1 |
+ |
2004-05-27 10:31 tim |
2 |
+ |
|
3 |
+ |
* libmdtools/SimInfo.cpp: groupList new bases on global index of |
4 |
+ |
atoms |
5 |
+ |
|
6 |
+ |
2004-05-27 10:21 gezelter |
7 |
+ |
|
8 |
+ |
* src/: oopse.cpp, oose.cpp: Modified the nifty banner |
9 |
+ |
|
10 |
+ |
2004-05-27 10:21 gezelter |
11 |
+ |
|
12 |
+ |
* libmdtools/: Make.dep, do_Forces.F90, simulation_module.F90: |
13 |
+ |
Fixed off-by-one error in groupStartRow and groupStartCol |
14 |
+ |
|
15 |
+ |
2004-05-26 19:48 tim |
16 |
+ |
|
17 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/DumpWriter.cpp, |
18 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
19 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
20 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/calc_LJ_FF.F90, |
21 |
+ |
libmdtools/calc_charge_charge.F90, |
22 |
+ |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, |
23 |
+ |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
24 |
+ |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
25 |
+ |
libmdtools/force_globals.F90, libmdtools/mdProfile.cpp, |
26 |
+ |
libmdtools/mpiComponentPlan.h, libmdtools/mpiSimulation.cpp, |
27 |
+ |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
28 |
+ |
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
29 |
+ |
libmdtools/simulation_module.F90: in the progress of fixing MPI |
30 |
+ |
version of cutoff group |
31 |
+ |
|
32 |
+ |
2004-05-26 11:41 gezelter |
33 |
+ |
|
34 |
+ |
* libmdtools/do_Forces.F90: Compacted all of the 8 copies of the |
35 |
+ |
force loop into one. |
36 |
+ |
|
37 |
+ |
2004-05-24 17:24 gezelter |
38 |
+ |
|
39 |
+ |
* libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes |
40 |
+ |
|
41 |
+ |
2004-05-24 16:23 chrisfen |
42 |
+ |
|
43 |
+ |
* libmdtools/Restraints.cpp: Removed unnecessary variables and |
44 |
+ |
changed error messages in Restraints.cpp |
45 |
+ |
|
46 |
+ |
2004-05-24 16:03 gezelter |
47 |
+ |
|
48 |
+ |
* libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90, |
49 |
+ |
calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
50 |
+ |
calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes |
51 |
+ |
for stress / pressure tensor by cutoff group |
52 |
+ |
|
53 |
+ |
2004-05-22 15:55 chrisfen |
54 |
+ |
|
55 |
+ |
* libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp... |
56 |
+ |
Too many arguements in a function call. |
57 |
+ |
|
58 |
+ |
2004-05-22 13:17 chrisfen |
59 |
+ |
|
60 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword |
61 |
+ |
useThermInt. |
62 |
+ |
|
63 |
+ |
2004-05-22 13:16 chrisfen |
64 |
+ |
|
65 |
+ |
* libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
66 |
+ |
ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp, |
67 |
+ |
Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp, |
68 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp, |
69 |
+ |
StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration |
70 |
+ |
code. |
71 |
+ |
|
72 |
+ |
2004-05-21 10:58 gezelter |
73 |
+ |
|
74 |
+ |
* libmdtools/: do_Forces.F90, simulation_module.F90: Major changes |
75 |
+ |
to skipThisPair for efficiency |
76 |
+ |
|
77 |
+ |
2004-05-21 09:22 gezelter |
78 |
+ |
|
79 |
+ |
* configure, ac-tools/configure.in, forceFields/LJ.vdw, |
80 |
+ |
forceFields/amber99.vdw, forceFields/charmm27.vdw, |
81 |
+ |
forceFields/gaff.vdw, forceFields/oplsaal.vdw, |
82 |
+ |
samples/argon/Makefile, samples/minimizer/argon/Makefile: Changes |
83 |
+ |
for SHAPES potential |
84 |
+ |
|
85 |
+ |
2004-05-20 15:27 chrisfen |
86 |
+ |
|
87 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit |
88 |
+ |
included the bass keywords |
89 |
+ |
|
90 |
+ |
2004-05-20 15:24 chrisfen |
91 |
+ |
|
92 |
+ |
* libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp, |
93 |
+ |
Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp, |
94 |
+ |
Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several |
95 |
+ |
additions... Restraints.cpp and .hpp were included for restraining |
96 |
+ |
particles in thermodynamic integration. By including these, |
97 |
+ |
changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, |
98 |
+ |
StatWriter, and possibly some other files. Two bass keywords were |
99 |
+ |
also added for performing thermodynamic integration: a lambda value |
100 |
+ |
one and a k power one. |
101 |
+ |
|
102 |
+ |
2004-05-13 16:08 gezelter |
103 |
+ |
|
104 |
+ |
* libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list |
105 |
+ |
|
106 |
+ |
2004-05-12 17:01 tim |
107 |
+ |
|
108 |
+ |
* samples/: argon/Makefile, argon/argonEM.bass, |
109 |
+ |
argon/init_argon.eor, minimizer/argon/Makefile, |
110 |
+ |
minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor, |
111 |
+ |
minimizer/water/Makefile, minimizer/water/Makefile.in, |
112 |
+ |
minimizer/water/WATER.frc, minimizer/water/init_ssd.eor, |
113 |
+ |
minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass, |
114 |
+ |
minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add |
115 |
+ |
minimizer sample |
116 |
+ |
|
117 |
+ |
2004-05-12 16:54 gezelter |
118 |
+ |
|
119 |
+ |
* libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X |
120 |
+ |
compilation |
121 |
+ |
|
122 |
+ |
2004-05-12 15:54 gezelter |
123 |
+ |
|
124 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes |
125 |
+ |
for compilation under Mac OS X with IBM's xl compilers |
126 |
+ |
|
127 |
+ |
2004-05-12 15:14 gezelter |
128 |
+ |
|
129 |
+ |
