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Comparing trunk/OOPSE-3.0/ChangeLog (file contents):
Revision 2102 by tim, Thu Mar 10 16:14:07 2005 UTC vs.
Revision 2116 by tim, Fri Mar 11 15:00:20 2005 UTC

# Line 1 | Line 1
1 < 2005-03-10 10:10  chrisfen
1 > 2005-03-11 00:43  chrisfen
2  
3 +        * samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md,
4 +        src/io/RestReader.cpp, src/restraints/Restraints.cpp,
5 +        src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in
6 +        MPI restraints
7 +
8 + 2005-03-10 23:56  tim
9 +
10 +        * doc/SelectionExpression.html, src/brains/SimInfo.cpp,
11 +        src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody
12 +        and cutoff group
13 +
14 + 2005-03-10 22:06  gezelter
15 +
16 +        * src/types/MorseBondType.hpp: fixed a doxygen problem
17 +
18 + 2005-03-10 21:51  gezelter
19 +
20 +        * samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with
21 +        the split dipole test cases
22 +
23 + 2005-03-10 21:51  gezelter
24 +
25 +        * doc/SelectionExpression.html: updated some documentation
26 +
27 + 2005-03-10 20:40  gezelter
28 +
29 +        * src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp,
30 +        Makefile: LinkedList removal project starts now
31 +
32 + 2005-03-10 20:28  tim
33 +
34 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
35 +        io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp:
36 +        using map to replace link list
37 +
38 + 2005-03-10 19:11  tim
39 +
40 +        * samples/dipole/: splitInWater.in, splitInWater.md: adding test
41 +        case  of split dipole
42 +
43 + 2005-03-10 19:10  chrisfen
44 +
45 +        * samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp,
46 +        src/io/RestWriter.cpp,
47 +        src/restraints/ThermoIntegrationForceManager.cpp: Oops...  MPI now
48 +        builds...
49 +
50 + 2005-03-10 18:44  tim
51 +
52 +        * samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in,
53 +        split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md:
54 +        adding test case for split dipole
55 +
56 + 2005-03-10 17:54  gezelter
57 +
58 +        * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side
59 +        support for split dipoles
60 +
61 + 2005-03-10 16:27  chrisfen
62 +
63 +        * samples/water/tip3p_ice/tp3.md,
64 +        src/restraints/ThermoIntegrationForceManager.cpp: fixes to
65 +        restraints
66 +
67 + 2005-03-10 16:15  chrisfen
68 +
69 +        * samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp,
70 +        src/UseTheForce/ForceFields.hpp,
71 +        src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints
72 +
73 + 2005-03-10 16:14  tim
74 +
75 +        * ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc,
76 +        src/io/MultipoleAtomTypesSectionParser.cpp,
77 +        src/selection/SelectionEvaluator.cpp: minor change
78 +
79 + 2005-03-10 15:10  chrisfen
80 +
81          * make/Makefile.in, samples/water/tip3p_ice/tp3.md,
82          src/brains/SimCreator.cpp, src/brains/SimInfo.hpp,
83          src/integrators/Integrator.cpp, src/integrators/Integrator.hpp,
# Line 15 | Line 93
93          src/restraints/ThermoIntegrationForceManager.hpp: First commit of
94          the new restraints code
95  
96 < 2005-03-09 13:48  tim
96 > 2005-03-09 18:48  tim
97  
98          * src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding
99          IndexFinder
100  
101 < 2005-03-09 13:46  tim
101 > 2005-03-09 18:46  tim
102  
103          * src/: applications/dump2Xyz/Dump2XYZ.ggo,
104          applications/dump2Xyz/Dump2XYZCmd.c,
# Line 28 | Line 106
106          selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp:
107          fix compilation issue
108  
109 < 2005-03-09 12:58  tim
109 > 2005-03-09 17:58  tim
110  
111          * forceFields/DUFF2.frc, scripts/filepp,
112          src/UseTheForce/EAM_FF.cpp,
# Line 36 | Line 114
114          src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug
115          in SectionParser (lineNo is not updated)
116  
117 < 2005-03-09 12:30  tim
117 > 2005-03-09 17:30  tim
118  
119          * src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp,
120          applications/dump2Xyz/Dump2XYZ.ggo,
# Line 58 | Line 136
136          MultipoleAtomTypesSectionParser;remove print dipole option from
137          Dump2XYZ;
138  
139 < 2005-03-09 12:28  tim
139 > 2005-03-09 17:28  tim
140  
141          * forceFields/DUFF2.frc: change the format of DUFF2
142  
143 < 2005-03-09 10:44  gezelter
143 > 2005-03-09 15:44  gezelter
144  
145          * src/UseTheForce/DarkSide/: electrostatic.F90,
146          electrostatic_interface.F90, electrostatic_interface.h: new
147          electrostatic module
148  
149 < 2005-03-09 09:26  gezelter
149 > 2005-03-09 14:26  gezelter
150  
151          * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
152          DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole
153          and fixed quadrupole stuff
154  
155 < 2005-03-09 09:25  gezelter
155 > 2005-03-09 14:25  gezelter
156  
157          * src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines
158          for outdated charge and dipole interfaces
159  
160 < 2005-03-08 16:08  gezelter
160 > 2005-03-08 21:08  gezelter
161  
162          * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in,
163          mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun
164          charge-dipole test cases
165  
166 < 2005-03-08 16:07  gezelter
166 > 2005-03-08 21:07  gezelter
167  
168          * src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp,
169          OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a
170          strange icc8 bug (we think).
171  
172 < 2005-03-08 16:07  gezelter
172 > 2005-03-08 21:07  gezelter
173  
174          * src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa!
175  
176 < 2005-03-08 16:07  gezelter
176 > 2005-03-08 21:07  gezelter
177  
178          * src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic
179          Unification Project
180  
181 < 2005-03-08 16:07  gezelter
181 > 2005-03-08 21:07  gezelter
182  
183          * src/io/Globals.cpp: Dunno
184  
185 < 2005-03-08 16:06  gezelter
185 > 2005-03-08 21:06  gezelter
186  
187          * src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using
188          OOPSE_itoa and checking a NULL left over from the LinkedList days
189  
190 < 2005-03-08 16:06  gezelter
190 > 2005-03-08 21:06  gezelter
191  
192          * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
193          atype_interface.F90, atype_interface.h, charge.F90,
# Line 117 | Line 195
195          dipole_interface.F90, dipole_interface.h: electrostatic unification
196          project fixed an uninitialized variable in Lennard Jones mixing map
197  
198 < 2005-03-08 16:05  gezelter
198 > 2005-03-08 21:05  gezelter
199  
200          * src/UseTheForce/doForces.F90: electrostatic unification project
201  
202 < 2005-03-08 16:05  gezelter
202 > 2005-03-08 21:05  gezelter
203  
204          * samples/water/dimer/: two.md, water.md: making some cool test
205          cases
206  
207 < 2005-03-08 16:05  gezelter
207 > 2005-03-08 21:05  gezelter
208  
209          * forceFields/DUFF2.frc: Added a charge for Chlorine
210  
211 < 2005-03-07 17:39  tim
211 > 2005-03-07 22:39  tim
212  
213          * src/: brains/SimInfo.cpp, io/DumpReader.cpp,
214          math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp,
215          primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp:
216          Fixing a bug in BitSet.cpp
217  
218 < 2005-03-04 10:28  gezelter
218 > 2005-03-04 15:28  gezelter
219  
220          * src/config.h.in: Cleaning up config.h.in by adding comments
221  
222 < 2005-03-04 10:28  gezelter
222 > 2005-03-04 15:28  gezelter
223  
224          * configure, ac-tools/configure.in, make/Makefile.in,
225          src/brains/SimCreator.cpp: SPRNG eradication project
226  
227 < 2005-03-03 09:40  tim
227 > 2005-03-03 14:40  tim
228  
229          * src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the
230          missing atom type problem)
231  
232 < 2005-03-02 11:29  tim
232 > 2005-03-02 16:29  tim
233  
234          * src/math/RandNumGen.hpp: adding base class of Random Number
235          generator
236  
237 < 2005-03-02 11:28  tim
237 > 2005-03-02 16:28  tim
238  
239          * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
240          math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in
241          Velocitizer is not initialized which causes a seg fault
242  
243 < 2005-03-02 10:36  tim
243 > 2005-03-02 15:36  tim
244  
245          * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
246          integrators/Velocitizer.hpp, math/Makefile,
# Line 172 | Line 250
250          MersenneTwister.hpp which causes all kinds of trouble.  Refactory
251          random number generator
252  
253 < 2005-03-02 02:32  tim
253 > 2005-03-02 07:32  tim
254  
255          * test/math/testRandNumGen.cpp: Adding unit test for random number
256          generator
257  
258 < 2005-03-01 18:17  tim
258 > 2005-03-01 23:17  tim
259  
260          * src/brains/Thermo.hpp: fixed a file inclusion problem
261  
262 < 2005-03-01 18:17  tim
262 > 2005-03-01 23:17  tim
263  
264          * test/math/: Makefile, OOPSERandNumGenTestCase.cpp,
265          OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp,
266          ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp,
267          RandNumGenTestCase.hpp: fixed compilation problem
268  
269 < 2005-03-01 18:02  tim
269 > 2005-03-01 23:02  tim
270  
271          * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
272          integrators/Velocitizer.hpp, math/Makefile,
# Line 196 | Line 274
274          math/ParallelRandNumGen.hpp, math/mt19937ar.c,
275          math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand
276  
277 < 2005-03-01 18:00  tim
277 > 2005-03-01 23:00  tim
278  
279          * test/math/: Makefile, ParallelandNumGenTestCase.cpp,
280          ParallelandNumGenTestCase.hpp: Change the name of test case
281  
282 < 2005-03-01 16:00  tim
282 > 2005-03-01 21:00  tim
283  
284          * test/math/: Makefile, OOPSERandNumGenTestCase.cpp,
285          OOPSERandNumGenTestCase.hpp: adding testcase for random number
286          generator
287  
288 < 2005-03-01 15:10  tim
288 > 2005-03-01 20:10  tim
289  
290          * src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp,
291          integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp,
# Line 218 | Line 296
296          utils/TypeContainer.hpp, visitors/AtomVisitor.cpp,
297          visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4
298  
299 < 2005-03-01 14:11  tim
299 > 2005-03-01 19:11  tim
300  
301          * src/: brains/SimCreator.cpp, brains/SimInfo.hpp,
302          integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
303          math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding
304          OOPSERandNumGen
305  
306 < 2005-03-01 10:44  gezelter
306 > 2005-03-01 15:44  gezelter
307  
308          * make/Makefile.in: Fixed the damned build problem with the
309          libraries not being removed in make clean and make distclean (at
310          least we think it is fixed).
311  
312 < 2005-03-01 10:26  gezelter
312 > 2005-03-01 15:26  gezelter
313  
314          * src/math/MersenneTwister.hpp: Making small modifications to allow
315          for use on MPI machines
316  
317 < 2005-03-01 09:45  tim
317 > 2005-03-01 14:45  tim
318  
319          * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp,
320          integrators/Velocitizer.cpp, io/DumpReader.cpp,
321          math/MersenneTwister.hpp: adding MersenneTwister random number
322          generator
323  
324 < 2005-02-28 22:55  tim
324 > 2005-03-01 03:55  tim
325  
326          * src/math/MersenneTwister.hpp: Adding a modified version of
327          MersenneTwister.hpp
328  
329 < 2005-02-28 12:24  tim
329 > 2005-02-28 17:24  tim
330  
331          * doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png,
332          definition.jpg: selection expression
333  
334 < 2005-02-25 16:22  tim
334 > 2005-02-25 21:22  tim
335  
336          * src/: UseTheForce/DarkSide/LJ.F90,
337          UseTheForce/DarkSide/lj_interface.F90,
# Line 261 | Line 339
339          io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp,
340          types/AtomType.hpp: adding soft potential to LJ Module
341  
342 < 2005-02-25 11:38  tim
342 > 2005-02-25 16:38  tim
343  
344          * doc/SelectionExpression.html: adding documentation for selection
345          expression
346  
347 < 2005-02-24 15:55  tim
347 > 2005-02-24 20:55  tim
348  
349          * src/: applications/simpleBuilder/simpleBuilder.cpp,
350          integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp,
# Line 274 | Line 352
352          adding basic_teebuf which can operate on multiple stream
353          simutaneously.
354  
355 < 2005-02-22 13:56  tim
355 > 2005-02-22 18:56  tim
356  
357          * src/: UseTheForce/DarkSide/reactionField.F90,
358          primitives/RigidBody.cpp: reactionfield get fixed
359  
360 < 2005-02-21 11:57  tim
360 > 2005-02-21 16:57  tim
361  
362          * src/: applications/staticProps/GofRAngle.cpp,
363          visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix
364          a bug in GofRAngle
365  
366 < 2005-02-21 10:28  tim
366 > 2005-02-21 15:28  tim
367  
368          * src/primitives/Molecule.cpp: Fix for compilation on the Sun
369  
370 < 2005-02-21 10:22  tim
370 > 2005-02-21 15:22  tim
371  
372          * src/utils/next_combination.hpp: fix for compilation on the Sun
373  
374 < 2005-02-21 10:21  tim
374 > 2005-02-21 15:21  tim
375  
376          * src/utils/GenericData.hpp: fix problem in sun
377  
378 < 2005-02-18 18:07  tim
378 > 2005-02-18 23:07  tim
379  
380          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
381          applications/dump2Xyz/Dump2XYZ.ggo,
# Line 314 | Line 392
392          visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
393          visitors/Makefile: adding LipidTransVisitor, GofXyz is working now
394  
395 < 2005-02-18 10:58  gezelter
395 > 2005-02-18 15:58  gezelter
396  
397          * src/brains/Register.cpp: Corrected filename collision for EAM on
398          Mac OS X
399  
400 < 2005-02-18 10:58  gezelter
400 > 2005-02-18 15:58  gezelter
401  
402          * src/applications/oopse/oopse.cpp: Updated copyright information
403  
404 < 2005-02-18 10:58  gezelter
404 > 2005-02-18 15:58  gezelter
405  
406          * src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp,
407          Makefile: corrected filename collision for EAM on operating systems
408          which are not case sensitive (aka Mac OS X)
409  
410 < 2005-02-17 15:15  tim
410 > 2005-02-17 20:15  tim
411  
412          * src/applications/staticProps/GofXyz.cpp: more bug get fixed
413  
414 < 2005-02-17 14:50  tim
414 > 2005-02-17 19:50  tim
415  
416          * src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug
417          in GofXyz
418  
419 < 2005-02-17 14:09  tim
419 > 2005-02-17 19:09  tim
420  
421          * src/applications/staticProps/RadialDistrFunc.hpp: make
422          processHistogram non-abstrct function
423  
424 < 2005-02-17 13:41  tim
424 > 2005-02-17 18:41  tim
425  
426          * src/applications/staticProps/GofXyz.cpp: [no log message]
427  
428 < 2005-02-17 13:30  tim
428 > 2005-02-17 18:30  tim
429  
430          * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp,
431          GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp:
432          finish GofXyz
433  
434 < 2005-02-17 11:21  tim
434 > 2005-02-17 16:21  tim
435  
436          * src/applications/staticProps/: GofAngle2.cpp, GofR.cpp,
437          GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial
438          distribution function
439  
440 < 2005-02-17 10:23  tim
440 > 2005-02-17 15:23  tim
441  
442          * src/utils/BitSet.hpp: forget the const correctness for BitSet
443  
444 < 2005-02-17 10:18  tim
444 > 2005-02-17 15:18  tim
445  
446          * src/: brains/BlockSnapshotManager.cpp,
447          selection/DistanceFinder.cpp: The change of interface of BitSet
448          cause a bug in SelectionEvaluation
449  
450 < 2005-02-16 16:13  tim
450 > 2005-02-16 21:13  tim
451  
452          * src/utils/residentMem.c: return residentMem in byte
453  
454 < 2005-02-16 16:00  tim
454 > 2005-02-16 21:00  tim
455  
456          * src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix
457          a bug in writing out the value of cosang
458  
459 < 2005-02-16 15:43  tim
459 > 2005-02-16 20:43  tim
460  
461          * src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to
462          estimate avaliable memory
463  
464 < 2005-02-16 15:30  tim
464 > 2005-02-16 20:30  tim
465  
466          * src/: applications/staticProps/GofAngle2.cpp,
467          applications/staticProps/GofAngle2.hpp,
# Line 399 | Line 477
477          applications/staticProps/StaticPropsCmd.h,
478          brains/BlockSnapshotManager.cpp: change the default bin number
479  
480 < 2005-02-16 14:36  tim
480 > 2005-02-16 19:36  tim
481  
482          * src/: applications/dynamicProps/DipoleCorrFunc.cpp,
483          applications/dynamicProps/RCorrFunc.cpp,
# Line 416 | Line 494
494          utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output
495          files;fix the problem of counting in staticProps
496  
497 < 2005-02-15 14:39  tim
497 > 2005-02-15 19:39  tim
498  
499          * src/brains/BlockSnapshotManager.cpp: fix a bug in
500          BlockSnapshotManager
501  
502 < 2005-02-15 14:36  tim
502 > 2005-02-15 19:36  tim
503  
504          * src/: applications/dynamicProps/TimeCorrFunc.cpp,
505          applications/staticProps/RadialDistrFunc.cpp,
# Line 429 | Line 507
507          selection/SelectionEvaluator.cpp: BlockSnapshotManager is using
508          reference counting now
509  
510 < 2005-02-15 12:49  tim
510 > 2005-02-15 17:49  tim
511  
512          * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
513          replace std::make_pair by VariablesType::value_type to make Sun
514          Compiler happy
515  
516 < 2005-02-15 12:35  tim
516 > 2005-02-15 17:35  tim
517  
518          * src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to
519          TokenMap, using TokenMapType::value_type instead of std::make_pair
520          to make Sun compiler happy
521  
522 < 2005-02-15 12:24  tim
522 > 2005-02-15 17:24  tim
523  
524          * src/applications/staticProps/: GofRAngle.cpp,
525          RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps
526  
527 < 2005-02-15 12:11  tim
527 > 2005-02-15 17:11  tim
528  
529          * src/: applications/staticProps/GofR.cpp,
530          applications/staticProps/RadialDistrFunc.cpp,
# Line 455 | Line 533
533          #ifdef __RWSTD to make sun compiler happy (2) fix pair density
534          calculation problem when two selections intersect with each other
535  
536 < 2005-02-15 10:24  gezelter
536 > 2005-02-15 15:24  gezelter
537  
538          * src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy
539          xlc++
540  
541 < 2005-02-15 10:17  gezelter
541 > 2005-02-15 15:17  gezelter
542  
543          * configure, ac-tools/configure.in, src/config.h.in,
544          src/utils/residentMem.c: [no log message]
545  
546 < 2005-02-15 01:17  gezelter
546 > 2005-02-15 06:17  gezelter
547  
548          * src/utils/residentMem.c: bug fix for null termination
549  
550 < 2005-02-15 01:11  gezelter
550 > 2005-02-15 06:11  gezelter
551  
552          * configure, ac-tools/configure.in, src/utils/residentMem.c:
553          bugfixing residentMem
554  
555 < 2005-02-15 00:59  gezelter
555 > 2005-02-15 05:59  gezelter
556  
557          * configure, ac-tools/configure.in, src/config.h.in,
558          src/utils/residentMem.c: bugfixes for residentMem on LINUX
559  
560 < 2005-02-15 00:08  gezelter
560 > 2005-02-15 05:08  gezelter
561  
562          * src/utils/Makefile.in: added residentMem
563  
564 < 2005-02-15 00:05  gezelter
564 > 2005-02-15 05:05  gezelter
565  
566          * configure, ac-tools/configure.in, make/Makefile.in,
567          src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c,
# Line 491 | Line 569
569          other processes autoconf fixes ps syntax checking config.h file
570          cleaning
571  
572 < 2005-02-14 18:26  gezelter
572 > 2005-02-14 23:26  gezelter
573  
574          * configure, ac-tools/configure.in, make/Makefile.in: ps niceness
575  
576 < 2005-02-14 18:16  gezelter
576 > 2005-02-14 23:16  gezelter
577  
578          * configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps
579          strangeness
580  
581 < 2005-02-14 14:42  tim
581 > 2005-02-14 19:42  tim
582  
583          * src/brains/BlockSnapshotManager.cpp: fix a bug in
584          BlockSnapshotManager.hpp
585  
586 < 2005-02-14 13:51  tim
586 > 2005-02-14 18:51  tim
587  
588          * src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo,
589          StaticPropsCmd.c: default length for staticProps is 1/2 smallest
590          length of first frame
591  
592 < 2005-02-14 13:12  tim
592 > 2005-02-14 18:12  tim
593  
594          * src/integrators/VelocityVerletIntegrator.cpp: fix a bug in
595          VelocityVerletIntegrator : last frame is written twice
596  
597 < 2005-02-14 12:57  tim
597 > 2005-02-14 17:57  tim
598  
599          * src/: applications/dynamicProps/TimeCorrFunc.cpp,
600          brains/SimInfo.cpp, primitives/RigidBody.cpp,
601          primitives/StuntDouble.hpp: begin bug fix
602  
603 < 2005-02-14 12:35  tim
603 > 2005-02-14 17:35  tim
604  
605          * src/applications/dynamicProps/: CorrelationFunction.cpp,
606          CorrelationFunction.hpp, CrossTimeCorrFunc.cpp,
