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, |
815 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
816 |
+ |
Adding GoldenSection and Brent LineSearch Method |
817 |
+ |
|
818 |
+ |
2004-01-30 16:47 tim |
819 |
+ |
|
820 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
821 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
822 |
+ |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
823 |
+ |
MinimizerBase instead of a functor to do line seach |
824 |
+ |
|
825 |
+ |
2004-01-30 10:00 chrisfen |
826 |
+ |
|
827 |
+ |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
828 |
+ |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
829 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
830 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
831 |
+ |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
832 |
+ |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
833 |
+ |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
834 |
+ |
has a working WATER.cpp forcefield and parser. This involved |
835 |
+ |
changes to WATER.cpp and ForceFields amoung other files. One |
836 |
+ |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
837 |
+ |
This will be removed on the next commit... |
838 |
+ |
|
839 |
+ |
2004-01-29 18:00 gezelter |
840 |
+ |
|
841 |
+ |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
842 |
+ |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
843 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
844 |
+ |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
845 |
+ |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
846 |
+ |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
847 |
+ |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
848 |
+ |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
849 |
+ |
member list fixes for rigid bodies |
850 |
+ |
|
851 |
+ |
2004-01-29 16:44 tim |
852 |
+ |
|
853 |
+ |
* libmdtools/MinimizerParameterSet.hpp: Adding |
854 |
+ |
MinimizerParameterSet class. |
855 |
+ |
|
856 |
+ |
2004-01-28 17:44 tim |
857 |
+ |
|
858 |
+ |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
859 |
+ |
NLModel0 and NLModel1 |
860 |
+ |
|
861 |
+ |
2004-01-28 15:40 tim |
862 |
+ |
|
863 |
+ |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
864 |
+ |
of NLModel |
865 |
+ |
|
866 |
+ |
2004-01-27 15:34 gezelter |
867 |
+ |
|
868 |
+ |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
869 |
+ |
water.mdl file, updated ssd.bass to use new SSD name |
870 |
+ |
|
871 |
+ |
2004-01-27 15:34 gezelter |
872 |
+ |
|
873 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
874 |
+ |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
875 |
+ |
stuff |
876 |
+ |
|
877 |
+ |
2004-01-27 14:39 gezelter |
878 |
+ |
|
879 |
+ |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
880 |
+ |
|
881 |
+ |
2004-01-27 14:39 gezelter |
882 |
+ |
|
883 |
+ |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
884 |
+ |
|
885 |
+ |
2004-01-27 14:38 gezelter |
886 |
+ |
|
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 |
+ |
|
892 |
+ |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
893 |
+ |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
894 |
+ |
morning |
895 |
+ |
|
896 |
+ |
2004-01-27 14:37 gezelter |
897 |
+ |
|
898 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
899 |
+ |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
900 |
+ |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
901 |
+ |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
902 |
+ |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
903 |
+ |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
904 |
+ |
do new rigidBody scheme |
905 |
+ |
|
906 |
+ |
2004-01-27 14:15 tim |
907 |
+ |
|
908 |
+ |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
909 |
+ |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
910 |
+ |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
911 |
+ |
constraint for Nonlinear Optimization Model |
912 |
+ |
|
913 |
+ |
2004-01-26 17:01 gezelter |
914 |
+ |
|
915 |
+ |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
916 |
+ |
Euler angles for orientation instead of unit vectors required |
917 |
+ |
changes in MoLocator |
918 |
+ |
|
919 |
+ |
2004-01-26 16:53 gezelter |
920 |
+ |
|
921 |
+ |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
922 |
+ |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
923 |
+ |
water/water.mdl: Changed orientation lines from unit vectors to |
924 |
+ |
euler angles |
925 |
+ |
|
926 |
+ |
2004-01-26 16:52 gezelter |
927 |
+ |
|
928 |
+ |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
929 |
+ |
|
930 |
+ |
2004-01-26 16:45 gezelter |
931 |
+ |
|
932 |
+ |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
933 |
+ |
use Euler angles in the following order: phi, theta, psi Removed |
934 |
+ |
the ability to set orientation using a unit vector |
935 |
+ |
|
936 |
+ |
2004-01-26 16:26 gezelter |
937 |
+ |
|
938 |
+ |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
939 |
+ |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
940 |
+ |
Euler angles in the following order: phi, theta, psi Removed the |
941 |
+ |
ability to set orientation using a unit vector |
942 |
+ |
|
943 |
+ |
2004-01-26 13:52 gezelter |
944 |
+ |
|
945 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
946 |
+ |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
947 |
+ |
|
948 |
+ |
2004-01-22 12:34 chrisfen |
949 |
+ |
|
950 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
951 |
+ |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
