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Comparing trunk/OOPSE-2.0/ChangeLog (file contents):
Revision 1490 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1603 by tim, Tue Oct 19 21:28:55 2004 UTC

#	Line 1 | Line 1
1	<	2004-07-23 15:31  tim
1	>	2004-10-18 23:34  tim
2
3	<	* samples/lipid/5x5.bass: modify 5x5.bass
3	>	* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs
4	>	are fixed in Vector class
5
6	<	2004-07-23 15:25  tim
6	>	2004-10-18 23:28  tim
7
8	<	* samples/water/tip3p_ice/: 200.in, tp3.bass: [no log message]
8	>	* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix
9	>	some bugs in RectMatrixTestCase
10
11	<	2004-07-23 15:18  tim
11	>	2004-10-18 23:21  tim
12
13	<	* samples/: water/ssde/ssde.bass, argon/500.bass,
14	<	argon/argonNVT.bass: [no log message]
13	>	* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp,
14	>	test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp,
15	>	test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp,
16	>	test/math/VectorTestCase.hpp: implement more test cases
17
18	<	2004-07-23 15:12  tim
18	>	2004-10-18 18:13  tim
19
20	<	* samples/water/: dimer/two.in, spce/spce.in, ssd/ssd.in,
21	<	ssde/ssde.in, tip3p_ice/tp3.in, tip4p/tp4.in: add init files
20	>	* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp,
21	>	src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
22	>	src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
23	>	src/utils/StringTokenizer.hpp, test/math/Makefile,
24	>	test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more
25	>	tests on math library
26
27	<	2004-07-23 15:10  tim
27	>	2004-10-18 16:03  tim
28
29	<	* samples/minimizer/: ssdEM.in, tip4p_two.in: add init file
29	>	* test/math/: Makefile, QuaternionTestCase.cpp,
30	>	QuaternionTestCase.hpp, RectMatrixTestCase.cpp,
31	>	SquareMatrix3TestCase.cpp, Vector3TestCase.cpp,
32	>	Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding
33	>	more testing units
34
35	<	2004-07-23 15:09  tim
35	>	2004-10-18 12:07  tim
36
37	<	* samples/argon/: NVT.bass, argonNVT.bass, argonNVT.in: rename
38	<	NVT.bass to argonNVT.bass
37	>	* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp,
38	>	math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp,
39	>	math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp,
40	>	utils/GenericFactory.hpp: fix some bugs in Quaternion class
41
42	<	2004-07-23 15:07  tim
42	>	2004-10-18 11:30  gezelter
43
44	<	* samples/lipid/5x5.in: add 5x5.in
44	>	* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
45	>	Your basic run of the mill real-valued versions of Y_l^m(\theta,
46	>	\phi)
47
48	<	2004-07-23 15:06  tim
48	>	2004-10-18 11:29  gezelter
49
50	<	* samples/alkane/: butane.in, init_butane.eor: add butane.in
50	>	* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp,
51	>	types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp,
52	>	utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting
53	>	Shapes into OOPSE
54
55	<	2004-07-23 14:57  gezelter
55	>	2004-10-18 10:21  gezelter
56
57	<	* libBASS/Globals.cpp, samples/minimizer/ssdEM.bass,
39	<	samples/minimizer/tip4p_two.bass: changed minimizer keywords
57	>	* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType
58
59	<	2004-07-23 14:34  gezelter
59	>	2004-10-18 00:23  tim
60
61	<	* configure, ac-tools/configure.in: fixed typo
61	>	* test/math/VectorTestCase.hpp: adding  vector test case
62
63	<	2004-07-23 14:32  gezelter
63	>	2004-10-18 00:23  tim
64
65	<	* samples/minimizer/Makefile.in: fixed sample makefile
65	>	* src/utils/GenericFactory.hpp: adding generic factory and vector
66	>	test case
67
68	<	2004-07-23 14:31  gezelter
68	>	2004-10-16 20:19  tim
69
70	<	* configure, ac-tools/configure.in, samples/minimizer/Makefile.in,
71	<	samples/minimizer/WATER.frc, samples/minimizer/ssdEM.bass,
72	<	samples/minimizer/tip4p_two.bass, samples/minimizer/water.mdl:
54	<	minimizer sample changes
70	>	* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp,
71	>	SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in
72	>	progress
73
74	<	2004-07-23 14:15  gezelter
74	>	2004-10-15 20:31  tim
75
76	<	* configure, ac-tools/configure.in: removed beadLipid
76	>	* src/math/Quaternion.hpp: add quaternion class
77
78	<	2004-07-23 14:08  tim
78	>	2004-10-15 16:11  tim
79
80	<	* samples/Makefile.in: remove beadLipid
80	>	* test/io/: DUFF.frc, IfstrstreamTestCase.cpp,
81	>	IfstrstreamTestCase.hpp: adding test file
82
83	<	2004-07-23 14:03  chuckv
83	>	2004-10-15 16:10  tim
84
85	<	* samples/metals/: Au_nanoparticle.eor,
67	<	Au_nanoparticle_coreshell_12-20.bass,
68	<	Au_nanoparticle_coreshell_12-20.in: Added core-shell nanoparticle
69	<	files.
85	>	* src/io/basic_ifstrstream.hpp: fix a bunch of bugs
86
87	<	2004-07-23 13:51  tim
87	>	2004-10-15 15:42  tim
88
89	<	* samples/water/tip4p/TP4init.in: remove TP4init.in
89	>	* src/io/basic_ifstrstream.hpp: change const_cast to statc_const
90
91	<	2004-07-23 13:50  tim
91	>	2004-10-15 15:35  tim
92
93	<	* samples/water/tip4p/: Makefile.in, tp4.bass: change init file
78	<	name for tip4p and tip3p_ice
93	>	* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp
94
95	<	2004-07-23 13:48  tim
95	>	2004-10-15 15:34  tim
96
97	<	* samples/water/ssde/: Makefile.in, SSDEinit.in: [no log message]
97	>	* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use
98	>	namespace oopse
99
100	<	2004-07-23 13:48  tim
100	>	2004-10-15 14:38  chuckv
101
102	<	* samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass: change
103	<	init file name for ssd
102	>	* configure, ac-tools/aclocal.m4: Changed optimization flags for
103	>	XLF and XLC.
