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Comparing trunk/OOPSE-2.0/ChangeLog (file contents):
Revision 2102 by tim, Thu Mar 10 16:14:07 2005 UTC vs.
Revision 2310 by chrisfen, Mon Sep 19 23:21:46 2005 UTC

# Line 1 | Line 1
1 + 2005-09-18 15:45  chrisfen
2 +
3 +        * ChangeLog, samples/water/ssdrf/ssdrf.md,
4 +        src/UseTheForce/doForces.F90,
5 +        src/UseTheForce/doForces_interface.F90,
6 +        src/UseTheForce/doForces_interface.h,
7 +        src/UseTheForce/DarkSide/electrostatic.F90,
8 +        src/UseTheForce/DarkSide/electrostatic_interface.h,
9 +        src/brains/SimInfo.cpp: reaction field seems to work now, still
10 +        need to do some testing...
11 +
12 + 2005-09-16 18:04  chuckv
13 +
14 +        * src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed
15 +        dump files.
16 +
17 + 2005-09-16 16:07  chrisfen
18 +
19 +        * src/: UseTheForce/doForces_interface.F90,
20 +        UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a
21 +        bug that ifc missed...
22 +
23 + 2005-09-16 15:36  chrisfen
24 +
25 +        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90:
26 +        fixing some summation method issues
27 +
28 + 2005-09-16 14:35  chrisfen
29 +
30 +        * src/brains/SimInfo.cpp: fixed a capitalization error
31 +
32 + 2005-09-16 14:34  chrisfen
33 +
34 +        * src/UseTheForce/: fElectrostaticSummationMethod.h,
35 +        DarkSide/fElectrostaticSummationMethod.h: moved a header file
36 +        around
37 +
38 + 2005-09-16 14:00  chrisfen
39 +
40 +        * src/: UseTheForce/DarkSide/electrostatic_interface.F90,
41 +        brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there
42 +        are known issues - particularly with reaction field...
43 +
44 + 2005-09-16 11:07  chrisfen
45 +
46 +        * src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp,
47 +        io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking
48 +        (cutting out the old way to do reaction field)
49 +
50 + 2005-09-15 17:05  gezelter
51 +
52 +        * src/UseTheForce/: doForces.F90, fCoulombicCorrection.h,
53 +        fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90,
54 +        DarkSide/electrostatic_interface.F90,
55 +        DarkSide/electrostatic_interface.h: Working on adding WOLF
56 +
57 + 2005-09-15 14:17  tim
58 +
59 +        * src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame
60 +        is called without calling getNFrames
61 +
62 + 2005-09-15 08:47  chrisfen
63 +
64 +        * src/UseTheForce/fCoulombicCorrection.h: forgot to add a header
65 +
66 + 2005-09-14 21:48  chuckv
67 +
68 +        * src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was
69 +        not initialized after creation. When maxval(gtypeMaxCutoff) was
70 +        called, the largest random garbage value was returned from the
71 +        array.
72 +
73 + 2005-09-14 19:14  chrisfen
74 +
75 +        * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp,
76 +        io/Globals.hpp: changes to include the coulombicCorrection selector
77 +
78 + 2005-09-14 19:13  chrisfen
79 +
80 +        * src/UseTheForce/DarkSide/: Makefile, electrostatic.F90,
81 +        reactionField.F90: added in the undamped wolf, in the process of
82 +        doing the damped wolf
83 +
84 + 2005-09-14 19:13  chrisfen
85 +
86 +        * src/UseTheForce/: doForces.F90, doForces_interface.F90,
87 +        doForces_interface.h, notifyCutoffs.F90: some changes to activate
88 +        the coulombicCorrection selector
89 +
90 + 2005-09-14 19:11  chrisfen
91 +
92 +        * samples/water/dimer/: cl.in, cl.md, water.md: just some testing
93 +
94 + 2005-09-14 19:11  chrisfen
95 +
96 +        * samples/argon/: 500.in, 500.md: Equilibrated the sample
97 +
98 + 2005-09-14 19:10  chrisfen
99 +
100 +        * forceFields/DUFF2.frc: re-added Cl- and Na+
101 +
102 + 2005-09-14 15:31  chuckv
103 +
104 +        * src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup
105 +        eamAtypes instead of assuming a 1-1 correspondence to atypes.
106 +
107 + 2005-09-14 15:28  gezelter
108 +
109 +        * src/UseTheForce/doForces.F90: fix to put back calculation of r in
110 +        do_prepair
111 +
112 + 2005-09-14 14:02  gezelter
113 +
114 +        * src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the
115 +        createMixingMap routine.  It should now set doShift correctly
116 +
117 + 2005-09-07 17:44  chuckv
118 +
119 +        * src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build.
120 +
121 + 2005-09-07 17:23  chuckv
122 +
123 +        * src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi
124 +        logical variables
125 +
126 + 2005-09-07 17:08  gezelter
127 +
128 +        * src/UseTheForce/doForces.F90: bugfix on the grouptype finding
129 +        algorithm
130 +
131 + 2005-09-07 15:46  gezelter
132 +
133 +        * src/: UseTheForce/doForces.F90,
134 +        UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90,
135 +        UseTheForce/notifyCutoffs_interface.F90,
136 +        UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp,
137 +        io/Globals.cpp, io/Globals.hpp: adding c-side interface to change
138 +        cutoff Policy
139 +
140 + 2005-09-07 14:18  gezelter
141 +
142 +        * src/UseTheForce/doForces.F90: Some bug hunting
143 +
144 + 2005-09-07 14:18  gezelter
145 +
146 +        * samples/argon/argonNVT.md: Just a longer test
147 +
148 + 2005-09-06 12:32  chuckv
149 +
150 +        * src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap
151 +        etc..
152 +
153 + 2005-09-01 17:56  gezelter
154 +
155 +        * src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to
156 +        zero
157 +
158 + 2005-09-01 15:17  gezelter
159 +
160 +        * src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote
161 +        createGtypeCutoffMap
162 +
163 + 2005-08-30 13:23  chrisfen
164 +
165 +        * src/: UseTheForce/doForces.F90,
166 +        UseTheForce/doForces_interface.F90,
167 +        UseTheForce/doForces_interface.h,
168 +        UseTheForce/DarkSide/electrostatic.F90,
169 +        UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp,
170 +        brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some
171 +        changes for implementing the wolf potential
172 +
173 + 2005-08-26 17:39  chrisfen
174 +
175 +        * src/UseTheForce/DarkSide/eam.F90: updated getEAMCut
176 +
177 + 2005-08-26 16:30  chrisfen
178 +
179 +        * src/UseTheForce/: doForces.F90, DarkSide/eam.F90,
180 +        DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added
181 +        some probably nonfunctional get*cut routines
182 +
183 + 2005-08-26 15:34  chuckv
184 +
185 +        * src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map.
186 +
187 + 2005-08-26 11:36  gezelter
188 +
189 +        * src/UseTheForce/doForces.F90: fixing some of the problems in the
190 +        interactionHash and gtypeCutoff routines
191 +
192 + 2005-08-17 10:26  gezelter
193 +
194 +        * src/UseTheForce/: doForces.F90, fCutoffPolicy.h,
195 +        DarkSide/simulation.F90: added fCutoffPolicy.h
196 +
197 + 2005-08-11 16:04  gezelter
198 +
199 +        * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in
200 +        progress
201 +
202 + 2005-08-10 14:17  gezelter
203 +
204 +        * src/primitives/StuntDouble.hpp: putting spaceballs back where
205 +        they belong
206 +
207 + 2005-08-09 17:33  gezelter
208 +
209 +        * src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard
210 +        Jones module
211 +
212 + 2005-08-09 17:33  gezelter
213 +
214 +        * src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky
215 +
216 + 2005-08-09 14:40  chuckv
217 +
218 +        * src/UseTheForce/doForces.F90: In process of re-write for group
219 +        based cutoff....
220 +
221 + 2005-07-29 14:38  gezelter
222 +
223 +        * src/UseTheForce/doForces.F90: fixes in progress
224 +
225 + 2005-07-29 12:34  tim
226 +
227 +        * src/UseTheForce/doForces.F90: fix a bug which does not update
228 +        me_i and me_j correctly
229 +
230 + 2005-07-28 17:12  chuckv
231 +
232 +        * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed
233 +        cutoffs... Segfaults nicely now...
234 +
235 + 2005-07-20 12:04  gezelter
236 +
237 +        * configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text
238 +        error messages from pathscale compiler
239 +
240 + 2005-07-13 11:48  tim
241 +
242 +        * src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in
243 +        <functional>
244 +
245 + 2005-07-13 10:54  tim
246 +
247 +        * src/: UseTheForce/fSwitchingFunction.h,
248 +        UseTheForce/mpiComponentPlan.h,
249 +        UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h,
250 +        io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h,
251 +        io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c,
252 +        io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c,
253 +        io/parse_tree.h, math/MatVec3.c, utils/residentMem.c,
254 +        utils/simError.c, utils/simError.h: replace c++ style comment in c
255 +        files
256 +
257 + 2005-07-03 15:53  chuckv
258 +
259 +        * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90,
260 +        UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added
261 +        subroutine to set cuttoff for Interaction map and function in
262 +        simulation.F90 to determine if a particular atype is present in a
263 +        simulation.
264 +
265 + 2005-06-28 08:58  gezelter
266 +
267 +        * src/UseTheForce/doForces.F90: [no log message]
268 +
269 + 2005-06-27 17:21  chuckv
270 +
271 +        * src/UseTheForce/doForces.F90: More breaking and destruction of
272 +        force code. Does not build at this point...
273 +
274 + 2005-06-27 16:01  gezelter
275 +
276 +        * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90,
277 +        UseTheForce/DarkSide/fInteractionMap.h,
278 +        UseTheForce/DarkSide/interactions.F90, utils/definitions.F90:
279 +        Breaky breaky!
280 +
281 + 2005-06-20 11:03  gezelter
282 +
283 +        * samples/water/ssd/ssd.md,
284 +        src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a
285 +        simulation
286 +
287 + 2005-06-13 13:25  tim
288 +
289 +        * src/: applications/staticProps/DensityPlot.cpp,
290 +        applications/staticProps/DensityPlot.hpp,
291 +        applications/staticProps/SCDOrderParameter.cpp,
292 +        applications/staticProps/StaticProps.cpp,
293 +        io/AtomTypesSectionParser.cpp: working version of DensityPlot
294 +
295 + 2005-05-31 17:31  chuckv
296 +
297 +        * src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to
298 +        remove angular momentum.
299 +
300 + 2005-05-31 12:34  chuckv
301 +
302 +        * src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in
303 +        typo in nanorodBuilder.
304 +
305 + 2005-05-30 09:01  chuckv
306 +
307 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
308 +        brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp,
309 +        brains/Stats.hpp, integrators/Velocitizer.cpp,
310 +        integrators/Velocitizer.hpp: Added method to remove system angular
311 +        momentum to velocitizer and added method to calculate system
312 +        angular momentum to siminfo.
313 +
314 + 2005-05-29 16:16  chrisfen
315 +
316 +        * src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed
317 +        balance from the Darkside (files)
318 +
319 + 2005-05-29 16:15  chrisfen
320 +
321 +        * src/UseTheForce/doForces.F90: Removed balance from doForces
322 +
323 + 2005-05-29 16:15  chrisfen
324 +
325 +        * samples/water/tap/: tap.in, tap.md: Updated tap sample
326 +
327 + 2005-05-29 16:15  chrisfen
328 +
329 +        * samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap
330 +        dimer for testing purposes
331 +
332 + 2005-05-29 16:14  chrisfen
333 +
334 +        * forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It
335 +        was apparently wiped earlier this month...
