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90,
1854	>	UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added
1855	>	subroutine to set cuttoff for Interaction map and function in
1856	>	simulation.F90 to determine if a particular atype is present in a
1857	>	simulation.
1858	>
1859	>	2005-06-28 08:58  gezelter
1860	>
1861	>	* src/UseTheForce/doForces.F90: [no log message]
1862	>
1863	>	2005-06-27 17:21  chuckv
1864	>
1865	>	* src/UseTheForce/doForces.F90: More breaking and destruction of
1866	>	force code. Does not build at this point...
1867	>
1868	>	2005-06-27 16:01  gezelter
1869	>
1870	>	* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90,
1871	>	UseTheForce/DarkSide/fInteractionMap.h,
1872	>	UseTheForce/DarkSide/interactions.F90, utils/definitions.F90:
1873	>	Breaky breaky!
1874	>
1875	>	2005-06-20 11:03  gezelter
1876	>
1877	>	* samples/water/ssd/ssd.md,
1878	>	src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a
1879	>	simulation
1880	>
1881	>	2005-06-13 13:25  tim
1882	>
1883	>	* src/: applications/staticProps/DensityPlot.cpp,
1884	>	applications/staticProps/DensityPlot.hpp,
1885	>	applications/staticProps/SCDOrderParameter.cpp,
1886	>	applications/staticProps/StaticProps.cpp,
1887	>	io/AtomTypesSectionParser.cpp: working version of DensityPlot
1888	>
1889	>	2005-05-31 17:31  chuckv
1890	>
1891	>	* src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to
1892	>	remove angular momentum.
1893	>
1894	>	2005-05-31 12:34  chuckv
1895	>
1896	>	* src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in
1897	>	typo in nanorodBuilder.
1898	>
1899	>	2005-05-30 09:01  chuckv
1900	>
1901	>	* src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
1902	>	brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp,
1903	>	brains/Stats.hpp, integrators/Velocitizer.cpp,
1904	>	integrators/Velocitizer.hpp: Added method to remove system angular
1905	>	momentum to velocitizer and added method to calculate system
1906	>	angular momentum to siminfo.
1907	>
1908	>	2005-05-29 16:16  chrisfen
1909	>
1910	>	* src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed
1911	>	balance from the Darkside (files)
1912	>
1913	>	2005-05-29 16:15  chrisfen
1914	>
1915	>	* src/UseTheForce/doForces.F90: Removed balance from doForces
1916	>
1917	>	2005-05-29 16:15  chrisfen
1918	>
1919	>	* samples/water/tap/: tap.in, tap.md: Updated tap sample
1920	>
1921	>	2005-05-29 16:15  chrisfen
1922	>
1923	>	* samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap
1924	>	dimer for testing purposes
1925	>
1926	>	2005-05-29 16:14  chrisfen
1927	>
1928	>	* forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It
1929	>	was apparently wiped earlier this month...
1930	>
1931	>	2005-05-29 16:13  chrisfen
1932	>
1933	>	* ChangeLog: ran make cvslog
1934	>
1935	>	2005-05-28 19:16  tim
1936	>
1937	>	* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding
1938	>	AtomNameVisitor
1939	>
1940	>	2005-05-28 19:09  tim
1941	>
1942	>	* src/integrators/Integrator.cpp: dding resetIntegrator
1943	>
1944	>	2005-05-28 19:06  tim
1945	>
1946	>	* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp,
1947	>	NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp,
1948	>	VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding
1949	>	resetIntegrator
1950	>
1951	>	2005-05-27 16:11  tim
1952	>
1953	>	* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp,
1954	>	Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp,
1955	>	SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo,
1956	>	StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into
1957	>	StaticProps
1958	>
1959	>	2005-05-26 23:41  tim
1960	>
1961	>	* src/: applications/staticProps/Makefile,
1962	>	applications/staticProps/P2OrderParameter.cpp,
1963	>	applications/staticProps/P2OrderParameter.hpp,
1964	>	applications/staticProps/StaticProps.cpp,
1965	>	applications/staticProps/StaticProps.ggo,