104
105	<	2004-07-23 13:46  tim
105	>	2004-10-15 13:28  tim
106
107	<	* samples/water/spce/: Makefile.in, SPCEinit.in, spce.bass: remove
108	<	SPCEInit.in
107	>	* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp:
108	>	adding ifstrstream test case
109
110	<	2004-07-23 13:45  tim
110	>	2004-10-15 13:20  tim
111
112	<	* samples/water/dimer/: Makefile.in, two.bass, two.init: change
97	<	names for init file
112	>	* src/io/basic_ifstrstream.hpp: fix include
113
114	<	2004-07-23 13:40  tim
114	>	2004-10-15 13:18  tim
115
116	<	* samples/lipid/: 5x5.bass, 5x5.eor, Makefile.in, init_5x5.eor:
102	<	change init file name in lipid directory
116	>	* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi
117
118	<	2004-07-23 13:36  tim
118	>	2004-10-15 13:17  tim
119
120	<	* samples/argon/init_argon.eor: remove init_argon.eor
120	>	* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile
121
122	<	2004-07-23 13:34  tim
122	>	2004-10-15 13:16  tim
123
124	<	* samples/: alkane/Makefile.in, alkane/butane.bass,
125	<	alkane/butane.eor, argon/500.eor, argon/ar864.eor: [no log message]
124	>	* test/io/: Makefile, ifstrstreamTestCase.cpp,
125	>	ifstrstreamTestCase.hpp: adding test case for ifstrstream
126
127	<	2004-07-23 13:33  tim
127	>	2004-10-15 10:37  tim
128
129	<	* samples/argon/Makefile.in: remove eor file
129	>	* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp,
130	>	ifstrstreamTestCase.hpp: add ifstrstreamTestCase
131
132	<	2004-07-23 13:31  tim
132	>	2004-10-15 10:20  tim
133
134	<	* samples/argon/: Makefile.in, argon.bass, argon.eor, argonEM.bass:
120	<	change names for argon
134	>	* src/io/basic_ifstrstream.hpp: add checkFilename Option
135
136	<	2004-07-23 11:47  tim
136	>	2004-10-15 10:19  tim
137
138	<	* samples/water/ssde/SSDEinit.in: [no log message]
138	>	* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp,
139	>	SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add
140	>	SquareMatrixTestCase class
141
142	<	2004-07-23 11:45  tim
142	>	2004-10-15 02:52  tim
143
144	<	* samples/water/ssde/SSDEinit.in: add init file for ssde
144	>	* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream
145
146	<	2004-07-23 11:43  chuckv
146	>	2004-10-14 18:28  tim
147
148	<	* libmdtools/calc_eam.F90: Fixed bug in calc_eam with mixtures and
149	<	cutoffs associated with mixture.
148	>	* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp,
149	>	Vector.hpp: math library in progress
150
151	<	2004-07-23 10:35  tim
151	>	2004-10-14 18:27  tim
152
153	<	* libmdtools/: AtomVisitor.cpp, AtomVisitor.hpp: support SSD_E
138	<	SSD_RF SSD1
153	>	* src/io/FileReader.hpp: FileReader in progress
154
155	<	2004-07-23 09:53  tim
155	>	2004-10-13 18:53  tim
156
157	<	* libmdtools/AtomVisitor.cpp: SSDVisitor support SSD_RF, SSD_E,
158	<	SSD1 now
157	>	* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress,
158	>	test in isOrthogonal of SquareMatrix is failed by some reasons
159
160	<	2004-07-23 09:19  tim
160	>	2004-10-13 17:28  tim
161
162	<	* libmdtools/ZConsReader.cpp: remove ^M from ZConsReader.cpp
162	>	* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap
163	>	class
164
165	<	2004-07-23 09:18  tim
165	>	2004-10-13 17:27  tim
166
167	<	* samples/lipid/5x5.bass: remove unsupport keyword
167	>	* test/math/: MainTest.cpp, RectMatrixTestCase.cpp,
168	>	RectMatrixTestCase.hpp: adding testing unit
169
170	<	2004-07-22 16:01  chuckv
170	>	2004-10-13 17:24  tim
171
172	<	* samples/metals/: init_Au_bulk.in, init_Au_nanoparticle.in:
156	<	Changed init files to be more OOPSE like...
172	>	* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix
173
174	<	2004-07-22 10:11  gezelter
174	>	2004-10-13 01:51  tim
175
176	<	* configure, ac-tools/configure.in: added sample directory
176	>	* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp,
177	>	Vector3.hpp: refactory vector and matrix classes
178
179	<	2004-07-22 10:06  chrisfen
179	>	2004-10-13 01:50  tim
180
181	<	* src/Makefile.in: fixed icc7 incompatibility in linking
181	>	* src/math/Vector3d.hpp: Remove some Makefile.in
182
183	<	2004-07-21 17:03  chrisfen
183	>	2004-10-12 18:57  tim
184
185	<	* samples/water/: Makefile.in, tip3p_ice/200.in,
186	<	tip3p_ice/Makefile.in, tip3p_ice/tp3.bass, tip3p_ice/water.mdl:
170	<	Added tip3p_ice to Makefile
185	>	* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and
186	>	Matrix3x3d.hpp
187
188	<	2004-07-21 16:46  chuckv
188	>	2004-10-12 14:08  tim
189
190	<	* 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.
