ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE-2.0/ChangeLog
(Generate patch)

Comparing trunk/OOPSE-2.0/ChangeLog (file contents):
Revision 2102 by tim, Thu Mar 10 16:14:07 2005 UTC vs.
Revision 2309 by chrisfen, Sun Sep 18 20:45:38 2005 UTC

# Line 1 | Line 1
1 + 2005-09-16 18:04  chuckv
2 +
3 +        * src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed
4 +        dump files.
5 +
6 + 2005-09-16 16:07  chrisfen
7 +
8 +        * src/: UseTheForce/doForces_interface.F90,
9 +        UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a
10 +        bug that ifc missed...
11 +
12 + 2005-09-16 15:36  chrisfen
13 +
14 +        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90:
15 +        fixing some summation method issues
16 +
17 + 2005-09-16 14:35  chrisfen
18 +
19 +        * src/brains/SimInfo.cpp: fixed a capitalization error
20 +
21 + 2005-09-16 14:34  chrisfen
22 +
23 +        * src/UseTheForce/: fElectrostaticSummationMethod.h,
24 +        DarkSide/fElectrostaticSummationMethod.h: moved a header file
25 +        around
26 +
27 + 2005-09-16 14:00  chrisfen
28 +
29 +        * src/: UseTheForce/DarkSide/electrostatic_interface.F90,
30 +        brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there
31 +        are known issues - particularly with reaction field...
32 +
33 + 2005-09-16 11:07  chrisfen
34 +
35 +        * src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp,
36 +        io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking
37 +        (cutting out the old way to do reaction field)
38 +
39 + 2005-09-15 17:05  gezelter
40 +
41 +        * src/UseTheForce/: doForces.F90, fCoulombicCorrection.h,
42 +        fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90,
43 +        DarkSide/electrostatic_interface.F90,
44 +        DarkSide/electrostatic_interface.h: Working on adding WOLF
45 +
46 + 2005-09-15 14:17  tim
47 +
48 +        * src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame
49 +        is called without calling getNFrames
50 +
51 + 2005-09-15 08:47  chrisfen
52 +
53 +        * src/UseTheForce/fCoulombicCorrection.h: forgot to add a header
54 +
55 + 2005-09-14 21:48  chuckv
56 +
57 +        * src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was
58 +        not initialized after creation. When maxval(gtypeMaxCutoff) was
59 +        called, the largest random garbage value was returned from the
60 +        array.
61 +
62 + 2005-09-14 19:14  chrisfen
63 +
64 +        * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp,
65 +        io/Globals.hpp: changes to include the coulombicCorrection selector
66 +
67 + 2005-09-14 19:13  chrisfen
68 +
69 +        * src/UseTheForce/DarkSide/: Makefile, electrostatic.F90,
70 +        reactionField.F90: added in the undamped wolf, in the process of
71 +        doing the damped wolf
72 +
73 + 2005-09-14 19:13  chrisfen
74 +
75 +        * src/UseTheForce/: doForces.F90, doForces_interface.F90,
76 +        doForces_interface.h, notifyCutoffs.F90: some changes to activate
77 +        the coulombicCorrection selector
78 +
79 + 2005-09-14 19:11  chrisfen
80 +
81 +        * samples/water/dimer/: cl.in, cl.md, water.md: just some testing
82 +
83 + 2005-09-14 19:11  chrisfen
84 +
85 +        * samples/argon/: 500.in, 500.md: Equilibrated the sample
86 +
87 + 2005-09-14 19:10  chrisfen
88 +
89 +        * forceFields/DUFF2.frc: re-added Cl- and Na+
90 +
91 + 2005-09-14 15:31  chuckv
92 +
93 +        * src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup
94 +        eamAtypes instead of assuming a 1-1 correspondence to atypes.
95 +
96 + 2005-09-14 15:28  gezelter
97 +
98 +        * src/UseTheForce/doForces.F90: fix to put back calculation of r in
99 +        do_prepair
100 +
101 + 2005-09-14 14:02  gezelter
102 +
103 +        * src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the
104 +        createMixingMap routine.  It should now set doShift correctly
105 +
106 + 2005-09-07 17:44  chuckv
107 +
108 +        * src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build.
109 +
110 + 2005-09-07 17:23  chuckv
111 +
112 +        * src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi
113 +        logical variables
114 +
115 + 2005-09-07 17:08  gezelter
116 +
117 +        * src/UseTheForce/doForces.F90: bugfix on the grouptype finding
118 +        algorithm
119 +
120 + 2005-09-07 15:46  gezelter
121 +
122 +        * src/: UseTheForce/doForces.F90,
123 +        UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90,
124 +        UseTheForce/notifyCutoffs_interface.F90,
125 +        UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp,
126 +        io/Globals.cpp, io/Globals.hpp: adding c-side interface to change
127 +        cutoff Policy
128 +
129 + 2005-09-07 14:18  gezelter
130 +
131 +        * src/UseTheForce/doForces.F90: Some bug hunting
132 +
133 + 2005-09-07 14:18  gezelter
134 +
135 +        * samples/argon/argonNVT.md: Just a longer test
136 +
137 + 2005-09-06 12:32  chuckv
138 +
139 +        * src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap
140 +        etc..
141 +
142 + 2005-09-01 17:56  gezelter
143 +
144 +        * src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to
145 +        zero
146 +
147 + 2005-09-01 15:17  gezelter
148 +
149 +        * src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote
150 +        createGtypeCutoffMap
151 +
152 + 2005-08-30 13:23  chrisfen
153 +
154 +        * src/: UseTheForce/doForces.F90,
155 +        UseTheForce/doForces_interface.F90,
156 +        UseTheForce/doForces_interface.h,
157 +        UseTheForce/DarkSide/electrostatic.F90,
158 +        UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp,
159 +        brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some
160 +        changes for implementing the wolf potential
161 +
162 + 2005-08-26 17:39  chrisfen
163 +
164 +        * src/UseTheForce/DarkSide/eam.F90: updated getEAMCut
165 +
166 + 2005-08-26 16:30  chrisfen
167 +
168 +        * src/UseTheForce/: doForces.F90, DarkSide/eam.F90,
169 +        DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added
170 +        some probably nonfunctional get*cut routines
171 +
172 + 2005-08-26 15:34  chuckv
173 +
174 +        * src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map.
175 +
176 + 2005-08-26 11:36  gezelter
177 +
178 +        * src/UseTheForce/doForces.F90: fixing some of the problems in the
179 +        interactionHash and gtypeCutoff routines
180 +
181 + 2005-08-17 10:26  gezelter
182 +
183 +        * src/UseTheForce/: doForces.F90, fCutoffPolicy.h,
184 +        DarkSide/simulation.F90: added fCutoffPolicy.h
185 +
186 + 2005-08-11 16:04  gezelter
187 +
188 +        * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in
189 +        progress
190 +
191 + 2005-08-10 14:17  gezelter
192 +
193 +        * src/primitives/StuntDouble.hpp: putting spaceballs back where
194 +        they belong
195 +
196 + 2005-08-09 17:33  gezelter
197 +
198 +        * src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard
199 +        Jones module
200 +
201 + 2005-08-09 17:33  gezelter
202 +
203 +        * src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky
204 +
205 + 2005-08-09 14:40  chuckv
206 +
207 +        * src/UseTheForce/doForces.F90: In process of re-write for group
208 +        based cutoff....
209 +
210 + 2005-07-29 14:38  gezelter
211 +
212 +        * src/UseTheForce/doForces.F90: fixes in progress
213 +
214 + 2005-07-29 12:34  tim
215 +
216 +        * src/UseTheForce/doForces.F90: fix a bug which does not update
217 +        me_i and me_j correctly
218 +
219 + 2005-07-28 17:12  chuckv
220 +
221 +        * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed
222 +        cutoffs... Segfaults nicely now...
223 +
224 + 2005-07-20 12:04  gezelter
225 +
226 +        * configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text
227 +        error messages from pathscale compiler
228 +
229 + 2005-07-13 11:48  tim
230 +
231 +        * src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in
232 +        <functional>
233 +
234 + 2005-07-13 10:54  tim
235 +
236 +        * src/: UseTheForce/fSwitchingFunction.h,
237 +        UseTheForce/mpiComponentPlan.h,
238 +        UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h,
239 +        io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h,
240 +        io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c,
241 +        io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c,
242 +        io/parse_tree.h, math/MatVec3.c, utils/residentMem.c,
243 +        utils/simError.c, utils/simError.h: replace c++ style comment in c
244 +        files
245 +
246 + 2005-07-03 15:53  chuckv
247 +
248 +        * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90,
249 +        UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added
250 +        subroutine to set cuttoff for Interaction map and function in
251 +        simulation.F90 to determine if a particular atype is present in a
252 +        simulation.
253 +
254 + 2005-06-28 08:58  gezelter
255 +
256 +        * src/UseTheForce/doForces.F90: [no log message]
257 +
258 + 2005-06-27 17:21  chuckv
259 +
260 +        * src/UseTheForce/doForces.F90: More breaking and destruction of
261 +        force code. Does not build at this point...
262 +
263 + 2005-06-27 16:01  gezelter
264 +
265 +        * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90,
266 +        UseTheForce/DarkSide/fInteractionMap.h,
267 +        UseTheForce/DarkSide/interactions.F90, utils/definitions.F90:
268 +        Breaky breaky!
269 +
270 + 2005-06-20 11:03  gezelter
271 +
272 +        * samples/water/ssd/ssd.md,
273 +        src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a
274 +        simulation
275 +
276 + 2005-06-13 13:25  tim
277 +
278 +        * src/: applications/staticProps/DensityPlot.cpp,
279 +        applications/staticProps/DensityPlot.hpp,
280 +        applications/staticProps/SCDOrderParameter.cpp,
281 +        applications/staticProps/StaticProps.cpp,
282 +        io/AtomTypesSectionParser.cpp: working version of DensityPlot
283 +
284 + 2005-05-31 17:31  chuckv
285 +
286 +        * src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to
287 +        remove angular momentum.
288 +
289 + 2005-05-31 12:34  chuckv
290 +
291 +        * src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in
292 +        typo in nanorodBuilder.
293 +
294 + 2005-05-30 09:01  chuckv
295 +
296 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
297 +        brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp,
298 +        brains/Stats.hpp, integrators/Velocitizer.cpp,
299 +        integrators/Velocitizer.hpp: Added method to remove system angular
300 +        momentum to velocitizer and added method to calculate system
301 +        angular momentum to siminfo.
302 +
303 + 2005-05-29 16:16  chrisfen
304 +
305 +        * src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed
306 +        balance from the Darkside (files)
307 +
308 + 2005-05-29 16:15  chrisfen
309 +
310 +        * src/UseTheForce/doForces.F90: Removed balance from doForces
311 +
312 + 2005-05-29 16:15  chrisfen
313 +
314 +        * samples/water/tap/: tap.in, tap.md: Updated tap sample
315 +
316 + 2005-05-29 16:15  chrisfen
317 +
318 +        * samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap
319 +        dimer for testing purposes
320 +
321 + 2005-05-29 16:14  chrisfen
322 +
323 +        * forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It
324 +        was apparently wiped earlier this month...
