1 |
+ |
2004-06-03 21:38 gezelter |
2 |
+ |
|
3 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
4 |
+ |
libBASS/Makefile.in, libBASS/mpiBASS.h, libBASS/simError.c, |
5 |
+ |
libBASS/simError.h, libmdtools/Makefile.in, libmdtools/config.h.in, |
6 |
+ |
libmdtools/notifyCutoffs.F90, src/Makefile.in: Config changes for |
7 |
+ |
fortran access to SimError |
8 |
+ |
|
9 |
+ |
2004-06-03 16:51 tim |
10 |
+ |
|
11 |
+ |
* libmdtools/: CallbackFunctor.cpp, CallbackFunctor.hpp, |
12 |
+ |
ConstraintAlgorithm.cpp, ConstraintAlgorithm.hpp, |
13 |
+ |
ConstraintElement.cpp, ConstraintElement.hpp, |
14 |
+ |
ConstraintIterator.hpp, ConstraintManager.cpp, |
15 |
+ |
ConstraintManager.hpp, ConstraintPair.hpp, Rattle.cpp, Rattle.hpp, |
16 |
+ |
Shake.cpp, Shake.hpp, ShakeMin.cpp, ShakeMin.hpp, TypeInfo.hpp: new |
17 |
+ |
implementation of constraint |
18 |
+ |
|
19 |
+ |
2004-06-03 16:06 tim |
20 |
+ |
|
21 |
+ |
* libmdtools/DumpWriter.cpp: fixed a bug which only writes out the |
22 |
+ |
first atom of a molecule |
23 |
+ |
|
24 |
+ |
2004-06-03 15:02 gezelter |
25 |
+ |
|
26 |
+ |
* libmdtools/SimSetup.cpp: Fixed groupOffset bug |
27 |
+ |
|
28 |
+ |
2004-06-03 15:02 gezelter |
29 |
+ |
|
30 |
+ |
* ac-tools/: aclocal.m4, configure.in: Working on MPI scripting for |
31 |
+ |
autoconf |
32 |
+ |
|
33 |
+ |
2004-06-02 13:28 gezelter |
34 |
+ |
|
35 |
+ |
* samples/: argon/Makefile, minimizer/argon/Makefile: Shouldn't |
36 |
+ |
have been in CVS |
37 |
+ |
|
38 |
+ |
2004-06-02 13:28 gezelter |
39 |
+ |
|
40 |
+ |
* samples/: argon/Makefile, minimizer/argon/Makefile: Why is this |
41 |
+ |
in CVS? |
42 |
+ |
|
43 |
+ |
2004-06-02 13:27 gezelter |
44 |
+ |
|
45 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Make.dep, |
46 |
+ |
Makefile.in, WATER.cpp: formatting error messages, dependency fixes |
47 |
+ |
|
48 |
+ |
2004-06-02 13:27 gezelter |
49 |
+ |
|
50 |
+ |
* libBASS/simError.h: starting fortran-usable version of simError |
51 |
+ |
|
52 |
+ |
2004-06-02 09:56 chrisfen |
53 |
+ |
|
54 |
+ |
* samples/: argon/Makefile, minimizer/argon/Makefile: Probably |
55 |
+ |
shouldn't be in CVS |
56 |
+ |
|
57 |
+ |
2004-06-02 09:56 chrisfen |
58 |
+ |
|
59 |
+ |
* libmdtools/: Integrator.cpp, NVT.cpp, ReadWrite.hpp, |
60 |
+ |
Restraints.cpp, SimInfo.cpp, StatWriter.cpp: Formatting Changes, |
61 |
+ |
removed writeRaw |
62 |
+ |
|
63 |
+ |
2004-06-02 09:56 chrisfen |
64 |
+ |
|
65 |
+ |
* libBASS/simError.c: Formatting Changes |
66 |
+ |
|
67 |
+ |
2004-06-02 09:21 gezelter |
68 |
+ |
|
69 |
+ |
* libBASS/simError.c, libBASS/simError.h, libmdtools/SimInfo.cpp: |
70 |
+ |
severity levels in simError |
71 |
+ |
|
72 |
+ |
2004-06-01 16:45 gezelter |
73 |
+ |
|
74 |
+ |
* libmdtools/: Exclude.cpp, SimInfo.cpp, calc_LJ_FF.F90, |
75 |
+ |
do_Forces.F90, mpiSimulation.cpp, neighborLists.F90, |
76 |
+ |
simulation_module.F90: Bug fix (fixes of skipList and neighbor list |
77 |
+ |
under MPI) |
78 |
+ |
|
79 |
+ |
2004-06-01 16:44 gezelter |
80 |
+ |
|
81 |
+ |
* libBASS/MoleculeStamp.cpp: Bug fix (memory leak) |
82 |
+ |
|
83 |
+ |
2004-06-01 13:43 gezelter |
84 |
+ |
|
85 |
+ |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Testing |
86 |
+ |
|
87 |
+ |
2004-06-01 13:42 gezelter |
88 |
+ |
|
89 |
+ |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
90 |
+ |
SimSetup.hpp, do_Forces.F90, fortranWrapDefines.hpp, |
91 |
+ |
mpiSimulation.cpp, mpiSimulation_module.F90, simulation_module.F90: |
92 |
+ |
Cutoff Groups for MPI |
93 |
+ |
|
94 |
+ |
2004-06-01 13:07 chrisfen |
95 |
+ |
|
96 |
+ |
* libmdtools/: ForceFields.cpp, StatWriter.cpp: Fixed bug in |
97 |
+ |
useLiquidThermInt routine in ForceFields.cpp |
98 |
+ |
|
99 |
+ |
2004-06-01 12:15 chrisfen |
100 |
+ |
|
101 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
102 |
+ |
SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Implemented a separate |
103 |
+ |
solid and liquid thermodynamic integration routines |
104 |
+ |
|
105 |
+ |
2004-06-01 10:57 tim |
106 |
+ |
|
107 |
+ |
* libmdtools/: CutoffGroup.hpp, SimSetup.cpp: cutoff group in |
108 |
+ |
progress |
109 |
+ |
|
110 |
+ |
2004-06-01 09:27 chrisfen |
111 |
+ |
|
112 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Added useLiquidThermInt |
113 |
+ |
keyword and changed useThermInt to useSolidThermInt |
114 |
+ |
|
115 |
+ |
2004-06-01 09:21 chrisfen |
116 |
+ |
|
117 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Paving the way for separate |
118 |
+ |
solid and liquid thermodynamic integration routines |
119 |
+ |
|
120 |
+ |
2004-05-28 10:21 gezelter |
121 |
+ |
|
122 |
+ |
* libmdtools/do_Forces.F90: bugfix starting |
123 |
+ |
|
124 |
+ |
2004-05-27 15:06 chrisfen |
125 |
+ |
|
126 |
+ |
* libmdtools/: Integrator.cpp, StatWriter.cpp: Fixed a bug in |
127 |
+ |
Integrator.cpp where it called writeRaw() when useThermInt = |
128 |
+ |
false... |
129 |
+ |
|
130 |
+ |
2004-05-27 14:51 tim |
131 |