190	>	* doc/: cppstyle.html, style.css: adding c++ coding style
191
192	<	2004-07-21 14:53  gezelter
192	>	2004-10-11 17:15  tim
193
194	<	* samples/water/dimer/two.bass: Checked a bug where eor file wasn't
195	<	being written at the end of the run
194	>	* src/: constraints/AbstractClasses.hpp,
195	>	integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp:
196	>	change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
197
198	<	2004-07-21 14:53  gezelter
198	>	2004-10-11 16:54  tim
199
200	<	* libmdtools/Integrator.cpp: Fixed a bug where eor file wasn't
188	<	being written at the end of the run
200	>	* scripts/filepp: fix a bug in filepp
201
202	<	2004-07-21 09:11  gezelter
202	>	2004-10-11 16:13  tim
203
204	<	* README: [no log message]
204	>	* make/Makefile.in: using filepp to generate dependencies instead
205	>	of compilers
206
207	<	2004-07-21 09:08  gezelter
207	>	2004-10-11 16:10  tim
208
209	<	* samples/argon/machines: cleaning up for export
209	>	* scripts/filepp: filepp can be used to generate dependencies for
210	>	c/c++ now
211
212	<	2004-07-21 09:04  gezelter
212	>	2004-10-11 13:40  tim
213
214	<	* NEWS, README: cleaning up for export
214	>	* make/Makefile.in: remove -module from F90Options
215
216	<	2004-07-21 08:45  gezelter
216	>	2004-10-11 13:01  tim
217
218	<	* configure, ac-tools/configure.in: removing staticProps from cvs
219	<	tree
218	>	* make/Makefile.in: adding rules to move fortran 90 module to
219	>	target directory
220
221	<	2004-07-20 12:07  gezelter
221	>	2004-10-11 10:43  gezelter
222
223	<	* configure, ac-tools/aclocal.m4, utils/Makefile.in,
210	<	utils/quickLate.c, utils/sysbuilder/Makefile.in: [no log message]
223	>	* make/Makefile.in: fixed makefile.in
224
225	<	2004-07-20 10:17  gezelter
225	>	2004-10-11 09:51  tim
226
227	<	* configure, ac-tools/aclocal.m4, ac-tools/configure.in,
228	<	third-party/gnugetopt.h, utils/getopt.c, utils/getopt1.c,
216	<	utils/gnugetopt.h: fixing getopt_long
227	>	* scripts/filepp: remove "use bytes" which causes problem in sgi
228	>	machine
229
230	<	2004-07-19 16:58  gezelter
230	>	2004-10-11 09:26  tim
231
232	<	* 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]
232	>	* forceFields/Makefile: add Makefile
233
234	<	2004-07-19 16:52  tim
234	>	2004-10-11 09:23  tim
235
236	<	* utils/quickLate.c: minor fix of format string in quicklate.c
236	>	* samples/: water/dimer/Makefile, water/spce/Makefile,
237	>	water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile,
238	>	water/tip4p/Makefile, zcons/Makefile: fix Makefile under water
239	>	directory
240
241	<	2004-07-19 16:30  tim
241	>	2004-10-11 09:23  tim
242
243	<	* utils/zsub: remove zsub from cvs tree
243	>	* samples/argon/Makefile: remove argon.dump and argon.eor from
244	>	Makefile
245
246	<	2004-07-19 16:25  tim
246	>	2004-10-09 01:01  tim
247
248	<	* libmdtools/ZConstraint.cpp, utils/Dump2XYZ.cpp: remove some
249	<	comment lines
248	>	* samples/: alkane/Makefile.in, argon/Makefile.in,
249	>	lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in:
250	>	Remove some Makefile.in
251
252	<	2004-07-19 16:00  tim
252	>	2004-10-08 18:15  tim
253
254	<	* libmdtools/OOPSEMinimizer.hpp: remove an extra semicolon from
242	<	OOPSEMinimizer.hpp
254	>	* make/Makefile.in: [no log message]
255
256	<	2004-07-19 13:55  gezelter
256	>	2004-10-08 17:51  tim
257
258	<	* libBASS/y.tab.h: Shouldn't have been in CVS
258	>	* make/Makefile.in: fix make install
259
260	<	2004-07-19 13:54  gezelter
260	>	2004-10-08 17:10  tim
261
262	<	* libBASS/y.tab.h, libmdtools/ForceFields.cpp: Fix for
251	<	thermodynamic integration of rigid bodies
262	>	* make/Makefile.in: adding make install
263
264	<	2004-07-19 12:00  gezelter
264	>	2004-10-08 17:04  tim
265
266	<	* libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: These can be
267	<	generated via lex and yacc at compile time
266	>	* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile,
267	>	metals/Makefile, minimizer/Makefile, water/Makefile.in,
268	>	water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile,
269	>	water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in,
270	>	water/ssde/Makefile, water/ssde/Makefile.in,
271	>	water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in,
272	>	water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile,
273	>	zcons/Makefile.in: add Makefile to sample directory
274
275	<	2004-07-19 11:47  gezelter
275	>	2004-10-06 18:03  gezelter
276
277	<	* libBASS/BASSlex.c, libBASS/BASSyacc.c, libBASS/BASSyacc.h,
278	<	libBASS/make_nodes.c, libBASS/y.tab.h, libmdtools/Makefile.in,
262	<	libmdtools/MatVec3.c, src/Makefile.in: [no log message]
277	>	* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt
278	>	stuff
279
280	<	2004-07-19 11:32  gezelter
280	>	2004-10-06 18:03  gezelter
281
282		* configure, ac-tools/aclocal.m4, ac-tools/configure.in,
283	<	third-party/gnugetopt.h, utils/Makefile.in,
284	<	utils/sysbuilder/Makefile.in: changes for gnu getopt and fixed
285	<	SPRNG configure script
283	>	make/Doxyfile, src/applications/getopt.c,
284	>	src/applications/getopt1.c, src/applications/gnugetopt.h: more
285	>	build fixes
286
287	<	2004-07-16 16:49  gezelter
287	>	2004-10-06 17:20  tim
288
289	<	* libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: fixing for machines
274	<	that don't have lex and yacc
289	>	* make/: Doxyfile, Makefile.in: adding doxygen configuration file
290
291	<	2004-07-16 15:55  gezelter
291	>	2004-10-06 17:19  tim
292
293	<	* Makefile: Makefiles don't belong in cvs repository
293	>	* scripts/filepp: filepp can handle different fortran module case
294	>	and suffix
295
296	<	2004-07-16 15:54  gezelter
296	>	2004-10-06 16:27  gezelter
297
298	<	* Makefile, forceFields/Makefile, libBASS/Makefile,
299	<	libmdtools/Makefile, samples/Makefile, src/Makefile,
284	<	third-party/Makefile, utils/Makefile, utils/sysbuilder/Makefile:
285	<	Makefiles don't belong in repository
298	>	* src/restraints/Restraints.cpp: Chris doesn't know about the
299	>	OOPSE-2.0 directory structure yet
300
301	<	2004-07-16 15:49  gezelter
301	>	2004-10-06 16:27  gezelter
302
303	<	* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile,
290	<	metals/Makefile: Makefiles don't belong in repository
303	>	* ChangeLog: Yeah yeah, we'lll get around to it later
304
305	<	2004-07-16 15:20  chrisfen
305	>	2004-10-06 16:22  gezelter
306
307	<	* Makefile, configure, ac-tools/configure.in, forceFields/Makefile,
308	<	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
307	>	* configure, ac-tools/configure.in, ac-tools/fortran90.m4,
308	>	make/Makefile.in: cleaning up build process
309
310	<	2004-07-16 14:57  chrisfen
310	>	2004-10-06 15:01  chrisfen
311
312	<	* samples/water/tip4p/Makefile.in: tip4p makefile.in added
312	>	* src/restraints/Restraints.cpp: made the file reading in
313	>	restraints more intelligent - no longer gives uninformative seg
314	>	faults
315
316	<	2004-07-16 14:57  chrisfen
316	>	2004-10-06 14:55  gezelter
317
