1 |
+ |
2004-06-09 11:16 tim |
2 |
+ |
|
3 |
+ |
* libmdtools/: ConstraintAlgorithm.hpp, ConstraintElement.hpp, |
4 |
+ |
Euler3.cpp, Euler3.hpp, Integrator.hpp, Make.dep, Makefile.in, |
5 |
+ |
Mat3x3d.cpp, Mat3x3d.hpp, Quaternion.cpp, Quaternion.hpp, |
6 |
+ |
Rattle.cpp, Rattle.hpp, RigidBody.cpp, RigidBody.hpp, Roll.cpp, |
7 |
+ |
Roll.hpp, Shake.cpp, Shake.hpp, Vector3d.cpp, Vector3d.hpp: 1. |
8 |
+ |
adding some useful math classes(Mat3x3d, Vector3d, Quaternion, |
9 |
+ |
Euler3) these classes use anonymous union and struct to support |
10 |
+ |
double[3], double[3][3] and double[4] 2. adding roll constraint |
11 |
+ |
algorithm |
12 |
+ |
|
13 |
+ |
2004-06-08 11:49 gezelter |
14 |
+ |
|
15 |
+ |
* libmdtools/: NPT.cpp, NPTf.cpp, StuntDouble.cpp, Thermo.cpp: |
16 |
+ |
Fixed a bug in NPTf (vScale was declared in the cpp file in |
17 |
+ |
addition to the declaration in Integrator.hpp file) |
18 |
+ |
|
19 |
+ |
2004-06-07 09:26 gezelter |
20 |
+ |
|
21 |
+ |
* libBASS/Globals.cpp, libmdtools/AtomVisitor.cpp, |
22 |
+ |
libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.hpp, |
23 |
+ |
libmdtools/ConstraintIterator.hpp, |
24 |
+ |
libmdtools/ConstraintManager.hpp, libmdtools/ConstraintPair.hpp, |
25 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpReader.cpp, |
26 |
+ |
libmdtools/DumpWriter.cpp, libmdtools/MatVec3.c, |
27 |
+ |
libmdtools/MatVec3.h, libmdtools/StreamTokenizer.hpp, |
28 |
+ |
libmdtools/ZConsReader.cpp: Fixes from gcc -Wall |
29 |
+ |
|
30 |
+ |
2004-06-07 09:09 chrisfen |
31 |
+ |
|
32 |
+ |
* libmdtools/Thermo.cpp: Dan cleaned up the pressure calculation a |
33 |
+ |
bit... Got rid of some unnecessary lines of code in Thermo.cpp |
34 |
+ |
|
35 |
+ |
2004-06-04 16:00 gezelter |
36 |
+ |
|
37 |
+ |
* libmdtools/: ConstraintIterator.hpp, OOPSEMinimizer.cpp, |
38 |
+ |
StuntDouble.cpp: small bugfixes |
39 |
+ |
|
40 |
+ |
2004-06-04 15:29 tim |
41 |
+ |
|
42 |
+ |
* libmdtools/Integrator.hpp: [no log message] |
43 |
+ |
|
44 |
+ |
2004-06-04 14:30 tim |
45 |
+ |
|
46 |
+ |
* ChangeLog, libmdtools/CallbackFunctor.cpp, |
47 |
+ |
libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.cpp, |
48 |
+ |
libmdtools/ConstraintAlgorithm.hpp, libmdtools/Integrator.hpp, |
49 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/Rattle.hpp, |
50 |
+ |
libmdtools/Shake.hpp, libmdtools/ShakeMin.cpp, |
51 |
+ |
libmdtools/ShakeMin.hpp: constraint algorithm for minimization is |
52 |
+ |
working |
53 |
+ |
|
54 |
+ |
2004-06-04 11:23 gezelter |
55 |
+ |
|
56 |
+ |
* forceFields/charmm27.vdw: Moved to SHAPES |
57 |
+ |
|
58 |
+ |
2004-06-04 11:23 gezelter |
59 |
+ |
|
60 |
+ |
* forceFields/: LJ.vdw, amber99.vdw, gaff.vdw, oplsaal.vdw: [no log |
61 |
+ |
message] |
62 |
+ |
|
63 |
+ |
2004-06-04 09:59 gezelter |
64 |
+ |
|
65 |
+ |
* libmdtools/: notifyCutoffs.F90, status_module.F90, wrappers.F90: |
66 |
+ |
More work on Fortran side of error handler |
67 |
+ |
|
68 |
+ |
2004-06-04 09:59 gezelter |
69 |
+ |
|
70 |
+ |
* configure, ac-tools/aclocal.m4: fixed a typo in autoconf script |
71 |
+ |
|
72 |
+ |
2004-06-04 09:35 gezelter |
73 |
+ |
|
74 |
+ |
* libmdtools/: Makefile.in, fInfo.c, status_module.F90: Unifying |
75 |
+ |
the error handlers |
76 |
+ |
|
77 |
+ |
2004-06-04 09:17 gezelter |
78 |
+ |
