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Revision 837 by tim, Wed Oct 29 00:19:10 2003 UTC vs.
Revision 1005 by tim, Tue Feb 3 15:21:32 2004 UTC

# Line 1 | Line 1
1 < 2003-10-24 18:17  mmeineke
1 > 2004-02-02 15:29  tim
2 >
3 >        * libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp,
4 >        Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp:
5 >        Adding GoldenSection and Brent LineSearch Method
6 >
7 > 2004-01-30 16:47  tim
8 >
9 >        * libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp,
10 >        MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp,
11 >        NLModel0.cpp, NLModel1.cpp: using class  Minimizer1D derived from
12 >        MinimizerBase instead of a functor to do line seach
13 >
14 > 2004-01-30 10:00  chrisfen
15 >
16 >        * forceFields/Makefile.in, libmdtools/Atom.cpp,
17 >        libmdtools/Atom.hpp, libmdtools/ForceFields.hpp,
18 >        libmdtools/Integrator.cpp, libmdtools/Makefile.in,
19 >        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
20 >        libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90,
21 >        libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90,
22 >        libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now
23 >        has a working WATER.cpp forcefield and parser.  This involved
24 >        changes to WATER.cpp and ForceFields amoung other files. One
25 >        important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90.
26 >        This will be removed on the next commit...
27 >
28 > 2004-01-29 18:00  gezelter
29 >
30 >        * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h,
31 >        libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y,
32 >        libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp,
33 >        libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp,
34 >        libBASS/RigidBodyStamp.hpp, libBASS/interface.c,
35 >        libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c,
36 >        libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h,
37 >        libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl:
38 >        member list fixes for rigid bodies
39 >
40 > 2004-01-29 16:44  tim
41 >
42 >        * libmdtools/MinimizerParameterSet.hpp: Adding
43 >        MinimizerParameterSet class.
44 >
45 > 2004-01-28 17:44  tim
46 >
47 >        * libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of
48 >        NLModel0 and NLModel1
49 >
50 > 2004-01-28 15:40  tim
51 >
52 >        * libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision
53 >        of NLModel
54 >
55 > 2004-01-27 15:34  gezelter
56 >
57 >        * samples/water/: ssd.bass, water.mdl: Added point-charge models to
58 >        water.mdl file, updated ssd.bass to use new SSD name
59 >
60 > 2004-01-27 15:34  gezelter
61 >
62 >        * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp,
63 >        MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody
64 >        stuff
65 >
66 > 2004-01-27 14:39  gezelter
67 >
68 >        * samples/water/ssd.bass: Longer run time to test SSD water in MPI
69 >
70 > 2004-01-27 14:39  gezelter
71 >
72 >        * samples/metals/Au.bass: Longer run time to test gold in MPI
73 >
74 > 2004-01-27 14:38  gezelter
75 >
76 >        * samples/argon/argon.bass: Longer run time to test argon
77 >
78 > 2004-01-27 14:38  gezelter
79 >
80 >        * libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS
81 >        changes to do new rigidBody scheme a copy of WATER.cpp from this
82 >        morning
83 >
84 > 2004-01-27 14:37  gezelter
85 >
86 >        * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c,
87 >        BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in,
88 >        MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp,
89 >        MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp,
90 >        interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h,
91 >        node_list.h, parse_interface.h, parse_tree.c: More BASS changes to
92 >        do new rigidBody scheme
93 >
94 > 2004-01-27 14:15  tim
95 >
96 >        * libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp,
97 >        Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp,
98 >        MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of
99 >        constraint for Nonlinear Optimization Model
100 >
101 > 2004-01-26 17:01  gezelter
102 >
103 >        * utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use
104 >        Euler angles for orientation instead of unit vectors required
105 >        changes in MoLocator
106 >
107 > 2004-01-26 16:53  gezelter
108 >
109 >        * samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl,
110 >        beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl,
111 >        water/water.mdl: Changed orientation lines from unit vectors to
112 >        euler angles
113 >
114 > 2004-01-26 16:52  gezelter
115 >
116 >        * libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians
117 >
118 > 2004-01-26 16:45  gezelter
119 >
120 >        * libmdtools/SimSetup.cpp: Changed default orientation in BASS to
121 >        use Euler angles in the following order: phi, theta, psi Removed
122 >        the ability to set orientation using a unit vector
123 >
124 > 2004-01-26 16:26  gezelter
125 >
126 >        * libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp,
127 >        RigidBodyStamp.hpp: Changed default orientation in BASS to use
128 >        Euler angles in the following order: phi, theta, psi Removed the
129 >        ability to set orientation using a unit vector
130 >
131 > 2004-01-26 13:52  gezelter
132 >
133 >        * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp,
134 >        MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies
135 >
136 > 2004-01-22 12:34  chrisfen
137 >
138 >        * libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp,
139 >        TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h:
140 >        Corrected spelling in several directories, and stated WATER.cpp
141 >
142 > 2004-01-21 17:16  tim
143 >
144 >        * libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp,
145 >        NLOPModel.hpp: constraint class in energy minimization
146 >
147 > 2004-01-20 15:34  tim
148 >
149 >        * libmdtools/MinimizerBase.hpp: Adding energy minimization
150 >
151 > 2004-01-20 15:32  tim
152 >
153 >        * libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp,
154 >        NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer
155 >
156 > 2004-01-19 16:17  gezelter
157 >
158 >        * libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages
159 >        more user-friendly
160 >
161 > 2004-01-19 13:51  chrisfen
162 >
163 >        * forceFields/DUFF.frc: Updated the default water to SSD/E
164 >
165 > 2004-01-19 13:36  tim
166 >
167 >        * libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample
168 >        time, status time, thermal time and reset time are not divisible by
169 >        dt
170 >
171 > 2004-01-19 11:10  gezelter
172 >
173 >        * third-party/Makefile.in: Added a bunch of dummy targets so make
174 >        won't complain
175 >
176 > 2004-01-19 11:10  gezelter
177 >
178 >        * samples/lipid/5x5.bass: Fixed old bass file
179 >
180 > 2004-01-19 11:09  gezelter
181 >
182 >        * libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies
183 >        required a change in how the MoleculeStamps are used by divideLabor
184 >        in mpiSimulation.cpp
185 >
186 > 2004-01-19 11:08  gezelter
187 >
188 >        * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c,
189 >        BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp,
190 >        MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp,
191 >        RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c,
192 >        make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h,
193 >        parse_tree.c: BASS changes to add RigidBodies and LJrcut
194 >
195 > 2004-01-16 16:55  tim
196 >
197 >        * libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating
198 >        eor file
199 >
200 > 2004-01-16 16:51  mmeineke
201 >
202 >        * libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could
203 >        write eor files
204 >
205 > 2004-01-16 10:01  mmeineke
206 >
207 >        * libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi
208 >        initialization of the AtomStruct
209 >
210 > 2004-01-15 16:57  chuckv
211 >
212 >        * configure, libmdtools/DumpWriter.cpp: Fixes for Dumps
213 >
214 > 2004-01-15 10:51  gezelter
215 >
216 >        * ac-tools/aclocal.m4: Changes for altivec
217 >
218 > 2004-01-15 09:22  gezelter
219 >
220 >        * libmdtools/DumpWriter.cpp: Documented the Spud Toss
221 >
222 > 2004-01-14 23:33  gezelter
223 >
224 >        * libmdtools/do_Forces.F90: changes for charge charge interactions
225 >
226 > 2004-01-14 20:14  gezelter
227 >
228 >        * libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90,
229 >        notifyCutoffs.F90: More work for adding charges
230 >
231 > 2004-01-14 17:41  gezelter
232 >
233 >        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
234 >        src/Makefile.in: autoconf fixes
235 >
236 > 2004-01-14 11:28  mmeineke
237 >
238 >        * utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug
239 >
240 > 2004-01-14 10:48  gezelter
241 >
242 >        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
243 >        src/Makefile.in, third-party/Makefile.in: autoconf compatibility
244 >        changes for icc8
245 >
246 > 2004-01-13 18:01  gezelter
247 >
248 >        * libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp,
249 >        SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90,
250 >        fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90:
251 >        Changes for adding direct charge-charge interactions (with
252 >        switching function)
253 >
254 > 2004-01-13 17:34  gezelter
255 >
256 >        * libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90,
257 >        oopseMPI_module.F90: Some changes for new MPI organization and
258 >        direct charge-charge interactions
259 >
260 > 2004-01-13 17:11  tim
261 >
262 >        * Functor.hpp, libmdtools/Functor.hpp: [no log message]
263 >
264 > 2004-01-13 16:22  tim
265 >
266 >        * Functor.hpp, samples/water/ssd.bass: Energy Minimization method
267 >
268 > 2004-01-13 15:35  tim
269 >
270 >        * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the
271 >        eor file whenever it is used instead of rewinding it
272 >
273 > 2004-01-13 15:04  tim
274 >
275 >        * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface
276 >        of writeFrame
277 >
278 > 2004-01-13 10:46  tim
279 >
280 >        * libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp:
281 >        Merge the code of writeFinal and writeDump;
282 >         Adding sortingIndex into DumpWriter;
283 >         Fix a bug of writing last frame twice in integrator
284 >
285 > 2004-01-12 17:54  tim
286 >
287 >        * ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix
288 >        a bug in copying string
289 >
290 > 2004-01-12 15:37  tim
291 >
292 >        * ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass,
293 >        samples/water/ssd.bass: Dumpwriter only write out the atoms on
294 >        master nodes
295 >
296 > 2004-01-10 04:46  tim
297 >
298 >        * ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just
299 >        roll it back fix a bug of copying string to a pointer Still have
300 >        Seg fault, it looks like a random MPI seg fault in totalview
301 >
302 > 2004-01-09 21:15  tim
303 >
304 >        * libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub
305 >
306 > 2004-01-09 15:29  gezelter
307 >
308 >        * libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4)
309 >
310 > 2004-01-08 17:25  chuckv
311 >
312 >        * libmdtools/DumpWriter.cpp: A work in progress...
313 >
314 > 2004-01-08 13:59  gezelter
315 >
316 >        * libmdtools/DumpWriter.cpp: null terminate some strings just in
317 >        case
318 >
319 > 2004-01-08 13:13  mmeineke
320 >
321 >        * libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS
322 >        state bug.