318	<	* samples/water/ssde/: 256init.in, Makefile.in, ssde.bass: ssde
307	<	makefile.in added
318	>	* src/applications/simpleBuilder/Make.ftemp.old: cleaning up
319
320	<	2004-07-16 14:57  chrisfen
320	>	2004-10-06 14:51  gezelter
321
322	<	* samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass,
323	<	water.mdl: ssd files sorted added
322	>	* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy,
323	>	scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit
324
325	<	2004-07-16 14:57  chrisfen
325	>	2004-10-06 13:53  tim
326
327	<	* samples/water/spce/Makefile.in: spce makefile.in added
327	>	* make/: Makefile, Makefile.in: fix make statistics
328
329	<	2004-07-16 14:56  chrisfen
329	>	2004-10-06 13:18  tim
330
331	<	* samples/water/dimer/: Makefile.in, two.bass, two.init, water.mdl:
332	<	dimer files added
331	>	* make/: Makefile, Makefile.in: adding GNU make functions to
332	>	combine all of the static libraries to a big library
333
334	<	2004-07-16 14:56  chrisfen
334	>	2004-10-05 17:57  tim
335
336	<	* samples/water/: 200.in, Makefile, Makefile.in, init_ssd.eor,
326	<	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
336	>	* make/: Makefile, Makefile.in:  adding shared library flag
337
338	<	2004-07-16 13:57  gezelter
338	>	2004-10-05 14:37  tim
339
340	<	* AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README,
341	<	configure, ac-tools/Make.conf.in, ac-tools/aclocal.m4,
342	<	ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in,
343	<	ac-tools/fortran90.m4, ac-tools/install-sh, ac-tools/shtool,
344	<	forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl,
345	<	forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl,
346	<	forceFields/Au.VC.funcfl, forceFields/Au.u3.funcfl,
340	>	* src/: Makefile, UseTheForce/Makefile,
341	>	UseTheForce/mpiSimulation_module.F90,
342	>	UseTheForce/DarkSide/Makefile,
343	>	UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move
344	>	mpiSimulation_module to DarkSide
345	>
346	>	2004-10-05 14:35  tim
347	>
348	>	* make/: Makefile, Makefile.in: building MPI version;using static
349	>	library instead of shared library
350	>
351	>	2004-10-05 09:14  tim
352	>
353	>	* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90
354	>	to filepp
355	>
356	>	2004-10-04 15:56  tim
357	>
358	>	* make/: Makefile, Makefile.in: add make cvslog
359	>
360	>	2004-10-04 11:24  gezelter
361	>
362	>	* make/: Makefile, Makefile.in: more work on the parallel build
363	>
364	>	2004-10-04 11:06  gezelter
365	>
366	>	* make/: Makefile, Makefile.in: changes to backport declare flags
367	>
368	>	2004-10-04 10:27  gezelter
369	>
370	>	* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp,
371	>	DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging
372	>	shapes
373	>
374	>	2004-10-01 23:40  tim
375	>
376	>	* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree
377	>
378	>	2004-10-01 23:22  tim
379	>
380	>	* make/: Makefile, Makefile.in: add oopse_ as library prefix
381	>
382	>	2004-10-01 16:59  tim
383	>
384	>	* make/: Makefile, Makefile.in: fix a space trimming bug in filepp
385	>
386	>	2004-10-01 16:22  gezelter
387	>
388	>	* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A
389	>	few minor build changes
390	>
391	>	2004-10-01 16:11  tim
392	>
393	>	* scripts/filepp: adding fortran90 make dependency tool
394	>
395	>	2004-09-30 10:41  tim
396	>
397	>	* make/: Makefile, Makefile.in: make clean is smart enough to only
398	>	remove object files belong to current package.  turn off silent
399	>	mode
400	>
401	>	2004-09-29 16:55  tim
402	>
403	>	* src/: Makefile, UseTheForce/Makefile,
404	>	UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile,
405	>	applications/oopse/Makefile, applications/simpleBuilder/Makefile,
406	>	brains/Makedepend, brains/Makefile, constraints/Makefile,
407	>	integrators/Makefile, io/Makefile, math/Makefile,
408	>	minimizers/Makefile, primitives/Makefile, profiling/Makefile,
409	>	restraints/Makefile, types/Makefile, utils/Makefile,
410	>	visitors/Makefile: define DEV_ROOT as relative path
411	>
412	>	2004-09-29 16:54  tim
413	>
414	>	* make/: Makefile, Makefile.in: get the relative path by shell
415	>	script
416	>
417	>	2004-09-29 16:32  tim
418	>
419	>	* make/Makefile: eliminate DEV_ROOT by relative path
420	>
421	>	2004-09-29 13:37  tim
422	>
423	>	* make/Makefile.in: add PackageLibs;  fix dependency rule
424	>
425	>	2004-09-29 12:57  gezelter
426	>
427	>	* configure, ac-tools/configure.in: updates
428	>
429	>	2004-09-29 12:56  gezelter
430	>
431	>	* make/: Make.conf.in, Makefile.in: Working on make stuff
432	>
433	>	2004-09-29 12:46  tim
434	>
435	>	* Makefile: If makefile does not exist, print error message
436	>
437	>	2004-09-29 12:12  tim
438	>
439	>	* make/: Make.conf.in, Makefile: fix dependencies rule
440	>
441	>	2004-09-29 10:58  gezelter
442	>
443	>	* Makefile, make/Makefile: still working on build process
444	>
445	>	2004-09-29 10:00  tim
446	>
447	>	* make/Makefile: add print statment to rules
448	>
449	>	2004-09-29 09:59  tim
450	>
451	>	* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile,
452	>	applications/dump2Xyz/Makefile, applications/oopse/Makefile,
453	>	applications/simpleBuilder/Makefile, brains/Makefile,
454	>	constraints/Makefile, integrators/Makefile, io/Makefile,
455	>	math/Makefile, minimizers/Makefile, primitives/Makefile,
456	>	profiling/Makefile, restraints/Makefile, types/Makefile,
457	>	utils/Makefile, visitors/Makefile: change Makefile to relative path
458	>
459	>	2004-09-28 21:55  tim
460	>
461	>	* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c
462	>	which cause headache in bulding libutils
463	>
464	>	2004-09-28 18:24  tim
465	>
466	>	* src/applications/: BaseLattice.cpp, BaseLattice.hpp,
467	>	Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h,
468	>	Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
469	>	LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp,
470	>	MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp,
471	>	nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo,
472	>	simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp,
473	>	dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c,
474	>	dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile,
475	>	oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp,
476	>	simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
477	>	simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
478	>	simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
479	>	simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old,
480	>	simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp,
481	>	simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp,
482	>	simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo,
483	>	simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h:
484	>	change directory structure of application. Every executable file is
485	>	replaced in seperate directory
486	>
487	>	2004-09-28 17:15  gezelter
488	>
489	>	* lib/dummy: Keep that lib around, please.