952 |
+ |
Corrected spelling in several directories, and stated WATER.cpp |
953 |
+ |
|
954 |
+ |
2004-01-21 17:16 tim |
955 |
+ |
|
956 |
+ |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
957 |
+ |
NLOPModel.hpp: constraint class in energy minimization |
958 |
+ |
|
959 |
+ |
2004-01-20 15:34 tim |
960 |
+ |
|
961 |
+ |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
962 |
+ |
|
963 |
+ |
2004-01-20 15:32 tim |
964 |
+ |
|
965 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
966 |
+ |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
967 |
+ |
|
968 |
+ |
2004-01-19 16:17 gezelter |
969 |
+ |
|
970 |
+ |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
971 |
+ |
more user-friendly |
972 |
+ |
|
973 |
+ |
2004-01-19 13:51 chrisfen |
974 |
+ |
|
975 |
+ |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
976 |
+ |
|
977 |
+ |
2004-01-19 13:36 tim |
978 |
+ |
|
979 |
+ |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
980 |
+ |
time, status time, thermal time and reset time are not divisible by |
981 |
+ |
dt |
982 |
+ |
|
983 |
+ |
2004-01-19 11:10 gezelter |
984 |
+ |
|
985 |
+ |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
986 |
+ |
won't complain |
987 |
+ |
|
988 |
+ |
2004-01-19 11:10 gezelter |
989 |
+ |
|
990 |
+ |
* samples/lipid/5x5.bass: Fixed old bass file |
991 |
+ |
|
992 |
+ |
2004-01-19 11:09 gezelter |
993 |
+ |
|
994 |
+ |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
995 |
+ |
required a change in how the MoleculeStamps are used by divideLabor |
996 |
+ |
in mpiSimulation.cpp |
997 |
+ |
|
998 |
+ |
2004-01-19 11:08 gezelter |
999 |
+ |
|
1000 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
1001 |
+ |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
1002 |
+ |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
1003 |
+ |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
1004 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
1005 |
+ |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
1006 |
+ |
|
1007 |
+ |
2004-01-16 16:55 tim |
1008 |
+ |
|
1009 |
+ |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
1010 |
+ |
eor file |
1011 |
+ |
|
1012 |
+ |
2004-01-16 16:51 mmeineke |
1013 |
+ |
|
1014 |
+ |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
1015 |
+ |
write eor files |
1016 |
+ |
|
1017 |
+ |
2004-01-16 10:01 mmeineke |
1018 |
+ |
|
1019 |
+ |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
1020 |
+ |
initialization of the AtomStruct |
1021 |
+ |
|
1022 |
+ |
2004-01-15 16:57 chuckv |
1023 |
+ |
|
1024 |
+ |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
1025 |
+ |
|
1026 |
+ |
2004-01-15 10:51 gezelter |
1027 |
+ |
|
1028 |
+ |
* ac-tools/aclocal.m4: Changes for altivec |
1029 |
+ |
|
1030 |
+ |
2004-01-15 09:22 gezelter |
1031 |
+ |
|
1032 |
+ |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
1033 |
+ |
|
1034 |
+ |
2004-01-14 23:33 gezelter |
1035 |
+ |
|
1036 |
+ |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
1037 |
+ |
|
1038 |
+ |
2004-01-14 20:14 gezelter |
1039 |
+ |
|
1040 |
+ |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
1041 |
+ |
notifyCutoffs.F90: More work for adding charges |
1042 |
+ |
|
1043 |
+ |
2004-01-14 17:41 gezelter |
1044 |
+ |
|
1045 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1046 |
+ |
src/Makefile.in: autoconf fixes |
1047 |
+ |
|
1048 |
+ |
2004-01-14 11:28 mmeineke |
1049 |
+ |
|
1050 |
+ |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
1051 |
+ |
|
1052 |
+ |
2004-01-14 10:48 gezelter |
1053 |
+ |
|
1054 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1055 |
+ |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
1056 |
+ |
changes for icc8 |
1057 |
+ |
|
1058 |
+ |
2004-01-13 18:01 gezelter |
1059 |
+ |
|
1060 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
1061 |
+ |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
1062 |
+ |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
1063 |
+ |
Changes for adding direct charge-charge interactions (with |
1064 |
+ |
switching function) |
1065 |
+ |
|
1066 |
+ |
2004-01-13 17:34 gezelter |
1067 |
+ |
|
1068 |
+ |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
1069 |
+ |
oopseMPI_module.F90: Some changes for new MPI organization and |
1070 |
+ |
direct charge-charge interactions |
1071 |
+ |
|
1072 |
+ |
2004-01-13 17:11 tim |
1073 |
+ |
|
1074 |
+ |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
1075 |
+ |
|
1076 |
+ |
2004-01-13 16:22 tim |
1077 |
+ |
|
1078 |
+ |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
1079 |
+ |
|
1080 |
+ |
2004-01-13 15:35 tim |
1081 |
+ |
|
1082 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
1083 |
+ |
eor file whenever it is used instead of rewinding it |
1084 |
+ |
|
1085 |
+ |
2004-01-13 15:04 tim |
1086 |
+ |
|
1087 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
1088 |
+ |
of writeFrame |
1089 |
+ |
|
1090 |
+ |
2004-01-13 10:46 tim |
1091 |
+ |
|
1092 |
+ |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
1093 |
+ |
Merge the code of writeFinal and writeDump; |
1094 |
+ |
Adding sortingIndex into DumpWriter; |
1095 |
+ |
Fix a bug of writing last frame twice in integrator |
1096 |
+ |
|
1097 |
+ |
2004-01-12 17:54 tim |
1098 |
+ |
|
1099 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
1100 |
+ |
a bug in copying string |
1101 |
+ |
|
1102 |
+ |
2004-01-12 15:37 tim |
1103 |
+ |
|
1104 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
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 |
+ |
|
1110 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
1111 |
+ |