325 +
326 + 2005-05-29 16:13  chrisfen
327 +
328 +        * ChangeLog: ran make cvslog
329 +
330 + 2005-05-28 19:16  tim
331 +
332 +        * src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding
333 +        AtomNameVisitor
334 +
335 + 2005-05-28 19:09  tim
336 +
337 +        * src/integrators/Integrator.cpp: dding resetIntegrator
338 +
339 + 2005-05-28 19:06  tim
340 +
341 +        * src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp,
342 +        NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp,
343 +        VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding
344 +        resetIntegrator
345 +
346 + 2005-05-27 16:11  tim
347 +
348 +        * src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp,
349 +        Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp,
350 +        SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo,
351 +        StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into
352 +        StaticProps
353 +
354 + 2005-05-26 23:41  tim
355 +
356 +        * src/: applications/staticProps/Makefile,
357 +        applications/staticProps/P2OrderParameter.cpp,
358 +        applications/staticProps/P2OrderParameter.hpp,
359 +        applications/staticProps/StaticProps.cpp,
360 +        applications/staticProps/StaticProps.ggo,
361 +        applications/staticProps/StaticPropsCmd.c,
362 +        applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp,
363 +        utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps
364 +
365 + 2005-05-26 17:45  tim
366 +
367 +        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
368 +        applications/dump2Xyz/Dump2XYZCmd.c,
369 +        applications/dump2Xyz/Dump2XYZCmd.h,
370 +        applications/staticProps/Makefile,
371 +        applications/staticProps/P2OrderParameter.cpp,
372 +        applications/staticProps/P2OrderParameter.hpp,
373 +        applications/staticProps/RadialDistrFunc.cpp,
374 +        applications/staticProps/RadialDistrFunc.hpp,
375 +        applications/staticProps/StaticAnalyser.hpp,
376 +        applications/staticProps/StaticProps.cpp,
377 +        applications/staticProps/StaticProps.ggo,
378 +        applications/staticProps/StaticPropsCmd.c,
379 +        applications/staticProps/StaticPropsCmd.h, visitors/Makefile,
380 +        visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding
381 +        AtomNameVisitor to convert atom name to its base name;
382 +        wrappingvisitor now wrap back to the center of the mass; adding
383 +        P2OrderParameter into StaticProps
384 +
385 + 2005-05-22 16:36  chuckv
386 +
387 +        * samples/metals/nanorod/Au_nanoparticle_FCC.md,
388 +        src/applications/nanoRodBuilder/Geometry.cpp,
389 +        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
390 +        src/applications/nanoRodBuilder/GeometryFactory.cpp,
391 +        src/applications/nanoRodBuilder/GeometryFactory.hpp,
392 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
393 +        src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure
394 +        tensor.
395 +
396 + 2005-05-22 16:05  tim
397 +
398 +        * src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
399 +        integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp,
400 +        io/Globals.hpp, io/SectionParserManager.cpp: adding keyword
401 +        printPressureTensor
402 +
403 + 2005-05-20 14:27  tim
404 +
405 +        * src/integrators/NPrT.cpp: NPrT in progress
406 +
407 + 2005-05-20 11:01  tim
408 +
409 +        * src/: integrators/NPrT.cpp, io/Globals.cpp,
410 +        utils/OOPSEConstant.hpp: NPrT in progress
411 +
412 + 2005-05-19 16:31  tim
413 +
414 +        * src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp,
415 +        integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp,
416 +        io/Globals.hpp: NPAT is working
417 +
418 + 2005-05-19 10:49  tim
419 +
420 +        * src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile,
421 +        integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT
422 +
423 + 2005-05-18 23:28  tim
424 +
425 +        * src/: brains/Register.cpp, integrators/NPAT.cpp,
426 +        integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp,
427 +        io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators
428 +
429 + 2005-05-18 14:06  chrisfen
430 +
431 +        * forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just
432 +        some tap changes
433 +
434 + 2005-05-18 13:31  chrisfen
435 +
436 +        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
437 +        DarkSide/sticky.F90: Modifications to temper the dipolar strength
438 +        in the first solvation shell for tap
439 +
440 + 2005-05-18 07:35  chrisfen
441 +
442 +        * samples/water/tap/: tap.in, tap.md, water.md: added a tap example
443 +        for testing purposes
444 +
445 + 2005-05-17 17:35  chrisfen
446 +
447 +        * ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md,
448 +        samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp,
449 +        src/UseTheForce/doForces.F90,
450 +        src/UseTheForce/DarkSide/electrostatic.F90,
451 +        src/UseTheForce/DarkSide/electrostatic_interface.F90,
452 +        src/UseTheForce/DarkSide/sticky.F90: Modifications to tap.  Also
453 +        correcting changes to the previous merge that were not caught
454 +
455 + 2005-05-16 23:20  chuckv
456 +
457 +        * src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp:
458 +        Fixed merge issues between Kyle and Chris so OOPSE will actually
459 +        build.
460 +
461 + 2005-05-16 22:46  kdaily
462 +
463 +        * src/io/: GayBerneAtomTypesSectionParser.cpp,
464 +        GayBerneAtomTypesSectionParser.hpp, Makefile: help
465 +
466 + 2005-05-16 21:08  kdaily
467 +
468 +        * forceFields/DUFF2.frc, src/UseTheForce/doForces.F90,
469 +        src/UseTheForce/DarkSide/gb.F90, src/io/Makefile,
470 +        src/types/DirectionalAtomType.cpp,
471 +        src/types/DirectionalAtomType.hpp: added gb
472 +
473 + 2005-05-13 15:36  chrisfen
474 +
475 +        * forceFields/DUFF2.frc: Better tap
476 +
477 + 2005-05-12 14:43  chrisfen
478 +
479 +        * forceFields/DUFF2.frc, samples/water/dimer/ssd.in,
480 +        samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90,
481 +        src/applications/dump2Xyz/Dump2XYZ.cpp,
482 +        src/visitors/AtomVisitor.hpp: Couple of changes for TAP water.
483 +        Need to parametrize.
484 +
485 + 2005-05-11 18:15  chuckv
486 +
487 +        * src/: io/ShapeAtomTypesSectionParser.cpp,
488 +        math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed
489 +        build issues under ifc7.
490 +
491 + 2005-05-09 17:07  chuckv
492 +
493 +        * src/applications/nanoRodBuilder/Geometry.hpp: More geometry
494 +        builder changes.
495 +
496 + 2005-05-05 10:06  chrisfen
497 +
498 +        * forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED
499 +        to TAP
500 +
501 + 2005-05-05 09:47  chrisfen
502 +
503 +        * forceFields/DUFF2.frc, samples/water/ssde/ssde.md,
504 +        samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp,
505 +        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile,
506 +        src/UseTheForce/DarkSide/atype.F90,
507 +        src/UseTheForce/DarkSide/atype_interface.F90,
508 +        src/UseTheForce/DarkSide/simulation.F90,
509 +        src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp,
510 +        src/brains/fSimulation.h, src/io/Makefile,
511 +        src/io/StickyAtomTypesSectionParser.cpp,
512 +        src/io/StickyPowerAtomTypesSectionParser.cpp,
513 +        src/io/StickyPowerAtomTypesSectionParser.hpp,
514 +        src/types/AtomType.cpp, src/types/AtomType.hpp,
515 +        src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp,
516 +        src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water.  It's
517 +        not parametrized, but OOPSE will now let me run it...
518 +
519 + 2005-05-03 17:55  chuckv
520 +
521 +        * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
522 +        GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp:
523 +        Adding support for generic geometry to nanorodbuilder.
524 +
525 + 2005-05-03 12:55  chuckv
526 +
527 +        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
528 +        nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c,
529 +        nanorodBuilderCmd.h: More changes to nanoRodBuilder....
530 +
531 + 2005-04-29 14:16  gezelter
532 +
533 +        * make/Makefile.in: [no log message]
534 +
535 + 2005-04-29 11:26  chrisfen
536 +
537 +        * forceFields/DUFF2.frc, samples/water/spce/water.md,
538 +        samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md,
539 +        samples/water/ssd-ion/water.md, samples/water/ssde/water.md,
540 +        samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md,
541 +        samples/water/tip4p/water.md: Added TIP4P-Ew
542 +
543 + 2005-04-27 19:24  chuckv
544 +
545 +        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
546 +        GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo,
547 +        nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with
548 +        nanoRodBuilder....
549 +
550 + 2005-04-27 15:13  chrisfen
551 +
552 +        * samples/shape/Shapes.frc, samples/shape/linear.shape,
553 +        src/UseTheForce/DarkSide/atype.F90,
554 +        src/UseTheForce/DarkSide/shapes.F90,
555 +        src/UseTheForce/DarkSide/shapes_interface.F90,
556 +        src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of
557 +        write statements and am closer to a working shapes
558 +
559 + 2005-04-22 16:57  chuckv
560 +
561 +        * src/utils/Predicate.hpp: Fixed gcc4 bug...
562 +
563 + 2005-04-22 16:52  tim
564 +
565 +        * src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp,
566 +        Trim.hpp: adding CharClassificationFunctor to fix the locale
567 +        problem  of c++
568 +
569 + 2005-04-21 09:12  chrisfen
570 +
571 +        * samples/shape/Shapes.frc, samples/shape/linear.in,
572 +        samples/shape/linear.md, src/UseTheForce/ForceField.hpp,
573 +        src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile,
574 +        src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp,
575 +        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90,
576 +        src/UseTheForce/DarkSide/shapes.F90,
577 +        src/UseTheForce/DarkSide/shapes_interface.F90,
578 +        src/UseTheForce/DarkSide/shapes_interface.h,
579 +        src/brains/Register.cpp, src/brains/SimCreator.cpp,
580 +        src/io/Makefile, src/io/SectionParser.cpp,
581 +        src/io/SectionParser.hpp, src/io/SectionParserManager.cpp,
582 +        src/io/ShapeAtomTypesSectionParser.cpp,
583 +        src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile,
584 +        src/types/AtomType.cpp, src/types/ShapeAtomType.cpp,
585 +        src/types/ShapeAtomType.hpp: Shapes is limping along with a array
586 +        bounds overwrite (I think...). At least the parser loads the
587 +        forcefield fine...
588 +
589 + 2005-04-18 10:44  chrisfen
590 +
591 +        * src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on
592 +        Mac (capitalization confusion of filenames)
593 +
594 + 2005-04-17 22:50  chrisfen
595 +
596 +        * src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp,
597 +        UseTheForce/Shapes_FF.cpp,
598 +        io/DirectionalAtomTypesSectionParser.cpp,
599 +        io/ShapeAtomTypesSectionParser.cpp,
600 +        io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser...
601 +
602 + 2005-04-15 17:43  gezelter
603 +
604 +        * README: gmake in case people forget
605 +
606 + 2005-04-15 17:40  gezelter
607 +
608 +        * src/applications/oopse/oopse.cpp: fixed the spacing on the
609 +        banner.  Vanity.