* src/: oopse.cpp, oose.cpp: Added a nifty neato banner |
130 |
+ |
|
131 |
+ |
2004-05-12 15:14 gezelter |
132 |
+ |
|
133 |
+ |
* libmdtools/LJFF.cpp: Removed an extraneous write |
134 |
+ |
|
135 |
+ |
2004-05-12 15:13 gezelter |
136 |
+ |
|
137 |
+ |
* libBASS/simError.h: Starting to change the error model |
138 |
+ |
|
139 |
+ |
2004-05-12 14:45 gezelter |
140 |
+ |
|
141 |
+ |
* utils/Dump2XYZ.cpp: const char* fix |
142 |
+ |
|
143 |
+ |
2004-05-12 14:44 gezelter |
144 |
+ |
|
145 |
+ |
* libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
146 |
+ |
src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous |
147 |
+ |
write statements |
148 |
+ |
|
149 |
+ |
2004-05-12 11:38 tim |
150 |
+ |
|
151 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
152 |
+ |
ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
153 |
+ |
SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and |
154 |
+ |
massratio from simState, creat cutoff group forevery atom which |
155 |
+ |
does not belong to cutoff group defined at mdl file |
156 |
+ |
|
157 |
+ |
2004-05-12 10:58 gezelter |
158 |
+ |
|
159 |
+ |
* libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in |
160 |
+ |
CutoffGroup |
161 |
+ |
|
162 |
+ |
2004-05-12 10:35 gezelter |
163 |
+ |
|
164 |
+ |
* samples/water/water.mdl: Added the cutoff Groups to the default |
165 |
+ |
water.mdl file |
166 |
+ |
|
167 |
+ |
2004-05-12 10:02 tim |
168 |
+ |
|
169 |
+ |
* ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp: |
170 |
+ |
fixed a bug in CutoffGroup::getCOM() |
171 |
+ |
|
172 |
+ |
2004-05-12 09:29 gezelter |
173 |
+ |
|
174 |
+ |
* libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
175 |
+ |
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
176 |
+ |
samples/water/ssd.bass: bug fixes for cutoffGroups |
177 |
+ |
|
178 |
+ |
2004-05-11 17:28 tim |
179 |
+ |
|
180 |
+ |
* utils/Vector3.hpp: adding generic Vector3 class |
181 |
+ |
|
182 |
+ |
2004-05-11 16:44 tim |
183 |
+ |
|
184 |
+ |
* libmdtools/Integrator.hpp: adding instantiation of |
185 |
+ |
Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8 |
186 |
+ |
|
187 |
+ |
2004-05-11 16:31 gezelter |
188 |
+ |
|
189 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90, |
190 |
+ |
calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90, |
191 |
+ |
calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90: |
192 |
+ |
Fortran-side changes for group-based cutoffs |
193 |
+ |
|
194 |
+ |
2004-05-11 16:20 tim |
195 |
+ |
|
196 |
+ |
* libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp |
197 |
+ |
|
198 |
+ |
2004-05-11 16:14 tim |
199 |
+ |
|
200 |
+ |
* libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp, |
201 |
+ |
SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix |
202 |
+ |
anoter one in CutoffGroup which causes seg fault |
203 |
+ |
|
204 |
+ |
2004-05-11 15:33 tim |
205 |
+ |
|
206 |
+ |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
207 |
+ |
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
208 |
+ |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup |
209 |
+ |
into OOPSE |
210 |
+ |
|
211 |
+ |
2004-05-11 15:07 gezelter |
212 |
+ |
|
213 |
+ |
* libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup |
214 |
+ |
|
215 |
+ |
2004-05-11 11:00 gezelter |
216 |
+ |
|
217 |
+ |
* libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
218 |
+ |
fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to |
219 |
+ |
use the simplified cutoff stuff in the BASS library |
220 |
+ |
|
221 |
+ |
2004-05-10 23:21 gezelter |
222 |
+ |
|
223 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, |
224 |
+ |
CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, |
225 |
+ |
Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
226 |
+ |
MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c, |
227 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
228 |
+ |
parse_tree.c: BASS changes for adding CutoffGroups to molecules. |
229 |
+ |
Also restructured the plethora of cutoff radii into one |
230 |
+ |
cutoffRadius and one switchingRadius. Also removed the |
231 |
+ |
useMolecularCutoffs keyword |
232 |
+ |
|
233 |
+ |
2004-05-10 15:28 tim |
234 |
+ |
|
235 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize |
236 |
+ |
DumpWriter |
237 |
+ |
|
238 |
+ |
2004-05-07 16:36 gezelter |
239 |
+ |
|
240 |
+ |
* libmdtools/: fSwitchingFunction.h, switch_module.F90: New module |
241 |
+ |
for fortran group-based switching function |
242 |
+ |
|
243 |
+ |
2004-05-07 16:35 gezelter |
244 |
+ |
|
245 |
+ |
* libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, |
246 |
+ |
Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, |
247 |
+ |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
248 |
+ |
calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, |
249 |
+ |
force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, |
250 |
+ |
mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, |
251 |
+ |
simulation_module.F90: Many changes to get group-based cutoffs to |
252 |
+ |
work |
253 |
+ |
|
254 |
+ |
2004-05-01 13:52 tim |
255 |
+ |
|
256 |
+ |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
257 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, |
258 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, |
259 |
+ |
libmdtools/do_Forces.F90, libmdtools/fSimulation.h, |
260 |
+ |
libmdtools/fortranWrapDefines.hpp, |
261 |
+ |
libmdtools/simulation_module.F90: C++ pass groupList to fortran |
