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Comparing trunk/OOPSE-4/ChangeLog (file contents):
Revision 1490 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1648 by tim, Tue Oct 26 22:19:22 2004 UTC

#	Line 1 | Line 1
1	<	2004-07-23 15:31  tim
1	>	2004-10-25 17:46  tim
2
3	<	* samples/lipid/5x5.bass: modify 5x5.bass
3	>	* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
4	>	src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
5	>	src/math/Vector3.hpp, test/brains/StuntDouble.hpp,
6	>	test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp,
7	>	test/math/VectorTestCase.cpp: add getArray function to  RectMatrix
8	>	and Vector classes
9
10	<	2004-07-23 15:25  tim
10	>	2004-10-25 12:03  tim
11
12	<	* samples/water/tip3p_ice/: 200.in, tp3.bass: [no log message]
12	>	* ChangeLog, src/utils/GenericFactory.hpp,
13	>	test/utils/GenericFactoryTestCase.cpp,
14	>	test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding
15	>	GenericFactory Test Case. GenericFactory now can bed used to creat
16	>	ForcefieldFactory and IntegratorFactory etc.
17
18	<	2004-07-23 15:18  tim
18	>	2004-10-24 23:08  tim
19
20	<	* samples/: water/ssde/ssde.bass, argon/500.bass,
21	<	argon/argonNVT.bass: [no log message]
20	>	* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp,
21	>	brains/SimSnapshotManager.hpp, brains/Snapshot.hpp,
22	>	brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes
23	>	get reconstructed
24
25	<	2004-07-23 15:12  tim
25	>	2004-10-24 02:55  tim
26
27	<	* samples/water/: dimer/two.in, spce/spce.in, ssd/ssd.in,
17	<	ssde/ssde.in, tip3p_ice/tp3.in, tip4p/tp4.in: add init files
27	>	* src/utils/GenericFactory.hpp: GenericFactory pass unit test
28
29	<	2004-07-23 15:10  tim
29	>	2004-10-23 18:09  tim
30
31	<	* samples/minimizer/: ssdEM.in, tip4p_two.in: add init file
31	>	* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp,
32	>	StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp,
33	>	RigidBody.cpp: Refactoring in progress
34
35	<	2004-07-23 15:09  tim
35	>	2004-10-22 18:09  tim
36
37	<	* samples/argon/: NVT.bass, argonNVT.bass, argonNVT.in: rename
38	<	NVT.bass to argonNVT.bass
37	>	* ChangeLog, src/brains/Snapshot.hpp,
38	>	src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp,
39	>	test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp,
40	>	test/brains/StuntDouble.hpp: more work in Snapshot
41
42	<	2004-07-23 15:07  tim
42	>	2004-10-22 17:59  chrisfen
43
44	<	* samples/lipid/5x5.in: add 5x5.in
44	>	* src/: UseTheForce/LJFF.cpp,
45	>	UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear
46	>	god!  It runs and conserves energy!
47
48	<	2004-07-23 15:06  tim
48	>	2004-10-22 17:54  chrisfen
49
50	<	* samples/alkane/: butane.in, init_butane.eor: add butane.in
50	>	* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY
51
52	<	2004-07-23 14:57  gezelter
52	>	2004-10-22 17:53  chrisfen
53
54	<	* libBASS/Globals.cpp, samples/minimizer/ssdEM.bass,
55	<	samples/minimizer/tip4p_two.bass: changed minimizer keywords
54	>	* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
55	>	UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
56	>	UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
57	>	brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey
58	>	breakey
59
60	<	2004-07-23 14:34  gezelter
60	>	2004-10-22 17:53  chrisfen
61
62	<	* configure, ac-tools/configure.in: fixed typo
62	>	* make/Makefile.in: compiler flags
63
64	<	2004-07-23 14:32  gezelter
64	>	2004-10-22 16:20  gezelter
65
66	<	* samples/minimizer/Makefile.in: fixed sample makefile
66	>	* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
67	>	UseTheForce/LJFF.cpp, UseTheForce/doForces.F90,
68	>	brains/fSimulation.h, types/AtomType.hpp,
69	>	types/DirectionalAtomType.hpp: fixey fixey
70
71	<	2004-07-23 14:31  gezelter
71	>	2004-10-22 15:22  gezelter
72
73	<	* configure, ac-tools/configure.in, samples/minimizer/Makefile.in,
74	<	samples/minimizer/WATER.frc, samples/minimizer/ssdEM.bass,
75	<	samples/minimizer/tip4p_two.bass, samples/minimizer/water.mdl:
76	<	minimizer sample changes
73	>	* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h,
74	>	charge.F90, charge_interface.h, dipole.F90, dipole_interface.h,
75	>	lj_interface.h, shapes.F90, simulation.F90: Added un-busticated
76	>	fortran files and c/Fortran interfaces
77
78	<	2004-07-23 14:15  gezelter
78	>	2004-10-22 15:21  gezelter
79
80	<	* configure, ac-tools/configure.in: removed beadLipid
80	>	* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
81	>	DirectionalAtomType.hpp, Makefile: More on AtomType and
82	>	DirectionalAtomType
83
84	<	2004-07-23 14:08  tim
84	>	2004-10-22 09:47  gezelter
85
86	<	* samples/Makefile.in: remove beadLipid
86	>	* src/types/AtomType.hpp: Adding AtomType
87
88	<	2004-07-23 14:03  chuckv
88	>	2004-10-21 16:31  tim
89
90	<	* samples/metals/: Au_nanoparticle.eor,
91	<	Au_nanoparticle_coreshell_12-20.bass,
92	<	Au_nanoparticle_coreshell_12-20.in: Added core-shell nanoparticle
93	<	files.
90	>	* ChangeLog, src/brains/Snapshot.hpp,
91	>	src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp,
92	>	src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
93	>	src/math/Vector.hpp, src/math/Vector3.hpp,
94	>	test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp:
95	>	Snapshot and SnapshotManager in progress
96
97	<	2004-07-23 13:51  tim
97	>	2004-10-21 16:30  tim
98
99	<	* samples/water/tip4p/TP4init.in: remove TP4init.in
99	>	* test/brains/: BrainsTest.cpp, Makefile,
100	>	SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp,
101	>	SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for
102	>	Snapshot and snapshotManager.
103
104	<	2004-07-23 13:50  tim
104	>	2004-10-21 15:15  gezelter
105
106	<	* samples/water/tip4p/: Makefile.in, tp4.bass: change init file
107	<	name for tip4p and tip3p_ice
106	>	* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
107	>	UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
108	>	UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
109	>	UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
110	>	UseTheForce/doForces_interface.h, UseTheForce/fForceField.h,
111	>	UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h,
112	>	brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky.
113	>	Fixey Fixey.
114
115	<	2004-07-23 13:48  tim
115	>	2004-10-21 11:32  tim
116
117	<	* samples/water/ssde/: Makefile.in, SSDEinit.in: [no log message]
117	>	* src/utils/GenericData.cpp, src/utils/Makefile,
118	>	test/utils/Makefile, test/utils/UtilTest: remove some junk files
119
120	<	2004-07-23 13:48  tim
120	>	2004-10-21 11:24  tim
121
122	<	* samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass: change
87	<	init file name for ssd
122	>	* test/utils/GenericData.hpp: remove backup of  GenericData.hpp
123
124	<	2004-07-23 13:46  tim
124	>	2004-10-21 11:22  tim
125
126	<	* samples/water/spce/: Makefile.in, SPCEinit.in, spce.bass: remove
127	<	SPCEInit.in
126	>	* ChangeLog, src/brains/SimSetup.cpp,
127	>	src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp,
128	>	src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
129	>	src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
130	>	src/integrators/NVT.cpp, src/io/DumpReader.cpp,
131	>	src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp,
132	>	src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp,
133	>	src/utils/GenericData.cpp, src/utils/GenericData.hpp,
134	>	src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp,
135	>	src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp,
136	>	src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp,
137	>	src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp,
138	>	src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
139	>	src/visitors/ZconsVisitor.hpp: replace old GebericData with  new
140	>	GenericData
141
142	<	2004-07-23 13:45  tim
142	>	2004-10-21 10:25  chuckv
143
144	<	* samples/water/dimer/: Makefile.in, two.bass, two.init: change
145	<	names for init file
144	>	* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj
145	>	module.
146
147	<	2004-07-23 13:40  tim
147	>	2004-10-21 10:24  chuckv
148
149	<	* samples/lipid/: 5x5.bass, 5x5.eor, Makefile.in, init_5x5.eor:
150	<	change init file name in lipid directory
149	>	* src/UseTheForce/DarkSide/lj_interface.h: Added interface for
150	>	fortran lj module.
151
152	<	2004-07-23 13:36  tim
152	>	2004-10-20 17:54  tim
153
154	<	* samples/argon/init_argon.eor: remove init_argon.eor
154	>	* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp,
155	>	test/utils/GenericDataTestCase.cpp, test/utils/Makefile,
156	>	test/utils/PropertyMapTestCase.cpp,
157	>	test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest:
158	>	GenericData and PropertyMap  pass unit test.
159
160	<	2004-07-23 13:34  tim
160	>	2004-10-20 16:52  gezelter
161
162	<	* samples/: alkane/Makefile.in, alkane/butane.bass,
163	<	alkane/butane.eor, argon/500.eor, argon/ar864.eor: [no log message]
162	>	* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90,
163	>	DarkSide/sticky_interface.h: fixed a fortran name problem
164
165	<	2004-07-23 13:33  tim
165	>	2004-10-20 16:38  tim
166
167	<	* samples/argon/Makefile.in: remove eor file
167	>	* test/utils/: GenericData.hpp, GenericDataTestCase.cpp,
168	>	GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp,
169	>	UtilTest, UtilTest.cpp: adding generic data test case
170
171	<	2004-07-23 13:31  tim
171	>	2004-10-20 16:16  chuckv
172
173	<	* samples/argon/: Makefile.in, argon.bass, argon.eor, argonEM.bass:
174	<	change names for argon
173	>	* configure, ac-tools/aclocal.m4,
174	>	src/UseTheForce/DarkSide/Makefile,
175	>	src/UseTheForce/DarkSide/mpiSimulation.F90,
176	>	src/UseTheForce/DarkSide/mpiSimulation_interface.h,
177	>	src/UseTheForce/DarkSide/simParallel.F90,
178	>	src/UseTheForce/DarkSide/simParallel_interface.h,
179	>	src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp:
180	>	Fortran/C++ interface de-obfuscation project appears to be
181	>	complete!  Woo hoo!
