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Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 760 by gezelter, Fri Sep 12 16:20:05 2003 UTC vs.
Revision 1091 by tim, Tue Mar 16 19:22:56 2004 UTC

# Line 1 | Line 1
1 < 2003-09-10 16:28  mmeineke
1 > 2004-03-02 15:32  tim
2  
3 <        * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more
4 <        work on getting gofR working.
3 >        * libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp,
4 >        StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to
5 >        support large file
6  
7 < 2003-09-09 16:50  mmeineke
7 > 2004-03-01 16:17  tim
8  
9 <        * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the
10 <        beginings of the GofR pair correlation.
11 <        
12 <        added identification of identI in matchI.
9 >        * utils/zsub.cpp: Fix a couple of bugs in zsub
10 >
11 > 2004-03-01 15:01  tim
12 >
13 >        * ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in,
14 >        libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp,
15 >        libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp,
16 >        utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in,
17 >        utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a
18 >        program which can be used to replace atom type for zconstraint into
19 >        OOPSE
20 >
21 > 2004-02-24 11:36  tim
22 >
23 >        * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp,
24 >        libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log
25 >        message]
26 >
27 > 2004-02-24 10:49  tim
28 >
29 >        * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp,
30 >        Constraint.cpp, Constraint.hpp, ConstraintList.cpp,
31 >        ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp,
32 >        Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp,
33 >        NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp,
34 >        OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp,
35 >        SymMatrix.hpp: remove the old implement of minimizer from cvs tree
36 >
37 > 2004-02-24 10:44  tim
38 >
39 >        * libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp,
40 >        Integrator.hpp, Makefile.in, Minimizer1D.cpp,
41 >        MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp,
42 >        OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp,
43 >        SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of
44 >        compose to implement Minimizer both versions are working
45 >
46 > 2004-02-17 14:23  tim
47 >
48 >        * ChangeLog, libmdtools/ConjugateMinimizer.cpp,
49 >        libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
50 >        libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp,
51 >        libmdtools/MinimizerParameterSet.hpp,
52 >        libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order
53 >        to remove the constraint force along bond direction
54 >
55 > 2004-02-10 16:33  tim
56 >
57 >        * ChangeLog, libmdtools/ConjugateMinimizer.cpp,
58 >        libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp:
59 >        single version of energy minimization is working.
60 >
61 > 2004-02-09 15:38  mmeineke
62 >
63 >        * staticProps/: AllCorr.cpp, staticProps.cpp:  started a bug fix on
64 >        the massive memory overusage by OOPSE
65 >
66 > 2004-02-09 09:48  chrisfen
67 >
68 >        * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the
69 >        hardwired LJ_rcut
70 >
71 > 2004-02-06 19:14  tim
72 >
73 >        * libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log
74 >        message]
75 >
76 > 2004-02-06 16:37  tim
77 >
78 >        * ChangeLog, libBASS/Globals.cpp,
79 >        libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp,
80 >        libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp,
81 >        libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of
82 >        energy minimization for argon is working, need to add constraint
83 >
84 > 2004-02-06 14:05  tim
85 >
86 >        * libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add
87 >        one more file into Makefile.in
88 >
89 > 2004-02-06 13:58  tim
90 >
91 >        * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp,
92 >        libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp,
93 >        libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp,
94 >        libmdtools/Integrator.hpp, libmdtools/Makefile.in,
95 >        libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp,
96 >        libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp,
97 >        libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp,
98 >        libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp,
99 >        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
100 >        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add
101 >        some lines into global.cpp to make it work with energy minimization
102 >
103 > 2004-02-04 17:26  tim
104 >
105 >        * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp,
106 >        Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp,
107 >        Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp,
108 >        NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs   :-)
109 >        Single version of conjugate gradient with golden search linesearch
110 >        pass a couple of functions test. Brent's  algorithm is still broken
111 >
112 > 2004-02-03 17:54  tim
113 >
114 >        * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp,
115 >        Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp,
116 >        NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp,
117 >        SteepestDescent.hpp: NLModel0, NLModel1 pass uit test
118 >
119 > 2004-02-03 15:47  tim
120 >
121 >        * libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp,
122 >        ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp,
123 >        NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp,
124 >        SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp,
125 >        SteepestDescent.hpp: [no log message]
126 >
127 > 2004-02-03 15:43  tim
128 >
129 >        * libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp,
130 >        Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp,
131 >        MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp,
132 >        NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory
133 >        constraint class
134 >
135 > 2004-02-03 12:10  tim
136 >
137 >        * libmdtools/Functor.hpp: Functor.hpp pass unit test
138 >
139 > 2004-02-03 10:21  tim
140 >
141 >        * ChangeLog, libmdtools/Minimizer1D.cpp,
142 >        libmdtools/Minimizer1D.hpp: begin unit test of minimizer
143 >
144 > 2004-02-02 15:29  tim
145 >
146 >        * libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp,
147 >        Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp:
148 >        Adding GoldenSection and Brent LineSearch Method
149 >
150 > 2004-01-30 16:47  tim
151 >
152 >        * libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp,
153 >        MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp,
154 >        NLModel0.cpp, NLModel1.cpp: using class  Minimizer1D derived from
155 >        MinimizerBase instead of a functor to do line seach
156 >
157 > 2004-01-30 10:00  chrisfen
158 >
159 >        * forceFields/Makefile.in, libmdtools/Atom.cpp,
160 >        libmdtools/Atom.hpp, libmdtools/ForceFields.hpp,
161 >        libmdtools/Integrator.cpp, libmdtools/Makefile.in,
162 >        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
163 >        libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90,
164 >        libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90,
165 >        libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now
166 >        has a working WATER.cpp forcefield and parser.  This involved
167 >        changes to WATER.cpp and ForceFields amoung other files. One
168 >        important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90.