323 >
324 > 2004-01-08 13:05  gezelter
325 >
326 >        * libmdtools/DumpWriter.cpp: added strncpy to DumpWriter
327 >
328 > 2004-01-08 12:57  mmeineke
329 >
330 >        * libmdtools/InitializeFromFile.cpp: fixed the restart from NVT
331 >        exstended state bug
332 >
333 > 2004-01-08 12:40  gezelter
334 >
335 >        * libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter
336 >
337 > 2004-01-08 10:44  mmeineke
338 >
339 >        * libmdtools/InitializeFromFile.cpp: added support for the ignore
340 >        XS state info  flag
341 >
342 > 2004-01-07 14:26  tim
343 >
344 >        * libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp,
345 >        samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of
346 >        sending message from master node to itself in DumpWriter.cpp and
347 >        InitializeFromFile.cpp
348 >
349 > 2004-01-06 14:49  chuckv
350 >
351 >        * libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90:
352 >        performance fixes in the dipole dipole and reaction field code
353 >
354 > 2004-01-06 13:54  chuckv
355 >
356 >        * libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a
357 >        little more sane
358 >
359 > 2004-01-05 17:49  chuckv
360 >
361 >        * libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90,
362 >        calc_eam.F90, calc_gb.F90, calc_reaction_field.F90,
363 >        calc_sticky_pair.F90, do_Forces.F90: Attempting to increase
364 >        performance by reducing spurious function calls
365 >
366 > 2004-01-05 17:18  chuckv
367 >
368 >        * libmdtools/do_Forces.F90: mangling forces even further
369 >
370 > 2004-01-05 17:18  chuckv
371 >
372 >        * configure, ac-tools/configure.in: mpich mucking
373 >
374 > 2004-01-05 17:12  chuckv
375 >
376 >        * libmdtools/do_Forces.F90: mangled do_forces...
377 >
378 > 2004-01-05 16:00  chuckv
379 >
380 >        * ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90,
381 >        libmdtools/do_Forces.F90: Added bitmask to do_forces property
382 >        lookup
383 >
384 > 2003-12-29 14:56  chuckv
385 >
386 >        * samples/metals/Au.bass, third-party/mt19937ar.c: Added
387 >        third-party directory for code not written by us. Also added
388 >        Mersenne Twister random number generator code. This will eventually
389 >        replace sprng as the random number generator used by OOPSE.
390 >
391 > 2003-12-22 16:26  chuckv
392 >
393 >        * libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
394 >        libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp:
395 >        Fixes to profile code.
396 >
397 > 2003-12-19 15:36  mmeineke
398 >
399 >        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp,
400 >        timing.F90, timing.f90: More profiling fixes.
401 >
402 > 2003-12-19 15:19  chuckv
403 >
404 >        * libmdtools/timing.f90: Another change for MPI in timing.
405 >
406 > 2003-12-19 15:17  chuckv
407 >
408 >        * libmdtools/timing.f90: Small update to timing in MPI
409 >
410 > 2003-12-19 13:53  mmeineke
411 >
412 >        * libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the
413 >        profiling commands work now. Will start adding PROFILE ifdefs into
414 >        the code
415 >
416 > 2003-12-19 12:25  mmeineke
417 >
418 >        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added
419 >        some profiling routines
420 >
421 > 2003-12-19 10:12  mmeineke
422 >
423 >        * utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta
424 >        and GofRomega
425 >        
426 >        additional work on randomBilayer
427 >
428 > 2003-12-19 10:12  mmeineke
429 >
430 >        * staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp,
431 >        PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and
432 >        GofRomega
433 >
434 > 2003-12-18 16:47  mmeineke
435 >
436 >        * libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added
437 >        some profile functionality
438 >
439 > 2003-12-18 15:46  chuckv
440 >
441 >        * libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90:
442 >        Added functions for simple profiling in fortran.
443 >
444 > 2003-12-17 15:13  chuckv
445 >
446 >        * libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90,
447 >        samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and
448 >        rho_col were scattered into the same array. Unfortunately, MPI
449 >        zeros the array between scatters so half of the sum was being lost.
450 >        Fixed by added a temp array for column scatter, then sum loop over
451 >        nlocal.
452 >
453 > 2003-12-16 15:49  mmeineke
454 >
455 >        * staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in,
456 >        PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added
457 >        gofRomega. both need to be debugged and tested.
458 >
459 > 2003-12-12 10:42  gezelter
460 >
461 >        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
462 >        libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for
463 >        gradients (to do minimizations)
464 >
465 > 2003-12-12 10:33  mmeineke
466 >
467 >        * utils/sysbuilder/randomBilayer.hpp:  removed the randombilayer
468 >        header
469 >
470 > 2003-12-10 11:52  mmeineke
471 >
472 >        * utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp,
473 >        randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add
474 >        randomBilayer to the build. Also move the random bilayer builder
475 >        from bilayerSys to randomBilayer
476 >
477 > 2003-11-25 10:44  mmeineke
478 >
479 >        * forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old
480 >        DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and
481 >        TB3 in DUFF.frc
482 >
483 > 2003-11-21 15:09  mmeineke
484 >
485 >        * libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp,
486 >        utils/sysbuilder/latticeBilayer.cpp: added a more verbose error
487 >        message in SimInfo. Added a more informative error message in
488 >        InitializeFromFile
489 >
490 > 2003-11-21 15:07  mmeineke
491 >
492 >        * staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add
493 >        ing in the GofR,CosTheta
494 >
495 > 2003-11-21 14:31  chrisfen
496 >
497 >        * libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed
498 >        a bug in SimInfo ordering of radii
499 >
500 > 2003-11-11 12:20  mmeineke
501 >
502 >        * libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline
503 >        a min function.
504 >
505 > 2003-11-10 16:50  mmeineke
506 >
507 >        * libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp:
508 >        reordered the rcut/ecr/boxSize initialization
509 >        
510 >        removed the rcut/ecr shrink and grow algorithm. the simulation will
511 >        now exit when it runs into rcut or ecr.
512 >
513 > 2003-11-07 16:46  chuckv
514 >
515 >        * libmdtools/: Makefile.in, mpiSimulation_module.F90,
516 >        oopseMPI_module.F90: Added support for compiling fortran without
517 >        use of mpich modules. We use mpif.h instead.:
518 >
519 > 2003-11-07 12:09  mmeineke
520 >
521 >        * libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp,
522 >        NPTxyz.cpp: moved the velocity scale matrix calculation outside of
523 >        the atom loop in the NPT family of integrators.
524 >
525 > 2003-11-06 17:01  mmeineke
526 >
527 >        * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep,
528 >        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp,
529 >        libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
530 >        libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep,
531 >        utils/sysbuilder/latticeBilayer.cpp: added the following parameters
532 >        to BASS:    * useInitialExtendedSystemState    * orthoBoxTolerance
533 >          * useIntiTime => useInitialTime
534 >
535 > 2003-11-06 14:24  mmeineke
536 >
537 >        * libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c,
538 >        make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c,
539 >        parse_tree.h: fixed the includes in the Make.dep
540 >
541 > 2003-11-06 14:11  mmeineke
542 >
543 >        * libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp,
544 >        NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the
545 >        new-templateless branch to the main trunk.
546 >        
547 >        bug Fixes include:   * fixed the switching function from ortho to
548 >        non-ortho box.           !!!!! THis was responsible for all of the
549 >        sudden deaths we saw.    * some formating in the string when we
550 >        write out the extended system state.    * added NPT.cpp to the
551 >        makefile.in
552 >
553 > 2003-11-06 13:20  mmeineke
554 >
555 >        * libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp,
556 >        SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death"
557 >        bug.    The box was not switching between orthorhombic and
558 >        non-orthorhombic wrapping correctly.         we added a fabs() to
559 >        the check.which should fix it.
560 >
561 > 2003-11-05 14:16  mmeineke
562 >
563 >        * libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp,
564 >        libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
565 >        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp,
566 >        libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp,
567 >        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp,
568 >        libmdtools/NVT.cpp, libmdtools/SimInfo.hpp,
569 >        libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep,
570 >        utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp:
571 >        some work on trying to find the compression bug
572 >
573 > 2003-11-03 17:07  mmeineke
574 >
575 >        * libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp,
576 >        InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp,
577 >        NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp,
578 >        SimSetup.cpp, SimSetup.hpp: begun work on removing templates and
579 >        most of standard template library from OOPSE.
580 >
581 > 2003-10-31 16:06  mmeineke
582 >
583 >        * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp,
584 >        Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp,
585 >        SimSetup.cpp: started work on template removal.
586 >
587 > 2003-10-31 13:28  mmeineke
588 >
589 >        * libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp:
590 >        added template stuff to the Maikefile template
591 >        
592 >        little changes to some printf format statements
593 >
594 > 2003-10-31 13:28  mmeineke
595 >
596 >        * libBASS/Makefile.in: added template stuff to the Maikefile
597 >        template
598 >
599 > 2003-10-30 13:59  gezelter
600 >
601 >        * libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp,
602 >        do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for
603 >        rList problems
604 >
605 > 2003-10-30 09:11  gezelter
606 >
607 >        * libmdtools/neighborLists.F90: Fixed bug that size(q0) was being
608 >        queried before q0 was allocated.
609 >
610 > 2003-10-29 15:41  mmeineke
611 >
612 >        * libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp,
613 >        SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90,
614 >        calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error
615 >        in bass.l
616 >        
617 >        fixed a little bug in the first time step, regarding the setting of
618 >        ecr and est in fortran
619 >
620 > 2003-10-29 15:40  mmeineke
621 >
622 >        * libBASS/BASSlex.l: fixed a stdlib.h include error
623 >
624 > 2003-10-29 12:55  mmeineke
625 >
626 >        * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
627 >        SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way
628 >        rcut is setup, as well as additional debugging comments.
629 >
630 > 2003-10-29 09:28  gezelter
631 >
632 >        * configure, ac-tools/configure.in, libBASS/Makefile.in,
633 >        libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for
634 >        templates
635 >
636 > 2003-10-28 22:16  gezelter
637 >
638 >        * src/Makefile.in: Refixed broken makefile
639 >
640 > 2003-10-28 22:06  gezelter
641 >
642 >        * configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility
643 >        fixes
644 >
645 > 2003-10-28 19:19  tim
646 >
647 >        * ChangeLog, libmdtools/AbstractClasses.hpp,
648 >        libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp,
649 >        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp,
650 >        libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp,
651 >        libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp,
652 >        libmdtools/ReadWrite.hpp, samples/argon/argon.bass,
653 >        samples/water/ssd.bass: add chi and eta to the comment line of dump
654 >        file.
655 >
656 > 2003-10-28 17:25  mmeineke
657 >
658 >        * libmdtools/: ForceFields.hpp, SimInfo.hpp,
659 >        fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp,
660 >        mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of
661 >        how c calls fortran. All function pointers and fortran calls are
662 >        rigidly typecast now.