336 +
337 + 2005-05-29 16:13  chrisfen
338 +
339 +        * ChangeLog: ran make cvslog
340 +
341 + 2005-05-28 19:16  tim
342 +
343 +        * src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding
344 +        AtomNameVisitor
345 +
346 + 2005-05-28 19:09  tim
347 +
348 +        * src/integrators/Integrator.cpp: dding resetIntegrator
349 +
350 + 2005-05-28 19:06  tim
351 +
352 +        * src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp,
353 +        NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp,
354 +        VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding
355 +        resetIntegrator
356 +
357 + 2005-05-27 16:11  tim
358 +
359 +        * src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp,
360 +        Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp,
361 +        SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo,
362 +        StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into
363 +        StaticProps
364 +
365 + 2005-05-26 23:41  tim
366 +
367 +        * src/: applications/staticProps/Makefile,
368 +        applications/staticProps/P2OrderParameter.cpp,
369 +        applications/staticProps/P2OrderParameter.hpp,
370 +        applications/staticProps/StaticProps.cpp,
371 +        applications/staticProps/StaticProps.ggo,
372 +        applications/staticProps/StaticPropsCmd.c,
373 +        applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp,
374 +        utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps
375 +
376 + 2005-05-26 17:45  tim
377 +
378 +        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
379 +        applications/dump2Xyz/Dump2XYZCmd.c,
380 +        applications/dump2Xyz/Dump2XYZCmd.h,
381 +        applications/staticProps/Makefile,
382 +        applications/staticProps/P2OrderParameter.cpp,
383 +        applications/staticProps/P2OrderParameter.hpp,
384 +        applications/staticProps/RadialDistrFunc.cpp,
385 +        applications/staticProps/RadialDistrFunc.hpp,
386 +        applications/staticProps/StaticAnalyser.hpp,
387 +        applications/staticProps/StaticProps.cpp,
388 +        applications/staticProps/StaticProps.ggo,
389 +        applications/staticProps/StaticPropsCmd.c,
390 +        applications/staticProps/StaticPropsCmd.h, visitors/Makefile,
391 +        visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding
392 +        AtomNameVisitor to convert atom name to its base name;
393 +        wrappingvisitor now wrap back to the center of the mass; adding
394 +        P2OrderParameter into StaticProps
395 +
396 + 2005-05-22 16:36  chuckv
397 +
398 +        * samples/metals/nanorod/Au_nanoparticle_FCC.md,
399 +        src/applications/nanoRodBuilder/Geometry.cpp,
400 +        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
401 +        src/applications/nanoRodBuilder/GeometryFactory.cpp,
402 +        src/applications/nanoRodBuilder/GeometryFactory.hpp,
403 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
404 +        src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure
405 +        tensor.
406 +
407 + 2005-05-22 16:05  tim
408 +
409 +        * src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
410 +        integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp,
411 +        io/Globals.hpp, io/SectionParserManager.cpp: adding keyword
412 +        printPressureTensor
413 +
414 + 2005-05-20 14:27  tim
415 +
416 +        * src/integrators/NPrT.cpp: NPrT in progress
417 +
418 + 2005-05-20 11:01  tim
419 +
420 +        * src/: integrators/NPrT.cpp, io/Globals.cpp,
421 +        utils/OOPSEConstant.hpp: NPrT in progress
422 +
423 + 2005-05-19 16:31  tim
424 +
425 +        * src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp,
426 +        integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp,
427 +        io/Globals.hpp: NPAT is working
428 +
429 + 2005-05-19 10:49  tim
430 +
431 +        * src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile,
432 +        integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT
433 +
434 + 2005-05-18 23:28  tim
435 +
436 +        * src/: brains/Register.cpp, integrators/NPAT.cpp,
437 +        integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp,
438 +        io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators
439 +
440 + 2005-05-18 14:06  chrisfen
441 +
442 +        * forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just
443 +        some tap changes
444 +
445 + 2005-05-18 13:31  chrisfen
446 +
447 +        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
448 +        DarkSide/sticky.F90: Modifications to temper the dipolar strength
449 +        in the first solvation shell for tap
450 +
451 + 2005-05-18 07:35  chrisfen
452 +
453 +        * samples/water/tap/: tap.in, tap.md, water.md: added a tap example
454 +        for testing purposes
455 +
456 + 2005-05-17 17:35  chrisfen
457 +
458 +        * ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md,
459 +        samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp,
460 +        src/UseTheForce/doForces.F90,
461 +        src/UseTheForce/DarkSide/electrostatic.F90,
462 +        src/UseTheForce/DarkSide/electrostatic_interface.F90,
463 +        src/UseTheForce/DarkSide/sticky.F90: Modifications to tap.  Also
464 +        correcting changes to the previous merge that were not caught
465 +
466 + 2005-05-16 23:20  chuckv
467 +
468 +        * src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp:
469 +        Fixed merge issues between Kyle and Chris so OOPSE will actually
470 +        build.
471 +
472 + 2005-05-16 22:46  kdaily
473 +
474 +        * src/io/: GayBerneAtomTypesSectionParser.cpp,
475 +        GayBerneAtomTypesSectionParser.hpp, Makefile: help
476 +
477 + 2005-05-16 21:08  kdaily
478 +
479 +        * forceFields/DUFF2.frc, src/UseTheForce/doForces.F90,
480 +        src/UseTheForce/DarkSide/gb.F90, src/io/Makefile,
481 +        src/types/DirectionalAtomType.cpp,
482 +        src/types/DirectionalAtomType.hpp: added gb
483 +
484 + 2005-05-13 15:36  chrisfen
485 +
486 +        * forceFields/DUFF2.frc: Better tap
487 +
488 + 2005-05-12 14:43  chrisfen
489 +
490 +        * forceFields/DUFF2.frc, samples/water/dimer/ssd.in,
491 +        samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90,
492 +        src/applications/dump2Xyz/Dump2XYZ.cpp,
493 +        src/visitors/AtomVisitor.hpp: Couple of changes for TAP water.
494 +        Need to parametrize.
495 +
496 + 2005-05-11 18:15  chuckv
497 +
498 +        * src/: io/ShapeAtomTypesSectionParser.cpp,
499 +        math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed
500 +        build issues under ifc7.
501 +
502 + 2005-05-09 17:07  chuckv
503 +
504 +        * src/applications/nanoRodBuilder/Geometry.hpp: More geometry
505 +        builder changes.
506 +
507 + 2005-05-05 10:06  chrisfen
508 +
509 +        * forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED
510 +        to TAP
511 +
512 + 2005-05-05 09:47  chrisfen
513 +
514 +        * forceFields/DUFF2.frc, samples/water/ssde/ssde.md,
515 +        samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp,
516 +        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile,
517 +        src/UseTheForce/DarkSide/atype.F90,
518 +        src/UseTheForce/DarkSide/atype_interface.F90,
519 +        src/UseTheForce/DarkSide/simulation.F90,
520 +        src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp,
521 +        src/brains/fSimulation.h, src/io/Makefile,
522 +        src/io/StickyAtomTypesSectionParser.cpp,
523 +        src/io/StickyPowerAtomTypesSectionParser.cpp,
524 +        src/io/StickyPowerAtomTypesSectionParser.hpp,
525 +        src/types/AtomType.cpp, src/types/AtomType.hpp,
526 +        src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp,
527 +        src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water.  It's
528 +        not parametrized, but OOPSE will now let me run it...
529 +
530 + 2005-05-03 17:55  chuckv
531 +
532 +        * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
533 +        GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp:
534 +        Adding support for generic geometry to nanorodbuilder.
535 +
536 + 2005-05-03 12:55  chuckv
537 +
538 +        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
539 +        nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c,
540 +        nanorodBuilderCmd.h: More changes to nanoRodBuilder....
541 +
542 + 2005-04-29 14:16  gezelter
543 +
544 +        * make/Makefile.in: [no log message]
545 +
546 + 2005-04-29 11:26  chrisfen
547 +
548 +        * forceFields/DUFF2.frc, samples/water/spce/water.md,
549 +        samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md,
550 +        samples/water/ssd-ion/water.md, samples/water/ssde/water.md,
551 +        samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md,
552 +        samples/water/tip4p/water.md: Added TIP4P-Ew
553 +
554 + 2005-04-27 19:24  chuckv
555 +
556 +        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
557 +        GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo,
558 +        nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with
559 +        nanoRodBuilder....
560 +
561 + 2005-04-27 15:13  chrisfen
562 +
563 +        * samples/shape/Shapes.frc, samples/shape/linear.shape,
564 +        src/UseTheForce/DarkSide/atype.F90,
565 +        src/UseTheForce/DarkSide/shapes.F90,
566 +        src/UseTheForce/DarkSide/shapes_interface.F90,
567 +        src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of
568 +        write statements and am closer to a working shapes
569 +
570 + 2005-04-22 16:57  chuckv
571 +
572 +        * src/utils/Predicate.hpp: Fixed gcc4 bug...
573 +
574 + 2005-04-22 16:52  tim
575 +
576 +        * src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp,
577 +        Trim.hpp: adding CharClassificationFunctor to fix the locale
578 +        problem  of c++
579 +
580 + 2005-04-21 09:12  chrisfen
581 +
582 +        * samples/shape/Shapes.frc, samples/shape/linear.in,
583 +        samples/shape/linear.md, src/UseTheForce/ForceField.hpp,
584 +        src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile,
585 +        src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp,
586 +        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90,
587 +        src/UseTheForce/DarkSide/shapes.F90,
588 +        src/UseTheForce/DarkSide/shapes_interface.F90,
589 +        src/UseTheForce/DarkSide/shapes_interface.h,
590 +        src/brains/Register.cpp, src/brains/SimCreator.cpp,
591 +        src/io/Makefile, src/io/SectionParser.cpp,
592 +        src/io/SectionParser.hpp, src/io/SectionParserManager.cpp,
593 +        src/io/ShapeAtomTypesSectionParser.cpp,
594 +        src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile,
595 +        src/types/AtomType.cpp, src/types/ShapeAtomType.cpp,
596 +        src/types/ShapeAtomType.hpp: Shapes is limping along with a array
597 +        bounds overwrite (I think...). At least the parser loads the
598 +        forcefield fine...
599 +
600 + 2005-04-18 10:44  chrisfen
601 +
602 +        * src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on
603 +        Mac (capitalization confusion of filenames)
604 +
605 + 2005-04-17 22:50  chrisfen
606 +
607 +        * src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp,
608 +        UseTheForce/Shapes_FF.cpp,
609 +        io/DirectionalAtomTypesSectionParser.cpp,
610 +        io/ShapeAtomTypesSectionParser.cpp,
611 +        io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser...
612 +
613 + 2005-04-15 17:43  gezelter
614 +
615 +        * README: gmake in case people forget
616 +
617 + 2005-04-15 17:40  gezelter
618 +
619 +        * src/applications/oopse/oopse.cpp: fixed the spacing on the
620 +        banner.  Vanity.