490	>
491	>	2004-09-28 17:14  gezelter
492	>
493	>	* Makefile, configure, ac-tools/configure.in, make/Make.conf.in:
494	>	starting a configure version
495	>
496	>	2004-09-28 16:08  tim
497	>
498	>	* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90,
499	>	UseTheForce/DarkSide/Makefile,
500	>	UseTheForce/DarkSide/notifyCutoffs.F90,
501	>	UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend,
502	>	brains/Makefile, brains/simulation_module.F90: move fortran files
503	>	around to solve dependency problem
504	>
505	>	2004-09-28 15:43  tim
506	>
507	>	* Makefile, src/UseTheForce/ForceFields.hpp,
508	>	src/UseTheForce/Makefile, src/applications/BaseLattice.hpp,
509	>	src/applications/Makedepend, src/applications/Makefile,
510	>	src/brains/Makedepend, src/brains/simulation_module.F90,
511	>	src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp,
512	>	src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp,
513	>	src/utils/Makefile: [no log message]
514	>
515	>	2004-09-28 15:41  tim
516	>
517	>	* make/Makefile, scripts/sfmakedepend: fix fortran dependency
518	>	problem
519	>
520	>	2004-09-28 11:13  tim
521	>
522	>	* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y,
523	>	src/io/Makefile: add yacc and lex rules
524	>
525	>	2004-09-27 15:24  tim
526	>
527	>	* make/Makefile: adding include path to F90Options
528	>
529	>	2004-09-27 15:13  tim
530	>
531	>	* make/Makefile: change suffix from .cc to .cpp
532	>
533	>	2004-09-24 11:27  tim
534	>
535	>	* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
536	>	UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
537	>	UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp,
538	>	UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp,
539	>	UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp,
540	>	UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90,
541	>	UseTheForce/DarkSide/calc_LJ_FF.F90,
542	>	UseTheForce/DarkSide/notifyCutoffs.F90,
543	>	UseTheForce/DarkSide/switch_module.F90,
544	>	applications/BaseLattice.cpp, applications/Dump2XYZ.cpp,
545	>	applications/Dump2XYZCmd.c, applications/Lattice.cpp,
546	>	applications/Lattice.hpp, applications/LatticeCreator.cpp,
547	>	applications/LatticeCreator.hpp, applications/LatticeFactory.cpp,
548	>	applications/MoLocator.cpp, applications/MoLocator.hpp,
549	>	applications/cmdline.c, applications/nanoBuilder.cpp,
550	>	applications/oopse.cpp, applications/simpleBuilder.cpp,
551	>	applications/simpleBuilderCmd.c, brains/Exclude.cpp,
552	>	brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
553	>	brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp,
554	>	brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp,
555	>	brains/mpiSimulation.cpp, brains/mpiSimulation.hpp,
556	>	constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp,
557	>	integrators/AbstractClasses.hpp, integrators/Integrator.cpp,
558	>	integrators/Integrator.hpp, integrators/NPT.cpp,
559	>	integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp,
560	>	integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c,
561	>	io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp,
562	>	io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp,
563	>	io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp,
564	>	io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
565	>	io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c,
566	>	io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h,
567	>	io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c,
568	>	math/MatVec3.h, math/randomSPRNG.cpp,
569	>	minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp,
570	>	minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp,
571	>	minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp,
572	>	primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp,
573	>	primitives/BendExtensions.cpp, primitives/Bond.cpp,
574	>	primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp,
575	>	primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
576	>	primitives/GhostBend.cpp, primitives/Molecule.cpp,
577	>	primitives/Molecule.hpp, primitives/RigidBody.cpp,
578	>	primitives/RigidBody.hpp, primitives/SRI.hpp,
579	>	primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
580	>	primitives/Torsion.cpp, primitives/TorsionExtensions.cpp,
581	>	profiling/mdProfile.cpp, restraints/Restraints.cpp,
582	>	restraints/Restraints.hpp, types/AtomStamp.cpp,
583	>	types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp,
584	>	types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp,
585	>	types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
586	>	types/MakeStamps.cpp, types/MakeStamps.hpp,
587	>	types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
588	>	types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
589	>	types/TorsionStamp.cpp, types/TorsionStamp.hpp,
590	>	types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp,
591	>	utils/StreamTokenizer.cpp, utils/StringUtils.c,
592	>	utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c,
593	>	utils/simError.c, visitors/AtomVisitor.cpp,
594	>	visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp,
595	>	visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp,
596	>	visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp,
597	>	visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
598	>	visitors/ZconsVisitor.hpp: change the #include in source files
599	>
600	>	2004-09-23 23:16  gezelter
601	>
602	>	* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
603	>	src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
604	>	src/constraints/Makefile, src/constraints/ZConstraint.cpp,
605	>	src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp,
606	>	src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp,
607	>	src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile,
608	>	src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90,
609	>	src/UseTheForce/fForceField.h,
610	>	src/UseTheForce/fSwitchingFunction.h,
611	>	src/UseTheForce/fortranWrapDefines.hpp,
612	>	src/UseTheForce/fortranWrappers.cpp,
613	>	src/UseTheForce/fortranWrappers.hpp,
614	>	src/UseTheForce/mpiComponentPlan.h,
615	>	src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h,
616	>	src/UseTheForce/mpiSimulation_module.F90,
617	>	src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile,
618	>	src/UseTheForce/DarkSide/atype_module.F90,
619	>	src/UseTheForce/DarkSide/calc_LJ_FF.F90,
620	>	src/UseTheForce/DarkSide/calc_charge_charge.F90,
621	>	src/UseTheForce/DarkSide/calc_dipole_dipole.F90,
622	>	src/UseTheForce/DarkSide/calc_eam.F90,
623	>	src/UseTheForce/DarkSide/calc_gb.F90,
624	>	src/UseTheForce/DarkSide/calc_reaction_field.F90,
625	>	src/UseTheForce/DarkSide/calc_sticky_pair.F90,
626	>	src/UseTheForce/DarkSide/force_globals.F90,
627	>	src/UseTheForce/DarkSide/neighborLists.F90,
628	>	src/UseTheForce/DarkSide/notifyCutoffs.F90,
629	>	src/UseTheForce/DarkSide/switch_module.F90,
630	>	src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h,