663 >
664 > 2003-10-28 15:42  gezelter
665 >
666 >        * staticProps/Makefile.in, utils/sysbuilder/Makefile.in:
667 >        Portability fixes
668 >
669 > 2003-10-28 15:09  gezelter
670 >
671 >        * libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90,
672 >        libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90,
673 >        src/Makefile.in: Compatibility fixes
674 >
675 > 2003-10-28 12:08  mmeineke
676 >
677 >        * libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in:
678 >        started work on template removal
679 >
680 > 2003-10-28 12:04  gezelter
681 >
682 >        * libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started
683 >        trying to understand extern "C" stuff for pointers
684 >
685 > 2003-10-28 11:20  gezelter
686 >
687 >        * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp,
688 >        ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility
689 >
690 > 2003-10-28 11:03  gezelter
691 >
692 >        * libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp,
693 >        DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp,
694 >        DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp,
695 >        ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp,
696 >        Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp,
697 >        ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp,
698 >        StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp,
699 >        calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp,
700 >        mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with
701 >        more portable c header stuff Also, mod file fixes and portability
702 >        changes Some fortran changes will need to be reversed.
703  
704 + 2003-10-28 11:03  gezelter
705 +
706 +        * libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp,
707 +        Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp,
708 +        Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more
709 +        portable c header stuff Also, mod file fixes and portability
710 +        changes
711 +
712 + 2003-10-28 11:02  gezelter
713 +
714 +        * configure, ac-tools/aclocal.m4: mod file fixes and portability
715 +        stuff
716 +
717 + 2003-10-27 18:00  gezelter
718 +
719 +        * Makefile.in, configure, ac-tools/aclocal.m4,
720 +        ac-tools/configure.in, ac-tools/fortran90.m4,
721 +        libmdtools/Makefile.in: Stuff for MOD support in other compilers
722 +
723 + 2003-10-27 17:08  mmeineke
724 +
725          * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp,
726 +        MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp:
727 +        added routines for the sysbuilder to work with simSetup
728 +        
729 +        remved the QuickBass routines, and had all parsing go through
730 +        SimSetup.  LatticeBilayer is in complete working order now.
731 +
732 + 2003-10-27 17:07  mmeineke
733 +
734 +        * libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added
735 +        routines for the sysbuilder to work with simSetup
736 +
737 + 2003-10-27 11:20  gezelter
738 +
739 +        * configure, ac-tools/configure.in, samples/water/ssd.bass,
740 +        utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild
741 +
742 + 2003-10-24 17:17  mmeineke
743 +
744 +        * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp,
745          MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp,
746          latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put
747          QuickBass, MoLocator, and latticeBuilder into a Builder Library
748          overhauled latticeBilayer into its own program. Removed sysBuild
749          from the Makefile
750  
751 < 2003-10-24 13:36  gezelter
751 > 2003-10-24 12:36  gezelter
752  
753          * utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp,
754          latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer
755          builder
756  
757 < 2003-10-24 13:35  gezelter
757 > 2003-10-24 12:35  gezelter
758  
759          * configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a
760          merge problem
761  
762 < 2003-10-23 15:57  mmeineke
762 > 2003-10-23 14:57  mmeineke
763  
764          * samples/metals/Makefile.in: added eam ForceField files to the
765          init
# Line 27 | Line 768
768          
769          added the init file to the makefile
770  
771 < 2003-10-23 15:57  mmeineke
771 > 2003-10-23 14:57  mmeineke
772  
773          * libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files
774          to the init
775          
776          fixed an eam mpi parmeter setup bug
777  
778 < 2003-10-23 15:57  mmeineke
778 > 2003-10-23 14:57  mmeineke
779  
780          * forceFields/Makefile.in: added eam ForceField files to the init
781  
782 < 2003-10-22 17:17  mmeineke
782 > 2003-10-22 16:17  mmeineke
783  
784          * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in,
785          NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT
786          integrator, NPTxyz. It scales the x, y, and z direction sepeartely.
787          no box skew allowed.
788  
789 < 2003-10-21 15:33  mmeineke
789 > 2003-10-21 14:33  mmeineke
790  
791          * libBASS/Globals.cpp, libBASS/Globals.hpp,
792          libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp,
# Line 54 | Line 795
795          of the time stamp in the .init file     * default=> useInitTime =
796          true;
797  
798 < 2003-10-17 17:19  mmeineke
798 > 2003-10-17 16:19  mmeineke
799  
800          * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp,
801          Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
# Line 64 | Line 805
805          fixed a number of bugs in the staticProps code. gofr is now
806          working.
807  
808 < 2003-10-17 17:18  mmeineke
808 > 2003-10-17 16:18  mmeineke
809  
810          * ac-tools/configure.in: added the staticProps directory to the
811          build list for both configure  and configure.in
812  
813 < 2003-10-17 17:17  mmeineke
813 > 2003-10-17 16:17  mmeineke
814  
815          * configure: added the staticProps directory to the build list
816  
817 < 2003-10-16 15:16  mmeineke
817 > 2003-10-16 14:16  mmeineke
818  
819          * libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp,
820          Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to
# Line 87 | Line 828
828          a frame is written.  This lets the .eor file represent the last
829          written frame of a simulation.
830  
831 < 2003-10-10 13:10  mmeineke
831 > 2003-10-10 12:10  mmeineke
832  
833 <        * props/AllCorr.cpp, props/AllCorr.hpp, props/CorrWrap.cpp,
834 <        props/CorrWrap.hpp, props/GofR.cpp, props/PairCorrList.cpp,
835 <        props/PairCorrList.hpp, props/PairCorrType.cpp,
836 <        props/PairCorrType.hpp, props/staticProps.cpp,
837 <        staticProps/AllCorr.cpp, staticProps/AllCorr.hpp,
97 <        staticProps/CorrWrap.cpp, staticProps/CorrWrap.hpp,
98 <        staticProps/GofR.cpp, staticProps/Makefile.in,
99 <        staticProps/PairCorrList.cpp, staticProps/PairCorrList.hpp,
100 <        staticProps/PairCorrType.cpp, staticProps/PairCorrType.hpp,
101 <        staticProps/staticProps.cpp: removed the props directory, and moved
102 <        everything over to staticProps
833 >        * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp,
834 >        CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp,
835 >        PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
836 >        staticProps.cpp: removed the props directory, and moved everything
837 >        over to staticProps
838  
839 < 2003-10-09 18:09  mmeineke
839 > 2003-10-09 17:09  mmeineke
840  
841 <        * libmdtools/Atom.hpp, props/AllCorr.cpp, props/AllCorr.hpp,
107 <        props/CorrWrap.cpp, props/CorrWrap.hpp, props/GofR.cpp,
108 <        props/PairCorrType.cpp, props/PairCorrType.hpp,
109 <        props/staticProps.cpp: Contiuned work on staticProps. should be in
841 >        * libmdtools/Atom.hpp: Contiuned work on staticProps. should be in
842          a position where it will compile and run first runs.
843  
844 < 2003-10-04 14:46  chuckv
844 > 2003-10-04 13:46  chuckv
845  
846          * libmdtools/calc_eam.F90, libmdtools/do_Forces.F90,
847          samples/metals/Au.bass: Fixed bug in calc_eam.
848  
849 < 2003-10-04 14:08  chuckv
849 > 2003-10-04 13:08  chuckv
850  
851          * samples/metals/init_au.in: added Au init file for eam.
852  
853 < 2003-10-03 18:11  mmeineke
853 > 2003-10-03 17:11  mmeineke
854  
855          * libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed
856          entahlpy from the statwriter and thermo.
857  
858 < 2003-10-03 18:02  mmeineke
858 > 2003-10-03 17:02  mmeineke
859  
128 –        * props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp,
129 –        PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
130 –        staticProps.cpp: changed the formating ogf the error statements in
131 –        simError
132 –        
133 –        added a function to get the maxCutoff
134 –        
135 –        near completion of the staticProps code. still needs the pair loop,
136 –        and the loop to allocate and read each frame.
137 –
138 – 2003-10-03 18:02  mmeineke
139 –
860          * libmdtools/SimInfo.hpp: changed the formating ogf the error
861          statements in simError
862          
863          added a function to get the maxCutoff
864  
865 < 2003-10-03 18:01  mmeineke
865 > 2003-10-03 17:01  mmeineke
866  
867          * libBASS/simError.c: changed the formating ogf the error
868          statements in simError
869  
870 < 2003-10-02 18:06  mmeineke
870 > 2003-09-30 11:00  mmeineke
871  
152 –        * props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp,
153 –        PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
154 –        staticProps.cpp: finishing up the constructs needed to get this
155 –        program up and running
156 –
157 – 2003-09-30 12:00  mmeineke
158 –
872          * configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed
873          f90Flags so they are no longer overwritten by the compiler.
874  
875 < 2003-09-29 18:06  mmeineke
875 > 2003-09-29 17:06  mmeineke
876  
877          * libmdtools/fortranWrappers.cpp: added mpif90 mod check back same
878          for conifig.in
879          
880          fixed wrappers to extern "C"
881  
882 < 2003-09-29 18:06  mmeineke
882 > 2003-09-29 17:06  mmeineke
883  
884          * ac-tools/configure.in: added mpif90 mod check back same for
885          conifig.in
886  
887 < 2003-09-29 18:05  mmeineke
887 > 2003-09-29 17:05  mmeineke
888  
889          * configure: added mpif90 mod check back
890  
891 < 2003-09-29 17:16  mmeineke
891 > 2003-09-29 16:16  mmeineke
892  
893          * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
894          libBASS/BendStamp.cpp, libBASS/BondStamp.cpp,
# Line 187 | Line 900
900          libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors
901          found with SUN's SUNWspro.s1s7
902  
903 < 2003-09-29 13:38  mmeineke
903 > 2003-09-29 12:38  mmeineke
904  
905          * libmdtools/GenericData.hpp: light change in syntax. no
906          signifigant change.
907  
908 < 2003-09-25 17:17  mmeineke
908 > 2003-09-25 16:17  mmeineke
909  
910          * libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some
911          additional remarks from icc -w3 (extra verbose output)
912  
913 < 2003-09-25 15:27  mmeineke
913 > 2003-09-25 14:27  mmeineke
914  
915          * libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
916          libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp,
# Line 211 | Line 924
924          libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with
925          gcc -Wall and g++ -Wall
926  
927 < 2003-09-25 14:54  gezelter
927 > 2003-09-25 13:54  gezelter
928  
929          * configure, ac-tools/configure.in: fixed a bug in configure
930  
931 < 2003-09-25 12:42  gezelter
931 > 2003-09-25 11:42  gezelter
932  
933          * Makefile.in, configure, ac-tools/aclocal.m4,
934          ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in,
935          src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in:
936          fixes for configure
937  
938 < 2003-09-24 15:34  mmeineke
938 > 2003-09-24 14:34  mmeineke
939  
940          * libmdtools/Integrator.cpp: moved readyCheck in the integrator so
941          that it is called before the first Statistics are written.