621 +
622 + 2005-04-15 17:22  gezelter
623 +
624 +        * src/: config.h.in, applications/oopse/oopse.cpp: Version string
625 +        in banner (and version numbers in config.h)
626 +
627 + 2005-04-15 17:22  gezelter
628 +
629 +        * ChangeLog, LICENSE, README: Documentation changes
630 +
631 + 2005-04-15 17:03  gezelter
632 +
633 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
634 +        UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp,
635 +        UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
636 +        UseTheForce/ForceFieldCreator.hpp,
637 +        UseTheForce/ForceFieldFactory.cpp,
638 +        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp,
639 +        UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90,
640 +        UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h,
641 +        UseTheForce/notifyCutoffs.F90,
642 +        UseTheForce/notifyCutoffs_interface.F90,
643 +        UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90,
644 +        UseTheForce/DarkSide/atype.F90,
645 +        UseTheForce/DarkSide/atype_interface.F90,
646 +        UseTheForce/DarkSide/eam.F90,
647 +        UseTheForce/DarkSide/eam_interface.F90,
648 +        UseTheForce/DarkSide/eam_interface.h,
649 +        UseTheForce/DarkSide/electrostatic.F90,
650 +        UseTheForce/DarkSide/electrostatic_interface.F90,
651 +        UseTheForce/DarkSide/electrostatic_interface.h,
652 +        UseTheForce/DarkSide/force_globals.F90,
653 +        UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h,
654 +        UseTheForce/DarkSide/lj_interface.F90,
655 +        UseTheForce/DarkSide/lj_interface.h,
656 +        UseTheForce/DarkSide/neighborLists.F90,
657 +        UseTheForce/DarkSide/reactionField.F90,
658 +        UseTheForce/DarkSide/shapes.F90,
659 +        UseTheForce/DarkSide/shapes_interface.F90,
660 +        UseTheForce/DarkSide/shapes_interface.h,
661 +        UseTheForce/DarkSide/simParallel.F90,
662 +        UseTheForce/DarkSide/simParallel_interface.F90,
663 +        UseTheForce/DarkSide/simParallel_interface.h,
664 +        UseTheForce/DarkSide/simulation.F90,
665 +        UseTheForce/DarkSide/simulation_interface.F90,
666 +        UseTheForce/DarkSide/simulation_interface.h,
667 +        UseTheForce/DarkSide/sticky.F90,
668 +        UseTheForce/DarkSide/sticky_interface.F90,
669 +        UseTheForce/DarkSide/sticky_interface.h,
670 +        UseTheForce/DarkSide/switcheroo.F90,
671 +        applications/dump2Xyz/Dump2XYZ.cpp,
672 +        applications/dump2Xyz/Dump2XYZCmd.c,
673 +        applications/dump2Xyz/Dump2XYZCmd.h,
674 +        applications/dynamicProps/CrossTimeCorrFunc.cpp,
675 +        applications/dynamicProps/CrossTimeCorrFunc.hpp,
676 +        applications/dynamicProps/DipoleCorrFunc.cpp,
677 +        applications/dynamicProps/DipoleCorrFunc.hpp,
678 +        applications/dynamicProps/DynamicProps.cpp,
679 +        applications/dynamicProps/DynamicPropsCmd.c,
680 +        applications/dynamicProps/DynamicPropsCmd.h,
681 +        applications/dynamicProps/FrameTimeCorrFunc.hpp,
682 +        applications/dynamicProps/ParticleTimeCorrFunc.cpp,
683 +        applications/dynamicProps/ParticleTimeCorrFunc.hpp,
684 +        applications/dynamicProps/RCorrFunc.cpp,
685 +        applications/dynamicProps/RCorrFunc.hpp,
686 +        applications/dynamicProps/TimeCorrFunc.cpp,
687 +        applications/dynamicProps/TimeCorrFunc.hpp,
688 +        applications/dynamicProps/VCorrFunc.cpp,
689 +        applications/dynamicProps/VCorrFunc.hpp,
690 +        applications/nanoRodBuilder/GeometryBuilder.cpp,
691 +        applications/nanoRodBuilder/GeometryBuilder.hpp,
692 +        applications/nanoRodBuilder/nanorodBuilder.cpp,
693 +        applications/nanoRodBuilder/nanorodBuilderCmd.c,
694 +        applications/nanoRodBuilder/nanorodBuilderCmd.h,
695 +        applications/oopse/oopse.cpp,
696 +        applications/simpleBuilder/simpleBuilder.cpp,
697 +        applications/simpleBuilder/simpleBuilderCmd.c,
698 +        applications/simpleBuilder/simpleBuilderCmd.h,
699 +        applications/staticProps/GofAngle2.cpp,
700 +        applications/staticProps/GofAngle2.hpp,
701 +        applications/staticProps/GofR.cpp,
702 +        applications/staticProps/GofR.hpp,
703 +        applications/staticProps/GofRAngle.cpp,
704 +        applications/staticProps/GofRAngle.hpp,
705 +        applications/staticProps/GofXyz.cpp,
706 +        applications/staticProps/GofXyz.hpp,
707 +        applications/staticProps/RadialDistrFunc.cpp,
708 +        applications/staticProps/RadialDistrFunc.hpp,
709 +        applications/staticProps/StaticProps.cpp,
710 +        applications/staticProps/StaticPropsCmd.c,
711 +        applications/staticProps/StaticPropsCmd.h,
712 +        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
713 +        brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp,
714 +        brains/Exclude.hpp, brains/ForceManager.cpp,
715 +        brains/ForceManager.hpp, brains/MoleculeCreator.cpp,
716 +        brains/MoleculeCreator.hpp, brains/Register.cpp,
717 +        brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
718 +        brains/SimInfo.hpp, brains/SimSnapshotManager.cpp,
719 +        brains/SimSnapshotManager.hpp, brains/Snapshot.cpp,
720 +        brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp,
721 +        brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp,
722 +        brains/fSimulation.h, constraints/ConstraintElem.hpp,
723 +        constraints/ConstraintPair.hpp, constraints/Rattle.cpp,
724 +        constraints/Rattle.hpp, constraints/ZconsStruct.hpp,
725 +        constraints/ZconstraintForceManager.cpp,
726 +        constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp,
727 +        integrators/DLM.hpp, integrators/Integrator.cpp,
728 +        integrators/Integrator.hpp, integrators/IntegratorCreator.hpp,
729 +        integrators/IntegratorFactory.cpp,
730 +        integrators/IntegratorFactory.hpp, integrators/NPT.cpp,
731 +        integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp,
732 +        integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp,
733 +        integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp,
734 +        integrators/NVT.cpp, integrators/NVT.hpp,
735 +        integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp,
736 +        integrators/Velocitizer.hpp,
737 +        integrators/VelocityVerletIntegrator.cpp,
738 +        integrators/VelocityVerletIntegrator.hpp,
739 +        io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp,
740 +        io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c,
741 +        io/BASS_parse.h, io/BendTypesSectionParser.cpp,
742 +        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
743 +        io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
744 +        io/ChargeAtomTypesSectionParser.hpp,
745 +        io/DirectionalAtomTypesSectionParser.cpp,
746 +        io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
747 +        io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp,
748 +        io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
749 +        io/Globals.cpp, io/Globals.hpp,
750 +        io/LennardJonesAtomTypesSectionParser.cpp,
751 +        io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp,
752 +        io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp,
753 +        io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp,
754 +        io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp,
755 +        io/SectionParser.cpp, io/SectionParser.hpp,
756 +        io/SectionParserManager.cpp, io/SectionParserManager.hpp,
757 +        io/StatWriter.cpp, io/StatWriter.hpp,
758 +        io/StickyAtomTypesSectionParser.cpp,
759 +        io/StickyAtomTypesSectionParser.hpp,
760 +        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
761 +        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
762 +        io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp,
763 +        io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c,
764 +        io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h,
765 +        io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp,
766 +        lattice/CubicLattice.hpp, lattice/FCCLattice.cpp,
767 +        lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
768 +        lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp,
769 +        lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp,
770 +        math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h,
771 +        math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp,
772 +        math/ParallelRandNumGen.hpp, math/Polynomial.hpp,
773 +        math/Quaternion.hpp, math/RandNumGen.hpp,
774 +        math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp,
775 +        math/RectMatrix.hpp, math/SeqRandNumGen.cpp,
776 +        math/SeqRandNumGen.hpp, math/SquareMatrix.hpp,
777 +        math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp,
778 +        minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp,
779 +        minimizers/Minimizer.cpp, minimizers/Minimizer.hpp,
780 +        minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp,
781 +        minimizers/MinimizerFactory.hpp,
782 +        minimizers/MinimizerParameterSet.cpp,
783 +        minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp,
784 +        minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp,
785 +        minimizers/SDMinimizer.hpp, primitives/Atom.cpp,
786 +        primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp,
787 +        primitives/Bond.hpp, primitives/CutoffGroup.hpp,
788 +        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
789 +        primitives/GhostBend.cpp, primitives/GhostBend.hpp,
790 +        primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp,
791 +        primitives/Molecule.cpp, primitives/Molecule.hpp,
792 +        primitives/RigidBody.cpp, primitives/RigidBody.hpp,
793 +        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
794 +        primitives/Torsion.cpp, primitives/Torsion.hpp,
795 +        primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp,
796 +        profiling/mdProfile.cpp, profiling/mdProfile.hpp,
797 +        profiling/timing.F90, restraints/Restraints.cpp,
798 +        restraints/Restraints.hpp,
799 +        restraints/ThermoIntegrationForceManager.cpp,
800 +        restraints/ThermoIntegrationForceManager.hpp,
801 +        selection/DistanceFinder.cpp, selection/DistanceFinder.hpp,
802 +        selection/IndexFinder.cpp, selection/IndexFinder.hpp,
803 +        selection/NameFinder.cpp, selection/NameFinder.hpp,
804 +        selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp,
805 +        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
806 +        selection/SelectionManager.cpp, selection/SelectionManager.hpp,
807 +        selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp,
808 +        selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp,
809 +        types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h,
810 +        types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp,
811 +        types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp,
812 +        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
813 +        types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp,
814 +        types/CubicBondType.hpp, types/CubicTorsionType.hpp,
815 +        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
816 +        types/DirectionalAtomType.hpp, types/FixedBondType.hpp,
817 +        types/HarmonicBendType.hpp, types/HarmonicBondType.hpp,
818 +        types/MakeStamps.cpp, types/MakeStamps.hpp,
819 +        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
820 +        types/MorseBondType.hpp, types/OplsTorsionType.hpp,
821 +        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
822 +        types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp,
823 +        types/QuarticBondType.hpp, types/QuarticTorsionType.hpp,
824 +        types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
825 +        types/ShapeAtomType.cpp, types/ShapeAtomType.hpp,
826 +        types/TorsionStamp.cpp, types/TorsionStamp.hpp,
827 +        types/TorsionType.hpp, types/UreyBradleyBendType.hpp,
828 +        types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp,
829 +        utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp,
830 +        utils/GenericFactory.hpp, utils/LocalIndexManager.hpp,
831 +        utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp,
832 +        utils/NumericConstant.hpp, utils/OOPSEConstant.hpp,
833 +        utils/PropertyMap.cpp, utils/PropertyMap.hpp,
834 +        utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
835 +        utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp,
836 +        utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp,
837 +        utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp,
838 +        utils/any.hpp, utils/definitions.F90, utils/fError.c,
839 +        utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h,
840 +        utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h,
841 +        utils/residentMem.h, utils/simError.c, utils/simError.h,
842 +        utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp,
843 +        visitors/AtomData.hpp, visitors/AtomVisitor.cpp,
844 +        visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp,
845 +        visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp,
846 +        visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
847 +        visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp,
848 +        visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp,
849 +        visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has
850 +        been drafted to perform our indentation services
851 +
852 + 2005-04-15 17:03  gezelter
853 +
854 +        * configure, ac-tools/configure.in: Jedi mind-trick warning
855 +        messages have been added to make users ignore CGAL.