|
79 |
+ |
* libBASS/: MemberStamp.cpp, MemberStamp.hpp: Not used anymore |
80 |
+ |
|
81 |
+ |
2004-06-04 09:11 gezelter |
82 |
+ |
|
83 |
+ |
* libBASS/: config.h.in, fError.c: forgot to add these |
84 |
+ |
|
85 |
+ |
2004-06-03 22:15 tim |
86 |
+ |
|
87 |
+ |
* ChangeLog, libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
88 |
+ |
libmdtools/CallbackFunctor.cpp, libmdtools/ConstraintAlgorithm.cpp, |
89 |
+ |
libmdtools/ConstraintManager.cpp, libmdtools/GenericData.cpp, |
90 |
+ |
libmdtools/GenericData.hpp, libmdtools/Integrator.cpp, |
91 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
92 |
+ |
libmdtools/Makefile.in, libmdtools/Molecule.cpp, |
93 |
+ |
libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NVT.cpp, |
94 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, |
95 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
96 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
97 |
+ |
libmdtools/SimSetup.cpp, libmdtools/StuntDouble.cpp, |
98 |
+ |
libmdtools/StuntDouble.hpp, utils/Vector3.hpp: new rattle algorithm |
99 |
+ |
is working |
100 |
+ |
|
101 |
+ |
2004-06-03 21:38 gezelter |
102 |
+ |
|
103 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
104 |
+ |
libBASS/Makefile.in, libBASS/mpiBASS.h, libBASS/simError.c, |
105 |
+ |
libBASS/simError.h, libmdtools/Makefile.in, libmdtools/config.h.in, |
106 |
+ |
libmdtools/notifyCutoffs.F90, src/Makefile.in: Config changes for |
107 |
+ |
fortran access to SimError |
108 |
+ |
|
109 |
+ |
2004-06-03 16:51 tim |
110 |
+ |
|
111 |
+ |
* libmdtools/: CallbackFunctor.cpp, CallbackFunctor.hpp, |
112 |
+ |
ConstraintAlgorithm.cpp, ConstraintAlgorithm.hpp, |
113 |
+ |
ConstraintElement.cpp, ConstraintElement.hpp, |
114 |
+ |
ConstraintIterator.hpp, ConstraintManager.cpp, |
115 |
+ |
ConstraintManager.hpp, ConstraintPair.hpp, Rattle.cpp, Rattle.hpp, |
116 |
+ |
Shake.cpp, Shake.hpp, ShakeMin.cpp, ShakeMin.hpp, TypeInfo.hpp: new |
117 |
+ |
implementation of constraint |
118 |
+ |
|
119 |
+ |
2004-06-03 16:06 tim |
120 |
+ |
|
121 |
+ |
* libmdtools/DumpWriter.cpp: fixed a bug which only writes out the |
122 |
+ |
first atom of a molecule |
123 |
+ |
|
124 |
+ |
2004-06-03 15:02 gezelter |
125 |
+ |
|
126 |
+ |
* libmdtools/SimSetup.cpp: Fixed groupOffset bug |
127 |
+ |
|
128 |
+ |
2004-06-03 15:02 gezelter |
129 |
+ |
|
130 |
+ |
* ac-tools/: aclocal.m4, configure.in: Working on MPI scripting for |
131 |
+ |
autoconf |
132 |
+ |
|
133 |
+ |
2004-06-02 13:28 gezelter |
134 |
+ |
|
135 |
+ |
* samples/: argon/Makefile, minimizer/argon/Makefile: Shouldn't |
136 |
+ |
have been in CVS |
137 |
+ |
|
138 |
+ |
2004-06-02 13:28 gezelter |
139 |
+ |
|
140 |
+ |
* samples/: argon/Makefile, minimizer/argon/Makefile: Why is this |
141 |
+ |
in CVS? |
142 |
+ |
|
143 |
+ |
2004-06-02 13:27 gezelter |
144 |
+ |
|
145 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Make.dep, |
146 |
+ |
Makefile.in, WATER.cpp: formatting error messages, dependency fixes |
147 |
+ |
|
148 |
+ |
2004-06-02 13:27 gezelter |
149 |
+ |
|
150 |
+ |
* libBASS/simError.h: starting fortran-usable version of simError |
151 |
+ |
|
152 |
+ |
2004-06-02 09:56 chrisfen |
153 |
+ |
|
154 |
+ |
* samples/: argon/Makefile, minimizer/argon/Makefile: Probably |
155 |
+ |
shouldn't be in CVS |