262 |
+ |
|
263 |
+ |
2004-04-29 11:03 tim |
264 |
+ |
|
265 |
+ |
* ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in |
266 |
+ |
calc_charge_charge when using molecular cutoff |
267 |
+ |
|
268 |
+ |
2004-04-28 21:11 tim |
269 |
+ |
|
270 |
+ |
* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
271 |
+ |
unmatched c/fortran interface |
272 |
+ |
|
273 |
+ |
2004-04-28 18:09 tim |
274 |
+ |
|
275 |
+ |
* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
276 |
+ |
keep the previous position of cantilever in SMD |
277 |
+ |
|
278 |
+ |
2004-04-28 17:34 tim |
279 |
+ |
|
280 |
+ |
* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
281 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
282 |
+ |
in Molecule.cpp which initialize massRatio before creat the array. |
283 |
+ |
fix two bugs in ZconsVisitor |
284 |
+ |
|
285 |
+ |
2004-04-28 17:06 gezelter |
286 |
+ |
|
287 |
+ |
* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
288 |
+ |
Adding molecular cutoffs |
289 |
+ |
|
290 |
+ |
2004-04-28 16:39 gezelter |
291 |
+ |
|
292 |
+ |
* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
293 |
+ |
fSimulation.h, force_globals.F90, simulation_module.F90: work on |
294 |
+ |
molecular cutoffs |
295 |
+ |
|
296 |
+ |
2004-04-28 16:39 gezelter |
297 |
+ |
|
298 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
299 |
+ |
Globals |
300 |
+ |
|
301 |
+ |
2004-04-27 11:26 tim |
302 |
+ |
|
303 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
304 |
+ |
ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
305 |
+ |
fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
306 |
+ |
molecule and massRation into atom class |
307 |
+ |
|
308 |
+ |
2004-04-26 16:16 mmeineke |
309 |
+ |
|
310 |
+ |
* libBASS/Globals.cpp: modified the defaults for the system init |
311 |
+ |
time and system init state. |
312 |
+ |
|
313 |
+ |
2004-04-26 09:29 gezelter |
314 |
+ |
|
315 |
+ |
* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
316 |
+ |
calc_charge_charge.F90 |
317 |
+ |
|
318 |
+ |
2004-04-23 23:31 tim |
319 |
+ |
|
320 |
+ |
* ChangeLog, libmdtools/AtomVisitor.cpp, |
321 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
322 |
+ |
reaction field correction to charge-charge interaction |
323 |
+ |
|
324 |
+ |
2004-04-22 16:33 tim |
325 |
+ |
|
326 |
+ |
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
327 |
+ |
Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
328 |
+ |
calculation of pressure tensor |
329 |
+ |
|
330 |
+ |
2004-04-22 09:55 tim |
331 |
+ |
|
332 |
+ |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
333 |
+ |
another bug in InitFromFile. MPI verion of OOPSE is working again |
334 |
+ |
|
335 |
+ |
2004-04-21 22:29 tim |
336 |
+ |
|
337 |
+ |
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
338 |
+ |
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
339 |
+ |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
340 |
+ |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
341 |
+ |
DumpWriter |
342 |
+ |
|
343 |
+ |
2004-04-21 00:32 tim |
344 |
+ |
|
345 |
+ |
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
346 |
+ |
libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
347 |
+ |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
348 |
+ |
useless files |
349 |
+ |
|
350 |
+ |
2004-04-20 11:56 tim |
351 |
+ |
|
352 |
+ |
* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
353 |
+ |
SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
354 |
+ |
velocitize at thermo |
355 |
+ |
|
356 |
+ |
2004-04-20 00:39 tim |
357 |
+ |
|
358 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
359 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
360 |
+ |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
361 |
+ |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
362 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
363 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
364 |
+ |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
365 |
+ |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
366 |
+ |
|
367 |
+ |
2004-04-19 17:13 gezelter |
368 |
+ |
|
369 |
+ |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
370 |
+ |
Thermo.cpp: Fixed a charge bug |
371 |
+ |
|
372 |
+ |
2004-04-19 15:54 tim |
373 |
+ |
|
374 |
+ |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
375 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
376 |
+ |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
377 |
+ |
a bug in CompositeVisitor which cause the double counting problem |
378 |
+ |
|
379 |
+ |
2004-04-19 12:44 tim |
380 |
+ |
|
381 |
+ |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
382 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
383 |
+ |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
384 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
385 |
+ |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
386 |
+ |
Dump2XYZ is almost working except atoms in rigidbody are double |
387 |
+ |
counted |
388 |
+ |
|
389 |
+ |
2004-04-18 22:52 tim |
390 |
+ |
|
391 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
392 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
393 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
394 |
+ |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
395 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
396 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
397 |
+ |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