856 +
857 + 2005-04-15 13:41  tim
858 +
859 +        * make/Makefile.in: fix make install
860 +
861 + 2005-04-15 13:41  tim
862 +
863 +        * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile:
864 +        add  Makefile of samples
865 +
866 + 2005-04-15 13:33  tim
867 +
868 +        * samples/: lipid/Makefile, water/dimer/Makefile,
869 +        water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not
870 +        installed correctly
871 +
872 + 2005-04-14 16:41  gezelter
873 +
874 +        * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in,
875 +        make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl,
876 +        scripts/filepp, scripts/filepp.in: configure now searches for perl
877 +        to use with filepp
878 +
879 + 2005-04-14 16:20  gezelter
880 +
881 +        * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of
882 +        MoLocator
883 +
884 + 2005-04-14 14:12  gezelter
885 +
886 +        * LICENSE: [no log message]
887 +
888 + 2005-04-14 11:10  chuckv
889 +
890 +        * src/applications/nanoRodBuilder/nanorodBuilder.cpp:
891 +        nanorodbuilder now exit's when libCGAL is not present.
892 +
893 + 2005-04-14 10:20  tim
894 +
895 +        * src/io/make_nodes.h: fix one more warning message in make_nodes
896 +
897 + 2005-04-13 18:36  chuckv
898 +
899 +        * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed
900 +        interface name for SGI Compiler
901 +
902 + 2005-04-13 18:29  chrisfen
903 +
904 +        * samples/water/ssde/ssde.md: oops...  bad sample
905 +
906 + 2005-04-13 18:00  chuckv
907 +
908 +        * src/config.h.in: Change typo in CGAL.
909 +
910 + 2005-04-13 17:43  tim
911 +
912 +        * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp,
913 +        selection/SelectionCompiler.hpp: fix some warning messages
914 +
915 + 2005-04-13 17:30  gezelter
916 +
917 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
918 +        make/Makefile.in, src/config.h.in,
919 +        src/applications/nanoRodBuilder/Makefile,
920 +        src/applications/nanoRodBuilder/Makefile.in,
921 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL
922 +        checks
923 +
924 + 2005-04-13 15:36  chuckv
925 +
926 +        * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp,
927 +        DarkSide/LJ.F90, DarkSide/electrostatic.F90,
928 +        DarkSide/electrostatic_interface.F90,
929 +        DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90,
930 +        DarkSide/lj_interface.h, DarkSide/sticky.F90,
931 +        DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added
932 +        destroy methods for Fortran modules.
933 +
934 + 2005-04-13 15:17  chuckv
935 +
936 +        * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90,
937 +        shapes_interface.h: Added destroy method to clean up memory
938 +
939 + 2005-04-13 13:41  tim
940 +
941 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
942 +        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
943 +        io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp,
944 +        primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp,
945 +        types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are
946 +        fixed
947 +
948 + 2005-04-12 17:44  chuckv
949 +
950 +        * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed
951 +        for nanoRodBuilder.
952 +
953 + 2005-04-12 17:42  tim
954 +
955 +        * src/applications/: nanoRodBuilder/nanorodBuilder.cpp,
956 +        simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder
957 +        and simpleBuilder(forget to delete lattice)
958 +
959 + 2005-04-12 17:33  tim
960 +
961 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
962 +        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp:
963 +        refactory lattice
964 +
965 + 2005-04-12 17:07  tim
966 +
967 +        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp,
968 +        CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp,
969 +        Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory
970 +        LatticeFactory and LatticeCreator
971 +
972 + 2005-04-12 16:58  tim
973 +
974 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
975 +        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp,
976 +        brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
977 +        lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp,
978 +        lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp,
979 +        lattice/Makefile: refactory LatticeFactory and LatticeCreator
980 +
981 + 2005-04-12 16:28  gezelter
982 +
983 +        * src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp,
984 +        vector_class.F90: cleaned up vector_class memory leak fix by
985 +        deallocating in reverse order of how we allocated.  Also migrated
986 +        MoLocator into utils directory
987 +
988 + 2005-04-12 16:27  gezelter
989 +
990 +        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp,
991 +        Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
992 +        LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice
993 +        directory
994 +
995 + 2005-04-12 16:27  gezelter
996 +
997 +        * src/applications/: nanoRodBuilder/BaseLattice.cpp,
998 +        nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp,
999 +        nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp,
1000 +        nanoRodBuilder/LatticeCreator.hpp,
1001 +        nanoRodBuilder/LatticeFactory.cpp,
1002 +        nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile,
1003 +        nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp,
1004 +        nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp,
1005 +        simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
1006 +        simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
1007 +        simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
1008 +        simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile,
1009 +        simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp,
1010 +        simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of
1011 +        these files are now redundant
1012 +
1013 + 2005-04-12 16:27  gezelter
1014 +
1015 +        * src/UseTheForce/DarkSide/: atype_interface.F90,
1016 +        atype_interface.h: cleaned up memory leak fix
1017 +
1018 + 2005-04-12 16:26  gezelter
1019 +
1020 +        * make/Makefile.in: added lattice subdirectory
1021 +
1022 + 2005-04-12 15:57  chrisfen
1023 +
1024 +        * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added
1025 +        a space by accident
1026 +
1027 + 2005-04-12 15:56  chrisfen
1028 +
1029 +        * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added
1030 +        quadrupole sample
1031 +
1032 + 2005-04-12 15:56  chrisfen
1033 +
1034 +        * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating
1035 +        samples
1036 +
1037 + 2005-04-12 13:30  tim
1038 +
1039 +        * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom
1040 +        type in fortran side
1041 +
1042 + 2005-04-12 12:45  chuckv
1043 +
1044 +        * src/utils/vector_class.F90: Further changes to vector_class
1045 +        destroy function.
1046 +
1047 + 2005-04-12 12:39  chuckv
1048 +
1049 +        * src/utils/vector_class.F90: Fixed pointer memory leak in
1050 +        vector_class.
1051 +
1052 + 2005-04-12 12:12  chuckv
1053 +
1054 +        * src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp,
1055 +        DarkSide/atype_interface.F90, DarkSide/atype_interface.h,
1056 +        DarkSide/eam.F90, DarkSide/eam_interface.F90,
1057 +        DarkSide/eam_interface.h: Updates to deallocate object in fortran.
1058 +
1059 + 2005-04-12 09:24  chrisfen
1060 +
1061 +        * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI
1062 +        output
1063 +
1064 + 2005-04-11 19:29  chuckv
1065 +
1066 +        * src/: UseTheForce/DarkSide/atype.F90,
1067 +        applications/nanoRodBuilder/Makefile: Changes to delete atypes...
1068 +
1069 + 2005-04-11 19:28  chuckv
1070 +
1071 +        * src/utils/vector_class.F90: Added code to delete vector.
1072 +
1073 + 2005-04-11 17:03  chuckv
1074 +
1075 +        * samples/metals/nanorod/: Au_nanoparticle.md,
1076 +        Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why
1077 +        aren't these here?
1078 +
1079 + 2005-04-11 16:58  tim
1080 +
1081 +        * src/io/basic_ifstrstream.hpp: avoid multiple inherit in
1082 +        basic_ifstrstream
1083 +
1084 + 2005-04-11 16:37  chuckv
1085 +
1086 +        * make/Makefile.in,
1087 +        src/applications/nanoRodBuilder/BaseLattice.cpp,
1088 +        src/applications/nanoRodBuilder/BaseLattice.hpp,
1089 +        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
1090 +        src/applications/nanoRodBuilder/GeometryBuilder.hpp,
1091 +        src/applications/nanoRodBuilder/Lattice.cpp,
1092 +        src/applications/nanoRodBuilder/Lattice.hpp,
1093 +        src/applications/nanoRodBuilder/LatticeCreator.cpp,
1094 +        src/applications/nanoRodBuilder/LatticeCreator.hpp,
1095 +        src/applications/nanoRodBuilder/LatticeFactory.cpp,
1096 +        src/applications/nanoRodBuilder/LatticeFactory.hpp,
1097 +        src/applications/nanoRodBuilder/Makefile,
1098 +        src/applications/nanoRodBuilder/MoLocator.cpp,
1099 +        src/applications/nanoRodBuilder/MoLocator.hpp,
1100 +        src/applications/nanoRodBuilder/nanoBuilder.ggo,
1101 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
1102 +        src/applications/nanoRodBuilder/nanorodBuilder.ggo,
1103 +        src/applications/nanoRodBuilder/nanorodBuilderCmd.c,
1104 +        src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing
1105 +        nanoRodBuilder application (may not work yet).  ((Doesn't work
1106 +        yet.)) (((May never work....)))
1107 +
1108 + 2005-04-11 15:54  tim
1109 +
1110 +        * src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete
1111 +        prepareVisitor in Dump2XYZ
1112 +
1113 + 2005-04-11 15:19  chrisfen
1114 +
1115 +        * src/UseTheForce/DarkSide/electrostatic.F90: fixing of the
1116 +        quadrupoles.  look!  it's divide by 3 like stone says!
1117 +
1118 + 2005-04-11 15:18  chrisfen
1119 +
1120 +        * forceFields/DUFF2.frc: fixing of the quadrupoles
1121 +
1122 + 2005-04-11 15:16  tim
1123 +
1124 +        * src/selection/Token.hpp: change the parameter name in
1125 +        constructors
1126 +
1127 + 2005-04-11 14:49  gezelter
1128 +
1129 +        * make/Makefile.in: One more bug fix for GNU make versions < 3.80
1130 +
1131 + 2005-04-11 14:06  gezelter
1132 +
1133 +        * make/Makefile.in: Fixed the uc and lc functions for GNU make
1134 +        versions < 3.80
1135 +
1136 + 2005-04-11 11:13  gezelter
1137 +
1138 +        * make/Makefile.in, src/UseTheForce/Makefile,
1139 +        src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added
1140 +        some stuff to clean out module files during "make clean"
1141 +
1142 + 2005-04-08 17:13  chrisfen
1143 +
1144 +        * src/UseTheForce/DarkSide/electrostatic.F90: quadrupole
1145 +        interactions should be working with a remaining question of
1146 +        interaction magnitude
1147 +
1148 + 2005-04-08 17:12  chrisfen
1149 +
1150 +        * samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with
1151 +        samples
1152 +
1153 + 2005-04-08 13:48  chrisfen
1154 +
1155 +        * samples/water/ssd/ssd.md: oops...  messed up a sample
1156 +
1157 + 2005-04-08 09:43  chrisfen
1158 +
1159 +        * src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix
1160 +        charge-dipole interactions
1161 +
1162 + 2005-04-08 09:42  chrisfen
1163 +
1164 +        * samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md,
1165 +        ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole
1166 +
1167 + 2005-04-08 09:41  chrisfen
1168 +
1169 +        * forceFields/DUFF2.frc: added Cl- and Na+
1170 +
1171 + 2005-04-06 18:59  tim
1172 +
1173 +        * src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser
1174 +
1175 + 2005-04-05 18:09  tim
1176 +
1177 +        * src/selection/: NameFinder.cpp, SelectionCompiler.cpp,
1178 +        SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-'
1179 +        in atom type name;clean the code a little bit
1180 +
1181 + 2005-03-29 16:00  tim
1182 +
1183 +        * src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug
1184 +        in converting rotation matrix to quaternion
1185 +
1186 + 2005-03-28 17:41  tim
1187 +
1188 +        * src/visitors/LipidTransVisitor.cpp: fixed the wrapping
1189 +
1190 + 2005-03-28 17:30  tim
1191 +
1192 +        * src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do
1193 +        the wrapping
1194 +
1195 + 2005-03-28 10:54  tim
1196 +
1197 +        * src/applications/staticProps/GofXyz.cpp: fix a bug in getting the
1198 +        dimension of histogram
1199 +
1200 + 2005-03-22 11:38  tim
1201 +
1202 +        * make/Makefile.in, src/applications/dump2Xyz/Makefile,
1203 +        src/applications/dynamicProps/Makefile,
1204 +        src/applications/oopse/Makefile,
1205 +        src/applications/simpleBuilder/Makefile,
1206 +        src/applications/staticProps/Makefile: avoid building parallel
1207 +        executable for dump2XYZ, simpleBuilder, staticProps and
1208 +        dynamicProps
1209 +
1210 + 2005-03-21 17:34  chrisfen
1211 +
1212 +        * forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the
1213 +        forcefield files
1214 +
1215 + 2005-03-21 15:51  chrisfen
1216 +
1217 +        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
1218 +        DarkSide/reactionField.F90: Make sure electrostatic_module provides
1219 +        data for reaction_field
1220 +
1221 + 2005-03-21 15:50  chrisfen
1222 +
1223 +        * forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff.  HE
1224 +        WILL CHANGE THIS BACK, RIGHT?