169 >        This will be removed on the next commit...
170 >
171 > 2004-01-29 18:00  gezelter
172 >
173 >        * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h,
174 >        libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y,
175 >        libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp,
176 >        libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp,
177 >        libBASS/RigidBodyStamp.hpp, libBASS/interface.c,
178 >        libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c,
179 >        libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h,
180 >        libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl:
181 >        member list fixes for rigid bodies
182 >
183 > 2004-01-29 16:44  tim
184 >
185 >        * libmdtools/MinimizerParameterSet.hpp: Adding
186 >        MinimizerParameterSet class.
187 >
188 > 2004-01-28 17:44  tim
189 >
190 >        * libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of
191 >        NLModel0 and NLModel1
192 >
193 > 2004-01-28 15:40  tim
194 >
195 >        * libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision
196 >        of NLModel
197 >
198 > 2004-01-27 15:34  gezelter
199 >
200 >        * samples/water/: ssd.bass, water.mdl: Added point-charge models to
201 >        water.mdl file, updated ssd.bass to use new SSD name
202 >
203 > 2004-01-27 15:34  gezelter
204 >
205 >        * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp,
206 >        MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody
207 >        stuff
208 >
209 > 2004-01-27 14:39  gezelter
210 >
211 >        * samples/water/ssd.bass: Longer run time to test SSD water in MPI
212 >
213 > 2004-01-27 14:39  gezelter
214 >
215 >        * samples/metals/Au.bass: Longer run time to test gold in MPI
216 >
217 > 2004-01-27 14:38  gezelter
218 >
219 >        * samples/argon/argon.bass: Longer run time to test argon
220 >
221 > 2004-01-27 14:38  gezelter
222 >
223 >        * libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS
224 >        changes to do new rigidBody scheme a copy of WATER.cpp from this
225 >        morning
226 >
227 > 2004-01-27 14:37  gezelter
228 >
229 >        * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c,
230 >        BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in,
231 >        MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp,
232 >        MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp,
233 >        interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h,
234 >        node_list.h, parse_interface.h, parse_tree.c: More BASS changes to
235 >        do new rigidBody scheme
236 >
237 > 2004-01-27 14:15  tim
238 >
239 >        * libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp,
240 >        Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp,
241 >        MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of
242 >        constraint for Nonlinear Optimization Model
243 >
244 > 2004-01-26 17:01  gezelter
245 >
246 >        * utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use
247 >        Euler angles for orientation instead of unit vectors required
248 >        changes in MoLocator
249 >
250 > 2004-01-26 16:53  gezelter
251 >
252 >        * samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl,
253 >        beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl,
254 >        water/water.mdl: Changed orientation lines from unit vectors to
255 >        euler angles
256 >
257 > 2004-01-26 16:52  gezelter
258 >
259 >        * libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians
260 >
261 > 2004-01-26 16:45  gezelter
262 >
263 >        * libmdtools/SimSetup.cpp: Changed default orientation in BASS to
264 >        use Euler angles in the following order: phi, theta, psi Removed
265 >        the ability to set orientation using a unit vector
266 >
267 > 2004-01-26 16:26  gezelter
268 >
269 >        * libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp,
270 >        RigidBodyStamp.hpp: Changed default orientation in BASS to use
271 >        Euler angles in the following order: phi, theta, psi Removed the
272 >        ability to set orientation using a unit vector
273 >
274 > 2004-01-26 13:52  gezelter
275 >
276 >        * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp,
277 >        MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies
278 >
279 > 2004-01-22 12:34  chrisfen
280 >
281 >        * libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp,
282 >        TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h:
283 >        Corrected spelling in several directories, and stated WATER.cpp
284 >
285 > 2004-01-21 17:16  tim
286 >
287 >        * libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp,
288 >        NLOPModel.hpp: constraint class in energy minimization
289 >
290 > 2004-01-20 15:34  tim
291 >
292 >        * libmdtools/MinimizerBase.hpp: Adding energy minimization
293 >
294 > 2004-01-20 15:32  tim
295 >
296 >        * libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp,
297 >        NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer
298 >
299 > 2004-01-19 16:17  gezelter
300 >
301 >        * libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages
302 >        more user-friendly
303 >
304 > 2004-01-19 13:51  chrisfen
305 >
306 >        * forceFields/DUFF.frc: Updated the default water to SSD/E
307 >
308 > 2004-01-19 13:36  tim
309  
310 +        * libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample
311 +        time, status time, thermal time and reset time are not divisible by
312 +        dt
313 +
314 + 2004-01-19 11:10  gezelter
315 +
316 +        * third-party/Makefile.in: Added a bunch of dummy targets so make
317 +        won't complain
318 +
319 + 2004-01-19 11:10  gezelter
320 +
321 +        * samples/lipid/5x5.bass: Fixed old bass file
322 +
323 + 2004-01-19 11:09  gezelter
324 +
325 +        * libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies
326 +        required a change in how the MoleculeStamps are used by divideLabor
327 +        in mpiSimulation.cpp
328 +
329 + 2004-01-19 11:08  gezelter
330 +
331 +        * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c,
332 +        BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp,
333 +        MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp,