roll it back fix a bug of copying string to a pointer Still have |
1112 |
+ |
Seg fault, it looks like a random MPI seg fault in totalview |
1113 |
+ |
|
1114 |
+ |
2004-01-09 21:15 tim |
1115 |
+ |
|
1116 |
+ |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
1117 |
+ |
|
1118 |
+ |
2004-01-09 15:29 gezelter |
1119 |
+ |
|
1120 |
+ |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
1121 |
+ |
|
1122 |
+ |
2004-01-08 17:25 chuckv |
1123 |
+ |
|
1124 |
+ |
* libmdtools/DumpWriter.cpp: A work in progress... |
1125 |
+ |
|
1126 |
+ |
2004-01-08 13:59 gezelter |
1127 |
+ |
|
1128 |
+ |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
1129 |
+ |
case |
1130 |
+ |
|
1131 |
+ |
2004-01-08 13:13 mmeineke |
1132 |
+ |
|
1133 |
+ |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
1134 |
+ |
state bug. |
1135 |
+ |
|
1136 |
+ |
2004-01-08 13:05 gezelter |
1137 |
+ |
|
1138 |
+ |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
1139 |
+ |
|
1140 |
+ |
2004-01-08 12:57 mmeineke |
1141 |
+ |
|
1142 |
+ |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
1143 |
+ |
exstended state bug |
1144 |
+ |
|
1145 |
+ |
2004-01-08 12:40 gezelter |
1146 |
+ |
|
1147 |
+ |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
1148 |
+ |
|
1149 |
+ |
2004-01-08 10:44 mmeineke |
1150 |
+ |
|
1151 |
+ |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
1152 |
+ |
XS state info flag |
1153 |
+ |
|
1154 |
+ |
2004-01-07 14:26 tim |
1155 |
+ |
|
1156 |
+ |
* libmdtools/DumpWriter.cpp, libmdtools/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 |
+ |
|
1163 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
1164 |
+ |
performance fixes in the dipole dipole and reaction field code |
1165 |
+ |
|
1166 |
+ |
2004-01-06 13:54 chuckv |
1167 |
+ |
|
1168 |
+ |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
1169 |
+ |
little more sane |
1170 |
+ |
|
1171 |
+ |
2004-01-05 17:49 chuckv |
1172 |
+ |
|
1173 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
1174 |
+ |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
1175 |
+ |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
1176 |
+ |
performance by reducing spurious function calls |
1177 |
+ |
|
1178 |
+ |
2004-01-05 17:18 chuckv |
1179 |
+ |
|
1180 |
+ |
* libmdtools/do_Forces.F90: mangling forces even further |
1181 |
+ |
|
1182 |
+ |
2004-01-05 17:18 chuckv |
1183 |
+ |
|
1184 |
+ |
* configure, ac-tools/configure.in: mpich mucking |
1185 |
+ |
|
1186 |
+ |
2004-01-05 17:12 chuckv |
1187 |
+ |
|
1188 |
+ |
* libmdtools/do_Forces.F90: mangled do_forces... |
1189 |
+ |
|
1190 |
+ |
2004-01-05 16:00 chuckv |
1191 |
+ |
|
1192 |
+ |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
1193 |
+ |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
1194 |
+ |
lookup |
1195 |
+ |
|
1196 |
+ |
2003-12-29 14:56 chuckv |
1197 |
+ |
|
1198 |
+ |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
1199 |
+ |
third-party directory for code not written by us. Also added |
1200 |
+ |
Mersenne Twister random number generator code. This will eventually |
1201 |
+ |
replace sprng as the random number generator used by OOPSE. |
1202 |
+ |
|
1203 |
+ |
2003-12-22 16:26 chuckv |
1204 |
+ |
|
1205 |
+ |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
1206 |
+ |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
1207 |
+ |
Fixes to profile code. |
1208 |
+ |
|
1209 |
+ |
2003-12-19 15:36 mmeineke |
1210 |
+ |
|
1211 |
+ |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
1212 |
+ |
timing.F90, timing.f90: More profiling fixes. |
1213 |
+ |
|
1214 |
+ |
2003-12-19 15:19 chuckv |
1215 |
+ |
|
1216 |
+ |
* libmdtools/timing.f90: Another change for MPI in timing. |
1217 |
+ |
|
1218 |
+ |
2003-12-19 15:17 chuckv |
1219 |
+ |
|
1220 |
+ |
* libmdtools/timing.f90: Small update to timing in MPI |
1221 |
+ |
|
1222 |
+ |
2003-12-19 13:53 mmeineke |
1223 |
+ |
|
1224 |
+ |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
1225 |
+ |
profiling commands work now. Will start adding PROFILE ifdefs into |
1226 |
+ |
the code |
1227 |
+ |
|
1228 |
+ |
2003-12-19 12:25 mmeineke |
1229 |
+ |
|
1230 |
+ |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
1231 |
+ |
some profiling routines |
1232 |
+ |
|
1233 |
+ |
2003-12-19 10:12 mmeineke |
1234 |
+ |
|
1235 |
+ |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
1236 |
+ |
and GofRomega |
1237 |
+ |
|
1238 |
+ |
additional work on randomBilayer |
1239 |
+ |
|
1240 |
+ |
2003-12-19 10:12 mmeineke |
1241 |
+ |
|
1242 |
+ |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
1243 |
+ |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
1244 |
+ |
GofRomega |
1245 |
+ |
|
1246 |
+ |
2003-12-18 16:47 mmeineke |
1247 |
+ |
|
1248 |
+ |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
1249 |
+ |
some profile functionality |
1250 |
+ |
|
1251 |
+ |
2003-12-18 15:46 chuckv |
1252 |
+ |
|
1253 |
+ |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
1254 |
+ |
Added functions for simple profiling in fortran. |
1255 |
+ |
|
1256 |
+ |
2003-12-17 15:13 chuckv |
1257 |
+ |
|
1258 |
+ |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
1259 |
+ |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
1260 |
+ |
rho_col were scattered into the same array. Unfortunately, MPI |
1261 |
+ |
zeros the array between scatters so half of the sum was being lost. |
1262 |
+ |
Fixed by added a temp array for column scatter, then sum loop over |
1263 |
+ |
nlocal. |
1264 |
+ |
|
1265 |
+ |
2003-12-16 15:49 mmeineke |
1266 |
+ |
|
1267 |
+ |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
1268 |