1225 +
1226 + 2005-03-21 14:23  gezelter
1227 +
1228 +        * src/UseTheForce/DarkSide/electrostatic.F90: constant back to
1229 +        correct value
1230 +
1231 + 2005-03-21 14:22  gezelter
1232 +
1233 +        * make/Makefile.in: fixed an install-related bug.
1234 +        $(InstallCommand) had been set to $(InstallData)
1235 +
1236 + 2005-03-15 09:21  gezelter
1237 +
1238 +        * src/integrators/Integrator.cpp: VelocityVerletIntegrator already
1239 +        deletes and Nullifies restWriter, so Integrator shouldn't do it.
1240 +
1241 + 2005-03-15 09:20  gezelter
1242 +
1243 +        * src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos
1244 +
1245 + 2005-03-13 02:39  gezelter
1246 +
1247 +        * src/UseTheForce/DarkSide/electrostatic.F90: first run at
1248 +        charge-quadrupole interactions
1249 +
1250 + 2005-03-12 14:12  chrisfen
1251 +
1252 +        * samples/: Makefile.in, thermoIntegration/liquid/Makefile,
1253 +        thermoIntegration/solid/Makefile: forgot a couple of makefiles
1254 +
1255 + 2005-03-12 14:05  chrisfen
1256 +
1257 +        * samples/thermoIntegration/liquid/ssde.in,
1258 +        samples/thermoIntegration/liquid/ssde.md,
1259 +        samples/thermoIntegration/liquid/water.md,
1260 +        samples/thermoIntegration/solid/idealCrystal.in,
1261 +        samples/thermoIntegration/solid/ssde.in,
1262 +        samples/thermoIntegration/solid/ssde.md,
1263 +        samples/thermoIntegration/solid/ssde.zang0,
1264 +        samples/thermoIntegration/solid/water.md,
1265 +        samples/water/tip3p_ice/tp3.md,
1266 +        src/UseTheForce/DarkSide/sticky.F90,
1267 +        src/restraints/ThermoIntegrationForceManager.cpp: added some
1268 +        samples
1269 +
1270 + 2005-03-11 12:50  tim
1271 +
1272 +        * src/: brains/SimCreator.cpp,
1273 +        io/MultipoleAtomTypesSectionParser.cpp: fix a typo in
1274 +        MultipoleAtomTypesSectionParser
1275 +
1276 + 2005-03-11 10:55  tim
1277 +
1278 +        * src/brains/SimInfo.cpp: pairs inside cutoff group should not be
1279 +        excluded
1280 +
1281 + 2005-03-11 10:53  gezelter
1282 +
1283 +        * src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for
1284 +        quadrupoles
1285 +
1286 + 2005-03-11 10:52  gezelter
1287 +
1288 +        * forceFields/DUFF2.frc: quadrupoles for SSD models
1289 +
1290 + 2005-03-11 10:00  tim
1291 +
1292 +        * ChangeLog, doc/SelectionExpression.html,
1293 +        doc/classoopse_1_1StuntDouble.png, doc/definition.jpg,
1294 +        doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png,
1295 +        src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp,
1296 +        src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp,
1297 +        src/selection/TokenMap.cpp: clean up SimInfo; modify the images of
1298 +        SelectionExpression.html
1299 +
1300 + 2005-03-10 19:43  chrisfen
1301 +
1302 +        * samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md,
1303 +        src/io/RestReader.cpp, src/restraints/Restraints.cpp,
1304 +        src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in
1305 +        MPI restraints
1306 +
1307 + 2005-03-10 18:56  tim
1308 +
1309 +        * doc/SelectionExpression.html, src/brains/SimInfo.cpp,
1310 +        src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody
1311 +        and cutoff group
1312 +
1313 + 2005-03-10 17:06  gezelter
1314 +
1315 +        * src/types/MorseBondType.hpp: fixed a doxygen problem
1316 +
1317 + 2005-03-10 16:51  gezelter
1318 +
1319 +        * samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with
1320 +        the split dipole test cases
1321 +
1322 + 2005-03-10 16:51  gezelter
1323 +
1324 +        * doc/SelectionExpression.html: updated some documentation
1325 +
1326 + 2005-03-10 15:40  gezelter
1327 +
1328 +        * src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp,
1329 +        Makefile: LinkedList removal project starts now
1330 +
1331 + 2005-03-10 15:28  tim
1332 +
1333 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
1334 +        io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp:
1335 +        using map to replace link list
1336 +
1337 + 2005-03-10 14:11  tim
1338 +
1339 +        * samples/dipole/: splitInWater.in, splitInWater.md: adding test
1340 +        case  of split dipole
1341 +
1342 + 2005-03-10 14:10  chrisfen
1343 +
1344 +        * samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp,
1345 +        src/io/RestWriter.cpp,
1346 +        src/restraints/ThermoIntegrationForceManager.cpp: Oops...  MPI now
1347 +        builds...
1348 +
1349 + 2005-03-10 13:44  tim
1350 +
1351 +        * samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in,
1352 +        split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md:
1353 +        adding test case for split dipole
1354 +
1355 + 2005-03-10 12:54  gezelter
1356 +
1357 +        * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side
1358 +        support for split dipoles
1359 +
1360 + 2005-03-10 11:27  chrisfen
1361 +
1362 +        * samples/water/tip3p_ice/tp3.md,
1363 +        src/restraints/ThermoIntegrationForceManager.cpp: fixes to
1364 +        restraints
1365 +
1366 + 2005-03-10 11:15  chrisfen
1367 +
1368 +        * samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp,
1369 +        src/UseTheForce/ForceFields.hpp,
1370 +        src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints
1371 +
1372 + 2005-03-10 11:14  tim
1373 +
1374 +        * ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc,
1375 +        src/io/MultipoleAtomTypesSectionParser.cpp,
1376 +        src/selection/SelectionEvaluator.cpp: minor change
1377 +
1378   2005-03-10 10:10  chrisfen
1379  
1380          * make/Makefile.in, samples/water/tip3p_ice/tp3.md,
# Line 273 | Line 1650
1650          io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp:
1651          adding basic_teebuf which can operate on multiple stream
1652          simutaneously.
1653 +
1654 + 2005-02-22 14:26  chrisfen
1655 +
1656 +        * samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf
1657 +        sample
1658  
1659   2005-02-22 13:56  tim
1660  
# Line 1479 | Line 2861
2861  
2862   2005-01-11 10:52  tim
2863  
2864 <        * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
2864 >        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
2865          on branch new_design.
2866  
2867   2005-01-11 10:52  tim
2868  
2869 <        * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
2869 >        * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
2870 >        on branch new_design.
2871  
2872   2005-01-11 10:52  tim
2873  
2874 <        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
1492 <        on branch new_design.
2874 >        * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
2875  
2876   2005-01-11 10:47  tim
2877  
# Line 1554 | Line 2936
2936  
2937          * src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was
2938          initially added on branch new_design.
2939 +
2940 + 2005-01-07 16:50  tim
2941 +
2942 +        * src/constraints/ZconstraintForceManager.cpp: file
2943 +        ZconstraintForceManager.cpp was initially added on branch
2944 +        new_design.
2945  
2946   2005-01-07 16:50  tim
2947  
2948 +        * src/constraints/ZconstraintForceManager.hpp: file
2949 +        ZconstraintForceManager.hpp was initially added on branch
2950 +        new_design.
2951 +
2952 + 2005-01-07 16:50  tim
2953 +
2954          * src/: applications/simpleBuilder/BaseLattice.hpp,
2955          applications/simpleBuilder/Lattice.hpp,
2956          applications/simpleBuilder/LatticeCreator.hpp,
# Line 1574 | Line 2968
2968          * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was
2969          initially added on branch new_design.
2970  
1577 – 2005-01-07 16:50  tim
1578 –
1579 –        * src/constraints/ZconstraintForceManager.cpp: file
1580 –        ZconstraintForceManager.cpp was initially added on branch
1581 –        new_design.
1582 –
1583 – 2005-01-07 16:50  tim
1584 –
1585 –        * src/constraints/ZconstraintForceManager.hpp: file
1586 –        ZconstraintForceManager.hpp was initially added on branch
1587 –        new_design.
1588 –
2971   2005-01-06 17:31  tim
2972  
2973          * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
# Line 1622 | Line 3004
3004  
3005   2005-01-05 12:35  tim
3006  
3007 +        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
3008 +        added on branch new_design.
3009 +
3010 + 2005-01-05 12:35  tim
3011 +
3012          * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
3013          Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp,
3014          MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp,
# Line 1630 | Line 3017
3017  
3018   2005-01-05 12:35  tim
3019  
3020 <        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
3021 <        added on branch new_design.
3020 >        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
3021 >        was initially added on branch new_design.
3022  
3023   2005-01-05 12:35  tim
3024  
3025 <        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
3025 >        * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
3026          was initially added on branch new_design.
3027  
3028   2005-01-05 12:35  tim
3029  
3030 <        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
3030 >        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
3031          was initially added on branch new_design.
3032  
3033   2005-01-05 12:35  tim
# Line 1648 | Line 3035
3035          * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially
3036          added on branch new_design.
3037  
1651 – 2005-01-05 12:35  tim
1652 –
1653 –        * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
1654 –        was initially added on branch new_design.
1655 –
3038   2005-01-04 17:18  tim
3039  
1658 –        * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was
1659 –        initially added on branch new_design.
1660 –
1661 – 2005-01-04 17:18  tim
1662 –
3040          * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
3041          brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp,
3042          brains/Thermo.cpp, constraints/ConstraintPair.hpp,
# Line 1671 | Line 3048
3048  
3049   2005-01-04 17:18  tim
3050  
3051 <        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
3052 <        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
1676 <        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
1677 <        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
3051 >        * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was
3052 >        initially added on branch new_design.
3053  
3054   2005-01-04 17:18  tim
3055  
1681 –        * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
1682 –        was initially added on branch new_design.
1683 –
1684 – 2005-01-04 17:18  tim
1685 –
3056          * src/minimizers/MinimizerParameterSet.cpp: file
3057          MinimizerParameterSet.cpp was initially added on branch new_design.
3058  
# Line 1693 | Line 3063
3063  
3064   2005-01-04 17:18  tim
3065  
3066 +        * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
3067 +        was initially added on branch new_design.
3068 +
3069 + 2005-01-04 17:18  tim
3070 +
3071 +        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
3072 +        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
3073 +        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
3074 +        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
3075 +
3076 + 2005-01-04 17:18  tim
3077 +
3078          * src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on
3079          branch new_design.
3080  
# Line 2011 | Line 3393
3393  
3394   2004-12-02 19:26  tim
3395  
3396 +        * src/utils/Trim.cpp: file Trim.cpp was initially added on branch
3397 +        new_design.
3398 +
3399 + 2004-12-02 19:26  tim
3400 +
3401          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3402          UseTheForce/ForceFieldCreator.cpp,
3403          UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp,
# Line 2020 | Line 3407
3407          utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a
3408          bug in countTokens in StringTokenizer
3409  
2023 – 2004-12-02 19:26  tim
2024 –
2025 –        * src/utils/Trim.cpp: file Trim.cpp was initially added on branch
2026 –        new_design.