631	>	src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp,
632	>	src/io/DumpWriter.cpp, src/io/Globals.cpp,
633	>	src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp,
634	>	src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp,
635	>	src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp,
636	>	src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
637	>	src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c,
638	>	src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h,
639	>	src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h,
640	>	src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp,
641	>	src/types/AtomStamp.hpp, src/types/BendStamp.cpp,
642	>	src/types/BendStamp.hpp, src/types/BondStamp.cpp,
643	>	src/types/BondStamp.hpp, src/types/Component.cpp,
644	>	src/types/Component.hpp, src/types/CutoffGroupStamp.cpp,
645	>	src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp,
646	>	src/types/MakeStamps.hpp, src/types/Makefile,
647	>	src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp,
648	>	src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp,
649	>	src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp,
650	>	src/types/ZconStamp.cpp, src/types/ZconStamp.hpp,
651	>	src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp,
652	>	src/brains/Exclude.hpp, src/brains/ForceFields.cpp,
653	>	src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp,
654	>	src/brains/SimInfo.hpp, src/brains/SimSetup.cpp,
655	>	src/brains/SimSetup.hpp, src/brains/SimState.cpp,
656	>	src/brains/SimState.hpp, src/brains/SkipList.cpp,
657	>	src/brains/SkipList.hpp, src/brains/Thermo.cpp,
658	>	src/brains/Thermo.hpp, src/brains/fSimulation.h,
659	>	src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp,
660	>	src/brains/simulation_module.F90, src/io/BASS_interface.cpp,
661	>	src/io/Globals.hpp, src/io/LinkedAssign.cpp,
662	>	src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp,
663	>	src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h,
664	>	src/math/mt19937ar.c, src/math/randomSPRNG.cpp,
665	>	src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp,
666	>	src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp,
667	>	src/minimizers/OOPSEMinimizer.cpp,
668	>	src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp,
669	>	src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp,
670	>	src/primitives/Atom.cpp, src/primitives/Atom.hpp,
671	>	src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp,
672	>	src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp,
673	>	src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp,
674	>	src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
675	>	src/primitives/Makefile, src/primitives/Molecule.cpp,
676	>	src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp,
677	>	src/primitives/RigidBody.hpp, src/primitives/SRI.hpp,
678	>	src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp,
679	>	src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp,
680	>	src/restraints/Makefile, src/restraints/Restraints.cpp,
681	>	src/restraints/Restraints.hpp, src/utils/GenericData.cpp,
682	>	src/utils/GenericData.hpp, src/utils/Makefile,
683	>	src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp,
684	>	src/utils/StringUtils.c, src/utils/StringUtils.cpp,
685	>	src/utils/StringUtils.h, src/utils/StringUtils.hpp,
686	>	src/utils/TypeInfo.hpp, src/utils/Utility.cpp,
687	>	src/utils/Utility.hpp, src/utils/definitions_module.F90,
688	>	src/utils/fError.c, src/utils/oopseMPI_module.F90,
689	>	src/utils/simError.c, src/utils/simError.h,
690	>	src/utils/status_module.F90, src/utils/vector_class.F90,
691	>	src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp,
692	>	src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp,
693	>	src/visitors/CompositeVisitor.hpp, src/visitors/Makefile,
694	>	src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
695	>	src/visitors/RigidBodyVisitor.cpp,
696	>	src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
697	>	src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
698	>	samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
699	>	samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
700	>	samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
701	>	samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in,
702	>	samples/zcons/Makefile.in, samples/zcons/water.md,
703	>	samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md,
704	>	samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md,
705	>	src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp,
706	>	src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo,
707	>	src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h,
708	>	src/applications/Lattice.cpp, src/applications/Lattice.hpp,
709	>	src/applications/LatticeCreator.cpp,
710	>	src/applications/LatticeCreator.hpp,
711	>	src/applications/LatticeFactory.cpp,
712	>	src/applications/LatticeFactory.hpp, src/applications/Makedepend,
713	>	src/applications/Makefile, src/applications/MoLocator.cpp,
714	>	src/applications/MoLocator.hpp, src/applications/Vector3d.hpp,
715	>	src/applications/cmdline.c, src/applications/cmdline.h,
716	>	src/applications/getopt.c, src/applications/getopt1.c,
717	>	src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp,
718	>	src/applications/nanoBuilder.hpp, src/applications/oopse.cpp,
719	>	src/applications/quickLate.c, src/applications/simpleBuilder.cpp,
720	>	src/applications/simpleBuilder.ggo,
721	>	src/applications/simpleBuilderCmd.c,
722	>	src/integrators/AbstractClasses.hpp,
723	>	src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp,
724	>	src/integrators/Integrator.hpp, src/integrators/Makefile,
725	>	src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
726	>	src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
727	>	src/integrators/NVT.cpp, src/profiling/Makefile,
728	>	src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp,
729	>	src/profiling/timing.F90, samples/metals/Au_bulk.in,
730	>	samples/metals/Au_nanoparticle.in, samples/metals/metals.md,
731	>	samples/water/Makefile.in, samples/water/dimer/Makefile.in,
732	>	samples/water/dimer/two.in, samples/water/dimer/two.md,
733	>	samples/water/dimer/water.md, samples/water/spce/Makefile.in,
734	>	samples/water/spce/spce.in, samples/water/spce/spce.md,
735	>	samples/water/spce/water.md, samples/water/ssde/Makefile.in,
736	>	samples/water/ssde/ssde.in, samples/water/ssde/ssde.md,
737	>	samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in,
738	>	samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md,
739	>	samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in,
740	>	samples/water/ssd/ssd.in, samples/water/ssd/ssd.md,
741	>	samples/water/ssd/water.md, samples/water/tip4p/tp4.in,
742	>	samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
743	>	samples/alkane/Makefile.in, samples/alkane/alkanes.md,
744	>	samples/alkane/butane.in, samples/alkane/butane.md,
745	>	samples/argon/500.in, samples/argon/500.md,