398 |
+ |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
399 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
400 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
401 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
402 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
403 |
+ |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
404 |
+ |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
405 |
+ |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
406 |
+ |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
407 |
+ |
implement of quickLate using visitor and composite pattern |
408 |
+ |
|
409 |
+ |
2004-04-15 17:15 tim |
410 |
+ |
|
411 |
+ |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
412 |
+ |
exclude list |
413 |
+ |
|
414 |
+ |
2004-04-15 11:18 tim |
415 |
+ |
|
416 |
+ |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
417 |
+ |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
418 |
+ |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
419 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
420 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
421 |
+ |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
422 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
423 |
+ |
whole bunch of bugs :-) |
424 |
+ |
|
425 |
+ |
2004-04-14 12:20 chrisfen |
426 |
+ |
|
427 |
+ |
* forceFields/WATER.frc: Added the WATER.frc force field |
428 |
+ |
|
429 |
+ |
2004-04-14 11:32 gezelter |
430 |
+ |
|
431 |
+ |
* libmdtools/Molecule.cpp: fixed for get_potential |
432 |
+ |
|
433 |
+ |
2004-04-14 10:37 tim |
434 |
+ |
|
435 |
+ |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
436 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
437 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
438 |
+ |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
439 |
+ |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
440 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
441 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
442 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
443 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
444 |
+ |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
445 |
+ |
Change DumpWriter and InitFromFile |
446 |
+ |
|
447 |
+ |
2004-04-13 11:26 gezelter |
448 |
+ |
|
449 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
450 |
+ |
molecules can keep track of their own IntegrableObjects (and |
451 |
+ |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
452 |
+ |
RigidBodies (which was done incorrectly before). |
453 |
+ |
|
454 |
+ |
2004-04-13 11:25 gezelter |
455 |
+ |
|
456 |
+ |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
457 |
+ |
(will back out momentarily) |
458 |
+ |
|
459 |
+ |
2004-04-13 10:10 gezelter |
460 |
+ |
|
461 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
462 |
+ |
Those were old. |
463 |
+ |
|
464 |
+ |
2004-04-13 10:09 gezelter |
465 |
+ |
|
466 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
467 |
+ |
to add IntegrableObjects |
468 |
+ |
|
469 |
+ |
2004-04-12 16:02 gezelter |
470 |
+ |
|
471 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
472 |
+ |
|
473 |
+ |
2004-04-12 15:32 gezelter |
474 |
+ |
|
475 |
+ |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
476 |
+ |
test run |
477 |
+ |
|
478 |
+ |
2004-04-12 15:32 gezelter |
479 |
+ |
|
480 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
481 |
+ |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
482 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
483 |
+ |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
484 |
+ |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
485 |
+ |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
486 |
+ |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
487 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
488 |
+ |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
489 |
+ |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
490 |
+ |
(Somewhat extensive) |
491 |
+ |
|
492 |
+ |
2004-04-12 15:31 gezelter |
493 |
+ |
|
494 |
+ |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
495 |
+ |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
496 |
+ |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
497 |
+ |
Changes for RigidBody dynamics |
498 |
+ |
|
499 |
+ |
2004-03-17 09:22 tim |
500 |
+ |
|
501 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
502 |
+ |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
503 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
504 |
+ |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
505 |
+ |
does not sound a good choice, next commit will seperate SMD and |
506 |
+ |
ZConstraint |
507 |
+ |
|
508 |
+ |
2004-03-16 14:22 tim |
509 |
+ |
|
510 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
511 |
+ |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
512 |
+ |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
513 |
+ |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
514 |
+ |
now can support sequential moving. Refactorying is needed to |
515 |
+ |
support SMD in ZConstraint |
516 |
+ |
|
517 |
+ |
2004-03-02 15:32 tim |
518 |
+ |
|
519 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
520 |
+ |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
521 |
+ |
support large file |
522 |
+ |
|
523 |
+ |
2004-03-01 16:17 tim |
524 |
+ |
|
525 |
+ |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