+ |
|
132 |
+ |
* ChangeLog, libmdtools/do_Forces.F90, |
133 |
+ |
libmdtools/simulation_module.F90: Bug fix for SkipList |
134 |
+ |
|
135 |
+ |
2004-05-27 14:26 gezelter |
136 |
+ |
|
137 |
+ |
* libmdtools/SimSetup.cpp: bugfix in simsetup? |
138 |
+ |
|
139 |
+ |
2004-05-27 13:59 gezelter |
140 |
+ |
|
141 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, |
142 |
+ |
InitializeFromFile.cpp, SimInfo.cpp, SimSetup.cpp, SimSetup.hpp, |
143 |
+ |
ZConsWriter.cpp, ZConstraint.cpp, fortranWrapDefines.hpp, |
144 |
+ |
mdProfile.cpp, mpiSimulation.cpp, mpiSimulation.hpp, |
145 |
+ |
mpiSimulation_module.F90, randomSPRNG.cpp, simulation_module.F90: |
146 |
+ |
Cutoff group changes under MPI |
147 |
+ |
|
148 |
+ |
2004-05-27 11:20 gezelter |
149 |
+ |
|
150 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: Fixes for |
151 |
+ |
xlc++ |
152 |
+ |
|
153 |
+ |
2004-05-27 10:31 tim |
154 |
+ |
|
155 |
+ |
* libmdtools/SimInfo.cpp: groupList new bases on global index of |
156 |
+ |
atoms |
157 |
+ |
|
158 |
+ |
2004-05-27 10:21 gezelter |
159 |
+ |
|
160 |
+ |
* src/: oopse.cpp, oose.cpp: Modified the nifty banner |
161 |
+ |
|
162 |
+ |
2004-05-27 10:21 gezelter |
163 |
+ |
|
164 |
+ |
* libmdtools/: Make.dep, do_Forces.F90, simulation_module.F90: |
165 |
+ |
Fixed off-by-one error in groupStartRow and groupStartCol |
166 |
+ |
|
167 |
+ |
2004-05-26 19:48 tim |
168 |
+ |
|
169 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/DumpWriter.cpp, |
170 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
171 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
172 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/calc_LJ_FF.F90, |
173 |
+ |
libmdtools/calc_charge_charge.F90, |
174 |
+ |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, |
175 |
+ |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
176 |
+ |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
177 |
+ |
libmdtools/force_globals.F90, libmdtools/mdProfile.cpp, |
178 |
+ |
libmdtools/mpiComponentPlan.h, libmdtools/mpiSimulation.cpp, |
179 |
+ |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
180 |
+ |
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
181 |
+ |
libmdtools/simulation_module.F90: in the progress of fixing MPI |
182 |
+ |
version of cutoff group |
183 |
+ |
|
184 |
+ |
2004-05-26 11:41 gezelter |
185 |
+ |
|
186 |
+ |
* libmdtools/do_Forces.F90: Compacted all of the 8 copies of the |
187 |
+ |
force loop into one. |
188 |
+ |
|
189 |
+ |
2004-05-24 17:24 gezelter |
190 |
+ |
|
191 |
+ |
* libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes |
192 |
+ |
|
193 |
+ |
2004-05-24 16:23 chrisfen |
194 |
+ |
|
195 |
+ |
* libmdtools/Restraints.cpp: Removed unnecessary variables and |
196 |
+ |
changed error messages in Restraints.cpp |
197 |
+ |
|
198 |
+ |
2004-05-24 16:03 gezelter |
199 |
+ |
|
200 |
+ |
* libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90, |
201 |
+ |
calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
202 |
+ |
calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes |
203 |
+ |
for stress / pressure tensor by cutoff group |
204 |
+ |
|
205 |
+ |
2004-05-22 15:55 chrisfen |
206 |
+ |
|
207 |
+ |
* libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp... |
208 |
+ |
Too many arguements in a function call. |
209 |
+ |
|
210 |
+ |
2004-05-22 13:17 chrisfen |
211 |
+ |
|
212 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword |
213 |
+ |
useThermInt. |
214 |
+ |
|
215 |
+ |
2004-05-22 13:16 chrisfen |
216 |
+ |
|
217 |
+ |
* libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
218 |
+ |
ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp, |
219 |
+ |
Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp, |
220 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp, |
221 |
+ |
StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration |
222 |
+ |
code. |
223 |
+ |
|
224 |
+ |
2004-05-21 10:58 gezelter |
225 |
+ |
|
226 |
+ |
* libmdtools/: do_Forces.F90, simulation_module.F90: Major changes |
227 |
+ |
to skipThisPair for efficiency |
228 |
+ |
|
229 |
+ |
2004-05-21 09:22 gezelter |
230 |
+ |
|
231 |
+ |
* configure, ac-tools/configure.in, forceFields/LJ.vdw, |
232 |
+ |
forceFields/amber99.vdw, forceFields/charmm27.vdw, |
233 |
+ |
forceFields/gaff.vdw, forceFields/oplsaal.vdw, |
234 |
+ |
samples/argon/Makefile, samples/minimizer/argon/Makefile: Changes |
235 |
+ |
for SHAPES potential |
236 |
+ |
|
237 |
+ |
2004-05-20 15:27 chrisfen |
238 |
+ |
|
239 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit |
240 |
+ |
included the bass keywords |
241 |
+ |
|
242 |
+ |
2004-05-20 15:24 chrisfen |
243 |
+ |
|
244 |
+ |
* libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp, |
245 |
+ |
Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp, |
246 |
+ |
Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several |
247 |
+ |
additions... Restraints.cpp and .hpp were included for restraining |