1966	>	applications/staticProps/StaticPropsCmd.c,
1967	>	applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp,
1968	>	utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps
1969	>
1970	>	2005-05-26 17:45  tim
1971	>
1972	>	* src/: applications/dump2Xyz/Dump2XYZ.cpp,
1973	>	applications/dump2Xyz/Dump2XYZCmd.c,
1974	>	applications/dump2Xyz/Dump2XYZCmd.h,
1975	>	applications/staticProps/Makefile,
1976	>	applications/staticProps/P2OrderParameter.cpp,
1977	>	applications/staticProps/P2OrderParameter.hpp,
1978	>	applications/staticProps/RadialDistrFunc.cpp,
1979	>	applications/staticProps/RadialDistrFunc.hpp,
1980	>	applications/staticProps/StaticAnalyser.hpp,
1981	>	applications/staticProps/StaticProps.cpp,
1982	>	applications/staticProps/StaticProps.ggo,
1983	>	applications/staticProps/StaticPropsCmd.c,
1984	>	applications/staticProps/StaticPropsCmd.h, visitors/Makefile,
1985	>	visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding
1986	>	AtomNameVisitor to convert atom name to its base name;
1987	>	wrappingvisitor now wrap back to the center of the mass; adding
1988	>	P2OrderParameter into StaticProps
1989	>
1990	>	2005-05-22 16:36  chuckv
1991	>
1992	>	* src/: applications/nanoRodBuilder/Geometry.cpp,
1993	>	applications/nanoRodBuilder/GeometryBuilder.cpp,
1994	>	applications/nanoRodBuilder/GeometryFactory.cpp,
1995	>	applications/nanoRodBuilder/GeometryFactory.hpp,
1996	>	applications/nanoRodBuilder/nanorodBuilder.cpp,
1997	>	integrators/VelocityVerletIntegrator.cpp: Fix to print pressure
1998	>	tensor.
1999	>
2000	>	2005-05-22 16:05  tim
2001	>
2002	>	* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
2003	>	integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp,
2004	>	io/Globals.hpp, io/SectionParserManager.cpp: adding keyword
2005	>	printPressureTensor
2006	>
2007	>	2005-05-20 14:27  tim
2008	>
2009	>	* src/integrators/NPrT.cpp: NPrT in progress
2010	>
2011	>	2005-05-20 11:01  tim
2012	>
2013	>	* src/: integrators/NPrT.cpp, io/Globals.cpp,
2014	>	utils/OOPSEConstant.hpp: NPrT in progress
2015	>
2016	>	2005-05-19 16:31  tim
2017	>
2018	>	* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp,
2019	>	integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp,
2020	>	io/Globals.hpp: NPAT is working
2021	>
2022	>	2005-05-19 10:49  tim
2023	>
2024	>	* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile,
2025	>	integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT
2026	>
2027	>	2005-05-18 23:28  tim
2028	>
2029	>	* src/: brains/Register.cpp, integrators/NPAT.cpp,
2030	>	integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp,
2031	>	io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators
2032	>
2033	>	2005-05-18 14:06  chrisfen
2034	>
2035	>	* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just
2036	>	some tap changes
2037	>
2038	>	2005-05-18 13:31  chrisfen
2039	>
2040	>	* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
2041	>	DarkSide/sticky.F90: Modifications to temper the dipolar strength
2042	>	in the first solvation shell for tap
2043	>
2044	>	2005-05-18 07:35  chrisfen
2045	>
2046	>	* samples/water/tap/: tap.in, tap.md, water.md: added a tap example
2047	>	for testing purposes
2048	>
2049	>	2005-05-17 17:35  chrisfen
2050	>
2051	>	* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md,
2052	>	samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp,
2053	>	src/UseTheForce/doForces.F90,
2054	>	src/UseTheForce/DarkSide/electrostatic.F90,
2055	>	src/UseTheForce/DarkSide/electrostatic_interface.F90,
2056	>	src/UseTheForce/DarkSide/sticky.F90: Modifications to tap.  Also
2057	>	correcting changes to the previous merge that were not caught
2058	>
2059	>	2005-05-16 23:20  chuckv
2060	>
2061	>	* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp:
2062	>	Fixed merge issues between Kyle and Chris so OOPSE will actually
2063	>	build.