610 +
611 + 2005-04-15 17:22  gezelter
612 +
613 +        * src/: config.h.in, applications/oopse/oopse.cpp: Version string
614 +        in banner (and version numbers in config.h)
615 +
616 + 2005-04-15 17:22  gezelter
617 +
618 +        * ChangeLog, LICENSE, README: Documentation changes
619 +
620 + 2005-04-15 17:03  gezelter
621 +
622 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
623 +        UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp,
624 +        UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
625 +        UseTheForce/ForceFieldCreator.hpp,
626 +        UseTheForce/ForceFieldFactory.cpp,
627 +        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp,
628 +        UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90,
629 +        UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h,
630 +        UseTheForce/notifyCutoffs.F90,
631 +        UseTheForce/notifyCutoffs_interface.F90,
632 +        UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90,
633 +        UseTheForce/DarkSide/atype.F90,
634 +        UseTheForce/DarkSide/atype_interface.F90,
635 +        UseTheForce/DarkSide/eam.F90,
636 +        UseTheForce/DarkSide/eam_interface.F90,
637 +        UseTheForce/DarkSide/eam_interface.h,
638 +        UseTheForce/DarkSide/electrostatic.F90,
639 +        UseTheForce/DarkSide/electrostatic_interface.F90,
640 +        UseTheForce/DarkSide/electrostatic_interface.h,
641 +        UseTheForce/DarkSide/force_globals.F90,
642 +        UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h,
643 +        UseTheForce/DarkSide/lj_interface.F90,
644 +        UseTheForce/DarkSide/lj_interface.h,
645 +        UseTheForce/DarkSide/neighborLists.F90,
646 +        UseTheForce/DarkSide/reactionField.F90,
647 +        UseTheForce/DarkSide/shapes.F90,
648 +        UseTheForce/DarkSide/shapes_interface.F90,
649 +        UseTheForce/DarkSide/shapes_interface.h,
650 +        UseTheForce/DarkSide/simParallel.F90,
651 +        UseTheForce/DarkSide/simParallel_interface.F90,
652 +        UseTheForce/DarkSide/simParallel_interface.h,
653 +        UseTheForce/DarkSide/simulation.F90,
654 +        UseTheForce/DarkSide/simulation_interface.F90,
655 +        UseTheForce/DarkSide/simulation_interface.h,
656 +        UseTheForce/DarkSide/sticky.F90,
657 +        UseTheForce/DarkSide/sticky_interface.F90,
658 +        UseTheForce/DarkSide/sticky_interface.h,
659 +        UseTheForce/DarkSide/switcheroo.F90,
660 +        applications/dump2Xyz/Dump2XYZ.cpp,
661 +        applications/dump2Xyz/Dump2XYZCmd.c,
662 +        applications/dump2Xyz/Dump2XYZCmd.h,
663 +        applications/dynamicProps/CrossTimeCorrFunc.cpp,
664 +        applications/dynamicProps/CrossTimeCorrFunc.hpp,
665 +        applications/dynamicProps/DipoleCorrFunc.cpp,
666 +        applications/dynamicProps/DipoleCorrFunc.hpp,
667 +        applications/dynamicProps/DynamicProps.cpp,
668 +        applications/dynamicProps/DynamicPropsCmd.c,
669 +        applications/dynamicProps/DynamicPropsCmd.h,
670 +        applications/dynamicProps/FrameTimeCorrFunc.hpp,
671 +        applications/dynamicProps/ParticleTimeCorrFunc.cpp,
672 +        applications/dynamicProps/ParticleTimeCorrFunc.hpp,
673 +        applications/dynamicProps/RCorrFunc.cpp,
674 +        applications/dynamicProps/RCorrFunc.hpp,
675 +        applications/dynamicProps/TimeCorrFunc.cpp,
676 +        applications/dynamicProps/TimeCorrFunc.hpp,
677 +        applications/dynamicProps/VCorrFunc.cpp,
678 +        applications/dynamicProps/VCorrFunc.hpp,
679 +        applications/nanoRodBuilder/GeometryBuilder.cpp,
680 +        applications/nanoRodBuilder/GeometryBuilder.hpp,
681 +        applications/nanoRodBuilder/nanorodBuilder.cpp,
682 +        applications/nanoRodBuilder/nanorodBuilderCmd.c,
683 +        applications/nanoRodBuilder/nanorodBuilderCmd.h,
684 +        applications/oopse/oopse.cpp,
685 +        applications/simpleBuilder/simpleBuilder.cpp,
686 +        applications/simpleBuilder/simpleBuilderCmd.c,
687 +        applications/simpleBuilder/simpleBuilderCmd.h,
688 +        applications/staticProps/GofAngle2.cpp,
689 +        applications/staticProps/GofAngle2.hpp,
690 +        applications/staticProps/GofR.cpp,
691 +        applications/staticProps/GofR.hpp,
692 +        applications/staticProps/GofRAngle.cpp,
693 +        applications/staticProps/GofRAngle.hpp,
694 +        applications/staticProps/GofXyz.cpp,
695 +        applications/staticProps/GofXyz.hpp,
696 +        applications/staticProps/RadialDistrFunc.cpp,
697 +        applications/staticProps/RadialDistrFunc.hpp,
698 +        applications/staticProps/StaticProps.cpp,
699 +        applications/staticProps/StaticPropsCmd.c,
700 +        applications/staticProps/StaticPropsCmd.h,
701 +        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
702 +        brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp,
703 +        brains/Exclude.hpp, brains/ForceManager.cpp,
704 +        brains/ForceManager.hpp, brains/MoleculeCreator.cpp,
705 +        brains/MoleculeCreator.hpp, brains/Register.cpp,
706 +        brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
707 +        brains/SimInfo.hpp, brains/SimSnapshotManager.cpp,
708 +        brains/SimSnapshotManager.hpp, brains/Snapshot.cpp,
709 +        brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp,
710 +        brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp,
711 +        brains/fSimulation.h, constraints/ConstraintElem.hpp,
712 +        constraints/ConstraintPair.hpp, constraints/Rattle.cpp,
713 +        constraints/Rattle.hpp, constraints/ZconsStruct.hpp,
714 +        constraints/ZconstraintForceManager.cpp,
715 +        constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp,
716 +        integrators/DLM.hpp, integrators/Integrator.cpp,
717 +        integrators/Integrator.hpp, integrators/IntegratorCreator.hpp,
718 +        integrators/IntegratorFactory.cpp,
719 +        integrators/IntegratorFactory.hpp, integrators/NPT.cpp,
720 +        integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp,
721 +        integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp,
722 +        integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp,
723 +        integrators/NVT.cpp, integrators/NVT.hpp,
724 +        integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp,
725 +        integrators/Velocitizer.hpp,
726 +        integrators/VelocityVerletIntegrator.cpp,
727 +        integrators/VelocityVerletIntegrator.hpp,
728 +        io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp,
729 +        io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c,
730 +        io/BASS_parse.h, io/BendTypesSectionParser.cpp,
731 +        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
732 +        io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
733 +        io/ChargeAtomTypesSectionParser.hpp,
734 +        io/DirectionalAtomTypesSectionParser.cpp,
735 +        io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
736 +        io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp,
737 +        io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
738 +        io/Globals.cpp, io/Globals.hpp,
739 +        io/LennardJonesAtomTypesSectionParser.cpp,
740 +        io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp,
741 +        io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp,
742 +        io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp,
743 +        io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp,
744 +        io/SectionParser.cpp, io/SectionParser.hpp,
745 +        io/SectionParserManager.cpp, io/SectionParserManager.hpp,
746 +        io/StatWriter.cpp, io/StatWriter.hpp,
747 +        io/StickyAtomTypesSectionParser.cpp,
748 +        io/StickyAtomTypesSectionParser.hpp,
749 +        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
750 +        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
751 +        io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp,
752 +        io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c,
753 +        io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h,
754 +        io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp,
755 +        lattice/CubicLattice.hpp, lattice/FCCLattice.cpp,
756 +        lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
757 +        lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp,
758 +        lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp,
759 +        math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h,
760 +        math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp,
761 +        math/ParallelRandNumGen.hpp, math/Polynomial.hpp,
762 +        math/Quaternion.hpp, math/RandNumGen.hpp,
763 +        math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp,
764 +        math/RectMatrix.hpp, math/SeqRandNumGen.cpp,
765 +        math/SeqRandNumGen.hpp, math/SquareMatrix.hpp,
766 +        math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp,
767 +        minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp,
768 +        minimizers/Minimizer.cpp, minimizers/Minimizer.hpp,
769 +        minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp,
770 +        minimizers/MinimizerFactory.hpp,
771 +        minimizers/MinimizerParameterSet.cpp,
772 +        minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp,
773 +        minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp,
774 +        minimizers/SDMinimizer.hpp, primitives/Atom.cpp,
775 +        primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp,
776 +        primitives/Bond.hpp, primitives/CutoffGroup.hpp,
777 +        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
778 +        primitives/GhostBend.cpp, primitives/GhostBend.hpp,
779 +        primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp,
780 +        primitives/Molecule.cpp, primitives/Molecule.hpp,
781 +        primitives/RigidBody.cpp, primitives/RigidBody.hpp,
782 +        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
783 +        primitives/Torsion.cpp, primitives/Torsion.hpp,
784 +        primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp,
785 +        profiling/mdProfile.cpp, profiling/mdProfile.hpp,
786 +        profiling/timing.F90, restraints/Restraints.cpp,
787 +        restraints/Restraints.hpp,
788 +        restraints/ThermoIntegrationForceManager.cpp,
789 +        restraints/ThermoIntegrationForceManager.hpp,
790 +        selection/DistanceFinder.cpp, selection/DistanceFinder.hpp,
791 +        selection/IndexFinder.cpp, selection/IndexFinder.hpp,
792 +        selection/NameFinder.cpp, selection/NameFinder.hpp,
793 +        selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp,
794 +        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
795 +        selection/SelectionManager.cpp, selection/SelectionManager.hpp,
796 +        selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp,
797 +        selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp,
798 +        types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h,
799 +        types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp,
800 +        types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp,
801 +        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
802 +        types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp,
803 +        types/CubicBondType.hpp, types/CubicTorsionType.hpp,
804 +        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
805 +        types/DirectionalAtomType.hpp, types/FixedBondType.hpp,
806 +        types/HarmonicBendType.hpp, types/HarmonicBondType.hpp,
807 +        types/MakeStamps.cpp, types/MakeStamps.hpp,
808 +        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
809 +        types/MorseBondType.hpp, types/OplsTorsionType.hpp,
810 +        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
811 +        types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp,
812 +        types/QuarticBondType.hpp, types/QuarticTorsionType.hpp,
813 +        types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
814 +        types/ShapeAtomType.cpp, types/ShapeAtomType.hpp,
815 +        types/TorsionStamp.cpp, types/TorsionStamp.hpp,
816 +        types/TorsionType.hpp, types/UreyBradleyBendType.hpp,
817 +        types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp,
818 +        utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp,
819 +        utils/GenericFactory.hpp, utils/LocalIndexManager.hpp,
820 +        utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp,
821 +        utils/NumericConstant.hpp, utils/OOPSEConstant.hpp,
822 +        utils/PropertyMap.cpp, utils/PropertyMap.hpp,
823 +        utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
824 +        utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp,
825 +        utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp,
826 +        utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp,
827 +        utils/any.hpp, utils/definitions.F90, utils/fError.c,
828 +        utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h,
829 +        utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h,
830 +        utils/residentMem.h, utils/simError.c, utils/simError.h,
831 +        utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp,
832 +        visitors/AtomData.hpp, visitors/AtomVisitor.cpp,
833 +        visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp,
834 +        visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp,
835 +        visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
836 +        visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp,
837 +        visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp,
838 +        visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has
839 +        been drafted to perform our indentation services
840 +
841 + 2005-04-15 17:03  gezelter
842 +
843 +        * configure, ac-tools/configure.in: Jedi mind-trick warning
844 +        messages have been added to make users ignore CGAL.