# Line 532 | Line 610
610          RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp,
611          VCorrFunc.hpp: refactory CorrelationFunction
612  
613 < 2005-02-14 10:18  gezelter
613 > 2005-02-14 15:18  gezelter
614  
615          * src/applications/dynamicProps/CorrelationFunction.cpp: bug fix
616          and start of switch for type of correlation function
617  
618 < 2005-02-13 16:18  tim
618 > 2005-02-13 21:18  tim
619  
620          * src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in
621          calculating  bytes per stuntdouble
622  
623 < 2005-02-13 16:03  tim
623 > 2005-02-13 21:03  tim
624  
625          * src/applications/dynamicProps/CorrelationFunction.cpp: more fix
626  
627 < 2005-02-13 15:57  tim
627 > 2005-02-13 20:57  tim
628  
629          * src/applications/dynamicProps/CorrelationFunction.cpp: fixed a
630          bug in CorrelationFunction
631  
632 < 2005-02-13 15:36  tim
632 > 2005-02-13 20:36  tim
633  
634          * src/: applications/staticProps/GofR.cpp,
635          applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a
636          bug in SimInfo::getCutoff()
637  
638 < 2005-02-13 15:08  tim
638 > 2005-02-13 20:08  tim
639  
640          * make/Makefile.in: adding staticProps and dynamicProps into
641          Makefile.in
642  
643 < 2005-02-13 15:05  tim
643 > 2005-02-13 20:05  tim
644  
645          * src/: applications/dynamicProps/CorrelationFunction.cpp,
646          applications/dynamicProps/CorrelationFunction.hpp,
# Line 573 | Line 651
651          brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length
652          defaults to the cutoff radius
653  
654 < 2005-02-13 14:14  tim
654 > 2005-02-13 19:14  tim
655  
656          * src/utils/Algorithm.hpp: adding Algorithm.hpp
657  
658 < 2005-02-13 14:10  tim
658 > 2005-02-13 19:10  tim
659  
660          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
661          applications/dynamicProps/CorrelationFunction.cpp,
# Line 591 | Line 669
669          utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h,
670          visitors/OtherVisitor.cpp: dynamicProps get built
671  
672 < 2005-02-13 10:56  tim
672 > 2005-02-13 15:56  tim
673  
674          * src/: applications/dynamicProps/CorrelationFunction.cpp,
675          brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
676          brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in
677          progress
678  
679 < 2005-02-13 03:04  tim
679 > 2005-02-13 08:04  tim
680  
681          * src/: applications/dynamicProps/CorrelationFunction.hpp,
682          brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
# Line 606 | Line 684
684          brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more
685          work in dynamicProps
686  
687 < 2005-02-13 02:25  tim
687 > 2005-02-13 07:25  tim
688  
689          * src/applications/dynamicProps/DynamicProps.cpp: adding
690          dynamicProps
691  
692 < 2005-02-13 02:14  tim
692 > 2005-02-13 07:14  tim
693  
694          * src/applications/dynamicProps/: DynamicPropsCmd.c,
695          DynamicPropsCmd.h: adding command line option to DynamicProps
696  
697 < 2005-02-13 02:13  tim
697 > 2005-02-13 07:13  tim
698  
699          * src/applications/dynamicProps/: DynamicProps.ggo, Makefile:
700          adding command line option for DynamicProps
701  
702 < 2005-02-13 01:57  tim
702 > 2005-02-13 06:57  tim
703  
704          * src/: applications/dynamicProps/CorrelationFunction.cpp,
705          applications/dynamicProps/CorrelationFunction.hpp,
# Line 638 | Line 716
716          primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding
717          dynamicProps
718  
719 < 2005-02-12 15:09  tim
719 > 2005-02-12 20:09  tim
720  
721          * src/selection/SelectionManager.cpp: adding SelectionManager.cpp
722  
723 < 2005-02-11 17:41  tim
723 > 2005-02-11 22:41  tim
724  
725          * src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one
726          more constructor to Snapshot to create customized DataStorage
727  
728 < 2005-02-11 17:39  tim
728 > 2005-02-11 22:39  tim
729  
730          * src/selection/: DistanceFinder.hpp, Makefile,
731          SelectionManager.hpp: adding beginSelected, nextSelected method to
732          SelectionManager
733  
734 < 2005-02-11 17:36  tim
734 > 2005-02-11 22:36  tim
735  
736          * src/config.h.in, configure: adding support for physmem
737  
738 < 2005-02-11 17:35  tim
738 > 2005-02-11 22:35  tim
739  
740          * ac-tools/configure.in: adding supprot for physmem
741  
742 < 2005-02-11 17:35  tim
742 > 2005-02-11 22:35  tim
743  
744          * src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding
745          physmem
746  
747 < 2005-02-10 17:37  tim
747 > 2005-02-10 22:37  tim
748  
749          * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp,
750          GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp,
# Line 674 | Line 752
752          StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
753          StaticPropsCmd.h: more work in StaticProps
754  
755 < 2005-02-10 13:14  tim
755 > 2005-02-10 18:14  tim
756  
757          * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp,
758          GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp,
# Line 683 | Line 761
761          StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
762          StaticPropsCmd.h: change the filenames
763  
764 < 2005-02-10 09:15  tim
764 > 2005-02-10 14:15  tim
765  
766          * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp,
767          GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp,
768          RadialDistrFunc.hpp: adding GofRAngle
769  
770 < 2005-02-09 13:21  tim
770 > 2005-02-09 18:21  tim
771  
772          * src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some
773          useless files
774  
775 < 2005-02-09 13:12  tim
775 > 2005-02-09 18:12  tim
776  
777          * src/applications/staticProps/: GofR.cpp, Makefile,
778          RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress
779  
780 < 2005-02-09 12:08  tim
780 > 2005-02-09 17:08  tim
781  
782          * src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp,
783          GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h,
784          RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR
785  
786 < 2005-02-07 17:39  tim
786 > 2005-02-07 22:39  tim
787  
788          * src/primitives/Molecule.hpp: add getRigidBodyAt  function into
789          Molecule class
790  
791 < 2005-02-07 17:38  tim
791 > 2005-02-07 22:38  tim
792  
793          * src/applications/dump2Xyz/Dump2XYZCmd.c: update help info
794  
795 < 2005-02-07 17:36  tim
795 > 2005-02-07 22:36  tim
796  
797          * src/selection/: NameFinder.cpp, NameFinder.hpp,
798          SelectionCompiler.cpp: support select internal index selection, for
799          example, select DMPC.3
800  
801 < 2005-02-07 16:11  tim
801 > 2005-02-07 21:11  tim
802  
803          * src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update
804          help info for Dump2XYZ
805  
806 < 2005-02-07 15:39  chrisfen
806 > 2005-02-07 20:39  chrisfen
807  
808          * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
809          selection librarys added
810  
811 < 2005-02-07 15:31  tim
811 > 2005-02-07 20:31  tim
812  
813          * src/selection/Makefile, make/Makefile.in: adding Makefile
814  
815 < 2005-02-07 15:20  chrisfen
815 > 2005-02-07 20:20  chrisfen
816  
817          * src/utils/wildcards.hpp: issue commented out in wildcards
818  
819 < 2005-02-07 15:06  tim
819 > 2005-02-07 20:06  tim
820  
821          * src/selection/SelectionEvaluator.cpp: forget to reset the pc
822          which cause reevaluate return NULL
823  
824 < 2005-02-07 14:14  tim
824 > 2005-02-07 19:14  tim
825  
826          * src/brains/: SimCreator.cpp, SimSnapshotManager.cpp,
827          SimSnapshotManager.hpp: fix a bug in determing the global index for
828          rigidbodies
829  
830 < 2005-02-07 14:13  tim
830 > 2005-02-07 19:13  tim
831  
832          * src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change
833          in Bitset
834  
835 < 2005-02-07 14:13  tim
835 > 2005-02-07 19:13  tim
836  
837          * src/selection/: DistanceFinder.cpp, DistanceFinder.hpp,
838          SelectionCompiler.cpp, SelectionCompiler.hpp,
839          SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp,
840          TokenMap.cpp: selection library is working
841  
842 < 2005-02-04 17:46  tim
842 > 2005-02-04 22:46  tim
843  
844          * src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor
845  
846 < 2005-02-04 17:45  tim
846 > 2005-02-04 22:45  tim
847  
848          * src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor
849          and XYZVisitor now use selection library
850  
851 < 2005-02-04 17:44  tim
851 > 2005-02-04 22:44  tim
852  
853          * src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp:
854          adding SelectionManager into SimInfo
855  
856 < 2005-02-04 17:43  tim
856 > 2005-02-04 22:43  tim
857  
858          * src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo,
859          Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of
860          selection library
861  
862 < 2005-02-04 17:42  tim
862 > 2005-02-04 22:42  tim
863  
864          * src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change
865          in BitSet
866  
867 < 2005-02-04 17:41  tim
867 > 2005-02-04 22:41  tim
868  
869          * src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing
870          implementation
871  
872 < 2005-02-04 17:39  tim
872 > 2005-02-04 22:39  tim
873  
874          * src/selection/: NameFinder.cpp, NameFinder.hpp,
875          SelectionCompiler.cpp, SelectionCompiler.hpp,
# Line 799 | Line 877
877          SelectionManager.hpp, Token.hpp: half of the selection utility is
878          working need to debug within keyword and atomproperty keyword
879  
880 < 2005-02-04 00:42  tim
880 > 2005-02-04 05:42  tim
881  
882          * src/selection/: NameFinder.cpp, NameFinder.hpp: selection library
883          get built
884  
885 < 2005-02-04 00:42  tim
885 > 2005-02-04 05:42  tim
886  
887          * src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet
888  
889 < 2005-02-04 00:26  tim
889 > 2005-02-04 05:26  tim
890  
891          * src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp:
892          remove some useless files
893  
894 < 2005-02-03 23:57  tim
894 > 2005-02-04 04:57  tim
895  
896          * src/: primitives/RigidBody.hpp, selection/NameFinder.cpp,
897          selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp:
898          adding wildcard class; NameFinder is finished
899  
900 < 2005-02-03 18:14  tim
900 > 2005-02-03 23:14  tim
901  
902          * src/selection/: NameFinder.cpp, NameFinder.hpp,
903          SelectionCompiler.cpp, SelectionCompiler.hpp,
# Line 827 | Line 905
905          SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in
906          selection library
907  
908 < 2005-02-03 09:04  tim
908 > 2005-02-03 14:04  tim
909  
910          * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
911          selection in progress
912  
913 < 2005-02-02 18:13  tim
913 > 2005-02-02 23:13  tim
914  
915          * src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp,
916          SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp,
917          Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in
918          progress, except SelectionEvaluator, other files are compiled
919  
920 < 2005-02-02 18:12  tim
920 > 2005-02-02 23:12  tim
921  
922          * src/utils/: Makefile.in, any.hpp: adding boost::any
923  
924 < 2005-02-02 07:51  tim
924 > 2005-02-02 12:51  tim
925  
926          * src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp
927  
928 < 2005-02-01 17:49  tim
928 > 2005-02-01 22:49  tim
929  
930          * src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp,
931          selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp,
932          selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp,
933          selection/Token.hpp: Selection in progress
934  
935 < 2005-02-01 01:55  tim
935 > 2005-02-01 06:55  tim
936  
937          * src/: selection/SelectionCompiler.hpp,
938          selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
939          selection/SelectionManager.hpp, selection/Token.hpp,
940          utils/BitSet.cpp, utils/BitSet.hpp: adding selection library
941  
942 < 2005-01-26 10:26  tim
942 > 2005-01-26 15:26  tim
943  
944          * src/integrators/: Integrator.cpp, Integrator.hpp,
945          VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget
946          to add eorWriter
947  
948 < 2005-01-26 10:15  tim
948 > 2005-01-26 15:15  tim
949  
950          * src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp:
951          (1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the
952          wrong column of electroframe
953  
954 < 2005-01-25 16:59  tim
954 > 2005-01-25 21:59  tim
955  
956          * src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in
957          SimInfo, use number of cutoff stamp as counter to loop over
958          rigidbody stamp
959  
960 < 2005-01-25 12:45  tim
960 > 2005-01-25 17:45  tim
961  
962          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
963          brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
# Line 899 | Line 977
977          inertial tensor from the directional atoms before calculate
978          rigidbody's inertial tensor
979  
980 < 2005-01-17 17:17  tim
980 > 2005-01-17 22:17  tim
981  
982          * forceFields/DUFF2.frc: forget to set dipole for lipid head group
983  
984 < 2005-01-17 11:58  tim
984 > 2005-01-17 16:58  tim
985  
986          * src/integrators/NVT.cpp: fix a bug in loading initial extended
987          system parameters
988  
989 < 2005-01-17 11:05  tim
989 > 2005-01-17 16:05  tim
990  
991          * src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT
992  
993 < 2005-01-14 17:02  tim
993 > 2005-01-14 22:02  tim
994  
995          * src/UseTheForce/WATER.cpp: remove WATER.cpp
996  
997 < 2005-01-14 16:37  tim
997 > 2005-01-14 21:37  tim
998  
999          * forceFields/Makefile: sync Makefile
1000  
1001 < 2005-01-14 16:13  gezelter
1001 > 2005-01-14 21:13  gezelter
1002  
1003          * make/Makefile.in, src/Makefile, src/UseTheForce/Makefile,
1004          src/UseTheForce/DarkSide/Makefile, src/applications/Makefile,
# Line 934 | Line 1012
1012          src/visitors/Makefile: moved Package variable into subdirectory
1013          makefiles to speed up the building process
1014  
1015 < 2005-01-14 15:48  gezelter
1015 > 2005-01-14 20:48  gezelter
1016  
1017          * src/applications/oopse/oopse.cpp: Fixed publication details in
1018          banner
1019  
1020 < 2005-01-14 15:48  gezelter
1020 > 2005-01-14 20:48  gezelter
1021  
1022          * src/UseTheForce/DarkSide/: simParallel_interface.F90,
1023          simParallel_interface.h: added dummy subroutine to avoid empty
1024          unit, synchronized this dummy routine between C and fortran
1025  
1026 < 2005-01-14 15:31  gezelter
1026 > 2005-01-14 20:31  gezelter
1027  
1028          * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90,
1029          notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90,
# Line 961 | Line 1039
1039          DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating
1040          modules and C/Fortran interface subroutines
1041  
1042 < 2005-01-14 15:15  gezelter
1042 > 2005-01-14 20:15  gezelter
1043  
1044          * configure, ac-tools/aclocal.m4: more fixes for gnugetopt
1045  
1046 < 2005-01-14 15:09  gezelter
1046 > 2005-01-14 20:09  gezelter
1047  
1048          * configure, ac-tools/configure.in, src/config.h.in,
1049          src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt
1050  
1051 < 2005-01-14 11:49  tim
1051 > 2005-01-14 16:49  tim
1052  
1053          * src/: io/EAMAtomTypesSectionParser.cpp,
1054          utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
1055          utils/StringUtils.hpp: using c library to do conversion instead of
1056          using iostream due to a bug in libstdc++(GCC 3.2)
1057  
1058 < 2005-01-13 21:40  tim
1058 > 2005-01-14 02:40  tim
1059  
1060          * src/brains/SimSetup.cpp: no message
1061  
1062 < 2005-01-13 20:56  tim
1062 > 2005-01-14 01:56  tim
1063  
1064          * src/primitives/Molecule.hpp: fix a bug in global index
1065  
1066 < 2005-01-13 20:04  tim
1066 > 2005-01-14 01:04  tim
1067  
1068          * src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include
1069          Integrator.hpp in Minimizer
1070  
1071 < 2005-01-13 17:14  gezelter
1071 > 2005-01-13 22:14  gezelter
1072  
1073          * src/utils/Makefile: compile getopt and getopt1 if we need to
1074  
1075 < 2005-01-13 16:56  gezelter
1075 > 2005-01-13 21:56  gezelter
1076  
1077          * make/Makefile.in: template flags
1078  
1079 < 2005-01-13 16:48  gezelter
1079 > 2005-01-13 21:48  gezelter
1080  
1081          * src/applications/oopse/Makefile: formatting
1082  
1083 < 2005-01-13 16:48  gezelter
1083 > 2005-01-13 21:48  gezelter
1084  
1085          * make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir
1086          target
1087  
1088 < 2005-01-13 14:40  tim
1088 > 2005-01-13 19:40  tim
1089  
1090          * src/: UseTheForce/fSwitchingFunction.h,
1091          UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile,
# Line 1015 | Line 1093
1093          primitives/RigidBody.cpp, types/AtomTypeProperties.h,
1094          types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform
1095  
1096 < 2005-01-13 13:26  tim
1096 > 2005-01-13 18:26  tim
1097  
1098          * make/Makefile.in: change the order of linking (object file comes
1099          first and then follow by user built library)
1100  
1101 < 2005-01-12 18:24  tim
1101 > 2005-01-12 23:24  tim
1102  
1103          * src/io/DumpWriter.cpp: remove useless debug info
1104  
1105 < 2005-01-12 18:21  tim
1105 > 2005-01-12 23:21  tim
1106  
1107          * src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix
1108  
1109 < 2005-01-12 18:17  tim
1109 > 2005-01-12 23:17  tim
1110  
1111          * make/: Makefile.in, Makefile.in: missing tab
1112  
1113 < 2005-01-12 18:15  tim
1113 > 2005-01-12 23:15  tim
1114  
1115          * src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor
1116          get fixed
1117  
1118 < 2005-01-12 17:40  gezelter
1118 > 2005-01-12 22:40  gezelter
1119  
1120          * make/Makefile.in, src/UseTheForce/DUFF.cpp,
1121          src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp,
# Line 1247 | Line 1325
1325          src/visitors/ZconsVisitor.hpp: merging new_design branch into
1326          OOPSE-2.0
1327  
1328 < 2005-01-12 13:13  tim
1328 > 2005-01-12 18:13  tim
1329  
1330          * src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp,
1331          utils/TypeContainer.hpp: forget to include <algorithm>
1332  
1333 < 2005-01-12 12:25  tim
1333 > 2005-01-12 17:25  tim
1334  
1335          * forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc,
1336          newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force
1337          fields
1338  
1339 < 2005-01-12 12:14  tim
1339 > 2005-01-12 17:14  tim
1340  
1341          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
1342          UseTheForce/EAM.cpp, UseTheForce/EAM.hpp,
# Line 1420 | Line 1498
1498          visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
1499          visitors/ZconsVisitor.hpp: change license
1500  
1501 < 2005-01-12 12:14  tim
1501 > 2005-01-12 17:14  tim
1502  
1503          * src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on
1504          branch new_design.
1505  
1506 < 2005-01-11 16:03  tim
1506 > 2005-01-11 21:03  tim
1507  
1508          * src/: constraints/ZconstraintForceManager.cpp,
1509          constraints/ZconstraintForceManager.hpp,
# Line 1433 | Line 1511
1511          minimizers/MinimizerParameterSet.hpp: change const static double
1512          data member to const double
1513  
1514 < 2005-01-11 15:50  tim
1514 > 2005-01-11 20:50  tim
1515  
1516          * src/io/basic_ifstrstream.hpp: forget namespace qualifier std::
1517  
1518 < 2005-01-11 15:39  tim
1518 > 2005-01-11 20:39  tim
1519  
1520          * src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h:
1521          change data type from logical to integer in AtomTypeProperties.h
1522  
1523 < 2005-01-11 11:36  tim
1523 > 2005-01-11 16:36  tim
1524  
1525          * forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding
1526          new format of EAM force field
1527  
1528 < 2005-01-11 11:24  tim
1528 > 2005-01-11 16:24  tim
1529  
1530          * src/UseTheForce/DUFF.cpp: change default name of DUFF force field
1531          to DUFF2.frc
1532  
1533 < 2005-01-11 11:23  tim
1533 > 2005-01-11 16:23  tim
1534  
1535          * forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to
1536          DUFF2.frc
1537  
1538 < 2005-01-11 11:09  tim
1538 > 2005-01-11 16:09  tim
1539  
1540          * make/Makefile.in: adding constraints and minimizers into
1541          Makefile.in
1542  
1543 < 2005-01-11 11:03  tim
1543 > 2005-01-11 16:03  tim
1544  
1545          * src/io/: ChargeAtomTypesSectionParser.cpp,
1546          ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp,
1547          DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless
1548          files
1549  
1550 < 2005-01-11 10:59  tim
1550 > 2005-01-11 15:59  tim
1551  
1552          * src/io/ZConsWriter.cpp: [no log message]
1553  
1554 < 2005-01-11 10:53  tim
1554 > 2005-01-11 15:53  tim
1555  
1556          * src/UseTheForce/EAM.cpp: minor fix
1557  
1558 < 2005-01-11 10:52  tim
1558 > 2005-01-11 15:52  tim
1559  
1560 +        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
1561 +        on branch new_design.