2064	>
2065	>	2005-05-16 22:46  kdaily
2066	>
2067	>	* src/io/: GayBerneAtomTypesSectionParser.cpp,
2068	>	GayBerneAtomTypesSectionParser.hpp, Makefile: help
2069	>
2070	>	2005-05-16 21:08  kdaily
2071	>
2072	>	* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90,
2073	>	src/UseTheForce/DarkSide/gb.F90, src/io/Makefile,
2074	>	src/types/DirectionalAtomType.cpp,
2075	>	src/types/DirectionalAtomType.hpp: added gb
2076	>
2077	>	2005-05-13 15:36  chrisfen
2078	>
2079	>	* forceFields/DUFF2.frc: Better tap
2080	>
2081	>	2005-05-12 14:43  chrisfen
2082	>
2083	>	* forceFields/DUFF2.frc, samples/water/dimer/ssd.in,
2084	>	samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90,
2085	>	src/applications/dump2Xyz/Dump2XYZ.cpp,
2086	>	src/visitors/AtomVisitor.hpp: Couple of changes for TAP water.
2087	>	Need to parametrize.
2088	>
2089	>	2005-05-11 18:15  chuckv
2090	>
2091	>	* src/: io/ShapeAtomTypesSectionParser.cpp,
2092	>	math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed
2093	>	build issues under ifc7.
2094	>
2095	>	2005-05-09 17:07  chuckv
2096	>
2097	>	* src/applications/nanoRodBuilder/Geometry.hpp: More geometry
2098	>	builder changes.
2099	>
2100	>	2005-05-05 10:06  chrisfen
2101	>
2102	>	* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED
2103	>	to TAP
2104	>
2105	>	2005-05-05 09:47  chrisfen
2106	>
2107	>	* forceFields/DUFF2.frc, samples/water/ssde/ssde.md,
2108	>	samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp,
2109	>	src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile,
2110	>	src/UseTheForce/DarkSide/atype.F90,
2111	>	src/UseTheForce/DarkSide/atype_interface.F90,
2112	>	src/UseTheForce/DarkSide/simulation.F90,
2113	>	src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp,
2114	>	src/brains/fSimulation.h, src/io/Makefile,
2115	>	src/io/StickyAtomTypesSectionParser.cpp,
2116	>	src/io/StickyPowerAtomTypesSectionParser.cpp,
2117	>	src/io/StickyPowerAtomTypesSectionParser.hpp,
2118	>	src/types/AtomType.cpp, src/types/AtomType.hpp,
2119	>	src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp,
2120	>	src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water.  It's
2121	>	not parametrized, but OOPSE will now let me run it...
2122	>
2123	>	2005-05-03 17:55  chuckv
2124	>
2125	>	* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
2126	>	GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp:
2127	>	Adding support for generic geometry to nanorodbuilder.
2128	>
2129	>	2005-05-03 12:55  chuckv
2130	>
2131	>	* src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
2132	>	nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c,
2133	>	nanorodBuilderCmd.h: More changes to nanoRodBuilder....
2134	>
2135	>	2005-04-29 14:16  gezelter
2136	>
2137	>	* make/Makefile.in: [no log message]
2138	>
2139	>	2005-04-29 11:26  chrisfen
2140	>
2141	>	* forceFields/DUFF2.frc, samples/water/spce/water.md,
2142	>	samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md,
2143	>	samples/water/ssd-ion/water.md, samples/water/ssde/water.md,
2144	>	samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md,
2145	>	samples/water/tip4p/water.md: Added TIP4P-Ew
2146	>
2147	>	2005-04-27 19:24  chuckv
2148	>
2149	>	* src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
2150	>	GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo,
2151	>	nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with
2152	>	nanoRodBuilder....
2153	>
2154	>	2005-04-27 15:13  chrisfen
2155	>
2156	>	* samples/shape/Shapes.frc, samples/shape/linear.shape,
2157	>	src/UseTheForce/DarkSide/atype.F90,
2158	>	src/UseTheForce/DarkSide/shapes.F90,
2159	>	src/UseTheForce/DarkSide/shapes_interface.F90,
2160	>	src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of
2161	>	write statements and am closer to a working shapes
2162	>
2163	>	2005-04-22 16:57  chuckv
2164	>
2165	>	* src/utils/Predicate.hpp: Fixed gcc4 bug...