182
183	<	2004-07-23 11:47  tim
183	>	2004-10-20 15:47  chuckv
184
185	<	* samples/water/ssde/SSDEinit.in: [no log message]
185	>	* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp,
186	>	fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project
187	>	continues
188
189	<	2004-07-23 11:45  tim
189	>	2004-10-20 15:46  chuckv
190
191	<	* samples/water/ssde/SSDEinit.in: add init file for ssde
191	>	* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
192	>	UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
193	>	UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp,
194	>	UseTheForce/doForces_interface.h,
195	>	UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90,
196	>	UseTheForce/DarkSide/atype_interface.h,
197	>	UseTheForce/DarkSide/eam_interface.h,
198	>	UseTheForce/DarkSide/gb_interface.h,
199	>	UseTheForce/DarkSide/mpiSimulation_interface.h,
200	>	UseTheForce/DarkSide/shapes_interface.h,
201	>	UseTheForce/DarkSide/simulation_interface.h,
202	>	UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp,
203	>	brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface
204	>	de-obfuscation project (It is a very long story)
205
206	<	2004-07-23 11:43  chuckv
206	>	2004-10-20 13:07  tim
207
208	<	* libmdtools/calc_eam.F90: Fixed bug in calc_eam with mixtures and
209	<	cutoffs associated with mixture.
208	>	* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
209	>	test/math/SquareMatrix3TestCase.cpp,
210	>	test/math/SquareMatrixTestCase.cpp,
211	>	test/math/SquareMatrixTestCase.hpp: Math library pass the unit test
212
213	<	2004-07-23 10:35  tim
213	>	2004-10-20 00:52  tim
214
215	<	* libmdtools/: AtomVisitor.cpp, AtomVisitor.hpp: support SSD_E
216	<	SSD_RF SSD1
215	>	* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and
216	>	SnapshotManager in design phase
217
218	<	2004-07-23 09:53  tim
218	>	2004-10-19 23:54  gezelter
219
220	<	* libmdtools/AtomVisitor.cpp: SSDVisitor support SSD_RF, SSD_E,
221	<	SSD1 now
220	>	* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace
221	>	problem prevented linking
222
223	<	2004-07-23 09:19  tim
223	>	2004-10-19 23:54  gezelter
224
225	<	* libmdtools/ZConsReader.cpp: remove ^M from ZConsReader.cpp
225	>	* src/UseTheForce/Shapes_FF.cpp: fixed include
226
227	<	2004-07-23 09:18  tim
227	>	2004-10-19 23:26  gezelter
228
229	<	* samples/lipid/5x5.bass: remove unsupport keyword
229	>	* src/utils/: Makefile, definitions.F90, definitions_module.F90,
230	>	oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90:
231	>	more fortran name mangling
232
233	<	2004-07-22 16:01  chuckv
233	>	2004-10-19 23:23  gezelter
234
235	<	* samples/metals/: init_Au_bulk.in, init_Au_nanoparticle.in:
156	<	Changed init files to be more OOPSE like...
157	<
158	<	2004-07-22 10:11  gezelter
235	>	* src/profiling/timing.F90: yet more fortran renaming
236
237	<	* configure, ac-tools/configure.in: added sample directory
237	>	2004-10-19 23:19  gezelter
238
239	<	2004-07-22 10:06  chrisfen
239	>	* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h,
240	>	do_Forces.F90, do_Forces.h, notifyCutoffs.F90,
241	>	notifyCutoffs_interface.h, notifycutoffs_module_interface.h,
242	>	wrappers.F90: Fortran name cleanup continues
243
244	<	* src/Makefile.in: fixed icc7 incompatibility in linking
244	>	2004-10-19 23:12  gezelter
245
246	<	2004-07-21 17:03  chrisfen
246	>	* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some
247	>	broken fortran stuff
248
249	<	* samples/water/: Makefile.in, tip3p_ice/200.in,
169	<	tip3p_ice/Makefile.in, tip3p_ice/tp3.bass, tip3p_ice/water.mdl:
170	<	Added tip3p_ice to Makefile
249	>	2004-10-19 23:02  gezelter
250
251	<	2004-07-21 16:46  chuckv
251	>	* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
252	>	atype_interface.h, atype_module.F90, atype_module_interface.h,
253	>	calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90,
254	>	calc_eam.F90, calc_gb.F90, calc_reaction_field.F90,
255	>	calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90,
256	>	eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90,
257	>	gb_interface.h, gb_module_interface.h, mpiSimulation.F90,
258	>	mpiSimulation_interface.h, mpiSimulation_module.F90,
259	>	mpisimulation_module_interface.h, reactionField.F90, shapes.F90,
260	>	shapes_interface.h, shapes_module.h, simulation.F90,
261	>	simulation_interface.h, simulation_module.F90,
262	>	simulation_module_interface.h, sticky.F90, sticky_interface.h,
263	>	sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90:
264	>	name sanity on the fortran side
265
266	<	* samples/metals/: Au.bass, Au.eor, Au_bulk_FBD.bass,
175	<	Au_bulk_voter.bass, Au_nanoparticle.bass, Au_nanoparticle.eor,
176	<	init_Au_bulk.in, init_Au_nanoparticle.in, init_au.in: Added sample
177	<	files for bulk metals and a bass file for both voter and FBD
178	<	formulations of EAM.
266	>	2004-10-19 19:18  tim
267
268	<	2004-07-21 14:53  gezelter
268	>	* test/math/SquareMatrix3TestCase.hpp: [no log message]
269
270	<	* samples/water/dimer/two.bass: Checked a bug where eor file wasn't
183	<	being written at the end of the run
270	>	2004-10-19 18:01  tim
271
272	<	2004-07-21 14:53  gezelter
272	>	* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
273	>	src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp:
274	>	except diagonalize(), all of functions in math library pass the
275	>	test
276
277	<	* libmdtools/Integrator.cpp: Fixed a bug where eor file wasn't
188	<	being written at the end of the run
277	>	2004-10-19 17:43  chuckv
278
279	<	2004-07-21 09:11  gezelter
279	>	* src/UseTheForce/do_Forces.h: Added correct prototypes for
280	>	C-fortran interface functions.
281
282	<	* README: [no log message]
282	>	2004-10-19 17:37  chuckv
283
284	<	2004-07-21 09:08  gezelter
284	>	* src/UseTheForce/DarkSide/: atype_module_interface.h,
285	>	eam_module_inteface.h, gb_module_interface.h,
286	>	mpisimulation_module_interface.h, simulation_module_interface.h,
287	>	sticky_pair_module_interface.h: Added correct prototypes for
288	>	C-fortran interface functions.
289
290	<	* samples/argon/machines: cleaning up for export
290	>	2004-10-19 16:28  tim
291
292	<	2004-07-21 09:04  gezelter
292	>	* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp,
293	>	src/math/SquareMatrix.hpp, src/math/Vector.hpp,
294	>	test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp,
295	>	test/math/RectMatrixTestCase.cpp,
296	>	test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp,
297	>	test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more
298	>	bugs get fixed at math library
299
300	<	* NEWS, README: cleaning up for export
300	>	2004-10-19 15:43  chuckv
301
302	<	2004-07-21 08:45  gezelter
302	>	* src/UseTheForce/: DarkSide/atype_module_interface.h,
303	>	DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h,
304	>	DarkSide/mpisimulation_module_interface.h,
305	>	DarkSide/simulation_module_interface.h,
306	>	DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90,
307	>	DarkSide/atype_module.F90, DarkSide/calc_gb.F90,
308	>	DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90,
309	>	DarkSide/simulation_module.F90, do_Forces.F90,
310	>	fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90,
311	>	notifycutoffs_module_interface.h: Added new files for fortran
312	>	interface.