2027 –
3410   2004-12-02 19:06  tim
3411  
3412          * forceFields/newDUFF.frc: minor fix
# Line 2035 | Line 3417
3417  
3418   2004-12-02 17:15  tim
3419  
2038 –        * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp
2039 –        was initially added on branch new_design.
2040 –
2041 – 2004-12-02 17:15  tim
2042 –
2043 –        * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp
2044 –        was initially added on branch new_design.
2045 –
2046 – 2004-12-02 17:15  tim
2047 –
2048 –        * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp
2049 –        was initially added on branch new_design.
2050 –
2051 – 2004-12-02 17:15  tim
2052 –
3420          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3421          UseTheForce/ForceFieldCreator.cpp,
3422          UseTheForce/ForceFieldCreator.hpp,
# Line 2070 | Line 3437
3437   2004-12-02 17:15  tim
3438  
3439          * src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp
3440 +        was initially added on branch new_design.
3441 +
3442 + 2004-12-02 17:15  tim
3443 +
3444 +        * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp
3445 +        was initially added on branch new_design.
3446 +
3447 + 2004-12-02 17:15  tim
3448 +
3449 +        * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp
3450          was initially added on branch new_design.
3451  
3452 + 2004-12-02 17:15  tim
3453 +
3454 +        * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp
3455 +        was initially added on branch new_design.
3456 +
3457   2004-12-02 11:53  tim
3458  
3459          * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp,
# Line 2230 | Line 3612
3612  
3613   2004-12-01 19:09  tim
3614  
3615 <        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
3616 <        was initially added on branch new_design.
3615 >        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
3616 >        branch new_design.
3617 >
3618 > 2004-12-01 19:09  tim
3619 >
3620 >        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
3621 >        branch new_design.
3622  
3623   2004-12-01 19:09  tim
3624  
# Line 2247 | Line 3634
3634  
3635   2004-12-01 19:09  tim
3636  
3637 <        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
3638 <        branch new_design.
3637 >        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
3638 >        was initially added on branch new_design.
3639  
2253 – 2004-12-01 19:09  tim
2254 –
2255 –        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
2256 –        branch new_design.
2257 –
3640   2004-12-01 17:45  tim
3641  
3642          * src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp,
# Line 2353 | Line 3735
3735  
3736   2004-11-30 14:58  tim
3737  
2356 –        * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially
2357 –        added on branch new_design.
2358 –
2359 – 2004-11-30 14:58  tim
2360 –
3738          * src/: brains/Exclude.cpp, brains/Exclude.hpp,
3739          brains/ForceManager.cpp, brains/ForceManager.hpp,
3740          brains/MoleculeCreator.cpp, brains/SimCreator.hpp,
# Line 2367 | Line 3744
3744          brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile,
3745          math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo
3746  
3747 + 2004-11-30 14:58  tim
3748 +
3749 +        * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially
3750 +        added on branch new_design.
3751 +
3752   2004-11-30 12:54  tim
3753  
3754          * src/: primitives/Bend.hpp, primitives/Bond.hpp,
# Line 2375 | Line 3757
3757  
3758   2004-11-30 00:03  tim
3759  
3760 <        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
3761 <        LocalndexManager.hpp to LocalIndexManager.hpp
3760 >        * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
3761 >        initially added on branch new_design.
3762  
3763   2004-11-30 00:03  tim
3764  
3765 <        * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
3766 <        initially added on branch new_design.
3765 >        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
3766 >        LocalndexManager.hpp to LocalIndexManager.hpp
3767  
3768   2004-11-29 23:43  tim
3769  
# Line 2506 | Line 3888
3888          io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp,
3889          types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some
3890          files
3891 +
3892 + 2004-11-25 15:18  tim
3893 +
3894 +        * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was
3895 +        initially added on branch new_design.
3896  
3897   2004-11-25 15:18  tim
3898  
# Line 2521 | Line 3908
3908          * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was
3909          initially added on branch new_design.
3910  
2524 – 2004-11-25 15:18  tim
2525 –
2526 –        * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was
2527 –        initially added on branch new_design.
2528 –
3911   2004-11-24 17:12  tim
3912  
3913          * src/: io/AtomTypesSectionParser.cpp,
# Line 2638 | Line 4020
4020  
4021   2004-11-23 12:53  tim
4022  
2641 –        * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
2642 –        ElectrostaticAtomTypesSectionParser.cpp was initially added on
2643 –        branch new_design.
2644 –
2645 – 2004-11-23 12:53  tim
2646 –
4023          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
4024          UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
4025          applications/simpleBuilder/simpleBuilder.cpp,
# Line 2661 | Line 4037
4037          ElectrostaticAtomTypesSectionParser.hpp was initially added on
4038          branch new_design.
4039  
4040 < 2004-11-23 01:03  tim
4040 > 2004-11-23 12:53  tim
4041  
4042 <        * src/io/EAMAtomTypesSectionParser.cpp: file
4043 <        EAMAtomTypesSectionParser.cpp was initially added on branch
4044 <        new_design.
4042 >        * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
4043 >        ElectrostaticAtomTypesSectionParser.cpp was initially added on
4044 >        branch new_design.
4045  
4046   2004-11-23 01:03  tim
4047  
# Line 2676 | Line 4052
4052  
4053   2004-11-23 01:03  tim
4054  
4055 +        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
4056 +        was initially added on branch new_design.
4057 +
4058 + 2004-11-23 01:03  tim
4059 +
4060          * src/io/EAMAtomTypesSectionParser.hpp: file
4061          EAMAtomTypesSectionParser.hpp was initially added on branch
4062          new_design.
4063  
4064   2004-11-23 01:03  tim
4065  
4066 <        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
4067 <        was initially added on branch new_design.
4066 >        * src/io/EAMAtomTypesSectionParser.cpp: file
4067 >        EAMAtomTypesSectionParser.cpp was initially added on branch
4068 >        new_design.
4069  
4070   2004-11-22 23:35  tim
4071  
4072 <        * src/io/TorsionTypesSectionParser.cpp: file
4073 <        TorsionTypesSectionParser.cpp was initially added on branch
4072 >        * src/io/TorsionTypesSectionParser.hpp: file
4073 >        TorsionTypesSectionParser.hpp was initially added on branch
4074          new_design.
4075  
4076   2004-11-22 23:35  tim
# Line 2699 | Line 4081
4081  
4082   2004-11-22 23:35  tim
4083  
2702 –        * src/io/BondTypesSectionParser.cpp: file
2703 –        BondTypesSectionParser.cpp was initially added on branch
2704 –        new_design.
2705 –
2706 – 2004-11-22 23:35  tim
2707 –
4084          * src/io/BondTypesSectionParser.hpp: file
4085          BondTypesSectionParser.hpp was initially added on branch
4086          new_design.
4087  
4088   2004-11-22 23:35  tim
4089  
4090 <        * src/io/TorsionTypesSectionParser.hpp: file
4091 <        TorsionTypesSectionParser.hpp was initially added on branch
4090 >        * src/io/BondTypesSectionParser.cpp: file
4091 >        BondTypesSectionParser.cpp was initially added on branch
4092          new_design.
4093  
4094   2004-11-22 23:35  tim
4095  
4096 <        * src/io/BendTypesSectionParser.cpp: file
4097 <        BendTypesSectionParser.cpp was initially added on branch
4096 >        * src/io/TorsionTypesSectionParser.cpp: file
4097 >        TorsionTypesSectionParser.cpp was initially added on branch
4098          new_design.
4099  
4100   2004-11-22 23:35  tim
# Line 2729 | Line 4105
4105          BondTypesSectionParser, BendTypesSectionParser and
4106          TorsionTypeSectionParser
4107  
4108 + 2004-11-22 23:35  tim
4109 +
4110 +        * src/io/BendTypesSectionParser.cpp: file
4111 +        BendTypesSectionParser.cpp was initially added on branch
4112 +        new_design.
4113 +
4114   2004-11-22 18:04  tim
4115  
4116          * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in
# Line 2736 | Line 4118
4118  
4119   2004-11-22 18:02  tim
4120  
4121 +        * src/io/: DirectionalAtomTypesParser.hpp,
4122 +        DirectionalAtomTypesSectionParser.hpp: adding section parsers
4123 +
4124 + 2004-11-22 18:02  tim
4125 +
4126          * src/io/DirectionalAtomTypesSectionParser.hpp: file
4127          DirectionalAtomTypesSectionParser.hpp was initially added on branch
4128          new_design.
4129  
4130 < 2004-11-22 18:02  tim
4130 > 2004-11-22 15:55  tim
4131  
4132 <        * src/io/: DirectionalAtomTypesParser.hpp,
4133 <        DirectionalAtomTypesSectionParser.hpp: adding section parsers
4132 >        * src/io/DipoleAtomTypesSectionParser.hpp: file
4133 >        DipoleAtomTypesSectionParser.hpp was initially added on branch
4134 >        new_design.
4135  
4136   2004-11-22 15:55  tim
4137  
4138 <        * src/io/DirectionalAtomTypesParser.hpp: file
4139 <        DirectionalAtomTypesParser.hpp was initially added on branch
4138 >        * src/io/AtomTypesSectionParser.hpp: file
4139 >        AtomTypesSectionParser.hpp was initially added on branch
4140          new_design.
4141  
4142   2004-11-22 15:55  tim
# Line 2759 | Line 4147
4147  
4148   2004-11-22 15:55  tim
4149  
4150 <        * src/io/ChargeAtomTypesSectionParser.hpp: file
4151 <        ChargeAtomTypesSectionParser.hpp was initially added on branch
4150 >        * src/io/StickyAtomTypesSectionParser.cpp: file
4151 >        StickyAtomTypesSectionParser.cpp was initially added on branch
4152          new_design.
4153  
4154   2004-11-22 15:55  tim
4155  
4156 <        * src/io/DirectionalAtomTypesSectionParser.cpp: file
4157 <        DirectionalAtomTypesSectionParser.cpp was initially added on branch
2770 <        new_design.
2771 <
2772 < 2004-11-22 15:55  tim
2773 <
2774 <        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
2775 <        LennardJonesAtomTypesSectionParser.cpp was initially added on
4156 >        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
4157 >        LennardJonesAtomTypesSectionParser.hpp was initially added on
4158          branch new_design.
4159  
4160   2004-11-22 15:55  tim
4161  
4162 <        * src/io/DipoleAtomTypesSectionParser.cpp: file
4163 <        DipoleAtomTypesSectionParser.cpp was initially added on branch
4162 >        * src/io/HarmonicBondTypesSectionParser.cpp: file
4163 >        HarmonicBondTypesSectionParser.cpp was initially added on branch
4164          new_design.
4165  
4166   2004-11-22 15:55  tim
4167  
4168 <        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
4169 <        brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
2788 <        brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp,
2789 <        integrators/NVT.hpp, io/AtomTypesSectionParser.cpp,
2790 <        io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
2791 <        io/ChargeAtomTypesSectionParser.hpp,
2792 <        io/DipoleAtomTypesSectionParser.cpp,
2793 <        io/DipoleAtomTypesSectionParser.hpp,
2794 <        io/DirectionalAtomTypesParser.hpp,
2795 <        io/DirectionalAtomTypesSectionParser.cpp,
2796 <        io/HarmonicBondTypesSectionParser.cpp,
2797 <        io/HarmonicBondTypesSectionParser.hpp,
2798 <        io/LennardJonesAtomTypesSectionParser.cpp,
2799 <        io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp,
2800 <        io/SectionParser.hpp, io/SectionParserManager.cpp,
2801 <        io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp,
2802 <        io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp,
2803 <        types/AtomType.hpp, types/DirectionalAtomType.hpp,
2804 <        utils/GenericData.hpp: adding section parsers
2805 <
2806 < 2004-11-22 15:55  tim
2807 <
2808 <        * src/io/DipoleAtomTypesSectionParser.hpp: file
2809 <        DipoleAtomTypesSectionParser.hpp was initially added on branch
4168 >        * src/io/DirectionalAtomTypesSectionParser.cpp: file
4169 >        DirectionalAtomTypesSectionParser.cpp was initially added on branch
4170          new_design.