942  
943 < 2003-09-23 16:36  gezelter
943 > 2003-09-23 15:36  gezelter
944  
945          * src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a
946          bunch of Make.dep files to CVS
947  
948 < 2003-09-23 16:34  mmeineke
948 > 2003-09-23 15:34  mmeineke
949  
950          * libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp,
951          SimSetup.cpp: Removed NPTfm from Integrator.hpp.
952          
953          Some small syntax cleaning in NPTfm and SimSetup
954  
955 < 2003-09-22 19:07  tim
955 > 2003-09-22 18:07  tim
956  
957          * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
958          SimInfo.hpp: fix bug in calculating maxCutoff
959  
960 < 2003-09-22 17:23  mmeineke
960 > 2003-09-22 16:23  mmeineke
961  
962          * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep,
963          Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp:
# Line 252 | Line 965
965          
966          Removed NPTfm and NPTim from cvs
967  
968 < 2003-09-19 16:00  mmeineke
968 > 2003-09-19 15:00  mmeineke
969  
970          * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp,
971          NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base
972          class. NPTi is up to date. NPTf is not.
973  
974 < 2003-09-19 12:03  mmeineke
974 > 2003-09-19 11:03  mmeineke
975  
976          * utils/Makefile.in, src/Makefile.in: removed mpi++ from the
977          makefile
978  
979 < 2003-09-19 12:01  gezelter
979 > 2003-09-19 11:01  gezelter
980  
981          * samples/water/ssd.bass: goofing off to test NPTf and NPTi
982  
983 < 2003-09-19 12:01  gezelter
983 > 2003-09-19 11:01  gezelter
984  
985          * libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found
986          (nearly) conserved quantities for both NPTi and NPTf
987  
988 < 2003-09-19 11:20  mmeineke
988 > 2003-09-19 10:20  mmeineke
989  
990          * utils/Makefile.in: fixed a typo in the makefile.
991  
992 < 2003-09-19 10:55  gezelter
992 > 2003-09-19 09:55  gezelter
993  
994          * libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp,
995          samples/water/ssd.bass: [no log message]
996  
997 < 2003-09-19 10:22  tim
997 > 2003-09-19 09:22  tim
998  
999          * libmdtools/: NPTi.cpp, NVT.cpp: [no log message]
1000  
1001 < 2003-09-17 10:22  mmeineke
1001 > 2003-09-17 09:22  mmeineke
1002  
1003          * libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now
1004          work with constraints.
1005  
1006 < 2003-09-16 16:02  tim
1006 > 2003-09-16 15:02  tim
1007  
1008          * libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp,
1009          SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo
# Line 299 | Line 1012
1012          
1013          NPTi appears very stable.
1014  
1015 < 2003-09-15 12:52  tim
1015 > 2003-09-15 11:52  tim
1016  
1017          * libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp,
1018          libmdtools/Integrator.hpp, libmdtools/NPTf.cpp,
# Line 310 | Line 1023
1023          utils/sysbuilder/bilayerSys.cpp: add conserved quantity to
1024          statWriter fix bug of vector wrapping at NPTi
1025  
1026 < 2003-09-12 16:51  mmeineke
314 <
315 <        * props/: AllCorr.cpp, AllCorr.hpp, GofR.cpp, PairCorrType.cpp,
316 <        PairCorrType.hpp: added AllCorr. It eill still need some work
1026 > 2003-09-12 11:20  gezelter
1027  
318 – 2003-09-12 12:20  gezelter
319 –
1028          * libmdtools/: Make.dep, Makefile.in: Added integrators to
1029          Makefile.in
1030  
1031 < 2003-09-12 12:20  gezelter
1031 > 2003-09-12 11:20  gezelter
1032  
1033          * ChangeLog: Entered changes for configure into ChangeLog
1034  
1035 < 2003-09-10 17:28  mmeineke
1035 > 2003-09-09 15:35  mmeineke
1036  
329 –        * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more
330 –        work on getting gofR working.
331 –
332 – 2003-09-09 17:50  mmeineke
333 –
334 –        * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the
335 –        beginings of the GofR pair correlation.
336 –        
337 –        added identification of identI in matchI.
338 –
339 – 2003-09-09 16:35  mmeineke
340 –
1037          * libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp,
1038          NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog
1039          
1040          added two new NPT integrators, they still need work.
1041  
1042 < 2003-09-09 16:34  mmeineke
1042 > 2003-09-09 15:34  mmeineke
1043  
1044          * ChangeLog: updated the ChangeLog
1045  
1046 < 2003-09-05 18:45  gezelter
1046 > 2003-09-05 17:45  gezelter
1047  
1048          * libmdtools/Make.dep: dependency on config.h
1049  
1050 < 2003-09-05 18:36  gezelter
1050 > 2003-09-05 17:36  gezelter
1051  
1052          * configure, ac-tools/aclocal.m4: fixed sprng problem
1053  
1054 < 2003-09-05 17:29  gezelter
1054 > 2003-09-05 16:29  gezelter
1055  
1056          * samples/metals/Makefile.in: New Makefile for metals sample
1057  
1058 < 2003-09-05 17:27  gezelter
1058 > 2003-09-05 16:27  gezelter
1059  
1060          * Makefile, Makefile.in, ac-tools/aclocal.m4,
1061          ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile,
# Line 383 | Line 1079
1079          utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to
1080          autoconf / configure method of configuring OOPSE
1081  
1082 < 2003-09-04 17:48  mmeineke
1082 > 2003-09-04 16:48  mmeineke
1083  
1084          * libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
1085          libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp,
# Line 393 | Line 1089
1089          
1090          added ability to reset the integrators in the NVT and NPT family.
1091  
1092 < 2003-09-04 17:48  mmeineke
1092 > 2003-09-04 16:48  mmeineke
1093  
1094          * libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global
1095          namespace.
1096  
1097 < 2003-09-02 10:30  tim
1097 > 2003-09-02 09:30  tim
1098  
1099          * libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp,
1100          ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of
1101          PolicyByMass
1102  
1103 < 2003-08-28 17:09  tim
1103 > 2003-08-28 16:09  tim
1104  
1105          * ChangeLog, libmdtools/GenericData.cpp,
1106          libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp,
1107          libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex
1108  
1109 < 2003-08-28 12:59  mmeineke
1109 > 2003-08-27 14:23  tim
1110  
415 –        * props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp:
416 –        added the first functional parts of the PairCorrType Abstract
417 –        classes.
418 –
419 – 2003-08-27 15:23  tim
420 –
1111          * libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix
1112          bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to
1113          MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we
1114          turn on the optimization flag, it causes a seg fault
1115  
1116 < 2003-08-27 12:25  gezelter
1116 > 2003-08-27 11:25  gezelter
1117  
1118          * libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90,
1119          calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for
1120          stress tensor parallel bug.
1121  
1122 < 2003-08-27 12:16  tim
1122 > 2003-08-27 11:16  tim
1123  
1124          * ChangeLog, libmdtools/DUFF.cpp,
1125          libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90:
1126          fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90
1127          molMembershipList use global index instead of local index
1128  
1129 < 2003-08-26 16:37  tim
1129 > 2003-08-26 15:37  tim
1130  
1131          * libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90,
1132          mpiSimulation.cpp: set default force substraction policy to
1133          PolicyByMass
1134  
1135 < 2003-08-26 16:29  tim
1135 > 2003-08-26 15:29  tim
1136  
1137          * libmdtools/Integrator.cpp: [no log message]
1138  
1139 < 2003-08-26 16:13  mmeineke
1139 > 2003-08-26 15:13  mmeineke
1140  
1141          * utils/sysbuilder/bilayerSys.cpp: added define statemewnt to
1142          Statwriter and Dumpwriter to handle files larger than 2 gb.
# Line 455 | Line 1145
1145          
1146          hard coding some system init into bilayer.sys
1147  
1148 < 2003-08-26 16:12  mmeineke
1148 > 2003-08-26 15:12  mmeineke
1149  
1150          * libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp:
1151          added define statemewnt to Statwriter and Dumpwriter to handle
# Line 463 | Line 1153
1153          
1154          commented out some print statements in Zconstraint
1155  
1156 < 2003-08-26 16:02  tim
1156 > 2003-08-26 15:02  tim
1157  
1158          * libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed
1159          and check the seed which is specified by user at least contains 9
1160          digits
1161  
1162 < 2003-08-26 14:32  mmeineke
1162 > 2003-08-26 13:32  mmeineke
1163  
1164          * libmdtools/DUFF.cpp: changed the Makefiel a litle.
1165          
# Line 477 | Line 1167
1167          constucted in MPI. (The MPI struct had 6 doubles declared versus
1168          the actual 11)
1169  
1170 < 2003-08-26 14:30  mmeineke
1170 > 2003-08-26 13:30  mmeineke
1171  
1172          * Makefile: changed the Makefiel a litle.
1173  
1174 < 2003-08-25 18:17  gezelter
1174 > 2003-08-25 17:17  gezelter
1175  
1176          * utils/sysbuilder/Makefile: More FreeBSD fixes
1177  
1178 < 2003-08-25 17:51  gezelter
1178 > 2003-08-25 16:51  gezelter
1179  
1180          * libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp,
1181          libmdtools/Makefile, src/Makefile: [no log message]
1182  
1183 < 2003-08-22 16:04  mmeineke
1183 > 2003-08-22 15:04  mmeineke
1184  
1185          * libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on
1186          frequency of output dumps.
1187  
1188 < 2003-08-20 18:23  tim
1188 > 2003-08-20 17:23  tim
1189  
1190          * libBASS/Globals.hpp, libmdtools/SimInfo.hpp,
1191          libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp,
# Line 503 | Line 1193
1193          if he does not specify any value for seed, oopse will take the
1194          value of seconds of system time as seed
1195  
1196 < 2003-08-20 15:42  mmeineke
1196 > 2003-08-20 14:42  mmeineke
1197  
1198          * libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
1199          libmdtools/GhostBend.cpp, libmdtools/SRI.hpp,
# Line 516 | Line 1206
1206          fixed a bug where ghostbend atom b was not being set. ( recent bug
1207          from SimState conversion)
1208  
1209 < 2003-08-20 15:41  mmeineke
1209 > 2003-08-20 14:41  mmeineke
1210  
1211          * libBASS/Globals.hpp: updated the Changelog.
1212          
1213          added some bug fixes for setting the random number generator seed
1214          value.
1215  
1216 < 2003-08-20 15:41  mmeineke
1216 > 2003-08-20 14:41  mmeineke
1217  
1218          * ChangeLog: updated the Changelog.
1219  
1220 < 2003-08-20 15:11  tim
1220 > 2003-08-20 14:11  tim
1221  
1222          * libBASS/Globals.cpp, libmdtools/DUFF.cpp,
1223          libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost
1224          bend class
1225  
1226 < 2003-08-20 11:13  mmeineke
1226 > 2003-08-20 10:13  mmeineke
1227  
1228          * utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in
1229          make links. added -f to ln -s.