1562 +
1563 + 2005-01-11 15:52  tim
1564 +
1565          * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
1566          on branch new_design.
1567  
1568 < 2005-01-11 10:52  tim
1568 > 2005-01-11 15:52  tim
1569  
1570          * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
1571  
1572 < 2005-01-11 10:52  tim
1572 > 2005-01-11 15:47  tim
1573  
1491 –        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
1492 –        on branch new_design.
1493 –
1494 – 2005-01-11 10:47  tim
1495 –
1574          * make/Makefile.in: forget a '$' sign
1575  
1576 < 2005-01-11 10:46  tim
1576 > 2005-01-11 15:46  tim
1577  
1578          * make/Makefile.in: missing tab in rules
1579  
1580 < 2005-01-10 17:04  tim
1580 > 2005-01-10 22:04  tim
1581  
1582          * src/: UseTheForce/ForceFieldCreator.cpp,
1583          UseTheForce/ForceFieldCreator.hpp,
# Line 1518 | Line 1596
1596          minimizers/MinimizerFactory.hpp: create a register module to
1597          register force fields, integrators and minimizers
1598  
1599 < 2005-01-10 17:04  tim
1599 > 2005-01-10 22:04  tim
1600  
1601          * src/brains/Register.cpp: file Register.cpp was initially added on
1602          branch new_design.
1603  
1604 < 2005-01-10 17:04  tim
1604 > 2005-01-10 22:04  tim
1605  
1606          * src/brains/Register.hpp: file Register.hpp was initially added on
1607          branch new_design.
1608  
1609 < 2005-01-10 15:52  tim
1609 > 2005-01-10 20:52  tim
1610  
1611          * src/: UseTheForce/ForceFieldFactory.cpp,
1612          applications/oopse/oopse.cpp, brains/ForceManager.hpp,
# Line 1540 | Line 1618
1618          visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint
1619          method is working now
1620  
1621 < 2005-01-10 13:05  tim
1621 > 2005-01-10 18:05  tim
1622  
1623          * src/: constraints/ConstraintElem.hpp,
1624          constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp,
# Line 1550 | Line 1628
1628          visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in
1629          zconstraint
1630  
1631 < 2005-01-10 13:05  tim
1631 > 2005-01-10 18:05  tim
1632  
1633          * src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was
1634          initially added on branch new_design.
1635  
1636 < 2005-01-07 16:50  tim
1636 > 2005-01-07 21:50  tim
1637  
1638 +        * src/constraints/ZconstraintForceManager.cpp: file
1639 +        ZconstraintForceManager.cpp was initially added on branch
1640 +        new_design.
1641 +
1642 + 2005-01-07 21:50  tim
1643 +
1644 +        * src/constraints/ZconstraintForceManager.hpp: file
1645 +        ZconstraintForceManager.hpp was initially added on branch
1646 +        new_design.
1647 +
1648 + 2005-01-07 21:50  tim
1649 +
1650          * src/: applications/simpleBuilder/BaseLattice.hpp,
1651          applications/simpleBuilder/Lattice.hpp,
1652          applications/simpleBuilder/LatticeCreator.hpp,
# Line 1569 | Line 1659
1659          integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp,
1660          utils/NumericConstant.hpp: ZConstraintForceManager in progress
1661  
1662 < 2005-01-07 16:50  tim
1662 > 2005-01-07 21:50  tim
1663  
1664          * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was
1665          initially added on branch new_design.
1666  
1667 < 2005-01-07 16:50  tim
1667 > 2005-01-06 22:31  tim
1668  
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 –
1589 – 2005-01-06 17:31  tim
1590 –
1669          * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
1670          brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
1671          constraints/ConstraintPair.hpp, integrators/Integrator.cpp,
# Line 1595 | Line 1673
1673          io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp:
1674          constraint is almost working
1675  
1676 < 2005-01-05 19:36  tim
1676 > 2005-01-06 00:36  tim
1677  
1678          * src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is
1679          working
1680  
1681 < 2005-01-05 19:16  tim
1681 > 2005-01-06 00:16  tim
1682  
1683          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
1684          applications/oopse/oopse.cpp,
# Line 1615 | Line 1693
1693          minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder
1694          in progress
1695  
1696 < 2005-01-05 12:35  tim
1696 > 2005-01-05 17:35  tim
1697  
1698          * src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp
1699          was initially added on branch new_design.
1700  
1701 < 2005-01-05 12:35  tim
1701 > 2005-01-05 17:35  tim
1702  
1703 +        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
1704 +        added on branch new_design.
1705 +
1706 + 2005-01-05 17:35  tim
1707 +
1708          * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
1709          Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp,
1710          MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp,
1711          OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp,
1712          SDMinimizer.hpp: minimizer in progress
1713  
1714 < 2005-01-05 12:35  tim
1714 > 2005-01-05 17:35  tim
1715  
1716 <        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
1717 <        added on branch new_design.
1716 >        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
1717 >        was initially added on branch new_design.
1718  
1719 < 2005-01-05 12:35  tim
1719 > 2005-01-05 17:35  tim
1720  
1721 <        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
1721 >        * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
1722          was initially added on branch new_design.
1723  
1724 < 2005-01-05 12:35  tim
1724 > 2005-01-05 17:35  tim
1725  
1726 <        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
1726 >        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
1727          was initially added on branch new_design.
1728  
1729 < 2005-01-05 12:35  tim
1729 > 2005-01-05 17:35  tim
1730  
1731          * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially
1732          added on branch new_design.
1733  
1734 < 2005-01-05 12:35  tim
1652 <
1653 <        * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
1654 <        was initially added on branch new_design.
1734 > 2005-01-04 22:18  tim
1735  
1656 – 2005-01-04 17:18  tim
1657 –
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 –
1736          * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
1737          brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp,
1738          brains/Thermo.cpp, constraints/ConstraintPair.hpp,
# Line 1669 | Line 1742
1742          primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in
1743          progress
1744  
1745 < 2005-01-04 17:18  tim
1745 > 2005-01-04 22:18  tim
1746  
1747 <        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
1748 <        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
1676 <        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
1677 <        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
1747 >        * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was
1748 >        initially added on branch new_design.
1749  
1750 < 2005-01-04 17:18  tim
1750 > 2005-01-04 22:18  tim
1751  
1681 –        * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
1682 –        was initially added on branch new_design.
1683 –
1684 – 2005-01-04 17:18  tim
1685 –
1752          * src/minimizers/MinimizerParameterSet.cpp: file
1753          MinimizerParameterSet.cpp was initially added on branch new_design.
1754  
1755 < 2005-01-04 17:18  tim
1755 > 2005-01-04 22:18  tim
1756  
1757          * src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was
1758          initially added on branch new_design.
1759  
1760 < 2005-01-04 17:18  tim
1760 > 2005-01-04 22:18  tim
1761  
1762 +        * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
1763 +        was initially added on branch new_design.
1764 +
1765 + 2005-01-04 22:18  tim
1766 +
1767 +        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
1768 +        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
1769 +        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
1770 +        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
1771 +
1772 + 2005-01-04 22:18  tim
1773 +
1774          * src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on
1775          branch new_design.
1776  
1777 < 2004-12-20 15:50  chuckv
1777 > 2004-12-20 20:50  chuckv
1778  
1779          * make/Makefile.in: Fixed Makefile test bug under OSX and possibly
1780          other BSD's, replaced test -f *.mod with ls function since BSD test
1781          apparently doesn't support wildcards.
1782  
1783 < 2004-12-20 15:36  tim
1783 > 2004-12-20 20:36  tim
1784  
1785          * make/Makefile.in: fix a test command incompatiable problem
1786  
1787 < 2004-12-20 14:49  tim
1787 > 2004-12-20 19:49  tim
1788  
1789          * src/integrators/NPTi.cpp: NPT is working now
1790  
1791 < 2004-12-16 14:20  tim
1791 > 2004-12-16 19:20  tim
1792  
1793          * src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the
1794          invalid stamp id
1795  
1796 < 2004-12-16 14:00  tim
1796 > 2004-12-16 19:00  tim
1797  
1798          * forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc,
1799          newEAM.u6.frc: adding new EAM force field files
1800  
1801 < 2004-12-16 13:55  tim
1801 > 2004-12-16 18:55  tim
1802  
1803          * src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays
1804          in  EAM parameter file is incorrect
1805  
1806 < 2004-12-16 12:27  tim
1806 > 2004-12-16 17:27  tim
1807  
1808          * src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp,
1809          brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp,
1810          utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM
1811  
1812 < 2004-12-15 17:34  tim
1812 > 2004-12-15 22:34  tim
1813  
1814          * src/: applications/simpleBuilder/BaseLattice.cpp,
1815          applications/simpleBuilder/BaseLattice.hpp,
# Line 1744 | Line 1822
1822          applications/simpleBuilder/simpleBuilder.cpp,
1823          io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream
1824  
1825 < 2004-12-15 16:07  tim
1825 > 2004-12-15 21:07  tim
1826  
1827          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
1828          UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile,
1829          applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp:
1830          add EAM Force Field
1831  
1832 < 2004-12-15 14:40  tim
1832 > 2004-12-15 19:40  tim
1833  
1834          * src/applications/oopse/oopse.cpp: add more force fields
1835  
1836 < 2004-12-15 11:44  tim
1836 > 2004-12-15 16:44  tim
1837  
1838          * src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget
1839          to call All_reduce in MPI version)
1840  
1841 < 2004-12-15 11:13  tim
1841 > 2004-12-15 16:13  tim
1842  
1843          * src/: brains/SimCreator.cpp, brains/SimInfo.cpp,
1844          io/DumpReader.cpp: MPI in NVE is working
1845  
1846 < 2004-12-14 16:57  tim
1846 > 2004-12-14 21:57  tim
1847  
1848          * src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader.
1849          Master nodes does not brocast the total number of frames
1850  
1851 < 2004-12-14 14:08  tim
1851 > 2004-12-14 19:08  tim
1852  
1853          * src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp,
1854          integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
# Line 1779 | Line 1857
1857          minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp,
1858          minimizers/SDMinimizer.cpp: more fix in MPI version
1859  
1860 < 2004-12-13 17:30  tim
1860 > 2004-12-13 22:30  tim
1861  
1862          * src/: UseTheForce/DarkSide/simParallel.F90,
1863          applications/oopse/oopse.cpp, brains/SimCreator.cpp,
# Line 1797 | Line 1875
1875          utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version
1876          is built
1877  
1878 < 2004-12-10 13:41  tim
1878 > 2004-12-10 18:41  tim
1879  
1880          * src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp
1881  
1882 < 2004-12-10 11:14  tim
1882 > 2004-12-10 16:14  tim
1883  
1884          * src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp,
1885          primitives/StuntDouble.hpp: forget to zero out the torque. Sticky
1886          and Dipole is working now
1887  
1888 < 2004-12-09 18:15  tim
1888 > 2004-12-09 23:15  tim
1889  
1890          * src/: UseTheForce/DarkSide/dipole.F90,
1891          UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp:
1892          fix an index problem in eFrame matrix
1893  
1894 < 2004-12-09 18:09  tim
1894 > 2004-12-09 23:09  tim
1895  
1896          * src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when
1897          initializing the new Charge AtomType
1898  
1899 < 2004-12-09 16:15  tim
1899 > 2004-12-09 21:15  tim
1900  
1901          * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90,
1902          types/DirectionalAtomType.cpp: sticky module get compiled
1903  
1904 < 2004-12-09 15:43  gezelter
1904 > 2004-12-09 20:43  gezelter
1905  
1906          * src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90,
1907          reactionField.F90: u_l -> eFrame  for electrostatics u_l -> A for
1908          GB
1909  
1910 < 2004-12-09 15:42  gezelter
1910 > 2004-12-09 20:42  gezelter
1911  
1912          * src/UseTheForce/doForces.F90: u_l -> eFrame
1913  
1914 < 2004-12-09 15:27  gezelter
1914 > 2004-12-09 20:27  gezelter
1915  
1916          * src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky
1917          module now has the option for multiple sticky types
1918  
1919 < 2004-12-09 15:27  gezelter
1919 > 2004-12-09 20:27  gezelter
1920  
1921          * src/UseTheForce/doForces.F90: sticky
1922  
1923 < 2004-12-09 11:22  tim
1923 > 2004-12-09 16:22  tim
1924  
1925          * src/integrators/: NPT.cpp, NVT.cpp: fix an interface
1926          inconsistency in lab2Bidy
1927  
1928 < 2004-12-09 10:45  tim
1928 > 2004-12-09 15:45  tim
1929  
1930          * src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug
1931          in calculating torque in rigid body
1932  
1933 < 2004-12-08 15:37  tim
1933 > 2004-12-08 20:37  tim
1934  
1935          * src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h,
1936          brains/SnapShot.cpp, brains/Snapshot.hpp,
# Line 1860 | Line 1938
1938          io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp:
1939          fix a parsing bug in ElectroStaticAtomTypesSectionParser
1940  
1941 < 2004-12-08 12:03  tim
1941 > 2004-12-08 17:03  tim
1942  
1943          * src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane
1944          in  NVT is working
1945  
1946 < 2004-12-07 18:08  tim
1946 > 2004-12-07 23:08  tim
1947  
1948          * src/: UseTheForce/Makefile, brains/SimInfo.hpp,
1949          integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp,
1950          integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp,
1951          io/DumpWriter.cpp: NPT in progress
1952  
1953 < 2004-12-07 09:43  tim
1953 > 2004-12-07 14:43  tim
1954  
1955          * test/utils/: Makefile, NextCombinationTestCase.hpp: [no log
1956          message]
1957  
1958 < 2004-12-07 00:12  tim
1958 > 2004-12-07 05:12  tim
1959  
1960          * src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in
1961          UseInitXSstate
1962  
1963 < 2004-12-07 00:00  tim
1963 > 2004-12-07 05:00  tim
1964  
1965          * src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message
1966  
1967 < 2004-12-06 23:47  tim
1967 > 2004-12-07 04:47  tim
1968  
1969          * src/types/DirectionalAtomType.cpp: [no log message]
1970  
1971 < 2004-12-06 21:18  tim
1971 > 2004-12-07 02:18  tim
1972  
1973          * forceFields/newDUFF.frc: merge WATER force field into DUFF
1974  
1975 < 2004-12-06 20:33  tim
1975 > 2004-12-07 01:33  tim
1976  
1977          * forceFields/newDUFF.frc: change the force constant of bonds
1978  
1979 < 2004-12-06 18:29  tim
1979 > 2004-12-06 23:29  tim
1980  
1981          * src/: UseTheForce/DarkSide/charge.F90,
1982          UseTheForce/DarkSide/charge_interface.h,
# Line 1906 | Line 1984
1984          UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp:
1985          fix atom type ident in Charge and Dipole Module
1986  
1987 < 2004-12-06 17:56  tim
1987 > 2004-12-06 22:56  tim
1988  
1989          * src/primitives/Torsion.cpp: butane is working now
1990  
1991 < 2004-12-06 15:15  tim
1991 > 2004-12-06 20:15  tim
1992  
1993          * src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp,
1994          primitives/Bond.hpp, primitives/Torsion.cpp: short range
1995          interaction for butane is correct.Still something wrong with long
1996          range one
1997  
1998 < 2004-12-05 23:49  tim
1998 > 2004-12-06 04:49  tim
1999  
2000          * src/: brains/Exclude.cpp, brains/Exclude.hpp,
2001          brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
# Line 1925 | Line 2003
2003          primitives/Atom.hpp, utils/NumericConstant.hpp,
2004          utils/TypeContainer.hpp: fix a bug in Exclude List
2005  
2006 < 2004-12-05 17:21  tim
2006 > 2004-12-05 22:21  tim
2007  
2008          * forceFields/newDUFF.frc: minor fix in DUFF
2009  
2010 < 2004-12-05 17:02  tim
2010 > 2004-12-05 22:02  tim
2011  
2012          * src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp,
2013          utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp:
2014          fix a bug in filling MolMembership
2015  
2016 < 2004-12-05 12:12  tim
2016 > 2004-12-05 17:12  tim
2017  
2018          * forceFields/newDUFF.frc: minor fix in force field file
2019  
2020 < 2004-12-05 12:09  tim
2020 > 2004-12-05 17:09  tim
2021  
2022          * src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp,
2023          integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp
2024  
2025 < 2004-12-04 15:09  tim
2025 > 2004-12-04 20:09  tim
2026  
2027          * src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp,
2028          math/Vector3.hpp: NVE is working now, get the same result as
2029          OOPSE-1.0
2030  
2031 < 2004-12-04 14:29  tim
2031 > 2004-12-04 19:29  tim
2032  
2033          * src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy
2034  
2035 < 2004-12-04 14:24  gezelter
2035 > 2004-12-04 19:24  gezelter
2036  
2037          * src/primitives/: Bend.cpp, Torsion.cpp: What?
2038  
2039 < 2004-12-04 14:24  gezelter
2039 > 2004-12-04 19:24  gezelter
2040  
2041          * src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion
2042  
2043 < 2004-12-04 00:24  tim
2043 > 2004-12-04 05:24  tim
2044  
2045          * src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp,
2046          integrators/Integrator.hpp,
# Line 1973 | Line 2051
2051          dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step
2052          4 EAM Step 5 Shape Step 6 Constraint & Restraint
2053  
2054 < 2004-12-03 19:01  tim
2054 > 2004-12-04 00:01  tim
2055  
2056          * src/: UseTheForce/DarkSide/LJ.F90,
2057          applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp,
# Line 1982 | Line 2060
2060          io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working,
2061          energy of NVE is not conserved
2062  
2063 < 2004-12-03 17:36  tim
2063 > 2004-12-03 22:36  tim
2064  
2065          * src/: brains/DataStorage.hpp, brains/Snapshot.hpp,
2066          primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running
2067  
2068 < 2004-12-03 16:30  tim
2068 > 2004-12-03 21:30  tim
2069  
2070          * src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp,
2071          brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile,
# Line 1995 | Line 2073
2073          primitives/Molecule.hpp, primitives/StuntDouble.hpp,
2074          primitives/Torsion.hpp: more missing function get implemented
2075  
2076 < 2004-12-03 15:30  tim
2076 > 2004-12-03 20:30  tim
2077  
2078          * src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp,
2079          SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo
2080  
2081 < 2004-12-03 12:59  tim
2081 > 2004-12-03 17:59  tim
2082  
2083          * src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp,
2084          brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
# Line 2009 | Line 2087
2087          io/SectionParserManager.cpp, utils/LocalIndexManager.hpp,
2088          utils/TypeContainer.hpp: begin to fix bugs
2089  
2090 < 2004-12-02 19:26  tim
2090 > 2004-12-03 00:26  tim
2091  
2092 +        * src/utils/Trim.cpp: file Trim.cpp was initially added on branch
2093 +        new_design.
2094 +
2095 + 2004-12-03 00:26  tim
2096 +
2097          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2098          UseTheForce/ForceFieldCreator.cpp,
2099          UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp,
# Line 2020 | Line 2103
2103          utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a
2104          bug in countTokens in StringTokenizer
2105  
2106 < 2004-12-02 19:26  tim
2106 > 2004-12-03 00:06  tim
2107  
2025 –        * src/utils/Trim.cpp: file Trim.cpp was initially added on branch
2026 –        new_design.
2027 –
2028 – 2004-12-02 19:06  tim
2029 –
2108          * forceFields/newDUFF.frc: minor fix
2109  
2110 < 2004-12-02 18:15  tim
2110 > 2004-12-02 23:15  tim
2111  
2112          * forceFields/newDUFF.frc: new ForceField format
2113  
2114 < 2004-12-02 17:15  tim
2114 > 2004-12-02 22:15  tim
2115  
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 –
2116          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2117          UseTheForce/ForceFieldCreator.cpp,
2118          UseTheForce/ForceFieldCreator.hpp,
# Line 2067 | Line 2130
2130          types/Makefile: refine factory pattern to make it initialized
2131          correctly
2132  
2133 < 2004-12-02 17:15  tim
2133 > 2004-12-02 22:15  tim
2134  
2135          * src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp
2136          was initially added on branch new_design.
2137  
2138 < 2004-12-02 11:53  tim
2138 > 2004-12-02 22:15  tim
2139  
2140 +        * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp
2141 +        was initially added on branch new_design.