313
314	<	* configure, ac-tools/configure.in: removing staticProps from cvs
205	<	tree
314	>	2004-10-19 15:43  gezelter
315
316	<	2004-07-20 12:07  gezelter
316	>	* src/UseTheForce/Makefile: regressing
317
318	<	* configure, ac-tools/aclocal.m4, utils/Makefile.in,
210	<	utils/quickLate.c, utils/sysbuilder/Makefile.in: [no log message]
318	>	2004-10-19 15:40  gezelter
319
320	<	2004-07-20 10:17  gezelter
320	>	* src/: UseTheForce/DarkSide/calc_shapes.F90,
321	>	UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp:
322	>	working on shapes for portability
323
324	<	* configure, ac-tools/aclocal.m4, ac-tools/configure.in,
215	<	third-party/gnugetopt.h, utils/getopt.c, utils/getopt1.c,
216	<	utils/gnugetopt.h: fixing getopt_long
324	>	2004-10-19 15:40  gezelter
325
326	<	2004-07-19 16:58  gezelter
326	>	* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes
327
328	<	* configure, ac-tools/configure.in, libmdtools/ReadWrite.hpp,
221	<	libmdtools/ZConsWriter.hpp, src/Makefile.in,
222	<	third-party/gnugetopt.h, utils/Dump2XYZCmd.c, utils/Make.dep,
223	<	utils/Makefile.in, utils/sysbuilder/Makefile.in,
224	<	utils/sysbuilder/latticeBuilder.cpp: [no log message]
328	>	2004-10-19 13:21  chrisfen
329
330	<	2004-07-19 16:52  tim
330	>	* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around
331	>	findBegin
332
333	<	* utils/quickLate.c: minor fix of format string in quicklate.c
333	>	2004-10-18 23:34  tim
334
335	<	2004-07-19 16:30  tim
335	>	* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs
336	>	are fixed in Vector class
337
338	<	* utils/zsub: remove zsub from cvs tree
338	>	2004-10-18 23:28  tim
339
340	<	2004-07-19 16:25  tim
340	>	* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix
341	>	some bugs in RectMatrixTestCase
342
343	<	* libmdtools/ZConstraint.cpp, utils/Dump2XYZ.cpp: remove some
237	<	comment lines
343	>	2004-10-18 23:21  tim
344
345	<	2004-07-19 16:00  tim
345	>	* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp,
346	>	test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp,
347	>	test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp,
348	>	test/math/VectorTestCase.hpp: implement more test cases
349
350	<	* libmdtools/OOPSEMinimizer.hpp: remove an extra semicolon from
242	<	OOPSEMinimizer.hpp
350	>	2004-10-18 18:13  tim
351
352	<	2004-07-19 13:55  gezelter
352	>	* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp,
353	>	src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
354	>	src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
355	>	src/utils/StringTokenizer.hpp, test/math/Makefile,
356	>	test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more
357	>	tests on math library
358
359	<	* libBASS/y.tab.h: Shouldn't have been in CVS
359	>	2004-10-18 16:03  tim
360
361	<	2004-07-19 13:54  gezelter
361	>	* test/math/: Makefile, QuaternionTestCase.cpp,
362	>	QuaternionTestCase.hpp, RectMatrixTestCase.cpp,
363	>	SquareMatrix3TestCase.cpp, Vector3TestCase.cpp,
364	>	Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding
365	>	more testing units
366
367	<	* libBASS/y.tab.h, libmdtools/ForceFields.cpp: Fix for
251	<	thermodynamic integration of rigid bodies
367	>	2004-10-18 12:07  tim
368
369	<	2004-07-19 12:00  gezelter
369	>	* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp,
370	>	math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp,
371	>	math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp,
372	>	utils/GenericFactory.hpp: fix some bugs in Quaternion class
373
374	<	* libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: These can be
256	<	generated via lex and yacc at compile time
374	>	2004-10-18 11:30  gezelter
375
376	<	2004-07-19 11:47  gezelter
376	>	* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
377	>	Your basic run of the mill real-valued versions of Y_l^m(\theta,
378	>	\phi)
379
380	<	* libBASS/BASSlex.c, libBASS/BASSyacc.c, libBASS/BASSyacc.h,
261	<	libBASS/make_nodes.c, libBASS/y.tab.h, libmdtools/Makefile.in,
262	<	libmdtools/MatVec3.c, src/Makefile.in: [no log message]
380	>	2004-10-18 11:29  gezelter
381
382	<	2004-07-19 11:32  gezelter
382	>	* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp,
383	>	types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp,
384	>	utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting
385	>	Shapes into OOPSE
386
387	<	* configure, ac-tools/aclocal.m4, ac-tools/configure.in,
388	<	third-party/gnugetopt.h, utils/Makefile.in,
389	<	utils/sysbuilder/Makefile.in: changes for gnu getopt and fixed
269	<	SPRNG configure script
387	>	2004-10-18 10:21  gezelter
388	>
389	>	* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType
390
391	<	2004-07-16 16:49  gezelter
391	>	2004-10-18 00:23  tim
392
393	<	* libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: fixing for machines
274	<	that don't have lex and yacc
393	>	* test/math/VectorTestCase.hpp: adding  vector test case
394
395	<	2004-07-16 15:55  gezelter
395	>	2004-10-18 00:23  tim
396
397	<	* Makefile: Makefiles don't belong in cvs repository
397	>	* src/utils/GenericFactory.hpp: adding generic factory and vector
398	>	test case
399
400	<	2004-07-16 15:54  gezelter
400	>	2004-10-16 20:19  tim
401
402	<	* Makefile, forceFields/Makefile, libBASS/Makefile,
403	<	libmdtools/Makefile, samples/Makefile, src/Makefile,
404	<	third-party/Makefile, utils/Makefile, utils/sysbuilder/Makefile:
285	<	Makefiles don't belong in repository
402	>	* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp,
403	>	SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in
404	>	progress
405
406	<	2004-07-16 15:49  gezelter
406	>	2004-10-15 20:31  tim
407
408	+	* src/math/Quaternion.hpp: add quaternion class
409	+
410	+	2004-10-15 16:11  tim
411	+
412	+	* test/io/: DUFF.frc, IfstrstreamTestCase.cpp,
413	+	IfstrstreamTestCase.hpp: adding test file
414	+
415	+	2004-10-15 16:10  tim
416	+
417	+	* src/io/basic_ifstrstream.hpp: fix a bunch of bugs
418	+
419	+	2004-10-15 15:42  tim
420	+
421	+	* src/io/basic_ifstrstream.hpp: change const_cast to statc_const
422	+
423	+	2004-10-15 15:35  tim
424	+
425	+	* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp
426	+
427	+	2004-10-15 15:34  tim
428	+
429	+	* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use
430	+	namespace oopse
431	+
432	+	2004-10-15 14:38  chuckv
433	+
434	+	* configure, ac-tools/aclocal.m4: Changed optimization flags for
435	+	XLF and XLC.
436	+
437	+	2004-10-15 13:28  tim
438	+
439	+	* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp:
440	+	adding ifstrstream test case
441	+
442	+	2004-10-15 13:20  tim
443	+
444	+	* src/io/basic_ifstrstream.hpp: fix include
445	+
446	+	2004-10-15 13:18  tim
447	+
448	+	* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi
449	+
450	+	2004-10-15 13:17  tim
451	+
452	+	* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile
453	+
454	+	2004-10-15 13:16  tim
455	+
456	+	* test/io/: Makefile, ifstrstreamTestCase.cpp,
457	+	ifstrstreamTestCase.hpp: adding test case for ifstrstream
458	+
459	+	2004-10-15 10:37  tim
460	+
461	+	* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp,
462	+	ifstrstreamTestCase.hpp: add ifstrstreamTestCase
463	+
464	+	2004-10-15 10:20  tim
465	+
466	+	* src/io/basic_ifstrstream.hpp: add checkFilename Option
467	+
468	+	2004-10-15 10:19  tim
469	+
470	+	* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp,
471	+	SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add
472	+	SquareMatrixTestCase class
473	+
474	+	2004-10-15 02:52  tim
475	+
476	+	* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream
477	+
478	+	2004-10-14 18:28  tim
479	+
480	+	* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp,
481	+	Vector.hpp: math library in progress
482	+
483	+	2004-10-14 18:27  tim
484	+
485	+	* src/io/FileReader.hpp: FileReader in progress
486	+
487	+	2004-10-13 18:53  tim
488	+
489	+	* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress,
490	+	test in isOrthogonal of SquareMatrix is failed by some reasons
491	+
492	+	2004-10-13 17:28  tim
493	+
494	+	* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap
495	+	class
496	+
497	+	2004-10-13 17:27  tim
498	+
499	+	* test/math/: MainTest.cpp, RectMatrixTestCase.cpp,
500	+	RectMatrixTestCase.hpp: adding testing unit
501	+
502	+	2004-10-13 17:24  tim
503	+
504	+	* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix
505	+
506	+	2004-10-13 01:51  tim
507	+
508	+	* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp,
509	+	Vector3.hpp: refactory vector and matrix classes
510	+
511	+	2004-10-13 01:50  tim
512	+
513	+	* src/math/Vector3d.hpp: Remove some Makefile.in
514	+
515	+	2004-10-12 18:57  tim
516	+
517	+	* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and
518	+	Matrix3x3d.hpp
519	+
520	+	2004-10-12 14:08  tim
521	+
522	+	* doc/: cppstyle.html, style.css: adding c++ coding style
523	+
524	+	2004-10-11 17:15  tim
525	+
526	+	* src/: constraints/AbstractClasses.hpp,
527	+	integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp:
528	+	change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
529	+
530	+	2004-10-11 16:54  tim
531	+
532	+	* scripts/filepp: fix a bug in filepp
533	+
534	+	2004-10-11 16:13  tim
535	+
536	+	* make/Makefile.in: using filepp to generate dependencies instead
537	+	of compilers
538	+
539	+	2004-10-11 16:10  tim
540	+
541	+	* scripts/filepp: filepp can be used to generate dependencies for
542	+	c/c++ now
543	+
544	+	2004-10-11 13:40  tim
545	+
546	+	* make/Makefile.in: remove -module from F90Options
547	+
548	+	2004-10-11 13:01  tim
549	+
550	+	* make/Makefile.in: adding rules to move fortran 90 module to
551	+	target directory
552	+
553	+	2004-10-11 10:43  gezelter
554	+
555	+	* make/Makefile.in: fixed makefile.in
556	+
557	+	2004-10-11 09:51  tim
558	+
559	+	* scripts/filepp: remove "use bytes" which causes problem in sgi
560	+	machine
561	+
562	+	2004-10-11 09:26  tim
563	+
564	+	* forceFields/Makefile: add Makefile
565	+
566	+	2004-10-11 09:23  tim
567	+
568	+	* samples/: water/dimer/Makefile, water/spce/Makefile,
569	+	water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile,
570	+	water/tip4p/Makefile, zcons/Makefile: fix Makefile under water