248 |
+ |
particles in thermodynamic integration. By including these, |
249 |
+ |
changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, |
250 |
+ |
StatWriter, and possibly some other files. Two bass keywords were |
251 |
+ |
also added for performing thermodynamic integration: a lambda value |
252 |
+ |
one and a k power one. |
253 |
+ |
|
254 |
+ |
2004-05-13 16:08 gezelter |
255 |
+ |
|
256 |
+ |
* libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list |
257 |
+ |
|
258 |
+ |
2004-05-12 17:01 tim |
259 |
+ |
|
260 |
+ |
* samples/: argon/Makefile, argon/argonEM.bass, |
261 |
+ |
argon/init_argon.eor, minimizer/argon/Makefile, |
262 |
+ |
minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor, |
263 |
+ |
minimizer/water/Makefile, minimizer/water/Makefile.in, |
264 |
+ |
minimizer/water/WATER.frc, minimizer/water/init_ssd.eor, |
265 |
+ |
minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass, |
266 |
+ |
minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add |
267 |
+ |
minimizer sample |
268 |
+ |
|
269 |
+ |
2004-05-12 16:54 gezelter |
270 |
+ |
|
271 |
+ |
* libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X |
272 |
+ |
compilation |
273 |
+ |
|
274 |
+ |
2004-05-12 15:54 gezelter |
275 |
+ |
|
276 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes |
277 |
+ |
for compilation under Mac OS X with IBM's xl compilers |
278 |
+ |
|
279 |
+ |
2004-05-12 15:14 gezelter |
280 |
+ |
|
281 |
+ |
* src/: oopse.cpp, oose.cpp: Added a nifty neato banner |
282 |
+ |
|
283 |
+ |
2004-05-12 15:14 gezelter |
284 |
+ |
|
285 |
+ |
* libmdtools/LJFF.cpp: Removed an extraneous write |
286 |
+ |
|
287 |
+ |
2004-05-12 15:13 gezelter |
288 |
+ |
|
289 |
+ |
* libBASS/simError.h: Starting to change the error model |
290 |
+ |
|
291 |
+ |
2004-05-12 14:45 gezelter |
292 |
+ |
|
293 |
+ |
* utils/Dump2XYZ.cpp: const char* fix |
294 |
+ |
|
295 |
+ |
2004-05-12 14:44 gezelter |
296 |
+ |
|
297 |
+ |
* libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
298 |
+ |
src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous |
299 |
+ |
write statements |
300 |
+ |
|
301 |
+ |
2004-05-12 11:38 tim |
302 |
+ |
|
303 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
304 |
+ |
ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
305 |
+ |
SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and |
306 |
+ |
massratio from simState, creat cutoff group forevery atom which |
307 |
+ |
does not belong to cutoff group defined at mdl file |
308 |
+ |
|
309 |
+ |
2004-05-12 10:58 gezelter |
310 |
+ |
|
311 |
+ |
* libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in |
312 |
+ |
CutoffGroup |
313 |
+ |
|
314 |
+ |
2004-05-12 10:35 gezelter |
315 |
+ |
|
316 |
+ |
* samples/water/water.mdl: Added the cutoff Groups to the default |
317 |
+ |
water.mdl file |
318 |
+ |
|
319 |
+ |
2004-05-12 10:02 tim |
320 |
+ |
|
321 |
+ |
* ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp: |
322 |
+ |
fixed a bug in CutoffGroup::getCOM() |
323 |
+ |
|
324 |
+ |
2004-05-12 09:29 gezelter |
325 |
+ |
|
326 |
+ |
* libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
327 |
+ |
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
328 |
+ |
samples/water/ssd.bass: bug fixes for cutoffGroups |
329 |
+ |
|
330 |
+ |
2004-05-11 17:28 tim |
331 |
+ |
|
332 |
+ |
* utils/Vector3.hpp: adding generic Vector3 class |
333 |
+ |
|
334 |
+ |
2004-05-11 16:44 tim |
335 |
+ |
|
336 |
+ |
* libmdtools/Integrator.hpp: adding instantiation of |
337 |
+ |
Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8 |
338 |
+ |
|
339 |
+ |
2004-05-11 16:31 gezelter |
340 |
+ |
|
341 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90, |
342 |
+ |
calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90, |
343 |
+ |
calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90: |
344 |
+ |
Fortran-side changes for group-based cutoffs |
345 |
+ |
|
346 |
+ |
2004-05-11 16:20 tim |
347 |
+ |
|
348 |
+ |
* libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp |
349 |
+ |
|
350 |
+ |
2004-05-11 16:14 tim |
351 |
+ |
|
352 |
+ |
* libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp, |
353 |
+ |
SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix |
354 |
+ |
anoter one in CutoffGroup which causes seg fault |
355 |
+ |
|
356 |
+ |
2004-05-11 15:33 tim |
357 |
+ |
|
358 |
+ |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
359 |
+ |
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
360 |
+ |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup |
361 |
+ |
into OOPSE |
362 |
+ |
|
363 |
+ |
2004-05-11 15:07 gezelter |
364 |
+ |
|
365 |
+ |
* libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup |
366 |
+ |
|
367 |
+ |
2004-05-11 11:00 gezelter |
368 |
+ |
|
369 |
+ |
* libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
370 |
+ |
fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to |