1230  
1231 < 2003-08-20 10:50  tim
1231 > 2003-08-20 09:50  tim
1232  
1233          * libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message]
1234  
1235 < 2003-08-20 10:34  tim
1235 > 2003-08-20 09:34  tim
1236  
1237          * libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp,
1238          ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg
1239          printing
1240  
1241 < 2003-08-18 16:59  chuckv
1241 > 2003-08-18 15:59  chuckv
1242  
1243          * utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp,
1244          latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp,
1245          sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works.
1246          Nanobuilder still broke.
1247  
1248 < 2003-08-15 15:24  tim
1248 > 2003-08-15 14:24  tim
1249  
1250          * libBASS/Globals.cpp, libBASS/Globals.hpp,
1251          libmdtools/GenericData.hpp, libmdtools/Integrator.hpp,
# Line 564 | Line 1254
1254          libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint
1255          Method
1256  
1257 < 2003-08-14 12:16  tim
1257 > 2003-08-14 11:16  tim
1258  
1259          * libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint
1260          with average force substraction strategy
1261  
1262 < 2003-08-13 17:20  chuckv
1262 > 2003-08-13 16:20  chuckv
1263  
1264          * libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some
1265          profiling code -DPROFILE.
1266  
1267 < 2003-08-13 15:21  tim
1267 > 2003-08-13 14:21  tim
1268  
1269          * libBASS/Globals.cpp, libBASS/Globals.hpp,
1270          libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
1271          libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic
1272          potential & z-contraint method
1273  
1274 < 2003-08-12 17:44  mmeineke
1274 > 2003-08-12 16:44  mmeineke
1275  
1276          * libBASS/BASS_interface.cpp, libBASS/Globals.hpp,
1277          libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
# Line 590 | Line 1280
1280          annoying bug in Directional Atom, where mu was getting written to
1281          pseudorandom memory location.
1282  
1283 < 2003-08-12 15:56  tim
1283 > 2003-08-12 14:56  tim
1284  
1285          * libBASS/BASS_interface.cpp, libBASS/Globals.cpp,
1286          libBASS/Globals.hpp, libmdtools/Atom.hpp,
1287          libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp,
1288          libmdtools/SimSetup.cpp: debugging globals
1289  
1290 < 2003-08-12 14:40  gezelter
1290 > 2003-08-12 13:40  gezelter
1291  
1292          * forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes
1293          and new atypes in LJFF
1294  
1295 < 2003-08-12 14:15  gezelter
1295 > 2003-08-12 13:15  gezelter
1296  
1297          * forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older
1298          stuff...
1299  
1300 < 2003-08-12 14:14  chuckv
1300 > 2003-08-12 13:14  chuckv
1301  
1302          * utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt.
1303  
1304 < 2003-08-12 14:04  chuckv
1304 > 2003-08-12 13:04  chuckv
1305  
1306          * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp:
1307          Missed del of files before.
1308  
1309 < 2003-08-12 14:03  chuckv
1309 > 2003-08-12 13:03  chuckv
1310  
1311          * utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log
1312          message]
1313  
1314 < 2003-08-12 14:01  chuckv
1314 > 2003-08-12 13:01  chuckv
1315  
1316          * utils/sysbuilder/Makefile: commit makefile
1317  
1318 < 2003-08-12 13:51  tim
1318 > 2003-08-12 12:51  tim
1319  
1320          * libBASS/Globals.cpp, libBASS/Globals.hpp,
1321          libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
# Line 633 | Line 1323
1323          libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added
1324          harmonical potential to z-constraint method
1325  
1326 < 2003-08-11 18:31  chuckv
1326 > 2003-08-11 17:31  chuckv
1327  
1328          * utils/Makefile: Changed makefile to only build quicklate.
1329  
1330 < 2003-08-11 18:25  chuckv
1330 > 2003-08-11 17:25  chuckv
1331  
1332          * ac-tools/configure.in: added utils/sysbuilder to be built.
1333  
1334 < 2003-08-11 18:12  chuckv
1334 > 2003-08-11 17:12  chuckv
1335  
1336          * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp,
1337          bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp,
# Line 655 | Line 1345
1345          sysbuilder into a subdirectory. Fixed some of sysbuilder to work
1346          with new atom allocation in libmdtools.
1347  
1348 < 2003-08-11 15:41  tim
1348 > 2003-08-11 14:41  tim
1349  
1350          * libmdtools/: Integrator.cpp, Integrator.hpp: added method of
1351          moving zconstraint molecules to specified positions
1352  
1353 < 2003-08-11 15:39  tim
1353 > 2003-08-11 14:39  tim
1354  
1355          * libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message]
1356  
1357 < 2003-08-11 15:38  mmeineke
1357 > 2003-08-11 14:38  mmeineke
1358  
1359          * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h,
1360          libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp,
# Line 675 | Line 1365
1365          libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint
1366          into the BASS language syntax.
1367  
1368 < 2003-08-11 14:29  mmeineke
1368 > 2003-08-11 13:29  mmeineke
1369  
1370          * libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of
1371          degrees of freedom to account for zConstreints
1372  
1373 < 2003-08-08 17:22  chuckv
1373 > 2003-08-08 16:22  chuckv
1374  
1375          * libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90,
1376          libmdtools/do_Forces.F90, libmdtools/neighborLists.F90,
1377          samples/metals/Au.bass: EAM works...... Neighbor list also
1378          works.....
1379  
1380 < 2003-08-08 14:32  mmeineke
1380 > 2003-08-08 12:48  mmeineke
1381  
692 –        * props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp:
693 –        moved frameCount's functionality into DumpReader. also split props
694 –        into staticProps and dynamicProps. (currently only have
695 –        staticProps)
696 –
697 – 2003-08-08 13:48  mmeineke
698 –
1382          * libmdtools/: Makefile, ZConstraint.cpp:  fixed a deprcated
1383          instance of Atom::setZ and Atom::getZ in ZConstaint.
1384  
1385 < 2003-08-07 17:47  mmeineke
1385 > 2003-08-07 16:47  mmeineke
1386  
1387          * libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp,
1388          DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp,
# Line 708 | Line 1391
1391          SimState.hpp, Torsion.cpp: switched SimInfo to use a system
1392          configuration from SimState rather than arrays from Atom
1393  
1394 < 2003-08-06 20:47  chuckv
1394 > 2003-08-06 19:47  chuckv
1395  
1396          * libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp,
1397          libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90,
1398          libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90,
1399          samples/metals/Au.bass: Bug fixes for eam...
1400  
1401 < 2003-08-01 12:18  tim
1401 > 2003-08-01 11:18  tim
1402  
1403          * libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of
1404          Z-Constraint
1405  
1406 < 2003-07-31 15:59  tim
1406 > 2003-07-31 14:59  tim
1407  
1408          * ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
1409          libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp,
1410          libmdtools/ZConstraint.cpp: add index range checking into
1411          ZConstraint
1412  
1413 < 2003-07-31 11:38  tim
1413 > 2003-07-31 10:38  tim
1414  
1415          * libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters
1416          to the globals
1417  
1418 < 2003-07-31 11:35  tim
1418 > 2003-07-31 10:35  tim
1419  
1420          * libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp,
1421          Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp,
# Line 740 | Line 1423
1423          SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp:
1424          Added Z constraint.
1425  
1426 < 2003-07-30 17:17  chuckv
1426 > 2003-07-30 16:17  chuckv
1427  
1428          * libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp,
1429          libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90,
1430          libmdtools/do_Forces.F90, libmdtools/wrappers.F90,
1431          samples/metals/Au.bass: More bug fixes for eam.
1432  
1433 < 2003-07-29 12:32  mmeineke
1433 > 2003-07-29 11:32  mmeineke
1434  
1435          * libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp,
1436 <        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp,
1437 <        props/frameCount.c, props/frameCount.h, props/props.cpp,
755 <        src/Makefile: working on the props code
1436 >        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile:
1437 >        working on the props code
1438  
1439 < 2003-07-29 12:32  mmeineke
1439 > 2003-07-29 11:32  mmeineke
1440  
1441          * libBASS/Globals.cpp: [no log message]
1442  
1443 < 2003-07-25 16:05  chuckv
1443 > 2003-07-25 15:05  chuckv
1444  
1445          * samples/metals/: Au.bass, metals.mdl: Added bass models for
1446          metals
1447  
1448 < 2003-07-25 16:00  chuckv
1448 > 2003-07-25 15:00  chuckv
1449  
1450          * libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90,
1451          notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam.
1452  
1453 < 2003-07-24 17:22  chuckv
1453 > 2003-07-24 16:22  chuckv
1454  
1455          * ac-tools/configure.in: Changed configure to look for both upper
1456          and lower cass .mod files
1457  
1458 < 2003-07-24 15:57  chuckv
1458 > 2003-07-24 14:57  chuckv
1459  
1460          * libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for
1461          eam and do_forces.
1462  
1463 < 2003-07-23 18:13  chuckv
1463 > 2003-07-23 17:13  chuckv
1464  
1465          * libmdtools/: Makefile, calc_eam.F90, do_Forces.F90,
1466          force_globals.F90, simulation_module.F90, status_module.F90:
1467          Finished most code for eam....
1468  
1469 < 2003-07-22 17:49  mmeineke
1469 > 2003-07-22 16:49  mmeineke
1470  
1471          * libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan
1472          function to the DumpReader. It should now save the start of each
1473          frame in a vector.
1474  
1475 < 2003-07-22 16:05  mmeineke
1475 > 2003-07-22 15:05  mmeineke
1476  
1477          * libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes
1478          to read dump files
1479  
1480 < 2003-07-22 15:54  tim
1480 > 2003-07-22 14:54  tim
1481  
1482          * libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp,
1483          Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp,
1484          NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log
1485          message]
1486  
1487 < 2003-07-22 12:41  mmeineke
1487 > 2003-07-22 11:41  mmeineke
1488  
1489          * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp,
1490          SimSetup.cpp: Fixed a current time initialization bug in
1491          InitFromFile.
1492  
1493 < 2003-07-21 17:27  mmeineke
1493 > 2003-07-21 16:27  mmeineke
1494  
1495          * libmdtools/: DumpReader.cpp, InitializeFromFile.cpp,
1496          Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and
1497          friends to accomadate random file access
1498  
1499 < 2003-07-21 12:23  mmeineke
1499 > 2003-07-21 11:23  mmeineke
1500  
1501          * libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no
1502          one sets it.
1503  
1504 < 2003-07-21 12:23  mmeineke
1504 > 2003-07-21 11:23  mmeineke
1505  
1506          * libmdtools/: InitializeFromFile.cpp, Integrator.cpp,
1507          ReadWrite.hpp: fixed Initializefrom file to start the simulation
1508          from the time specified in the init file.