2166	>
2167	>	2005-04-22 16:52  tim
2168	>
2169	>	* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp,
2170	>	Trim.hpp: adding CharClassificationFunctor to fix the locale
2171	>	problem  of c++
2172	>
2173	>	2005-04-21 09:12  chrisfen
2174	>
2175	>	* samples/shape/Shapes.frc, samples/shape/linear.in,
2176	>	samples/shape/linear.md, src/UseTheForce/ForceField.hpp,
2177	>	src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile,
2178	>	src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp,
2179	>	src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90,
2180	>	src/UseTheForce/DarkSide/shapes.F90,
2181	>	src/UseTheForce/DarkSide/shapes_interface.F90,
2182	>	src/UseTheForce/DarkSide/shapes_interface.h,
2183	>	src/brains/Register.cpp, src/brains/SimCreator.cpp,
2184	>	src/io/Makefile, src/io/SectionParser.cpp,
2185	>	src/io/SectionParser.hpp, src/io/SectionParserManager.cpp,
2186	>	src/io/ShapeAtomTypesSectionParser.cpp,
2187	>	src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile,
2188	>	src/types/AtomType.cpp, src/types/ShapeAtomType.cpp,
2189	>	src/types/ShapeAtomType.hpp: Shapes is limping along with a array
2190	>	bounds overwrite (I think...). At least the parser loads the
2191	>	forcefield fine...
2192	>
2193	>	2005-04-18 10:44  chrisfen
2194	>
2195	>	* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on
2196	>	Mac (capitalization confusion of filenames)
2197	>
2198	>	2005-04-17 22:50  chrisfen
2199	>
2200	>	* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp,
2201	>	UseTheForce/Shapes_FF.cpp,
2202	>	io/DirectionalAtomTypesSectionParser.cpp,
2203	>	io/ShapeAtomTypesSectionParser.cpp,
2204	>	io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser...
2205	>
2206	>	2005-04-15 17:43  gezelter
2207	>
2208	>	* README: gmake in case people forget
2209	>
2210	>	2005-04-15 17:40  gezelter
2211	>
2212	>	* src/applications/oopse/oopse.cpp: fixed the spacing on the
2213	>	banner.  Vanity.
2214	>
2215	>	2005-04-15 17:22  gezelter
2216	>
2217	>	* src/: config.h.in, applications/oopse/oopse.cpp: Version string
2218	>	in banner (and version numbers in config.h)
2219	>
2220	>	2005-04-15 17:22  gezelter
2221	>
2222	>	* ChangeLog, LICENSE, README: Documentation changes
2223	>
2224	>	2005-04-15 17:03  gezelter
2225	>
2226	>	* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2227	>	UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp,
2228	>	UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
2229	>	UseTheForce/ForceFieldCreator.hpp,
2230	>	UseTheForce/ForceFieldFactory.cpp,
2231	>	UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp,
2232	>	UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90,
2233	>	UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h,
2234	>	UseTheForce/notifyCutoffs.F90,
2235	>	UseTheForce/notifyCutoffs_interface.F90,
2236	>	UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90,
2237	>	UseTheForce/DarkSide/atype.F90,
2238	>	UseTheForce/DarkSide/atype_interface.F90,
2239	>	UseTheForce/DarkSide/eam.F90,
2240	>	UseTheForce/DarkSide/eam_interface.F90,
2241	>	UseTheForce/DarkSide/eam_interface.h,
2242	>	UseTheForce/DarkSide/electrostatic.F90,
2243	>	UseTheForce/DarkSide/electrostatic_interface.F90,
2244	>	UseTheForce/DarkSide/electrostatic_interface.h,
2245	>	UseTheForce/DarkSide/force_globals.F90,
2246	>	UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h,
2247	>	UseTheForce/DarkSide/lj_interface.F90,
2248	>	UseTheForce/DarkSide/lj_interface.h,
2249	>	UseTheForce/DarkSide/neighborLists.F90,
2250	>	UseTheForce/DarkSide/reactionField.F90,
2251	>	UseTheForce/DarkSide/shapes.F90,
2252	>	UseTheForce/DarkSide/shapes_interface.F90,
2253	>	UseTheForce/DarkSide/shapes_interface.h,
2254	>	UseTheForce/DarkSide/simParallel.F90,
2255	>	UseTheForce/DarkSide/simParallel_interface.F90,
2256	>	UseTheForce/DarkSide/simParallel_interface.h,
2257	>	UseTheForce/DarkSide/simulation.F90,
2258	>	UseTheForce/DarkSide/simulation_interface.F90,
2259	>	UseTheForce/DarkSide/simulation_interface.h,
2260	>	UseTheForce/DarkSide/sticky.F90,
2261	>	UseTheForce/DarkSide/sticky_interface.F90,
2262	>	UseTheForce/DarkSide/sticky_interface.h,
2263	>	UseTheForce/DarkSide/switcheroo.F90,
2264	>	applications/dump2Xyz/Dump2XYZ.cpp,
2265	>	applications/dump2Xyz/Dump2XYZCmd.c,
2266	>	applications/dump2Xyz/Dump2XYZCmd.h,