845 +
846 + 2005-04-15 13:41  tim
847 +
848 +        * make/Makefile.in: fix make install
849 +
850 + 2005-04-15 13:41  tim
851 +
852 +        * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile:
853 +        add  Makefile of samples
854 +
855 + 2005-04-15 13:33  tim
856 +
857 +        * samples/: lipid/Makefile, water/dimer/Makefile,
858 +        water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not
859 +        installed correctly
860 +
861 + 2005-04-14 16:41  gezelter
862 +
863 +        * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in,
864 +        make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl,
865 +        scripts/filepp, scripts/filepp.in: configure now searches for perl
866 +        to use with filepp
867 +
868 + 2005-04-14 16:20  gezelter
869 +
870 +        * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of
871 +        MoLocator
872 +
873 + 2005-04-14 14:12  gezelter
874 +
875 +        * LICENSE: [no log message]
876 +
877 + 2005-04-14 11:10  chuckv
878 +
879 +        * src/applications/nanoRodBuilder/nanorodBuilder.cpp:
880 +        nanorodbuilder now exit's when libCGAL is not present.
881 +
882 + 2005-04-14 10:20  tim
883 +
884 +        * src/io/make_nodes.h: fix one more warning message in make_nodes
885 +
886 + 2005-04-13 18:36  chuckv
887 +
888 +        * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed
889 +        interface name for SGI Compiler
890 +
891 + 2005-04-13 18:29  chrisfen
892 +
893 +        * samples/water/ssde/ssde.md: oops...  bad sample
894 +
895 + 2005-04-13 18:00  chuckv
896 +
897 +        * src/config.h.in: Change typo in CGAL.
898 +
899 + 2005-04-13 17:43  tim
900 +
901 +        * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp,
902 +        selection/SelectionCompiler.hpp: fix some warning messages
903 +
904 + 2005-04-13 17:30  gezelter
905 +
906 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
907 +        make/Makefile.in, src/config.h.in,
908 +        src/applications/nanoRodBuilder/Makefile,
909 +        src/applications/nanoRodBuilder/Makefile.in,
910 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL
911 +        checks
912 +
913 + 2005-04-13 15:36  chuckv
914 +
915 +        * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp,
916 +        DarkSide/LJ.F90, DarkSide/electrostatic.F90,
917 +        DarkSide/electrostatic_interface.F90,
918 +        DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90,
919 +        DarkSide/lj_interface.h, DarkSide/sticky.F90,
920 +        DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added
921 +        destroy methods for Fortran modules.
922 +
923 + 2005-04-13 15:17  chuckv
924 +
925 +        * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90,
926 +        shapes_interface.h: Added destroy method to clean up memory
927 +
928 + 2005-04-13 13:41  tim
929 +
930 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
931 +        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
932 +        io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp,
933 +        primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp,
934 +        types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are
935 +        fixed
936 +
937 + 2005-04-12 17:44  chuckv
938 +
939 +        * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed
940 +        for nanoRodBuilder.
941 +
942 + 2005-04-12 17:42  tim
943 +
944 +        * src/applications/: nanoRodBuilder/nanorodBuilder.cpp,
945 +        simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder
946 +        and simpleBuilder(forget to delete lattice)
947 +
948 + 2005-04-12 17:33  tim
949 +
950 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
951 +        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp:
952 +        refactory lattice
953 +
954 + 2005-04-12 17:07  tim
955 +
956 +        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp,
957 +        CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp,
958 +        Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory
959 +        LatticeFactory and LatticeCreator
960 +
961 + 2005-04-12 16:58  tim
962 +
963 +        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
964 +        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp,
965 +        brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
966 +        lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp,
967 +        lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp,
968 +        lattice/Makefile: refactory LatticeFactory and LatticeCreator
969 +
970 + 2005-04-12 16:28  gezelter
971 +
972 +        * src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp,
973 +        vector_class.F90: cleaned up vector_class memory leak fix by
974 +        deallocating in reverse order of how we allocated.  Also migrated
975 +        MoLocator into utils directory
976 +
977 + 2005-04-12 16:27  gezelter
978 +
979 +        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp,
980 +        Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
981 +        LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice
982 +        directory
983 +
984 + 2005-04-12 16:27  gezelter
985 +
986 +        * src/applications/: nanoRodBuilder/BaseLattice.cpp,
987 +        nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp,
988 +        nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp,
989 +        nanoRodBuilder/LatticeCreator.hpp,
990 +        nanoRodBuilder/LatticeFactory.cpp,
991 +        nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile,
992 +        nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp,
993 +        nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp,
994 +        simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
995 +        simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
996 +        simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
997 +        simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile,
998 +        simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp,
999 +        simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of
1000 +        these files are now redundant
1001 +
1002 + 2005-04-12 16:27  gezelter
1003 +
1004 +        * src/UseTheForce/DarkSide/: atype_interface.F90,
1005 +        atype_interface.h: cleaned up memory leak fix
1006 +
1007 + 2005-04-12 16:26  gezelter
1008 +
1009 +        * make/Makefile.in: added lattice subdirectory
1010 +
1011 + 2005-04-12 15:57  chrisfen
1012 +
1013 +        * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added
1014 +        a space by accident
1015 +
1016 + 2005-04-12 15:56  chrisfen
1017 +
1018 +        * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added
1019 +        quadrupole sample
1020 +
1021 + 2005-04-12 15:56  chrisfen
1022 +
1023 +        * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating
1024 +        samples
1025 +
1026 + 2005-04-12 13:30  tim
1027 +
1028 +        * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom
1029 +        type in fortran side
1030 +
1031 + 2005-04-12 12:45  chuckv
1032 +
1033 +        * src/utils/vector_class.F90: Further changes to vector_class
1034 +        destroy function.
1035 +
1036 + 2005-04-12 12:39  chuckv
1037 +
1038 +        * src/utils/vector_class.F90: Fixed pointer memory leak in
1039 +        vector_class.
1040 +
1041 + 2005-04-12 12:12  chuckv
1042 +
1043 +        * src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp,
1044 +        DarkSide/atype_interface.F90, DarkSide/atype_interface.h,
1045 +        DarkSide/eam.F90, DarkSide/eam_interface.F90,
1046 +        DarkSide/eam_interface.h: Updates to deallocate object in fortran.
1047 +
1048 + 2005-04-12 09:24  chrisfen
1049 +
1050 +        * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI
1051 +        output
1052 +
1053 + 2005-04-11 19:29  chuckv
1054 +
1055 +        * src/: UseTheForce/DarkSide/atype.F90,
1056 +        applications/nanoRodBuilder/Makefile: Changes to delete atypes...
1057 +
1058 + 2005-04-11 19:28  chuckv
1059 +
1060 +        * src/utils/vector_class.F90: Added code to delete vector.
1061 +
1062 + 2005-04-11 17:03  chuckv
1063 +
1064 +        * samples/metals/nanorod/: Au_nanoparticle.md,
1065 +        Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why
1066 +        aren't these here?
1067 +
1068 + 2005-04-11 16:58  tim
1069 +
1070 +        * src/io/basic_ifstrstream.hpp: avoid multiple inherit in
1071 +        basic_ifstrstream
1072 +
1073 + 2005-04-11 16:37  chuckv
1074 +
1075 +        * make/Makefile.in,
1076 +        src/applications/nanoRodBuilder/BaseLattice.cpp,
1077 +        src/applications/nanoRodBuilder/BaseLattice.hpp,
1078 +        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
1079 +        src/applications/nanoRodBuilder/GeometryBuilder.hpp,
1080 +        src/applications/nanoRodBuilder/Lattice.cpp,
1081 +        src/applications/nanoRodBuilder/Lattice.hpp,
1082 +        src/applications/nanoRodBuilder/LatticeCreator.cpp,
1083 +        src/applications/nanoRodBuilder/LatticeCreator.hpp,
1084 +        src/applications/nanoRodBuilder/LatticeFactory.cpp,
1085 +        src/applications/nanoRodBuilder/LatticeFactory.hpp,
1086 +        src/applications/nanoRodBuilder/Makefile,
1087 +        src/applications/nanoRodBuilder/MoLocator.cpp,
1088 +        src/applications/nanoRodBuilder/MoLocator.hpp,
1089 +        src/applications/nanoRodBuilder/nanoBuilder.ggo,
1090 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
1091 +        src/applications/nanoRodBuilder/nanorodBuilder.ggo,
1092 +        src/applications/nanoRodBuilder/nanorodBuilderCmd.c,
1093 +        src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing
1094 +        nanoRodBuilder application (may not work yet).  ((Doesn't work
1095 +        yet.)) (((May never work....)))
1096 +
1097 + 2005-04-11 15:54  tim
1098 +
1099 +        * src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete
1100 +        prepareVisitor in Dump2XYZ
1101 +
1102 + 2005-04-11 15:19  chrisfen
1103 +
1104 +        * src/UseTheForce/DarkSide/electrostatic.F90: fixing of the
1105 +        quadrupoles.  look!  it's divide by 3 like stone says!