2142 +
2143 + 2004-12-02 22:15  tim
2144 +
2145 +        * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp
2146 +        was initially added on branch new_design.
2147 +
2148 + 2004-12-02 22:15  tim
2149 +
2150 +        * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp
2151 +        was initially added on branch new_design.
2152 +
2153 + 2004-12-02 16:53  tim
2154 +
2155          * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp,
2156          types/DirectionalAtomType.cpp, types/Makefile: oopse get built
2157  
2158 < 2004-12-02 11:04  tim
2158 > 2004-12-02 16:04  tim
2159  
2160          * src/: applications/simpleBuilder/LatticeCreator.cpp,
2161          applications/simpleBuilder/LatticeCreator.hpp,
# Line 2101 | Line 2179
2179          visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still
2180          have two linking problem
2181  
2182 < 2004-12-02 00:17  tim
2182 > 2004-12-02 05:17  tim
2183  
2184          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
2185          applications/simpleBuilder/Lattice.cpp,
# Line 2113 | Line 2191
2191          visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp,
2192          visitors/ZconsVisitor.cpp: change endl to std::endl
2193  
2194 < 2004-12-02 00:14  tim
2194 > 2004-12-02 05:14  tim
2195  
2196          * src/: UseTheForce/Shapes_FF.cpp,
2197          applications/dump2Xyz/Dump2XYZ.cpp,
# Line 2129 | Line 2207
2207          visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
2208          visitors/RigidBodyVisitor.hpp: minor fix
2209  
2210 < 2004-12-02 00:09  tim
2210 > 2004-12-02 05:09  tim
2211  
2212          * src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp:
2213          remove StreamTokenizer
2214  
2215 < 2004-12-02 00:06  tim
2215 > 2004-12-02 05:06  tim
2216  
2217          * src/: UseTheForce/Shapes_FF.cpp,
2218          applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp,
# Line 2143 | Line 2221
2221          restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using
2222          namespace std in .cpp file
2223  
2224 < 2004-12-02 00:04  tim
2224 > 2004-12-02 05:04  tim
2225  
2226          * src/: UseTheForce/Shapes_FF.cpp,
2227          applications/dump2Xyz/Dump2XYZ.cpp,
# Line 2167 | Line 2245
2245          visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding
2246          qulified name prefix std
2247  
2248 < 2004-12-01 23:55  tim
2248 > 2004-12-02 04:55  tim
2249  
2250          * src/: UseTheForce/Shapes_FF.cpp,
2251          applications/dump2Xyz/Dump2XYZ.cpp,
# Line 2183 | Line 2261
2261          visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
2262          visitors/RigidBodyVisitor.hpp: replace string by std::string
2263  
2264 < 2004-12-01 22:12  tim
2264 > 2004-12-02 03:12  tim
2265  
2266          * make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp,
2267          src/applications/simpleBuilder/BaseLattice.hpp,
# Line 2204 | Line 2282
2282          test/brains/RigidBody.cpp: replace misuse of using namespace std in
2283          header files
2284  
2285 < 2004-12-01 21:23  tim
2285 > 2004-12-02 02:23  tim
2286  
2287          * src/: primitives/Atom.hpp, primitives/RigidBody.hpp,
2288          primitives/StuntDouble.hpp, utils/TypeContainer.hpp,
2289          utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp:
2290          begin to fix linking problem
2291  
2292 < 2004-12-01 21:08  tim
2292 > 2004-12-02 02:08  tim
2293  
2294          * src/: applications/oopse/oopse.cpp, brains/Stats.cpp,
2295          brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile,
# Line 2223 | Line 2301
2301          utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled,
2302          still has some linking problem
2303  
2304 < 2004-12-01 19:26  tim
2304 > 2004-12-02 00:26  tim
2305  
2306          * src/: integrators/NVT.cpp, integrators/NVT.hpp,
2307          utils/OOPSEConstant.hpp: NVT get built
2308  
2309 < 2004-12-01 19:09  tim
2309 > 2004-12-02 00:09  tim
2310  
2311 <        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
2312 <        was initially added on branch new_design.
2311 >        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
2312 >        branch new_design.
2313  
2314 < 2004-12-01 19:09  tim
2314 > 2004-12-02 00:09  tim
2315  
2316 +        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
2317 +        branch new_design.
2318 +
2319 + 2004-12-02 00:09  tim
2320 +
2321          * src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp,
2322          brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
2323          brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp,
# Line 2245 | Line 2328
2328          integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE
2329          get built
2330  
2331 < 2004-12-01 19:09  tim
2331 > 2004-12-02 00:09  tim
2332  
2333 <        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
2334 <        branch new_design.
2333 >        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
2334 >        was initially added on branch new_design.
2335  
2336 < 2004-12-01 19:09  tim
2336 > 2004-12-01 22:45  tim
2337  
2255 –        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
2256 –        branch new_design.
2257 –
2258 – 2004-12-01 17:45  tim
2259 –
2338          * src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp,
2339          integrators/IntegratorFactory.cpp,
2340          integrators/IntegratorFactory.hpp, integrators/Makefile,
# Line 2266 | Line 2344
2344          io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp,
2345          io/StatWriter.hpp: rename DumpWrite to DumpWriter
2346  
2347 < 2004-12-01 17:45  tim
2347 > 2004-12-01 22:45  tim
2348  
2349          * src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on
2350          branch new_design.
2351  
2352 < 2004-12-01 15:05  tim
2352 > 2004-12-01 20:05  tim
2353  
2354          * src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp,
2355          io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile,
# Line 2280 | Line 2358
2358          visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp,
2359          visitors/ZconsVisitor.hpp: visitors get built
2360  
2361 < 2004-12-01 14:32  chrisfen
2361 > 2004-12-01 19:32  chrisfen
2362  
2363          * samples/water/tip3p_ice/tp3.md: fixed a sample
2364  
2365 < 2004-12-01 14:10  tim
2365 > 2004-12-01 19:10  tim
2366  
2367          * src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp,
2368          src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
# Line 2293 | Line 2371
2371          src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp:
2372          spell check
2373  
2374 < 2004-12-01 13:42  tim
2374 > 2004-12-01 18:42  tim
2375  
2376          * src/: UseTheForce/DarkSide/atype.F90,
2377          io/ElectrostaticAtomTypesSectionParser.cpp,
# Line 2302 | Line 2380
2380          primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator
2381          and constraint, other directories get built
2382  
2383 < 2004-12-01 12:38  tim
2383 > 2004-12-01 17:38  tim
2384  
2385          * src/: brains/DataStorage.cpp, brains/DataStorage.hpp,
2386          brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
# Line 2315 | Line 2393
2393          types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp:
2394          refactory AtomType
2395  
2396 < 2004-11-30 22:11  tim
2396 > 2004-12-01 03:11  tim
2397  
2398          * src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change
2399  
2400 < 2004-11-30 21:30  tim
2400 > 2004-12-01 02:30  tim
2401  
2402          * src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change
2403          NumericConstant
2404  
2405 < 2004-11-30 21:24  tim
2405 > 2004-12-01 02:24  tim
2406  
2407          * src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp,
2408          primitives/RigidBody.cpp: minor fix
2409  
2410 < 2004-11-30 18:14  tim
2410 > 2004-11-30 23:14  tim
2411  
2412          * src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp,
2413          io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile,
2414          io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io
2415          get built, next is integrator
2416  
2417 < 2004-11-30 17:43  tim
2417 > 2004-11-30 22:43  tim
2418  
2419          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2420          UseTheForce/ForceField.hpp, brains/SimCreator.cpp,
# Line 2344 | Line 2422
2422          io/BASS_interface.cpp, primitives/StuntDouble.hpp,
2423          utils/StringUtils.hpp: brains get built
2424  
2425 < 2004-11-30 15:50  tim
2425 > 2004-11-30 20:50  tim
2426  
2427          * src/: brains/ForceManager.cpp, brains/Makefile,
2428          brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
2429          primitives/RigidBody.cpp, primitives/RigidBody.hpp,
2430          utils/StringUtils.hpp: brains get built, io is next
2431  
2432 < 2004-11-30 14:58  tim
2432 > 2004-11-30 19:58  tim
2433  
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 –
2434          * src/: brains/Exclude.cpp, brains/Exclude.hpp,
2435          brains/ForceManager.cpp, brains/ForceManager.hpp,
2436          brains/MoleculeCreator.cpp, brains/SimCreator.hpp,
# Line 2367 | Line 2440
2440          brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile,
2441          math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo
2442  
2443 < 2004-11-30 12:54  tim
2443 > 2004-11-30 19:58  tim
2444  
2445 +        * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially
2446 +        added on branch new_design.
2447 +
2448 + 2004-11-30 17:54  tim
2449 +
2450          * src/: primitives/Bend.hpp, primitives/Bond.hpp,
2451          primitives/StuntDouble.hpp, primitives/Torsion.hpp,
2452          utils/LocalIndexManager.hpp: more get fixed
2453  
2454 < 2004-11-30 00:03  tim
2454 > 2004-11-30 05:03  tim
2455  
2378 –        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
2379 –        LocalndexManager.hpp to LocalIndexManager.hpp
2380 –
2381 – 2004-11-30 00:03  tim
2382 –
2456          * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
2457          initially added on branch new_design.
2458  
2459 < 2004-11-29 23:43  tim
2459 > 2004-11-30 05:03  tim
2460  
2461 +        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
2462 +        LocalndexManager.hpp to LocalIndexManager.hpp
2463 +
2464 + 2004-11-30 04:43  tim
2465 +
2466          * src/: io/BendTypesSectionParser.cpp,
2467          io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
2468          io/BondTypesSectionParser.hpp, io/SectionParserManager.cpp,
# Line 2392 | Line 2470
2470          types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
2471          types/PolynomialTorsionType.hpp: Section Parsers get compiled
2472  
2473 < 2004-11-29 23:14  tim
2473 > 2004-11-30 04:14  tim
2474  
2475          * src/: io/BendTypesSectionParser.cpp,
2476          io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
# Line 2400 | Line 2478
2478          types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor
2479          fixed
2480  
2481 < 2004-11-29 22:49  tim
2481 > 2004-11-30 03:49  tim
2482  
2483          * src/: io/TorsionTypesSectionParser.cpp,
2484          io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp,
# Line 2408 | Line 2486
2486          types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp,
2487          types/QuarticTorsionType.hpp: minor fixed
2488  
2489 < 2004-11-29 22:32  tim
2489 > 2004-11-30 03:32  tim
2490  
2491          * src/: io/TorsionTypesSectionParser.cpp,
2492          types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
2493          types/PolynomialTorsionType.hpp: #inlcude statement can not be
2494          embedded
2495  
2496 < 2004-11-29 16:42  tim
2496 > 2004-11-29 21:42  tim
2497  
2498          * test/math/: Makefile, PolynomialTestCase.cpp,
2499          PolynomialTestCase.hpp: add PolynomialTestCase
2500  
2501 < 2004-11-29 16:42  tim
2501 > 2004-11-29 21:42  tim
2502  
2503          * src/math/Polynomial.hpp: Polynomial passes unit test
2504  
2505 < 2004-11-29 15:03  tim
2505 > 2004-11-29 20:03  tim
2506  
2507          * src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename
2508          QuarticTorsion.hpp to QuarticTorsionType.hpp
2509  
2510 < 2004-11-29 15:03  tim
2510 > 2004-11-29 20:03  tim
2511  
2512          * src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was
2513          initially added on branch new_design.
2514  
2515 < 2004-11-29 14:56  tim
2515 > 2004-11-29 19:56  tim
2516  
2517          * src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was
2518          initially added on branch new_design.
2519  
2520 < 2004-11-29 14:56  tim
2520 > 2004-11-29 19:56  tim
2521  
2522          * src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add
2523          CubicTorsionType and QuarticTorsionType
2524  
2525 < 2004-11-29 14:56  tim
2525 > 2004-11-29 19:56  tim
2526  
2527          * src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was
2528          initially added on branch new_design.
2529  
2530 < 2004-11-29 13:00  tim
2530 > 2004-11-29 18:00  tim
2531  
2532          * src/: brains/DataStorage.hpp, brains/Snapshot.hpp,
2533          types/CubicBendType.hpp, types/CubicBondType.hpp,
2534          types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get
2535          fixed
2536  
2537 < 2004-11-29 12:59  tim
2537 > 2004-11-29 17:59  tim
2538  
2539          * src/utils/Trim.hpp: file Trim.hpp was initially added on branch
2540          new_design.
2541  
2542 < 2004-11-29 12:59  tim
2542 > 2004-11-29 17:59  tim
2543  
2544          * src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim
2545          Algorithm for std::string
2546  
2547 < 2004-11-29 10:52  tim
2547 > 2004-11-29 15:52  tim
2548  
2549          * src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove
2550          some useless files
2551  
2552 < 2004-11-29 10:50  tim
2552 > 2004-11-29 15:50  tim
2553  
2554          * src/io/: BondTypesSectionParser.cpp,
2555          ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp,
# Line 2482 | Line 2560
2560          SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp,
2561          StickyAtomTypesSectionParser.hpp: more files get fixed
2562  
2563 < 2004-11-29 10:27  tim
2563 > 2004-11-29 15:27  tim
2564  
2565          * src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp,
2566          DirectionalAtomTypesSectionParser.cpp,
# Line 2491 | Line 2569
2569          SectionParserManager.cpp, SectionParserManager.hpp: part of io get
2570          built
2571  
2572 < 2004-11-29 09:49  tim
2572 > 2004-11-29 14:49  tim
2573  
2574          * src/types/UreyBradleyBendType.hpp: types get built
2575  
2576 < 2004-11-29 09:40  tim
2576 > 2004-11-29 14:40  tim
2577  
2578          * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp:
2579          types  get built
2580  
2581 < 2004-11-25 21:13  tim
2581 > 2004-11-26 02:13  tim
2582  
2583          * src/: UseTheForce/ForceField.hpp,
2584          io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp,
2585          types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some
2586          files
2587  
2588 < 2004-11-25 15:18  tim
2588 > 2004-11-25 20:18  tim
2589  
2590 +        * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was
2591 +        initially added on branch new_design.
2592 +
2593 + 2004-11-25 20:18  tim
2594 +
2595          * src/: io/AtomTypesSectionParser.cpp,
2596          io/BondTypesSectionParser.cpp,
2597          io/DirectionalAtomTypesSectionParser.cpp,
# Line 2516 | Line 2599
2599          types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some
2600          files
2601  
2602 < 2004-11-25 15:18  tim
2602 > 2004-11-25 20:18  tim
2603  
2604          * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was
2605          initially added on branch new_design.
2606  
2607 < 2004-11-25 15:18  tim
2607 > 2004-11-24 22:12  tim
2608  
2526 –        * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was
2527 –        initially added on branch new_design.
2528 –
2529 – 2004-11-24 17:12  tim
2530 –
2609          * src/: io/AtomTypesSectionParser.cpp,
2610          io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp,
2611          io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
# Line 2549 | Line 2627
2627          io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
2628          utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built
2629  
2630 < 2004-11-24 16:33  tim
2630 > 2004-11-24 21:33  tim
2631  
2632          * src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp,
2633          ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp,
2634          LJFF.cpp, Makefile: UseTheForce get built
2635  
2636 < 2004-11-24 15:55  tim
2636 > 2004-11-24 20:55  tim
2637  
2638          * src/: math/RectMatrix.hpp, primitives/Bend.cpp,
2639          primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp,
# Line 2565 | Line 2643
2643          primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp,
2644          primitives/UreyBradleyBend.hpp: types and primitives get built
2645  
2646 < 2004-11-24 14:49  tim
2646 > 2004-11-24 19:49  tim
2647  
2648          * test/utils/: Makefile, NextCombinationTestCase.cpp,
2649          StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint
2650          StringTokenizerTestCase
2651  
2652 < 2004-11-24 14:49  tim
2652 > 2004-11-24 19:49  tim
2653  
2654          * src/utils/: GenericData.hpp, StringTokenizer.cpp,
2655          StringTokenizer.hpp: StringTokenizer passes unit test
2656  
2657 < 2004-11-24 13:20  tim
2657 > 2004-11-24 18:20  tim
2658  
2659          * ChangeLog, make/Makefile.in, src/UseTheForce/Makefile,
2660          src/io/Makefile, src/primitives/Makefile, src/utils/Makefile:
2661          change Makefile
2662  
2663 < 2004-11-24 13:06  chrisfen
2663 > 2004-11-24 18:06  chrisfen
2664  
2665          * src/io/RestraintReader.cpp: improved restraints - mpi should work
2666          fine
2667  
2668 < 2004-11-24 13:06  chrisfen
2668 > 2004-11-24 18:06  chrisfen
2669  
2670          * src/integrators/Integrator.cpp: improved restraints
2671  
2672 < 2004-11-24 13:05  chrisfen
2672 > 2004-11-24 18:05  chrisfen
2673  
2674          * samples/water/tip3p_ice/tp3.md: oops...
2675  
2676 < 2004-11-24 12:42  tim
2676 > 2004-11-24 17:42  tim
2677  
2678          * src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp,
2679          brains/DataStorage.hpp, brains/SimCreator.cpp,
# Line 2604 | Line 2682
2682          primitives/DirectionalAtom.cpp: add SetForceManager method to
2683          integrator
2684  
2685 < 2004-11-23 18:12  tim
2685 > 2004-11-23 23:12  tim
2686  
2687          * src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp,
2688          integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp,
# Line 2616 | Line 2694
2694          integrators/VelocityVerletIntegrator.hpp,
2695          types/UreyBradleyBendType.hpp: refactory NPT integrator
2696  
2697 < 2004-11-23 17:50  chrisfen
2697 > 2004-11-23 22:50  chrisfen
2698  
2699          * samples/water/tip3p_ice/tp3.md: Back to normal... Oh...
2700          Restraints should work in parallel now
2701  
2702 < 2004-11-23 17:48  chrisfen
2702 > 2004-11-23 22:48  chrisfen
2703  
2704          * src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
2705          brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
# Line 2631 | Line 2709
2709          restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements
2710          to restraints
2711  
2712 < 2004-11-23 17:47  chrisfen
2712 > 2004-11-23 22:47  chrisfen
2713  
2714          * samples/water/tip3p_ice/tp3.md: just some testing changes, I'll
2715          return to the original on next commit
2716  
2717 < 2004-11-23 12:53  tim
2717 > 2004-11-23 17:53  tim
2718  
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 –
2719          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2720          UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
2721          applications/simpleBuilder/simpleBuilder.cpp,
# Line 2655 | Line 2727
2727          io/SectionParser.hpp, types/DirectionalAtomType.cpp,
2728          utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser
2729  
2730 < 2004-11-23 12:53  tim
2730 > 2004-11-23 17:53  tim
2731  
2732          * src/io/ElectrostaticAtomTypesSectionParser.hpp: file
2733          ElectrostaticAtomTypesSectionParser.hpp was initially added on
2734          branch new_design.
2735  
2736 < 2004-11-23 01:03  tim
2736 > 2004-11-23 17:53  tim
2737  
2738 <        * src/io/EAMAtomTypesSectionParser.cpp: file
2739 <        EAMAtomTypesSectionParser.cpp was initially added on branch
2740 <        new_design.
2738 >        * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
2739 >        ElectrostaticAtomTypesSectionParser.cpp was initially added on
2740 >        branch new_design.
2741  
2742 < 2004-11-23 01:03  tim
2742 > 2004-11-23 06:03  tim
2743  
2744          * src/: io/EAMAtomTypesSectionParser.cpp,
2745          io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp,
2746          types/AtomType.hpp, types/DirectionalAtomType.cpp,
2747          types/DirectionalAtomType.hpp: add EAM AtomType Section Parser
2748  
2749 < 2004-11-23 01:03  tim
2749 > 2004-11-23 06:03  tim
2750  
2751 +        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
2752 +        was initially added on branch new_design.
2753 +
2754 + 2004-11-23 06:03  tim
2755 +
2756          * src/io/EAMAtomTypesSectionParser.hpp: file
2757          EAMAtomTypesSectionParser.hpp was initially added on branch
2758          new_design.
2759  
2760 < 2004-11-23 01:03  tim
2760 > 2004-11-23 06:03  tim
2761  
2762 <        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
2763 <        was initially added on branch new_design.
2762 >        * src/io/EAMAtomTypesSectionParser.cpp: file
2763 >        EAMAtomTypesSectionParser.cpp was initially added on branch
2764 >        new_design.
2765  
2766 < 2004-11-22 23:35  tim
2766 > 2004-11-23 04:35  tim
2767  
2768 <        * src/io/TorsionTypesSectionParser.cpp: file
2769 <        TorsionTypesSectionParser.cpp was initially added on branch
2768 >        * src/io/TorsionTypesSectionParser.hpp: file
2769 >        TorsionTypesSectionParser.hpp was initially added on branch
2770          new_design.