+ |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
1269 |
+ |
gofRomega. both need to be debugged and tested. |
1270 |
+ |
|
1271 |
+ |
2003-12-12 10:42 gezelter |
1272 |
+ |
|
1273 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1274 |
+ |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
1275 |
+ |
gradients (to do minimizations) |
1276 |
+ |
|
1277 |
+ |
2003-12-12 10:33 mmeineke |
1278 |
+ |
|
1279 |
+ |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
1280 |
+ |
header |
1281 |
+ |
|
1282 |
+ |
2003-12-10 11:52 mmeineke |
1283 |
+ |
|
1284 |
+ |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
1285 |
+ |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
1286 |
+ |
randomBilayer to the build. Also move the random bilayer builder |
1287 |
+ |
from bilayerSys to randomBilayer |
1288 |
+ |
|
1289 |
+ |
2003-11-25 10:44 mmeineke |
1290 |
+ |
|
1291 |
+ |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
1292 |
+ |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
1293 |
+ |
TB3 in DUFF.frc |
1294 |
+ |
|
1295 |
+ |
2003-11-21 15:09 mmeineke |
1296 |
+ |
|
1297 |
+ |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
1298 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
1299 |
+ |
message in SimInfo. Added a more informative error message in |
1300 |
+ |
InitializeFromFile |
1301 |
+ |
|
1302 |
+ |
2003-11-21 15:07 mmeineke |
1303 |
+ |
|
1304 |
+ |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
1305 |
+ |
ing in the GofR,CosTheta |
1306 |
+ |
|
1307 |
+ |
2003-11-21 14:31 chrisfen |
1308 |
+ |
|
1309 |
+ |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
1310 |
+ |
a bug in SimInfo ordering of radii |
1311 |
+ |
|
1312 |
+ |
2003-11-11 12:20 mmeineke |
1313 |
+ |
|
1314 |
+ |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
1315 |
+ |
a min function. |
1316 |
+ |
|
1317 |
+ |
2003-11-10 16:50 mmeineke |
1318 |
+ |
|
1319 |
+ |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
1320 |
+ |
reordered the rcut/ecr/boxSize initialization |
1321 |
+ |
|
1322 |
+ |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
1323 |
+ |
now exit when it runs into rcut or ecr. |
1324 |
+ |
|
1325 |
+ |
2003-11-07 16:46 chuckv |
1326 |
+ |
|
1327 |
+ |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
1328 |
+ |
oopseMPI_module.F90: Added support for compiling fortran without |
1329 |
+ |
use of mpich modules. We use mpif.h instead.: |
1330 |
+ |
|
1331 |
+ |
2003-11-07 12:09 mmeineke |
1332 |
+ |
|
1333 |
+ |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
1334 |
+ |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
1335 |
+ |
the atom loop in the NPT family of integrators. |
1336 |
+ |
|
1337 |
+ |
2003-11-06 17:01 mmeineke |
1338 |
+ |
|
1339 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
1340 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
1341 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1342 |
+ |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
1343 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
1344 |
+ |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
1345 |
+ |
* useIntiTime => useInitialTime |
1346 |
+ |
|
1347 |
+ |
2003-11-06 14:24 mmeineke |
1348 |
+ |
|
1349 |
+ |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
1350 |
+ |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
1351 |
+ |
parse_tree.h: fixed the includes in the Make.dep |
1352 |
+ |
|
1353 |
+ |
2003-11-06 14:11 mmeineke |
1354 |
+ |
|
1355 |
+ |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
1356 |
+ |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
1357 |
+ |
new-templateless branch to the main trunk. |
1358 |
+ |
|
1359 |
+ |
bug Fixes include: * fixed the switching function from ortho to |
1360 |
+ |
non-ortho box. !!!!! THis was responsible for all of the |
1361 |
+ |
sudden deaths we saw. * some formating in the string when we |
1362 |
+ |
write out the extended system state. * added NPT.cpp to the |
1363 |
+ |
makefile.in |
1364 |
+ |
|
1365 |
+ |
2003-11-06 13:20 mmeineke |
1366 |
+ |
|
1367 |
+ |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
1368 |
+ |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
1369 |
+ |
bug. The box was not switching between orthorhombic and |
1370 |
+ |
non-orthorhombic wrapping correctly. we added a fabs() to |
1371 |
+ |
the check.which should fix it. |
1372 |
+ |
|
1373 |
+ |
2003-11-05 14:16 mmeineke |
1374 |
+ |
|
1375 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
1376 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
1377 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
1378 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
1379 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
1380 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
1381 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
1382 |
+ |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
1383 |
+ |
some work on trying to find the compression bug |
1384 |
+ |
|
1385 |
+ |
2003-11-03 17:07 mmeineke |
1386 |
+ |
|
1387 |
+ |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
1388 |
+ |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
1389 |
+ |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
1390 |
+ |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
1391 |
+ |
most of standard template library from OOPSE. |
1392 |
+ |
|
1393 |
+ |
2003-10-31 16:06 mmeineke |
1394 |
+ |
|
1395 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1396 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
1397 |
+ |
SimSetup.cpp: started work on template removal. |