1106 +
1107 + 2005-04-11 15:18  chrisfen
1108 +
1109 +        * forceFields/DUFF2.frc: fixing of the quadrupoles
1110 +
1111 + 2005-04-11 15:16  tim
1112 +
1113 +        * src/selection/Token.hpp: change the parameter name in
1114 +        constructors
1115 +
1116 + 2005-04-11 14:49  gezelter
1117 +
1118 +        * make/Makefile.in: One more bug fix for GNU make versions < 3.80
1119 +
1120 + 2005-04-11 14:06  gezelter
1121 +
1122 +        * make/Makefile.in: Fixed the uc and lc functions for GNU make
1123 +        versions < 3.80
1124 +
1125 + 2005-04-11 11:13  gezelter
1126 +
1127 +        * make/Makefile.in, src/UseTheForce/Makefile,
1128 +        src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added
1129 +        some stuff to clean out module files during "make clean"
1130 +
1131 + 2005-04-08 17:13  chrisfen
1132 +
1133 +        * src/UseTheForce/DarkSide/electrostatic.F90: quadrupole
1134 +        interactions should be working with a remaining question of
1135 +        interaction magnitude
1136 +
1137 + 2005-04-08 17:12  chrisfen
1138 +
1139 +        * samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with
1140 +        samples
1141 +
1142 + 2005-04-08 13:48  chrisfen
1143 +
1144 +        * samples/water/ssd/ssd.md: oops...  messed up a sample
1145 +
1146 + 2005-04-08 09:43  chrisfen
1147 +
1148 +        * src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix
1149 +        charge-dipole interactions
1150 +
1151 + 2005-04-08 09:42  chrisfen
1152 +
1153 +        * samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md,
1154 +        ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole
1155 +
1156 + 2005-04-08 09:41  chrisfen
1157 +
1158 +        * forceFields/DUFF2.frc: added Cl- and Na+
1159 +
1160 + 2005-04-06 18:59  tim
1161 +
1162 +        * src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser
1163 +
1164 + 2005-04-05 18:09  tim
1165 +
1166 +        * src/selection/: NameFinder.cpp, SelectionCompiler.cpp,
1167 +        SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-'
1168 +        in atom type name;clean the code a little bit
1169 +
1170 + 2005-03-29 16:00  tim
1171 +
1172 +        * src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug
1173 +        in converting rotation matrix to quaternion
1174 +
1175 + 2005-03-28 17:41  tim
1176 +
1177 +        * src/visitors/LipidTransVisitor.cpp: fixed the wrapping
1178 +
1179 + 2005-03-28 17:30  tim
1180 +
1181 +        * src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do
1182 +        the wrapping
1183 +
1184 + 2005-03-28 10:54  tim
1185 +
1186 +        * src/applications/staticProps/GofXyz.cpp: fix a bug in getting the
1187 +        dimension of histogram
1188 +
1189 + 2005-03-22 11:38  tim
1190 +
1191 +        * make/Makefile.in, src/applications/dump2Xyz/Makefile,
1192 +        src/applications/dynamicProps/Makefile,
1193 +        src/applications/oopse/Makefile,
1194 +        src/applications/simpleBuilder/Makefile,
1195 +        src/applications/staticProps/Makefile: avoid building parallel
1196 +        executable for dump2XYZ, simpleBuilder, staticProps and
1197 +        dynamicProps
1198 +
1199 + 2005-03-21 17:34  chrisfen
1200 +
1201 +        * forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the
1202 +        forcefield files
1203 +
1204 + 2005-03-21 15:51  chrisfen
1205 +
1206 +        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
1207 +        DarkSide/reactionField.F90: Make sure electrostatic_module provides
1208 +        data for reaction_field
1209 +
1210 + 2005-03-21 15:50  chrisfen
1211 +
1212 +        * forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff.  HE
1213 +        WILL CHANGE THIS BACK, RIGHT?
1214 +
1215 + 2005-03-21 14:23  gezelter
1216 +
1217 +        * src/UseTheForce/DarkSide/electrostatic.F90: constant back to
1218 +        correct value
1219 +
1220 + 2005-03-21 14:22  gezelter
1221 +
1222 +        * make/Makefile.in: fixed an install-related bug.
1223 +        $(InstallCommand) had been set to $(InstallData)
1224 +
1225 + 2005-03-15 09:21  gezelter
1226 +
1227 +        * src/integrators/Integrator.cpp: VelocityVerletIntegrator already
1228 +        deletes and Nullifies restWriter, so Integrator shouldn't do it.
1229 +
1230 + 2005-03-15 09:20  gezelter
1231 +
1232 +        * src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos
1233 +
1234 + 2005-03-13 02:39  gezelter
1235 +
1236 +        * src/UseTheForce/DarkSide/electrostatic.F90: first run at
1237 +        charge-quadrupole interactions
1238 +
1239 + 2005-03-12 14:12  chrisfen
1240 +
1241 +        * samples/: Makefile.in, thermoIntegration/liquid/Makefile,
1242 +        thermoIntegration/solid/Makefile: forgot a couple of makefiles
1243 +
1244 + 2005-03-12 14:05  chrisfen
1245 +
1246 +        * samples/thermoIntegration/liquid/ssde.in,
1247 +        samples/thermoIntegration/liquid/ssde.md,
1248 +        samples/thermoIntegration/liquid/water.md,
1249 +        samples/thermoIntegration/solid/idealCrystal.in,
1250 +        samples/thermoIntegration/solid/ssde.in,
1251 +        samples/thermoIntegration/solid/ssde.md,
1252 +        samples/thermoIntegration/solid/ssde.zang0,
1253 +        samples/thermoIntegration/solid/water.md,
1254 +        samples/water/tip3p_ice/tp3.md,
1255 +        src/UseTheForce/DarkSide/sticky.F90,
1256 +        src/restraints/ThermoIntegrationForceManager.cpp: added some
1257 +        samples
1258 +
1259 + 2005-03-11 12:50  tim
1260 +
1261 +        * src/: brains/SimCreator.cpp,
1262 +        io/MultipoleAtomTypesSectionParser.cpp: fix a typo in
1263 +        MultipoleAtomTypesSectionParser
1264 +
1265 + 2005-03-11 10:55  tim
1266 +
1267 +        * src/brains/SimInfo.cpp: pairs inside cutoff group should not be
1268 +        excluded
1269 +
1270 + 2005-03-11 10:53  gezelter
1271 +
1272 +        * src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for
1273 +        quadrupoles
1274 +
1275 + 2005-03-11 10:52  gezelter
1276 +
1277 +        * forceFields/DUFF2.frc: quadrupoles for SSD models
1278 +
1279 + 2005-03-11 10:00  tim
1280 +
1281 +        * ChangeLog, doc/SelectionExpression.html,
1282 +        doc/classoopse_1_1StuntDouble.png, doc/definition.jpg,
1283 +        doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png,
1284 +        src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp,
1285 +        src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp,
1286 +        src/selection/TokenMap.cpp: clean up SimInfo; modify the images of
1287 +        SelectionExpression.html
1288 +
1289 + 2005-03-10 19:43  chrisfen
1290 +
1291 +        * samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md,
1292 +        src/io/RestReader.cpp, src/restraints/Restraints.cpp,
1293 +        src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in
1294 +        MPI restraints
1295 +
1296 + 2005-03-10 18:56  tim
1297 +
1298 +        * doc/SelectionExpression.html, src/brains/SimInfo.cpp,
1299 +        src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody
1300 +        and cutoff group
1301 +
1302 + 2005-03-10 17:06  gezelter
1303 +
1304 +        * src/types/MorseBondType.hpp: fixed a doxygen problem
1305 +
1306 + 2005-03-10 16:51  gezelter
1307 +
1308 +        * samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with
1309 +        the split dipole test cases
1310 +
1311 + 2005-03-10 16:51  gezelter
1312 +
1313 +        * doc/SelectionExpression.html: updated some documentation
1314 +
1315 + 2005-03-10 15:40  gezelter
1316 +
1317 +        * src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp,
1318 +        Makefile: LinkedList removal project starts now
1319 +
1320 + 2005-03-10 15:28  tim
1321 +
1322 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
1323 +        io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp:
1324 +        using map to replace link list
1325 +
1326 + 2005-03-10 14:11  tim
1327 +
1328 +        * samples/dipole/: splitInWater.in, splitInWater.md: adding test
1329 +        case  of split dipole
1330 +
1331 + 2005-03-10 14:10  chrisfen
1332 +
1333 +        * samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp,
1334 +        src/io/RestWriter.cpp,
1335 +        src/restraints/ThermoIntegrationForceManager.cpp: Oops...  MPI now
1336 +        builds...
1337 +
1338 + 2005-03-10 13:44  tim
1339 +
1340 +        * samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in,
1341 +        split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md:
1342 +        adding test case for split dipole
1343 +
1344 + 2005-03-10 12:54  gezelter
1345 +
1346 +        * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side
1347 +        support for split dipoles
1348 +
1349 + 2005-03-10 11:27  chrisfen
1350 +
1351 +        * samples/water/tip3p_ice/tp3.md,
1352 +        src/restraints/ThermoIntegrationForceManager.cpp: fixes to
1353 +        restraints
1354 +
1355 + 2005-03-10 11:15  chrisfen
1356 +
1357 +        * samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp,
1358 +        src/UseTheForce/ForceFields.hpp,
1359 +        src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints
1360 +
1361 + 2005-03-10 11:14  tim
1362 +
1363 +        * ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc,
1364 +        src/io/MultipoleAtomTypesSectionParser.cpp,
1365 +        src/selection/SelectionEvaluator.cpp: minor change
1366 +
1367   2005-03-10 10:10  chrisfen
1368  
1369          * make/Makefile.in, samples/water/tip3p_ice/tp3.md,
# Line 274 | Line 1640
1640          adding basic_teebuf which can operate on multiple stream
1641          simutaneously.
1642  
1643 + 2005-02-22 14:26  chrisfen
1644 +
1645 +        * samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf
1646 +        sample
1647 +
1648   2005-02-22 13:56  tim
1649  
1650          * src/: UseTheForce/DarkSide/reactionField.F90,
# Line 1479 | Line 2850
2850  
2851   2005-01-11 10:52  tim
2852  
2853 <        * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
2853 >        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
2854          on branch new_design.
2855  
2856   2005-01-11 10:52  tim
2857  
2858 <        * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
2858 >        * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
2859 >        on branch new_design.
2860  
2861   2005-01-11 10:52  tim
2862  
2863 <        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
1492 <        on branch new_design.
2863 >        * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
2864  
2865   2005-01-11 10:47  tim
2866  
# Line 1557 | Line 2928
2928  
2929   2005-01-07 16:50  tim
2930  
2931 +        * src/constraints/ZconstraintForceManager.cpp: file
2932 +        ZconstraintForceManager.cpp was initially added on branch
2933 +        new_design.
2934 +
2935 + 2005-01-07 16:50  tim
2936 +
2937 +        * src/constraints/ZconstraintForceManager.hpp: file
2938 +        ZconstraintForceManager.hpp was initially added on branch
2939 +        new_design.
2940 +
2941 + 2005-01-07 16:50  tim
2942 +
2943          * src/: applications/simpleBuilder/BaseLattice.hpp,
2944          applications/simpleBuilder/Lattice.hpp,
2945          applications/simpleBuilder/LatticeCreator.hpp,
# Line 1574 | Line 2957
2957          * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was
2958          initially added on branch new_design.
2959  
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 –
2960   2005-01-06 17:31  tim
2961  
2962          * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
# Line 1622 | Line 2993
2993  
2994   2005-01-05 12:35  tim
2995  
2996 +        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
2997 +        added on branch new_design.
2998 +
2999 + 2005-01-05 12:35  tim
3000 +
3001          * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
3002          Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp,
3003          MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp,
# Line 1630 | Line 3006
3006  
3007   2005-01-05 12:35  tim
3008  
3009 <        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
3010 <        added on branch new_design.
3009 >        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
3010 >        was initially added on branch new_design.