746	>	samples/argon/Makefile.in, samples/argon/ar864.in,
747	>	samples/argon/ar864.md, samples/argon/argonNVT.in,
748	>	samples/argon/argonNVT.md, samples/argon/lj.md,
749	>	samples/lipid/5x5.in, samples/lipid/5x5.md,
750	>	samples/lipid/Makefile.in, samples/lipid/lipid.md,
751	>	samples/lipid/water.md, samples/minimizer/Makefile.in,
752	>	samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in,
753	>	samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in,
754	>	samples/minimizer/tip4p_two.md, samples/minimizer/water.md,
755	>	samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl,
756	>	forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl,
757		forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl,
758		forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl,
759		forceFields/DUFF.frc, forceFields/DipoleTest.frc,
760		forceFields/EAM.VC.frc, forceFields/EAM.frc,
761		forceFields/EAM.u3.frc, forceFields/EAM.u6.frc,
762	<	forceFields/LJFF.frc, forceFields/Makefile,
763	<	forceFields/Makefile.in, forceFields/Ni.VC.funcfl,
764	<	forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl,
765	<	forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl,
766	<	forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl,
767	<	forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl,
768	<	forceFields/WATER.frc, libBASS/AtomStamp.cpp,
769	<	libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp,
770	<	libBASS/BASS_interface.h, libBASS/BASS_parse.c,
771	<	libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y,
772	<	libBASS/BendStamp.cpp, libBASS/BendStamp.hpp,
773	<	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
489	<
490	<	2004-07-16 13:57  gezelter
762	>	forceFields/Makefile.in, forceFields/Ni.u3.funcfl,
763	>	forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl,
764	>	forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl,
765	>	forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc,
766	>	scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend,
767	>	ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess,
768	>	ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4,
769	>	ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf,
770	>	forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl,
771	>	forceFields/Au.u3.funcfl, forceFields/LJFF.frc,
772	>	forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
773	>	forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0
774
775	<	* AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README,
776	<	configure, ac-tools/Make.conf.in, ac-tools/aclocal.m4,
777	<	ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in,
778	<	ac-tools/fortran90.m4, ac-tools/install-sh, ac-tools/shtool,
779	<	forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl,
780	<	forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl,
781	<	forceFields/Au.VC.funcfl, forceFields/Au.u3.funcfl,
775	>	2004-09-23 23:16  gezelter
776	>
777	>	* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
778	>	src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
779	>	src/constraints/Makefile, src/constraints/ZConstraint.cpp,
780	>	src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp,
781	>	src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp,
782	>	src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile,
783	>	src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90,
784	>	src/UseTheForce/fForceField.h,
785	>	src/UseTheForce/fSwitchingFunction.h,
786	>	src/UseTheForce/fortranWrapDefines.hpp,
787	>	src/UseTheForce/fortranWrappers.cpp,
788	>	src/UseTheForce/fortranWrappers.hpp,
789	>	src/UseTheForce/mpiComponentPlan.h,
790	>	src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h,
791	>	src/UseTheForce/mpiSimulation_module.F90,
792	>	src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile,
793	>	src/UseTheForce/DarkSide/atype_module.F90,
794	>	src/UseTheForce/DarkSide/calc_LJ_FF.F90,
795	>	src/UseTheForce/DarkSide/calc_charge_charge.F90,
796	>	src/UseTheForce/DarkSide/calc_dipole_dipole.F90,
797	>	src/UseTheForce/DarkSide/calc_eam.F90,
798	>	src/UseTheForce/DarkSide/calc_gb.F90,
799	>	src/UseTheForce/DarkSide/calc_reaction_field.F90,
800	>	src/UseTheForce/DarkSide/calc_sticky_pair.F90,
801	>	src/UseTheForce/DarkSide/force_globals.F90,
802	>	src/UseTheForce/DarkSide/neighborLists.F90,
803	>	src/UseTheForce/DarkSide/notifyCutoffs.F90,
804	>	src/UseTheForce/DarkSide/switch_module.F90,
805	>	src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h,
806	>	src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp,
807	>	src/io/DumpWriter.cpp, src/io/Globals.cpp,
808	>	src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp,
809	>	src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp,
810	>	src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp,
811	>	src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
812	>	src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c,
813	>	src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h,
814	>	src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h,
815	>	src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp,
816	>	src/types/AtomStamp.hpp, src/types/BendStamp.cpp,
817	>	src/types/BendStamp.hpp, src/types/BondStamp.cpp,
818	>	src/types/BondStamp.hpp, src/types/Component.cpp,
819	>	src/types/Component.hpp, src/types/CutoffGroupStamp.cpp,
820	>	src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp,
821	>	src/types/MakeStamps.hpp, src/types/Makefile,
822	>	src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp,
823	>	src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp,
824	>	src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp,
825	>	src/types/ZconStamp.cpp, src/types/ZconStamp.hpp,
826	>	src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp,
827	>	src/brains/Exclude.hpp, src/brains/ForceFields.cpp,
828	>	src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp,
829	>	src/brains/SimInfo.hpp, src/brains/SimSetup.cpp,
830	>	src/brains/SimSetup.hpp, src/brains/SimState.cpp,
831	>	src/brains/SimState.hpp, src/brains/SkipList.cpp,
832	>	src/brains/SkipList.hpp, src/brains/Thermo.cpp,
833	>	src/brains/Thermo.hpp, src/brains/fSimulation.h,
834	>	src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp,
835	>	src/brains/simulation_module.F90, src/io/BASS_interface.cpp,
836	>	src/io/Globals.hpp, src/io/LinkedAssign.cpp,
837	>	src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp,
838	>	src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h,
839	>	src/math/mt19937ar.c, src/math/randomSPRNG.cpp,
840	>	src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp,
841	>	src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp,
842	>	src/minimizers/OOPSEMinimizer.cpp,
843	>	src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp,
844	>	src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp,
845	>	src/primitives/Atom.cpp, src/primitives/Atom.hpp,
846	>	src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp,