156 |
+ |
|
157 |
+ |
2004-06-02 09:56 chrisfen |
158 |
+ |
|
159 |
+ |
* libmdtools/: Integrator.cpp, NVT.cpp, ReadWrite.hpp, |
160 |
+ |
Restraints.cpp, SimInfo.cpp, StatWriter.cpp: Formatting Changes, |
161 |
+ |
removed writeRaw |
162 |
+ |
|
163 |
+ |
2004-06-02 09:56 chrisfen |
164 |
+ |
|
165 |
+ |
* libBASS/simError.c: Formatting Changes |
166 |
+ |
|
167 |
+ |
2004-06-02 09:21 gezelter |
168 |
+ |
|
169 |
+ |
* libBASS/simError.c, libBASS/simError.h, libmdtools/SimInfo.cpp: |
170 |
+ |
severity levels in simError |
171 |
+ |
|
172 |
+ |
2004-06-01 16:45 gezelter |
173 |
+ |
|
174 |
+ |
* libmdtools/: Exclude.cpp, SimInfo.cpp, calc_LJ_FF.F90, |
175 |
+ |
do_Forces.F90, mpiSimulation.cpp, neighborLists.F90, |
176 |
+ |
simulation_module.F90: Bug fix (fixes of skipList and neighbor list |
177 |
+ |
under MPI) |
178 |
+ |
|
179 |
+ |
2004-06-01 16:44 gezelter |
180 |
+ |
|
181 |
+ |
* libBASS/MoleculeStamp.cpp: Bug fix (memory leak) |
182 |
+ |
|
183 |
+ |
2004-06-01 13:43 gezelter |
184 |
+ |
|
185 |
+ |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Testing |
186 |
+ |
|
187 |
+ |
2004-06-01 13:42 gezelter |
188 |
+ |
|
189 |
+ |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
190 |
+ |
SimSetup.hpp, do_Forces.F90, fortranWrapDefines.hpp, |
191 |
+ |
mpiSimulation.cpp, mpiSimulation_module.F90, simulation_module.F90: |
192 |
+ |
Cutoff Groups for MPI |
193 |
+ |
|
194 |
+ |
2004-06-01 13:07 chrisfen |
195 |
+ |
|
196 |
+ |
* libmdtools/: ForceFields.cpp, StatWriter.cpp: Fixed bug in |
197 |
+ |
useLiquidThermInt routine in ForceFields.cpp |
198 |
+ |
|
199 |
+ |
2004-06-01 12:15 chrisfen |
200 |
+ |
|
201 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
202 |
+ |
SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Implemented a separate |
203 |
+ |
solid and liquid thermodynamic integration routines |
204 |
+ |
|
205 |
+ |
2004-06-01 10:57 tim |
206 |
+ |
|
207 |
+ |
* libmdtools/: CutoffGroup.hpp, SimSetup.cpp: cutoff group in |
208 |
+ |
progress |
209 |
+ |
|
210 |
+ |
2004-06-01 09:27 chrisfen |
211 |
+ |
|
212 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Added useLiquidThermInt |
213 |
+ |
keyword and changed useThermInt to useSolidThermInt |
214 |
+ |
|
215 |
+ |
2004-06-01 09:21 chrisfen |
216 |
+ |
|
217 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Paving the way for separate |
218 |
+ |
solid and liquid thermodynamic integration routines |
219 |
+ |
|
220 |
+ |
2004-05-28 10:21 gezelter |
221 |
+ |
|
222 |
+ |
* libmdtools/do_Forces.F90: bugfix starting |
223 |
+ |
|
224 |
+ |
2004-05-27 15:06 chrisfen |
225 |
+ |
|
226 |
+ |
* libmdtools/: Integrator.cpp, StatWriter.cpp: Fixed a bug in |
227 |
+ |
Integrator.cpp where it called writeRaw() when useThermInt = |
228 |
+ |
false... |
229 |
+ |
|
230 |
+ |
2004-05-27 14:51 tim |
231 |
+ |
|
232 |
+ |
* ChangeLog, libmdtools/do_Forces.F90, |
233 |
+ |
libmdtools/simulation_module.F90: Bug fix for SkipList |
234 |
+ |
|
235 |
+ |
2004-05-27 14:26 gezelter |
236 |
+ |
|
237 |
+ |
* libmdtools/SimSetup.cpp: bugfix in simsetup? |
238 |
+ |
|
239 |
+ |
2004-05-27 13:59 gezelter |
240 |
+ |
|
241 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, |
242 |
+ |
InitializeFromFile.cpp, SimInfo.cpp, SimSetup.cpp, SimSetup.hpp, |