3011  
3012   2005-01-05 12:35  tim
3013  
3014 <        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
3014 >        * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
3015          was initially added on branch new_design.
3016  
3017   2005-01-05 12:35  tim
3018  
3019 <        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
3019 >        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
3020          was initially added on branch new_design.
3021  
3022   2005-01-05 12:35  tim
3023  
3024          * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially
3025          added on branch new_design.
1650 –
1651 – 2005-01-05 12:35  tim
1652 –
1653 –        * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
1654 –        was initially added on branch new_design.
3026  
3027   2005-01-04 17:18  tim
3028  
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 –
3029          * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
3030          brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp,
3031          brains/Thermo.cpp, constraints/ConstraintPair.hpp,
# Line 1671 | Line 3037
3037  
3038   2005-01-04 17:18  tim
3039  
3040 <        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
3041 <        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
1676 <        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
1677 <        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
1678 <
1679 < 2005-01-04 17:18  tim
1680 <
1681 <        * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
1682 <        was initially added on branch new_design.
3040 >        * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was
3041 >        initially added on branch new_design.
3042  
3043   2005-01-04 17:18  tim
3044  
# Line 1690 | Line 3049
3049  
3050          * src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was
3051          initially added on branch new_design.
3052 +
3053 + 2005-01-04 17:18  tim
3054 +
3055 +        * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
3056 +        was initially added on branch new_design.
3057 +
3058 + 2005-01-04 17:18  tim
3059 +
3060 +        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
3061 +        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
3062 +        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
3063 +        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
3064  
3065   2005-01-04 17:18  tim
3066  
# Line 2011 | Line 3382
3382  
3383   2004-12-02 19:26  tim
3384  
3385 +        * src/utils/Trim.cpp: file Trim.cpp was initially added on branch
3386 +        new_design.
3387 +
3388 + 2004-12-02 19:26  tim
3389 +
3390          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3391          UseTheForce/ForceFieldCreator.cpp,
3392          UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp,
# Line 2020 | Line 3396
3396          utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a
3397          bug in countTokens in StringTokenizer
3398  
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 –
3399   2004-12-02 19:06  tim
3400  
3401          * forceFields/newDUFF.frc: minor fix
# Line 2035 | Line 3406
3406  
3407   2004-12-02 17:15  tim
3408  
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 –
3409          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3410          UseTheForce/ForceFieldCreator.cpp,
3411          UseTheForce/ForceFieldCreator.hpp,
# Line 2070 | Line 3426
3426   2004-12-02 17:15  tim
3427  
3428          * src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp
3429 +        was initially added on branch new_design.
3430 +
3431 + 2004-12-02 17:15  tim
3432 +
3433 +        * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp
3434 +        was initially added on branch new_design.
3435 +
3436 + 2004-12-02 17:15  tim
3437 +
3438 +        * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp
3439          was initially added on branch new_design.
3440  
3441 + 2004-12-02 17:15  tim
3442 +
3443 +        * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp
3444 +        was initially added on branch new_design.
3445 +
3446   2004-12-02 11:53  tim
3447  
3448          * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp,
# Line 2230 | Line 3601
3601  
3602   2004-12-01 19:09  tim
3603  
3604 <        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
3605 <        was initially added on branch new_design.
3604 >        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
3605 >        branch new_design.
3606 >
3607 > 2004-12-01 19:09  tim
3608 >
3609 >        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
3610 >        branch new_design.
3611  
3612   2004-12-01 19:09  tim
3613  
# Line 2247 | Line 3623
3623  
3624   2004-12-01 19:09  tim
3625  
3626 <        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
3627 <        branch new_design.
3626 >        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
3627 >        was initially added on branch new_design.
3628  
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 –
3629   2004-12-01 17:45  tim
3630  
3631          * src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp,
# Line 2353 | Line 3724
3724  
3725   2004-11-30 14:58  tim
3726  
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 –
3727          * src/: brains/Exclude.cpp, brains/Exclude.hpp,
3728          brains/ForceManager.cpp, brains/ForceManager.hpp,
3729          brains/MoleculeCreator.cpp, brains/SimCreator.hpp,
# Line 2366 | Line 3732
3732          brains/SnapShot.cpp, brains/Stats.cpp, brains/Stats.hpp,
3733          brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile,
3734          math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo
3735 +
3736 + 2004-11-30 14:58  tim
3737  
3738 +        * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially
3739 +        added on branch new_design.
3740 +
3741   2004-11-30 12:54  tim
3742  
3743          * src/: primitives/Bend.hpp, primitives/Bond.hpp,
# Line 2375 | Line 3746
3746  
3747   2004-11-30 00:03  tim
3748  
3749 <        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
3750 <        LocalndexManager.hpp to LocalIndexManager.hpp
3749 >        * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
3750 >        initially added on branch new_design.
3751  
3752   2004-11-30 00:03  tim
3753  
3754 <        * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
3755 <        initially added on branch new_design.
3754 >        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
3755 >        LocalndexManager.hpp to LocalIndexManager.hpp
3756  
3757   2004-11-29 23:43  tim
3758  
# Line 2509 | Line 3880
3880  
3881   2004-11-25 15:18  tim
3882  
3883 +        * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was
3884 +        initially added on branch new_design.
3885 +
3886 + 2004-11-25 15:18  tim
3887 +
3888          * src/: io/AtomTypesSectionParser.cpp,
3889          io/BondTypesSectionParser.cpp,
3890          io/DirectionalAtomTypesSectionParser.cpp,
# Line 2521 | Line 3897
3897          * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was
3898          initially added on branch new_design.
3899  
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 –
3900   2004-11-24 17:12  tim
3901  
3902          * src/: io/AtomTypesSectionParser.cpp,
# Line 2638 | Line 4009
4009  
4010   2004-11-23 12:53  tim
4011  
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 –
4012          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
4013          UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
4014          applications/simpleBuilder/simpleBuilder.cpp,
# Line 2661 | Line 4026
4026          ElectrostaticAtomTypesSectionParser.hpp was initially added on
4027          branch new_design.
4028  
4029 < 2004-11-23 01:03  tim
4029 > 2004-11-23 12:53  tim
4030  
4031 <        * src/io/EAMAtomTypesSectionParser.cpp: file
4032 <        EAMAtomTypesSectionParser.cpp was initially added on branch
4033 <        new_design.
4031 >        * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
4032 >        ElectrostaticAtomTypesSectionParser.cpp was initially added on
4033 >        branch new_design.
4034  
4035   2004-11-23 01:03  tim
4036  
# Line 2676 | Line 4041
4041  
4042   2004-11-23 01:03  tim
4043  
4044 +        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
4045 +        was initially added on branch new_design.
4046 +
4047 + 2004-11-23 01:03  tim
4048 +
4049          * src/io/EAMAtomTypesSectionParser.hpp: file
4050          EAMAtomTypesSectionParser.hpp was initially added on branch
4051          new_design.
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.
4055 >        * src/io/EAMAtomTypesSectionParser.cpp: file
4056 >        EAMAtomTypesSectionParser.cpp was initially added on branch
4057 >        new_design.
4058  
4059   2004-11-22 23:35  tim
4060  
4061 <        * src/io/TorsionTypesSectionParser.cpp: file
4062 <        TorsionTypesSectionParser.cpp was initially added on branch
4061 >        * src/io/TorsionTypesSectionParser.hpp: file
4062 >        TorsionTypesSectionParser.hpp was initially added on branch
4063          new_design.
4064  
4065   2004-11-22 23:35  tim
# Line 2699 | Line 4070
4070  
4071   2004-11-22 23:35  tim
4072  
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 –
4073          * src/io/BondTypesSectionParser.hpp: file
4074          BondTypesSectionParser.hpp was initially added on branch
4075          new_design.
4076  
4077   2004-11-22 23:35  tim
4078  
4079 <        * src/io/TorsionTypesSectionParser.hpp: file
4080 <        TorsionTypesSectionParser.hpp was initially added on branch
4079 >        * src/io/BondTypesSectionParser.cpp: file
4080 >        BondTypesSectionParser.cpp was initially added on branch
4081          new_design.
4082  
4083   2004-11-22 23:35  tim
4084  
4085 <        * src/io/BendTypesSectionParser.cpp: file
4086 <        BendTypesSectionParser.cpp was initially added on branch
4085 >        * src/io/TorsionTypesSectionParser.cpp: file
4086 >        TorsionTypesSectionParser.cpp was initially added on branch
4087          new_design.
4088  
4089   2004-11-22 23:35  tim
# Line 2729 | Line 4094
4094          BondTypesSectionParser, BendTypesSectionParser and
4095          TorsionTypeSectionParser
4096  
4097 + 2004-11-22 23:35  tim
4098 +
4099 +        * src/io/BendTypesSectionParser.cpp: file
4100 +        BendTypesSectionParser.cpp was initially added on branch
4101 +        new_design.
4102 +
4103   2004-11-22 18:04  tim
4104  
4105          * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in
# Line 2736 | Line 4107
4107  
4108   2004-11-22 18:02  tim
4109  
4110 +        * src/io/: DirectionalAtomTypesParser.hpp,
4111 +        DirectionalAtomTypesSectionParser.hpp: adding section parsers
4112 +
4113 + 2004-11-22 18:02  tim
4114 +
4115          * src/io/DirectionalAtomTypesSectionParser.hpp: file
4116          DirectionalAtomTypesSectionParser.hpp was initially added on branch
4117          new_design.
4118  
4119 < 2004-11-22 18:02  tim
4119 > 2004-11-22 15:55  tim
4120  
4121 <        * src/io/: DirectionalAtomTypesParser.hpp,
4122 <        DirectionalAtomTypesSectionParser.hpp: adding section parsers
4121 >        * src/io/DipoleAtomTypesSectionParser.hpp: file
4122 >        DipoleAtomTypesSectionParser.hpp was initially added on branch
4123 >        new_design.
4124  
4125   2004-11-22 15:55  tim
4126  
4127 <        * src/io/DirectionalAtomTypesParser.hpp: file
4128 <        DirectionalAtomTypesParser.hpp was initially added on branch
4127 >        * src/io/AtomTypesSectionParser.hpp: file
4128 >        AtomTypesSectionParser.hpp was initially added on branch
4129          new_design.
4130  
4131   2004-11-22 15:55  tim
# Line 2759 | Line 4136
4136  
4137   2004-11-22 15:55  tim
4138  
4139 <        * src/io/ChargeAtomTypesSectionParser.hpp: file
4140 <        ChargeAtomTypesSectionParser.hpp was initially added on branch
4139 >        * src/io/StickyAtomTypesSectionParser.cpp: file
4140 >        StickyAtomTypesSectionParser.cpp was initially added on branch
4141          new_design.
4142  
4143   2004-11-22 15:55  tim
4144  
4145 <        * src/io/DirectionalAtomTypesSectionParser.cpp: file
4146 <        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
4145 >        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
4146 >        LennardJonesAtomTypesSectionParser.hpp was initially added on
4147          branch new_design.