2267	>	applications/dynamicProps/CrossTimeCorrFunc.cpp,
2268	>	applications/dynamicProps/CrossTimeCorrFunc.hpp,
2269	>	applications/dynamicProps/DipoleCorrFunc.cpp,
2270	>	applications/dynamicProps/DipoleCorrFunc.hpp,
2271	>	applications/dynamicProps/DynamicProps.cpp,
2272	>	applications/dynamicProps/DynamicPropsCmd.c,
2273	>	applications/dynamicProps/DynamicPropsCmd.h,
2274	>	applications/dynamicProps/FrameTimeCorrFunc.hpp,
2275	>	applications/dynamicProps/ParticleTimeCorrFunc.cpp,
2276	>	applications/dynamicProps/ParticleTimeCorrFunc.hpp,
2277	>	applications/dynamicProps/RCorrFunc.cpp,
2278	>	applications/dynamicProps/RCorrFunc.hpp,
2279	>	applications/dynamicProps/TimeCorrFunc.cpp,
2280	>	applications/dynamicProps/TimeCorrFunc.hpp,
2281	>	applications/dynamicProps/VCorrFunc.cpp,
2282	>	applications/dynamicProps/VCorrFunc.hpp,
2283	>	applications/nanoRodBuilder/GeometryBuilder.cpp,
2284	>	applications/nanoRodBuilder/GeometryBuilder.hpp,
2285	>	applications/nanoRodBuilder/nanorodBuilder.cpp,
2286	>	applications/nanoRodBuilder/nanorodBuilderCmd.c,
2287	>	applications/nanoRodBuilder/nanorodBuilderCmd.h,
2288	>	applications/oopse/oopse.cpp,
2289	>	applications/simpleBuilder/simpleBuilder.cpp,
2290	>	applications/simpleBuilder/simpleBuilderCmd.c,
2291	>	applications/simpleBuilder/simpleBuilderCmd.h,
2292	>	applications/staticProps/GofAngle2.cpp,
2293	>	applications/staticProps/GofAngle2.hpp,
2294	>	applications/staticProps/GofR.cpp,
2295	>	applications/staticProps/GofR.hpp,
2296	>	applications/staticProps/GofRAngle.cpp,
2297	>	applications/staticProps/GofRAngle.hpp,
2298	>	applications/staticProps/GofXyz.cpp,
2299	>	applications/staticProps/GofXyz.hpp,
2300	>	applications/staticProps/RadialDistrFunc.cpp,
2301	>	applications/staticProps/RadialDistrFunc.hpp,
2302	>	applications/staticProps/StaticProps.cpp,
2303	>	applications/staticProps/StaticPropsCmd.c,
2304	>	applications/staticProps/StaticPropsCmd.h,
2305	>	brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
2306	>	brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp,
2307	>	brains/Exclude.hpp, brains/ForceManager.cpp,
2308	>	brains/ForceManager.hpp, brains/MoleculeCreator.cpp,
2309	>	brains/MoleculeCreator.hpp, brains/Register.cpp,
2310	>	brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
2311	>	brains/SimInfo.hpp, brains/SimSnapshotManager.cpp,
2312	>	brains/SimSnapshotManager.hpp, brains/Snapshot.cpp,
2313	>	brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp,
2314	>	brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp,
2315	>	brains/fSimulation.h, constraints/ConstraintElem.hpp,
2316	>	constraints/ConstraintPair.hpp, constraints/Rattle.cpp,
2317	>	constraints/Rattle.hpp, constraints/ZconsStruct.hpp,
2318	>	constraints/ZconstraintForceManager.cpp,
2319	>	constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp,
2320	>	integrators/DLM.hpp, integrators/Integrator.cpp,
2321	>	integrators/Integrator.hpp, integrators/IntegratorCreator.hpp,
2322	>	integrators/IntegratorFactory.cpp,
2323	>	integrators/IntegratorFactory.hpp, integrators/NPT.cpp,
2324	>	integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp,
2325	>	integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp,
2326	>	integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp,
2327	>	integrators/NVT.cpp, integrators/NVT.hpp,
2328	>	integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp,
2329	>	integrators/Velocitizer.hpp,
2330	>	integrators/VelocityVerletIntegrator.cpp,
2331	>	integrators/VelocityVerletIntegrator.hpp,
2332	>	io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp,
2333	>	io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c,
2334	>	io/BASS_parse.h, io/BendTypesSectionParser.cpp,
2335	>	io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
2336	>	io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
2337	>	io/ChargeAtomTypesSectionParser.hpp,
2338	>	io/DirectionalAtomTypesSectionParser.cpp,
2339	>	io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
2340	>	io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp,
2341	>	io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
2342	>	io/Globals.cpp, io/Globals.hpp,
2343	>	io/LennardJonesAtomTypesSectionParser.cpp,
2344	>	io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp,
2345	>	io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp,