243 |
+ |
ZConsWriter.cpp, ZConstraint.cpp, fortranWrapDefines.hpp, |
244 |
+ |
mdProfile.cpp, mpiSimulation.cpp, mpiSimulation.hpp, |
245 |
+ |
mpiSimulation_module.F90, randomSPRNG.cpp, simulation_module.F90: |
246 |
+ |
Cutoff group changes under MPI |
247 |
+ |
|
248 |
+ |
2004-05-27 11:20 gezelter |
249 |
+ |
|
250 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: Fixes for |
251 |
+ |
xlc++ |
252 |
+ |
|
253 |
+ |
2004-05-27 10:31 tim |
254 |
+ |
|
255 |
+ |
* libmdtools/SimInfo.cpp: groupList new bases on global index of |
256 |
+ |
atoms |
257 |
+ |
|
258 |
+ |
2004-05-27 10:21 gezelter |
259 |
+ |
|
260 |
+ |
* src/: oopse.cpp, oose.cpp: Modified the nifty banner |
261 |
+ |
|
262 |
+ |
2004-05-27 10:21 gezelter |
263 |
+ |
|
264 |
+ |
* libmdtools/: Make.dep, do_Forces.F90, simulation_module.F90: |
265 |
+ |
Fixed off-by-one error in groupStartRow and groupStartCol |
266 |
+ |
|
267 |
+ |
2004-05-26 19:48 tim |
268 |
+ |
|
269 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/DumpWriter.cpp, |
270 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
271 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
272 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/calc_LJ_FF.F90, |
273 |
+ |
libmdtools/calc_charge_charge.F90, |
274 |
+ |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, |
275 |
+ |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
276 |
+ |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
277 |
+ |
libmdtools/force_globals.F90, libmdtools/mdProfile.cpp, |
278 |
+ |
libmdtools/mpiComponentPlan.h, libmdtools/mpiSimulation.cpp, |
279 |
+ |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
280 |
+ |
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
281 |
+ |
libmdtools/simulation_module.F90: in the progress of fixing MPI |
282 |
+ |
version of cutoff group |
283 |
+ |
|
284 |
+ |
2004-05-26 11:41 gezelter |
285 |
+ |
|
286 |
+ |
* libmdtools/do_Forces.F90: Compacted all of the 8 copies of the |
287 |
+ |
force loop into one. |
288 |
+ |
|
289 |
+ |
2004-05-24 17:24 gezelter |
290 |
+ |
|
291 |
+ |
* libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes |
292 |
+ |
|
293 |
+ |
2004-05-24 16:23 chrisfen |
294 |
+ |
|
295 |
+ |
* libmdtools/Restraints.cpp: Removed unnecessary variables and |
296 |
+ |
changed error messages in Restraints.cpp |
297 |
+ |
|
298 |
+ |
2004-05-24 16:03 gezelter |
299 |
+ |
|
300 |
+ |
* libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90, |
301 |
+ |
calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
302 |
+ |
calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes |
303 |
+ |
for stress / pressure tensor by cutoff group |
304 |
+ |
|
305 |
+ |
2004-05-22 15:55 chrisfen |
306 |
+ |
|
307 |
+ |
* libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp... |
308 |
+ |
Too many arguements in a function call. |
309 |
+ |
|
310 |
+ |
2004-05-22 13:17 chrisfen |
311 |
+ |
|
312 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword |
313 |
+ |
useThermInt. |
314 |
+ |
|
315 |
+ |
2004-05-22 13:16 chrisfen |
316 |
+ |
|
317 |
+ |
* libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
318 |
+ |
ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp, |
319 |
+ |
Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp, |