4148  
4149   2004-11-22 15:55  tim
4150  
4151 <        * src/io/DipoleAtomTypesSectionParser.cpp: file
4152 <        DipoleAtomTypesSectionParser.cpp was initially added on branch
4151 >        * src/io/HarmonicBondTypesSectionParser.cpp: file
4152 >        HarmonicBondTypesSectionParser.cpp was initially added on branch
4153          new_design.
4154  
4155   2004-11-22 15:55  tim
4156  
4157 <        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
4158 <        brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
4159 <        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
4157 >        * src/io/DirectionalAtomTypesSectionParser.cpp: file
4158 >        DirectionalAtomTypesSectionParser.cpp was initially added on branch
4159 >        new_design.
4160  
4161   2004-11-22 15:55  tim
4162  
4163 <        * src/io/DipoleAtomTypesSectionParser.hpp: file
4164 <        DipoleAtomTypesSectionParser.hpp was initially added on branch
2810 <        new_design.
4163 >        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
4164 >        was initially added on branch new_design.
4165  
4166   2004-11-22 15:55  tim
4167  
4168 <        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
4169 <        added on branch new_design.
4168 >        * src/io/AtomTypesSectionParser.cpp: file
4169 >        AtomTypesSectionParser.cpp was initially added on branch
4170 >        new_design.
4171  
4172   2004-11-22 15:55  tim
4173  
4174 <        * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
4175 <        was initially added on branch new_design.
4174 >        * src/io/ChargeAtomTypesSectionParser.cpp: file
4175 >        ChargeAtomTypesSectionParser.cpp was initially added on branch
4176 >        new_design.
4177  
4178   2004-11-22 15:55  tim
4179  
4180 <        * src/io/AtomTypesSectionParser.cpp: file
4181 <        AtomTypesSectionParser.cpp was initially added on branch
4180 >        * src/io/DipoleAtomTypesSectionParser.cpp: file
4181 >        DipoleAtomTypesSectionParser.cpp was initially added on branch
4182          new_design.
4183  
4184   2004-11-22 15:55  tim
4185  
4186 <        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
4187 <        LennardJonesAtomTypesSectionParser.hpp was initially added on
4186 >        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
4187 >        LennardJonesAtomTypesSectionParser.cpp was initially added on
4188          branch new_design.
4189  
4190   2004-11-22 15:55  tim
4191  
4192 <        * src/io/HarmonicBondTypesSectionParser.cpp: file
4193 <        HarmonicBondTypesSectionParser.cpp was initially added on branch
4192 >        * src/io/ChargeAtomTypesSectionParser.hpp: file
4193 >        ChargeAtomTypesSectionParser.hpp was initially added on branch
4194          new_design.
4195  
4196   2004-11-22 15:55  tim
4197  
4198 <        * src/io/AtomTypesSectionParser.hpp: file
4199 <        AtomTypesSectionParser.hpp was initially added on branch
4198 >        * src/io/StickyAtomTypesSectionParser.hpp: file
4199 >        StickyAtomTypesSectionParser.hpp was initially added on branch
4200          new_design.
4201  
4202   2004-11-22 15:55  tim
4203  
4204 <        * src/io/StickyAtomTypesSectionParser.cpp: file
4205 <        StickyAtomTypesSectionParser.cpp was initially added on branch
2850 <        new_design.
4204 >        * src/io/SectionParser.hpp: file SectionParser.hpp was initially
4205 >        added on branch new_design.
4206  
4207   2004-11-22 15:55  tim
4208  
4209 <        * src/io/SectionParser.hpp: file SectionParser.hpp was initially
4210 <        added on branch new_design.
4209 >        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
4210 >        brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
4211 >        brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp,
4212 >        integrators/NVT.hpp, io/AtomTypesSectionParser.cpp,
4213 >        io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
4214 >        io/ChargeAtomTypesSectionParser.hpp,
4215 >        io/DipoleAtomTypesSectionParser.cpp,
4216 >        io/DipoleAtomTypesSectionParser.hpp,
4217 >        io/DirectionalAtomTypesParser.hpp,
4218 >        io/DirectionalAtomTypesSectionParser.cpp,
4219 >        io/HarmonicBondTypesSectionParser.cpp,
4220 >        io/HarmonicBondTypesSectionParser.hpp,
4221 >        io/LennardJonesAtomTypesSectionParser.cpp,
4222 >        io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp,
4223 >        io/SectionParser.hpp, io/SectionParserManager.cpp,
4224 >        io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp,
4225 >        io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp,
4226 >        types/AtomType.hpp, types/DirectionalAtomType.hpp,
4227 >        utils/GenericData.hpp: adding section parsers
4228  
4229   2004-11-22 15:55  tim
4230  
4231 <        * src/io/ChargeAtomTypesSectionParser.cpp: file
4232 <        ChargeAtomTypesSectionParser.cpp was initially added on branch
4231 >        * src/io/DirectionalAtomTypesParser.hpp: file
4232 >        DirectionalAtomTypesParser.hpp was initially added on branch
4233          new_design.
4234  
4235   2004-11-22 15:55  tim
4236  
4237 <        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
4237 >        * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
4238          was initially added on branch new_design.
4239  
4240   2004-11-22 15:55  tim
4241  
4242 <        * src/io/StickyAtomTypesSectionParser.hpp: file
4243 <        StickyAtomTypesSectionParser.hpp was initially added on branch
2872 <        new_design.
4242 >        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
4243 >        added on branch new_design.
4244  
4245   2004-11-19 17:12  tim
4246  
4247 +        * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
4248 +        added on branch new_design.
4249 +
4250 + 2004-11-19 17:12  tim
4251 +
4252          * src/: brains/SimState.cpp, brains/SimState.hpp,
4253          io/InitializeFromFile.cpp, types/FixBondType.hpp,
4254          types/FixedBondType.hpp: remove more useless files
4255  
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 –
4256   2004-11-19 16:47  tim
4257  
4258          * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp,
# Line 2890 | Line 4261
4261  
4262   2004-11-19 16:38  tim
4263  
4264 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
4265 +        UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp,
4266 +        integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp,
4267 +        integrators/NVT.hpp: refactory integrator
4268 +
4269 + 2004-11-19 16:38  tim
4270 +
4271          * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on
4272          branch new_design.
4273  
4274   2004-11-19 16:38  tim
4275  
4276 <        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
4277 <        on branch new_design.
4276 >        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
4277 >        branch new_design.
4278  
4279   2004-11-19 16:38  tim
4280  
# Line 2905 | Line 4283
4283  
4284   2004-11-19 16:38  tim
4285  
4286 <        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
4287 <        branch new_design.
4286 >        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
4287 >        on branch new_design.
4288  
4289   2004-11-19 16:38  tim
4290  
4291 <        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
4291 >        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
4292          branch new_design.
4293  
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 –
4294   2004-11-19 15:37  tim
4295  
4296          * forceFields/newDUFF.frc: new DUFF forcefield
4297  
4298   2004-11-19 15:23  tim
4299  
4300 +        * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
4301 +        branch new_design.
4302 +
4303 + 2004-11-19 15:23  tim
4304 +
4305          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp,
4306          UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp,
4307          utils/TypeContainer.hpp: add EAM
# Line 2935 | Line 4311
4311          * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on
4312          branch new_design.
4313  
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 –
4314   2004-11-19 13:02  tim
4315  
4316          * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except
# Line 2947 | Line 4318
4318  
4319   2004-11-19 12:56  tim
4320  
4321 <        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
4321 >        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
4322          was initially added on branch new_design.
4323  
4324   2004-11-19 12:56  tim
4325  
4326 <        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
4326 >        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
4327          was initially added on branch new_design.
4328  
4329   2004-11-19 12:56  tim
# Line 2977 | Line 4348
4348  
4349   2004-11-18 18:26  tim
4350  
4351 +        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
4352 +        initially added on branch new_design.
4353 +
4354 + 2004-11-18 18:26  tim
4355 +
4356          * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp,
4357          integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
4358          integrators/VelocityVerletIntegrator.cpp,
# Line 2987 | Line 4363
4363          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding
4364          DUFF parser
4365  
2990 – 2004-11-18 18:26  tim
2991 –
2992 –        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
2993 –        initially added on branch new_design.
2994 –
4366   2004-11-18 16:42  tim
4367  
4368          * forceFields/newDUFF.frc: adding new format DUFF force field
# Line 3003 | Line 4374
4374  
4375   2004-11-18 00:42  tim
4376  
4377 <        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
4377 >        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
4378          initially added on branch new_design.
4379  
4380   2004-11-18 00:42  tim
4381  
4382 <        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
4382 >        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
4383          initially added on branch new_design.
4384  
4385   2004-11-18 00:42  tim
# Line 3051 | Line 4422
4422  
4423   2004-11-17 16:47  tim
4424  
4425 +        * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp
4426 +        was initially added on branch new_design.
4427 +
4428 + 2004-11-17 16:47  tim
4429 +
4430          * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially
4431          added on branch new_design.
4432  
4433   2004-11-17 16:47  tim
4434  
4435 +        * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially
4436 +        added on branch new_design.
4437 +
4438 + 2004-11-17 16:47  tim
4439 +
4440          * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was
4441          initially added on branch new_design.
4442  
4443   2004-11-17 16:47  tim
4444  
4445 <        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
4445 >        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
4446          initially added on branch new_design.
4447  
4448   2004-11-17 16:47  tim
4449  
4450 <        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
4450 >        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
4451          initially added on branch new_design.
4452  
4453   2004-11-17 16:47  tim
# Line 3086 | Line 4467
4467          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp:
4468          UreyBradleyBend and GhostBend
4469  
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 –
4470   2004-11-17 13:58  tim
4471  
4472          * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp
# Line 3103 | Line 4474
4474  
4475   2004-11-17 13:58  tim
4476  
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 –
4477          * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp
4478          was initially added on branch new_design.
4479  
# Line 3120 | Line 4486
4486          types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types
4487          stuff and Chebyshev Polynomial
4488  
4489 < 2004-11-17 01:37  tim
4489 > 2004-11-17 13:58  tim
4490  
4491 <        * 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
4491 >        * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
4492          initially added on branch new_design.
4493  
4494   2004-11-17 01:37  tim
4495  
4496 <        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
4497 <        initially added on branch new_design.
4496 >        * src/types/PolynomialTorsionType.hpp: file
4497 >        PolynomialTorsionType.hpp was initially added on branch new_design.
4498  
4499   2004-11-17 01:37  tim
4500  
# Line 3142 | Line 4503
4503  
4504   2004-11-17 01:37  tim
4505  
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 –
4506          * src/: math/Polynomial.hpp, primitives/Bend.cpp,
4507          primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp,
4508          types/BondType.hpp, types/CharmmTorsionType.cpp,
# Line 3159 | Line 4515
4515          CharmmTorsionType. Need to refine the design and add document for
4516          them
4517  
4518 + 2004-11-17 01:37  tim
4519 +
4520 +        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
4521 +        initially added on branch new_design.
4522 +
4523 + 2004-11-17 01:37  tim
4524 +
4525 +        * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was
4526 +        initially added on branch new_design.