2346	>	io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp,
2347	>	io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp,
2348	>	io/SectionParser.cpp, io/SectionParser.hpp,
2349	>	io/SectionParserManager.cpp, io/SectionParserManager.hpp,
2350	>	io/StatWriter.cpp, io/StatWriter.hpp,
2351	>	io/StickyAtomTypesSectionParser.cpp,
2352	>	io/StickyAtomTypesSectionParser.hpp,
2353	>	io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
2354	>	io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
2355	>	io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp,
2356	>	io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c,
2357	>	io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h,
2358	>	io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp,
2359	>	lattice/CubicLattice.hpp, lattice/FCCLattice.cpp,
2360	>	lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
2361	>	lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp,
2362	>	lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp,
2363	>	math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h,
2364	>	math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp,
2365	>	math/ParallelRandNumGen.hpp, math/Polynomial.hpp,
2366	>	math/Quaternion.hpp, math/RandNumGen.hpp,
2367	>	math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp,
2368	>	math/RectMatrix.hpp, math/SeqRandNumGen.cpp,
2369	>	math/SeqRandNumGen.hpp, math/SquareMatrix.hpp,
2370	>	math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp,
2371	>	minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp,
2372	>	minimizers/Minimizer.cpp, minimizers/Minimizer.hpp,
2373	>	minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp,
2374	>	minimizers/MinimizerFactory.hpp,
2375	>	minimizers/MinimizerParameterSet.cpp,
2376	>	minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp,
2377	>	minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp,
2378	>	minimizers/SDMinimizer.hpp, primitives/Atom.cpp,
2379	>	primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp,
2380	>	primitives/Bond.hpp, primitives/CutoffGroup.hpp,
2381	>	primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
2382	>	primitives/GhostBend.cpp, primitives/GhostBend.hpp,
2383	>	primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp,
2384	>	primitives/Molecule.cpp, primitives/Molecule.hpp,
2385	>	primitives/RigidBody.cpp, primitives/RigidBody.hpp,
2386	>	primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
2387	>	primitives/Torsion.cpp, primitives/Torsion.hpp,
2388	>	primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp,
2389	>	profiling/mdProfile.cpp, profiling/mdProfile.hpp,
2390	>	profiling/timing.F90, restraints/Restraints.cpp,
2391	>	restraints/Restraints.hpp,
2392	>	restraints/ThermoIntegrationForceManager.cpp,
2393	>	restraints/ThermoIntegrationForceManager.hpp,
2394	>	selection/DistanceFinder.cpp, selection/DistanceFinder.hpp,
2395	>	selection/IndexFinder.cpp, selection/IndexFinder.hpp,
2396	>	selection/NameFinder.cpp, selection/NameFinder.hpp,
2397	>	selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp,
2398	>	selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
2399	>	selection/SelectionManager.cpp, selection/SelectionManager.hpp,
2400	>	selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp,
2401	>	selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp,
2402	>	types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h,
2403	>	types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp,
2404	>	types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp,
2405	>	types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
2406	>	types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp,
2407	>	types/CubicBondType.hpp, types/CubicTorsionType.hpp,
2408	>	types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
2409	>	types/DirectionalAtomType.hpp, types/FixedBondType.hpp,
2410	>	types/HarmonicBendType.hpp, types/HarmonicBondType.hpp,
2411	>	types/MakeStamps.cpp, types/MakeStamps.hpp,
2412	>	types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
2413	>	types/MorseBondType.hpp, types/OplsTorsionType.hpp,
2414	>	types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
2415	>	types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp,
2416	>	types/QuarticBondType.hpp, types/QuarticTorsionType.hpp,