371 |
+ |
use the simplified cutoff stuff in the BASS library |
372 |
+ |
|
373 |
+ |
2004-05-10 23:21 gezelter |
374 |
+ |
|
375 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, |
376 |
+ |
CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, |
377 |
+ |
Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
378 |
+ |
MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c, |
379 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
380 |
+ |
parse_tree.c: BASS changes for adding CutoffGroups to molecules. |
381 |
+ |
Also restructured the plethora of cutoff radii into one |
382 |
+ |
cutoffRadius and one switchingRadius. Also removed the |
383 |
+ |
useMolecularCutoffs keyword |
384 |
+ |
|
385 |
+ |
2004-05-10 15:28 tim |
386 |
+ |
|
387 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize |
388 |
+ |
DumpWriter |
389 |
+ |
|
390 |
+ |
2004-05-07 16:36 gezelter |
391 |
+ |
|
392 |
+ |
* libmdtools/: fSwitchingFunction.h, switch_module.F90: New module |
393 |
+ |
for fortran group-based switching function |
394 |
+ |
|
395 |
+ |
2004-05-07 16:35 gezelter |
396 |
+ |
|
397 |
+ |
* libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, |
398 |
+ |
Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, |
399 |
+ |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
400 |
+ |
calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, |
401 |
+ |
force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, |
402 |
+ |
mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, |
403 |
+ |
simulation_module.F90: Many changes to get group-based cutoffs to |
404 |
+ |
work |
405 |
+ |
|
406 |
+ |
2004-05-01 13:52 tim |
407 |
+ |
|
408 |
+ |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
409 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, |
410 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, |
411 |
+ |
libmdtools/do_Forces.F90, libmdtools/fSimulation.h, |
412 |
+ |
libmdtools/fortranWrapDefines.hpp, |
413 |
+ |
libmdtools/simulation_module.F90: C++ pass groupList to fortran |
414 |
+ |
|
415 |
+ |
2004-04-29 11:03 tim |
416 |
+ |
|
417 |
+ |
* ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in |
418 |
+ |
calc_charge_charge when using molecular cutoff |
419 |
+ |
|
420 |
+ |
2004-04-28 21:11 tim |
421 |
+ |
|
422 |
+ |
* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
423 |
+ |
unmatched c/fortran interface |
424 |
+ |
|
425 |
+ |
2004-04-28 18:09 tim |
426 |
+ |
|
427 |
+ |
* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
428 |
+ |
keep the previous position of cantilever in SMD |
429 |
+ |
|
430 |
+ |
2004-04-28 17:34 tim |
431 |
+ |
|
432 |
+ |
* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
433 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
434 |
+ |
in Molecule.cpp which initialize massRatio before creat the array. |
435 |
+ |
fix two bugs in ZconsVisitor |
436 |
+ |
|
437 |
+ |
2004-04-28 17:06 gezelter |
438 |
+ |
|
439 |
+ |
* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
440 |
+ |
Adding molecular cutoffs |
441 |
+ |
|
442 |
+ |
2004-04-28 16:39 gezelter |
443 |
+ |
|
444 |
+ |
* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
445 |
+ |
fSimulation.h, force_globals.F90, simulation_module.F90: work on |
446 |
+ |
molecular cutoffs |
447 |
+ |
|
448 |
+ |
2004-04-28 16:39 gezelter |
449 |
+ |
|
450 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
451 |
+ |
Globals |
452 |
+ |
|
453 |
+ |
2004-04-27 11:26 tim |
454 |
+ |
|
455 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
456 |
+ |
ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
457 |
+ |
fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
458 |
+ |
molecule and massRation into atom class |
459 |
+ |
|
460 |
+ |
2004-04-26 16:16 mmeineke |
461 |
+ |
|
462 |
+ |
* libBASS/Globals.cpp: modified the defaults for the system init |
463 |
+ |
time and system init state. |
464 |
+ |
|
465 |
+ |
2004-04-26 09:29 gezelter |
466 |
+ |
|
467 |
+ |
* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
468 |
+ |
calc_charge_charge.F90 |
469 |
+ |
|
470 |
+ |
2004-04-23 23:31 tim |
471 |
+ |
|
472 |
+ |
* ChangeLog, libmdtools/AtomVisitor.cpp, |
473 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
474 |
+ |
reaction field correction to charge-charge interaction |
475 |
+ |
|
476 |
+ |
2004-04-22 16:33 tim |
477 |
+ |
|
478 |
+ |
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
479 |
+ |
Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
480 |
+ |
calculation of pressure tensor |
481 |
+ |
|
482 |
+ |
2004-04-22 09:55 tim |
483 |
+ |
|
484 |
+ |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
485 |
+ |
another bug in InitFromFile. MPI verion of OOPSE is working again |
486 |
+ |
|
487 |
+ |
2004-04-21 22:29 tim |
488 |
+ |
|
489 |
+ |
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
490 |
+ |
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
491 |