334 +        RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c,
335 +        make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h,
336 +        parse_tree.c: BASS changes to add RigidBodies and LJrcut
337 +
338 + 2004-01-16 16:55  tim
339 +
340 +        * libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating
341 +        eor file
342 +
343 + 2004-01-16 16:51  mmeineke
344 +
345 +        * libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could
346 +        write eor files
347 +
348 + 2004-01-16 10:01  mmeineke
349 +
350 +        * libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi
351 +        initialization of the AtomStruct
352 +
353 + 2004-01-15 16:57  chuckv
354 +
355 +        * configure, libmdtools/DumpWriter.cpp: Fixes for Dumps
356 +
357 + 2004-01-15 10:51  gezelter
358 +
359 +        * ac-tools/aclocal.m4: Changes for altivec
360 +
361 + 2004-01-15 09:22  gezelter
362 +
363 +        * libmdtools/DumpWriter.cpp: Documented the Spud Toss
364 +
365 + 2004-01-14 23:33  gezelter
366 +
367 +        * libmdtools/do_Forces.F90: changes for charge charge interactions
368 +
369 + 2004-01-14 20:14  gezelter
370 +
371 +        * libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90,
372 +        notifyCutoffs.F90: More work for adding charges
373 +
374 + 2004-01-14 17:41  gezelter
375 +
376 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
377 +        src/Makefile.in: autoconf fixes
378 +
379 + 2004-01-14 11:28  mmeineke
380 +
381 +        * utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug
382 +
383 + 2004-01-14 10:48  gezelter
384 +
385 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
386 +        src/Makefile.in, third-party/Makefile.in: autoconf compatibility
387 +        changes for icc8
388 +
389 + 2004-01-13 18:01  gezelter
390 +
391 +        * libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp,
392 +        SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90,
393 +        fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90:
394 +        Changes for adding direct charge-charge interactions (with
395 +        switching function)
396 +
397 + 2004-01-13 17:34  gezelter
398 +
399 +        * libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90,
400 +        oopseMPI_module.F90: Some changes for new MPI organization and
401 +        direct charge-charge interactions
402 +
403 + 2004-01-13 17:11  tim
404 +
405 +        * Functor.hpp, libmdtools/Functor.hpp: [no log message]
406 +
407 + 2004-01-13 16:22  tim
408 +
409 +        * Functor.hpp, samples/water/ssd.bass: Energy Minimization method
410 +
411 + 2004-01-13 15:35  tim
412 +
413 +        * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the
414 +        eor file whenever it is used instead of rewinding it
415 +
416 + 2004-01-13 15:04  tim
417 +
418 +        * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface
419 +        of writeFrame
420 +
421 + 2004-01-13 10:46  tim
422 +
423 +        * libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp:
424 +        Merge the code of writeFinal and writeDump;
425 +         Adding sortingIndex into DumpWriter;
426 +         Fix a bug of writing last frame twice in integrator
427 +
428 + 2004-01-12 17:54  tim
429 +
430 +        * ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix
431 +        a bug in copying string
432 +
433 + 2004-01-12 15:37  tim
434 +
435 +        * ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass,
436 +        samples/water/ssd.bass: Dumpwriter only write out the atoms on
437 +        master nodes
438 +
439 + 2004-01-10 04:46  tim
440 +
441 +        * ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just
442 +        roll it back fix a bug of copying string to a pointer Still have
443 +        Seg fault, it looks like a random MPI seg fault in totalview
444 +
445 + 2004-01-09 21:15  tim
446 +
447 +        * libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub
448 +
449 + 2004-01-09 15:29  gezelter
450 +
451 +        * libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4)
452 +
453 + 2004-01-08 17:25  chuckv
454 +
455 +        * libmdtools/DumpWriter.cpp: A work in progress...
456 +
457 + 2004-01-08 13:59  gezelter
458 +
459 +        * libmdtools/DumpWriter.cpp: null terminate some strings just in
460 +        case
461 +
462 + 2004-01-08 13:13  mmeineke
463 +
464 +        * libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS
465 +        state bug.
466 +
467 + 2004-01-08 13:05  gezelter
468 +
469 +        * libmdtools/DumpWriter.cpp: added strncpy to DumpWriter
470 +
471 + 2004-01-08 12:57  mmeineke
472 +
473 +        * libmdtools/InitializeFromFile.cpp: fixed the restart from NVT
474 +        exstended state bug
475 +
476 + 2004-01-08 12:40  gezelter
477 +
478 +        * libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter
479 +
480 + 2004-01-08 10:44  mmeineke
481 +
482 +        * libmdtools/InitializeFromFile.cpp: added support for the ignore
483 +        XS state info  flag
484 +
485 + 2004-01-07 14:26  tim
486 +
487 +        * libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp,
488 +        samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of
489 +        sending message from master node to itself in DumpWriter.cpp and
490 +        InitializeFromFile.cpp
491 +
492 + 2004-01-06 14:49  chuckv
493 +
494 +        * libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90:
495 +        performance fixes in the dipole dipole and reaction field code
496 +
497 + 2004-01-06 13:54  chuckv
498 +
499 +        * libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a
500 +        little more sane
501 +
502 + 2004-01-05 17:49  chuckv
503 +
504 +        * libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90,
505 +        calc_eam.F90, calc_gb.F90, calc_reaction_field.F90,
506 +        calc_sticky_pair.F90, do_Forces.F90: Attempting to increase
507 +        performance by reducing spurious function calls
508 +
509 + 2004-01-05 17:18  chuckv
510 +
511 +        * libmdtools/do_Forces.F90: mangling forces even further
512 +
513 + 2004-01-05 17:18  chuckv
514 +
515 +        * configure, ac-tools/configure.in: mpich mucking
516 +
517 + 2004-01-05 17:12  chuckv
518 +
519 +        * libmdtools/do_Forces.F90: mangled do_forces...