2771  
2772 < 2004-11-22 23:35  tim
2772 > 2004-11-23 04:35  tim
2773  
2774          * src/io/BendTypesSectionParser.hpp: file
2775          BendTypesSectionParser.hpp was initially added on branch
2776          new_design.
2777  
2778 < 2004-11-22 23:35  tim
2778 > 2004-11-23 04:35  tim
2779  
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 –
2780          * src/io/BondTypesSectionParser.hpp: file
2781          BondTypesSectionParser.hpp was initially added on branch
2782          new_design.
2783  
2784 < 2004-11-22 23:35  tim
2784 > 2004-11-23 04:35  tim
2785  
2786 <        * src/io/TorsionTypesSectionParser.hpp: file
2787 <        TorsionTypesSectionParser.hpp was initially added on branch
2786 >        * src/io/BondTypesSectionParser.cpp: file
2787 >        BondTypesSectionParser.cpp was initially added on branch
2788          new_design.
2789  
2790 < 2004-11-22 23:35  tim
2790 > 2004-11-23 04:35  tim
2791  
2792 <        * src/io/BendTypesSectionParser.cpp: file
2793 <        BendTypesSectionParser.cpp was initially added on branch
2792 >        * src/io/TorsionTypesSectionParser.cpp: file
2793 >        TorsionTypesSectionParser.cpp was initially added on branch
2794          new_design.
2795  
2796 < 2004-11-22 23:35  tim
2796 > 2004-11-23 04:35  tim
2797  
2798          * src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp,
2799          BondTypesSectionParser.cpp, BondTypesSectionParser.hpp,
# Line 2729 | Line 2801
2801          BondTypesSectionParser, BendTypesSectionParser and
2802          TorsionTypeSectionParser
2803  
2804 < 2004-11-22 18:04  tim
2804 > 2004-11-23 04:35  tim
2805  
2806 +        * src/io/BendTypesSectionParser.cpp: file
2807 +        BendTypesSectionParser.cpp was initially added on branch
2808 +        new_design.
2809 +
2810 + 2004-11-22 23:04  tim
2811 +
2812          * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in
2813          DUFF and EAM
2814  
2815 < 2004-11-22 18:02  tim
2815 > 2004-11-22 23:02  tim
2816  
2817 +        * src/io/: DirectionalAtomTypesParser.hpp,
2818 +        DirectionalAtomTypesSectionParser.hpp: adding section parsers
2819 +
2820 + 2004-11-22 23:02  tim
2821 +
2822          * src/io/DirectionalAtomTypesSectionParser.hpp: file
2823          DirectionalAtomTypesSectionParser.hpp was initially added on branch
2824          new_design.
2825  
2826 < 2004-11-22 18:02  tim
2826 > 2004-11-22 20:55  tim
2827  
2828 <        * src/io/: DirectionalAtomTypesParser.hpp,
2829 <        DirectionalAtomTypesSectionParser.hpp: adding section parsers
2828 >        * src/io/DipoleAtomTypesSectionParser.hpp: file
2829 >        DipoleAtomTypesSectionParser.hpp was initially added on branch
2830 >        new_design.
2831  
2832 < 2004-11-22 15:55  tim
2832 > 2004-11-22 20:55  tim
2833  
2834 <        * src/io/DirectionalAtomTypesParser.hpp: file
2835 <        DirectionalAtomTypesParser.hpp was initially added on branch
2834 >        * src/io/AtomTypesSectionParser.hpp: file
2835 >        AtomTypesSectionParser.hpp was initially added on branch
2836          new_design.
2837  
2838 < 2004-11-22 15:55  tim
2838 > 2004-11-22 20:55  tim
2839  
2840          * src/io/HarmonicBondTypesSectionParser.hpp: file
2841          HarmonicBondTypesSectionParser.hpp was initially added on branch
2842          new_design.
2843  
2844 < 2004-11-22 15:55  tim
2844 > 2004-11-22 20:55  tim
2845  
2846 <        * src/io/ChargeAtomTypesSectionParser.hpp: file
2847 <        ChargeAtomTypesSectionParser.hpp was initially added on branch
2846 >        * src/io/StickyAtomTypesSectionParser.cpp: file
2847 >        StickyAtomTypesSectionParser.cpp was initially added on branch
2848          new_design.
2849  
2850 < 2004-11-22 15:55  tim
2850 > 2004-11-22 20:55  tim
2851  
2852 <        * src/io/DirectionalAtomTypesSectionParser.cpp: file
2853 <        DirectionalAtomTypesSectionParser.cpp was initially added on branch
2854 <        new_design.
2852 >        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
2853 >        LennardJonesAtomTypesSectionParser.hpp was initially added on
2854 >        branch new_design.
2855  
2856 < 2004-11-22 15:55  tim
2856 > 2004-11-22 20:55  tim
2857  
2858 +        * src/io/HarmonicBondTypesSectionParser.cpp: file
2859 +        HarmonicBondTypesSectionParser.cpp was initially added on branch
2860 +        new_design.
2861 +
2862 + 2004-11-22 20:55  tim
2863 +
2864 +        * src/io/DirectionalAtomTypesSectionParser.cpp: file
2865 +        DirectionalAtomTypesSectionParser.cpp was initially added on branch
2866 +        new_design.
2867 +
2868 + 2004-11-22 20:55  tim
2869 +
2870 +        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
2871 +        was initially added on branch new_design.
2872 +
2873 + 2004-11-22 20:55  tim
2874 +
2875 +        * src/io/AtomTypesSectionParser.cpp: file
2876 +        AtomTypesSectionParser.cpp was initially added on branch
2877 +        new_design.
2878 +
2879 + 2004-11-22 20:55  tim
2880 +
2881 +        * src/io/ChargeAtomTypesSectionParser.cpp: file
2882 +        ChargeAtomTypesSectionParser.cpp was initially added on branch
2883 +        new_design.
2884 +
2885 + 2004-11-22 20:55  tim
2886 +
2887 +        * src/io/DipoleAtomTypesSectionParser.cpp: file
2888 +        DipoleAtomTypesSectionParser.cpp was initially added on branch
2889 +        new_design.
2890 +
2891 + 2004-11-22 20:55  tim
2892 +
2893          * src/io/LennardJonesAtomTypesSectionParser.cpp: file
2894          LennardJonesAtomTypesSectionParser.cpp was initially added on
2895          branch new_design.
2896  
2897 < 2004-11-22 15:55  tim
2897 > 2004-11-22 20:55  tim
2898  
2899 <        * src/io/DipoleAtomTypesSectionParser.cpp: file
2900 <        DipoleAtomTypesSectionParser.cpp was initially added on branch
2899 >        * src/io/ChargeAtomTypesSectionParser.hpp: file
2900 >        ChargeAtomTypesSectionParser.hpp was initially added on branch
2901          new_design.
2902  
2903 < 2004-11-22 15:55  tim
2903 > 2004-11-22 20:55  tim
2904  
2905 +        * src/io/StickyAtomTypesSectionParser.hpp: file
2906 +        StickyAtomTypesSectionParser.hpp was initially added on branch
2907 +        new_design.
2908 +
2909 + 2004-11-22 20:55  tim
2910 +
2911 +        * src/io/SectionParser.hpp: file SectionParser.hpp was initially
2912 +        added on branch new_design.
2913 +
2914 + 2004-11-22 20:55  tim
2915 +
2916          * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
2917          brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
2918          brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp,
# Line 2803 | Line 2933
2933          types/AtomType.hpp, types/DirectionalAtomType.hpp,
2934          utils/GenericData.hpp: adding section parsers
2935  
2936 < 2004-11-22 15:55  tim
2936 > 2004-11-22 20:55  tim
2937  
2938 <        * src/io/DipoleAtomTypesSectionParser.hpp: file
2939 <        DipoleAtomTypesSectionParser.hpp was initially added on branch
2938 >        * src/io/DirectionalAtomTypesParser.hpp: file
2939 >        DirectionalAtomTypesParser.hpp was initially added on branch
2940          new_design.
2941  
2942 < 2004-11-22 15:55  tim
2942 > 2004-11-22 20:55  tim
2943  
2814 –        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
2815 –        added on branch new_design.
2816 –
2817 – 2004-11-22 15:55  tim
2818 –
2944          * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
2945          was initially added on branch new_design.
2946  
2947 < 2004-11-22 15:55  tim
2947 > 2004-11-22 20:55  tim
2948  
2949 <        * src/io/AtomTypesSectionParser.cpp: file
2950 <        AtomTypesSectionParser.cpp was initially added on branch
2826 <        new_design.
2949 >        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
2950 >        added on branch new_design.
2951  
2952 < 2004-11-22 15:55  tim
2952 > 2004-11-19 22:12  tim
2953  
2954 <        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
2831 <        LennardJonesAtomTypesSectionParser.hpp was initially added on
2832 <        branch new_design.
2833 <
2834 < 2004-11-22 15:55  tim
2835 <
2836 <        * src/io/HarmonicBondTypesSectionParser.cpp: file
2837 <        HarmonicBondTypesSectionParser.cpp was initially added on branch
2838 <        new_design.
2839 <
2840 < 2004-11-22 15:55  tim
2841 <
2842 <        * src/io/AtomTypesSectionParser.hpp: file
2843 <        AtomTypesSectionParser.hpp was initially added on branch
2844 <        new_design.
2845 <
2846 < 2004-11-22 15:55  tim
2847 <
2848 <        * src/io/StickyAtomTypesSectionParser.cpp: file
2849 <        StickyAtomTypesSectionParser.cpp was initially added on branch
2850 <        new_design.
2851 <
2852 < 2004-11-22 15:55  tim
2853 <
2854 <        * src/io/SectionParser.hpp: file SectionParser.hpp was initially
2954 >        * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
2955          added on branch new_design.
2956  
2957 < 2004-11-22 15:55  tim
2957 > 2004-11-19 22:12  tim
2958  
2859 –        * src/io/ChargeAtomTypesSectionParser.cpp: file
2860 –        ChargeAtomTypesSectionParser.cpp was initially added on branch
2861 –        new_design.
2862 –
2863 – 2004-11-22 15:55  tim
2864 –
2865 –        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
2866 –        was initially added on branch new_design.
2867 –
2868 – 2004-11-22 15:55  tim
2869 –
2870 –        * src/io/StickyAtomTypesSectionParser.hpp: file
2871 –        StickyAtomTypesSectionParser.hpp was initially added on branch
2872 –        new_design.
2873 –
2874 – 2004-11-19 17:12  tim
2875 –
2959          * src/: brains/SimState.cpp, brains/SimState.hpp,
2960          io/InitializeFromFile.cpp, types/FixBondType.hpp,
2961          types/FixedBondType.hpp: remove more useless files
2962  
2963 < 2004-11-19 17:12  tim
2963 > 2004-11-19 21:47  tim
2964  
2882 –        * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
2883 –        added on branch new_design.
2884 –
2885 – 2004-11-19 16:47  tim
2886 –
2965          * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp,
2966          integrators/Integrator.cpp, applications/Makedepend: remove more
2967          useless files
2968  
2969 < 2004-11-19 16:38  tim
2969 > 2004-11-19 21:38  tim
2970  
2971 +        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
2972 +        UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp,
2973 +        integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp,
2974 +        integrators/NVT.hpp: refactory integrator
2975 +
2976 + 2004-11-19 21:38  tim
2977 +
2978          * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on
2979          branch new_design.
2980  
2981 < 2004-11-19 16:38  tim
2981 > 2004-11-19 21:38  tim
2982  
2983 <        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
2984 <        on branch new_design.
2983 >        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
2984 >        branch new_design.
2985  
2986 < 2004-11-19 16:38  tim
2986 > 2004-11-19 21:38  tim
2987  
2988          * src/integrators/NPT.hpp: file NPT.hpp was initially added on
2989          branch new_design.
2990  
2991 < 2004-11-19 16:38  tim
2991 > 2004-11-19 21:38  tim
2992  
2993 <        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
2994 <        branch new_design.
2993 >        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
2994 >        on branch new_design.
2995  
2996 < 2004-11-19 16:38  tim
2996 > 2004-11-19 21:38  tim
2997  
2998 <        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
2998 >        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
2999          branch new_design.
3000  
3001 < 2004-11-19 16:38  tim
3001 > 2004-11-19 20:37  tim
3002  
3003 <        * 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
3003 >        * forceFields/newDUFF.frc: new DUFF forcefield
3004  
3005 < 2004-11-19 15:37  tim
3005 > 2004-11-19 20:23  tim
3006  
3007 <        * forceFields/newDUFF.frc: new DUFF forcefield
3007 >        * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
3008 >        branch new_design.
3009  
3010 < 2004-11-19 15:23  tim
3010 > 2004-11-19 20:23  tim
3011  
3012          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp,
3013          UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp,
3014          utils/TypeContainer.hpp: add EAM
3015  
3016 < 2004-11-19 15:23  tim
3016 > 2004-11-19 20:23  tim
3017  
3018          * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on
3019          branch new_design.
3020  
3021 < 2004-11-19 15:23  tim
3021 > 2004-11-19 18:02  tim
3022  
2940 –        * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
2941 –        branch new_design.
2942 –
2943 – 2004-11-19 13:02  tim
2944 –
3023          * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except
3024          error checking
3025  
3026 < 2004-11-19 12:56  tim
3026 > 2004-11-19 17:56  tim
3027  
3028 <        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
3028 >        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
3029          was initially added on branch new_design.
3030  
3031 < 2004-11-19 12:56  tim
3031 > 2004-11-19 17:56  tim
3032  
3033 <        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
3033 >        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
3034          was initially added on branch new_design.
3035  
3036 < 2004-11-19 12:56  tim
3036 > 2004-11-19 17:56  tim
3037  
3038          * src/types/FixBondType.hpp: file FixBondType.hpp was initially
3039          added on branch new_design.
3040  
3041 < 2004-11-19 12:56  tim
3041 > 2004-11-19 17:56  tim
3042  
3043          * src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp,
3044          UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp,
# Line 2971 | Line 3049
3049          utils/StringTokenizer.cpp: DUFF is almost done except error
3050          checking
3051  
3052 < 2004-11-18 19:11  tim
3052 > 2004-11-19 00:11  tim
3053  
3054          * src/UseTheForce/DUFF.cpp: adding DUFF parser
3055  
3056 < 2004-11-18 18:26  tim
3056 > 2004-11-18 23:26  tim
3057  
3058 +        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
3059 +        initially added on branch new_design.
3060 +
3061 + 2004-11-18 23:26  tim
3062 +
3063          * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp,
3064          integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
3065          integrators/VelocityVerletIntegrator.cpp,
# Line 2987 | Line 3070
3070          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding
3071          DUFF parser
3072  
3073 < 2004-11-18 18:26  tim
3073 > 2004-11-18 21:42  tim
3074  
2992 –        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
2993 –        initially added on branch new_design.
2994 –
2995 – 2004-11-18 16:42  tim
2996 –
3075          * forceFields/newDUFF.frc: adding new format DUFF force field
3076  
3077 < 2004-11-18 10:57  chrisfen
3077 > 2004-11-18 15:57  chrisfen
3078  
3079          * src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that
3080          slowed down the force loop
3081  
3082 < 2004-11-18 00:42  tim
3082 > 2004-11-18 05:42  tim
3083  
3084 <        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
3084 >        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
3085          initially added on branch new_design.
3086  
3087 < 2004-11-18 00:42  tim
3087 > 2004-11-18 05:42  tim
3088  
3089 <        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
3089 >        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
3090          initially added on branch new_design.
3091  
3092 < 2004-11-18 00:42  tim
3092 > 2004-11-18 05:42  tim
3093  
3094          * src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp,
3095          primitives/Bend.cpp, utils/NumericConstant.cpp,
3096          utils/NumericConstant.hpp: Adding NumericConstant class
3097  
3098 < 2004-11-17 23:16  tim
3098 > 2004-11-18 04:16  tim
3099  
3100          * src/: applications/quickLate.c, UseTheForce/ForceFields.cpp,
3101          UseTheForce/ForceFields.hpp: remove more junk files
3102  
3103 < 2004-11-17 23:12  tim
3103 > 2004-11-18 04:12  tim
3104  
3105          * src/: brains/ForceFields.cpp, brains/SimSetup.cpp,
3106          brains/SimSetup.hpp, constraints/AbstractClasses.hpp,
# Line 3031 | Line 3109
3109          primitives/BondExtensions.cpp, primitives/SRI.hpp,
3110          primitives/TorsionExtensions.cpp: remove some junk files
3111  
3112 < 2004-11-17 23:07  tim
3112 > 2004-11-18 04:07  tim
3113  
3114          * src/primitives/BendExtensions.cpp: remove some junk files
3115  
3116 < 2004-11-17 23:04  tim
3116 > 2004-11-18 04:04  tim
3117  
3118          * src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp,
3119          QuadraticBondType.hpp: refine QudraticBond
3120  
3121 < 2004-11-17 22:57  tim
3121 > 2004-11-18 03:57  tim
3122  
3123          * src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp
3124  
3125 < 2004-11-17 22:57  tim
3125 > 2004-11-18 03:57  tim
3126  
3127          * src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was
3128          initially added on branch new_design.
3129  
3130 < 2004-11-17 16:47  tim
3130 > 2004-11-17 21:47  tim
3131  
3132 +        * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp
3133 +        was initially added on branch new_design.
3134 +
3135 + 2004-11-17 21:47  tim
3136 +
3137          * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially
3138          added on branch new_design.
3139  
3140 < 2004-11-17 16:47  tim
3140 > 2004-11-17 21:47  tim
3141  
3142 +        * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially
3143 +        added on branch new_design.
3144 +
3145 + 2004-11-17 21:47  tim
3146 +
3147          * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was
3148          initially added on branch new_design.
3149  
3150 < 2004-11-17 16:47  tim
3150 > 2004-11-17 21:47  tim
3151  
3152 <        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
3152 >        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
3153          initially added on branch new_design.
3154  
3155 < 2004-11-17 16:47  tim
3155 > 2004-11-17 21:47  tim
3156  
3157 <        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
3157 >        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
3158          initially added on branch new_design.
3159  
3160 < 2004-11-17 16:47  tim
3160 > 2004-11-17 21:47  tim
3161  
3162          * src/types/CubicBondType.hpp: file CubicBondType.hpp was initially
3163          added on branch new_design.
3164  
3165 < 2004-11-17 16:47  tim
3165 > 2004-11-17 21:47  tim
3166  
3167          * src/: math/ChebyshevPolynomials.cpp,
3168          math/ChebyshevPolynomials.hpp, primitives/Bend.cpp,
# Line 3086 | Line 3174
3174          types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp:
3175          UreyBradleyBend and GhostBend
3176  
3177 < 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 <
3099 < 2004-11-17 13:58  tim
3177 > 2004-11-17 18:58  tim
3178  
3179          * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp
3180          was initially added on branch new_design.
3181  
3182 < 2004-11-17 13:58  tim
3182 > 2004-11-17 18:58  tim
3183  
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 –
3184          * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp
3185          was initially added on branch new_design.
3186  
3187 < 2004-11-17 13:58  tim
3187 > 2004-11-17 18:58  tim
3188  
3189          * src/: math/ChebyshevPolynomials.cpp,
3190          math/ChebyshevPolynomials.hpp, math/Polynomial.hpp,
# Line 3120 | Line 3193
3193          types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types
3194          stuff and Chebyshev Polynomial
3195  
3196 < 2004-11-17 01:37  tim
3196 > 2004-11-17 18:58  tim
3197  
3198 <        * 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
3198 >        * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
3199          initially added on branch new_design.
3200  
3201 < 2004-11-17 01:37  tim
3201 > 2004-11-17 06:37  tim
3202  
3203 <        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
3204 <        initially added on branch new_design.
3203 >        * src/types/PolynomialTorsionType.hpp: file
3204 >        PolynomialTorsionType.hpp was initially added on branch new_design.
3205  
3206 < 2004-11-17 01:37  tim
3206 > 2004-11-17 06:37  tim
3207  
3208          * src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was
3209          initially added on branch new_design.
3210  
3211 < 2004-11-17 01:37  tim
3211 > 2004-11-17 06:37  tim
3212  
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 –
3213          * src/: math/Polynomial.hpp, primitives/Bend.cpp,
3214          primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp,
3215          types/BondType.hpp, types/CharmmTorsionType.cpp,
# Line 3159 | Line 3222
3222          CharmmTorsionType. Need to refine the design and add document for
3223          them
3224  
3225 < 2004-11-16 20:11  tim
3225 > 2004-11-17 06:37  tim
3226  
3227 +        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
3228 +        initially added on branch new_design.
3229 +
3230 + 2004-11-17 06:37  tim
3231 +
3232 +        * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was
3233 +        initially added on branch new_design.
3234 +
3235 + 2004-11-17 06:37  tim
3236 +
3237 +        * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
3238 +        initially added on branch new_design.