+ |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
492 |
+ |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
493 |
+ |
DumpWriter |
494 |
+ |
|
495 |
+ |
2004-04-21 00:32 tim |
496 |
+ |
|
497 |
+ |
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
498 |
+ |
libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
499 |
+ |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
500 |
+ |
useless files |
501 |
+ |
|
502 |
+ |
2004-04-20 11:56 tim |
503 |
+ |
|
504 |
+ |
* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
505 |
+ |
SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
506 |
+ |
velocitize at thermo |
507 |
+ |
|
508 |
+ |
2004-04-20 00:39 tim |
509 |
+ |
|
510 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
511 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
512 |
+ |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
513 |
+ |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
514 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
515 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
516 |
+ |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
517 |
+ |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
518 |
+ |
|
519 |
+ |
2004-04-19 17:13 gezelter |
520 |
+ |
|
521 |
+ |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
522 |
+ |
Thermo.cpp: Fixed a charge bug |
523 |
+ |
|
524 |
+ |
2004-04-19 15:54 tim |
525 |
+ |
|
526 |
+ |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
527 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
528 |
+ |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
529 |
+ |
a bug in CompositeVisitor which cause the double counting problem |
530 |
+ |
|
531 |
+ |
2004-04-19 12:44 tim |
532 |
+ |
|
533 |
+ |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
534 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
535 |
+ |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
536 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
537 |
+ |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
538 |
+ |
Dump2XYZ is almost working except atoms in rigidbody are double |
539 |
+ |
counted |
540 |
+ |
|
541 |
+ |
2004-04-18 22:52 tim |
542 |
+ |
|
543 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
544 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
545 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
546 |
+ |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
547 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
548 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
549 |
+ |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
550 |
+ |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
551 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
552 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
553 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
554 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
555 |
+ |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
556 |
+ |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
557 |
+ |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
558 |
+ |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
559 |
+ |
implement of quickLate using visitor and composite pattern |
560 |
+ |
|
561 |
+ |
2004-04-15 17:15 tim |
562 |
+ |
|
563 |
+ |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
564 |
+ |
exclude list |
565 |
+ |
|
566 |
+ |
2004-04-15 11:18 tim |
567 |
+ |
|
568 |
+ |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
569 |
+ |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
570 |
+ |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
571 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
572 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
573 |
+ |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
574 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
575 |
+ |
whole bunch of bugs :-) |
576 |
+ |
|
577 |
+ |
2004-04-14 12:20 chrisfen |
578 |
+ |
|
579 |
+ |
* forceFields/WATER.frc: Added the WATER.frc force field |
580 |
+ |
|
581 |
+ |
2004-04-14 11:32 gezelter |
582 |
+ |
|
583 |
+ |
* libmdtools/Molecule.cpp: fixed for get_potential |
584 |
+ |
|
585 |
+ |
2004-04-14 10:37 tim |
586 |
+ |
|
587 |
+ |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
588 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
589 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
590 |
+ |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
591 |
+ |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
592 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
593 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
594 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
595 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
596 |
+ |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
597 |
+ |
Change DumpWriter and InitFromFile |
598 |
+ |
|
599 |
+ |
2004-04-13 11:26 gezelter |
600 |
+ |
|