847	>	src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp,
848	>	src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp,
849	>	src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
850	>	src/primitives/Makefile, src/primitives/Molecule.cpp,
851	>	src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp,
852	>	src/primitives/RigidBody.hpp, src/primitives/SRI.hpp,
853	>	src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp,
854	>	src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp,
855	>	src/restraints/Makefile, src/restraints/Restraints.cpp,
856	>	src/restraints/Restraints.hpp, src/utils/GenericData.cpp,
857	>	src/utils/GenericData.hpp, src/utils/Makefile,
858	>	src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp,
859	>	src/utils/StringUtils.c, src/utils/StringUtils.cpp,
860	>	src/utils/StringUtils.h, src/utils/StringUtils.hpp,
861	>	src/utils/TypeInfo.hpp, src/utils/Utility.cpp,
862	>	src/utils/Utility.hpp, src/utils/definitions_module.F90,
863	>	src/utils/fError.c, src/utils/oopseMPI_module.F90,
864	>	src/utils/simError.c, src/utils/simError.h,
865	>	src/utils/status_module.F90, src/utils/vector_class.F90,
866	>	src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp,
867	>	src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp,
868	>	src/visitors/CompositeVisitor.hpp, src/visitors/Makefile,
869	>	src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
870	>	src/visitors/RigidBodyVisitor.cpp,
871	>	src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
872	>	src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
873	>	samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
874	>	samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
875	>	samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
876	>	samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in,
877	>	samples/zcons/Makefile.in, samples/zcons/water.md,
878	>	samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md,
879	>	samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md,
880	>	src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp,
881	>	src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo,
882	>	src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h,
883	>	src/applications/Lattice.cpp, src/applications/Lattice.hpp,
884	>	src/applications/LatticeCreator.cpp,
885	>	src/applications/LatticeCreator.hpp,
886	>	src/applications/LatticeFactory.cpp,
887	>	src/applications/LatticeFactory.hpp, src/applications/Makedepend,
888	>	src/applications/Makefile, src/applications/MoLocator.cpp,
889	>	src/applications/MoLocator.hpp, src/applications/Vector3d.hpp,
890	>	src/applications/cmdline.c, src/applications/cmdline.h,
891	>	src/applications/getopt.c, src/applications/getopt1.c,
892	>	src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp,
893	>	src/applications/nanoBuilder.hpp, src/applications/oopse.cpp,
894	>	src/applications/quickLate.c, src/applications/simpleBuilder.cpp,
895	>	src/applications/simpleBuilder.ggo,
896	>	src/applications/simpleBuilderCmd.c,
897	>	src/integrators/AbstractClasses.hpp,
898	>	src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp,
899	>	src/integrators/Integrator.hpp, src/integrators/Makefile,
900	>	src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
901	>	src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
902	>	src/integrators/NVT.cpp, src/profiling/Makefile,
903	>	src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp,
904	>	src/profiling/timing.F90, samples/metals/Au_bulk.in,
905	>	samples/metals/Au_nanoparticle.in, samples/metals/metals.md,
906	>	samples/water/Makefile.in, samples/water/dimer/Makefile.in,
907	>	samples/water/dimer/two.in, samples/water/dimer/two.md,
908	>	samples/water/dimer/water.md, samples/water/spce/Makefile.in,
909	>	samples/water/spce/spce.in, samples/water/spce/spce.md,
910	>	samples/water/spce/water.md, samples/water/ssde/Makefile.in,
911	>	samples/water/ssde/ssde.in, samples/water/ssde/ssde.md,
912	>	samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in,
913	>	samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md,
914	>	samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in,
915	>	samples/water/ssd/ssd.in, samples/water/ssd/ssd.md,
916	>	samples/water/ssd/water.md, samples/water/tip4p/tp4.in,
917	>	samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
918	>	samples/alkane/Makefile.in, samples/alkane/alkanes.md,
919	>	samples/alkane/butane.in, samples/alkane/butane.md,
920	>	samples/argon/500.in, samples/argon/500.md,
921	>	samples/argon/Makefile.in, samples/argon/ar864.in,
922	>	samples/argon/ar864.md, samples/argon/argonNVT.in,
923	>	samples/argon/argonNVT.md, samples/argon/lj.md,
924	>	samples/lipid/5x5.in, samples/lipid/5x5.md,
925	>	samples/lipid/Makefile.in, samples/lipid/lipid.md,
926	>	samples/lipid/water.md, samples/minimizer/Makefile.in,
927	>	samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in,
928	>	samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in,
929	>	samples/minimizer/tip4p_two.md, samples/minimizer/water.md,
930	>	samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl,
931	>	forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl,
932		forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl,
933		forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl,
934		forceFields/DUFF.frc, forceFields/DipoleTest.frc,
935		forceFields/EAM.VC.frc, forceFields/EAM.frc,
936		forceFields/EAM.u3.frc, forceFields/EAM.u6.frc,
937	<	forceFields/LJFF.frc, forceFields/Makefile,
938	<	forceFields/Makefile.in, forceFields/Ni.VC.funcfl,
939	<	forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl,
940	<	forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl,
941	<	forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl,
942	<	forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl,
943	<	forceFields/WATER.frc, libBASS/AtomStamp.cpp,
944	<	libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp,
945	<	libBASS/BASS_interface.h, libBASS/BASS_parse.c,
946	<	libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y,
947	<	libBASS/BendStamp.cpp, libBASS/BendStamp.hpp,
948	<	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
937	>	forceFields/Makefile.in, forceFields/Ni.u3.funcfl,
938	>	forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl,
939	>	forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl,
940	>	forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc,
941	>	scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend,
942	>	ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess,
943	>	ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4,
944	>	ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf,
945	>	forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl,
946	>	forceFields/Au.u3.funcfl, forceFields/LJFF.frc,
947	>	forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
948	>	forceFields/Pt.VC.funcfl: Initial revision
949

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