2417	>	types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
2418	>	types/ShapeAtomType.cpp, types/ShapeAtomType.hpp,
2419	>	types/TorsionStamp.cpp, types/TorsionStamp.hpp,
2420	>	types/TorsionType.hpp, types/UreyBradleyBendType.hpp,
2421	>	types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp,
2422	>	utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp,
2423	>	utils/GenericFactory.hpp, utils/LocalIndexManager.hpp,
2424	>	utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp,
2425	>	utils/NumericConstant.hpp, utils/OOPSEConstant.hpp,
2426	>	utils/PropertyMap.cpp, utils/PropertyMap.hpp,
2427	>	utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
2428	>	utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp,
2429	>	utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp,
2430	>	utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp,
2431	>	utils/any.hpp, utils/definitions.F90, utils/fError.c,
2432	>	utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h,
2433	>	utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h,
2434	>	utils/residentMem.h, utils/simError.c, utils/simError.h,
2435	>	utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp,
2436	>	visitors/AtomData.hpp, visitors/AtomVisitor.cpp,
2437	>	visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp,
2438	>	visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp,
2439	>	visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
2440	>	visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp,
2441	>	visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp,
2442	>	visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has
2443	>	been drafted to perform our indentation services
2444	>
2445	>	2005-04-15 17:03  gezelter
2446	>
2447	>	* configure, ac-tools/configure.in: Jedi mind-trick warning
2448	>	messages have been added to make users ignore CGAL.
2449	>
2450	>	2005-04-15 13:41  tim
2451	>
2452	>	* make/Makefile.in: fix make install
2453	>
2454	>	2005-04-15 13:41  tim
2455	>
2456	>	* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile:
2457	>	add  Makefile of samples
2458	>
2459	>	2005-04-15 13:33  tim
2460	>
2461	>	* samples/: lipid/Makefile, water/dimer/Makefile,
2462	>	water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not
2463	>	installed correctly
2464	>
2465	>	2005-04-14 16:41  gezelter
2466	>
2467	>	* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in,
2468	>	make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl,
2469	>	scripts/filepp, scripts/filepp.in: configure now searches for perl
2470	>	to use with filepp
2471	>
2472	>	2005-04-14 16:20  gezelter
2473	>
2474	>	* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of
2475	>	MoLocator
2476	>
2477	>	2005-04-14 14:12  gezelter
2478	>
2479	>	* LICENSE: [no log message]
2480	>
2481	>	2005-04-14 11:10  chuckv
2482	>
2483	>	* src/applications/nanoRodBuilder/nanorodBuilder.cpp:
2484	>	nanorodbuilder now exit's when libCGAL is not present.
2485	>
2486	>	2005-04-14 10:20  tim
2487	>
2488	>	* src/io/make_nodes.h: fix one more warning message in make_nodes
2489	>
2490	>	2005-04-13 18:36  chuckv
2491	>
2492	>	* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed
2493	>	interface name for SGI Compiler
2494	>
2495	>	2005-04-13 18:29  chrisfen
2496	>
2497	>	* samples/water/ssde/ssde.md: oops...  bad sample
2498	>
2499	>	2005-04-13 18:00  chuckv
2500	>
2501	>	* src/config.h.in: Change typo in CGAL.
2502	>
2503	>	2005-04-13 17:43  tim
2504	>
2505	>	* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp,
2506	>	selection/SelectionCompiler.hpp: fix some warning messages
2507	>
2508	>	2005-04-13 17:30  gezelter
2509	>
2510	>	* configure, ac-tools/aclocal.m4, ac-tools/configure.in,
2511	>	make/Makefile.in, src/config.h.in,
2512	>	src/applications/nanoRodBuilder/Makefile,
2513	>	src/applications/nanoRodBuilder/Makefile.in,
2514	>	src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL
2515	>	checks
2516	>
2517	>	2005-04-13 15:36  chuckv
2518	>
2519	>	* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp,
2520	>	DarkSide/LJ.F90, DarkSide/electrostatic.F90,
2521	>	DarkSide/electrostatic_interface.F90,
2522	>	DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90,
2523	>	DarkSide/lj_interface.h, DarkSide/sticky.F90,
2524	>	DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added
2525	>	destroy methods for Fortran modules.