3239 +
3240 + 2004-11-17 01:11  tim
3241 +
3242          * src/types/: BendType.hpp, PolynomialBondType.hpp,
3243          TorsionType.hpp: add PolynomialBondType
3244  
3245 < 2004-11-16 20:11  tim
3245 > 2004-11-17 01:11  tim
3246  
3247          * src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was
3248          initially added on branch new_design.
3249  
3250 < 2004-11-16 18:20  tim
3250 > 2004-11-16 23:20  tim
3251  
3174 –        * src/math/Polynomial.hpp: Adding Polynomial class
3175 –
3176 – 2004-11-16 18:20  tim
3177 –
3252          * src/math/Polynomial.hpp: file Polynomial.hpp was initially added
3253          on branch new_design.
3254  
3255 < 2004-11-16 17:04  gezelter
3255 > 2004-11-16 23:20  tim
3256  
3257 <        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
3184 <        initially added on branch new_design.
3257 >        * src/math/Polynomial.hpp: Adding Polynomial class
3258  
3259 < 2004-11-16 17:04  gezelter
3259 > 2004-11-16 22:04  gezelter
3260  
3261          * src/types/MorseBondType.hpp: file MorseBondType.hpp was initially
3262          added on branch new_design.
3263  
3264 < 2004-11-16 17:04  gezelter
3264 > 2004-11-16 22:04  gezelter
3265  
3266 +        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
3267 +        initially added on branch new_design.
3268 +
3269 + 2004-11-16 22:04  gezelter
3270 +
3271          * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp,
3272          MorseBondType.hpp, TorsionType.hpp: added some new stuff
3273  
3274 < 2004-11-16 15:36  tim
3274 > 2004-11-16 20:36  tim
3275  
3276          * src/: primitives/Bend.cpp, primitives/Bend.hpp,
3277          primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp,
3278          types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and
3279          TorsionType
3280  
3281 < 2004-11-15 21:07  tim
3281 > 2004-11-16 02:07  tim
3282  
3283 +        * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
3284 +        branch new_design.
3285 +
3286 + 2004-11-16 02:07  tim
3287 +
3288          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3289          UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp,
3290          utils/StringTokenizer.cpp: adding DUFF class; adding checking
3291          statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer
3292  
3293 < 2004-11-15 21:07  tim
3293 > 2004-11-15 23:00  tim
3294  
3295 <        * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
3296 <        branch new_design.
3295 >        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
3296 >        UseTheForce/ForceFieldFactory.cpp,
3297 >        UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp,
3298 >        UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp,
3299 >        types/AtomType.hpp: adding ForceFieldFactory and LJFF classes
3300  
3301 < 2004-11-15 18:00  tim
3301 > 2004-11-15 23:00  tim
3302  
3303          * src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp
3304          was initially added on branch new_design.
3305  
3306 < 2004-11-15 18:00  tim
3306 > 2004-11-15 23:00  tim
3307  
3308 +        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
3309 +        was initially added on branch new_design.
3310 +
3311 + 2004-11-15 23:00  tim
3312 +
3313          * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
3314          branch new_design.
3315  
3316 < 2004-11-15 18:00  tim
3316 > 2004-11-15 18:02  tim
3317  
3318 <        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
3319 <        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
3318 >        * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was
3319 >        initially added on branch new_design.
3320  
3321 < 2004-11-15 18:00  tim
3321 > 2004-11-15 18:02  tim
3322  
3235 –        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
3236 –        was initially added on branch new_design.
3237 –
3238 – 2004-11-15 13:02  tim
3239 –
3323          * src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on
3324          branch new_design.
3325  
3326 < 2004-11-15 13:02  tim
3326 > 2004-11-15 18:02  tim
3327  
3328          * src/io/DumpReader.hpp: file DumpReader.hpp was initially added on
3329          branch new_design.
3330  
3331 < 2004-11-15 13:02  tim
3331 > 2004-11-15 18:02  tim
3332  
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 –
3333          * src/: brains/SimInfo.cpp, brains/SimInfo.hpp,
3334          brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
3335          integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp,
3336          io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader,
3337          DumpWriter.Next Step is LJFF and integrators
3338  
3339 < 2004-11-13 00:08  tim
3339 > 2004-11-13 05:08  tim
3340  
3341          * src/: brains/ForceManager.cpp, brains/ForceManager.hpp,
3342          brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
# Line 3266 | Line 3344
3344          primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory,
3345          refactory, refactory
3346  
3347 < 2004-11-12 17:43  tim
3347 > 2004-11-12 22:43  tim
3348  
3349          * src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp,
3350          StringTokenizer.cpp: bug fix in hasMoreTokens
3351  
3352 < 2004-11-12 17:28  tim
3352 > 2004-11-12 22:28  tim
3353  
3354          * src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was
3355          initially added on branch new_design.
3356  
3357 < 2004-11-12 17:28  tim
3357 > 2004-11-12 22:28  tim
3358  
3359          * src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding
3360          StringUtils, a c-style strtok like class, need unit test
3361  
3362 < 2004-11-12 12:40  tim
3362 > 2004-11-12 17:40  tim
3363  
3364          * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
3365          brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
3366          brains/SimInfo.hpp: SimCreator and SimInfo are  ready for unit test
3367  
3368 < 2004-11-12 02:05  tim
3368 > 2004-11-12 07:05  tim
3369  
3370          * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
3371          primitives/CutoffGroup.hpp, primitives/Molecule.cpp:
3372          MoleculeCreator forget to create CutoffGroups for free atoms
3373  
3374 < 2004-11-12 01:19  tim
3374 > 2004-11-12 06:19  tim
3375  
3376          * src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
3377          brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
# Line 3301 | Line 3379
3379          io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp:
3380          OOPSE = Object-Obfuscated Parallel Simulation Engine
3381  
3382 < 2004-11-11 16:48  chrisfen
3382 > 2004-11-11 21:48  chrisfen
3383  
3384          * samples/water/tip3p_ice/tp3.md: working sample
3385  
3386 < 2004-11-11 16:47  chrisfen
3386 > 2004-11-11 21:47  chrisfen
3387  
3388          * src/restraints/Restraints.cpp: working towards parallel
3389          restraints
3390  
3391 < 2004-11-11 16:47  chrisfen
3391 > 2004-11-11 21:47  chrisfen
3392  
3393          * src/integrators/Integrator.cpp: Commented out some write
3394          statements
3395  
3396 < 2004-11-11 16:46  chrisfen
3396 > 2004-11-11 21:46  chrisfen
3397  
3398          * src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some
3399          write statements
3400  
3401 < 2004-11-11 16:46  chrisfen
3401 > 2004-11-11 21:46  chrisfen
3402  
3403          * samples/water/tip3p_ice/tp3.md: Fun with ice
3404  
3405 < 2004-11-11 11:41  tim
3405 > 2004-11-11 16:41  tim
3406  
3407          * src/: brains/Exclude.cpp, brains/Exclude.hpp,
3408          brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
# Line 3333 | Line 3411
3411          io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove
3412          useless mpiSimulation
3413  
3414 < 2004-11-11 11:41  tim
3414 > 2004-11-11 16:41  tim
3415  
3416          * src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on
3417          branch new_design.
3418  
3419 < 2004-11-10 17:50  tim
3419 > 2004-11-10 22:50  tim
3420  
3421          * src/: brains/ForceManager.cpp, brains/SimInfo.cpp,
3422          brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp,
3423          integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo
3424  
3425 < 2004-11-10 17:01  tim
3425 > 2004-11-10 22:01  tim
3426  
3427          * src/: brains/SimCreator.cpp, brains/SimCreator.hpp,
3428          brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
# Line 3358 | Line 3436
3436          BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors &
3437          Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint
3438  
3439 < 2004-11-10 09:52  tim
3439 > 2004-11-10 14:52  tim
3440  
3441          * src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a
3442          configurable StatWriter
3443  
3444 < 2004-11-10 09:52  tim
3444 > 2004-11-10 14:52  tim
3445  
3446          * src/io/StatWriter.hpp: file StatWriter.hpp was initially added on
3447          branch new_design.
3448  
3449 < 2004-11-09 21:58  tim
3449 > 2004-11-10 02:58  tim
3450  
3451          * src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation
3452          in progress
3453  
3454 < 2004-11-09 18:11  tim
3454 > 2004-11-09 23:11  tim
3455  
3456 +        * src/brains/ForceManager.cpp: file ForceManager.cpp was initially
3457 +        added on branch new_design.
3458 +
3459 + 2004-11-09 23:11  tim
3460 +
3461 +        * src/integrators/VelocityVerletIntegrator.cpp: file
3462 +        VelocityVerletIntegrator.cpp was initially added on branch
3463 +        new_design.
3464 +
3465 + 2004-11-09 23:11  tim
3466 +
3467          * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp,
3468          brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
3469          brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp,
# Line 3382 | Line 3471
3471          integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp,
3472          integrators/VelocityVerletIntegrator.hpp: adding ForceManager
3473  
3474 < 2004-11-09 18:11  tim
3474 > 2004-11-09 23:11  tim
3475  
3476          * src/brains/ForceManager.hpp: file ForceManager.hpp was initially
3477          added on branch new_design.
3478  
3479 < 2004-11-09 18:11  tim
3479 > 2004-11-09 23:11  tim
3480  
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 –
3481          * src/integrators/NVE.cpp: file NVE.cpp was initially added on
3482          branch new_design.
3483  
3484 < 2004-11-09 18:11  tim
3484 > 2004-11-09 01:08  tim
3485  
3403 –        * src/brains/ForceManager.cpp: file ForceManager.cpp was initially
3404 –        added on branch new_design.
3405 –
3406 – 2004-11-08 20:08  tim
3407 –
3486          * src/integrators/VelocityVerletIntegrator.hpp: file
3487          VelocityVerletIntegrator.hpp was initially added on branch
3488          new_design.
3489  
3490 < 2004-11-08 20:08  tim
3490 > 2004-11-09 01:08  tim
3491  
3492 +        * src/integrators/NVE.hpp: file NVE.hpp was initially added on
3493 +        branch new_design.
3494 +
3495 + 2004-11-09 01:08  tim
3496 +
3497          * src/: brains/Exclude.hpp, brains/Stats.hpp,
3498          integrators/Integrator.hpp, integrators/NVE.hpp,
3499          integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
3500          utils/TypeContainer.hpp: More to break
3501  
3502 < 2004-11-08 20:08  tim
3502 > 2004-11-06 05:21  tim
3503  
3421 –        * src/integrators/NVE.hpp: file NVE.hpp was initially added on
3422 –        branch new_design.
3423 –
3424 – 2004-11-06 00:21  tim
3425 –
3504          * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially
3505          added on branch new_design.
3506  
3507 < 2004-11-06 00:21  tim
3507 > 2004-11-06 05:21  tim
3508  
3509          * src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp,
3510          UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp,
3511          utils/TypeContainer.hpp, utils/next_combination.hpp: adding
3512          ForceField and TypeContainer classes
3513  
3514 < 2004-11-05 18:38  tim
3514 > 2004-11-05 23:38  tim
3515  
3516 +        * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
3517 +        initially added on branch new_design.
3518 +
3519 + 2004-11-05 23:38  tim
3520 +
3521          * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was
3522          initially added on branch new_design.
3523  
3524 < 2004-11-05 18:38  tim
3524 > 2004-11-05 23:38  tim
3525  
3526          * src/: brains/Exclude.cpp, brains/Exclude.hpp,
3527          brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
# Line 3446 | Line 3529
3529          brains/SimInfo.hpp, primitives/Molecule.hpp,
3530          utils/LocalndexManager.hpp: Fix Exclude class etc.
3531  
3532 < 2004-11-05 18:38  tim
3532 > 2004-11-05 21:45  chrisfen
3533  
3451 –        * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
3452 –        initially added on branch new_design.
3453 –
3454 – 2004-11-05 16:45  chrisfen
3455 –
3534          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
3535          visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the
3536          linear visitor
3537  
3538 < 2004-11-05 16:04  chrisfen
3538 > 2004-11-05 21:04  chrisfen
3539  
3540          * src/UseTheForce/DarkSide/shapes.F90: current status of the
3541          debugging process
3542  
3543 < 2004-11-05 16:04  chrisfen
3543 > 2004-11-05 21:04  chrisfen
3544  
3545          * make/Makefile.in: included visitors and minimizer
3546  
3547 < 2004-11-05 16:03  chrisfen
3547 > 2004-11-05 21:03  chrisfen
3548  
3549          * ChangeLog: new changes
3550  
3551 < 2004-11-04 21:56  tim
3551 > 2004-11-05 02:56  tim
3552  
3553          * src/: brains/SimCreator.cpp, brains/SimCreator.hpp,
3554          primitives/Molecule.hpp: Pain......
3555  
3556 < 2004-11-04 15:55  tim
3556 > 2004-11-04 20:55  tim
3557  
3558          * ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp,
3559          src/brains/SimCreator.hpp, src/brains/SimInfo.hpp,
3560          src/brains/Stats.hpp: time to break SimSetup
3561  
3562 < 2004-11-04 15:51  gezelter
3562 > 2004-11-04 20:51  gezelter
3563  
3564          * src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new
3565          classes in progress
3566  
3567 < 2004-11-04 14:48  tim
3567 > 2004-11-04 19:48  tim
3568  
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 –
3569          * src/brains/Stats.cpp: file Stats.cpp was initially added on
3570          branch new_design.
3571  
3572 < 2004-11-04 14:48  tim
3572 > 2004-11-04 19:48  tim
3573  
3574          * src/brains/Stats.hpp: file Stats.hpp was initially added on
3575          branch new_design.
3576  
3577 < 2004-11-04 11:22  gezelter
3577 > 2004-11-04 19:48  tim
3578  
3579 +        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
3580 +        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
3581 +        class
3582 +
3583 + 2004-11-04 16:22  gezelter
3584 +
3585          * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp,
3586          RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and
3587          linearAxis are virtual in StuntDouble, but are implemented by
# Line 3511 | Line 3589
3589          false and "-1" but there should be logic to figure them out in the
3590          other two classes
3591  
3592 < 2004-11-04 11:20  gezelter
3592 > 2004-11-04 16:20  gezelter
3593  
3594          * src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't
3595          remember what I did
3596  
3597 < 2004-11-04 11:20  gezelter
3597 > 2004-11-04 16:20  gezelter
3598  
3599          * src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky
3600  
3601 < 2004-11-04 11:20  gezelter
3601 > 2004-11-04 16:20  gezelter
3602  
3603          * src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX
3604          in the entry_plug so that it only is set if the atoms really are in
3605          the simulation
3606  
3607 < 2004-11-04 11:20  gezelter
3607 > 2004-11-04 16:20  gezelter
3608  
3609          * samples/water/ssd/ssd.md: testing force fields
3610  
3611 < 2004-11-04 11:19  gezelter
3611 > 2004-11-04 16:19  gezelter
3612  
3613          * samples/shape/linear.in: testing shapes
3614  
3615 < 2004-11-03 14:56  tim
3615 > 2004-11-03 19:56  tim
3616  
3617          * src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator
3618          class(similar as SimSetup)
3619  
3620 < 2004-11-03 14:56  tim
3620 > 2004-11-03 19:56  tim
3621  
3622          * src/brains/SimCreator.hpp: file SimCreator.hpp was initially
3623          added on branch new_design.
3624  
3625 < 2004-11-03 14:56  tim
3625 > 2004-11-03 19:56  tim
3626  
3627          * src/brains/SimCreator.cpp: file SimCreator.cpp was initially
3628          added on branch new_design.
3629  
3630 < 2004-11-03 13:00  tim
3630 > 2004-11-03 18:00  tim
3631  
3632          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
3633          UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp,
# Line 3559 | Line 3637
3637          visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get
3638          compiled. Still a long way to go ......
3639  
3640 < 2004-11-03 11:08  tim
3640 > 2004-11-03 16:08  tim
3641  
3642          * ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp,
3643          src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp,
# Line 3574 | Line 3652
3652          src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp,
3653          src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ......
3654  
3655 < 2004-11-02 17:41  tim
3655 > 2004-11-02 22:41  tim
3656  
3657 <        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
3658 <        branch new_design.
3657 >        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
3658 >        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
3659 >        Need unit test
3660  
3661 < 2004-11-02 17:41  tim
3661 > 2004-11-02 22:41  tim
3662  
3663          * src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was
3664          initially added on branch new_design.
3665  
3666 < 2004-11-02 17:41  tim
3666 > 2004-11-02 22:41  tim
3667  
3668 <        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
3669 <        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
3591 <        Need unit test
3668 >        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
3669 >        branch new_design.
3670  
3671 < 2004-11-02 11:59  tim
3671 > 2004-11-02 16:59  tim
3672  
3595 –        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
3596 –        SimSnapshotManager.hpp: SimModel in progress
3597 –
3598 – 2004-11-02 11:59  tim
3599 –
3673          * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
3674          branch new_design.
3675  
3676 < 2004-11-02 10:28  chrisfen
3676 > 2004-11-02 16:59  tim
3677  
3678 +        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
3679 +        SimSnapshotManager.hpp: SimModel in progress
3680 +
3681 + 2004-11-02 15:28  chrisfen
3682 +
3683          * src/: UseTheForce/DarkSide/shapes.F90,
3684          primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes
3685          looks like it's working
3686  
3687 < 2004-11-02 10:27  tim
3687 > 2004-11-02 15:27  tim
3688  
3611 –        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
3612 –        added on branch new_design.
3613 –
3614 – 2004-11-02 10:27  tim
3615 –
3689          * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
3690          functions for dealing with memory issue
3691  
3692 < 2004-11-02 10:23  tim
3692 > 2004-11-02 15:27  tim
3693  
3694 +        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
3695 +        added on branch new_design.
3696 +
3697 + 2004-11-02 15:23  tim
3698 +
3699          * src/: brains/SimModel.hpp, brains/Snapshot.hpp,
3700          brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding
3701          SimModel(something similar as SimInfo)
3702  
3703 < 2004-11-01 17:52  tim
3703 > 2004-11-01 22:52  tim
3704  
3705          * src/: applications/simpleBuilder/MoLocator.hpp,
3706          applications/simpleBuilder/simpleBuilder.cpp,
# Line 3641 | Line 3719
3719          visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom,
3720          RigidBody and StuntDouble classes get compiled
3721  
3722 < 2004-11-01 16:40  tim
3722 > 2004-11-01 21:40  tim
3723  
3724 +        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
3725 +        on branch new_design.
3726 +
3727 + 2004-11-01 21:40  tim
3728 +
3729          * src/primitives/Bend.hpp: file Bend.hpp was initially added on
3730          branch new_design.
3731  
3732 < 2004-11-01 16:40  tim
3732 > 2004-11-01 21:40  tim
3733  
3651 –        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
3652 –        version of Bond, Bend and Torsion.
3653 –
3654 – 2004-11-01 16:40  tim
3655 –
3734          * src/primitives/Bond.hpp: file Bond.hpp was initially added on
3735          branch new_design.
3736  
3737 < 2004-11-01 16:40  tim
3737 > 2004-11-01 21:40  tim
3738  
3739 <        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
3740 <        on branch new_design.
3739 >        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
3740 >        version of Bond, Bend and Torsion.
3741  
3742 < 2004-11-01 16:37  tim
3742 > 2004-11-01 21:37  tim
3743  
3744          * src/types/BendType.hpp: file BendType.hpp was initially added on
3745          branch new_design.
3746  
3747 < 2004-11-01 16:37  tim
3747 > 2004-11-01 21:37  tim
3748  
3749 <        * src/types/BondType.hpp: file BondType.hpp was initially added on
3750 <        branch new_design.
3749 >        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
3750 >        BondType, BendType, TorsionType
3751  
3752 < 2004-11-01 16:37  tim
3752 > 2004-11-01 21:37  tim
3753  
3754          * src/types/TorsionType.hpp: file TorsionType.hpp was initially
3755          added on branch new_design.
3756  
3757 < 2004-11-01 16:37  tim
3757 > 2004-11-01 21:37  tim
3758  
3759 <        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
3760 <        BondType, BendType, TorsionType
3759 >        * src/types/BondType.hpp: file BondType.hpp was initially added on
3760 >        branch new_design.
3761  
3762 < 2004-11-01 15:15  tim
3762 > 2004-11-01 20:15  tim
3763  
3764          * src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp,
3765          CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp,
# Line 3689 | Line 3767
3767          RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp:
3768          break, break and break.....