1398 |
+ |
|
1399 |
+ |
2003-10-31 13:28 mmeineke |
1400 |
+ |
|
1401 |
+ |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
1402 |
+ |
added template stuff to the Maikefile template |
1403 |
+ |
|
1404 |
+ |
little changes to some printf format statements |
1405 |
+ |
|
1406 |
+ |
2003-10-31 13:28 mmeineke |
1407 |
+ |
|
1408 |
+ |
* libBASS/Makefile.in: added template stuff to the Maikefile |
1409 |
+ |
template |
1410 |
+ |
|
1411 |
+ |
2003-10-30 13:59 gezelter |
1412 |
+ |
|
1413 |
+ |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
1414 |
+ |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
1415 |
+ |
rList problems |
1416 |
+ |
|
1417 |
+ |
2003-10-30 09:11 gezelter |
1418 |
+ |
|
1419 |
+ |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
1420 |
+ |
queried before q0 was allocated. |
1421 |
+ |
|
1422 |
+ |
2003-10-29 15:41 mmeineke |
1423 |
+ |
|
1424 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
1425 |
+ |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
1426 |
+ |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
1427 |
+ |
in bass.l |
1428 |
+ |
|
1429 |
+ |
fixed a little bug in the first time step, regarding the setting of |
1430 |
+ |
ecr and est in fortran |
1431 |
+ |
|
1432 |
+ |
2003-10-29 15:40 mmeineke |
1433 |
+ |
|
1434 |
+ |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
1435 |
+ |
|
1436 |
+ |
2003-10-29 12:55 mmeineke |
1437 |
+ |
|
1438 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1439 |
+ |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
1440 |
+ |
rcut is setup, as well as additional debugging comments. |
1441 |
+ |
|
1442 |
+ |
2003-10-29 09:28 gezelter |
1443 |
+ |
|
1444 |
+ |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
1445 |
+ |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
1446 |
+ |
templates |
1447 |
+ |
|
1448 |
+ |
2003-10-28 22:16 gezelter |
1449 |
+ |
|
1450 |
+ |
* src/Makefile.in: Refixed broken makefile |
1451 |
+ |
|
1452 |
+ |
2003-10-28 22:06 gezelter |
1453 |
+ |
|
1454 |
+ |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
1455 |
+ |
fixes |
1456 |
+ |
|
1457 |
+ |
2003-10-28 19:19 tim |
1458 |
+ |
|
1459 |
+ |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
1460 |
+ |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
1461 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
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/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 |
+ |
|
1470 |
+ |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
1471 |
+ |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
1472 |
+ |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
1473 |
+ |
how c calls fortran. All function pointers and fortran calls are |
1474 |
+ |
rigidly typecast now. |
1475 |
+ |
|
1476 |
+ |
2003-10-28 15:42 gezelter |
1477 |
+ |
|
1478 |
+ |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
1479 |
+ |
Portability fixes |
1480 |
+ |
|
1481 |
+ |
2003-10-28 15:09 gezelter |
1482 |
+ |
|
1483 |
+ |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
1484 |
+ |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
1485 |
+ |
src/Makefile.in: Compatibility fixes |
1486 |
+ |
|
1487 |
+ |
2003-10-28 12:08 mmeineke |
1488 |
+ |
|
1489 |
+ |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
1490 |
+ |
started work on template removal |
1491 |
+ |
|
1492 |
+ |
2003-10-28 12:04 gezelter |
1493 |
+ |
|
1494 |
+ |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
1495 |
+ |
trying to understand extern "C" stuff for pointers |
1496 |
+ |
|
1497 |
+ |
2003-10-28 11:20 gezelter |
1498 |
+ |
|
1499 |
+ |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
1500 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
1501 |
+ |
|
1502 |
+ |
2003-10-28 11:03 gezelter |
1503 |
+ |
|
1504 |
+ |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
1505 |
+ |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
1506 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
1507 |
+ |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
1508 |
+ |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
1509 |
+ |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
1510 |
+ |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
1511 |
+ |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
1512 |
+ |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
1513 |
+ |
more portable c header stuff Also, mod file fixes and portability |
1514 |
+ |
changes Some fortran changes will need to be reversed. |
1515 |
+ |
|
1516 |
+ |
2003-10-28 11:03 gezelter |
1517 |
+ |
|
1518 |
+ |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
1519 |
+ |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
1520 |
+ |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
1521 |
+ |
portable c header stuff Also, mod file fixes and portability |
1522 |
+ |
changes |
1523 |
+ |
|
1524 |
+ |
2003-10-28 11:02 gezelter |
1525 |
+ |
|
1526 |
+ |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
1527 |
+ |
stuff |
1528 |
+ |
|
1529 |
+ |
2003-10-27 18:00 gezelter |
1530 |
+ |
|
1531 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1532 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, |
1533 |
+ |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
1534 |
+ |
|
1535 |
+ |
2003-10-27 17:08 mmeineke |
1536 |
+ |
|
1537 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1538 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
1539 |
+ |
added routines for the sysbuilder to work with simSetup |
1540 |
+ |
|
1541 |
+ |
remved the QuickBass routines, and had all parsing go through |