526 |
+ |
|
527 |
+ |
2004-03-01 15:01 tim |
528 |
+ |
|
529 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
530 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
531 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
532 |
+ |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
533 |
+ |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
534 |
+ |
program which can be used to replace atom type for zconstraint into |
535 |
+ |
OOPSE |
536 |
+ |
|
537 |
+ |
2004-02-24 11:36 tim |
538 |
+ |
|
539 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
540 |
+ |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
541 |
+ |
message] |
542 |
+ |
|
543 |
+ |
2004-02-24 10:49 tim |
544 |
+ |
|
545 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
546 |
+ |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
547 |
+ |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
548 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
549 |
+ |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
550 |
+ |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
551 |
+ |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
552 |
+ |
|
553 |
+ |
2004-02-24 10:44 tim |
554 |
+ |
|
555 |
+ |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
556 |
+ |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
557 |
+ |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
558 |
+ |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
559 |
+ |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
560 |
+ |
compose to implement Minimizer both versions are working |
561 |
+ |
|
562 |
+ |
2004-02-17 14:23 tim |
563 |
+ |
|
564 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
565 |
+ |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
566 |
+ |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
567 |
+ |
libmdtools/MinimizerParameterSet.hpp, |
568 |
+ |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
569 |
+ |
to remove the constraint force along bond direction |
570 |
+ |
|
571 |
+ |
2004-02-10 16:33 tim |
572 |
+ |
|
573 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
574 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
575 |
+ |
single version of energy minimization is working. |
576 |
+ |
|
577 |
+ |
2004-02-09 15:38 mmeineke |
578 |
+ |
|
579 |
+ |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
580 |
+ |
the massive memory overusage by OOPSE |
581 |
+ |
|
582 |
+ |
2004-02-09 09:48 chrisfen |
583 |
+ |
|
584 |
+ |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
585 |
+ |
hardwired LJ_rcut |
586 |
+ |
|
587 |
+ |
2004-02-06 19:14 tim |
588 |
+ |
|
589 |
+ |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
590 |
+ |
message] |
591 |
+ |
|
592 |
+ |
2004-02-06 16:37 tim |
593 |
+ |
|
594 |
+ |
* ChangeLog, libBASS/Globals.cpp, |
595 |
+ |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
596 |
+ |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
597 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
598 |
+ |
energy minimization for argon is working, need to add constraint |
599 |
+ |
|
600 |
+ |
2004-02-06 14:05 tim |
601 |
+ |
|
602 |
+ |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
603 |
+ |
one more file into Makefile.in |
604 |
+ |
|
605 |
+ |
2004-02-06 13:58 tim |
606 |
+ |
|
607 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
608 |
+ |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
609 |
+ |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
610 |
+ |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
611 |
+ |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
612 |
+ |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
613 |
+ |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
614 |
+ |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
615 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
616 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
617 |
+ |
some lines into global.cpp to make it work with energy minimization |
618 |
+ |
|
619 |
+ |
2004-02-04 17:26 tim |
620 |
+ |
|
621 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
622 |
+ |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
623 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
624 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
625 |
+ |
Single version of conjugate gradient with golden search linesearch |
626 |
+ |
pass a couple of functions test. Brent's algorithm is still broken |
627 |
+ |
|
628 |
+ |
2004-02-03 17:54 tim |
629 |
+ |
|
630 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
631 |
+ |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
632 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
633 |
+ |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
634 |
+ |
|
635 |
+ |
2004-02-03 15:47 tim |
636 |
+ |
|
637 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
638 |
+ |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
639 |
+ |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
640 |
+ |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
641 |
+ |
SteepestDescent.hpp: [no log message] |
642 |
+ |
|
643 |
+ |
2004-02-03 15:43 tim |
644 |
+ |
|
645 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
646 |
+ |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
647 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
648 |
+ |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
649 |
+ |
constraint class |
650 |
+ |
|
651 |
+ |