3769  
3770 < 2004-11-01 14:57  tim
3770 > 2004-11-01 19:57  tim
3771  
3772          * test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp,
3773          DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp,
3774          StuntDouble.hpp: these core classes get compiled
3775  
3776 < 2004-10-29 17:37  tim
3776 > 2004-10-29 22:37  tim
3777  
3778          * test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule
3779          class
3780  
3781 < 2004-10-29 17:28  chrisfen
3781 > 2004-10-29 22:28  chrisfen
3782  
3783          * src/: UseTheForce/DarkSide/atype.F90,
3784          UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp,
3785          types/ShapeAtomType.cpp: still debugging
3786  
3787 < 2004-10-29 17:28  chrisfen
3787 > 2004-10-29 22:28  chrisfen
3788  
3789          * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90:
3790          shapes rcut calculator added
3791  
3792 < 2004-10-29 17:27  chrisfen
3792 > 2004-10-29 22:27  chrisfen
3793  
3794          * samples/shape/linear.md: shorter run
3795  
3796 < 2004-10-29 15:54  tim
3796 > 2004-10-29 20:54  tim
3797  
3798          * test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class.
3799  
3800 < 2004-10-29 11:22  tim
3800 > 2004-10-29 16:22  tim
3801  
3802          * test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp,
3803          ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove
3804          some deprecated files
3805  
3806 < 2004-10-29 11:20  tim
3806 > 2004-10-29 16:20  tim
3807  
3808          * test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp,
3809          DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp:
3810          More painful reconstruction is coming !!!
3811  
3812 < 2004-10-28 17:34  tim
3812 > 2004-10-28 22:34  tim
3813  
3814          * src/brains/DataStorage.hpp, src/utils/next_combination.hpp,
3815          test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp,
# Line 3739 | Line 3817
3817          test/brains/StuntDouble.hpp: More work on StuntDouble, Atom,
3818          DirectionalAtom and RigidBody
3819  
3820 < 2004-10-28 17:26  tim
3820 > 2004-10-28 22:26  tim
3821  
3822          * ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp,
3823          src/applications/simpleBuilder/MoLocator.cpp,
# Line 3747 | Line 3825
3825          src/utils/GenericFactory.hpp, src/utils/next_combination.hpp:
3826          remove old Vector3d.hpp from application/simpleBuilder
3827  
3828 < 2004-10-28 16:42  tim
3828 > 2004-10-28 21:42  tim
3829  
3830          * src/utils/next_combination.hpp: Minor change in next_combination
3831  
3832 < 2004-10-28 16:28  tim
3832 > 2004-10-28 21:28  tim
3833  
3834          * src/utils/next_combination.hpp,
3835          test/utils/NextCombinationTestCase.cpp,
3836          test/utils/ReplaceWildCardTestCase.cpp: Done with combination
3837  
3838 < 2004-10-28 16:11  tim
3838 > 2004-10-28 21:11  tim
3839  
3840          * src/utils/next_combination.hpp: change documentation of
3841          next_combination.hpp
3842  
3843 < 2004-10-28 15:41  tim
3843 > 2004-10-28 20:41  tim
3844  
3845          * ChangeLog, src/utils/next_combination.hpp,
3846          test/utils/NextCombinationTestCase.cpp,
3847          test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working
3848  
3849 < 2004-10-28 15:01  tim
3849 > 2004-10-28 20:01  tim
3850  
3851          * src/utils/next_combination.hpp: adding replace wildcard function
3852  
3853 < 2004-10-28 14:33  tim
3853 > 2004-10-28 19:33  tim
3854  
3855          * src/utils/next_combination.hpp: Minor change
3856  
3857 < 2004-10-28 14:06  tim
3857 > 2004-10-28 19:06  tim
3858  
3859          * ChangeLog, src/applications/simpleBuilder/MoLocator.hpp,
3860          src/applications/simpleBuilder/simpleBuilder.cpp,
# Line 3786 | Line 3864
3864          test/utils/next_combination.hpp: STL next_permutation like
3865          next_combination is working
3866  
3867 < 2004-10-28 12:22  chrisfen
3867 > 2004-10-28 17:22  chrisfen
3868  
3869          * src/UseTheForce/WATER.cpp: fix of setDipoles
3870  
3871 < 2004-10-28 12:20  gezelter
3871 > 2004-10-28 17:20  gezelter
3872  
3873          * src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the
3874          shapeFile
3875  
3876 < 2004-10-28 12:20  gezelter
3876 > 2004-10-28 17:20  gezelter
3877  
3878          * samples/shape/linear.md: forgot the orientation line
3879  
3880 < 2004-10-28 11:56  gezelter
3880 > 2004-10-28 16:56  gezelter
3881  
3882          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
3883          UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
3884          UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate
3885          declaration foo
3886  
3887 < 2004-10-28 11:55  gezelter
3887 > 2004-10-28 16:55  gezelter
3888  
3889          * samples/lipid/5x5.md: uncommented .in line
3890  
3891 < 2004-10-28 10:42  tim
3891 > 2004-10-28 15:42  tim
3892  
3893          * test/utils/: Makefile, NextCombinationTestCase.cpp,
3894          NextCombinationTestCase.hpp, next_combination.hpp: next_combination
3895          in progress
3896  
3897 < 2004-10-28 10:15  tim
3897 > 2004-10-28 15:15  tim
3898  
3899          * test/utils/: NextCombinationTestCase.cpp,
3900          NextCombinationTestCase.hpp: adding next_combination test case
3901  
3902 < 2004-10-28 10:02  tim
3902 > 2004-10-28 15:02  tim
3903  
3904          * test/utils/next_combination.hpp: STL Compatible combination
3905          sequence generator
3906  
3907 < 2004-10-28 01:23  tim
3907 > 2004-10-28 06:23  tim
3908  
3909          * test/utils/: GenerateCombination.hpp,
3910          ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp
3911  
3912 < 2004-10-28 01:16  tim
3912 > 2004-10-28 06:16  tim
3913  
3914          * test/utils/GenerateCombination.hpp: a STL next_permutaion like
3915          next_combination function.
3916  
3917 < 2004-10-27 22:27  tim
3917 > 2004-10-28 03:27  tim
3918  
3919          * test/utils/ReplaceWildCard.hpp: no message
3920  
3921 < 2004-10-27 22:14  tim
3921 > 2004-10-28 03:14  tim
3922  
3923          * test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp:
3924          ReplaceWildCard(recursive version) is working, need refactoring. An
3925          iterative version is on the way
3926  
3927 < 2004-10-27 21:28  tim
3927 > 2004-10-28 02:28  tim
3928  
3929          * test/utils/: Makefile, ReplaceWildCard.hpp,
3930          ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress
3931  
3932 < 2004-10-27 21:08  tim
3932 > 2004-10-28 02:08  tim
3933  
3934          * test/utils/: ReplaceWildCardTestCase.cpp,
3935          ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard
3936  
3937 < 2004-10-27 18:17  tim
3937 > 2004-10-27 23:17  tim
3938  
3939          * test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need
3940          test
3941  
3942 < 2004-10-27 01:25  tim
3942 > 2004-10-27 06:25  tim
3943  
3944          * src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild
3945          char matching is on the way
3946  
3947 < 2004-10-27 01:07  tim
3947 > 2004-10-27 06:07  tim
3948  
3949          * src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4
3950  
3951 < 2004-10-26 22:00  gezelter
3951 > 2004-10-27 03:00  gezelter
3952  
3953          * src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix
3954  
3955 < 2004-10-26 21:20  gezelter
3955 > 2004-10-27 02:20  gezelter
3956  
3957          * src/UseTheForce/ForceFields.hpp: subclass foo
3958  
3959 < 2004-10-26 21:16  gezelter
3959 > 2004-10-27 02:16  gezelter
3960  
3961          * src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* ->
3962          string conversion
3963  
3964 < 2004-10-26 19:01  gezelter
3964 > 2004-10-27 00:01  gezelter
3965  
3966          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
3967          UseTheForce/ForceFields.hpp, brains/SimSetup.cpp,
3968          brains/SimSetup.hpp: char* -> string
3969  
3970 < 2004-10-26 17:25  gezelter
3970 > 2004-10-26 22:25  gezelter
3971  
3972          * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp,
3973          Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp,
3974          ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some
3975          isXXX
3976  
3977 < 2004-10-26 17:25  gezelter
3977 > 2004-10-26 22:25  gezelter
3978  
3979          * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
3980          define name collision
3981  
3982 < 2004-10-26 17:24  gezelter
3982 > 2004-10-26 22:24  gezelter
3983  
3984          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
3985          UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
# Line 3910 | Line 3988
3988          UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp:
3989          forcefield refactoring for shapes
3990  
3991 < 2004-10-26 17:24  gezelter
3991 > 2004-10-26 22:24  gezelter
3992  
3993          * samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape,
3994          Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in,
3995          linear.md, linear.shape, toluene.shape: adding sample shape
3996          directory
3997  
3998 < 2004-10-26 17:19  tim
3998 > 2004-10-26 22:19  tim
3999  
4000          * ChangeLog, src/brains/DataStorage.cpp,
4001          src/brains/DataStorage.hpp, src/brains/Snapshot.hpp,
# Line 3925 | Line 4003
4003          test/brains/DataStorageTestCase.hpp, test/brains/Makefile:
4004          DataStorage passes unit test
4005  
4006 < 2004-10-26 13:03  chrisfen
4006 > 2004-10-26 18:03  chrisfen
4007  
4008          * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h:
4009          Changes to help advance shapes
4010  
4011 < 2004-10-26 13:02  chrisfen
4011 > 2004-10-26 18:02  chrisfen
4012  
4013          * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to
4014          Shapes force field reader
4015  
4016 < 2004-10-26 12:28  tim
4016 > 2004-10-26 17:28  tim
4017  
4018          * src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and
4019          SnapshotTestCase in progress
4020  
4021 < 2004-10-25 17:46  tim
4021 > 2004-10-25 22:46  tim
4022  
4023          * ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
4024          src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
# Line 3949 | Line 4027
4027          test/math/VectorTestCase.cpp: add getArray function to  RectMatrix
4028          and Vector classes
4029  
4030 < 2004-10-25 12:03  tim
4030 > 2004-10-25 17:03  tim
4031  
4032          * ChangeLog, src/utils/GenericFactory.hpp,
4033          test/utils/GenericFactoryTestCase.cpp,
# Line 3957 | Line 4035
4035          GenericFactory Test Case. GenericFactory now can bed used to creat
4036          ForcefieldFactory and IntegratorFactory etc.
4037  
4038 < 2004-10-24 23:08  tim
4038 > 2004-10-25 04:08  tim
4039  
4040          * src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp,
4041          brains/SimSnapshotManager.hpp, brains/Snapshot.hpp,
4042          brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes
4043          get reconstructed
4044  
4045 < 2004-10-24 02:55  tim
4045 > 2004-10-24 07:55  tim
4046  
4047          * src/utils/GenericFactory.hpp: GenericFactory pass unit test
4048  
4049 < 2004-10-23 18:09  tim
4049 > 2004-10-23 23:09  tim
4050  
4051          * test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp,
4052          StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp,
4053          RigidBody.cpp: Refactoring in progress
4054  
4055 < 2004-10-22 18:09  tim
4055 > 2004-10-22 23:09  tim
4056  
4057          * ChangeLog, src/brains/Snapshot.hpp,
4058          src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp,
4059          test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp,
4060          test/brains/StuntDouble.hpp: more work in Snapshot
4061  
4062 < 2004-10-22 17:59  chrisfen
4062 > 2004-10-22 22:59  chrisfen
4063  
4064          * src/: UseTheForce/LJFF.cpp,
4065          UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear
4066          god!  It runs and conserves energy!
4067  
4068 < 2004-10-22 17:54  chrisfen
4068 > 2004-10-22 22:54  chrisfen
4069  
4070          * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY
4071  
4072 < 2004-10-22 17:53  chrisfen
4072 > 2004-10-22 22:53  chrisfen
4073  
4074          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4075          UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
# Line 3999 | Line 4077
4077          brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey
4078          breakey
4079  
4080 < 2004-10-22 17:53  chrisfen
4080 > 2004-10-22 22:53  chrisfen
4081  
4082          * make/Makefile.in: compiler flags
4083  
4084 < 2004-10-22 16:20  gezelter
4084 > 2004-10-22 21:20  gezelter
4085  
4086          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4087          UseTheForce/LJFF.cpp, UseTheForce/doForces.F90,
4088          brains/fSimulation.h, types/AtomType.hpp,
4089          types/DirectionalAtomType.hpp: fixey fixey
4090  
4091 < 2004-10-22 15:22  gezelter
4091 > 2004-10-22 20:22  gezelter
4092  
4093          * src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h,
4094          charge.F90, charge_interface.h, dipole.F90, dipole_interface.h,
4095          lj_interface.h, shapes.F90, simulation.F90: Added un-busticated
4096          fortran files and c/Fortran interfaces
4097  
4098 < 2004-10-22 15:21  gezelter
4098 > 2004-10-22 20:21  gezelter
4099  
4100          * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
4101          DirectionalAtomType.hpp, Makefile: More on AtomType and
4102          DirectionalAtomType
4103  
4104 < 2004-10-22 09:47  gezelter
4104 > 2004-10-22 14:47  gezelter
4105  
4106          * src/types/AtomType.hpp: Adding AtomType
4107  
4108 < 2004-10-21 16:31  tim
4108 > 2004-10-21 21:31  tim
4109  
4110          * ChangeLog, src/brains/Snapshot.hpp,
4111          src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp,
# Line 4036 | Line 4114
4114          test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp:
4115          Snapshot and SnapshotManager in progress
4116  
4117 < 2004-10-21 16:30  tim
4117 > 2004-10-21 21:30  tim
4118  
4119          * test/brains/: BrainsTest.cpp, Makefile,
4120          SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp,
4121          SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for
4122          Snapshot and snapshotManager.
4123  
4124 < 2004-10-21 15:15  gezelter
4124 > 2004-10-21 20:15  gezelter
4125  
4126          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4127          UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
# Line 4054 | Line 4132
4132          brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky.  
4133          Fixey Fixey.
4134  
4135 < 2004-10-21 11:32  tim
4135 > 2004-10-21 16:32  tim
4136  
4137          * src/utils/GenericData.cpp, src/utils/Makefile,
4138          test/utils/Makefile, test/utils/UtilTest: remove some junk files
4139  
4140 < 2004-10-21 11:24  tim
4140 > 2004-10-21 16:24  tim
4141  
4142          * test/utils/GenericData.hpp: remove backup of  GenericData.hpp
4143  
4144 < 2004-10-21 11:22  tim
4144 > 2004-10-21 16:22  tim
4145  
4146          * ChangeLog, src/brains/SimSetup.cpp,
4147          src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp,
# Line 4081 | Line 4159
4159          src/visitors/ZconsVisitor.hpp: replace old GebericData with  new
4160          GenericData
4161  
4162 < 2004-10-21 10:25  chuckv
4162 > 2004-10-21 15:25  chuckv
4163  
4164          * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj
4165          module.
4166  
4167 < 2004-10-21 10:24  chuckv
4167 > 2004-10-21 15:24  chuckv
4168  
4169          * src/UseTheForce/DarkSide/lj_interface.h: Added interface for
4170          fortran lj module.
4171  
4172 < 2004-10-20 17:54  tim
4172 > 2004-10-20 22:54  tim
4173  
4174          * ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp,
4175          test/utils/GenericDataTestCase.cpp, test/utils/Makefile,
# Line 4099 | Line 4177
4177          test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest:
4178          GenericData and PropertyMap  pass unit test.
4179  
4180 < 2004-10-20 16:52  gezelter
4180 > 2004-10-20 21:52  gezelter
4181  
4182          * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90,
4183          DarkSide/sticky_interface.h: fixed a fortran name problem
4184  
4185 < 2004-10-20 16:38  tim
4185 > 2004-10-20 21:38  tim
4186  
4187          * test/utils/: GenericData.hpp, GenericDataTestCase.cpp,
4188          GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp,
4189          UtilTest, UtilTest.cpp: adding generic data test case
4190  
4191 < 2004-10-20 16:16  chuckv
4191 > 2004-10-20 21:16  chuckv
4192  
4193          * configure, ac-tools/aclocal.m4,
4194          src/UseTheForce/DarkSide/Makefile,
# Line 4122 | Line 4200
4200          Fortran/C++ interface de-obfuscation project appears to be
4201          complete!  Woo hoo!
4202  
4203 < 2004-10-20 15:47  chuckv
4203 > 2004-10-20 20:47  chuckv
4204  
4205          * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp,
4206          fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project
4207          continues
4208  
4209 < 2004-10-20 15:46  chuckv
4209 > 2004-10-20 20:46  chuckv
4210  
4211          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4212          UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
# Line 4145 | Line 4223
4223          brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface
4224          de-obfuscation project (It is a very long story)
4225  
4226 < 2004-10-20 13:07  tim
4226 > 2004-10-20 18:07  tim
4227  
4228          * ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
4229          test/math/SquareMatrix3TestCase.cpp,
4230          test/math/SquareMatrixTestCase.cpp,
4231          test/math/SquareMatrixTestCase.hpp: Math library pass the unit test
4232  
4233 < 2004-10-20 00:52  tim
4233 > 2004-10-20 05:52  tim
4234  
4235          * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and
4236          SnapshotManager in design phase
4237  
4238 < 2004-10-19 23:54  gezelter
4238 > 2004-10-20 04:54  gezelter
4239  
4240          * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace
4241          problem prevented linking
4242  
4243 < 2004-10-19 23:54  gezelter
4243 > 2004-10-20 04:54  gezelter
4244  
4245          * src/UseTheForce/Shapes_FF.cpp: fixed include
4246  
4247 < 2004-10-19 23:26  gezelter
4247 > 2004-10-20 04:26  gezelter
4248  
4249          * src/utils/: Makefile, definitions.F90, definitions_module.F90,
4250          oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90:
4251          more fortran name mangling
4252  
4253 < 2004-10-19 23:23  gezelter
4253 > 2004-10-20 04:23  gezelter
4254  
4255          * src/profiling/timing.F90: yet more fortran renaming
4256  
4257 < 2004-10-19 23:19  gezelter
4257 > 2004-10-20 04:19  gezelter
4258  
4259          * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h,
4260          do_Forces.F90, do_Forces.h, notifyCutoffs.F90,
4261          notifyCutoffs_interface.h, notifycutoffs_module_interface.h,
4262          wrappers.F90: Fortran name cleanup continues
4263  
4264 < 2004-10-19 23:12  gezelter
4264 > 2004-10-20 04:12  gezelter
4265  
4266          * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some
4267          broken fortran stuff
4268  
4269 < 2004-10-19 23:02  gezelter
4269 > 2004-10-20 04:02  gezelter
4270  
4271          * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
4272          atype_interface.h, atype_module.F90, atype_module_interface.h,
# Line 4205 | Line 4283
4283          sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90:
4284          name sanity on the fortran side
4285  
4286 < 2004-10-19 19:18  tim
4286 > 2004-10-20 00:18  tim
4287  
4288          * test/math/SquareMatrix3TestCase.hpp: [no log message]
4289  
4290 < 2004-10-19 18:01  tim
4290 > 2004-10-19 23:01  tim
4291  
4292          * src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
4293          src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp:
4294          except diagonalize(), all of functions in math library pass the
4295          test
4296  
4297 < 2004-10-19 17:43  chuckv
4297 > 2004-10-19 22:43  chuckv
4298  
4299          * src/UseTheForce/do_Forces.h: Added correct prototypes for
4300          C-fortran interface functions.
4301  
4302 < 2004-10-19 17:37  chuckv
4302 > 2004-10-19 22:37  chuckv
4303  
4304          * src/UseTheForce/DarkSide/: atype_module_interface.h,
4305          eam_module_inteface.h, gb_module_interface.h,
# Line 4229 | Line 4307
4307          sticky_pair_module_interface.h: Added correct prototypes for
4308          C-fortran interface functions.
4309  
4310 < 2004-10-19 16:28  tim
4310 > 2004-10-19 21:28  tim
4311  
4312          * ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp,
4313          src/math/SquareMatrix.hpp, src/math/Vector.hpp,
# Line 4239 | Line 4317
4317          test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more
4318          bugs get fixed at math library
4319  
4320 < 2004-10-19 15:43  chuckv
4320 > 2004-10-19 20:43  chuckv
4321  
4322          * src/UseTheForce/: DarkSide/atype_module_interface.h,
4323          DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h,
# Line 4253 | Line 4331
4331          notifycutoffs_module_interface.h: Added new files for fortran
4332          interface.