571	+	directory
572	+
573	+	2004-10-11 09:23  tim
574	+
575	+	* samples/argon/Makefile: remove argon.dump and argon.eor from
576	+	Makefile
577	+
578	+	2004-10-09 01:01  tim
579	+
580	+	* samples/: alkane/Makefile.in, argon/Makefile.in,
581	+	lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in:
582	+	Remove some Makefile.in
583	+
584	+	2004-10-08 18:15  tim
585	+
586	+	* make/Makefile.in: [no log message]
587	+
588	+	2004-10-08 17:51  tim
589	+
590	+	* make/Makefile.in: fix make install
591	+
592	+	2004-10-08 17:10  tim
593	+
594	+	* make/Makefile.in: adding make install
595	+
596	+	2004-10-08 17:04  tim
597	+
598		* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile,
599	<	metals/Makefile: Makefiles don't belong in repository
599	>	metals/Makefile, minimizer/Makefile, water/Makefile.in,
600	>	water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile,
601	>	water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in,
602	>	water/ssde/Makefile, water/ssde/Makefile.in,
603	>	water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in,
604	>	water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile,
605	>	zcons/Makefile.in: add Makefile to sample directory
606
607	<	2004-07-16 15:20  chrisfen
607	>	2004-10-06 18:03  gezelter
608
609	<	* Makefile, configure, ac-tools/configure.in, forceFields/Makefile,
610	<	libBASS/Makefile, libmdtools/Makefile, samples/alkane/Makefile,
296	<	samples/argon/Makefile, samples/lipid/Makefile,
297	<	samples/metals/Makefile, src/Makefile, utils/Makefile,
298	<	utils/sysbuilder/Makefile: Updated configure for new samples
609	>	* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt
610	>	stuff
611
612	<	2004-07-16 14:57  chrisfen
612	>	2004-10-06 18:03  gezelter
613
614	<	* samples/water/tip4p/Makefile.in: tip4p makefile.in added
614	>	* configure, ac-tools/aclocal.m4, ac-tools/configure.in,
615	>	make/Doxyfile, src/applications/getopt.c,
616	>	src/applications/getopt1.c, src/applications/gnugetopt.h: more
617	>	build fixes
618
619	<	2004-07-16 14:57  chrisfen
619	>	2004-10-06 17:20  tim
620
621	<	* samples/water/ssde/: 256init.in, Makefile.in, ssde.bass: ssde
307	<	makefile.in added
621	>	* make/: Doxyfile, Makefile.in: adding doxygen configuration file
622
623	<	2004-07-16 14:57  chrisfen
623	>	2004-10-06 17:19  tim
624
625	<	* samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass,
626	<	water.mdl: ssd files sorted added
625	>	* scripts/filepp: filepp can handle different fortran module case
626	>	and suffix
627
628	<	2004-07-16 14:57  chrisfen
628	>	2004-10-06 16:27  gezelter
629
630	<	* samples/water/spce/Makefile.in: spce makefile.in added
630	>	* src/restraints/Restraints.cpp: Chris doesn't know about the
631	>	OOPSE-2.0 directory structure yet
632
633	<	2004-07-16 14:56  chrisfen
633	>	2004-10-06 16:27  gezelter
634
635	<	* samples/water/dimer/: Makefile.in, two.bass, two.init, water.mdl:
321	<	dimer files added
635	>	* ChangeLog: Yeah yeah, we'lll get around to it later
636
637	<	2004-07-16 14:56  chrisfen
637	>	2004-10-06 16:22  gezelter
638
639	<	* samples/water/: 200.in, Makefile, Makefile.in, init_ssd.eor,
640	<	spce.bass, spce.eor, ssd.bass, ssd.eor, tim.bass, tim.eor,
327	<	tim.init, tim.xyz, tip3p.bass, tip3p.eor, tip3p.init, two.bass,
328	<	two.eor, two.init, two.xyz, water.mdl: Cleaned up this file
329	<	considerably
639	>	* configure, ac-tools/configure.in, ac-tools/fortran90.m4,
640	>	make/Makefile.in: cleaning up build process
641
642	<	2004-07-16 13:57  gezelter
642	>	2004-10-06 15:01  chrisfen
643
644	<	* AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README,
645	<	configure, ac-tools/Make.conf.in, ac-tools/aclocal.m4,
646	<	ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in,
647	<	ac-tools/fortran90.m4, ac-tools/install-sh, ac-tools/shtool,
648	<	forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl,
649	<	forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl,
650	<	forceFields/Au.VC.funcfl, forceFields/Au.u3.funcfl,
644	>	* src/restraints/Restraints.cpp: made the file reading in
645	>	restraints more intelligent - no longer gives uninformative seg
646	>	faults
647	>
648	>	2004-10-06 14:55  gezelter
649	>
650	>	* src/applications/simpleBuilder/Make.ftemp.old: cleaning up
651	>
652	>	2004-10-06 14:51  gezelter
653	>
654	>	* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy,
655	>	scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit
656	>
657	>	2004-10-06 13:53  tim
658	>
659	>	* make/: Makefile, Makefile.in: fix make statistics
660	>
661	>	2004-10-06 13:18  tim
662	>
663	>	* make/: Makefile, Makefile.in: adding GNU make functions to
664	>	combine all of the static libraries to a big library
665	>
666	>	2004-10-05 17:57  tim
667	>
668	>	* make/: Makefile, Makefile.in:  adding shared library flag
669	>
670	>	2004-10-05 14:37  tim
671	>
672	>	* src/: Makefile, UseTheForce/Makefile,
673	>	UseTheForce/mpiSimulation_module.F90,
674	>	UseTheForce/DarkSide/Makefile,
675	>	UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move
676	>	mpiSimulation_module to DarkSide
677	>
678	>	2004-10-05 14:35  tim
679	>
680	>	* make/: Makefile, Makefile.in: building MPI version;using static
681	>	library instead of shared library
682	>
683	>	2004-10-05 09:14  tim
684	>
685	>	* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90
686	>	to filepp
687	>
688	>	2004-10-04 15:56  tim
689	>
690	>	* make/: Makefile, Makefile.in: add make cvslog
691	>
692	>	2004-10-04 11:24  gezelter
693	>
694	>	* make/: Makefile, Makefile.in: more work on the parallel build
695	>
696	>	2004-10-04 11:06  gezelter
697	>
698	>	* make/: Makefile, Makefile.in: changes to backport declare flags
699	>
700	>	2004-10-04 10:27  gezelter
701	>
702	>	* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp,
703	>	DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging
704	>	shapes
705	>
706	>	2004-10-01 23:40  tim
707	>
708	>	* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree
709	>
710	>	2004-10-01 23:22  tim
711	>
712	>	* make/: Makefile, Makefile.in: add oopse_ as library prefix
713	>
714	>	2004-10-01 16:59  tim
715	>
716	>	* make/: Makefile, Makefile.in: fix a space trimming bug in filepp
717	>
718	>	2004-10-01 16:22  gezelter
719	>
720	>	* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A
721	>	few minor build changes
722	>
723	>	2004-10-01 16:11  tim
724	>
725	>	* scripts/filepp: adding fortran90 make dependency tool
726	>
727	>	2004-09-30 10:41  tim
728	>
729	>	* make/: Makefile, Makefile.in: make clean is smart enough to only
730	>	remove object files belong to current package.  turn off silent
731	>	mode
732	>
733	>	2004-09-29 16:55  tim
734	>
735	>	* src/: Makefile, UseTheForce/Makefile,
736	>	UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile,
737	>	applications/oopse/Makefile, applications/simpleBuilder/Makefile,
738	>	brains/Makedepend, brains/Makefile, constraints/Makefile,
739	>	integrators/Makefile, io/Makefile, math/Makefile,
740	>	minimizers/Makefile, primitives/Makefile, profiling/Makefile,
741	>	restraints/Makefile, types/Makefile, utils/Makefile,
742	>	visitors/Makefile: define DEV_ROOT as relative path
743	>
744	>	2004-09-29 16:54  tim
745	>
746	>	* make/: Makefile, Makefile.in: get the relative path by shell
747	>	script
748	>
749	>	2004-09-29 16:32  tim
750	>
751	>	* make/Makefile: eliminate DEV_ROOT by relative path
752	>
753	>	2004-09-29 13:37  tim
754	>
755	>	* make/Makefile.in: add PackageLibs;  fix dependency rule
756	>
757	>	2004-09-29 12:57  gezelter
758	>
759	>	* configure, ac-tools/configure.in: updates
760	>
761	>	2004-09-29 12:56  gezelter
762	>
763	>	* make/: Make.conf.in, Makefile.in: Working on make stuff
764	>
765	>	2004-09-29 12:46  tim
766	>
767	>	* Makefile: If makefile does not exist, print error message
768	>
769	>	2004-09-29 12:12  tim
770	>
771	>	* make/: Make.conf.in, Makefile: fix dependencies rule
772	>
773	>	2004-09-29 10:58  gezelter
774	>
775	>	* Makefile, make/Makefile: still working on build process
776	>
777	>	2004-09-29 10:00  tim
778	>
779	>	* make/Makefile: add print statment to rules
780	>
781	>	2004-09-29 09:59  tim
782	>
783	>	* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile,
784	>	applications/dump2Xyz/Makefile, applications/oopse/Makefile,
785	>	applications/simpleBuilder/Makefile, brains/Makefile,
786	>	constraints/Makefile, integrators/Makefile, io/Makefile,
787	>	math/Makefile, minimizers/Makefile, primitives/Makefile,
788	>	profiling/Makefile, restraints/Makefile, types/Makefile,
789	>	utils/Makefile, visitors/Makefile: change Makefile to relative path
790	>
791	>	2004-09-28 21:55  tim
792	>
793	>	* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c
794	>	which cause headache in bulding libutils
795	>
796	>	2004-09-28 18:24  tim
797	>
798	>	* src/applications/: BaseLattice.cpp, BaseLattice.hpp,
799	>	Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h,
800	>	Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
801	>	LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp,
802	>	MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp,
803	>	nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo,
804	>	simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp,
805	>	dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c,
806	>	dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile,
807	>	oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp,
808	>	simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
809	>	simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
810	>	simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
811	>	simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old,
812	>	simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp,
813	>	simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp,
814	>	simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo,
815	>	simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h:
816	>	change directory structure of application. Every executable file is
817	>	replaced in seperate directory
818	>
819	>	2004-09-28 17:15  gezelter
820	>
821	>	* lib/dummy: Keep that lib around, please.