520 +
521 + 2004-01-05 16:00  chuckv
522 +
523 +        * ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90,
524 +        libmdtools/do_Forces.F90: Added bitmask to do_forces property
525 +        lookup
526 +
527 + 2003-12-29 14:56  chuckv
528 +
529 +        * samples/metals/Au.bass, third-party/mt19937ar.c: Added
530 +        third-party directory for code not written by us. Also added
531 +        Mersenne Twister random number generator code. This will eventually
532 +        replace sprng as the random number generator used by OOPSE.
533 +
534 + 2003-12-22 16:26  chuckv
535 +
536 +        * libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
537 +        libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp:
538 +        Fixes to profile code.
539 +
540 + 2003-12-19 15:36  mmeineke
541 +
542 +        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp,
543 +        timing.F90, timing.f90: More profiling fixes.
544 +
545 + 2003-12-19 15:19  chuckv
546 +
547 +        * libmdtools/timing.f90: Another change for MPI in timing.
548 +
549 + 2003-12-19 15:17  chuckv
550 +
551 +        * libmdtools/timing.f90: Small update to timing in MPI
552 +
553 + 2003-12-19 13:53  mmeineke
554 +
555 +        * libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the
556 +        profiling commands work now. Will start adding PROFILE ifdefs into
557 +        the code
558 +
559 + 2003-12-19 12:25  mmeineke
560 +
561 +        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added
562 +        some profiling routines
563 +
564 + 2003-12-19 10:12  mmeineke
565 +
566 +        * utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta
567 +        and GofRomega
568 +        
569 +        additional work on randomBilayer
570 +
571 + 2003-12-19 10:12  mmeineke
572 +
573 +        * staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp,
574 +        PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and
575 +        GofRomega
576 +
577 + 2003-12-18 16:47  mmeineke
578 +
579 +        * libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added
580 +        some profile functionality
581 +
582 + 2003-12-18 15:46  chuckv
583 +
584 +        * libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90:
585 +        Added functions for simple profiling in fortran.
586 +
587 + 2003-12-17 15:13  chuckv
588 +
589 +        * libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90,
590 +        samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and
591 +        rho_col were scattered into the same array. Unfortunately, MPI
592 +        zeros the array between scatters so half of the sum was being lost.
593 +        Fixed by added a temp array for column scatter, then sum loop over
594 +        nlocal.
595 +
596 + 2003-12-16 15:49  mmeineke
597 +
598 +        * staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in,
599 +        PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added
600 +        gofRomega. both need to be debugged and tested.
601 +
602 + 2003-12-12 10:42  gezelter
603 +
604 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
605 +        libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for
606 +        gradients (to do minimizations)
607 +
608 + 2003-12-12 10:33  mmeineke
609 +
610 +        * utils/sysbuilder/randomBilayer.hpp:  removed the randombilayer
611 +        header
612 +
613 + 2003-12-10 11:52  mmeineke
614 +
615 +        * utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp,
616 +        randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add
617 +        randomBilayer to the build. Also move the random bilayer builder
618 +        from bilayerSys to randomBilayer
619 +
620 + 2003-11-25 10:44  mmeineke
621 +
622 +        * forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old
623 +        DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and
624 +        TB3 in DUFF.frc
625 +
626 + 2003-11-21 15:09  mmeineke
627 +
628 +        * libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp,
629 +        utils/sysbuilder/latticeBilayer.cpp: added a more verbose error
630 +        message in SimInfo. Added a more informative error message in
631 +        InitializeFromFile
632 +
633 + 2003-11-21 15:07  mmeineke
634 +
635 +        * staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add
636 +        ing in the GofR,CosTheta
637 +
638 + 2003-11-21 14:31  chrisfen
639 +
640 +        * libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed
641 +        a bug in SimInfo ordering of radii
642 +
643 + 2003-11-11 12:20  mmeineke
644 +
645 +        * libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline
646 +        a min function.
647 +
648 + 2003-11-10 16:50  mmeineke
649 +
650 +        * libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp:
651 +        reordered the rcut/ecr/boxSize initialization
652 +        
653 +        removed the rcut/ecr shrink and grow algorithm. the simulation will
654 +        now exit when it runs into rcut or ecr.
655 +
656 + 2003-11-07 16:46  chuckv
657 +
658 +        * libmdtools/: Makefile.in, mpiSimulation_module.F90,
659 +        oopseMPI_module.F90: Added support for compiling fortran without
660 +        use of mpich modules. We use mpif.h instead.:
661 +
662 + 2003-11-07 12:09  mmeineke
663 +
664 +        * libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp,
665 +        NPTxyz.cpp: moved the velocity scale matrix calculation outside of
666 +        the atom loop in the NPT family of integrators.