601 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
602 |
+ |
molecules can keep track of their own IntegrableObjects (and |
603 |
+ |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
604 |
+ |
RigidBodies (which was done incorrectly before). |
605 |
+ |
|
606 |
+ |
2004-04-13 11:25 gezelter |
607 |
+ |
|
608 |
+ |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
609 |
+ |
(will back out momentarily) |
610 |
+ |
|
611 |
+ |
2004-04-13 10:10 gezelter |
612 |
+ |
|
613 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
614 |
+ |
Those were old. |
615 |
+ |
|
616 |
+ |
2004-04-13 10:09 gezelter |
617 |
+ |
|
618 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
619 |
+ |
to add IntegrableObjects |
620 |
+ |
|
621 |
+ |
2004-04-12 16:02 gezelter |
622 |
+ |
|
623 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
624 |
+ |
|
625 |
+ |
2004-04-12 15:32 gezelter |
626 |
+ |
|
627 |
+ |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
628 |
+ |
test run |
629 |
+ |
|
630 |
+ |
2004-04-12 15:32 gezelter |
631 |
+ |
|
632 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
633 |
+ |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
634 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
635 |
+ |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
636 |
+ |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
637 |
+ |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
638 |
+ |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
639 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
640 |
+ |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
641 |
+ |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
642 |
+ |
(Somewhat extensive) |
643 |
+ |
|
644 |
+ |
2004-04-12 15:31 gezelter |
645 |
+ |
|
646 |
+ |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
647 |
+ |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
648 |
+ |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
649 |
+ |
Changes for RigidBody dynamics |
650 |
+ |
|
651 |
+ |
2004-03-17 09:22 tim |
652 |
+ |
|
653 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
654 |
+ |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
655 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
656 |
+ |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
657 |
+ |
does not sound a good choice, next commit will seperate SMD and |
658 |
+ |
ZConstraint |
659 |
+ |
|
660 |
+ |
2004-03-16 14:22 tim |
661 |
+ |
|
662 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
663 |
+ |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
664 |
+ |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
665 |
+ |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
666 |
+ |
now can support sequential moving. Refactorying is needed to |
667 |
+ |
support SMD in ZConstraint |
668 |
+ |
|
669 |
+ |
2004-03-02 15:32 tim |
670 |
+ |
|
671 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
672 |
+ |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
673 |
+ |
support large file |
674 |
+ |
|
675 |
+ |
2004-03-01 16:17 tim |
676 |
+ |
|
677 |
+ |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
678 |
+ |
|
679 |
+ |
2004-03-01 15:01 tim |
680 |
+ |
|
681 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
682 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
683 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
684 |
+ |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
685 |
+ |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
686 |
+ |
program which can be used to replace atom type for zconstraint into |
687 |
+ |
OOPSE |
688 |
+ |
|
689 |
+ |
2004-02-24 11:36 tim |
690 |
+ |
|
691 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
692 |
+ |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
693 |
+ |
message] |
694 |
+ |
|
695 |
+ |
2004-02-24 10:49 tim |
696 |
+ |
|
697 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
698 |
+ |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
699 |
+ |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
700 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
701 |
+ |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
702 |
+ |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
703 |
+ |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
704 |
+ |
|
705 |
+ |
2004-02-24 10:44 tim |
706 |
+ |
|
707 |
+ |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
708 |
+ |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
709 |
+ |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
710 |
+ |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
711 |
+ |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
712 |
+ |
compose to implement Minimizer both versions are working |
713 |
+ |
|
714 |
+ |
2004-02-17 14:23 tim |
715 |
+ |
|
716 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
717 |
+ |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
718 |