320 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp, |
321 |
+ |
StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration |
322 |
+ |
code. |
323 |
+ |
|
324 |
+ |
2004-05-21 10:58 gezelter |
325 |
+ |
|
326 |
+ |
* libmdtools/: do_Forces.F90, simulation_module.F90: Major changes |
327 |
+ |
to skipThisPair for efficiency |
328 |
+ |
|
329 |
+ |
2004-05-21 09:22 gezelter |
330 |
+ |
|
331 |
+ |
* configure, ac-tools/configure.in, forceFields/LJ.vdw, |
332 |
+ |
forceFields/amber99.vdw, forceFields/charmm27.vdw, |
333 |
+ |
forceFields/gaff.vdw, forceFields/oplsaal.vdw, |
334 |
+ |
samples/argon/Makefile, samples/minimizer/argon/Makefile: Changes |
335 |
+ |
for SHAPES potential |
336 |
+ |
|
337 |
+ |
2004-05-20 15:27 chrisfen |
338 |
+ |
|
339 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit |
340 |
+ |
included the bass keywords |
341 |
+ |
|
342 |
+ |
2004-05-20 15:24 chrisfen |
343 |
+ |
|
344 |
+ |
* libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp, |
345 |
+ |
Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp, |
346 |
+ |
Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several |
347 |
+ |
additions... Restraints.cpp and .hpp were included for restraining |
348 |
+ |
particles in thermodynamic integration. By including these, |
349 |
+ |
changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, |
350 |
+ |
StatWriter, and possibly some other files. Two bass keywords were |
351 |
+ |
also added for performing thermodynamic integration: a lambda value |
352 |
+ |
one and a k power one. |
353 |
+ |
|
354 |
+ |
2004-05-13 16:08 gezelter |
355 |
+ |
|
356 |
+ |
* libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list |
357 |
+ |
|
358 |
+ |
2004-05-12 17:01 tim |
359 |
+ |
|
360 |
+ |
* samples/: argon/Makefile, argon/argonEM.bass, |
361 |
+ |
argon/init_argon.eor, minimizer/argon/Makefile, |
362 |
+ |
minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor, |
363 |
+ |
minimizer/water/Makefile, minimizer/water/Makefile.in, |
364 |
+ |
minimizer/water/WATER.frc, minimizer/water/init_ssd.eor, |
365 |
+ |
minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass, |
366 |
+ |
minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add |
367 |
+ |
minimizer sample |
368 |
+ |
|
369 |
+ |
2004-05-12 16:54 gezelter |
370 |
+ |
|
371 |
+ |
* libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X |
372 |
+ |
compilation |
373 |
+ |
|
374 |
+ |
2004-05-12 15:54 gezelter |
375 |
+ |
|
376 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes |
377 |
+ |
for compilation under Mac OS X with IBM's xl compilers |
378 |
+ |
|
379 |
+ |
2004-05-12 15:14 gezelter |
380 |
+ |
|
381 |
+ |
* src/: oopse.cpp, oose.cpp: Added a nifty neato banner |
382 |
+ |
|
383 |
+ |
2004-05-12 15:14 gezelter |
384 |
+ |
|
385 |
+ |
* libmdtools/LJFF.cpp: Removed an extraneous write |
386 |
+ |
|
387 |
+ |
2004-05-12 15:13 gezelter |
388 |
+ |
|
389 |
+ |
* libBASS/simError.h: Starting to change the error model |
390 |
+ |
|
391 |
+ |
2004-05-12 14:45 gezelter |
392 |
+ |
|
393 |
+ |
* utils/Dump2XYZ.cpp: const char* fix |
394 |
+ |
|
395 |
+ |
2004-05-12 14:44 gezelter |
396 |
+ |
|
397 |
+ |
* libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
398 |
+ |
src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous |
399 |
+ |
write statements |
400 |
+ |
|
401 |
+ |
2004-05-12 11:38 tim |
402 |
+ |
|
403 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
404 |
+ |
ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
405 |
+ |
SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and |
406 |
+ |
massratio from simState, creat cutoff group forevery atom which |
407 |
+ |
does not belong to cutoff group defined at mdl file |
408 |
+ |
|
409 |
+ |
2004-05-12 10:58 gezelter |
410 |
+ |
|
411 |
+ |
* libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in |
412 |
+ |
CutoffGroup |
413 |
+ |
|
414 |
+ |
2004-05-12 10:35 gezelter |
415 |
+ |
|
416 |
+ |
* samples/water/water.mdl: Added the cutoff Groups to the default |
417 |
+ |
water.mdl file |
418 |
+ |
|
419 |
+ |
2004-05-12 10:02 tim |
420 |
+ |
|
421 |
+ |
* ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp: |
422 |
+ |
fixed a bug in CutoffGroup::getCOM() |
423 |
+ |
|
424 |
+ |
2004-05-12 09:29 gezelter |
425 |
+ |
|
426 |
+ |
* libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
427 |
+ |
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
428 |
+ |
samples/water/ssd.bass: bug fixes for cutoffGroups |
429 |
+ |
|
430 |
+ |
2004-05-11 17:28 tim |
431 |
+ |
|
432 |
+ |
* utils/Vector3.hpp: adding generic Vector3 class |
433 |
+ |
|
434 |
+ |
2004-05-11 16:44 tim |
435 |
+ |
|
436 |
+ |
* libmdtools/Integrator.hpp: adding instantiation of |
437 |
+ |
Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8 |
438 |
+ |
|
439 |
+ |
2004-05-11 16:31 gezelter |
440 |
+ |
|
441 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90, |
442 |
+ |
calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90, |
443 |
+ |
calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90: |
444 |
+ |
Fortran-side changes for group-based cutoffs |
445 |
+ |
|
446 |
+ |
2004-05-11 16:20 tim |
447 |
+ |
|
448 |
+ |
* libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp |
449 |
+ |
|
450 |
+ |
2004-05-11 16:14 tim |
451 |
+ |
|
452 |
+ |
* libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp, |
453 |
+ |
SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix |
454 |
+ |
anoter one in CutoffGroup which causes seg fault |
455 |
+ |
|
456 |
+ |
2004-05-11 15:33 tim |
457 |
+ |
|
458 |
+ |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
459 |
+ |
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
460 |
+ |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup |
461 |
+ |
into OOPSE |
462 |
+ |
|
463 |
+ |
2004-05-11 15:07 gezelter |
464 |
+ |
|
465 |
+ |
* libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup |
466 |
+ |
|
467 |
+ |
2004-05-11 11:00 gezelter |
468 |
+ |
|
469 |
+ |
* libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
470 |
+ |
fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to |
471 |
+ |
use the simplified cutoff stuff in the BASS library |
472 |
+ |
|
473 |
+ |
2004-05-10 23:21 gezelter |
474 |
+ |
|
475 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, |
476 |
+ |
CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, |
477 |
+ |
Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
478 |
+ |
MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c, |
479 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
480 |