667 +
668 + 2003-11-06 17:01  mmeineke
669 +
670 +        * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep,
671 +        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp,
672 +        libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
673 +        libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep,
674 +        utils/sysbuilder/latticeBilayer.cpp: added the following parameters
675 +        to BASS:    * useInitialExtendedSystemState    * orthoBoxTolerance
676 +          * useIntiTime => useInitialTime
677 +
678 + 2003-11-06 14:24  mmeineke
679 +
680 +        * libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c,
681 +        make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c,
682 +        parse_tree.h: fixed the includes in the Make.dep
683 +
684 + 2003-11-06 14:11  mmeineke
685 +
686 +        * libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp,
687 +        NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the
688 +        new-templateless branch to the main trunk.
689 +        
690 +        bug Fixes include:   * fixed the switching function from ortho to
691 +        non-ortho box.           !!!!! THis was responsible for all of the
692 +        sudden deaths we saw.    * some formating in the string when we
693 +        write out the extended system state.    * added NPT.cpp to the
694 +        makefile.in
695 +
696 + 2003-11-06 13:20  mmeineke
697 +
698 +        * libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp,
699 +        SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death"
700 +        bug.    The box was not switching between orthorhombic and
701 +        non-orthorhombic wrapping correctly.         we added a fabs() to
702 +        the check.which should fix it.
703 +
704 + 2003-11-05 14:16  mmeineke
705 +
706 +        * libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp,
707 +        libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
708 +        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp,
709 +        libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp,
710 +        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp,
711 +        libmdtools/NVT.cpp, libmdtools/SimInfo.hpp,
712 +        libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep,
713 +        utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp:
714 +        some work on trying to find the compression bug
715 +
716 + 2003-11-03 17:07  mmeineke
717 +
718 +        * libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp,
719 +        InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp,
720 +        NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp,
721 +        SimSetup.cpp, SimSetup.hpp: begun work on removing templates and
722 +        most of standard template library from OOPSE.
723 +
724 + 2003-10-31 16:06  mmeineke
725 +
726 +        * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp,
727 +        Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp,
728 +        SimSetup.cpp: started work on template removal.
729 +
730 + 2003-10-31 13:28  mmeineke
731 +
732 +        * libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp:
733 +        added template stuff to the Maikefile template
734 +        
735 +        little changes to some printf format statements
736 +
737 + 2003-10-31 13:28  mmeineke
738 +
739 +        * libBASS/Makefile.in: added template stuff to the Maikefile
740 +        template
741 +
742 + 2003-10-30 13:59  gezelter
743 +
744 +        * libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp,
745 +        do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for
746 +        rList problems
747 +
748 + 2003-10-30 09:11  gezelter
749 +
750 +        * libmdtools/neighborLists.F90: Fixed bug that size(q0) was being
751 +        queried before q0 was allocated.
752 +
753 + 2003-10-29 15:41  mmeineke
754 +
755 +        * libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp,
756 +        SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90,
757 +        calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error
758 +        in bass.l
759 +        
760 +        fixed a little bug in the first time step, regarding the setting of
761 +        ecr and est in fortran
762 +
763 + 2003-10-29 15:40  mmeineke
764 +
765 +        * libBASS/BASSlex.l: fixed a stdlib.h include error
766 +
767 + 2003-10-29 12:55  mmeineke
768 +
769 +        * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
770 +        SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way
771 +        rcut is setup, as well as additional debugging comments.
772 +
773 + 2003-10-29 09:28  gezelter
774 +
775 +        * configure, ac-tools/configure.in, libBASS/Makefile.in,
776 +        libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for
777 +        templates
778 +
779 + 2003-10-28 22:16  gezelter
780 +
781 +        * src/Makefile.in: Refixed broken makefile
782 +
783 + 2003-10-28 22:06  gezelter
784 +
785 +        * configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility
786 +        fixes
787 +
788 + 2003-10-28 19:19  tim
789 +
790 +        * ChangeLog, libmdtools/AbstractClasses.hpp,
791 +        libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp,
792 +        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp,
793 +        libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp,
794 +        libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp,
795 +        libmdtools/ReadWrite.hpp, samples/argon/argon.bass,
796 +        samples/water/ssd.bass: add chi and eta to the comment line of dump
797 +        file.
798 +
799 + 2003-10-28 17:25  mmeineke
800 +
801 +        * libmdtools/: ForceFields.hpp, SimInfo.hpp,
802 +        fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp,
803 +        mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of
804 +        how c calls fortran. All function pointers and fortran calls are
805 +        rigidly typecast now.
806 +
807 + 2003-10-28 15:42  gezelter
808 +
809 +        * staticProps/Makefile.in, utils/sysbuilder/Makefile.in:
810 +        Portability fixes
811 +
812 + 2003-10-28 15:09  gezelter
813 +
814 +        * libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90,
815 +        libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90,
816 +        src/Makefile.in: Compatibility fixes
817 +
818 + 2003-10-28 12:08  mmeineke
819 +
820 +        * libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in:
821 +        started work on template removal
822 +
823 + 2003-10-28 12:04  gezelter
824 +
825 +        * libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started
826 +        trying to understand extern "C" stuff for pointers
827 +
828 + 2003-10-28 11:20  gezelter
829 +
830 +        * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp,
831 +        ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility
832 +
833 + 2003-10-28 11:03  gezelter
834 +
835 +        * libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp,
836 +        DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp,
837 +        DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp,
838 +        ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp,
839 +        Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp,
840 +        ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp,
841 +        StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp,
842 +        calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp,
843 +        mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with
844 +        more portable c header stuff Also, mod file fixes and portability
845 +        changes Some fortran changes will need to be reversed.