822	>
823	>	2004-09-28 17:14  gezelter
824	>
825	>	* Makefile, configure, ac-tools/configure.in, make/Make.conf.in:
826	>	starting a configure version
827	>
828	>	2004-09-28 16:08  tim
829	>
830	>	* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90,
831	>	UseTheForce/DarkSide/Makefile,
832	>	UseTheForce/DarkSide/notifyCutoffs.F90,
833	>	UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend,
834	>	brains/Makefile, brains/simulation_module.F90: move fortran files
835	>	around to solve dependency problem
836	>
837	>	2004-09-28 15:43  tim
838	>
839	>	* Makefile, src/UseTheForce/ForceFields.hpp,
840	>	src/UseTheForce/Makefile, src/applications/BaseLattice.hpp,
841	>	src/applications/Makedepend, src/applications/Makefile,
842	>	src/brains/Makedepend, src/brains/simulation_module.F90,
843	>	src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp,
844	>	src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp,
845	>	src/utils/Makefile: [no log message]
846	>
847	>	2004-09-28 15:41  tim
848	>
849	>	* make/Makefile, scripts/sfmakedepend: fix fortran dependency
850	>	problem
851	>
852	>	2004-09-28 11:13  tim
853	>
854	>	* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y,
855	>	src/io/Makefile: add yacc and lex rules
856	>
857	>	2004-09-27 15:24  tim
858	>
859	>	* make/Makefile: adding include path to F90Options
860	>
861	>	2004-09-27 15:13  tim
862	>
863	>	* make/Makefile: change suffix from .cc to .cpp
864	>
865	>	2004-09-24 11:27  tim
866	>
867	>	* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
868	>	UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
869	>	UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp,
870	>	UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp,
871	>	UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp,
872	>	UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90,
873	>	UseTheForce/DarkSide/calc_LJ_FF.F90,
874	>	UseTheForce/DarkSide/notifyCutoffs.F90,
875	>	UseTheForce/DarkSide/switch_module.F90,
876	>	applications/BaseLattice.cpp, applications/Dump2XYZ.cpp,
877	>	applications/Dump2XYZCmd.c, applications/Lattice.cpp,
878	>	applications/Lattice.hpp, applications/LatticeCreator.cpp,
879	>	applications/LatticeCreator.hpp, applications/LatticeFactory.cpp,
880	>	applications/MoLocator.cpp, applications/MoLocator.hpp,
881	>	applications/cmdline.c, applications/nanoBuilder.cpp,
882	>	applications/oopse.cpp, applications/simpleBuilder.cpp,
883	>	applications/simpleBuilderCmd.c, brains/Exclude.cpp,
884	>	brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
885	>	brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp,
886	>	brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp,
887	>	brains/mpiSimulation.cpp, brains/mpiSimulation.hpp,
888	>	constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp,
889	>	integrators/AbstractClasses.hpp, integrators/Integrator.cpp,
890	>	integrators/Integrator.hpp, integrators/NPT.cpp,
891	>	integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp,
892	>	integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c,
893	>	io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp,
894	>	io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp,
895	>	io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp,
896	>	io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
897	>	io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c,
898	>	io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h,
899	>	io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c,
900	>	math/MatVec3.h, math/randomSPRNG.cpp,
901	>	minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp,
902	>	minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp,
903	>	minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp,
904	>	primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp,
905	>	primitives/BendExtensions.cpp, primitives/Bond.cpp,
906	>	primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp,
907	>	primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
908	>	primitives/GhostBend.cpp, primitives/Molecule.cpp,
909	>	primitives/Molecule.hpp, primitives/RigidBody.cpp,
910	>	primitives/RigidBody.hpp, primitives/SRI.hpp,
911	>	primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
912	>	primitives/Torsion.cpp, primitives/TorsionExtensions.cpp,
913	>	profiling/mdProfile.cpp, restraints/Restraints.cpp,
914	>	restraints/Restraints.hpp, types/AtomStamp.cpp,
915	>	types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp,
916	>	types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp,
917	>	types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
918	>	types/MakeStamps.cpp, types/MakeStamps.hpp,
919	>	types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
920	>	types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
921	>	types/TorsionStamp.cpp, types/TorsionStamp.hpp,
922	>	types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp,
923	>	utils/StreamTokenizer.cpp, utils/StringUtils.c,
924	>	utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c,
925	>	utils/simError.c, visitors/AtomVisitor.cpp,
926	>	visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp,
927	>	visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp,
928	>	visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp,
929	>	visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
930	>	visitors/ZconsVisitor.hpp: change the #include in source files
931	>
932	>	2004-09-23 23:16  gezelter
933	>
934	>	* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
935	>	src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
936	>	src/constraints/Makefile, src/constraints/ZConstraint.cpp,
937	>	src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp,
938	>	src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp,
939	>	src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile,
940	>	src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90,
941	>	src/UseTheForce/fForceField.h,
942	>	src/UseTheForce/fSwitchingFunction.h,
943	>	src/UseTheForce/fortranWrapDefines.hpp,
944	>	src/UseTheForce/fortranWrappers.cpp,
945	>	src/UseTheForce/fortranWrappers.hpp,
946	>	src/UseTheForce/mpiComponentPlan.h,
947	>	src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h,
948	>	src/UseTheForce/mpiSimulation_module.F90,
949	>	src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile,
950	>	src/UseTheForce/DarkSide/atype_module.F90,
951	>	src/UseTheForce/DarkSide/calc_LJ_FF.F90,
952	>	src/UseTheForce/DarkSide/calc_charge_charge.F90,
953	>	src/UseTheForce/DarkSide/calc_dipole_dipole.F90,
954	>	src/UseTheForce/DarkSide/calc_eam.F90,
955	>	src/UseTheForce/DarkSide/calc_gb.F90,
956	>	src/UseTheForce/DarkSide/calc_reaction_field.F90,
957	>	src/UseTheForce/DarkSide/calc_sticky_pair.F90,
958	>	src/UseTheForce/DarkSide/force_globals.F90,
959	>	src/UseTheForce/DarkSide/neighborLists.F90,
960	>	src/UseTheForce/DarkSide/notifyCutoffs.F90,
961	>	src/UseTheForce/DarkSide/switch_module.F90,
962	>	src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h,
963	>	src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp,
964	>	src/io/DumpWriter.cpp, src/io/Globals.cpp,
965	>	src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp,
966	>	src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp,
967	>	src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp,
968	>	src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
969	>	src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c,
970	>	src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h,
971	>	src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h,
972	>	src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp,
973	>	src/types/AtomStamp.hpp, src/types/BendStamp.cpp,
974	>	src/types/BendStamp.hpp, src/types/BondStamp.cpp,
975	>	src/types/BondStamp.hpp, src/types/Component.cpp,
976	>	src/types/Component.hpp, src/types/CutoffGroupStamp.cpp,
977	>	src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp,
978	>	src/types/MakeStamps.hpp, src/types/Makefile,
979	>	src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp,
980	>	src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp,
981	>	src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp,
982	>	src/types/ZconStamp.cpp, src/types/ZconStamp.hpp,
983	>	src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp,
984	>	src/brains/Exclude.hpp, src/brains/ForceFields.cpp,
985	>	src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp,
986	>	src/brains/SimInfo.hpp, src/brains/SimSetup.cpp,
987	>	src/brains/SimSetup.hpp, src/brains/SimState.cpp,
988	>	src/brains/SimState.hpp, src/brains/SkipList.cpp,
989	>	src/brains/SkipList.hpp, src/brains/Thermo.cpp,
990	>	src/brains/Thermo.hpp, src/brains/fSimulation.h,
991	>	src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp,
992	>	src/brains/simulation_module.F90, src/io/BASS_interface.cpp,
993	>	src/io/Globals.hpp, src/io/LinkedAssign.cpp,
994	>	src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp,
995	>	src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h,
996	>	src/math/mt19937ar.c, src/math/randomSPRNG.cpp,
997	>	src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp,
998	>	src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp,
999	>	src/minimizers/OOPSEMinimizer.cpp,
1000	>	src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp,
1001	>	src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp,
1002	>	src/primitives/Atom.cpp, src/primitives/Atom.hpp,
1003	>	src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp,
1004	>	src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp,
1005	>	src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp,
1006	>	src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
1007	>	src/primitives/Makefile, src/primitives/Molecule.cpp,
1008	>	src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp,
1009	>	src/primitives/RigidBody.hpp, src/primitives/SRI.hpp,
1010	>	src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp,
1011	>	src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp,
1012	>	src/restraints/Makefile, src/restraints/Restraints.cpp,
1013	>	src/restraints/Restraints.hpp, src/utils/GenericData.cpp,
1014	>	src/utils/GenericData.hpp, src/utils/Makefile,
1015	>	src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp,
1016	>	src/utils/StringUtils.c, src/utils/StringUtils.cpp,
1017	>	src/utils/StringUtils.h, src/utils/StringUtils.hpp,
1018	>	src/utils/TypeInfo.hpp, src/utils/Utility.cpp,
1019	>	src/utils/Utility.hpp, src/utils/definitions_module.F90,
1020	>	src/utils/fError.c, src/utils/oopseMPI_module.F90,
1021	>	src/utils/simError.c, src/utils/simError.h,
1022	>	src/utils/status_module.F90, src/utils/vector_class.F90,
1023	>	src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp,
1024	>	src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp,
1025	>	src/visitors/CompositeVisitor.hpp, src/visitors/Makefile,
1026	>	src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
1027	>	src/visitors/RigidBodyVisitor.cpp,
1028	>	src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
1029	>	src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