1542 |
+ |
SimSetup. LatticeBilayer is in complete working order now. |
1543 |
+ |
|
1544 |
+ |
2003-10-27 17:07 mmeineke |
1545 |
+ |
|
1546 |
+ |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
1547 |
+ |
routines for the sysbuilder to work with simSetup |
1548 |
+ |
|
1549 |
+ |
2003-10-27 11:20 gezelter |
1550 |
+ |
|
1551 |
+ |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
1552 |
+ |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
1553 |
+ |
|
1554 |
+ |
2003-10-24 17:17 mmeineke |
1555 |
+ |
|
1556 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1557 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
1558 |
+ |
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
1559 |
+ |
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
1560 |
+ |
overhauled latticeBilayer into its own program. Removed sysBuild |
1561 |
+ |
from the Makefile |
1562 |
+ |
|
1563 |
+ |
2003-10-24 12:36 gezelter |
1564 |
+ |
|
1565 |
+ |
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
1566 |
+ |
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
1567 |
+ |
builder |
1568 |
+ |
|
1569 |
+ |
2003-10-24 12:35 gezelter |
1570 |
+ |
|
1571 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
1572 |
+ |
merge problem |
1573 |
+ |
|
1574 |
+ |
2003-10-23 14:57 mmeineke |
1575 |
+ |
|
1576 |
+ |
* samples/metals/Makefile.in: added eam ForceField files to the |
1577 |
+ |
init |
1578 |
+ |
|
1579 |
+ |
fixed an eam mpi parmeter setup bug |
1580 |
+ |
|
1581 |
+ |
added the init file to the makefile |
1582 |
+ |
|
1583 |
+ |
2003-10-23 14:57 mmeineke |
1584 |
+ |
|
1585 |
+ |
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
1586 |
+ |
to the init |
1587 |
+ |
|
1588 |
+ |
fixed an eam mpi parmeter setup bug |
1589 |
+ |
|
1590 |
+ |
2003-10-23 14:57 mmeineke |
1591 |
+ |
|
1592 |
+ |
* forceFields/Makefile.in: added eam ForceField files to the init |
1593 |
+ |
|
1594 |
+ |
2003-10-22 16:17 mmeineke |
1595 |
+ |
|
1596 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
1597 |
+ |
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
1598 |
+ |
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
1599 |
+ |
no box skew allowed. |
1600 |
+ |
|
1601 |
+ |
2003-10-21 14:33 mmeineke |
1602 |
+ |
|
1603 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1604 |
+ |
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
1605 |
+ |
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
1606 |
+ |
* useInitTime = false: sets the origin time to 0.0 regardless |
1607 |
+ |
of the time stamp in the .init file * default=> useInitTime = |
1608 |
+ |
true; |
1609 |
+ |
|
1610 |
+ |
2003-10-17 16:19 mmeineke |
1611 |
+ |
|
1612 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
1613 |
+ |
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1614 |
+ |
staticProps.cpp, obj/placeholder: added the staticProps directory |
1615 |
+ |
to the build list for both configure and configure.in |
1616 |
+ |
|
1617 |
+ |
fixed a number of bugs in the staticProps code. gofr is now |
1618 |
+ |
working. |
1619 |
+ |
|
1620 |
+ |
2003-10-17 16:18 mmeineke |
1621 |
+ |
|
1622 |
+ |
* ac-tools/configure.in: added the staticProps directory to the |
1623 |
+ |
build list for both configure and configure.in |
1624 |
+ |
|
1625 |
+ |
2003-10-17 16:17 mmeineke |
1626 |
+ |
|
1627 |
+ |
* configure: added the staticProps directory to the build list |
1628 |
+ |
|
1629 |
+ |
2003-10-16 14:16 mmeineke |
1630 |
+ |
|
1631 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
1632 |
+ |
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
1633 |
+ |
use linked lists instead of a vector. |
1634 |
+ |
|
1635 |
+ |
Fixed the makefile to build DumpReader.cpp |
1636 |
+ |
|
1637 |
+ |
Removed a comment output in Exclude.cpp |
1638 |
+ |
|
1639 |
+ |
Modified DumpWriter and Integrator to write an eor file every time |
1640 |
+ |
a frame is written. This lets the .eor file represent the last |
1641 |
+ |
written frame of a simulation. |
1642 |
+ |
|
1643 |
+ |
2003-10-10 12:10 mmeineke |
1644 |
+ |
|
1645 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
1646 |
+ |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
1647 |
+ |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1648 |
+ |
staticProps.cpp: removed the props directory, and moved everything |
1649 |
+ |
over to staticProps |
1650 |
+ |
|
1651 |
+ |
2003-10-09 17:09 mmeineke |
1652 |
+ |
|
1653 |
+ |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
1654 |
+ |
a position where it will compile and run first runs. |
1655 |
+ |
|
1656 |
+ |
2003-10-04 13:46 chuckv |
1657 |
+ |
|
1658 |
+ |
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
1659 |
+ |
samples/metals/Au.bass: Fixed bug in calc_eam. |
1660 |
+ |
|
1661 |
+ |
2003-10-04 13:08 chuckv |
1662 |
+ |
|
1663 |
+ |
* samples/metals/init_au.in: added Au init file for eam. |
1664 |
+ |
|
1665 |
+ |
2003-10-03 17:11 mmeineke |
1666 |
+ |
|
1667 |
+ |
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
1668 |
+ |
entahlpy from the statwriter and thermo. |
1669 |
+ |
|
1670 |
+ |
2003-10-03 17:02 mmeineke |
1671 |
+ |
|
1672 |
+ |
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
1673 |
+ |
statements in simError |
1674 |
+ |
|
1675 |
+ |
added a function to get the maxCutoff |
1676 |
+ |
|
1677 |
+ |
2003-10-03 17:01 mmeineke |
1678 |
+ |
|
1679 |
+ |
* libBASS/simError.c: changed the formating ogf the error |
1680 |
+ |
statements in simError |
1681 |
+ |
|
1682 |
+ |
2003-09-30 11:00 mmeineke |
1683 |
+ |
|
1684 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
1685 |
+ |