846 +
847 + 2003-10-28 11:03  gezelter
848 +
849 +        * libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp,
850 +        Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp,
851 +        Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more
852 +        portable c header stuff Also, mod file fixes and portability
853 +        changes
854 +
855 + 2003-10-28 11:02  gezelter
856 +
857 +        * configure, ac-tools/aclocal.m4: mod file fixes and portability
858 +        stuff
859 +
860 + 2003-10-27 18:00  gezelter
861 +
862 +        * Makefile.in, configure, ac-tools/aclocal.m4,
863 +        ac-tools/configure.in, ac-tools/fortran90.m4,
864 +        libmdtools/Makefile.in: Stuff for MOD support in other compilers
865 +
866 + 2003-10-27 17:08  mmeineke
867 +
868 +        * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp,
869 +        MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp:
870 +        added routines for the sysbuilder to work with simSetup
871 +        
872 +        remved the QuickBass routines, and had all parsing go through
873 +        SimSetup.  LatticeBilayer is in complete working order now.
874 +
875 + 2003-10-27 17:07  mmeineke
876 +
877 +        * libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added
878 +        routines for the sysbuilder to work with simSetup
879 +
880 + 2003-10-27 11:20  gezelter
881 +
882 +        * configure, ac-tools/configure.in, samples/water/ssd.bass,
883 +        utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild
884 +
885 + 2003-10-24 17:17  mmeineke
886 +
887 +        * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp,
888 +        MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp,
889 +        latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put
890 +        QuickBass, MoLocator, and latticeBuilder into a Builder Library
891 +        overhauled latticeBilayer into its own program. Removed sysBuild
892 +        from the Makefile
893 +
894 + 2003-10-24 12:36  gezelter
895 +
896 +        * utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp,
897 +        latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer
898 +        builder
899 +
900 + 2003-10-24 12:35  gezelter
901 +
902 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a
903 +        merge problem
904 +
905 + 2003-10-23 14:57  mmeineke
906 +
907 +        * samples/metals/Makefile.in: added eam ForceField files to the
908 +        init
909 +        
910 +        fixed an eam mpi parmeter setup bug
911 +        
912 +        added the init file to the makefile
913 +
914 + 2003-10-23 14:57  mmeineke
915 +
916 +        * libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files
917 +        to the init
918 +        
919 +        fixed an eam mpi parmeter setup bug
920 +
921 + 2003-10-23 14:57  mmeineke
922 +
923 +        * forceFields/Makefile.in: added eam ForceField files to the init
924 +
925 + 2003-10-22 16:17  mmeineke
926 +
927 +        * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in,
928 +        NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT
929 +        integrator, NPTxyz. It scales the x, y, and z direction sepeartely.
930 +        no box skew allowed.
931 +
932 + 2003-10-21 14:33  mmeineke
933 +
934 +        * libBASS/Globals.cpp, libBASS/Globals.hpp,
935 +        libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp,
936 +        staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax.
937 +            * useInitTime = false: sets the origin time to 0.0 regardless
938 +        of the time stamp in the .init file     * default=> useInitTime =
939 +        true;
940 +
941 + 2003-10-17 16:19  mmeineke
942 +
943 +        * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp,
944 +        Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
945 +        staticProps.cpp, obj/placeholder: added the staticProps directory
946 +        to the build list for both configure  and configure.in
947 +        
948 +        fixed a number of bugs in the staticProps code. gofr is now
949 +        working.
950 +
951 + 2003-10-17 16:18  mmeineke
952 +
953 +        * ac-tools/configure.in: added the staticProps directory to the
954 +        build list for both configure  and configure.in
955 +
956 + 2003-10-17 16:17  mmeineke
957 +
958 +        * configure: added the staticProps directory to the build list
959 +
960 + 2003-10-16 14:16  mmeineke
961 +
962 +        * libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp,
963 +        Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to
964 +        use linked lists instead of a vector.
965 +        
966 +        Fixed the makefile to build DumpReader.cpp
967 +        
968 +        Removed a comment output in Exclude.cpp
969 +        
970 +        Modified DumpWriter and Integrator to write an eor file every time
971 +        a frame is written.  This lets the .eor file represent the last
972 +        written frame of a simulation.
973 +
974 + 2003-10-10 12:10  mmeineke
975 +
976 +        * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp,
977 +        CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp,
978 +        PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
979 +        staticProps.cpp: removed the props directory, and moved everything
980 +        over to staticProps
981 +
982 + 2003-10-09 17:09  mmeineke
983 +
984 +        * libmdtools/Atom.hpp: Contiuned work on staticProps. should be in
985 +        a position where it will compile and run first runs.
986 +
987 + 2003-10-04 13:46  chuckv
988 +
989 +        * libmdtools/calc_eam.F90, libmdtools/do_Forces.F90,
990 +        samples/metals/Au.bass: Fixed bug in calc_eam.
991 +
992 + 2003-10-04 13:08  chuckv
993 +
994 +        * samples/metals/init_au.in: added Au init file for eam.
995 +
996 + 2003-10-03 17:11  mmeineke
997 +
998 +        * libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed
999 +        entahlpy from the statwriter and thermo.