1030	>	samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
1031	>	samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
1032	>	samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
1033	>	samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in,
1034	>	samples/zcons/Makefile.in, samples/zcons/water.md,
1035	>	samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md,
1036	>	samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md,
1037	>	src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp,
1038	>	src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo,
1039	>	src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h,
1040	>	src/applications/Lattice.cpp, src/applications/Lattice.hpp,
1041	>	src/applications/LatticeCreator.cpp,
1042	>	src/applications/LatticeCreator.hpp,
1043	>	src/applications/LatticeFactory.cpp,
1044	>	src/applications/LatticeFactory.hpp, src/applications/Makedepend,
1045	>	src/applications/Makefile, src/applications/MoLocator.cpp,
1046	>	src/applications/MoLocator.hpp, src/applications/Vector3d.hpp,
1047	>	src/applications/cmdline.c, src/applications/cmdline.h,
1048	>	src/applications/getopt.c, src/applications/getopt1.c,
1049	>	src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp,
1050	>	src/applications/nanoBuilder.hpp, src/applications/oopse.cpp,
1051	>	src/applications/quickLate.c, src/applications/simpleBuilder.cpp,
1052	>	src/applications/simpleBuilder.ggo,
1053	>	src/applications/simpleBuilderCmd.c,
1054	>	src/integrators/AbstractClasses.hpp,
1055	>	src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp,
1056	>	src/integrators/Integrator.hpp, src/integrators/Makefile,
1057	>	src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
1058	>	src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
1059	>	src/integrators/NVT.cpp, src/profiling/Makefile,
1060	>	src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp,
1061	>	src/profiling/timing.F90, samples/metals/Au_bulk.in,
1062	>	samples/metals/Au_nanoparticle.in, samples/metals/metals.md,
1063	>	samples/water/Makefile.in, samples/water/dimer/Makefile.in,
1064	>	samples/water/dimer/two.in, samples/water/dimer/two.md,
1065	>	samples/water/dimer/water.md, samples/water/spce/Makefile.in,
1066	>	samples/water/spce/spce.in, samples/water/spce/spce.md,
1067	>	samples/water/spce/water.md, samples/water/ssde/Makefile.in,
1068	>	samples/water/ssde/ssde.in, samples/water/ssde/ssde.md,
1069	>	samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in,
1070	>	samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md,
1071	>	samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in,
1072	>	samples/water/ssd/ssd.in, samples/water/ssd/ssd.md,
1073	>	samples/water/ssd/water.md, samples/water/tip4p/tp4.in,
1074	>	samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
1075	>	samples/alkane/Makefile.in, samples/alkane/alkanes.md,
1076	>	samples/alkane/butane.in, samples/alkane/butane.md,
1077	>	samples/argon/500.in, samples/argon/500.md,
1078	>	samples/argon/Makefile.in, samples/argon/ar864.in,
1079	>	samples/argon/ar864.md, samples/argon/argonNVT.in,
1080	>	samples/argon/argonNVT.md, samples/argon/lj.md,
1081	>	samples/lipid/5x5.in, samples/lipid/5x5.md,
1082	>	samples/lipid/Makefile.in, samples/lipid/lipid.md,
1083	>	samples/lipid/water.md, samples/minimizer/Makefile.in,
1084	>	samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in,
1085	>	samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in,
1086	>	samples/minimizer/tip4p_two.md, samples/minimizer/water.md,
1087	>	samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl,
1088	>	forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl,
1089		forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl,
1090		forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl,
1091		forceFields/DUFF.frc, forceFields/DipoleTest.frc,
1092		forceFields/EAM.VC.frc, forceFields/EAM.frc,
1093		forceFields/EAM.u3.frc, forceFields/EAM.u6.frc,
1094	<	forceFields/LJFF.frc, forceFields/Makefile,
1095	<	forceFields/Makefile.in, forceFields/Ni.VC.funcfl,
1096	<	forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl,
1097	<	forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl,
1098	<	forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl,
1099	<	forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl,
1100	<	forceFields/WATER.frc, libBASS/AtomStamp.cpp,
1101	<	libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp,
1102	<	libBASS/BASS_interface.h, libBASS/BASS_parse.c,
1103	<	libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y,
1104	<	libBASS/BendStamp.cpp, libBASS/BendStamp.hpp,
1105	<	libBASS/BondStamp.cpp, libBASS/BondStamp.hpp,
357	<	libBASS/Component.cpp, libBASS/Component.hpp,
358	<	libBASS/CutoffGroupStamp.cpp, libBASS/CutoffGroupStamp.hpp,
359	<	libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/LinkedAssign.cpp,
360	<	libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp,
361	<	libBASS/LinkedCommand.hpp, libBASS/Make.dep,
362	<	libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile,
363	<	libBASS/Makefile.in, libBASS/MoleculeStamp.cpp,
364	<	libBASS/MoleculeStamp.hpp, libBASS/RigidBodyStamp.cpp,
365	<	libBASS/RigidBodyStamp.hpp, libBASS/TorsionStamp.cpp,
366	<	libBASS/TorsionStamp.hpp, libBASS/ZconStamp.cpp,
367	<	libBASS/ZconStamp.hpp, libBASS/config.h.in, libBASS/fError.c,
368	<	libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h,
369	<	libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h,
370	<	libBASS/parse_interface.h, libBASS/parse_me.h,
371	<	libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c,
372	<	libBASS/simError.h, libBASS/y.tab.h, libBASS/MPIobj/dummy,
373	<	libBASS/obj/dummy, libmdtools/AbstractClasses.hpp,
374	<	libmdtools/AllIntegrator.hpp, libmdtools/Atom.cpp,
375	<	libmdtools/Atom.hpp, libmdtools/AtomVisitor.cpp,
376	<	libmdtools/AtomVisitor.hpp, libmdtools/BaseVisitor.hpp,
377	<	libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp,
378	<	libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp,
379	<	libmdtools/CGFamilyMinimizer.cpp, libmdtools/CompositeVisitor.cpp,
380	<	libmdtools/CompositeVisitor.hpp, libmdtools/CutoffGroup.hpp,
381	<	libmdtools/DUFF.cpp, libmdtools/DirectionalAtom.cpp,
382	<	libmdtools/DirectionalAtom.hpp, libmdtools/DumpReader.cpp,
383	<	libmdtools/DumpWriter.cpp, libmdtools/EAM_FF.cpp,
384	<	libmdtools/Euler3.cpp, libmdtools/Euler3.hpp,
385	<	libmdtools/Exclude.cpp, libmdtools/Exclude.hpp,
386	<	libmdtools/ForceFields.cpp, libmdtools/ForceFields.hpp,
387	<	libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
388	<	libmdtools/GhostBend.cpp, libmdtools/InitializeFromFile.cpp,
389	<	libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
390	<	libmdtools/LJFF.cpp, libmdtools/Make.dep, libmdtools/Makefile,
391	<	libmdtools/Makefile.in, libmdtools/MatVec3.c, libmdtools/MatVec3.h,
392	<	libmdtools/MinimizerParameterSet.hpp, libmdtools/Molecule.cpp,
393	<	libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp,
394	<	libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp,
395	<	libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp,
396	<	libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp,
397	<	libmdtools/PRCG.cpp, libmdtools/ReadWrite.hpp,
398	<	libmdtools/Restraints.cpp, libmdtools/Restraints.hpp,
399	<	libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp,
400	<	libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp,
401	<	libmdtools/SDMinimizer.cpp, libmdtools/SRI.hpp,
402	<	libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
403	<	libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp,
404	<	libmdtools/SimState.cpp, libmdtools/SimState.hpp,
405	<	libmdtools/SkipList.cpp, libmdtools/SkipList.hpp,
406	<	libmdtools/StatWriter.cpp, libmdtools/StreamTokenizer.cpp,
407	<	libmdtools/StreamTokenizer.hpp, libmdtools/StringUtils.c,
408	<	libmdtools/StringUtils.h, libmdtools/StuntDouble.cpp,
409	<	libmdtools/StuntDouble.hpp, libmdtools/Thermo.cpp,
410	<	libmdtools/Thermo.hpp, libmdtools/Torsion.cpp,
411	<	libmdtools/TorsionExtensions.cpp, libmdtools/TypeInfo.hpp,
412	<	libmdtools/Utility.cpp, libmdtools/Utility.hpp,
413	<	libmdtools/WATER.cpp, libmdtools/ZConsReader.cpp,
414	<	libmdtools/ZConsReader.hpp, libmdtools/ZConsWriter.cpp,
415	<	libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp,
416	<	libmdtools/ZconsVisitor.cpp, libmdtools/ZconsVisitor.hpp,
417	<	libmdtools/atype_module.F90, libmdtools/calc_LJ_FF.F90,
418	<	libmdtools/calc_charge_charge.F90,
419	<	libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90,
420	<	libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90,
421	<	libmdtools/calc_sticky_pair.F90, libmdtools/config.h.in,
422	<	libmdtools/definitions_module.F90, libmdtools/do_Forces.F90,
423	<	libmdtools/fForceField.h, libmdtools/fSimulation.h,
424	<	libmdtools/fSwitchingFunction.h, libmdtools/forceFactory.hpp,
425	<	libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp,
426	<	libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp,
427	<	libmdtools/mdProfile.cpp, libmdtools/mdProfile.hpp,
428	<	libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c,
429	<	libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp,
430	<	libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90,
431	<	libmdtools/neighborLists.F90, libmdtools/notifyCutoffs.F90,
432	<	libmdtools/oopseMPI_module.F90, libmdtools/randomSPRNG.cpp,
433	<	libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90,
434	<	libmdtools/status_module.F90, libmdtools/switch_module.F90,
435	<	libmdtools/timing.F90, libmdtools/vector_class.F90,
436	<	libmdtools/wrappers.F90, libmdtools/MPIobj/dummy,
437	<	libmdtools/obj/dummy, samples/Makefile, samples/Makefile.in,
438	<	samples/alkane/Makefile, samples/alkane/Makefile.in,
439	<	samples/alkane/alkanes.mdl, samples/alkane/butane.bass,
440	<	samples/alkane/butane.eor, samples/alkane/init_butane.eor,
441	<	samples/argon/500.bass, samples/argon/500.eor,
442	<	samples/argon/500.in, samples/argon/Makefile,
443	<	samples/argon/Makefile.in, samples/argon/NVT.bass,
444	<	samples/argon/ar864.bass, samples/argon/ar864.eor,
445	<	samples/argon/ar864.in, samples/argon/argon.bass,
446	<	samples/argon/argon.eor, samples/argon/argonEM.bass,
447	<	samples/argon/init_argon.eor, samples/argon/lj.mdl,
448	<	samples/argon/machines, samples/lipid/5x5.bass,
449	<	samples/lipid/5x5.eor, samples/lipid/Makefile,
450	<	samples/lipid/Makefile.in, samples/lipid/init_5x5.eor,
451	<	samples/lipid/lipid.mdl, samples/lipid/water.mdl,
452	<	samples/metals/Au.bass, samples/metals/Au.eor,
453	<	samples/metals/Makefile, samples/metals/Makefile.in,
454	<	samples/metals/init_au.in, samples/metals/metals.mdl,
455	<	samples/water/200.in, samples/water/Makefile,
456	<	samples/water/Makefile.in, samples/water/init_ssd.eor,
457	<	samples/water/spce.bass, samples/water/spce.eor,
458	<	samples/water/ssd.bass, samples/water/ssd.eor,
459	<	samples/water/tim.bass, samples/water/tim.eor,
460	<	samples/water/tim.init, samples/water/tim.xyz,
461	<	samples/water/tip3p.bass, samples/water/tip3p.eor,
462	<	samples/water/tip3p.init, samples/water/two.bass,