4171  
4172   2004-11-22 15:55  tim
4173  
4174 <        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
2815 <        added on branch new_design.
2816 <
2817 < 2004-11-22 15:55  tim
2818 <
2819 <        * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
4174 >        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
4175          was initially added on branch new_design.
4176  
4177   2004-11-22 15:55  tim
# Line 2827 | Line 4182
4182  
4183   2004-11-22 15:55  tim
4184  
4185 <        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
4186 <        LennardJonesAtomTypesSectionParser.hpp was initially added on
4187 <        branch new_design.
4185 >        * src/io/ChargeAtomTypesSectionParser.cpp: file
4186 >        ChargeAtomTypesSectionParser.cpp was initially added on branch
4187 >        new_design.
4188  
4189   2004-11-22 15:55  tim
4190  
4191 <        * src/io/HarmonicBondTypesSectionParser.cpp: file
4192 <        HarmonicBondTypesSectionParser.cpp was initially added on branch
4191 >        * src/io/DipoleAtomTypesSectionParser.cpp: file
4192 >        DipoleAtomTypesSectionParser.cpp was initially added on branch
4193          new_design.
4194  
4195   2004-11-22 15:55  tim
4196  
4197 <        * src/io/AtomTypesSectionParser.hpp: file
4198 <        AtomTypesSectionParser.hpp was initially added on branch
4197 >        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
4198 >        LennardJonesAtomTypesSectionParser.cpp was initially added on
4199 >        branch new_design.
4200 >
4201 > 2004-11-22 15:55  tim
4202 >
4203 >        * src/io/ChargeAtomTypesSectionParser.hpp: file
4204 >        ChargeAtomTypesSectionParser.hpp was initially added on branch
4205          new_design.
4206  
4207   2004-11-22 15:55  tim
4208  
4209 <        * src/io/StickyAtomTypesSectionParser.cpp: file
4210 <        StickyAtomTypesSectionParser.cpp was initially added on branch
4209 >        * src/io/StickyAtomTypesSectionParser.hpp: file
4210 >        StickyAtomTypesSectionParser.hpp was initially added on branch
4211          new_design.
4212  
4213   2004-11-22 15:55  tim
# Line 2856 | Line 4217
4217  
4218   2004-11-22 15:55  tim
4219  
4220 <        * src/io/ChargeAtomTypesSectionParser.cpp: file
4221 <        ChargeAtomTypesSectionParser.cpp was initially added on branch
4220 >        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
4221 >        brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
4222 >        brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp,
4223 >        integrators/NVT.hpp, io/AtomTypesSectionParser.cpp,
4224 >        io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
4225 >        io/ChargeAtomTypesSectionParser.hpp,
4226 >        io/DipoleAtomTypesSectionParser.cpp,
4227 >        io/DipoleAtomTypesSectionParser.hpp,
4228 >        io/DirectionalAtomTypesParser.hpp,
4229 >        io/DirectionalAtomTypesSectionParser.cpp,
4230 >        io/HarmonicBondTypesSectionParser.cpp,
4231 >        io/HarmonicBondTypesSectionParser.hpp,
4232 >        io/LennardJonesAtomTypesSectionParser.cpp,
4233 >        io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp,
4234 >        io/SectionParser.hpp, io/SectionParserManager.cpp,
4235 >        io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp,
4236 >        io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp,
4237 >        types/AtomType.hpp, types/DirectionalAtomType.hpp,
4238 >        utils/GenericData.hpp: adding section parsers
4239 >
4240 > 2004-11-22 15:55  tim
4241 >
4242 >        * src/io/DirectionalAtomTypesParser.hpp: file
4243 >        DirectionalAtomTypesParser.hpp was initially added on branch
4244          new_design.
4245  
4246   2004-11-22 15:55  tim
4247  
4248 <        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
4248 >        * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
4249          was initially added on branch new_design.
4250  
4251   2004-11-22 15:55  tim
4252  
4253 <        * src/io/StickyAtomTypesSectionParser.hpp: file
4254 <        StickyAtomTypesSectionParser.hpp was initially added on branch
2872 <        new_design.
4253 >        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
4254 >        added on branch new_design.
4255  
4256   2004-11-19 17:12  tim
4257  
4258 +        * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
4259 +        added on branch new_design.
4260 +
4261 + 2004-11-19 17:12  tim
4262 +
4263          * src/: brains/SimState.cpp, brains/SimState.hpp,
4264          io/InitializeFromFile.cpp, types/FixBondType.hpp,
4265          types/FixedBondType.hpp: remove more useless files
4266  
2880 – 2004-11-19 17:12  tim
2881 –
2882 –        * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
2883 –        added on branch new_design.
2884 –
4267   2004-11-19 16:47  tim
4268  
4269          * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp,
# Line 2890 | Line 4272
4272  
4273   2004-11-19 16:38  tim
4274  
4275 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
4276 +        UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp,
4277 +        integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp,
4278 +        integrators/NVT.hpp: refactory integrator
4279 +
4280 + 2004-11-19 16:38  tim
4281 +
4282          * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on
4283          branch new_design.
4284  
4285   2004-11-19 16:38  tim
4286  
4287 <        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
4288 <        on branch new_design.
4287 >        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
4288 >        branch new_design.
4289  
4290   2004-11-19 16:38  tim
4291  
# Line 2905 | Line 4294
4294  
4295   2004-11-19 16:38  tim
4296  
4297 <        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
4298 <        branch new_design.
4297 >        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
4298 >        on branch new_design.
4299  
4300   2004-11-19 16:38  tim
4301  
4302 <        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
4302 >        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
4303          branch new_design.
4304  
2916 – 2004-11-19 16:38  tim
2917 –
2918 –        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2919 –        UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp,
2920 –        integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp,
2921 –        integrators/NVT.hpp: refactory integrator
2922 –
4305   2004-11-19 15:37  tim
4306  
4307          * forceFields/newDUFF.frc: new DUFF forcefield
4308  
4309   2004-11-19 15:23  tim
4310  
4311 +        * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
4312 +        branch new_design.
4313 +
4314 + 2004-11-19 15:23  tim
4315 +
4316          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp,
4317          UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp,
4318          utils/TypeContainer.hpp: add EAM
# Line 2935 | Line 4322
4322          * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on
4323          branch new_design.
4324  
2938 – 2004-11-19 15:23  tim
2939 –
2940 –        * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
2941 –        branch new_design.
2942 –
4325   2004-11-19 13:02  tim
4326  
4327          * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except
# Line 2947 | Line 4329
4329  
4330   2004-11-19 12:56  tim
4331  
4332 <        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
4332 >        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
4333          was initially added on branch new_design.
4334  
4335   2004-11-19 12:56  tim
4336  
4337 <        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
4337 >        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
4338          was initially added on branch new_design.
4339  
4340   2004-11-19 12:56  tim
# Line 2977 | Line 4359
4359  
4360   2004-11-18 18:26  tim
4361  
4362 +        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
4363 +        initially added on branch new_design.
4364 +
4365 + 2004-11-18 18:26  tim
4366 +
4367          * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp,
4368          integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
4369          integrators/VelocityVerletIntegrator.cpp,
# Line 2986 | Line 4373
4373          types/HarmonicBondType.hpp, types/QuadraticBendType.hpp,
4374          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding
4375          DUFF parser
2989 –
2990 – 2004-11-18 18:26  tim
2991 –
2992 –        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
2993 –        initially added on branch new_design.
4376  
4377   2004-11-18 16:42  tim
4378  
# Line 3003 | Line 4385
4385  
4386   2004-11-18 00:42  tim
4387  
4388 <        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
4388 >        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
4389          initially added on branch new_design.
4390  
4391   2004-11-18 00:42  tim
4392  
4393 <        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
4393 >        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
4394          initially added on branch new_design.
4395  
4396   2004-11-18 00:42  tim
# Line 3051 | Line 4433
4433  
4434   2004-11-17 16:47  tim
4435  
4436 +        * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp
4437 +        was initially added on branch new_design.
4438 +
4439 + 2004-11-17 16:47  tim
4440 +
4441          * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially
4442          added on branch new_design.
4443  
4444   2004-11-17 16:47  tim
4445  
4446 +        * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially
4447 +        added on branch new_design.
4448 +
4449 + 2004-11-17 16:47  tim
4450 +
4451          * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was
4452          initially added on branch new_design.
4453  
4454   2004-11-17 16:47  tim
4455  
4456 <        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
4456 >        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
4457          initially added on branch new_design.
4458  
4459   2004-11-17 16:47  tim
4460  
4461 <        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
4461 >        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
4462          initially added on branch new_design.
4463  
4464   2004-11-17 16:47  tim
# Line 3086 | Line 4478
4478          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp:
4479          UreyBradleyBend and GhostBend
4480  
3089 – 2004-11-17 16:47  tim
3090 –
3091 –        * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially
3092 –        added on branch new_design.
3093 –
3094 – 2004-11-17 16:47  tim
3095 –
3096 –        * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp
3097 –        was initially added on branch new_design.
3098 –
4481   2004-11-17 13:58  tim
4482  
4483          * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp
# Line 3103 | Line 4485
4485  
4486   2004-11-17 13:58  tim
4487  
3106 –        * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
3107 –        initially added on branch new_design.
3108 –
3109 – 2004-11-17 13:58  tim
3110 –
4488          * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp
4489          was initially added on branch new_design.
4490  
# Line 3120 | Line 4497
4497          types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types
4498          stuff and Chebyshev Polynomial
4499  
4500 < 2004-11-17 01:37  tim
4500 > 2004-11-17 13:58  tim
4501  
4502 <        * src/types/PolynomialTorsionType.hpp: file
3126 <        PolynomialTorsionType.hpp was initially added on branch new_design.
3127 <
3128 < 2004-11-17 01:37  tim
3129 <
3130 <        * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
4502 >        * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
4503          initially added on branch new_design.
4504  
4505   2004-11-17 01:37  tim
4506  
4507 <        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
4508 <        initially added on branch new_design.
4507 >        * src/types/PolynomialTorsionType.hpp: file
4508 >        PolynomialTorsionType.hpp was initially added on branch new_design.
4509  
4510   2004-11-17 01:37  tim
4511  
# Line 3142 | Line 4514
4514  
4515   2004-11-17 01:37  tim
4516  
3145 –        * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was
3146 –        initially added on branch new_design.
3147 –
3148 – 2004-11-17 01:37  tim
3149 –
4517          * src/: math/Polynomial.hpp, primitives/Bend.cpp,
4518          primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp,
4519          types/BondType.hpp, types/CharmmTorsionType.cpp,
# Line 3159 | Line 4526
4526          CharmmTorsionType. Need to refine the design and add document for
4527          them
4528  
4529 + 2004-11-17 01:37  tim
4530 +
4531 +        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
4532 +        initially added on branch new_design.
4533 +
4534 + 2004-11-17 01:37  tim
4535 +
4536 +        * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was
4537 +        initially added on branch new_design.
4538 +
4539 + 2004-11-17 01:37  tim
4540 +
4541 +        * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
4542 +        initially added on branch new_design.
4543 +
4544   2004-11-16 20:11  tim
4545  
4546          * src/types/: BendType.hpp, PolynomialBondType.hpp,
# Line 3171 | Line 4553
4553  
4554   2004-11-16 18:20  tim
4555  
3174 –        * src/math/Polynomial.hpp: Adding Polynomial class
3175 –
3176 – 2004-11-16 18:20  tim
3177 –
4556          * src/math/Polynomial.hpp: file Polynomial.hpp was initially added
4557          on branch new_design.