1000 +
1001 + 2003-10-03 17:02  mmeineke
1002 +
1003 +        * libmdtools/SimInfo.hpp: changed the formating ogf the error
1004 +        statements in simError
1005 +        
1006 +        added a function to get the maxCutoff
1007 +
1008 + 2003-10-03 17:01  mmeineke
1009 +
1010 +        * libBASS/simError.c: changed the formating ogf the error
1011 +        statements in simError
1012 +
1013 + 2003-09-30 11:00  mmeineke
1014 +
1015 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed
1016 +        f90Flags so they are no longer overwritten by the compiler.
1017 +
1018 + 2003-09-29 17:06  mmeineke
1019 +
1020 +        * libmdtools/fortranWrappers.cpp: added mpif90 mod check back same
1021 +        for conifig.in
1022 +        
1023 +        fixed wrappers to extern "C"
1024 +
1025 + 2003-09-29 17:06  mmeineke
1026 +
1027 +        * ac-tools/configure.in: added mpif90 mod check back same for
1028 +        conifig.in
1029 +
1030 + 2003-09-29 17:05  mmeineke
1031 +
1032 +        * configure: added mpif90 mod check back
1033 +
1034 + 2003-09-29 16:16  mmeineke
1035 +
1036 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
1037 +        libBASS/BendStamp.cpp, libBASS/BondStamp.cpp,
1038 +        libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp,
1039 +        libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp,
1040 +        libBASS/ZconStamp.cpp, libBASS/simError.c,
1041 +        libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp,
1042 +        libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90,
1043 +        libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors
1044 +        found with SUN's SUNWspro.s1s7
1045 +
1046 + 2003-09-29 12:38  mmeineke
1047 +
1048 +        * libmdtools/GenericData.hpp: light change in syntax. no
1049 +        signifigant change.
1050 +
1051 + 2003-09-25 16:17  mmeineke
1052 +
1053 +        * libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some
1054 +        additional remarks from icc -w3 (extra verbose output)
1055 +
1056 + 2003-09-25 14:27  mmeineke
1057 +
1058 +        * libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
1059 +        libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp,
1060 +        libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp,
1061 +        libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp,
1062 +        libmdtools/Integrator.cpp, libmdtools/LJFF.cpp,
1063 +        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp,
1064 +        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
1065 +        libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp,
1066 +        libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp,
1067 +        libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with
1068 +        gcc -Wall and g++ -Wall
1069 +
1070 + 2003-09-25 13:54  gezelter
1071 +
1072 +        * configure, ac-tools/configure.in: fixed a bug in configure
1073 +
1074 + 2003-09-25 11:42  gezelter
1075 +
1076 +        * Makefile.in, configure, ac-tools/aclocal.m4,
1077 +        ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in,
1078 +        src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in:
1079 +        fixes for configure
1080 +
1081 + 2003-09-24 14:34  mmeineke
1082 +
1083 +        * libmdtools/Integrator.cpp: moved readyCheck in the integrator so
1084 +        that it is called before the first Statistics are written.
1085 +
1086 + 2003-09-23 15:36  gezelter
1087 +
1088 +        * src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a
1089 +        bunch of Make.dep files to CVS
1090 +
1091 + 2003-09-23 15:34  mmeineke
1092 +
1093 +        * libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp,
1094 +        SimSetup.cpp: Removed NPTfm from Integrator.hpp.
1095 +        
1096 +        Some small syntax cleaning in NPTfm and SimSetup
1097 +
1098 + 2003-09-22 18:07  tim
1099 +
1100 +        * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
1101 +        SimInfo.hpp: fix bug in calculating maxCutoff
1102 +
1103 + 2003-09-22 16:23  mmeineke
1104 +
1105 +        * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep,
1106 +        Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp:
1107 +        Converted NPTf to work with the NPT base class.
1108 +        
1109 +        Removed NPTfm and NPTim from cvs
1110 +
1111 + 2003-09-19 15:00  mmeineke
1112 +
1113 +        * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp,
1114 +        NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base
1115 +        class. NPTi is up to date. NPTf is not.
1116 +
1117 + 2003-09-19 11:03  mmeineke
1118 +
1119 +        * utils/Makefile.in, src/Makefile.in: removed mpi++ from the
1120 +        makefile
1121 +
1122 + 2003-09-19 11:01  gezelter
1123 +
1124 +        * samples/water/ssd.bass: goofing off to test NPTf and NPTi
1125 +
1126 + 2003-09-19 11:01  gezelter
1127 +
1128 +        * libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found
1129 +        (nearly) conserved quantities for both NPTi and NPTf
1130 +
1131 + 2003-09-19 10:20  mmeineke
1132 +
1133 +        * utils/Makefile.in: fixed a typo in the makefile.
1134 +
1135 + 2003-09-19 09:55  gezelter
1136 +
1137 +        * libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp,
1138 +        samples/water/ssd.bass: [no log message]
1139 +
1140 + 2003-09-19 09:22  tim
1141 +
1142 +        * libmdtools/: NPTi.cpp, NVT.cpp: [no log message]
1143 +
1144 + 2003-09-17 09:22  mmeineke
1145 +
1146 +        * libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now
1147 +        work with constraints.
1148 +
1149 + 2003-09-16 15:02  tim
1150 +
1151 +        * libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp,
1152 +        SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo
1153 +        
1154 +        fixed conserved quantity in NPT (Still some small bug)
1155 +        
1156 +        NPTi appears very stable.
1157 +
1158 + 2003-09-15 11:52  tim
1159 +
1160 +        * libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp,
1161 +        libmdtools/Integrator.hpp, libmdtools/NPTf.cpp,
1162 +        libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp,
1163 +        libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
1164 +        libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp,
1165 +        libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp,
1166 +        utils/sysbuilder/bilayerSys.cpp: add conserved quantity to
1167 +        statWriter fix bug of vector wrapping at NPTi
1168 +
1169 + 2003-09-12 11:20  gezelter
1170 +
1171 +        * libmdtools/: Make.dep, Makefile.in: Added integrators to
1172 +        Makefile.in
1173 +
1174 + 2003-09-12 11:20  gezelter
1175 +
1176 +        * ChangeLog: Entered changes for configure into ChangeLog
1177 +
1178   2003-09-09 15:35  mmeineke
1179  
1180          * libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp,
# Line 84 | Line 1249
1249          libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp,
1250          libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex
1251  
87 – 2003-08-28 11:59  mmeineke
88 –
89 –        * props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp:
90 –        added the first functional parts of the PairCorrType Abstract
91 –        classes.
92 –
1252   2003-08-27 14:23  tim
1253  
1254          * libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix
# Line 360 | Line 1519
1519          libmdtools/do_Forces.F90, libmdtools/neighborLists.F90,
1520          samples/metals/Au.bass: EAM works...... Neighbor list also
1521          works.....
363 –
364 – 2003-08-08 13:32  mmeineke
365 –
366 –        * props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp:
367 –        moved frameCount's functionality into DumpReader. also split props
368 –        into staticProps and dynamicProps. (currently only have
369 –        staticProps)
1522  
1523   2003-08-08 12:48  mmeineke
1524  
# Line 424 | Line 1576
1576   2003-07-29 11:32  mmeineke
1577  
1578          * libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp,
1579 <        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp,
1580 <        props/frameCount.c, props/frameCount.h, props/props.cpp,
429 <        src/Makefile: working on the props code
1579 >        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile:
1580 >        working on the props code
1581  
1582   2003-07-29 11:32  mmeineke
1583  
# Line 1553 | Line 2704
2704  
2705   2003-03-25 09:29  mmeineke
2706  
2707 <        * libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy,
2707 >        * libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy,
2708          src/MPIobj/dummy, src/obj/dummy: [no log message]
2709  
2710   2003-03-25 09:29  mmeineke
# Line 1563 | Line 2714
2714  
2715   2003-03-24 20:07  gezelter
2716  
2717 <        * samples/Makefile, tests/Makefile: moving tests to samples
2717 >        * samples/Makefile: moving tests to samples
2718  
2719   2003-03-24 20:06  gezelter
2720  
2721 <        * samples/alkane/Makefile, samples/alkane/alkanes.mdl,
2722 <        samples/alkane/butane.bass, samples/alkane/init_butane.eor,
2723 <        samples/argon/Makefile, samples/argon/argon.bass,
2724 <        samples/argon/init_argon.eor, samples/argon/lj.mdl,
2725 <        samples/lipid/5x5.bass, samples/lipid/Makefile,
2726 <        samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl,
2727 <        samples/lipid/water.mdl, samples/water/Makefile,
1577 <        samples/water/init_ssd.eor, samples/water/ssd.bass,
1578 <        samples/water/water.mdl, tests/alkane/Makefile,
1579 <        tests/alkane/alkanes.mdl, tests/alkane/butane.bass,
1580 <        tests/alkane/init_butane.eor, tests/argon/Makefile,
1581 <        tests/argon/argon.bass, tests/argon/init_argon.eor,
1582 <        tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile,
1583 <        tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl,
1584 <        tests/lipid/water.mdl, tests/water/Makefile,
1585 <        tests/water/init_ssd.eor, tests/water/ssd.bass,
1586 <        tests/water/water.mdl: moved tests to samples
2721 >        * samples/: alkane/Makefile, alkane/alkanes.mdl,
2722 >        alkane/butane.bass, alkane/init_butane.eor, argon/Makefile,
2723 >        argon/argon.bass, argon/init_argon.eor, argon/lj.mdl,
2724 >        lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor,
2725 >        lipid/lipid.mdl, lipid/water.mdl, water/Makefile,
2726 >        water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to
2727 >        samples
2728  
2729   2003-03-24 19:51  gezelter
2730  
# Line 1591 | Line 2732
2732  
2733   2003-03-24 19:46  gezelter
2734  
2735 <        * ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile,
1595 <        tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile:
1596 <        Added makefiles in tests directories
2735 >        * ac-tools/Make.conf.in: Added makefiles in tests directories
2736  
2737   2003-03-24 16:55  gezelter
2738  
# Line 1610 | Line 2749
2749          * libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp,
2750          do_Forces.F90: little bug fixes here and there
2751  
1613 – 2003-03-24 11:04  mmeineke
1614 –
1615 –        * tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon
1616 –        test simulation
1617 –
1618 – 2003-03-24 11:02  mmeineke
1619 –
1620 –        * tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl,
1621 –        lipid/water.mdl, water/init_ssd.eor, water/ssd.bass,
1622 –        water/water.mdl: [no log message]
1623 –
1624 – 2003-03-24 11:02  mmeineke
1625 –
1626 –        * tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added
1627 –        some test bass files for experimenting with
1628 –
2752   2003-03-24 10:26  mmeineke
2753  
2754          * libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug

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