f90Flags so they are no longer overwritten by the compiler. |
1686 |
+ |
|
1687 |
+ |
2003-09-29 17:06 mmeineke |
1688 |
+ |
|
1689 |
+ |
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
1690 |
+ |
for conifig.in |
1691 |
+ |
|
1692 |
+ |
fixed wrappers to extern "C" |
1693 |
+ |
|
1694 |
+ |
2003-09-29 17:06 mmeineke |
1695 |
+ |
|
1696 |
+ |
* ac-tools/configure.in: added mpif90 mod check back same for |
1697 |
+ |
conifig.in |
1698 |
+ |
|
1699 |
+ |
2003-09-29 17:05 mmeineke |
1700 |
+ |
|
1701 |
+ |
* configure: added mpif90 mod check back |
1702 |
+ |
|
1703 |
+ |
2003-09-29 16:16 mmeineke |
1704 |
+ |
|
1705 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1706 |
+ |
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
1707 |
+ |
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
1708 |
+ |
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
1709 |
+ |
libBASS/ZconStamp.cpp, libBASS/simError.c, |
1710 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
1711 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
1712 |
+ |
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
1713 |
+ |
found with SUN's SUNWspro.s1s7 |
1714 |
+ |
|
1715 |
+ |
2003-09-29 12:38 mmeineke |
1716 |
+ |
|
1717 |
+ |
* libmdtools/GenericData.hpp: light change in syntax. no |
1718 |
+ |
signifigant change. |
1719 |
+ |
|
1720 |
+ |
2003-09-25 16:17 mmeineke |
1721 |
+ |
|
1722 |
+ |
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
1723 |
+ |
additional remarks from icc -w3 (extra verbose output) |
1724 |
+ |
|
1725 |
+ |
2003-09-25 14:27 mmeineke |
1726 |
+ |
|
1727 |
+ |
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1728 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
1729 |
+ |
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
1730 |
+ |
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
1731 |
+ |
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
1732 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
1733 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1734 |
+ |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1735 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
1736 |
+ |
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
1737 |
+ |
gcc -Wall and g++ -Wall |
1738 |
+ |
|
1739 |
+ |
2003-09-25 13:54 gezelter |
1740 |
+ |
|
1741 |
+ |
* configure, ac-tools/configure.in: fixed a bug in configure |
1742 |
+ |
|
1743 |
+ |
2003-09-25 11:42 gezelter |
1744 |
+ |
|
1745 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1746 |
+ |
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
1747 |
+ |
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
1748 |
+ |
fixes for configure |
1749 |
+ |
|
1750 |
+ |
2003-09-24 14:34 mmeineke |
1751 |
+ |
|
1752 |
+ |
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
1753 |
+ |
that it is called before the first Statistics are written. |
1754 |
+ |
|
1755 |
+ |
2003-09-23 15:36 gezelter |
1756 |
+ |
|
1757 |
+ |
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
1758 |
+ |
bunch of Make.dep files to CVS |
1759 |
+ |
|
1760 |
+ |
2003-09-23 15:34 mmeineke |
1761 |
+ |
|
1762 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
1763 |
+ |
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
1764 |
+ |
|
1765 |
+ |
Some small syntax cleaning in NPTfm and SimSetup |
1766 |
+ |
|
1767 |
+ |
2003-09-22 18:07 tim |
1768 |
+ |
|
1769 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1770 |
+ |
SimInfo.hpp: fix bug in calculating maxCutoff |
1771 |
+ |
|
1772 |
+ |
2003-09-22 16:23 mmeineke |
1773 |
+ |
|
1774 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
1775 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
1776 |
+ |
Converted NPTf to work with the NPT base class. |
1777 |
+ |
|
1778 |
+ |
Removed NPTfm and NPTim from cvs |
1779 |
+ |
|
1780 |
+ |
2003-09-19 15:00 mmeineke |
1781 |
+ |
|
1782 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1783 |
+ |
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
1784 |
+ |
class. NPTi is up to date. NPTf is not. |
1785 |
+ |
|
1786 |
+ |
2003-09-19 11:03 mmeineke |
1787 |
+ |
|
1788 |
+ |
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
1789 |
+ |
makefile |
1790 |
+ |
|
1791 |
+ |
2003-09-19 11:01 gezelter |
1792 |
+ |
|
1793 |
+ |
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
1794 |
+ |
|
1795 |
+ |
2003-09-19 11:01 gezelter |
1796 |
+ |
|
1797 |
+ |
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
1798 |
+ |
(nearly) conserved quantities for both NPTi and NPTf |
1799 |
+ |
|
1800 |
+ |
2003-09-19 10:20 mmeineke |
1801 |
+ |
|
1802 |
+ |
* utils/Makefile.in: fixed a typo in the makefile. |
1803 |
+ |
|
1804 |
+ |
2003-09-19 09:55 gezelter |
1805 |
+ |
|
1806 |
+ |
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
1807 |
+ |
samples/water/ssd.bass: [no log message] |
1808 |
+ |
|
1809 |
+ |
2003-09-19 09:22 tim |
1810 |
+ |
|
1811 |
+ |
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
1812 |
+ |
|
1813 |
+ |
2003-09-17 09:22 mmeineke |
1814 |
+ |
|
1815 |
+ |
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
1816 |
+ |
work with constraints. |
1817 |
+ |
|
1818 |
+ |
2003-09-16 15:02 tim |
1819 |
+ |
|
1820 |
+ |
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
1821 |
+ |
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
1822 |
+ |
|
1823 |
+ |
fixed conserved quantity in NPT (Still some small bug) |
1824 |
+ |
|
1825 |
+ |
NPTi appears very stable. |
1826 |
+ |
|
1827 |
+ |
2003-09-15 11:52 tim |
1828 |
+ |
|
1829 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