1509  
1510 < 2003-07-17 17:49  gezelter
1510 > 2003-07-17 16:49  gezelter
1511  
1512          * libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp,
1513          DumpReader.cpp: Started work on a DumpReader
1514  
1515 < 2003-07-17 16:38  gezelter
1515 > 2003-07-17 15:38  gezelter
1516  
1517          * libmdtools/calc_sticky_pair.F90: Fixes for SSD/E
1518  
1519 < 2003-07-17 16:32  gezelter
1519 > 2003-07-17 15:32  gezelter
1520  
1521          * forceFields/DUFF.frc, libmdtools/DUFF.cpp,
1522          libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp:
1523          Changes for SSD/E
1524  
1525 < 2003-07-17 15:38  mmeineke
1525 > 2003-07-17 14:38  mmeineke
1526  
1527          * libmdtools/do_Forces.F90: commented out an eam line
1528  
1529 < 2003-07-17 15:32  chuckv
1529 > 2003-07-17 14:32  chuckv
1530  
1531          * libmdtools/atype_module.F90: fixed spelling issue
1532  
1533 < 2003-07-17 15:29  chuckv
1533 > 2003-07-17 14:29  chuckv
1534  
1535          * libmdtools/: fInfo.c, status_module.F90: added info module
1536  
1537 < 2003-07-17 15:25  chuckv
1537 > 2003-07-17 14:25  chuckv
1538  
1539          * libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile,
1540          atype_module.F90, calc_eam.F90, do_Forces.F90,
1541          fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp,
1542          mpiSimulation_module.F90: Added massive changes for eam....
1543  
1544 < 2003-07-16 17:49  chuckv
1544 > 2003-07-16 16:49  chuckv
1545  
1546          * libmdtools/EAM_FF.cpp: More up to date version of EAM_FF
1547  
1548 < 2003-07-16 17:30  mmeineke
1548 > 2003-07-16 16:30  mmeineke
1549  
1550          * libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp,
1551          SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90,
# Line 874 | Line 1556
1556          notifyCutoffs in Fortran notifies those who need the information of
1557          any changes to cutoffs.
1558  
1559 < 2003-07-16 13:35  gezelter
1559 > 2003-07-16 12:35  gezelter
1560  
1561          * utils/: Makefile, quickLate.c: Made quickLate aware of Hmat.
1562          quickLate is now somewhat more intelligent about periodic
1563          boundaries and wrapping.
1564  
1565 < 2003-07-16 12:40  chuckv
1565 > 2003-07-16 11:40  chuckv
1566  
1567          * libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists
1568  
1569 < 2003-07-16 11:34  mmeineke
1569 > 2003-07-16 10:34  mmeineke
1570  
1571          * scripts/cleanSrc: added a quick wipe-and-update script for quick
1572          rebuilds on BoB
1573  
1574 < 2003-07-15 22:11  gezelter
1574 > 2003-07-15 21:11  gezelter
1575  
1576          * libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp,
1577          SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more
1578          fixes for box changes
1579  
1580 < 2003-07-15 18:29  mmeineke
1580 > 2003-07-15 17:29  mmeineke
1581  
1582          * libmdtools/simulation_module.F90: removed some debugging print
1583          statements.
1584  
1585 < 2003-07-15 18:22  mmeineke
1585 > 2003-07-15 17:22  mmeineke
1586  
1587          * libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90,
1588          do_Forces.F90, simulation_module.F90: fixed a long lived bug in
# Line 909 | Line 1591
1591          cutoff region to be to small. Also led to the removal of the taper
1592          region to buffer the dipole cutoff.
1593  
1594 < 2003-07-15 17:34  mmeineke
1594 > 2003-07-15 16:34  mmeineke
1595  
1596          * libmdtools/: SimInfo.cpp, simulation_module.F90: working on
1597          fixing ssd bug
1598  
1599 < 2003-07-15 15:56  gezelter
1599 > 2003-07-15 14:56  gezelter
1600  
1601          * libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes
1602          for the NPT ensembles
1603  
1604 < 2003-07-15 14:52  mmeineke
1604 > 2003-07-15 13:52  mmeineke
1605  
1606          * libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up
1607          simSetup
1608  
1609 < 2003-07-15 13:57  mmeineke
1609 > 2003-07-15 12:57  mmeineke
1610  
1611          * libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp,
1612          SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90:
1613          fixed some bugs, Changed entry_plug to info where appropriate
1614  
1615 < 2003-07-15 13:25  chuckv
1615 > 2003-07-15 12:25  chuckv
1616  
1617          * utils/sysBuild.ggo: added more command line arguments
1618  
1619 < 2003-07-15 13:11  gezelter
1619 > 2003-07-15 12:11  gezelter
1620  
1621          * samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass:
1622          Fixing force field line
1623  
1624 < 2003-07-15 13:10  gezelter
1624 > 2003-07-15 12:10  gezelter
1625  
1626          * libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp,
1627          calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90,
1628          calc_reaction_field.F90, calc_sticky_pair.F90: Fixing  pressure
1629          tensor
1630  
1631 < 2003-07-15 11:50  gezelter
1631 > 2003-07-15 10:50  gezelter
1632  
1633          * libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes
1634  
1635 < 2003-07-15 11:42  gezelter
1635 > 2003-07-15 10:42  gezelter
1636  
1637          * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp:
1638          removed old outdated code
1639  
1640 < 2003-07-15 10:45  gezelter
1640 > 2003-07-15 09:45  gezelter
1641  
1642          * libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx
1643  
1644 < 2003-07-15 10:28  gezelter
1644 > 2003-07-15 09:28  gezelter
1645  
1646          * libmdtools/Molecule.cpp: removing get_vx
1647  
1648 < 2003-07-14 23:28  gezelter
1648 > 2003-07-14 22:28  gezelter
1649  
1650          * libmdtools/NPTfm.cpp: Added NPTfm
1651  
1652 < 2003-07-14 23:27  gezelter
1652 > 2003-07-14 22:27  gezelter
1653  
1654          * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp:
1655          Bugfix in NPTim, fixes for NPTfm
1656  
1657 < 2003-07-14 23:08  gezelter
1657 > 2003-07-14 22:08  gezelter
1658  
1659          * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp:
1660          Checking in changes for NPTim
1661  
1662 < 2003-07-14 19:06  gezelter
1662 > 2003-07-14 18:06  gezelter
1663  
1664          * utils/Makefile: Broken SysBuilder
1665  
1666 < 2003-07-14 19:06  gezelter
1666 > 2003-07-14 18:06  gezelter
1667  
1668          * samples/: alkane/init_butane.eor, argon/argon.bass,
1669          argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes
1670          for samples
1671  
1672 < 2003-07-14 19:06  gezelter
1672 > 2003-07-14 18:06  gezelter
1673  
1674          * libmdtools/: Integrator.cpp, do_Forces.F90: Removed some
1675          debugging write statements
1676  
1677 < 2003-07-14 18:38  gezelter
1677 > 2003-07-14 17:38  gezelter
1678  
1679          * libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp,
1680          NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom
1681  
1682 < 2003-07-14 17:48  mmeineke
1682 > 2003-07-14 16:48  mmeineke
1683  
1684          * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get
1685          and set routines to Atom and DirectionalAtom
1686  
1687 < 2003-07-14 17:35  chuckv
1687 > 2003-07-14 16:35  chuckv
1688  
1689          * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp,
1690          sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder
1691          that takes different cmd line arguments.
1692  
1693 < 2003-07-14 17:28  mmeineke
1693 > 2003-07-14 16:28  mmeineke
1694  
1695          * libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp,
1696          ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile,
1697          SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors
1698          were not being updated
1699  
1700 < 2003-07-14 11:04  gezelter
1700 > 2003-07-14 10:04  gezelter
1701  
1702          * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on
1703          NPTim
1704  
1705 < 2003-07-14 10:55  mmeineke
1705 > 2003-07-14 09:55  mmeineke
1706  
1707          * forceFields/DUFF.frc: Switched the bond in the force field back
1708          to constrained, to preserve energy
1709  
1710 < 2003-07-11 18:34  mmeineke
1710 > 2003-07-11 17:34  mmeineke
1711  
1712          * libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp,
1713          Integrator.hpp: working on som integrator bugs
1714  
1715 < 2003-07-11 11:26  gezelter
1715 > 2003-07-11 10:26  gezelter
1716  
1717          * libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting
1718          to worry about all the strtok() calls in our code
1719  
1720 < 2003-07-11 10:49  gezelter
1720 > 2003-07-11 09:49  gezelter
1721  
1722          * utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness
1723  
1724 < 2003-07-10 21:15  gezelter
1724 > 2003-07-10 20:15  gezelter
1725  
1726          * libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and
1727          eor.
1728  
1729 < 2003-07-10 18:15  mmeineke
1729 > 2003-07-10 17:15  mmeineke
1730  
1731          * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp,
1732          SimInfo.cpp, Thermo.cpp: fixed some bugs
1733  
1734 < 2003-07-10 15:53  chuckv
1734 > 2003-07-10 14:53  chuckv
1735  
1736          * utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp,
1737          nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added
1738          nanoBuilder and a general Lattice builder.
1739  
1740 < 2003-07-10 13:10  gezelter
1740 > 2003-07-10 12:10  gezelter
1741  
1742          * libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp,
1743          Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff
1744  
1745 < 2003-07-09 18:14  mmeineke
1745 > 2003-07-09 17:14  mmeineke
1746  
1747          * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp,
1748          Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp,
1749          SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the
1750          caclulation of HmatInverse.
1751  
1752 < 2003-07-09 11:34  mmeineke
1752 > 2003-07-09 10:34  mmeineke
1753  
1754          * libBASS/MoleculeStamp.hpp: starting some work for xlate
1755  
1756 < 2003-07-09 11:33  mmeineke
1756 > 2003-07-09 10:33  mmeineke
1757  
1758          * libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff
1759  
1760 < 2003-07-09 09:56  gezelter
1760 > 2003-07-09 08:56  gezelter
1761  
1762          * libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf
1763  
1764 < 2003-07-09 09:56  gezelter
1764 > 2003-07-09 08:56  gezelter
1765  
1766          * libBASS/Globals.cpp: Removed Qmass
1767  
1768 < 2003-07-08 22:15  gezelter
1768 > 2003-07-08 21:15  gezelter
1769  
1770          * libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf
1771          and NPTi
1772  
1773 < 2003-07-08 21:41  gezelter
1773 > 2003-07-08 20:41  gezelter
1774  
1775          * libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf
1776  
1777 < 2003-07-08 17:10  gezelter
1777 > 2003-07-08 16:10  gezelter
1778  
1779          * libmdtools/: Integrator.hpp, NPTf.cpp: [no log message]
1780  
1781 < 2003-07-08 17:06  gezelter
1781 > 2003-07-08 16:06  gezelter
1782  
1783          * libmdtools/NPTi.cpp: fixed box scaling
1784  
1785 < 2003-07-08 16:56  gezelter
1785 > 2003-07-08 15:56  gezelter
1786  
1787          * libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp,
1788          SimInfo.hpp, Thermo.cpp: NPTi
1789  
1790 < 2003-07-03 15:41  mmeineke
1790 > 2003-07-03 14:41  mmeineke
1791  
1792          * libBASS/Makefile, libmdtools/Makefile, src/Makefile,
1793          utils/Makefile, utils/bilayerSys.cpp:  cleaned up the dependecy
1794          scripts in the makefiles
1795  
1796 < 2003-07-02 17:26  mmeineke
1796 > 2003-07-02 16:26  mmeineke
1797  
1798          * libBASS/Makefile, libmdtools/DumpWriter.cpp,
1799          libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
# Line 1122 | Line 1804
1804          utils/Makefile: fixed the bugs introduced by switching the periodic
1805          box to a matrix
1806  
1807 < 2003-07-01 18:39  gezelter
1807 > 2003-07-01 17:39  gezelter
1808  
1809          * libmdtools/do_Forces.F90: Fortran flexi-BOX
1810  
1811 < 2003-07-01 18:29  gezelter
1811 > 2003-07-01 17:29  gezelter
1812  
1813          * libmdtools/simulation_module.F90: Fixes for flexi-BOX
1814  
1815 < 2003-07-01 17:33  mmeineke
1815 > 2003-07-01 16:33  mmeineke
1816  
1817          * libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h,
1818          fortranWrapDefines.hpp, simulation_module.F90: working on adding
1819          the box matrix to everything.