2004-02-03 12:10 tim |
652 |
+ |
|
653 |
+ |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
654 |
+ |
|
655 |
+ |
2004-02-03 10:21 tim |
656 |
+ |
|
657 |
+ |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
658 |
+ |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
659 |
+ |
|
660 |
+ |
2004-02-02 15:29 tim |
661 |
+ |
|
662 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
663 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
664 |
+ |
Adding GoldenSection and Brent LineSearch Method |
665 |
+ |
|
666 |
+ |
2004-01-30 16:47 tim |
667 |
+ |
|
668 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
669 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
670 |
+ |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
671 |
+ |
MinimizerBase instead of a functor to do line seach |
672 |
+ |
|
673 |
+ |
2004-01-30 10:00 chrisfen |
674 |
+ |
|
675 |
+ |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
676 |
+ |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
677 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
678 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
679 |
+ |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
680 |
+ |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
681 |
+ |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
682 |
+ |
has a working WATER.cpp forcefield and parser. This involved |
683 |
+ |
changes to WATER.cpp and ForceFields amoung other files. One |
684 |
+ |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
685 |
+ |
This will be removed on the next commit... |
686 |
+ |
|
687 |
+ |
2004-01-29 18:00 gezelter |
688 |
+ |
|
689 |
+ |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
690 |
+ |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
691 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
692 |
+ |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
693 |
+ |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
694 |
+ |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
695 |
+ |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
696 |
+ |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
697 |
+ |
member list fixes for rigid bodies |
698 |
+ |
|
699 |
+ |
2004-01-29 16:44 tim |
700 |
+ |
|
701 |
+ |
* libmdtools/MinimizerParameterSet.hpp: Adding |
702 |
+ |
MinimizerParameterSet class. |
703 |
+ |
|
704 |
+ |
2004-01-28 17:44 tim |
705 |
+ |
|
706 |
+ |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
707 |
+ |
NLModel0 and NLModel1 |
708 |
+ |
|
709 |
+ |
2004-01-28 15:40 tim |
710 |
+ |
|
711 |
+ |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
712 |
+ |
of NLModel |
713 |
+ |
|
714 |
+ |
2004-01-27 15:34 gezelter |
715 |
+ |
|
716 |
+ |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
717 |
+ |
water.mdl file, updated ssd.bass to use new SSD name |
718 |
+ |
|
719 |
+ |
2004-01-27 15:34 gezelter |
720 |
+ |
|
721 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
722 |
+ |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
723 |
+ |
stuff |
724 |
+ |
|
725 |
+ |
2004-01-27 14:39 gezelter |
726 |
+ |
|
727 |
+ |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
728 |
+ |
|
729 |
+ |
2004-01-27 14:39 gezelter |
730 |
+ |
|
731 |
+ |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
732 |
+ |
|
733 |
+ |
2004-01-27 14:38 gezelter |
734 |
+ |
|
735 |
+ |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer |
736 |
+ |
run time to test argon |
737 |
+ |
|
738 |
+ |
2004-01-27 14:38 gezelter |
739 |
+ |
|
740 |
+ |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
741 |
+ |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
742 |
+ |
morning |
743 |
+ |
|
744 |
+ |
2004-01-27 14:37 gezelter |
745 |
+ |
|
746 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
747 |
+ |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
748 |
+ |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
749 |
+ |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
750 |
+ |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
751 |
+ |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
752 |
+ |
do new rigidBody scheme |
753 |
+ |
|
754 |
+ |
2004-01-27 14:15 tim |
755 |
+ |
|
756 |
+ |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
757 |
+ |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
758 |
+ |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
759 |
+ |
constraint for Nonlinear Optimization Model |
760 |
+ |
|
761 |
+ |
2004-01-26 17:01 gezelter |
762 |
+ |
|
763 |
+ |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
764 |
+ |
Euler angles for orientation instead of unit vectors required |
765 |
+ |
changes in MoLocator |
766 |
+ |
|
767 |
+ |
2004-01-26 16:53 gezelter |
768 |
+ |
|
769 |
+ |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
770 |
+ |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
771 |
+ |
water/water.mdl: Changed orientation lines from unit vectors to |
772 |
+ |
euler angles |
773 |
+ |
|
774 |
+ |
2004-01-26 16:52 gezelter |
775 |
+ |
|
776 |
+ |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
777 |
+ |
|
778 |
+ |
2004-01-26 16:45 gezelter |
779 |
+ |
|
780 |
+ |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
781 |
+ |
use Euler angles in the following order: phi, theta, psi Removed |
782 |
+ |
the ability to set orientation using a unit vector |
783 |
+ |
|
784 |
+ |
2004-01-26 16:26 gezelter |
785 |
+ |
|
786 |
+ |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