463	<	samples/water/two.eor, samples/water/two.init,
464	<	samples/water/two.xyz, samples/water/water.mdl,
465	<	samples/water/spce/SPCEinit.in, samples/water/spce/spce.bass,
466	<	samples/water/spce/water.mdl, samples/water/ssde/256init.in,
467	<	samples/water/ssde/ssde.bass, samples/water/ssde/water.mdl,
468	<	samples/water/tip4p/TP4init.in, samples/water/tip4p/tp4.bass,
469	<	samples/water/tip4p/water.mdl, scripts/cleanSrc, scripts/cvs2cl.pl,
470	<	scripts/sfmakedepend, src/Make.dep, src/Makefile, src/Makefile.in,
471	<	src/oopse.cpp, src/oose.cpp, src/MPIobj/dummy, src/obj/dummy,
472	<	third-party/Makefile, third-party/Makefile.in,
473	<	third-party/mt19937ar.c, utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo,
474	<	utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h, utils/Make.dep,
475	<	utils/Makefile, utils/Makefile.in, utils/quickLate.c, utils/zsub,
476	<	utils/MPIobj/placeHolder, utils/obj/placeHolder,
477	<	utils/sysbuilder/Make.dep, utils/sysbuilder/Makefile,
478	<	utils/sysbuilder/Makefile.in, utils/sysbuilder/MoLocator.cpp,
479	<	utils/sysbuilder/MoLocator.hpp, utils/sysbuilder/cmdline.c,
480	<	utils/sysbuilder/cmdline.h, utils/sysbuilder/latticeBilayer.cpp,
481	<	utils/sysbuilder/latticeBuilder.cpp,
482	<	utils/sysbuilder/latticeBuilder.hpp,
483	<	utils/sysbuilder/nanoBuilder.cpp, utils/sysbuilder/nanoBuilder.hpp,
484	<	utils/sysbuilder/randomBilayer.cpp, utils/sysbuilder/sysBuild.cpp,
485	<	utils/sysbuilder/sysBuild.ggo, utils/sysbuilder/sysBuild.hpp,
486	<	utils/sysbuilder/MPIobj/placeHolder,
487	<	utils/sysbuilder/obj/placeHolder: Initial import of OOPSE-1.0
488	<	source tree
1094	>	forceFields/Makefile.in, forceFields/Ni.u3.funcfl,
1095	>	forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl,
1096	>	forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl,
1097	>	forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc,
1098	>	scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend,
1099	>	ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess,
1100	>	ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4,
1101	>	ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf,
1102	>	forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl,
1103	>	forceFields/Au.u3.funcfl, forceFields/LJFF.frc,
1104	>	forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
1105	>	forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0
1106
1107	<	2004-07-16 13:57  gezelter
1107	>	2004-09-23 23:16  gezelter
1108
1109	<	* AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README,
1110	<	configure, ac-tools/Make.conf.in, ac-tools/aclocal.m4,
1111	<	ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in,
1112	<	ac-tools/fortran90.m4, ac-tools/install-sh, ac-tools/shtool,
1113	<	forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl,
1114	<	forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl,
1115	<	forceFields/Au.VC.funcfl, forceFields/Au.u3.funcfl,
1109	>	* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
1110	>	src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
1111	>	src/constraints/Makefile, src/constraints/ZConstraint.cpp,
1112	>	src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp,
1113	>	src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp,
1114	>	src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile,
1115	>	src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90,
1116	>	src/UseTheForce/fForceField.h,
1117	>	src/UseTheForce/fSwitchingFunction.h,
1118	>	src/UseTheForce/fortranWrapDefines.hpp,
1119	>	src/UseTheForce/fortranWrappers.cpp,
1120	>	src/UseTheForce/fortranWrappers.hpp,
1121	>	src/UseTheForce/mpiComponentPlan.h,
1122	>	src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h,
1123	>	src/UseTheForce/mpiSimulation_module.F90,
1124	>	src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile,
1125	>	src/UseTheForce/DarkSide/atype_module.F90,
1126	>	src/UseTheForce/DarkSide/calc_LJ_FF.F90,
1127	>	src/UseTheForce/DarkSide/calc_charge_charge.F90,
1128	>	src/UseTheForce/DarkSide/calc_dipole_dipole.F90,
1129	>	src/UseTheForce/DarkSide/calc_eam.F90,
1130	>	src/UseTheForce/DarkSide/calc_gb.F90,
1131	>	src/UseTheForce/DarkSide/calc_reaction_field.F90,
1132	>	src/UseTheForce/DarkSide/calc_sticky_pair.F90,
1133	>	src/UseTheForce/DarkSide/force_globals.F90,
1134	>	src/UseTheForce/DarkSide/neighborLists.F90,
1135	>	src/UseTheForce/DarkSide/notifyCutoffs.F90,
1136	>	src/UseTheForce/DarkSide/switch_module.F90,
1137	>	src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h,
1138	>	src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp,
1139	>	src/io/DumpWriter.cpp, src/io/Globals.cpp,
1140	>	src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp,
1141	>	src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp,
1142	>	src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp,
1143	>	src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
1144	>	src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c,
1145	>	src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h,
1146	>	src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h,
1147	>	src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp,
1148	>	src/types/AtomStamp.hpp, src/types/BendStamp.cpp,
1149	>	src/types/BendStamp.hpp, src/types/BondStamp.cpp,
1150	>	src/types/BondStamp.hpp, src/types/Component.cpp,
1151	>	src/types/Component.hpp, src/types/CutoffGroupStamp.cpp,
1152	>	src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp,
1153	>	src/types/MakeStamps.hpp, src/types/Makefile,
1154	>	src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp,
1155	>	src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp,
1156	>	src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp,
1157	>	src/types/ZconStamp.cpp, src/types/ZconStamp.hpp,
1158	>	src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp,
1159	>	src/brains/Exclude.hpp, src/brains/ForceFields.cpp,
1160	>	src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp,
1161	>	src/brains/SimInfo.hpp, src/brains/SimSetup.cpp,
1162	>	src/brains/SimSetup.hpp, src/brains/SimState.cpp,
1163	>	src/brains/SimState.hpp, src/brains/SkipList.cpp,
1164	>	src/brains/SkipList.hpp, src/brains/Thermo.cpp,
1165	>	src/brains/Thermo.hpp, src/brains/fSimulation.h,
1166	>	src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp,
1167	>	src/brains/simulation_module.F90, src/io/BASS_interface.cpp,
1168	>	src/io/Globals.hpp, src/io/LinkedAssign.cpp,
1169	>	src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp,
1170	>	src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h,
1171	>	src/math/mt19937ar.c, src/math/randomSPRNG.cpp,
1172	>	src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp,
1173	>	src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp,
1174	>	src/minimizers/OOPSEMinimizer.cpp,
1175	>	src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp,
1176	>	src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp,
1177	>	src/primitives/Atom.cpp, src/primitives/Atom.hpp,
1178	>	src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp,
1179	>	src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp,
1180	>	src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp,
1181	>	src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
1182	>	src/primitives/Makefile, src/primitives/Molecule.cpp,
1183	>	src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp,
1184	>	src/primitives/RigidBody.hpp, src/primitives/SRI.hpp,
1185	>	src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp,
1186	>	src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp,
1187	>	src/restraints/Makefile, src/restraints/Restraints.cpp,
1188	>	src/restraints/Restraints.hpp, src/utils/GenericData.cpp,
1189	>	src/utils/GenericData.hpp, src/utils/Makefile,
1190	>	src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp,
1191	>	src/utils/StringUtils.c, src/utils/StringUtils.cpp,
1192	>	src/utils/StringUtils.h, src/utils/StringUtils.hpp,
1193	>	src/utils/TypeInfo.hpp, src/utils/Utility.cpp,
1194	>	src/utils/Utility.hpp, src/utils/definitions_module.F90,
1195	>	src/utils/fError.c, src/utils/oopseMPI_module.F90,
1196	>	src/utils/simError.c, src/utils/simError.h,
1197	>	src/utils/status_module.F90, src/utils/vector_class.F90,
1198	>	src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp,
1199	>	src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp,
1200	>	src/visitors/CompositeVisitor.hpp, src/visitors/Makefile,
1201	>	src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
1202	>	src/visitors/RigidBodyVisitor.cpp,
1203	>	src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
1204	>	src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
1205	>	samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
1206	>	samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
1207	>	samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
1208	>	samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in,
1209	>	samples/zcons/Makefile.in, samples/zcons/water.md,
1210	>	samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md,
1211	>	samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md,
1212	>	src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp,
1213	>	src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo,
1214	>	src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h,
1215	>	src/applications/Lattice.cpp, src/applications/Lattice.hpp,
1216	>	src/applications/LatticeCreator.cpp,
1217	>	src/applications/LatticeCreator.hpp,
1218	>	src/applications/LatticeFactory.cpp,
1219	>	src/applications/LatticeFactory.hpp, src/applications/Makedepend,
1220	>	src/applications/Makefile, src/applications/MoLocator.cpp,
1221	>	src/applications/MoLocator.hpp, src/applications/Vector3d.hpp,
1222	>	src/applications/cmdline.c, src/applications/cmdline.h,
1223	>	src/applications/getopt.c, src/applications/getopt1.c,
1224	>	src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp,
1225	>	src/applications/nanoBuilder.hpp, src/applications/oopse.cpp,
1226	>	src/applications/quickLate.c, src/applications/simpleBuilder.cpp,
1227	>	src/applications/simpleBuilder.ggo,
1228	>	src/applications/simpleBuilderCmd.c,
1229	>	src/integrators/AbstractClasses.hpp,
1230	>	src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp,
1231	>	src/integrators/Integrator.hpp, src/integrators/Makefile,
1232	>	src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
1233	>	src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
1234	>	src/integrators/NVT.cpp, src/profiling/Makefile,
1235	>	src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp,
1236	>	src/profiling/timing.F90, samples/metals/Au_bulk.in,
1237	>	samples/metals/Au_nanoparticle.in, samples/metals/metals.md,
1238	>	samples/water/Makefile.in, samples/water/dimer/Makefile.in,
1239	>	samples/water/dimer/two.in, samples/water/dimer/two.md,
1240	>	samples/water/dimer/water.md, samples/water/spce/Makefile.in,
1241	>	samples/water/spce/spce.in, samples/water/spce/spce.md,
1242	>	samples/water/spce/water.md, samples/water/ssde/Makefile.in,
1243	>	samples/water/ssde/ssde.in, samples/water/ssde/ssde.md,