+ |
parse_tree.c: BASS changes for adding CutoffGroups to molecules. |
481 |
+ |
Also restructured the plethora of cutoff radii into one |
482 |
+ |
cutoffRadius and one switchingRadius. Also removed the |
483 |
+ |
useMolecularCutoffs keyword |
484 |
+ |
|
485 |
+ |
2004-05-10 15:28 tim |
486 |
+ |
|
487 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize |
488 |
+ |
DumpWriter |
489 |
+ |
|
490 |
+ |
2004-05-07 16:36 gezelter |
491 |
+ |
|
492 |
+ |
* libmdtools/: fSwitchingFunction.h, switch_module.F90: New module |
493 |
+ |
for fortran group-based switching function |
494 |
+ |
|
495 |
+ |
2004-05-07 16:35 gezelter |
496 |
+ |
|
497 |
+ |
* libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, |
498 |
+ |
Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, |
499 |
+ |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
500 |
+ |
calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, |
501 |
+ |
force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, |
502 |
+ |
mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, |
503 |
+ |
simulation_module.F90: Many changes to get group-based cutoffs to |
504 |
+ |
work |
505 |
+ |
|
506 |
+ |
2004-05-01 13:52 tim |
507 |
+ |
|
508 |
+ |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
509 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, |
510 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, |
511 |
+ |
libmdtools/do_Forces.F90, libmdtools/fSimulation.h, |
512 |
+ |
libmdtools/fortranWrapDefines.hpp, |
513 |
+ |
libmdtools/simulation_module.F90: C++ pass groupList to fortran |
514 |
+ |
|
515 |
+ |
2004-04-29 11:03 tim |
516 |
+ |
|
517 |
+ |
* ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in |
518 |
+ |
calc_charge_charge when using molecular cutoff |
519 |
+ |
|
520 |
|
2004-04-28 21:11 tim |
521 |
|
|
522 |
|
* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
984 |
|
|
985 |
|
2004-01-27 14:38 gezelter |
986 |
|
|
987 |
< |
* samples/argon/argon.bass: Longer run time to test argon |
987 |
> |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer |
988 |
> |
run time to test argon |
989 |
|
|
990 |
|
2004-01-27 14:38 gezelter |
991 |
|
|
1202 |
|
2004-01-12 15:37 tim |
1203 |
|
|
1204 |
|
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
1205 |
< |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
1206 |
< |
master nodes |
1205 |
> |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: |
1206 |
> |
Dumpwriter only write out the atoms on master nodes |
1207 |
|
|
1208 |
|
2004-01-10 04:46 tim |
1209 |
|
|
1254 |
|
2004-01-07 14:26 tim |
1255 |
|
|
1256 |
|
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
1257 |
< |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
1258 |
< |
sending message from master node to itself in DumpWriter.cpp and |
1259 |
< |
InitializeFromFile.cpp |
1257 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass, |
1258 |
> |
samples/water/ssd.bass: Fixed a bug of sending message from master |
1259 |
> |
node to itself in DumpWriter.cpp and InitializeFromFile.cpp |
1260 |
|
|
1261 |
|
2004-01-06 14:49 chuckv |
1262 |
|
|
1562 |
|
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
1563 |
|
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
1564 |
|
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