787 |
+ |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
788 |
+ |
Euler angles in the following order: phi, theta, psi Removed the |
789 |
+ |
ability to set orientation using a unit vector |
790 |
+ |
|
791 |
+ |
2004-01-26 13:52 gezelter |
792 |
+ |
|
793 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
794 |
+ |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
795 |
+ |
|
796 |
+ |
2004-01-22 12:34 chrisfen |
797 |
+ |
|
798 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
799 |
+ |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
800 |
+ |
Corrected spelling in several directories, and stated WATER.cpp |
801 |
+ |
|
802 |
+ |
2004-01-21 17:16 tim |
803 |
+ |
|
804 |
+ |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
805 |
+ |
NLOPModel.hpp: constraint class in energy minimization |
806 |
+ |
|
807 |
+ |
2004-01-20 15:34 tim |
808 |
+ |
|
809 |
+ |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
810 |
+ |
|
811 |
+ |
2004-01-20 15:32 tim |
812 |
+ |
|
813 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
814 |
+ |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
815 |
+ |
|
816 |
+ |
2004-01-19 16:17 gezelter |
817 |
+ |
|
818 |
+ |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
819 |
+ |
more user-friendly |
820 |
+ |
|
821 |
+ |
2004-01-19 13:51 chrisfen |
822 |
+ |
|
823 |
+ |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
824 |
+ |
|
825 |
+ |
2004-01-19 13:36 tim |
826 |
+ |
|
827 |
+ |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
828 |
+ |
time, status time, thermal time and reset time are not divisible by |
829 |
+ |
dt |
830 |
+ |
|
831 |
+ |
2004-01-19 11:10 gezelter |
832 |
+ |
|
833 |
+ |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
834 |
+ |
won't complain |
835 |
+ |
|
836 |
+ |
2004-01-19 11:10 gezelter |
837 |
+ |
|
838 |
+ |
* samples/lipid/5x5.bass: Fixed old bass file |
839 |
+ |
|
840 |
+ |
2004-01-19 11:09 gezelter |
841 |
+ |
|
842 |
+ |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
843 |
+ |
required a change in how the MoleculeStamps are used by divideLabor |
844 |
+ |
in mpiSimulation.cpp |
845 |
+ |
|
846 |
+ |
2004-01-19 11:08 gezelter |
847 |
+ |
|
848 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
849 |
+ |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
850 |
+ |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
851 |
+ |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
852 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
853 |
+ |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
854 |
+ |
|
855 |
+ |
2004-01-16 16:55 tim |
856 |
+ |
|
857 |
+ |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
858 |
+ |
eor file |
859 |
+ |
|
860 |
+ |
2004-01-16 16:51 mmeineke |
861 |
+ |
|
862 |
+ |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
863 |
+ |
write eor files |
864 |
+ |
|
865 |
+ |
2004-01-16 10:01 mmeineke |
866 |
+ |
|
867 |
+ |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
868 |
+ |
initialization of the AtomStruct |
869 |
+ |
|
870 |
+ |
2004-01-15 16:57 chuckv |
871 |
+ |
|
872 |
+ |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
873 |
+ |
|
874 |
+ |
2004-01-15 10:51 gezelter |
875 |
+ |
|
876 |
+ |
* ac-tools/aclocal.m4: Changes for altivec |
877 |
+ |
|
878 |
+ |
2004-01-15 09:22 gezelter |
879 |
+ |
|
880 |
+ |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
881 |
+ |
|
882 |
+ |
2004-01-14 23:33 gezelter |
883 |
+ |
|
884 |
+ |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
885 |
+ |
|
886 |
+ |
2004-01-14 20:14 gezelter |
887 |
+ |
|
888 |
+ |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
889 |
+ |
notifyCutoffs.F90: More work for adding charges |
890 |
+ |
|
891 |
+ |
2004-01-14 17:41 gezelter |
892 |
+ |
|
893 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
894 |
+ |
src/Makefile.in: autoconf fixes |
895 |
+ |
|
896 |
+ |
2004-01-14 11:28 mmeineke |
897 |
+ |
|
898 |
+ |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
899 |
+ |
|
900 |
+ |
2004-01-14 10:48 gezelter |
901 |
+ |
|
902 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
903 |
+ |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
904 |
+ |
changes for icc8 |
905 |
+ |
|
906 |
+ |
2004-01-13 18:01 gezelter |
907 |
+ |
|
908 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
909 |
+ |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
910 |
+ |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
911 |
+ |
Changes for adding direct charge-charge interactions (with |
912 |
+ |
switching function) |
913 |
+ |
|
914 |
+ |
2004-01-13 17:34 gezelter |
915 |
+ |
|
916 |
+ |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
917 |
+ |
oopseMPI_module.F90: Some changes for new MPI organization and |
918 |
+ |
direct charge-charge interactions |
919 |
+ |
|
920 |
+ |
2004-01-13 17:11 tim |
921 |
+ |
|
922 |
+ |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
923 |
+ |
|
924 |
+ |
2004-01-13 16:22 tim |
925 |
+ |
|
926 |
+ |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
927 |
+ |
|
928 |
+ |
2004-01-13 15:35 tim |
929 |
+ |
|
930 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
931 |
+ |
eor file whenever it is used instead of rewinding it |
932 |
+ |
|
933 |
+ |
2004-01-13 15:04 tim |
934 |
+ |
|
935 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
936 |
+ |
of writeFrame |
937 |
+ |
|
938 |
+ |
2004-01-13 10:46 tim |
939 |
+ |
|
940 |