1820  
1821 < 2003-06-30 18:03  mmeineke
1821 > 2003-06-30 17:03  mmeineke
1822  
1823          * ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
1824          src/oopse.cpp:
1825          Updated the ChangeLog, and Converted most of the SImInfo to use
1826          non-Isotropic boxes. wrapVector needs to be finished.
1827  
1828 < 2003-06-25 17:12  mmeineke
1828 > 2003-06-25 16:12  mmeineke
1829  
1830          * libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds
1831          to Harmonic bonds in the DUFF frc file
1832          
1833          fixed constraints.
1834  
1835 < 2003-06-25 17:11  mmeineke
1835 > 2003-06-25 16:11  mmeineke
1836  
1837          * forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in
1838          the DUFF frc file
1839  
1840 < 2003-06-24 18:51  gezelter
1840 > 2003-06-24 17:51  gezelter
1841  
1842          * libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT.  Check them!
1843  
1844 < 2003-06-24 15:57  mmeineke
1844 > 2003-06-24 14:57  mmeineke
1845  
1846          * forceFields/DUFF.frc, libmdtools/BondExtensions.cpp,
1847          libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into
1848          the DUFF forcefield and BondExtensions.cpp
1849  
1850 < 2003-06-23 17:24  mmeineke
1850 > 2003-06-23 16:24  mmeineke
1851  
1852          * libmdtools/Integrator.cpp: Doing some work to debug the
1853          constraint code.
1854  
1855 < 2003-06-20 16:50  gezelter
1855 > 2003-06-20 15:50  gezelter
1856  
1857          * libmdtools/Integrator.hpp: NPT fix
1858  
1859 < 2003-06-20 16:29  mmeineke
1859 > 2003-06-20 15:29  mmeineke
1860  
1861          * libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
1862          libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
# Line 1183 | Line 1865
1865          libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the
1866          integrator and NVT seem to be working now.
1867  
1868 < 2003-06-20 12:49  gezelter
1868 > 2003-06-20 11:49  gezelter
1869  
1870          * libmdtools/: Integrator.hpp, NVT.cpp: NVT additions
1871  
1872 < 2003-06-19 18:02  mmeineke
1872 > 2003-06-19 17:02  mmeineke
1873  
1874          * forceFields/DUFF.frc, forceFields/LJFF.frc,
1875          forceFields/LJ_FF.frc, forceFields/Makefile,
# Line 1198 | Line 1880
1880          libmdtools/TraPPEFF.cpp: slowly converting to new integrator and
1881          forcefield names.
1882  
1883 < 2003-06-19 15:21  mmeineke
1883 > 2003-06-19 14:21  mmeineke
1884  
1885          * libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp:
1886          finished the basics of the integrator and SimSetup.cpp
1887  
1888 < 2003-06-19 15:11  mmeineke
1888 > 2003-06-19 14:11  mmeineke
1889  
1890          * libmdtools/SimSetup.cpp:  doing some work on SimSetup to clean it
1891          up / get it to work with the new Integrator.
1892  
1893 < 2003-06-18 18:20  mmeineke
1893 > 2003-06-18 17:20  mmeineke
1894  
1895          * libmdtools/Symplectic.cpp: minor changes in an attempt to fix
1896          output times.
1897  
1898 < 2003-06-17 17:56  mmeineke
1898 > 2003-06-17 16:56  mmeineke
1899  
1900          * libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters
1901          fro the ghost Bend in TraPPE_Ex
1902          
1903          some work on the integrator. ( incomplete)
1904  
1905 < 2003-06-17 17:55  mmeineke
1905 > 2003-06-17 16:55  mmeineke
1906  
1907          * forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost
1908          Bend in TraPPE_Ex
1909  
1910 < 2003-06-04 17:06  mmeineke
1910 > 2003-06-04 16:06  mmeineke
1911  
1912          * libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and
1913          constrainB to the Symplectic integrator
1914  
1915 < 2003-05-30 17:32  mmeineke
1915 > 2003-05-30 16:32  mmeineke
1916  
1917          * utils/bilayerSys.cpp: currently modifiying Symplectic to become
1918          the basic integrator.
1919          
1920          bilayerSys.cpp altered for building tb3.
1921  
1922 < 2003-05-30 17:31  mmeineke
1922 > 2003-05-30 16:31  mmeineke
1923  
1924          * libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp,
1925          TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently
1926          modifiying Symplectic to become the basic integrator.
1927  
1928 < 2003-05-30 16:19  mmeineke
1928 > 2003-05-30 15:19  mmeineke
1929  
1930          * libmdtools/Integrator.hpp: added some member variables for
1931          position, velocity, etc.
1932  
1933 < 2003-05-30 15:07  mmeineke
1933 > 2003-05-30 14:07  mmeineke
1934  
1935          * libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT
1936          is now derived from Integrator
1937  
1938 < 2003-05-20 12:44  mmeineke
1938 > 2003-05-20 11:44  mmeineke
1939  
1940          * libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug.
1941  
1942 < 2003-05-17 12:57  mmeineke
1942 > 2003-05-17 11:57  mmeineke
1943  
1944          * utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be
1945          working
1946  
1947 < 2003-05-16 17:37  mmeineke
1947 > 2003-05-16 16:37  mmeineke
1948  
1949          * utils/bilayerSys.cpp: still working on the bilayer code
1950  
1951 < 2003-05-16 10:28  mmeineke
1951 > 2003-05-16 09:28  mmeineke
1952  
1953          * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some
1954          work to overhaul sysbuild.
1955  
1956 < 2003-05-13 17:23  mmeineke
1956 > 2003-05-13 16:23  mmeineke
1957  
1958          * libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop
1959  
1960 < 2003-05-13 16:47  mmeineke
1960 > 2003-05-13 15:47  mmeineke
1961  
1962          * samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl,
1963          beadLipid/water.mdl: Added bead lipid model to the sample directory
1964  
1965 < 2003-05-13 16:34  mmeineke
1965 > 2003-05-13 15:34  mmeineke
1966  
1967          * forceFields/TraPPE_Ex.frc: finished adding the Tail beads into
1968          the Trappe extended force field
1969  
1970 < 2003-05-13 13:01  mmeineke
1970 > 2003-05-13 12:01  mmeineke
1971  
1972          * forceFields/TraPPE_Ex.frc: added the TailBead atom types to the
1973          TraPPe_Ex forceField
1974  
1975 < 2003-05-09 15:51  mmeineke
1975 > 2003-05-09 14:51  mmeineke
1976  
1977          * samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field.
1978          there were some duplicate entries
1979          
1980          added a two chain lipid to the lipid.mdl in sample
1981  
1982 < 2003-05-09 15:51  mmeineke
1982 > 2003-05-09 14:51  mmeineke
1983  
1984          * forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field.
1985          there were some duplicate entries
1986  
1987 < 2003-05-09 12:56  mmeineke
1987 > 2003-05-09 11:56  mmeineke
1988  
1989          * forceFields/TraPPE_Ex.frc: added the utils subdirectory to the
1990          configure script
1991          
1992          added the CH branching group to the TraPPE_Ex fource field
1993  
1994 < 2003-05-09 12:55  mmeineke
1994 > 2003-05-09 11:55  mmeineke
1995  
1996          * ac-tools/configure.in: added the utils subdirectory to the
1997          configure script
1998  
1999 < 2003-04-25 12:02  mmeineke
1999 > 2003-04-25 11:02  mmeineke
2000  
2001          * utils/bilayerSys.cpp: i quick fix to th distance in the random
2002          bilayer builder
2003  
2004 < 2003-04-24 22:00  mmeineke
2004 > 2003-04-24 21:00  mmeineke
2005  
2006          * libmdtools/f_verlet_constrained.F90: added a new test for
2007          constraint failure
2008  
2009 < 2003-04-17 17:54  mmeineke
2009 > 2003-04-17 16:54  mmeineke
2010  
2011          * libBASS/BASS_interface.h, libmdtools/SimSetup.cpp,
2012          utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp,
2013          utils/bilayerSys.cpp: fixed up sysBuild to where it should now
2014          build our systems
2015  
2016 < 2003-04-16 17:11  mmeineke
2016 > 2003-04-16 16:11  mmeineke
2017  
2018          * utils/: MoLocator.cpp, MoLocator.hpp: almost finished.
2019  
2020 < 2003-04-15 17:47  mmeineke
2020 > 2003-04-15 16:47  mmeineke
2021  
2022          * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys
2023          and sysBuild both will build now. woot!
2024  
2025 < 2003-04-15 17:20  mmeineke
2025 > 2003-04-15 16:20  mmeineke
2026  
2027          * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp,
2028          bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp
# Line 1349 | Line 2031
2031          
2032          MoLocator.cpp is currently empty
2033  
2034 < 2003-04-15 16:40  chuckv
2034 > 2003-04-15 15:40  chuckv
2035  
2036          * forceFields/EAM_FF.frc, forceFields/agu3.eam,
2037          forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam,
2038          forceFields/pdu3.eam, forceFields/ptu3.eam,
2039          libmdtools/ForceFields.hpp: Added eam force files...
2040  
2041 < 2003-04-15 12:37  chuckv
2041 > 2003-04-15 11:37  chuckv
2042  
2043          * libmdtools/EAM_FF.cpp: More eam work.