+ |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
719 |
+ |
libmdtools/MinimizerParameterSet.hpp, |
720 |
+ |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
721 |
+ |
to remove the constraint force along bond direction |
722 |
+ |
|
723 |
+ |
2004-02-10 16:33 tim |
724 |
+ |
|
725 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
726 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
727 |
+ |
single version of energy minimization is working. |
728 |
+ |
|
729 |
+ |
2004-02-09 15:38 mmeineke |
730 |
+ |
|
731 |
+ |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
732 |
+ |
the massive memory overusage by OOPSE |
733 |
+ |
|
734 |
+ |
2004-02-09 09:48 chrisfen |
735 |
+ |
|
736 |
+ |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
737 |
+ |
hardwired LJ_rcut |
738 |
+ |
|
739 |
+ |
2004-02-06 19:14 tim |
740 |
+ |
|
741 |
+ |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
742 |
+ |
message] |
743 |
+ |
|
744 |
+ |
2004-02-06 16:37 tim |
745 |
+ |
|
746 |
+ |
* ChangeLog, libBASS/Globals.cpp, |
747 |
+ |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
748 |
+ |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
749 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
750 |
+ |
energy minimization for argon is working, need to add constraint |
751 |
+ |
|
752 |
+ |
2004-02-06 14:05 tim |
753 |
+ |
|
754 |
+ |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
755 |
+ |
one more file into Makefile.in |
756 |
+ |
|
757 |
+ |
2004-02-06 13:58 tim |
758 |
+ |
|
759 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
760 |
+ |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
761 |
+ |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
762 |
+ |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
763 |
+ |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
764 |
+ |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
765 |
+ |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
766 |
+ |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
767 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
768 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
769 |
+ |
some lines into global.cpp to make it work with energy minimization |
770 |
+ |
|
771 |
+ |
2004-02-04 17:26 tim |
772 |
+ |
|
773 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
774 |
+ |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
775 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
776 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
777 |
+ |
Single version of conjugate gradient with golden search linesearch |
778 |
+ |
pass a couple of functions test. Brent's algorithm is still broken |
779 |
+ |
|
780 |
+ |
2004-02-03 17:54 tim |
781 |
+ |
|
782 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
783 |
+ |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
784 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
785 |
+ |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
786 |
+ |
|
787 |
+ |
2004-02-03 15:47 tim |
788 |
+ |
|
789 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
790 |
+ |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
791 |
+ |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
792 |
+ |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
793 |
+ |
SteepestDescent.hpp: [no log message] |
794 |
+ |
|
795 |
+ |
2004-02-03 15:43 tim |
796 |
+ |
|
797 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
798 |
+ |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
799 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
800 |
+ |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
801 |
+ |
constraint class |
802 |
+ |
|
803 |
+ |
2004-02-03 12:10 tim |
804 |
+ |
|
805 |
+ |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
806 |
+ |
|
807 |
+ |
2004-02-03 10:21 tim |
808 |
+ |
|
809 |
+ |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
810 |
+ |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
811 |
+ |
|
812 |
|
2004-02-02 15:29 tim |
813 |
|
|
814 |
|
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
884 |
|
|
885 |
|
2004-01-27 14:38 gezelter |
886 |
|
|
887 |
< |
* samples/argon/argon.bass: Longer run time to test argon |
887 |
> |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer |
888 |
> |
run time to test argon |
889 |
|
|
890 |
|
2004-01-27 14:38 gezelter |
891 |
|
|
1102 |
|
2004-01-12 15:37 tim |
1103 |
|
|
1104 |
|
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
1105 |
< |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
1106 |
< |
master nodes |
1105 |
> |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: |
1106 |
> |
Dumpwriter only write out the atoms on master nodes |
1107 |
|
|
1108 |
|
2004-01-10 04:46 tim |
1109 |
|
|
1154 |
|
2004-01-07 14:26 tim |
1155 |
|
|
1156 |
|
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
1157 |
< |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
1158 |
< |