4333  
4334 < 2004-10-19 15:43  gezelter
4334 > 2004-10-19 20:43  gezelter
4335  
4336          * src/UseTheForce/Makefile: regressing
4337  
4338 < 2004-10-19 15:40  gezelter
4338 > 2004-10-19 20:40  gezelter
4339  
4340          * src/: UseTheForce/DarkSide/calc_shapes.F90,
4341          UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp:
4342          working on shapes for portability
4343  
4344 < 2004-10-19 15:40  gezelter
4344 > 2004-10-19 20:40  gezelter
4345  
4346          * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes
4347  
4348 < 2004-10-19 13:21  chrisfen
4348 > 2004-10-19 18:21  chrisfen
4349  
4350          * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around
4351          findBegin
4352  
4353 < 2004-10-18 23:34  tim
4353 > 2004-10-19 04:34  tim
4354  
4355          * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs
4356          are fixed in Vector class
4357  
4358 < 2004-10-18 23:28  tim
4358 > 2004-10-19 04:28  tim
4359  
4360          * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix
4361          some bugs in RectMatrixTestCase
4362  
4363 < 2004-10-18 23:21  tim
4363 > 2004-10-19 04:21  tim
4364  
4365          * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp,
4366          test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp,
4367          test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp,
4368          test/math/VectorTestCase.hpp: implement more test cases
4369  
4370 < 2004-10-18 18:13  tim
4370 > 2004-10-18 23:13  tim
4371  
4372          * ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp,
4373          src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
# Line 4298 | Line 4376
4376          test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more
4377          tests on math library
4378  
4379 < 2004-10-18 16:03  tim
4379 > 2004-10-18 21:03  tim
4380  
4381          * test/math/: Makefile, QuaternionTestCase.cpp,
4382          QuaternionTestCase.hpp, RectMatrixTestCase.cpp,
# Line 4306 | Line 4384
4384          Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding
4385          more testing units
4386  
4387 < 2004-10-18 12:07  tim
4387 > 2004-10-18 17:07  tim
4388  
4389          * src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp,
4390          math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp,
4391          math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp,
4392          utils/GenericFactory.hpp: fix some bugs in Quaternion class
4393  
4394 < 2004-10-18 11:30  gezelter
4394 > 2004-10-18 16:30  gezelter
4395  
4396          * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
4397          Your basic run of the mill real-valued versions of Y_l^m(\theta,
4398          \phi)
4399  
4400 < 2004-10-18 11:29  gezelter
4400 > 2004-10-18 16:29  gezelter
4401  
4402          * src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp,
4403          types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp,
4404          utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting
4405          Shapes into OOPSE
4406  
4407 < 2004-10-18 10:21  gezelter
4407 > 2004-10-18 15:21  gezelter
4408  
4409          * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType
4410  
4411 < 2004-10-18 00:23  tim
4411 > 2004-10-18 05:23  tim
4412  
4413          * test/math/VectorTestCase.hpp: adding  vector test case
4414  
4415 < 2004-10-18 00:23  tim
4415 > 2004-10-18 05:23  tim
4416  
4417          * src/utils/GenericFactory.hpp: adding generic factory and vector
4418          test case
4419  
4420 < 2004-10-16 20:19  tim
4420 > 2004-10-17 01:19  tim
4421  
4422          * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp,
4423          SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in
4424          progress
4425  
4426 < 2004-10-15 20:31  tim
4426 > 2004-10-16 01:31  tim
4427  
4428          * src/math/Quaternion.hpp: add quaternion class
4429  
4430 < 2004-10-15 16:11  tim
4430 > 2004-10-15 21:11  tim
4431  
4432          * test/io/: DUFF.frc, IfstrstreamTestCase.cpp,
4433          IfstrstreamTestCase.hpp: adding test file
4434  
4435 < 2004-10-15 16:10  tim
4435 > 2004-10-15 21:10  tim
4436  
4437          * src/io/basic_ifstrstream.hpp: fix a bunch of bugs
4438  
4439 < 2004-10-15 15:42  tim
4439 > 2004-10-15 20:42  tim
4440  
4441          * src/io/basic_ifstrstream.hpp: change const_cast to statc_const
4442  
4443 < 2004-10-15 15:35  tim
4443 > 2004-10-15 20:35  tim
4444  
4445          * src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp
4446  
4447 < 2004-10-15 15:34  tim
4447 > 2004-10-15 20:34  tim
4448  
4449          * test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use
4450          namespace oopse
4451  
4452 < 2004-10-15 14:38  chuckv
4452 > 2004-10-15 19:38  chuckv
4453  
4454          * configure, ac-tools/aclocal.m4: Changed optimization flags for
4455          XLF and XLC.
4456  
4457 < 2004-10-15 13:28  tim
4457 > 2004-10-15 18:28  tim
4458  
4459          * test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp:
4460          adding ifstrstream test case
4461  
4462 < 2004-10-15 13:20  tim
4462 > 2004-10-15 18:20  tim
4463  
4464          * src/io/basic_ifstrstream.hpp: fix include
4465  
4466 < 2004-10-15 13:18  tim
4466 > 2004-10-15 18:18  tim
4467  
4468          * src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi
4469  
4470 < 2004-10-15 13:17  tim
4470 > 2004-10-15 18:17  tim
4471  
4472          * test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile
4473  
4474 < 2004-10-15 13:16  tim
4474 > 2004-10-15 18:16  tim
4475  
4476          * test/io/: Makefile, ifstrstreamTestCase.cpp,
4477          ifstrstreamTestCase.hpp: adding test case for ifstrstream
4478  
4479 < 2004-10-15 10:37  tim
4479 > 2004-10-15 15:37  tim
4480  
4481          * test/io/: IOTest.cpp, ifstrstreamTestCase.cpp,
4482          ifstrstreamTestCase.hpp: add ifstrstreamTestCase
4483  
4484 < 2004-10-15 10:20  tim
4484 > 2004-10-15 15:20  tim
4485  
4486          * src/io/basic_ifstrstream.hpp: add checkFilename Option
4487  
4488 < 2004-10-15 10:19  tim
4488 > 2004-10-15 15:19  tim
4489  
4490          * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp,
4491          SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add
4492          SquareMatrixTestCase class
4493  
4494 < 2004-10-15 02:52  tim
4494 > 2004-10-15 07:52  tim
4495  
4496          * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream
4497  
4498 < 2004-10-14 18:28  tim
4498 > 2004-10-14 23:28  tim
4499  
4500          * src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp,
4501          Vector.hpp: math library in progress
4502  
4503 < 2004-10-14 18:27  tim
4503 > 2004-10-14 23:27  tim
4504  
4505          * src/io/FileReader.hpp: FileReader in progress
4506  
4507 < 2004-10-13 18:53  tim
4507 > 2004-10-13 23:53  tim
4508  
4509          * src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress,
4510          test in isOrthogonal of SquareMatrix is failed by some reasons
4511  
4512 < 2004-10-13 17:28  tim
4512 > 2004-10-13 22:28  tim
4513  
4514          * src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap
4515          class
4516  
4517 < 2004-10-13 17:27  tim
4517 > 2004-10-13 22:27  tim
4518  
4519          * test/math/: MainTest.cpp, RectMatrixTestCase.cpp,
4520          RectMatrixTestCase.hpp: adding testing unit
4521  
4522 < 2004-10-13 17:24  tim
4522 > 2004-10-13 22:24  tim
4523  
4524          * src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix
4525  
4526 < 2004-10-13 01:51  tim
4526 > 2004-10-13 06:51  tim
4527  
4528          * src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp,
4529          Vector3.hpp: refactory vector and matrix classes
4530  
4531 < 2004-10-13 01:50  tim
4531 > 2004-10-13 06:50  tim
4532  
4533          * src/math/Vector3d.hpp: Remove some Makefile.in
4534  
4535 < 2004-10-12 18:57  tim
4535 > 2004-10-12 23:57  tim
4536  
4537          * src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and
4538          Matrix3x3d.hpp
4539  
4540 < 2004-10-12 14:08  tim
4540 > 2004-10-12 19:08  tim
4541  
4542          * doc/: cppstyle.html, style.css: adding c++ coding style
4543  
4544 < 2004-10-11 17:15  tim
4544 > 2004-10-11 22:15  tim
4545  
4546          * src/: constraints/AbstractClasses.hpp,
4547          integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp:
4548          change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
4549  
4550 < 2004-10-11 16:54  tim
4550 > 2004-10-11 21:54  tim
4551  
4552          * scripts/filepp: fix a bug in filepp
4553  
4554 < 2004-10-11 16:13  tim
4554 > 2004-10-11 21:13  tim
4555  
4556          * make/Makefile.in: using filepp to generate dependencies instead
4557          of compilers
4558  
4559 < 2004-10-11 16:10  tim
4559 > 2004-10-11 21:10  tim
4560  
4561          * scripts/filepp: filepp can be used to generate dependencies for
4562          c/c++ now
4563  
4564 < 2004-10-11 13:40  tim
4564 > 2004-10-11 18:40  tim
4565  
4566          * make/Makefile.in: remove -module from F90Options
4567  
4568 < 2004-10-11 13:01  tim
4568 > 2004-10-11 18:01  tim
4569  
4570          * make/Makefile.in: adding rules to move fortran 90 module to
4571          target directory
4572  
4573 < 2004-10-11 10:43  gezelter
4573 > 2004-10-11 15:43  gezelter
4574  
4575          * make/Makefile.in: fixed makefile.in
4576  
4577 < 2004-10-11 09:51  tim
4577 > 2004-10-11 14:51  tim
4578  
4579          * scripts/filepp: remove "use bytes" which causes problem in sgi
4580          machine
4581  
4582 < 2004-10-11 09:26  tim
4582 > 2004-10-11 14:26  tim
4583  
4584          * forceFields/Makefile: add Makefile
4585  
4586 < 2004-10-11 09:23  tim
4586 > 2004-10-11 14:23  tim
4587  
4588          * samples/: water/dimer/Makefile, water/spce/Makefile,
4589          water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile,
4590          water/tip4p/Makefile, zcons/Makefile: fix Makefile under water
4591          directory
4592  
4593 < 2004-10-09 01:01  tim
4593 > 2004-10-09 06:01  tim
4594  
4595          * samples/: alkane/Makefile.in, lipid/Makefile.in,
4596          metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in
4597  
4598 < 2004-10-08 18:15  tim
4598 > 2004-10-08 23:15  tim
4599  
4600          * make/Makefile.in: [no log message]
4601  
4602 < 2004-10-08 17:51  tim
4602 > 2004-10-08 22:51  tim
4603  
4604          * make/Makefile.in: fix make install
4605  
4606 < 2004-10-08 17:10  tim
4606 > 2004-10-08 22:10  tim
4607  
4608          * make/Makefile.in: adding make install
4609  
4610 < 2004-10-08 17:04  tim
4610 > 2004-10-08 22:04  tim
4611  
4612          * samples/: alkane/Makefile, lipid/Makefile, metals/Makefile,
4613          minimizer/Makefile, water/Makefile.in, water/dimer/Makefile,
# Line 4540 | Line 4618
4618          water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile,
4619          zcons/Makefile.in: add Makefile to sample directory
4620  
4621 < 2004-10-06 18:03  gezelter
4621 > 2004-10-06 23:03  gezelter
4622  
4623          * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt
4624          stuff
4625  
4626 < 2004-10-06 18:03  gezelter
4626 > 2004-10-06 23:03  gezelter
4627  
4628          * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
4629          make/Doxyfile, src/applications/getopt.c,
4630          src/applications/getopt1.c, src/applications/gnugetopt.h: more
4631          build fixes
4632  
4633 < 2004-10-06 17:20  tim
4633 > 2004-10-06 22:20  tim
4634  
4635          * make/: Doxyfile, Makefile.in: adding doxygen configuration file
4636  
4637 < 2004-10-06 17:19  tim
4637 > 2004-10-06 22:19  tim
4638  
4639          * scripts/filepp: filepp can handle different fortran module case
4640          and suffix
4641  
4642 < 2004-10-06 16:27  gezelter
4642 > 2004-10-06 21:27  gezelter
4643  
4644          * src/restraints/Restraints.cpp: Chris doesn't know about the
4645          OOPSE-2.0 directory structure yet
4646  
4647 < 2004-10-06 16:27  gezelter
4647 > 2004-10-06 21:27  gezelter
4648  
4649          * ChangeLog: Yeah yeah, we'lll get around to it later
4650  
4651 < 2004-10-06 16:22  gezelter
4651 > 2004-10-06 21:22  gezelter
4652  
4653          * configure, ac-tools/configure.in, ac-tools/fortran90.m4,
4654          make/Makefile.in: cleaning up build process
4655  
4656 < 2004-10-06 15:01  chrisfen
4656 > 2004-10-06 20:01  chrisfen
4657  
4658          * src/restraints/Restraints.cpp: made the file reading in
4659          restraints more intelligent - no longer gives uninformative seg
4660          faults
4661  
4662 < 2004-10-06 14:55  gezelter
4662 > 2004-10-06 19:55  gezelter
4663  
4664          * src/applications/simpleBuilder/Make.ftemp.old: cleaning up
4665  
4666 < 2004-10-06 14:51  gezelter
4666 > 2004-10-06 19:51  gezelter
4667  
4668          * LICENSE, MPIobj/dummy, make/Makefile, obj/dummy,
4669          scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit
4670  
4671 < 2004-10-06 13:53  tim
4671 > 2004-10-06 18:53  tim
4672  
4673          * make/: Makefile, Makefile.in: fix make statistics
4674  
4675 < 2004-10-06 13:18  tim
4675 > 2004-10-06 18:18  tim
4676  
4677          * make/: Makefile, Makefile.in: adding GNU make functions to
4678          combine all of the static libraries to a big library
4679  
4680 < 2004-10-05 17:57  tim
4680 > 2004-10-05 22:57  tim
4681  
4682          * make/: Makefile, Makefile.in:  adding shared library flag
4683  
4684 < 2004-10-05 14:37  tim
4684 > 2004-10-05 19:37  tim
4685  
4686          * src/: Makefile, UseTheForce/Makefile,
4687          UseTheForce/mpiSimulation_module.F90,
# Line 4611 | Line 4689
4689          UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move
4690          mpiSimulation_module to DarkSide
4691  
4692 < 2004-10-05 14:35  tim
4692 > 2004-10-05 19:35  tim
4693  
4694          * make/: Makefile, Makefile.in: building MPI version;using static
4695          library instead of shared library
4696  
4697 < 2004-10-05 09:14  tim
4697 > 2004-10-05 14:14  tim
4698  
4699          * make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90
4700          to filepp
4701  
4702 < 2004-10-04 15:56  tim
4702 > 2004-10-04 20:56  tim
4703  
4704          * make/: Makefile, Makefile.in: add make cvslog
4705  
4706 < 2004-10-04 11:24  gezelter
4706 > 2004-10-04 16:24  gezelter
4707  
4708          * make/: Makefile, Makefile.in: more work on the parallel build
4709  
4710 < 2004-10-04 11:06  gezelter
4710 > 2004-10-04 16:06  gezelter
4711  
4712          * make/: Makefile, Makefile.in: changes to backport declare flags
4713  
4714 < 2004-10-04 10:27  gezelter
4714 > 2004-10-04 15:27  gezelter
4715  
4716          * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp,
4717          DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging
4718          shapes
4719  
4720 < 2004-10-01 23:40  tim
4720 > 2004-10-02 04:40  tim
4721  
4722          * scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree
4723  
4724 < 2004-10-01 23:22  tim
4724 > 2004-10-02 04:22  tim
4725  
4726          * make/: Makefile, Makefile.in: add oopse_ as library prefix
4727  
4728 < 2004-10-01 16:59  tim
4728 > 2004-10-01 21:59  tim
4729  
4730          * make/: Makefile, Makefile.in: fix a space trimming bug in filepp
4731  
4732 < 2004-10-01 16:22  gezelter
4732 > 2004-10-01 21:22  gezelter
4733  
4734          * Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A
4735          few minor build changes
4736  
4737 < 2004-10-01 16:11  tim
4737 > 2004-10-01 21:11  tim
4738  
4739          * scripts/filepp: adding fortran90 make dependency tool
4740  
4741 < 2004-09-30 10:41  tim
4741 > 2004-09-30 15:41  tim
4742  
4743          * make/: Makefile, Makefile.in: make clean is smart enough to only
4744          remove object files belong to current package.  turn off silent
4745          mode
4746  
4747 < 2004-09-29 16:55  tim
4747 > 2004-09-29 21:55  tim
4748  
4749          * src/: Makefile, UseTheForce/Makefile,
4750          UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile,
# Line 4677 | Line 4755
4755          restraints/Makefile, types/Makefile, utils/Makefile,
4756          visitors/Makefile: define DEV_ROOT as relative path
4757  
4758 < 2004-09-29 16:54  tim
4758 > 2004-09-29 21:54  tim
4759  
4760          * make/: Makefile, Makefile.in: get the relative path by shell
4761          script
4762  
4763 < 2004-09-29 16:32  tim
4763 > 2004-09-29 21:32  tim
4764  
4765          * make/Makefile: eliminate DEV_ROOT by relative path
4766  
4767 < 2004-09-29 13:37  tim
4767 > 2004-09-29 18:37  tim
4768  
4769          * make/Makefile.in: add PackageLibs;  fix dependency rule
4770  
4771 < 2004-09-29 12:57  gezelter
4771 > 2004-09-29 17:57  gezelter
4772  
4773          * configure, ac-tools/configure.in: updates
4774  
4775 < 2004-09-29 12:56  gezelter
4775 > 2004-09-29 17:56  gezelter
4776  
4777          * make/: Make.conf.in, Makefile.in, _files/style.css: Working on
4778          make stuff
4779  
4780 < 2004-09-29 12:46  tim
4780 > 2004-09-29 17:46  tim
4781  
4782          * Makefile: If makefile does not exist, print error message
4783  
4784 < 2004-09-29 12:12  tim
4784 > 2004-09-29 17:12  tim
4785  
4786          * make/: Make.conf.in, Makefile: fix dependencies rule
4787  
4788 < 2004-09-29 10:58  gezelter
4788 > 2004-09-29 15:58  gezelter
4789  
4790          * Makefile, make/Makefile: still working on build process
4791  
4792 < 2004-09-29 10:00  tim
4792 > 2004-09-29 15:00  tim
4793  
4794          * make/Makefile: add print statment to rules
4795  
4796 < 2004-09-29 09:59  tim
4796 > 2004-09-29 14:59  tim
4797  
4798          * src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile,
4799          applications/dump2Xyz/Makefile, applications/oopse/Makefile,
# Line 4725 | Line 4803
4803          profiling/Makefile, restraints/Makefile, types/Makefile,
4804          utils/Makefile, visitors/Makefile: change Makefile to relative path
4805  
4806 < 2004-09-28 21:55  tim
4806 > 2004-09-29 02:55  tim
4807  
4808          * src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c
4809          which cause headache in bulding libutils
4810  
4811 < 2004-09-28 18:24  tim
4811 > 2004-09-28 23:24  tim
4812  
4813          * src/applications/: BaseLattice.cpp, BaseLattice.hpp,
4814          Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h,
# Line 4753 | Line 4831
4831          change directory structure of application. Every executable file is
4832          replaced in seperate directory
4833  
4834 < 2004-09-28 17:15  gezelter
4834 > 2004-09-28 22:15  gezelter
4835  
4836          * lib/dummy: Keep that lib around, please.
4837  
4838 < 2004-09-28 17:14  gezelter
4838 > 2004-09-28 22:14  gezelter
4839  
4840          * Makefile, configure, ac-tools/configure.in, make/Make.conf.in:
4841          starting a configure version
4842  
4843 < 2004-09-28 16:08  tim
4843 > 2004-09-28 21:08  tim
4844  
4845          * src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90,
4846          UseTheForce/DarkSide/Makefile,
# Line 4771 | Line 4849
4849          brains/Makefile, brains/simulation_module.F90: move fortran files
4850          around to solve dependency problem
4851  
4852 < 2004-09-28 15:43  tim
4852 > 2004-09-28 20:43  tim
4853  
4854          * Makefile, src/UseTheForce/ForceFields.hpp,
4855          src/UseTheForce/Makefile, src/applications/BaseLattice.hpp,
# Line 4781 | Line 4859
4859          src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp,
4860          src/utils/Makefile: [no log message]
4861  
4862 < 2004-09-28 15:41  tim
4862 > 2004-09-28 20:41  tim
4863  
4864          * make/Makefile, scripts/sfmakedepend: fix fortran dependency
4865          problem
4866  
4867 < 2004-09-28 11:13  tim
4867 > 2004-09-28 16:13  tim
4868  
4869          * make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y,
4870          src/io/Makefile: add yacc and lex rules
4871  
4872 < 2004-09-27 15:24  tim
4872 > 2004-09-27 20:24  tim
4873  
4874          * make/Makefile: adding include path to F90Options
4875  
4876 < 2004-09-27 15:13  tim
4876 > 2004-09-27 20:13  tim
4877  
4878          * make/Makefile: change suffix from .cc to .cpp
4879  
4880 < 2004-09-24 11:27  tim
4880 > 2004-09-24 16:27  tim
4881  
4882          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
4883          UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
# Line 4866 | Line 4944
4944          visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
4945          visitors/ZconsVisitor.hpp: change the #include in source files
4946  
4947 < 2004-09-23 23:16  gezelter
4947 > 2004-09-24 04:16  gezelter
4948  
4949          * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
4950          src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
# Line 5038 | Line 5116
5116          forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
5117          forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0
5118  
5119 < 2004-09-23 23:16  gezelter
5119 > 2004-09-24 04:16  gezelter
5120  
5121          * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
5122          src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,

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