4558  
4559 < 2004-11-16 17:04  gezelter
4559 > 2004-11-16 18:20  tim
4560  
4561 <        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
3184 <        initially added on branch new_design.
4561 >        * src/math/Polynomial.hpp: Adding Polynomial class
4562  
4563   2004-11-16 17:04  gezelter
4564  
# Line 3190 | Line 4567
4567  
4568   2004-11-16 17:04  gezelter
4569  
4570 +        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
4571 +        initially added on branch new_design.
4572 +
4573 + 2004-11-16 17:04  gezelter
4574 +
4575          * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp,
4576          MorseBondType.hpp, TorsionType.hpp: added some new stuff
4577  
# Line 3202 | Line 4584
4584  
4585   2004-11-15 21:07  tim
4586  
4587 +        * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
4588 +        branch new_design.
4589 +
4590 + 2004-11-15 21:07  tim
4591 +
4592          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
4593          UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp,
4594          utils/StringTokenizer.cpp: adding DUFF class; adding checking
4595          statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer
4596  
4597 < 2004-11-15 21:07  tim
4597 > 2004-11-15 18:00  tim
4598  
4599 <        * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
4600 <        branch new_design.
4599 >        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
4600 >        UseTheForce/ForceFieldFactory.cpp,
4601 >        UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp,
4602 >        UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp,
4603 >        types/AtomType.hpp: adding ForceFieldFactory and LJFF classes
4604  
4605   2004-11-15 18:00  tim
4606  
# Line 3219 | Line 4609
4609  
4610   2004-11-15 18:00  tim
4611  
4612 <        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
4613 <        branch new_design.
4612 >        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
4613 >        was initially added on branch new_design.
4614  
4615   2004-11-15 18:00  tim
4616  
4617 <        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
4618 <        UseTheForce/ForceFieldFactory.cpp,
3229 <        UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp,
3230 <        UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp,
3231 <        types/AtomType.hpp: adding ForceFieldFactory and LJFF classes
4617 >        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
4618 >        branch new_design.
4619  
4620 < 2004-11-15 18:00  tim
4620 > 2004-11-15 13:02  tim
4621  
4622 <        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
4623 <        was initially added on branch new_design.
4622 >        * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was
4623 >        initially added on branch new_design.
4624  
4625   2004-11-15 13:02  tim
4626  
# Line 3247 | Line 4634
4634  
4635   2004-11-15 13:02  tim
4636  
3250 –        * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was
3251 –        initially added on branch new_design.
3252 –
3253 – 2004-11-15 13:02  tim
3254 –
4637          * src/: brains/SimInfo.cpp, brains/SimInfo.hpp,
4638          brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
4639          integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp,
# Line 3375 | Line 4757
4757  
4758   2004-11-09 18:11  tim
4759  
4760 +        * src/brains/ForceManager.cpp: file ForceManager.cpp was initially
4761 +        added on branch new_design.
4762 +
4763 + 2004-11-09 18:11  tim
4764 +
4765 +        * src/integrators/VelocityVerletIntegrator.cpp: file
4766 +        VelocityVerletIntegrator.cpp was initially added on branch
4767 +        new_design.
4768 +
4769 + 2004-11-09 18:11  tim
4770 +
4771          * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp,
4772          brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
4773          brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp,
# Line 3389 | Line 4782
4782  
4783   2004-11-09 18:11  tim
4784  
3392 –        * src/integrators/VelocityVerletIntegrator.cpp: file
3393 –        VelocityVerletIntegrator.cpp was initially added on branch
3394 –        new_design.
3395 –
3396 – 2004-11-09 18:11  tim
3397 –
4785          * src/integrators/NVE.cpp: file NVE.cpp was initially added on
4786          branch new_design.
4787  
3401 – 2004-11-09 18:11  tim
3402 –
3403 –        * src/brains/ForceManager.cpp: file ForceManager.cpp was initially
3404 –        added on branch new_design.
3405 –
4788   2004-11-08 20:08  tim
4789  
4790          * src/integrators/VelocityVerletIntegrator.hpp: file
# Line 3411 | Line 4793
4793  
4794   2004-11-08 20:08  tim
4795  
4796 +        * src/integrators/NVE.hpp: file NVE.hpp was initially added on
4797 +        branch new_design.
4798 +
4799 + 2004-11-08 20:08  tim
4800 +
4801          * src/: brains/Exclude.hpp, brains/Stats.hpp,
4802          integrators/Integrator.hpp, integrators/NVE.hpp,
4803          integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
4804          utils/TypeContainer.hpp: More to break
4805  
3419 – 2004-11-08 20:08  tim
3420 –
3421 –        * src/integrators/NVE.hpp: file NVE.hpp was initially added on
3422 –        branch new_design.
3423 –
4806   2004-11-06 00:21  tim
4807  
4808          * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially
# Line 3435 | Line 4817
4817  
4818   2004-11-05 18:38  tim
4819  
4820 +        * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
4821 +        initially added on branch new_design.
4822 +
4823 + 2004-11-05 18:38  tim
4824 +
4825          * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was
4826          initially added on branch new_design.
4827  
# Line 3446 | Line 4833
4833          brains/SimInfo.hpp, primitives/Molecule.hpp,
4834          utils/LocalndexManager.hpp: Fix Exclude class etc.
4835  
3449 – 2004-11-05 18:38  tim
3450 –
3451 –        * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
3452 –        initially added on branch new_design.
3453 –
4836   2004-11-05 16:45  chrisfen
4837  
4838          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
# Line 3488 | Line 4870
4870  
4871   2004-11-04 14:48  tim
4872  
3491 –        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
3492 –        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
3493 –        class
3494 –
3495 – 2004-11-04 14:48  tim
3496 –
4873          * src/brains/Stats.cpp: file Stats.cpp was initially added on
4874          branch new_design.
4875  
# Line 3502 | Line 4878
4878          * src/brains/Stats.hpp: file Stats.hpp was initially added on
4879          branch new_design.
4880  
4881 + 2004-11-04 14:48  tim
4882 +
4883 +        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
4884 +        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
4885 +        class
4886 +
4887   2004-11-04 11:22  gezelter
4888  
4889          * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp,
# Line 3576 | Line 4958
4958  
4959   2004-11-02 17:41  tim
4960  
4961 <        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
4962 <        branch new_design.
4961 >        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
4962 >        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
4963 >        Need unit test
4964  
4965   2004-11-02 17:41  tim
4966  
# Line 3586 | Line 4969
4969  
4970   2004-11-02 17:41  tim
4971  
4972 <        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
4973 <        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
3591 <        Need unit test
4972 >        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
4973 >        branch new_design.
4974  
4975   2004-11-02 11:59  tim
4976  
4977 <        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
4978 <        SimSnapshotManager.hpp: SimModel in progress
4977 >        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
4978 >        branch new_design.
4979  
4980   2004-11-02 11:59  tim
4981  
4982 <        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
4983 <        branch new_design.
4982 >        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
4983 >        SimSnapshotManager.hpp: SimModel in progress
4984  
4985   2004-11-02 10:28  chrisfen
4986  
# Line 3608 | Line 4990
4990  
4991   2004-11-02 10:27  tim
4992  
4993 <        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
4994 <        added on branch new_design.
4993 >        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
4994 >        functions for dealing with memory issue
4995  
4996   2004-11-02 10:27  tim
4997  
4998 <        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
4999 <        functions for dealing with memory issue
4998 >        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
4999 >        added on branch new_design.
5000  
5001   2004-11-02 10:23  tim
5002  
# Line 3643 | Line 5025
5025  
5026   2004-11-01 16:40  tim
5027  
5028 <        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
5029 <        branch new_design.
5028 >        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
5029 >        on branch new_design.
5030  
5031   2004-11-01 16:40  tim
5032  
5033 <        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
5034 <        version of Bond, Bend and Torsion.
5033 >        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
5034 >        branch new_design.
5035  
5036   2004-11-01 16:40  tim
5037  
# Line 3658 | Line 5040
5040  
5041   2004-11-01 16:40  tim
5042  
5043 <        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
5044 <        on branch new_design.
5043 >        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
5044 >        version of Bond, Bend and Torsion.
5045  
5046   2004-11-01 16:37  tim
5047  
# Line 3668 | Line 5050
5050  
5051   2004-11-01 16:37  tim
5052  
5053 <        * src/types/BondType.hpp: file BondType.hpp was initially added on
5054 <        branch new_design.
5053 >        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
5054 >        BondType, BendType, TorsionType
5055  
5056   2004-11-01 16:37  tim
5057  
# Line 3678 | Line 5060
5060  
5061   2004-11-01 16:37  tim
5062  
5063 <        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
5064 <        BondType, BendType, TorsionType
5063 >        * src/types/BondType.hpp: file BondType.hpp was initially added on
5064 >        branch new_design.
5065  
5066   2004-11-01 15:15  tim
5067  
# Line 4512 | Line 5894
5894          water/tip4p/Makefile, zcons/Makefile: fix Makefile under water
5895          directory
5896  
5897 + 2004-10-11 09:23  tim
5898 +
5899 +        * samples/argon/Makefile: remove argon.dump and argon.eor from
5900 +        Makefile
5901 +
5902   2004-10-09 01:01  tim
5903  
5904 <        * samples/: alkane/Makefile.in, lipid/Makefile.in,
5905 <        metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in
5904 >        * samples/: alkane/Makefile.in, argon/Makefile.in,
5905 >        lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in:
5906 >        Remove some Makefile.in
5907  
5908   2004-10-08 18:15  tim
5909  
# Line 4531 | Line 5919
5919  
5920   2004-10-08 17:04  tim
5921  
5922 <        * samples/: alkane/Makefile, lipid/Makefile, metals/Makefile,
5923 <        minimizer/Makefile, water/Makefile.in, water/dimer/Makefile,
5924 <        water/dimer/Makefile.in, water/spce/Makefile,
5922 >        * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile,
5923 >        metals/Makefile, minimizer/Makefile, water/Makefile.in,
5924 >        water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile,
5925          water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in,
5926          water/ssde/Makefile, water/ssde/Makefile.in,
5927          water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in,
# Line 5012 | Line 6400
6400          samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
6401          samples/alkane/Makefile.in, samples/alkane/alkanes.md,
6402          samples/alkane/butane.in, samples/alkane/butane.md,
6403 +        samples/argon/500.in, samples/argon/500.md,
6404 +        samples/argon/Makefile.in, samples/argon/ar864.in,
6405 +        samples/argon/ar864.md, samples/argon/argonNVT.in,
6406 +        samples/argon/argonNVT.md, samples/argon/lj.md,
6407          samples/lipid/5x5.in, samples/lipid/5x5.md,
6408          samples/lipid/Makefile.in, samples/lipid/lipid.md,
6409          samples/lipid/water.md, samples/minimizer/Makefile.in,
# Line 5184 | Line 6576
6576          samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
6577          samples/alkane/Makefile.in, samples/alkane/alkanes.md,
6578          samples/alkane/butane.in, samples/alkane/butane.md,
6579 +        samples/argon/500.in, samples/argon/500.md,
6580 +        samples/argon/Makefile.in, samples/argon/ar864.in,
6581 +        samples/argon/ar864.md, samples/argon/argonNVT.in,
6582 +        samples/argon/argonNVT.md, samples/argon/lj.md,
6583          samples/lipid/5x5.in, samples/lipid/5x5.md,
6584          samples/lipid/Makefile.in, samples/lipid/lipid.md,
6585          samples/lipid/water.md, samples/minimizer/Makefile.in,

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