sending message from master node to itself in DumpWriter.cpp and |
1159 |
< |
InitializeFromFile.cpp |
1157 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass, |
1158 |
> |
samples/water/ssd.bass: Fixed a bug of sending message from master |
1159 |
> |
node to itself in DumpWriter.cpp and InitializeFromFile.cpp |
1160 |
|
|
1161 |
|
2004-01-06 14:49 chuckv |
1162 |
|
|
1462 |
|
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
1463 |
|
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
1464 |
|
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
1465 |
< |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
1466 |
< |
file. |
1465 |
> |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi |
1466 |
> |
and eta to the comment line of dump file. |
1467 |
|
|
1468 |
|
2003-10-28 17:25 mmeineke |
1469 |
|
|
1884 |
|
samples/Makefile.in, samples/alkane/Makefile, |
1885 |
|
samples/alkane/Makefile.in, samples/argon/Makefile, |
1886 |
|
samples/argon/Makefile.in, samples/argon/argon.bass, |
1887 |
< |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
1888 |
< |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
1889 |
< |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
1890 |
< |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
1891 |
< |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
1892 |
< |
autoconf / configure method of configuring OOPSE |
1887 |
> |
samples/minimizer/argon/Makefile, |
1888 |
> |
samples/minimizer/argon/Makefile.in, |
1889 |
> |
samples/minimizer/argon/argon.bass, samples/beadLipid/Makefile, |
1890 |
> |
samples/beadLipid/Makefile.in, samples/lipid/Makefile, |
1891 |
> |
samples/lipid/Makefile.in, samples/water/Makefile, |
1892 |
> |
samples/water/Makefile.in, src/Makefile, src/Makefile.in, |
1893 |
> |
utils/Makefile, utils/Makefile.in, utils/sysbuilder/Makefile, |
1894 |
> |
utils/sysbuilder/Makefile.in: Changes to autoconf / configure |
1895 |
> |
method of configuring OOPSE |
1896 |
|
|
1897 |
|
2003-09-04 16:48 mmeineke |
1898 |
|
|
2481 |
|
2003-07-14 18:06 gezelter |
2482 |
|
|
2483 |
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
2484 |
< |
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
2485 |
< |
for samples |
2484 |
> |
argon/init_argon.eor, minimizer/argon/argon.bass, |
2485 |
> |
minimizer/argon/init_argon.eor, lipid/init_5x5.eor, |
2486 |
> |
water/init_ssd.eor: Fixes for samples |
2487 |
|
|
2488 |
|
2003-07-14 18:06 gezelter |
2489 |
|
|
3156 |
|
|
3157 |
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
3158 |
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
3159 |
< |
samples/argon/argon.bass: more bug fixes.... |
3159 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more |
3160 |
> |
bug fixes.... |
3161 |
|
|
3162 |
|
2003-04-01 11:49 mmeineke |
3163 |
|
|
3364 |
|
2003-03-26 10:37 chuckv |
3365 |
|
|
3366 |
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
3367 |
< |
samples/argon/argon.bass: Fixes for Parallel thermalization |
3367 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes |
3368 |
> |
for Parallel thermalization |
3369 |
|
|
3370 |
|
2003-03-26 09:55 mmeineke |
3371 |
|
|
3379 |
|
|
3380 |
|
2003-03-25 09:29 mmeineke |
3381 |
|
|
3382 |
< |
* libBASS/obj/dummy, libmdtools/obj/dummy, src/MPIobj/dummy, |
3383 |
< |
src/obj/dummy: [no log message] |
3382 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
3383 |
> |
src/MPIobj/dummy, src/obj/dummy: [no log message] |
3384 |
|
|
3385 |
|
2003-03-25 09:29 mmeineke |
3386 |
|
|
3397 |
|
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
3398 |
|
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
3399 |
|
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
3400 |
< |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
3401 |
< |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
3402 |
< |
samples |
3400 |
> |
lipid/lipid.mdl, lipid/water.mdl, minimizer/argon/Makefile, |
3401 |
> |
minimizer/argon/argon.bass, minimizer/argon/init_argon.eor, |
3402 |
> |
minimizer/argon/lj.mdl, water/Makefile, water/init_ssd.eor, |
3403 |
> |
water/ssd.bass, water/water.mdl: moved tests to samples |
3404 |
|
|
3405 |
|
2003-03-24 19:51 gezelter |
3406 |
|
|
3534 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
3535 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
3536 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
3537 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
3538 |
< |
revision |
3537 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
3538 |
> |
Tree |
3539 |
|
|
3540 |
|
2003-03-21 12:42 mmeineke |
3541 |
|
|
3592 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
3593 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
3594 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
3595 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
3596 |
< |
Tree |
3595 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
3596 |
> |
revision |
3597 |
|
|