1565 |
< |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
1566 |
< |
file. |
1565 |
> |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi |
1566 |
> |
and eta to the comment line of dump file. |
1567 |
|
|
1568 |
|
2003-10-28 17:25 mmeineke |
1569 |
|
|
1984 |
|
samples/Makefile.in, samples/alkane/Makefile, |
1985 |
|
samples/alkane/Makefile.in, samples/argon/Makefile, |
1986 |
|
samples/argon/Makefile.in, samples/argon/argon.bass, |
1987 |
< |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
1988 |
< |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
1989 |
< |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
1990 |
< |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
1991 |
< |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
1992 |
< |
autoconf / configure method of configuring OOPSE |
1987 |
> |
samples/minimizer/argon/Makefile, |
1988 |
> |
samples/minimizer/argon/Makefile.in, |
1989 |
> |
samples/minimizer/argon/argon.bass, samples/beadLipid/Makefile, |
1990 |
> |
samples/beadLipid/Makefile.in, samples/lipid/Makefile, |
1991 |
> |
samples/lipid/Makefile.in, samples/water/Makefile, |
1992 |
> |
samples/water/Makefile.in, src/Makefile, src/Makefile.in, |
1993 |
> |
utils/Makefile, utils/Makefile.in, utils/sysbuilder/Makefile, |
1994 |
> |
utils/sysbuilder/Makefile.in: Changes to autoconf / configure |
1995 |
> |
method of configuring OOPSE |
1996 |
|
|
1997 |
|
2003-09-04 16:48 mmeineke |
1998 |
|
|
2581 |
|
2003-07-14 18:06 gezelter |
2582 |
|
|
2583 |
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
2584 |
< |
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
2585 |
< |
for samples |
2584 |
> |
argon/init_argon.eor, minimizer/argon/argon.bass, |
2585 |
> |
minimizer/argon/init_argon.eor, lipid/init_5x5.eor, |
2586 |
> |
water/init_ssd.eor: Fixes for samples |
2587 |
|
|
2588 |
|
2003-07-14 18:06 gezelter |
2589 |
|
|
3256 |
|
|
3257 |
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
3258 |
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
3259 |
< |
samples/argon/argon.bass: more bug fixes.... |
3259 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more |
3260 |
> |
bug fixes.... |
3261 |
|
|
3262 |
|
2003-04-01 11:49 mmeineke |
3263 |
|
|
3464 |
|
2003-03-26 10:37 chuckv |
3465 |
|
|
3466 |
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
3467 |
< |
samples/argon/argon.bass: Fixes for Parallel thermalization |
3467 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes |
3468 |
> |
for Parallel thermalization |
3469 |
|
|
3470 |
|
2003-03-26 09:55 mmeineke |
3471 |
|
|
3497 |
|
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
3498 |
|
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
3499 |
|
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
3500 |
< |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
3501 |
< |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
3502 |
< |
samples |
3500 |
> |
lipid/lipid.mdl, lipid/water.mdl, minimizer/argon/Makefile, |
3501 |
> |
minimizer/argon/argon.bass, minimizer/argon/init_argon.eor, |
3502 |
> |
minimizer/argon/lj.mdl, water/Makefile, water/init_ssd.eor, |
3503 |
> |
water/ssd.bass, water/water.mdl: moved tests to samples |
3504 |
|
|
3505 |
|
2003-03-24 19:51 gezelter |
3506 |
|
|