2044  
2045 < 2003-04-14 17:22  mmeineke
2045 > 2003-04-14 16:22  mmeineke
2046  
2047          * libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp,
2048          utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp:
2049          working on the system builder
2050  
2051 < 2003-04-14 17:16  chuckv
2051 > 2003-04-14 16:16  chuckv
2052  
2053          * libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed
2054          ordering on NVT calculation in integrators.
2055  
2056 < 2003-04-14 15:51  mmeineke
2056 > 2003-04-14 14:51  mmeineke
2057  
2058          * utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder,
2059          obj/placeHolder:  working on a system builder
2060  
2061 < 2003-04-14 15:04  mmeineke
2061 > 2003-04-14 14:04  mmeineke
2062  
2063          * utils/Makefile: added Ghost bends to the TraPPE_Ex forceField
2064          
2065          added sysBuild to the utils Makefile
2066  
2067 < 2003-04-14 15:03  mmeineke
2067 > 2003-04-14 14:03  mmeineke
2068  
2069          * forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added
2070          Ghost bends to the TraPPE_Ex forceField
2071  
2072 < 2003-04-14 14:19  chuckv
2072 > 2003-04-14 13:19  chuckv
2073  
2074          * libmdtools/calc_eam.F90: Added first mangling of EAM.
2075  
2076 < 2003-04-11 14:46  mmeineke
2076 > 2003-04-11 13:46  mmeineke
2077  
2078          * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90,
2079          simulation_module.F90: fixed a memory bug in Fortran, where
2080          molMembershipArray was declared nLocal instead of nGlobal.
2081  
2082 < 2003-04-11 11:16  gezelter
2082 > 2003-04-11 10:16  gezelter
2083  
2084          * libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp,
2085          SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90,
2086          fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress
2087          for NPT
2088  
2089 < 2003-04-10 16:08  mmeineke
2089 > 2003-04-10 15:08  mmeineke
2090  
2091          * libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp:  added a
2092          globalIndex counter to Molecule
2093  
2094 < 2003-04-10 12:35  gezelter
2094 > 2003-04-10 11:35  gezelter
2095  
2096          * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on
2097          ConstantStress
2098  
2099 < 2003-04-10 12:27  mmeineke
2099 > 2003-04-10 11:27  mmeineke
2100  
2101          * libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup.
2102          caused a miscalculation of nLocal.
2103  
2104 < 2003-04-10 12:21  mmeineke
2104 > 2003-04-10 11:21  mmeineke
2105  
2106          * libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90,
2107          do_Forces.F90: fixed a bug in symplectic, where presure was only
2108          being calculated the first time through.
2109  
2110 < 2003-04-09 12:20  chuckv
2110 > 2003-04-09 11:20  chuckv
2111  
2112          * samples/alkane/alkanes.mdl: added pentane to the alkane model
2113          file
2114  
2115 < 2003-04-09 09:59  gezelter
2115 > 2003-04-09 08:59  gezelter
2116  
2117          * libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp,
2118          Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file
2119  
2120 < 2003-04-09 00:06  gezelter
2120 > 2003-04-08 23:06  gezelter
2121  
2122          * libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp,
2123          ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp,
# Line 1445 | Line 2127
2127          fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and
2128          NVT
2129  
2130 < 2003-04-08 18:38  chuckv
2130 > 2003-04-08 17:38  chuckv
2131  
2132          * libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp,
2133          libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90,
# Line 1453 | Line 2135
2135          libmdtools/simulation_module.F90, samples/water/ssd.bass: It works
2136          (kinda)...
2137  
2138 < 2003-04-08 17:35  gezelter
2138 > 2003-04-08 16:35  gezelter
2139  
2140          * libBASS/Globals.cpp, libBASS/Globals.hpp,
2141          libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp,
2142          libmdtools/SimSetup.cpp: Fixes for NPT / NVT
2143  
2144 < 2003-04-08 13:16  chuckv
2144 > 2003-04-08 12:16  chuckv
2145  
2146          * libmdtools/: do_Forces.F90, neighborLists.F90,
2147          simulation_module.F90: Moved expand neighborlist to init_FF.
2148  
2149 < 2003-04-08 11:20  chuckv
2149 > 2003-04-08 10:20  chuckv
2150  
2151          * libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for
2152          NVT
2153  
2154 < 2003-04-08 10:39  gezelter
2154 > 2003-04-08 09:39  gezelter
2155  
2156          * libmdtools/Verlet.cpp: fixes for nvt / npt
2157  
2158 < 2003-04-08 10:34  gezelter
2158 > 2003-04-08 09:34  gezelter
2159  
2160          * libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp,
2161          Thermo.cpp, Verlet.cpp: dt/2 fix in nvt
2162  
2163 < 2003-04-08 08:50  gezelter
2163 > 2003-04-08 07:50  gezelter
2164  
2165          * libmdtools/ExtendedSystem.cpp: Fixes for affine transform
2166  
2167 < 2003-04-08 08:44  gezelter
2167 > 2003-04-08 07:44  gezelter
2168  
2169          * libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp,
2170          Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the
2171          NVT and NPT ensembles
2172  
2173 < 2003-04-07 17:42  gezelter
2173 > 2003-04-07 16:42  gezelter
2174  
2175          * libBASS/Globals.cpp, libBASS/Globals.hpp,
2176          libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp,
2177          libmdtools/SimSetup.cpp: Fixes for NPT and NVT
2178  
2179 < 2003-04-07 17:20  mmeineke
2179 > 2003-04-07 16:20  mmeineke
2180  
2181          * libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial
2182          portion of SSD.
2183  
2184 < 2003-04-07 17:16  mmeineke
2184 > 2003-04-07 16:16  mmeineke
2185  
2186          * libmdtools/: ForceFields.cpp, Symplectic.cpp:
2187          doing some testing in sticky through Symplectic.
2188  
2189 < 2003-04-07 16:51  gezelter
2189 > 2003-04-07 15:51  gezelter
2190  
2191          * libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT
2192  
2193 < 2003-04-07 16:50  chuckv
2193 > 2003-04-07 15:50  chuckv
2194  
2195          * libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for
2196          tau and virial.
2197  
2198 < 2003-04-07 16:06  mmeineke
2198 > 2003-04-07 15:06  mmeineke
2199  
2200          * libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp,
2201          libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp,
2202          libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90,
2203          src/Makefile: bug fixes
2204  
2205 < 2003-04-07 12:56  gezelter
2205 > 2003-04-07 11:56  gezelter
2206  
2207          * libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp,
2208          StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp:
2209          Many fixes to add extended system
2210  
2211 < 2003-04-07 10:30  gezelter
2211 > 2003-04-07 09:30  gezelter
2212  
2213          * src/Makefile: Fixed a bug caused by my experimentation
2214  
2215 < 2003-04-07 10:30  gezelter
2215 > 2003-04-07 09:30  gezelter
2216  
2217          * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp,
2218          Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp:
2219          Added ExtendedSystem infrastructure for NPT and NVT calculations
2220  
2221 < 2003-04-07 10:30  gezelter
2221 > 2003-04-07 09:30  gezelter
2222  
2223          * libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS
2224  
# Line 1879 | Line 2561
2561  
2562   2003-03-25 09:29  mmeineke
2563  
2564 <        * libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy,
2565 <        src/MPIobj/dummy, src/obj/dummy: [no log message]
2564 >        * libBASS/obj/dummy, libmdtools/obj/dummy, src/MPIobj/dummy,
2565 >        src/obj/dummy: [no log message]
2566  
2567   2003-03-25 09:29  mmeineke
2568  
# Line 1889 | Line 2571
2571  
2572   2003-03-24 20:07  gezelter
2573  
2574 <        * samples/Makefile, tests/Makefile: moving tests to samples
2574 >        * samples/Makefile: moving tests to samples
2575  
2576   2003-03-24 20:06  gezelter
2577  
2578 <        * samples/alkane/Makefile, samples/alkane/alkanes.mdl,
2579 <        samples/alkane/butane.bass, samples/alkane/init_butane.eor,
2580 <        samples/argon/Makefile, samples/argon/argon.bass,
2581 <        samples/argon/init_argon.eor, samples/argon/lj.mdl,
2582 <        samples/lipid/5x5.bass, samples/lipid/Makefile,
2583 <        samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl,
2584 <        samples/lipid/water.mdl, samples/water/Makefile,
1903 <        samples/water/init_ssd.eor, samples/water/ssd.bass,
1904 <        samples/water/water.mdl, tests/alkane/Makefile,
1905 <        tests/alkane/alkanes.mdl, tests/alkane/butane.bass,
1906 <        tests/alkane/init_butane.eor, tests/argon/Makefile,
1907 <        tests/argon/argon.bass, tests/argon/init_argon.eor,
1908 <        tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile,
1909 <        tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl,
1910 <        tests/lipid/water.mdl, tests/water/Makefile,
1911 <        tests/water/init_ssd.eor, tests/water/ssd.bass,
1912 <        tests/water/water.mdl: moved tests to samples
2578 >        * samples/: alkane/Makefile, alkane/alkanes.mdl,
2579 >        alkane/butane.bass, alkane/init_butane.eor, argon/Makefile,
2580 >        argon/argon.bass, argon/init_argon.eor, argon/lj.mdl,
2581 >        lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor,
2582 >        lipid/lipid.mdl, lipid/water.mdl, water/Makefile,
2583 >        water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to
2584 >        samples
2585  
2586   2003-03-24 19:51  gezelter
2587  
# Line 1917 | Line 2589
2589  
2590   2003-03-24 19:46  gezelter
2591  
2592 <        * ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile,
1921 <        tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile:
1922 <        Added makefiles in tests directories
2592 >        * ac-tools/Make.conf.in: Added makefiles in tests directories
2593  
2594   2003-03-24 16:55  gezelter
2595  
# Line 1936 | Line 2606
2606          * libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp,
2607          do_Forces.F90: little bug fixes here and there
2608  
1939 – 2003-03-24 11:04  mmeineke
1940 –
1941 –        * tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon
1942 –        test simulation
1943 –
1944 – 2003-03-24 11:02  mmeineke
1945 –
1946 –        * tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl,
1947 –        lipid/water.mdl, water/init_ssd.eor, water/ssd.bass,
1948 –        water/water.mdl: [no log message]
1949 –
1950 – 2003-03-24 11:02  mmeineke
1951 –
1952 –        * tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added
1953 –        some test bass files for experimenting with
1954 –
2609   2003-03-24 10:26  mmeineke
2610  
2611          * libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug
# Line 2061 | Line 2715
2715          libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90,
2716          libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp,
2717          libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90,
2718 <        libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE
2719 <        Tree
2718 >        libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial
2719 >        revision
2720  
2721   2003-03-21 12:42  mmeineke
2722  
# Line 2119 | Line 2773
2773          libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90,
2774          libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp,
2775          libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90,
2776 <        libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial
2777 <        revision
2776 >        libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE
2777 >        Tree
2778  

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