2526	>
2527	>	2005-04-13 15:17  chuckv
2528	>
2529	>	* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90,
2530	>	shapes_interface.h: Added destroy method to clean up memory
2531	>
2532	>	2005-04-13 13:41  tim
2533	>
2534	>	* src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
2535	>	brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
2536	>	io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp,
2537	>	primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp,
2538	>	types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are
2539	>	fixed
2540	>
2541	>	2005-04-12 17:44  chuckv
2542	>
2543	>	* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed
2544	>	for nanoRodBuilder.
2545	>
2546	>	2005-04-12 17:42  tim
2547	>
2548	>	* src/applications/: nanoRodBuilder/nanorodBuilder.cpp,
2549	>	simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder
2550	>	and simpleBuilder(forget to delete lattice)
2551	>
2552	>	2005-04-12 17:33  tim
2553	>
2554	>	* src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
2555	>	applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp:
2556	>	refactory lattice
2557	>
2558	>	2005-04-12 17:07  tim
2559	>
2560	>	* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp,
2561	>	CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp,
2562	>	Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory
2563	>	LatticeFactory and LatticeCreator
2564	>
2565	>	2005-04-12 16:58  tim
2566	>
2567	>	* src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
2568	>	applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp,
2569	>	brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
2570	>	lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp,
2571	>	lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp,
2572	>	lattice/Makefile: refactory LatticeFactory and LatticeCreator
2573	>
2574	>	2005-04-12 16:28  gezelter
2575	>
2576	>	* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp,
2577	>	vector_class.F90: cleaned up vector_class memory leak fix by
2578	>	deallocating in reverse order of how we allocated.  Also migrated
2579	>	MoLocator into utils directory
2580	>
2581	>	2005-04-12 16:27  gezelter
2582	>
2583	>	* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp,
2584	>	Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
2585	>	LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice
2586	>	directory
2587	>
2588	>	2005-04-12 16:27  gezelter
2589	>
2590	>	* src/applications/: nanoRodBuilder/BaseLattice.cpp,
2591	>	nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp,
2592	>	nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp,
2593	>	nanoRodBuilder/LatticeCreator.hpp,
2594	>	nanoRodBuilder/LatticeFactory.cpp,
2595	>	nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile,
2596	>	nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp,
2597	>	nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp,
2598	>	simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
2599	>	simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
2600	>	simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
2601	>	simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile,
2602	>	simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp,
2603	>	simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of
2604	>	these files are now redundant
2605	>
2606	>	2005-04-12 16:27  gezelter
2607	>
2608	>	* src/UseTheForce/DarkSide/: atype_interface.F90,
2609	>	atype_interface.h: cleaned up memory leak fix
2610	>
2611	>	2005-04-12 16:26  gezelter
2612	>
2613	>	* make/Makefile.in: added lattice subdirectory
2614	>
2615	>	2005-04-12 15:57  chrisfen
2616	>
2617	>	* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added
2618	>	a space by accident
2619	>
2620	>	2005-04-12 15:56  chrisfen
2621	>
2622	>	* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added
2623	>	quadrupole sample
2624	>
2625	>	2005-04-12 15:56  chrisfen
2626	>
2627	>	* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating
2628	>	samples
2629	>
2630	>	2005-04-12 13:30  tim
2631	>
2632	>	* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom
2633	>	type in fortran side
2634	>
2635	>	2005-04-12 12:45  chuckv
2636	>
2637	>	* src/utils/vector_class.F90: Further changes to vector_class
2638	>	destroy function.
2639	>
2640	>	2005-04-12 12:39  chuckv
2641	>
2642	>	* src/utils/vector_class.F90: Fixed pointer memory leak in
2643	>	vector_class.
2644	>
2645	>	2005-04-12 12:12  chuckv
2646	>
2647	>	* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp,
2648	>	DarkSide/atype_interface.F90, DarkSide/atype_interface.h,
2649	>	DarkSide/eam.F90, DarkSide/eam_interface.F90,
2650	>	DarkSide/eam_interface.h: Updates to deallocate object in fortran.
2651	>
2652	>	2005-04-12 09:24  chrisfen
2653	>
2654	>	* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI
2655	>	output
2656	>
2657	>	2005-04-11 19:29  chuckv
2658	>
2659	>	* src/: UseTheForce/DarkSide/atype.F90,
2660	>	applications/nanoRodBuilder/Makefile: Changes to delete atypes...
2661	>
2662	>	2005-04-11 19:28  chuckv
2663	>
2664	>	* src/utils/vector_class.F90: Added code to delete vector.
2665
2666		2005-04-11 16:58  tim
2667

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