1244	>	samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in,
1245	>	samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md,
1246	>	samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in,
1247	>	samples/water/ssd/ssd.in, samples/water/ssd/ssd.md,
1248	>	samples/water/ssd/water.md, samples/water/tip4p/tp4.in,
1249	>	samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
1250	>	samples/alkane/Makefile.in, samples/alkane/alkanes.md,
1251	>	samples/alkane/butane.in, samples/alkane/butane.md,
1252	>	samples/argon/500.in, samples/argon/500.md,
1253	>	samples/argon/Makefile.in, samples/argon/ar864.in,
1254	>	samples/argon/ar864.md, samples/argon/argonNVT.in,
1255	>	samples/argon/argonNVT.md, samples/argon/lj.md,
1256	>	samples/lipid/5x5.in, samples/lipid/5x5.md,
1257	>	samples/lipid/Makefile.in, samples/lipid/lipid.md,
1258	>	samples/lipid/water.md, samples/minimizer/Makefile.in,
1259	>	samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in,
1260	>	samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in,
1261	>	samples/minimizer/tip4p_two.md, samples/minimizer/water.md,
1262	>	samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl,
1263	>	forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl,
1264		forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl,
1265		forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl,
1266		forceFields/DUFF.frc, forceFields/DipoleTest.frc,
1267		forceFields/EAM.VC.frc, forceFields/EAM.frc,
1268		forceFields/EAM.u3.frc, forceFields/EAM.u6.frc,
1269	<	forceFields/LJFF.frc, forceFields/Makefile,
1270	<	forceFields/Makefile.in, forceFields/Ni.VC.funcfl,
1271	<	forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl,
1272	<	forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl,
1273	<	forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl,
1274	<	forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl,
1275	<	forceFields/WATER.frc, libBASS/AtomStamp.cpp,
1276	<	libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp,
1277	<	libBASS/BASS_interface.h, libBASS/BASS_parse.c,
1278	<	libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y,
1279	<	libBASS/BendStamp.cpp, libBASS/BendStamp.hpp,
1280	<	libBASS/BondStamp.cpp, libBASS/BondStamp.hpp,
516	<	libBASS/Component.cpp, libBASS/Component.hpp,
517	<	libBASS/CutoffGroupStamp.cpp, libBASS/CutoffGroupStamp.hpp,
518	<	libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/LinkedAssign.cpp,
519	<	libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp,
520	<	libBASS/LinkedCommand.hpp, libBASS/Make.dep,
521	<	libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile,
522	<	libBASS/Makefile.in, libBASS/MoleculeStamp.cpp,
523	<	libBASS/MoleculeStamp.hpp, libBASS/RigidBodyStamp.cpp,
524	<	libBASS/RigidBodyStamp.hpp, libBASS/TorsionStamp.cpp,
525	<	libBASS/TorsionStamp.hpp, libBASS/ZconStamp.cpp,
526	<	libBASS/ZconStamp.hpp, libBASS/config.h.in, libBASS/fError.c,
527	<	libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h,
528	<	libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h,
529	<	libBASS/parse_interface.h, libBASS/parse_me.h,
530	<	libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c,
531	<	libBASS/simError.h, libBASS/y.tab.h, libBASS/MPIobj/dummy,
532	<	libBASS/obj/dummy, libmdtools/AbstractClasses.hpp,
533	<	libmdtools/AllIntegrator.hpp, libmdtools/Atom.cpp,
534	<	libmdtools/Atom.hpp, libmdtools/AtomVisitor.cpp,
535	<	libmdtools/AtomVisitor.hpp, libmdtools/BaseVisitor.hpp,
536	<	libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp,
537	<	libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp,
538	<	libmdtools/CGFamilyMinimizer.cpp, libmdtools/CompositeVisitor.cpp,
539	<	libmdtools/CompositeVisitor.hpp, libmdtools/CutoffGroup.hpp,
540	<	libmdtools/DUFF.cpp, libmdtools/DirectionalAtom.cpp,
541	<	libmdtools/DirectionalAtom.hpp, libmdtools/DumpReader.cpp,
542	<	libmdtools/DumpWriter.cpp, libmdtools/EAM_FF.cpp,
543	<	libmdtools/Euler3.cpp, libmdtools/Euler3.hpp,
544	<	libmdtools/Exclude.cpp, libmdtools/Exclude.hpp,
545	<	libmdtools/ForceFields.cpp, libmdtools/ForceFields.hpp,
546	<	libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
547	<	libmdtools/GhostBend.cpp, libmdtools/InitializeFromFile.cpp,
548	<	libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
549	<	libmdtools/LJFF.cpp, libmdtools/Make.dep, libmdtools/Makefile,
550	<	libmdtools/Makefile.in, libmdtools/MatVec3.c, libmdtools/MatVec3.h,
551	<	libmdtools/MinimizerParameterSet.hpp, libmdtools/Molecule.cpp,
552	<	libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp,
553	<	libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp,
554	<	libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp,
555	<	libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp,
556	<	libmdtools/PRCG.cpp, libmdtools/ReadWrite.hpp,
557	<	libmdtools/Restraints.cpp, libmdtools/Restraints.hpp,
558	<	libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp,
559	<	libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp,
560	<	libmdtools/SDMinimizer.cpp, libmdtools/SRI.hpp,
561	<	libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
562	<	libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp,
563	<	libmdtools/SimState.cpp, libmdtools/SimState.hpp,
564	<	libmdtools/SkipList.cpp, libmdtools/SkipList.hpp,
565	<	libmdtools/StatWriter.cpp, libmdtools/StreamTokenizer.cpp,
566	<	libmdtools/StreamTokenizer.hpp, libmdtools/StringUtils.c,
567	<	libmdtools/StringUtils.h, libmdtools/StuntDouble.cpp,
568	<	libmdtools/StuntDouble.hpp, libmdtools/Thermo.cpp,
569	<	libmdtools/Thermo.hpp, libmdtools/Torsion.cpp,
570	<	libmdtools/TorsionExtensions.cpp, libmdtools/TypeInfo.hpp,
571	<	libmdtools/Utility.cpp, libmdtools/Utility.hpp,
572	<	libmdtools/WATER.cpp, libmdtools/ZConsReader.cpp,
573	<	libmdtools/ZConsReader.hpp, libmdtools/ZConsWriter.cpp,
574	<	libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp,
575	<	libmdtools/ZconsVisitor.cpp, libmdtools/ZconsVisitor.hpp,
576	<	libmdtools/atype_module.F90, libmdtools/calc_LJ_FF.F90,
577	<	libmdtools/calc_charge_charge.F90,
578	<	libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90,
579	<	libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90,
580	<	libmdtools/calc_sticky_pair.F90, libmdtools/config.h.in,
581	<	libmdtools/definitions_module.F90, libmdtools/do_Forces.F90,
582	<	libmdtools/fForceField.h, libmdtools/fSimulation.h,
583	<	libmdtools/fSwitchingFunction.h, libmdtools/forceFactory.hpp,
584	<	libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp,
585	<	libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp,
586	<	libmdtools/mdProfile.cpp, libmdtools/mdProfile.hpp,
587	<	libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c,
588	<	libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp,
589	<	libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90,
590	<	libmdtools/neighborLists.F90, libmdtools/notifyCutoffs.F90,
591	<	libmdtools/oopseMPI_module.F90, libmdtools/randomSPRNG.cpp,
592	<	libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90,
593	<	libmdtools/status_module.F90, libmdtools/switch_module.F90,
594	<	libmdtools/timing.F90, libmdtools/vector_class.F90,
595	<	libmdtools/wrappers.F90, libmdtools/MPIobj/dummy,
596	<	libmdtools/obj/dummy, samples/Makefile, samples/Makefile.in,
597	<	samples/alkane/Makefile, samples/alkane/Makefile.in,
598	<	samples/alkane/alkanes.mdl, samples/alkane/butane.bass,
599	<	samples/alkane/butane.eor, samples/alkane/init_butane.eor,
600	<	samples/argon/500.bass, samples/argon/500.eor,
601	<	samples/argon/500.in, samples/argon/Makefile,
602	<	samples/argon/Makefile.in, samples/argon/NVT.bass,
603	<	samples/argon/ar864.bass, samples/argon/ar864.eor,
604	<	samples/argon/ar864.in, samples/argon/argon.bass,
605	<	samples/argon/argon.eor, samples/argon/argonEM.bass,
606	<	samples/argon/init_argon.eor, samples/argon/lj.mdl,
607	<	samples/argon/machines, samples/lipid/5x5.bass,
608	<	samples/lipid/5x5.eor, samples/lipid/Makefile,
609	<	samples/lipid/Makefile.in, samples/lipid/init_5x5.eor,
610	<	samples/lipid/lipid.mdl, samples/lipid/water.mdl,
611	<	samples/metals/Au.bass, samples/metals/Au.eor,
612	<	samples/metals/Makefile, samples/metals/Makefile.in,
613	<	samples/metals/init_au.in, samples/metals/metals.mdl,
614	<	samples/water/200.in, samples/water/Makefile,
615	<	samples/water/Makefile.in, samples/water/init_ssd.eor,
616	<	samples/water/spce.bass, samples/water/spce.eor,
617	<	samples/water/ssd.bass, samples/water/ssd.eor,
618	<	samples/water/tim.bass, samples/water/tim.eor,
619	<	samples/water/tim.init, samples/water/tim.xyz,
620	<	samples/water/tip3p.bass, samples/water/tip3p.eor,
621	<	samples/water/tip3p.init, samples/water/two.bass,
622	<	samples/water/two.eor, samples/water/two.init,
623	<	samples/water/two.xyz, samples/water/water.mdl,
624	<	samples/water/spce/SPCEinit.in, samples/water/spce/spce.bass,
625	<	samples/water/spce/water.mdl, samples/water/ssde/256init.in,
626	<	samples/water/ssde/ssde.bass, samples/water/ssde/water.mdl,
627	<	samples/water/tip4p/TP4init.in, samples/water/tip4p/tp4.bass,
628	<	samples/water/tip4p/water.mdl, scripts/cleanSrc, scripts/cvs2cl.pl,
629	<	scripts/sfmakedepend, src/Make.dep, src/Makefile, src/Makefile.in,
630	<	src/oopse.cpp, src/oose.cpp, src/MPIobj/dummy, src/obj/dummy,
631	<	third-party/Makefile, third-party/Makefile.in,
632	<	third-party/mt19937ar.c, utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo,
633	<	utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h, utils/Make.dep,
634	<	utils/Makefile, utils/Makefile.in, utils/quickLate.c, utils/zsub,
635	<	utils/MPIobj/placeHolder, utils/obj/placeHolder,
636	<	utils/sysbuilder/Make.dep, utils/sysbuilder/Makefile,
637	<	utils/sysbuilder/Makefile.in, utils/sysbuilder/MoLocator.cpp,
638	<	utils/sysbuilder/MoLocator.hpp, utils/sysbuilder/cmdline.c,
639	<	utils/sysbuilder/cmdline.h, utils/sysbuilder/latticeBilayer.cpp,
640	<	utils/sysbuilder/latticeBuilder.cpp,
641	<	utils/sysbuilder/latticeBuilder.hpp,
642	<	utils/sysbuilder/nanoBuilder.cpp, utils/sysbuilder/nanoBuilder.hpp,
643	<	utils/sysbuilder/randomBilayer.cpp, utils/sysbuilder/sysBuild.cpp,
644	<	utils/sysbuilder/sysBuild.ggo, utils/sysbuilder/sysBuild.hpp,
645	<	utils/sysbuilder/MPIobj/placeHolder,
646	<	utils/sysbuilder/obj/placeHolder: Initial revision
1269	>	forceFields/Makefile.in, forceFields/Ni.u3.funcfl,
1270	>	forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl,
1271	>	forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl,
1272	>	forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc,
1273	>	scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend,
1274	>	ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess,
1275	>	ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4,
1276	>	ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf,
1277	>	forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl,
1278	>	forceFields/Au.u3.funcfl, forceFields/LJFF.frc,
1279	>	forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
1280	>	forceFields/Pt.VC.funcfl: Initial revision
1281

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