1830 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
1831 |
+ |
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
1832 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1833 |
+ |
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
1834 |
+ |
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
1835 |
+ |
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
1836 |
+ |
statWriter fix bug of vector wrapping at NPTi |
1837 |
+ |
|
1838 |
+ |
2003-09-12 11:20 gezelter |
1839 |
+ |
|
1840 |
+ |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
1841 |
+ |
Makefile.in |
1842 |
+ |
|
1843 |
+ |
2003-09-12 11:20 gezelter |
1844 |
+ |
|
1845 |
+ |
* ChangeLog: Entered changes for configure into ChangeLog |
1846 |
+ |
|
1847 |
+ |
2003-09-09 15:35 mmeineke |
1848 |
+ |
|
1849 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
1850 |
+ |
NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog |
1851 |
+ |
|
1852 |
+ |
added two new NPT integrators, they still need work. |
1853 |
+ |
|
1854 |
+ |
2003-09-09 15:34 mmeineke |
1855 |
+ |
|
1856 |
+ |
* ChangeLog: updated the ChangeLog |
1857 |
+ |
|
1858 |
+ |
2003-09-05 17:45 gezelter |
1859 |
+ |
|
1860 |
+ |
* libmdtools/Make.dep: dependency on config.h |
1861 |
+ |
|
1862 |
+ |
2003-09-05 17:36 gezelter |
1863 |
+ |
|
1864 |
+ |
* configure, ac-tools/aclocal.m4: fixed sprng problem |
1865 |
+ |
|
1866 |
+ |
2003-09-05 16:29 gezelter |
1867 |
+ |
|
1868 |
+ |
* samples/metals/Makefile.in: New Makefile for metals sample |
1869 |
+ |
|
1870 |
+ |
2003-09-05 16:27 gezelter |
1871 |
+ |
|
1872 |
+ |
* Makefile, Makefile.in, ac-tools/aclocal.m4, |
1873 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, |
1874 |
+ |
forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp, |
1875 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
1876 |
+ |
libBASS/Makefile.in, libmdtools/Integrator.hpp, |
1877 |
+ |
libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep, |
1878 |
+ |
libmdtools/Makefile, libmdtools/Makefile.in, |
1879 |
+ |
libmdtools/calc_eam.F90, libmdtools/config.h.in, |
1880 |
+ |
libmdtools/definitions_module.F90, libmdtools/fInfo.c, |
1881 |
+ |
libmdtools/fortranWrappers.cpp, |
1882 |
+ |
libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, |
1883 |
+ |
libmdtools/simulation_module.F90, samples/Makefile, |
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/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 |
+ |
|
1899 |
+ |
* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
1900 |
+ |
libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, |
1901 |
+ |
libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp, |
1902 |
+ |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile: |
1903 |
+ |
added resetTime to the Global namespace. |
1904 |
+ |
|
1905 |
+ |
added ability to reset the integrators in the NVT and NPT family. |
1906 |
+ |
|
1907 |
+ |
2003-09-04 16:48 mmeineke |
1908 |
+ |
|
1909 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global |
1910 |
+ |
namespace. |
1911 |
+ |
|
1912 |
+ |
2003-09-02 09:30 tim |
1913 |
+ |
|
1914 |
+ |
* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, |
1915 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of |
1916 |
+ |
PolicyByMass |
1917 |
+ |
|
1918 |
+ |
2003-08-28 16:09 tim |
1919 |
+ |
|
1920 |
+ |
* ChangeLog, libmdtools/GenericData.cpp, |
1921 |
+ |
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
1922 |
+ |
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
1923 |
+ |
|
1924 |
+ |
2003-08-27 14:23 tim |
1925 |
+ |
|
1926 |
+ |
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
1927 |
+ |
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
1928 |
+ |
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
1929 |
+ |
turn on the optimization flag, it causes a seg fault |
1930 |
+ |
|
1931 |
+ |
2003-08-27 11:25 gezelter |
1932 |
+ |
|
1933 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
1934 |
+ |
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
1935 |
+ |
stress tensor parallel bug. |
1936 |
+ |
|
1937 |
+ |
2003-08-27 11:16 tim |
1938 |
+ |
|
1939 |
+ |
* ChangeLog, libmdtools/DUFF.cpp, |
1940 |
+ |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
1941 |
+ |
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
1942 |
+ |
molMembershipList use global index instead of local index |
1943 |
+ |
|
1944 |
|
2003-08-26 15:37 tim |
1945 |
|
|
1946 |
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
2191 |
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
2192 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
2193 |
|
works..... |
251 |
– |
|
252 |
– |
2003-08-08 13:32 mmeineke |
253 |
– |
|
254 |
– |
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
255 |
– |
moved frameCount's functionality into DumpReader. also split props |
256 |
– |
into staticProps and dynamicProps. (currently only have |
257 |
– |
staticProps) |
2194 |
|
|
2195 |
|
2003-08-08 12:48 mmeineke |
2196 |
|
|
2248 |
|
2003-07-29 11:32 mmeineke |
2249 |
|
|
2250 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
2251 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
2252 |
< |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
317 |
< |
src/Makefile: working on the props code |
2251 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
2252 |
> |
working on the props code |
2253 |
|
|
2254 |
|
2003-07-29 11:32 mmeineke |
2255 |
|
|
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/MPIobj/dummy, libmdtools/obj/dummy, |
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 |
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 |
|
|