4527 +
4528 + 2004-11-17 01:37  tim
4529 +
4530 +        * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
4531 +        initially added on branch new_design.
4532 +
4533   2004-11-16 20:11  tim
4534  
4535          * src/types/: BendType.hpp, PolynomialBondType.hpp,
# Line 3171 | Line 4542
4542  
4543   2004-11-16 18:20  tim
4544  
3174 –        * src/math/Polynomial.hpp: Adding Polynomial class
3175 –
3176 – 2004-11-16 18:20  tim
3177 –
4545          * src/math/Polynomial.hpp: file Polynomial.hpp was initially added
4546          on branch new_design.
4547  
4548 < 2004-11-16 17:04  gezelter
4548 > 2004-11-16 18:20  tim
4549  
4550 <        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
3184 <        initially added on branch new_design.
4550 >        * src/math/Polynomial.hpp: Adding Polynomial class
4551  
4552   2004-11-16 17:04  gezelter
4553  
# Line 3190 | Line 4556
4556  
4557   2004-11-16 17:04  gezelter
4558  
4559 +        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
4560 +        initially added on branch new_design.
4561 +
4562 + 2004-11-16 17:04  gezelter
4563 +
4564          * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp,
4565          MorseBondType.hpp, TorsionType.hpp: added some new stuff
4566  
# Line 3202 | Line 4573
4573  
4574   2004-11-15 21:07  tim
4575  
4576 +        * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
4577 +        branch new_design.
4578 +
4579 + 2004-11-15 21:07  tim
4580 +
4581          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
4582          UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp,
4583          utils/StringTokenizer.cpp: adding DUFF class; adding checking
4584          statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer
4585  
4586 < 2004-11-15 21:07  tim
4586 > 2004-11-15 18:00  tim
4587  
4588 <        * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
4589 <        branch new_design.
4588 >        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
4589 >        UseTheForce/ForceFieldFactory.cpp,
4590 >        UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp,
4591 >        UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp,
4592 >        types/AtomType.hpp: adding ForceFieldFactory and LJFF classes
4593  
4594   2004-11-15 18:00  tim
4595  
# Line 3219 | Line 4598
4598  
4599   2004-11-15 18:00  tim
4600  
4601 <        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
4602 <        branch new_design.
4601 >        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
4602 >        was initially added on branch new_design.
4603  
4604   2004-11-15 18:00  tim
4605  
4606 <        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
4607 <        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
4606 >        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
4607 >        branch new_design.
4608  
4609 < 2004-11-15 18:00  tim
4609 > 2004-11-15 13:02  tim
4610  
4611 <        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
4612 <        was initially added on branch new_design.
4611 >        * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was
4612 >        initially added on branch new_design.
4613  
4614   2004-11-15 13:02  tim
4615  
# Line 3247 | Line 4623
4623  
4624   2004-11-15 13:02  tim
4625  
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 –
4626          * src/: brains/SimInfo.cpp, brains/SimInfo.hpp,
4627          brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
4628          integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp,
# Line 3372 | Line 4743
4743  
4744          * src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation
4745          in progress
4746 +
4747 + 2004-11-09 18:11  tim
4748 +
4749 +        * src/brains/ForceManager.cpp: file ForceManager.cpp was initially
4750 +        added on branch new_design.
4751 +
4752 + 2004-11-09 18:11  tim
4753  
4754 +        * src/integrators/VelocityVerletIntegrator.cpp: file
4755 +        VelocityVerletIntegrator.cpp was initially added on branch
4756 +        new_design.
4757 +
4758   2004-11-09 18:11  tim
4759  
4760          * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp,
# Line 3389 | Line 4771
4771  
4772   2004-11-09 18:11  tim
4773  
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 –
4774          * src/integrators/NVE.cpp: file NVE.cpp was initially added on
4775          branch new_design.
4776  
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 –
4777   2004-11-08 20:08  tim
4778  
4779          * src/integrators/VelocityVerletIntegrator.hpp: file
# Line 3411 | Line 4782
4782  
4783   2004-11-08 20:08  tim
4784  
4785 +        * src/integrators/NVE.hpp: file NVE.hpp was initially added on
4786 +        branch new_design.
4787 +
4788 + 2004-11-08 20:08  tim
4789 +
4790          * src/: brains/Exclude.hpp, brains/Stats.hpp,
4791          integrators/Integrator.hpp, integrators/NVE.hpp,
4792          integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
4793          utils/TypeContainer.hpp: More to break
4794  
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 –
4795   2004-11-06 00:21  tim
4796  
4797          * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially
# Line 3435 | Line 4806
4806  
4807   2004-11-05 18:38  tim
4808  
4809 +        * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
4810 +        initially added on branch new_design.
4811 +
4812 + 2004-11-05 18:38  tim
4813 +
4814          * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was
4815          initially added on branch new_design.
4816  
# Line 3446 | Line 4822
4822          brains/SimInfo.hpp, primitives/Molecule.hpp,
4823          utils/LocalndexManager.hpp: Fix Exclude class etc.
4824  
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 –
4825   2004-11-05 16:45  chrisfen
4826  
4827          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
# Line 3488 | Line 4859
4859  
4860   2004-11-04 14:48  tim
4861  
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 –
4862          * src/brains/Stats.cpp: file Stats.cpp was initially added on
4863          branch new_design.
4864  
# Line 3502 | Line 4867
4867          * src/brains/Stats.hpp: file Stats.hpp was initially added on
4868          branch new_design.
4869  
4870 + 2004-11-04 14:48  tim
4871 +
4872 +        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
4873 +        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
4874 +        class
4875 +
4876   2004-11-04 11:22  gezelter
4877  
4878          * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp,
# Line 3576 | Line 4947
4947  
4948   2004-11-02 17:41  tim
4949  
4950 <        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
4951 <        branch new_design.
4950 >        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
4951 >        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
4952 >        Need unit test
4953  
4954   2004-11-02 17:41  tim
4955  
# Line 3586 | Line 4958
4958  
4959   2004-11-02 17:41  tim
4960  
4961 <        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
4962 <        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
3591 <        Need unit test
4961 >        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
4962 >        branch new_design.
4963  
4964   2004-11-02 11:59  tim
4965  
4966 <        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
4967 <        SimSnapshotManager.hpp: SimModel in progress
4966 >        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
4967 >        branch new_design.
4968  
4969   2004-11-02 11:59  tim
4970  
4971 <        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
4972 <        branch new_design.
4971 >        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
4972 >        SimSnapshotManager.hpp: SimModel in progress
4973  
4974   2004-11-02 10:28  chrisfen
4975  
# Line 3608 | Line 4979
4979  
4980   2004-11-02 10:27  tim
4981  
4982 <        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
4983 <        added on branch new_design.
4982 >        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
4983 >        functions for dealing with memory issue
4984  
4985   2004-11-02 10:27  tim
4986  
4987 <        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
4988 <        functions for dealing with memory issue
4987 >        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
4988 >        added on branch new_design.
4989  
4990   2004-11-02 10:23  tim
4991  
# Line 3643 | Line 5014
5014  
5015   2004-11-01 16:40  tim
5016  
5017 <        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
5018 <        branch new_design.
5017 >        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
5018 >        on branch new_design.
5019  
5020   2004-11-01 16:40  tim
5021  
5022 <        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
5023 <        version of Bond, Bend and Torsion.
5022 >        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
5023 >        branch new_design.
5024  
5025   2004-11-01 16:40  tim
5026  
# Line 3658 | Line 5029
5029  
5030   2004-11-01 16:40  tim
5031  
5032 <        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
5033 <        on branch new_design.
5032 >        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
5033 >        version of Bond, Bend and Torsion.
5034  
5035   2004-11-01 16:37  tim
5036  
# Line 3668 | Line 5039
5039  
5040   2004-11-01 16:37  tim
5041  
5042 <        * src/types/BondType.hpp: file BondType.hpp was initially added on
5043 <        branch new_design.
5042 >        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
5043 >        BondType, BendType, TorsionType
5044  
5045   2004-11-01 16:37  tim
5046  
# Line 3678 | Line 5049
5049  
5050   2004-11-01 16:37  tim
5051  
5052 <        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
5053 <        BondType, BendType, TorsionType
5052 >        * src/types/BondType.hpp: file BondType.hpp was initially added on
5053 >        branch new_design.
5054  
5055   2004-11-01 15:15  tim
5056  
# Line 4511 | Line 5882
5882          water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile,
5883          water/tip4p/Makefile, zcons/Makefile: fix Makefile under water
5884          directory
5885 +
5886 + 2004-10-11 09:23  tim
5887 +
5888 +        * samples/argon/Makefile: remove argon.dump and argon.eor from
5889 +        Makefile
5890  
5891   2004-10-09 01:01  tim
5892  
5893 <        * samples/: alkane/Makefile.in, lipid/Makefile.in,
5894 <        metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in
5893 >        * samples/: alkane/Makefile.in, argon/Makefile.in,
5894 >        lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in:
5895 >        Remove some Makefile.in
5896  
5897   2004-10-08 18:15  tim
5898  
# Line 4531 | Line 5908
5908  
5909   2004-10-08 17:04  tim
5910  
5911 <        * samples/: alkane/Makefile, lipid/Makefile, metals/Makefile,
5912 <        minimizer/Makefile, water/Makefile.in, water/dimer/Makefile,
5913 <        water/dimer/Makefile.in, water/spce/Makefile,
5911 >        * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile,
5912 >        metals/Makefile, minimizer/Makefile, water/Makefile.in,
5913 >        water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile,
5914          water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in,
5915          water/ssde/Makefile, water/ssde/Makefile.in,
5916          water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in,
# Line 5012 | Line 6389
6389          samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
6390          samples/alkane/Makefile.in, samples/alkane/alkanes.md,
6391          samples/alkane/butane.in, samples/alkane/butane.md,
6392 +        samples/argon/500.in, samples/argon/500.md,
6393 +        samples/argon/Makefile.in, samples/argon/ar864.in,
6394 +        samples/argon/ar864.md, samples/argon/argonNVT.in,
6395 +        samples/argon/argonNVT.md, samples/argon/lj.md,
6396          samples/lipid/5x5.in, samples/lipid/5x5.md,
6397          samples/lipid/Makefile.in, samples/lipid/lipid.md,
6398          samples/lipid/water.md, samples/minimizer/Makefile.in,
# Line 5184 | Line 6565
6565          samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
6566          samples/alkane/Makefile.in, samples/alkane/alkanes.md,
6567          samples/alkane/butane.in, samples/alkane/butane.md,
6568 +        samples/argon/500.in, samples/argon/500.md,
6569 +        samples/argon/Makefile.in, samples/argon/ar864.in,
6570 +        samples/argon/ar864.md, samples/argon/argonNVT.in,
6571 +        samples/argon/argonNVT.md, samples/argon/lj.md,
6572          samples/lipid/5x5.in, samples/lipid/5x5.md,
6573          samples/lipid/Makefile.in, samples/lipid/lipid.md,
6574          samples/lipid/water.md, samples/minimizer/Makefile.in,

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines