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Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 660 by tim, Thu Jul 31 19:59:34 2003 UTC vs.
Revision 894 by chuckv, Mon Jan 5 21:00:05 2004 UTC

# Line 1 | Line 1
1 + 2003-12-29 14:56  chuckv
2 +
3 +        * samples/metals/Au.bass, third-party/mt19937ar.c: Added
4 +        third-party directory for code not written by us. Also added
5 +        Mersenne Twister random number generator code. This will eventually
6 +        replace sprng as the random number generator used by OOPSE.
7 +
8 + 2003-12-22 16:26  chuckv
9 +
10 +        * libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
11 +        libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp:
12 +        Fixes to profile code.
13 +
14 + 2003-12-19 15:36  mmeineke
15 +
16 +        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp,
17 +        timing.F90, timing.f90: More profiling fixes.
18 +
19 + 2003-12-19 15:19  chuckv
20 +
21 +        * libmdtools/timing.f90: Another change for MPI in timing.
22 +
23 + 2003-12-19 15:17  chuckv
24 +
25 +        * libmdtools/timing.f90: Small update to timing in MPI
26 +
27 + 2003-12-19 13:53  mmeineke
28 +
29 +        * libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the
30 +        profiling commands work now. Will start adding PROFILE ifdefs into
31 +        the code
32 +
33 + 2003-12-19 12:25  mmeineke
34 +
35 +        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added
36 +        some profiling routines
37 +
38 + 2003-12-19 10:12  mmeineke
39 +
40 +        * utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta
41 +        and GofRomega
42 +        
43 +        additional work on randomBilayer
44 +
45 + 2003-12-19 10:12  mmeineke
46 +
47 +        * staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp,
48 +        PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and
49 +        GofRomega
50 +
51 + 2003-12-18 16:47  mmeineke
52 +
53 +        * libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added
54 +        some profile functionality
55 +
56 + 2003-12-18 15:46  chuckv
57 +
58 +        * libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90:
59 +        Added functions for simple profiling in fortran.
60 +
61 + 2003-12-17 15:13  chuckv
62 +
63 +        * libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90,
64 +        samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and
65 +        rho_col were scattered into the same array. Unfortunately, MPI
66 +        zeros the array between scatters so half of the sum was being lost.
67 +        Fixed by added a temp array for column scatter, then sum loop over
68 +        nlocal.
69 +
70 + 2003-12-16 15:49  mmeineke
71 +
72 +        * staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in,
73 +        PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added
74 +        gofRomega. both need to be debugged and tested.
75 +
76 + 2003-12-12 10:42  gezelter
77 +
78 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
79 +        libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for
80 +        gradients (to do minimizations)
81 +
82 + 2003-12-12 10:33  mmeineke
83 +
84 +        * utils/sysbuilder/randomBilayer.hpp:  removed the randombilayer
85 +        header
86 +
87 + 2003-12-10 11:52  mmeineke
88 +
89 +        * utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp,
90 +        randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add
91 +        randomBilayer to the build. Also move the random bilayer builder
92 +        from bilayerSys to randomBilayer
93 +
94 + 2003-11-25 10:44  mmeineke
95 +
96 +        * forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old
97 +        DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and
98 +        TB3 in DUFF.frc
99 +
100 + 2003-11-21 15:09  mmeineke
101 +
102 +        * libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp,
103 +        utils/sysbuilder/latticeBilayer.cpp: added a more verbose error
104 +        message in SimInfo. Added a more informative error message in
105 +        InitializeFromFile
106 +
107 + 2003-11-21 15:07  mmeineke
108 +
109 +        * staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add
110 +        ing in the GofR,CosTheta
111 +
112 + 2003-11-21 14:31  chrisfen
113 +
114 +        * libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed
115 +        a bug in SimInfo ordering of radii
116 +
117 + 2003-11-11 12:20  mmeineke
118 +
119 +        * libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline
120 +        a min function.
121 +
122 + 2003-11-10 16:50  mmeineke
123 +
124 +        * libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp:
125 +        reordered the rcut/ecr/boxSize initialization
126 +        
127 +        removed the rcut/ecr shrink and grow algorithm. the simulation will
128 +        now exit when it runs into rcut or ecr.
129 +
130 + 2003-11-07 16:46  chuckv
131 +
132 +        * libmdtools/: Makefile.in, mpiSimulation_module.F90,
133 +        oopseMPI_module.F90: Added support for compiling fortran without
134 +        use of mpich modules. We use mpif.h instead.:
135 +
136 + 2003-11-07 12:09  mmeineke
137 +
138 +        * libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp,
139 +        NPTxyz.cpp: moved the velocity scale matrix calculation outside of
140 +        the atom loop in the NPT family of integrators.
141 +
142 + 2003-11-06 17:01  mmeineke
143 +
144 +        * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep,
145 +        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp,
146 +        libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
147 +        libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep,
148 +        utils/sysbuilder/latticeBilayer.cpp: added the following parameters
149 +        to BASS:    * useInitialExtendedSystemState    * orthoBoxTolerance
150 +          * useIntiTime => useInitialTime
151 +
152 + 2003-11-06 14:24  mmeineke
153 +
154 +        * libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c,
155 +        make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c,
156 +        parse_tree.h: fixed the includes in the Make.dep
157 +
158 + 2003-11-06 14:11  mmeineke
159 +
160 +        * libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp,
161 +        NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the
162 +        new-templateless branch to the main trunk.
163 +        
164 +        bug Fixes include:   * fixed the switching function from ortho to
165 +        non-ortho box.           !!!!! THis was responsible for all of the
166 +        sudden deaths we saw.    * some formating in the string when we
167 +        write out the extended system state.    * added NPT.cpp to the
168 +        makefile.in
169 +
170 + 2003-11-06 13:20  mmeineke
171 +
172 +        * libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp,
173 +        SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death"
174 +        bug.    The box was not switching between orthorhombic and
175 +        non-orthorhombic wrapping correctly.         we added a fabs() to
176 +        the check.which should fix it.
177 +
178 + 2003-11-05 14:16  mmeineke
179 +
180 +        * libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp,
181 +        libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
182 +        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp,
183 +        libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp,
184 +        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp,
185 +        libmdtools/NVT.cpp, libmdtools/SimInfo.hpp,
186 +        libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep,
187 +        utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp:
188 +        some work on trying to find the compression bug
189 +
190 + 2003-11-03 17:07  mmeineke
191 +
192 +        * libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp,
193 +        InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp,
194 +        NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp,
195 +        SimSetup.cpp, SimSetup.hpp: begun work on removing templates and
196 +        most of standard template library from OOPSE.
197 +
198 + 2003-10-31 16:06  mmeineke
199 +
200 +        * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp,
201 +        Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp,
202 +        SimSetup.cpp: started work on template removal.
203 +
204 + 2003-10-31 13:28  mmeineke
205 +
206 +        * libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp:
207 +        added template stuff to the Maikefile template
208 +        
209 +        little changes to some printf format statements
210 +
211 + 2003-10-31 13:28  mmeineke
212 +
213 +        * libBASS/Makefile.in: added template stuff to the Maikefile
214 +        template
215 +
216 + 2003-10-30 13:59  gezelter
217 +
218 +        * libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp,
219 +        do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for
220 +        rList problems
221 +
222 + 2003-10-30 09:11  gezelter
223 +
224 +        * libmdtools/neighborLists.F90: Fixed bug that size(q0) was being
225 +        queried before q0 was allocated.
226 +
227 + 2003-10-29 15:41  mmeineke
228 +
229 +        * libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp,
230 +        SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90,
231 +        calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error
232 +        in bass.l
233 +        
234 +        fixed a little bug in the first time step, regarding the setting of
235 +        ecr and est in fortran
236 +
237 + 2003-10-29 15:40  mmeineke
238 +
239 +        * libBASS/BASSlex.l: fixed a stdlib.h include error
240 +
241 + 2003-10-29 12:55  mmeineke
242 +
243 +        * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
244 +        SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way
245 +        rcut is setup, as well as additional debugging comments.
246 +
247 + 2003-10-29 09:28  gezelter
248 +
249 +        * configure, ac-tools/configure.in, libBASS/Makefile.in,
250 +        libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for
251 +        templates
252 +
253 + 2003-10-28 22:16  gezelter
254 +
255 +        * src/Makefile.in: Refixed broken makefile
256 +
257 + 2003-10-28 22:06  gezelter
258 +
259 +        * configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility
260 +        fixes
261 +
262 + 2003-10-28 19:19  tim
263 +
264 +        * ChangeLog, libmdtools/AbstractClasses.hpp,
265 +        libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp,
266 +        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp,
267 +        libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp,
268 +        libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp,
269 +        libmdtools/ReadWrite.hpp, samples/argon/argon.bass,
270 +        samples/water/ssd.bass: add chi and eta to the comment line of dump
271 +        file.
272 +
273 + 2003-10-28 17:25  mmeineke
274 +
275 +        * libmdtools/: ForceFields.hpp, SimInfo.hpp,
276 +        fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp,
277 +        mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of
278 +        how c calls fortran. All function pointers and fortran calls are
279 +        rigidly typecast now.
280 +
281 + 2003-10-28 15:42  gezelter
282 +
283 +        * staticProps/Makefile.in, utils/sysbuilder/Makefile.in:
284 +        Portability fixes
285 +
286 + 2003-10-28 15:09  gezelter
287 +
288 +        * libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90,
289 +        libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90,
290 +        src/Makefile.in: Compatibility fixes
291 +
292 + 2003-10-28 12:08  mmeineke
293 +
294 +        * libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in:
295 +        started work on template removal
296 +
297 + 2003-10-28 12:04  gezelter
298 +
299 +        * libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started
300 +        trying to understand extern "C" stuff for pointers
301 +
302 + 2003-10-28 11:20  gezelter
303 +
304 +        * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp,
305 +        ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility
306 +
307 + 2003-10-28 11:03  gezelter
308 +
309 +        * libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp,
310 +        DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp,
311 +        DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp,
312 +        ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp,
313 +        Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp,
314 +        ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp,
315 +        StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp,
316 +        calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp,
317 +        mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with
318 +        more portable c header stuff Also, mod file fixes and portability
319 +        changes Some fortran changes will need to be reversed.
320 +
321 + 2003-10-28 11:03  gezelter
322 +
323 +        * libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp,
324 +        Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp,
325 +        Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more
326 +        portable c header stuff Also, mod file fixes and portability
327 +        changes
328 +
329 + 2003-10-28 11:02  gezelter
330 +
331 +        * configure, ac-tools/aclocal.m4: mod file fixes and portability
332 +        stuff
333 +
334 + 2003-10-27 18:00  gezelter
335 +
336 +        * Makefile.in, configure, ac-tools/aclocal.m4,
337 +        ac-tools/configure.in, ac-tools/fortran90.m4,
338 +        libmdtools/Makefile.in: Stuff for MOD support in other compilers
339 +
340 + 2003-10-27 17:08  mmeineke
341 +
342 +        * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp,
343 +        MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp:
344 +        added routines for the sysbuilder to work with simSetup
345 +        
346 +        remved the QuickBass routines, and had all parsing go through
347 +        SimSetup.  LatticeBilayer is in complete working order now.
348 +
349 + 2003-10-27 17:07  mmeineke
350 +
351 +        * libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added
352 +        routines for the sysbuilder to work with simSetup
353 +
354 + 2003-10-27 11:20  gezelter
355 +
356 +        * configure, ac-tools/configure.in, samples/water/ssd.bass,
357 +        utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild
358 +
359 + 2003-10-24 17:17  mmeineke
360 +
361 +        * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp,
362 +        MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp,
363 +        latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put
364 +        QuickBass, MoLocator, and latticeBuilder into a Builder Library
365 +        overhauled latticeBilayer into its own program. Removed sysBuild
366 +        from the Makefile
367 +
368 + 2003-10-24 12:36  gezelter
369 +
370 +        * utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp,
371 +        latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer
372 +        builder
373 +
374 + 2003-10-24 12:35  gezelter
375 +
376 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a
377 +        merge problem
378 +
379 + 2003-10-23 14:57  mmeineke
380 +
381 +        * samples/metals/Makefile.in: added eam ForceField files to the
382 +        init
383 +        
384 +        fixed an eam mpi parmeter setup bug
385 +        
386 +        added the init file to the makefile
387 +
388 + 2003-10-23 14:57  mmeineke
389 +
390 +        * libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files
391 +        to the init
392 +        
393 +        fixed an eam mpi parmeter setup bug
394 +
395 + 2003-10-23 14:57  mmeineke
396 +
397 +        * forceFields/Makefile.in: added eam ForceField files to the init
398 +
399 + 2003-10-22 16:17  mmeineke
400 +
401 +        * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in,
402 +        NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT
403 +        integrator, NPTxyz. It scales the x, y, and z direction sepeartely.
404 +        no box skew allowed.
405 +
406 + 2003-10-21 14:33  mmeineke
407 +
408 +        * libBASS/Globals.cpp, libBASS/Globals.hpp,
409 +        libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp,
410 +        staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax.
411 +            * useInitTime = false: sets the origin time to 0.0 regardless
412 +        of the time stamp in the .init file     * default=> useInitTime =
413 +        true;
414 +
415 + 2003-10-17 16:19  mmeineke
416 +
417 +        * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp,
418 +        Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
419 +        staticProps.cpp, obj/placeholder: added the staticProps directory
420 +        to the build list for both configure  and configure.in
421 +        
422 +        fixed a number of bugs in the staticProps code. gofr is now
423 +        working.
424 +
425 + 2003-10-17 16:18  mmeineke
426 +
427 +        * ac-tools/configure.in: added the staticProps directory to the
428 +        build list for both configure  and configure.in
429 +
430 + 2003-10-17 16:17  mmeineke
431 +
432 +        * configure: added the staticProps directory to the build list
433 +
434 + 2003-10-16 14:16  mmeineke
435 +
436 +        * libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp,
437 +        Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to
438 +        use linked lists instead of a vector.
439 +        
440 +        Fixed the makefile to build DumpReader.cpp
441 +        
442 +        Removed a comment output in Exclude.cpp
443 +        
444 +        Modified DumpWriter and Integrator to write an eor file every time
445 +        a frame is written.  This lets the .eor file represent the last
446 +        written frame of a simulation.
447 +
448 + 2003-10-10 12:10  mmeineke
449 +
450 +        * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp,
451 +        CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp,
452 +        PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
453 +        staticProps.cpp: removed the props directory, and moved everything
454 +        over to staticProps
455 +
456 + 2003-10-09 17:09  mmeineke
457 +
458 +        * libmdtools/Atom.hpp: Contiuned work on staticProps. should be in
459 +        a position where it will compile and run first runs.
460 +
461 + 2003-10-04 13:46  chuckv
462 +
463 +        * libmdtools/calc_eam.F90, libmdtools/do_Forces.F90,
464 +        samples/metals/Au.bass: Fixed bug in calc_eam.
465 +
466 + 2003-10-04 13:08  chuckv
467 +
468 +        * samples/metals/init_au.in: added Au init file for eam.
469 +
470 + 2003-10-03 17:11  mmeineke
471 +
472 +        * libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed
473 +        entahlpy from the statwriter and thermo.
474 +
475 + 2003-10-03 17:02  mmeineke
476 +
477 +        * libmdtools/SimInfo.hpp: changed the formating ogf the error
478 +        statements in simError
479 +        
480 +        added a function to get the maxCutoff
481 +
482 + 2003-10-03 17:01  mmeineke
483 +
484 +        * libBASS/simError.c: changed the formating ogf the error
485 +        statements in simError
486 +
487 + 2003-09-30 11:00  mmeineke
488 +
489 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed
490 +        f90Flags so they are no longer overwritten by the compiler.
491 +
492 + 2003-09-29 17:06  mmeineke
493 +
494 +        * libmdtools/fortranWrappers.cpp: added mpif90 mod check back same
495 +        for conifig.in
496 +        
497 +        fixed wrappers to extern "C"
498 +
499 + 2003-09-29 17:06  mmeineke
500 +
501 +        * ac-tools/configure.in: added mpif90 mod check back same for
502 +        conifig.in
503 +
504 + 2003-09-29 17:05  mmeineke
505 +
506 +        * configure: added mpif90 mod check back
507 +
508 + 2003-09-29 16:16  mmeineke
509 +
510 +        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
511 +        libBASS/BendStamp.cpp, libBASS/BondStamp.cpp,
512 +        libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp,
513 +        libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp,
514 +        libBASS/ZconStamp.cpp, libBASS/simError.c,
515 +        libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp,
516 +        libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90,
517 +        libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors
518 +        found with SUN's SUNWspro.s1s7
519 +
520 + 2003-09-29 12:38  mmeineke
521 +
522 +        * libmdtools/GenericData.hpp: light change in syntax. no
523 +        signifigant change.
524 +
525 + 2003-09-25 16:17  mmeineke
526 +
527 +        * libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some
528 +        additional remarks from icc -w3 (extra verbose output)
529 +
530 + 2003-09-25 14:27  mmeineke
531 +
532 +        * libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
533 +        libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp,
534 +        libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp,
535 +        libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp,
536 +        libmdtools/Integrator.cpp, libmdtools/LJFF.cpp,
537 +        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp,
538 +        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
539 +        libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp,
540 +        libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp,
541 +        libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with
542 +        gcc -Wall and g++ -Wall
543 +
544 + 2003-09-25 13:54  gezelter
545 +
546 +        * configure, ac-tools/configure.in: fixed a bug in configure
547 +
548 + 2003-09-25 11:42  gezelter
549 +
550 +        * Makefile.in, configure, ac-tools/aclocal.m4,
551 +        ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in,
552 +        src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in:
553 +        fixes for configure
554 +
555 + 2003-09-24 14:34  mmeineke
556 +
557 +        * libmdtools/Integrator.cpp: moved readyCheck in the integrator so
558 +        that it is called before the first Statistics are written.
559 +
560 + 2003-09-23 15:36  gezelter
561 +
562 +        * src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a
563 +        bunch of Make.dep files to CVS
564 +
565 + 2003-09-23 15:34  mmeineke
566 +
567 +        * libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp,
568 +        SimSetup.cpp: Removed NPTfm from Integrator.hpp.
569 +        
570 +        Some small syntax cleaning in NPTfm and SimSetup
571 +
572 + 2003-09-22 18:07  tim
573 +
574 +        * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
575 +        SimInfo.hpp: fix bug in calculating maxCutoff
576 +
577 + 2003-09-22 16:23  mmeineke
578 +
579 +        * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep,
580 +        Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp:
581 +        Converted NPTf to work with the NPT base class.
582 +        
583 +        Removed NPTfm and NPTim from cvs
584 +
585 + 2003-09-19 15:00  mmeineke
586 +
587 +        * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp,
588 +        NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base
589 +        class. NPTi is up to date. NPTf is not.
590 +
591 + 2003-09-19 11:03  mmeineke
592 +
593 +        * utils/Makefile.in, src/Makefile.in: removed mpi++ from the
594 +        makefile
595 +
596 + 2003-09-19 11:01  gezelter
597 +
598 +        * samples/water/ssd.bass: goofing off to test NPTf and NPTi
599 +
600 + 2003-09-19 11:01  gezelter
601 +
602 +        * libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found
603 +        (nearly) conserved quantities for both NPTi and NPTf
604 +
605 + 2003-09-19 10:20  mmeineke
606 +
607 +        * utils/Makefile.in: fixed a typo in the makefile.
608 +
609 + 2003-09-19 09:55  gezelter
610 +
611 +        * libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp,
612 +        samples/water/ssd.bass: [no log message]
613 +
614 + 2003-09-19 09:22  tim
615 +
616 +        * libmdtools/: NPTi.cpp, NVT.cpp: [no log message]
617 +
618 + 2003-09-17 09:22  mmeineke
619 +
620 +        * libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now
621 +        work with constraints.
622 +
623 + 2003-09-16 15:02  tim
624 +
625 +        * libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp,
626 +        SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo
627 +        
628 +        fixed conserved quantity in NPT (Still some small bug)
629 +        
630 +        NPTi appears very stable.
631 +
632 + 2003-09-15 11:52  tim
633 +
634 +        * libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp,
635 +        libmdtools/Integrator.hpp, libmdtools/NPTf.cpp,
636 +        libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp,
637 +        libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
638 +        libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp,
639 +        libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp,
640 +        utils/sysbuilder/bilayerSys.cpp: add conserved quantity to
641 +        statWriter fix bug of vector wrapping at NPTi
642 +
643 + 2003-09-12 11:20  gezelter
644 +
645 +        * libmdtools/: Make.dep, Makefile.in: Added integrators to
646 +        Makefile.in
647 +
648 + 2003-09-12 11:20  gezelter
649 +
650 +        * ChangeLog: Entered changes for configure into ChangeLog
651 +
652 + 2003-09-09 15:35  mmeineke
653 +
654 +        * libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp,
655 +        NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog
656 +        
657 +        added two new NPT integrators, they still need work.
658 +
659 + 2003-09-09 15:34  mmeineke
660 +
661 +        * ChangeLog: updated the ChangeLog
662 +
663 + 2003-09-05 17:45  gezelter
664 +
665 +        * libmdtools/Make.dep: dependency on config.h
666 +
667 + 2003-09-05 17:36  gezelter
668 +
669 +        * configure, ac-tools/aclocal.m4: fixed sprng problem
670 +
671 + 2003-09-05 16:29  gezelter
672 +
673 +        * samples/metals/Makefile.in: New Makefile for metals sample
674 +
675 + 2003-09-05 16:27  gezelter
676 +
677 +        * Makefile, Makefile.in, ac-tools/aclocal.m4,
678 +        ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile,
679 +        forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp,
680 +        libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile,
681 +        libBASS/Makefile.in, libmdtools/Integrator.hpp,
682 +        libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep,
683 +        libmdtools/Makefile, libmdtools/Makefile.in,
684 +        libmdtools/calc_eam.F90, libmdtools/config.h.in,
685 +        libmdtools/definitions_module.F90, libmdtools/fInfo.c,
686 +        libmdtools/fortranWrappers.cpp,
687 +        libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90,
688 +        libmdtools/simulation_module.F90, samples/Makefile,
689 +        samples/Makefile.in, samples/alkane/Makefile,
690 +        samples/alkane/Makefile.in, samples/argon/Makefile,
691 +        samples/argon/Makefile.in, samples/argon/argon.bass,
692 +        samples/beadLipid/Makefile, samples/beadLipid/Makefile.in,
693 +        samples/lipid/Makefile, samples/lipid/Makefile.in,
694 +        samples/water/Makefile, samples/water/Makefile.in, src/Makefile,
695 +        src/Makefile.in, utils/Makefile, utils/Makefile.in,
696 +        utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to
697 +        autoconf / configure method of configuring OOPSE
698 +
699 + 2003-09-04 16:48  mmeineke
700 +
701 +        * libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
702 +        libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp,
703 +        libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp,
704 +        libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile:
705 +        added resetTime to the Global namespace.
706 +        
707 +        added ability to reset the integrators in the NVT and NPT family.
708 +
709 + 2003-09-04 16:48  mmeineke
710 +
711 +        * libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global
712 +        namespace.
713 +
714 + 2003-09-02 09:30  tim
715 +
716 +        * libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp,
717 +        ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of
718 +        PolicyByMass
719 +
720 + 2003-08-28 16:09  tim
721 +
722 +        * ChangeLog, libmdtools/GenericData.cpp,
723 +        libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp,
724 +        libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex
725 +
726 + 2003-08-27 14:23  tim
727 +
728 +        * libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix
729 +        bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to
730 +        MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we
731 +        turn on the optimization flag, it causes a seg fault
732 +
733 + 2003-08-27 11:25  gezelter
734 +
735 +        * libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90,
736 +        calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for
737 +        stress tensor parallel bug.
738 +
739 + 2003-08-27 11:16  tim
740 +
741 +        * ChangeLog, libmdtools/DUFF.cpp,
742 +        libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90:
743 +        fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90
744 +        molMembershipList use global index instead of local index
745 +
746 + 2003-08-26 15:37  tim
747 +
748 +        * libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90,
749 +        mpiSimulation.cpp: set default force substraction policy to
750 +        PolicyByMass
751 +
752 + 2003-08-26 15:29  tim
753 +
754 +        * libmdtools/Integrator.cpp: [no log message]
755 +
756 + 2003-08-26 15:13  mmeineke
757 +
758 +        * utils/sysbuilder/bilayerSys.cpp: added define statemewnt to
759 +        Statwriter and Dumpwriter to handle files larger than 2 gb.
760 +        
761 +        commented out some print statements in Zconstraint
762 +        
763 +        hard coding some system init into bilayer.sys
764 +
765 + 2003-08-26 15:12  mmeineke
766 +
767 +        * libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp:
768 +        added define statemewnt to Statwriter and Dumpwriter to handle
769 +        files larger than 2 gb.
770 +        
771 +        commented out some print statements in Zconstraint
772 +
773 + 2003-08-26 15:02  tim
774 +
775 +        * libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed
776 +        and check the seed which is specified by user at least contains 9
777 +        digits
778 +
779 + 2003-08-26 13:32  mmeineke
780 +
781 +        * libmdtools/DUFF.cpp: changed the Makefiel a litle.
782 +        
783 +        Fixed a bug in MPI_DUFF. The atom block type was not being properly
784 +        constucted in MPI. (The MPI struct had 6 doubles declared versus
785 +        the actual 11)
786 +
787 + 2003-08-26 13:30  mmeineke
788 +
789 +        * Makefile: changed the Makefiel a litle.
790 +
791 + 2003-08-25 17:17  gezelter
792 +
793 +        * utils/sysbuilder/Makefile: More FreeBSD fixes
794 +
795 + 2003-08-25 16:51  gezelter
796 +
797 +        * libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp,
798 +        libmdtools/Makefile, src/Makefile: [no log message]
799 +
800 + 2003-08-22 15:04  mmeineke
801 +
802 +        * libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on
803 +        frequency of output dumps.
804 +
805 + 2003-08-20 17:23  tim
806 +
807 +        * libBASS/Globals.hpp, libmdtools/SimInfo.hpp,
808 +        libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp,
809 +        libmdtools/mpiSimulation.cpp: user can setup seed in bass file now,
810 +        if he does not specify any value for seed, oopse will take the
811 +        value of seconds of system time as seed
812 +
813 + 2003-08-20 14:42  mmeineke
814 +
815 +        * libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
816 +        libmdtools/GhostBend.cpp, libmdtools/SRI.hpp,
817 +        libmdtools/SimSetup.cpp, libmdtools/SimState.cpp,
818 +        utils/sysbuilder/bilayerSys.cpp: updated the Changelog.
819 +        
820 +        added some bug fixes for setting the random number generator seed
821 +        value.
822 +        
823 +        fixed a bug where ghostbend atom b was not being set. ( recent bug
824 +        from SimState conversion)
825 +
826 + 2003-08-20 14:41  mmeineke
827 +
828 +        * libBASS/Globals.hpp: updated the Changelog.
829 +        
830 +        added some bug fixes for setting the random number generator seed
831 +        value.
832 +
833 + 2003-08-20 14:41  mmeineke
834 +
835 +        * ChangeLog: updated the Changelog.
836 +
837 + 2003-08-20 14:11  tim
838 +
839 +        * libBASS/Globals.cpp, libmdtools/DUFF.cpp,
840 +        libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost
841 +        bend class
842 +
843 + 2003-08-20 10:13  mmeineke
844 +
845 +        * utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in
846 +        make links. added -f to ln -s.
847 +
848 + 2003-08-20 09:50  tim
849 +
850 +        * libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message]
851 +
852 + 2003-08-20 09:34  tim
853 +
854 +        * libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp,
855 +        ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg
856 +        printing
857 +
858 + 2003-08-18 15:59  chuckv
859 +
860 +        * utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp,
861 +        latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp,
862 +        sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works.
863 +        Nanobuilder still broke.
864 +
865 + 2003-08-15 14:24  tim
866 +
867 +        * libBASS/Globals.cpp, libBASS/Globals.hpp,
868 +        libmdtools/GenericData.hpp, libmdtools/Integrator.hpp,
869 +        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
870 +        libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp,
871 +        libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint
872 +        Method
873 +
874 + 2003-08-14 11:16  tim
875 +
876 +        * libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint
877 +        with average force substraction strategy
878 +
879 + 2003-08-13 16:20  chuckv
880 +
881 +        * libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some
882 +        profiling code -DPROFILE.
883 +
884 + 2003-08-13 14:21  tim
885 +
886 +        * libBASS/Globals.cpp, libBASS/Globals.hpp,
887 +        libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
888 +        libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic
889 +        potential & z-contraint method
890 +
891 + 2003-08-12 16:44  mmeineke
892 +
893 +        * libBASS/BASS_interface.cpp, libBASS/Globals.hpp,
894 +        libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
895 +        libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp,
896 +        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really
897 +        annoying bug in Directional Atom, where mu was getting written to
898 +        pseudorandom memory location.
899 +
900 + 2003-08-12 14:56  tim
901 +
902 +        * libBASS/BASS_interface.cpp, libBASS/Globals.cpp,
903 +        libBASS/Globals.hpp, libmdtools/Atom.hpp,
904 +        libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp,
905 +        libmdtools/SimSetup.cpp: debugging globals
906 +
907 + 2003-08-12 13:40  gezelter
908 +
909 +        * forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes
910 +        and new atypes in LJFF
911 +
912 + 2003-08-12 13:15  gezelter
913 +
914 +        * forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older
915 +        stuff...
916 +
917 + 2003-08-12 13:14  chuckv
918 +
919 +        * utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt.
920 +
921 + 2003-08-12 13:04  chuckv
922 +
923 +        * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp:
924 +        Missed del of files before.
925 +
926 + 2003-08-12 13:03  chuckv
927 +
928 +        * utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log
929 +        message]
930 +
931 + 2003-08-12 13:01  chuckv
932 +
933 +        * utils/sysbuilder/Makefile: commit makefile
934 +
935 + 2003-08-12 12:51  tim
936 +
937 +        * libBASS/Globals.cpp, libBASS/Globals.hpp,
938 +        libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
939 +        libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp,
940 +        libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added
941 +        harmonical potential to z-constraint method
942 +
943 + 2003-08-11 17:31  chuckv
944 +
945 +        * utils/Makefile: Changed makefile to only build quicklate.
946 +
947 + 2003-08-11 17:25  chuckv
948 +
949 +        * ac-tools/configure.in: added utils/sysbuilder to be built.
950 +
951 + 2003-08-11 17:12  chuckv
952 +
953 +        * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp,
954 +        bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp,
955 +        sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp,
956 +        sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp,
957 +        sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c,
958 +        sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp,
959 +        sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp,
960 +        sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp,
961 +        sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged
962 +        sysbuilder into a subdirectory. Fixed some of sysbuilder to work
963 +        with new atom allocation in libmdtools.
964 +
965 + 2003-08-11 14:41  tim
966 +
967 +        * libmdtools/: Integrator.cpp, Integrator.hpp: added method of
968 +        moving zconstraint molecules to specified positions
969 +
970 + 2003-08-11 14:39  tim
971 +
972 +        * libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message]
973 +
974 + 2003-08-11 14:38  mmeineke
975 +
976 +        * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h,
977 +        libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp,
978 +        libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp,
979 +        libBASS/ZconStamp.hpp, libBASS/interface.c, libBASS/make_nodes.c,
980 +        libBASS/make_nodes.h, libBASS/mpiBASS.c, libBASS/mpiBASS.h,
981 +        libBASS/node_list.h, libBASS/parse_interface.h,
982 +        libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint
983 +        into the BASS language syntax.
984 +
985 + 2003-08-11 13:29  mmeineke
986 +
987 +        * libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of
988 +        degrees of freedom to account for zConstreints
989 +
990 + 2003-08-08 16:22  chuckv
991 +
992 +        * libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90,
993 +        libmdtools/do_Forces.F90, libmdtools/neighborLists.F90,
994 +        samples/metals/Au.bass: EAM works...... Neighbor list also
995 +        works.....
996 +
997 + 2003-08-08 12:48  mmeineke
998 +
999 +        * libmdtools/: Makefile, ZConstraint.cpp:  fixed a deprcated
1000 +        instance of Atom::setZ and Atom::getZ in ZConstaint.
1001 +
1002 + 2003-08-07 16:47  mmeineke
1003 +
1004 +        * libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp,
1005 +        DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp,
1006 +        GhostBend.cpp, InitializeFromFile.cpp, Makefile, SimInfo.cpp,
1007 +        SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SimState.cpp,
1008 +        SimState.hpp, Torsion.cpp: switched SimInfo to use a system
1009 +        configuration from SimState rather than arrays from Atom
1010 +
1011 + 2003-08-06 19:47  chuckv
1012 +
1013 +        * libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp,
1014 +        libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90,
1015 +        libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90,
1016 +        samples/metals/Au.bass: Bug fixes for eam...
1017 +
1018 + 2003-08-01 11:18  tim
1019 +
1020 +        * libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of
1021 +        Z-Constraint
1022 +
1023 + 2003-07-31 14:59  tim
1024 +
1025 +        * ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
1026 +        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp,
1027 +        libmdtools/ZConstraint.cpp: add index range checking into
1028 +        ZConstraint
1029 +
1030   2003-07-31 10:38  tim
1031  
1032          * libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters
# Line 13 | Line 1042
1042  
1043   2003-07-30 16:17  chuckv
1044  
1045 <        * libmdtools/: EAM_FF.cpp, ForceFields.hpp, ReadWrite.hpp,
1046 <        calc_eam.F90, do_Forces.F90, wrappers.F90: More bug fixes for eam.
1045 >        * libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp,
1046 >        libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90,
1047 >        libmdtools/do_Forces.F90, libmdtools/wrappers.F90,
1048 >        samples/metals/Au.bass: More bug fixes for eam.
1049  
1050   2003-07-29 11:32  mmeineke
1051  
# Line 26 | Line 1057
1057  
1058          * libBASS/Globals.cpp: [no log message]
1059  
1060 + 2003-07-25 15:05  chuckv
1061 +
1062 +        * samples/metals/: Au.bass, metals.mdl: Added bass models for
1063 +        metals
1064 +
1065   2003-07-25 15:00  chuckv
1066  
1067          * libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90,

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