+ |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
941 |
+ |
Merge the code of writeFinal and writeDump; |
942 |
+ |
Adding sortingIndex into DumpWriter; |
943 |
+ |
Fix a bug of writing last frame twice in integrator |
944 |
+ |
|
945 |
+ |
2004-01-12 17:54 tim |
946 |
+ |
|
947 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
948 |
+ |
a bug in copying string |
949 |
+ |
|
950 |
+ |
2004-01-12 15:37 tim |
951 |
+ |
|
952 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
953 |
+ |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: |
954 |
+ |
Dumpwriter only write out the atoms on master nodes |
955 |
+ |
|
956 |
+ |
2004-01-10 04:46 tim |
957 |
+ |
|
958 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
959 |
+ |
roll it back fix a bug of copying string to a pointer Still have |
960 |
+ |
Seg fault, it looks like a random MPI seg fault in totalview |
961 |
+ |
|
962 |
+ |
2004-01-09 21:15 tim |
963 |
+ |
|
964 |
+ |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
965 |
+ |
|
966 |
+ |
2004-01-09 15:29 gezelter |
967 |
+ |
|
968 |
+ |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
969 |
+ |
|
970 |
+ |
2004-01-08 17:25 chuckv |
971 |
+ |
|
972 |
+ |
* libmdtools/DumpWriter.cpp: A work in progress... |
973 |
+ |
|
974 |
+ |
2004-01-08 13:59 gezelter |
975 |
+ |
|
976 |
+ |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
977 |
+ |
case |
978 |
+ |
|
979 |
+ |
2004-01-08 13:13 mmeineke |
980 |
+ |
|
981 |
+ |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
982 |
+ |
state bug. |
983 |
+ |
|
984 |
+ |
2004-01-08 13:05 gezelter |
985 |
+ |
|
986 |
+ |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
987 |
+ |
|
988 |
+ |
2004-01-08 12:57 mmeineke |
989 |
+ |
|
990 |
+ |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
991 |
+ |
exstended state bug |
992 |
+ |
|
993 |
+ |
2004-01-08 12:40 gezelter |
994 |
+ |
|
995 |
+ |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
996 |
+ |
|
997 |
+ |
2004-01-08 10:44 mmeineke |
998 |
+ |
|
999 |
+ |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
1000 |
+ |
XS state info flag |
1001 |
+ |
|
1002 |
+ |
2004-01-07 14:26 tim |
1003 |
+ |
|
1004 |
+ |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
1005 |
+ |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass, |
1006 |
+ |
samples/water/ssd.bass: Fixed a bug of sending message from master |
1007 |
+ |
node to itself in DumpWriter.cpp and InitializeFromFile.cpp |
1008 |
+ |
|
1009 |
+ |
2004-01-06 14:49 chuckv |
1010 |
+ |
|
1011 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
1012 |
+ |
performance fixes in the dipole dipole and reaction field code |
1013 |
+ |
|
1014 |
+ |
2004-01-06 13:54 chuckv |
1015 |
+ |
|
1016 |
+ |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
1017 |
+ |
little more sane |
1018 |
+ |
|
1019 |
+ |
2004-01-05 17:49 chuckv |
1020 |
+ |
|
1021 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
1022 |
+ |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
1023 |
+ |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
1024 |
+ |
performance by reducing spurious function calls |
1025 |
+ |
|
1026 |
+ |
2004-01-05 17:18 chuckv |
1027 |
+ |
|
1028 |
+ |
* libmdtools/do_Forces.F90: mangling forces even further |
1029 |
+ |
|
1030 |
+ |
2004-01-05 17:18 chuckv |
1031 |
+ |
|
1032 |
+ |
* configure, ac-tools/configure.in: mpich mucking |
1033 |
+ |
|
1034 |
+ |
2004-01-05 17:12 chuckv |
1035 |
+ |
|
1036 |
+ |
* libmdtools/do_Forces.F90: mangled do_forces... |
1037 |
+ |
|
1038 |
+ |
2004-01-05 16:00 chuckv |
1039 |
+ |
|
1040 |
+ |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
1041 |
+ |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
1042 |
+ |
lookup |
1043 |
+ |
|
1044 |
|
2003-12-29 14:56 chuckv |
1045 |
|
|
1046 |
|
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
1310 |
|
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
1311 |
|
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
1312 |
|
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
1313 |
< |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
1314 |
< |
file. |
1313 |
> |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi |
1314 |
> |
and eta to the comment line of dump file. |
1315 |
|
|
1316 |
|
2003-10-28 17:25 mmeineke |
1317 |
|
|
1732 |
|
samples/Makefile.in, samples/alkane/Makefile, |
1733 |
|
samples/alkane/Makefile.in, samples/argon/Makefile, |
1734 |
|
samples/argon/Makefile.in, samples/argon/argon.bass, |
1735 |
< |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
1736 |
< |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
1737 |
< |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
1738 |
< |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
1739 |
< |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
1740 |
< |
autoconf / configure method of configuring OOPSE |
1735 |
> |
samples/minimizer/argon/Makefile, |
1736 |
> |
samples/minimizer/argon/Makefile.in, |
1737 |
> |
samples/minimizer/argon/argon.bass, samples/beadLipid/Makefile, |
1738 |
> |
samples/beadLipid/Makefile.in, samples/lipid/Makefile, |
1739 |
> |
samples/lipid/Makefile.in, samples/water/Makefile, |
1740 |
> |
samples/water/Makefile.in, src/Makefile, src/Makefile.in, |
1741 |
> |
utils/Makefile, utils/Makefile.in, utils/sysbuilder/Makefile, |
1742 |
> |
utils/sysbuilder/Makefile.in: Changes to autoconf / configure |
1743 |
> |
method of configuring OOPSE |
1744 |
|
|
1745 |
|
2003-09-04 16:48 mmeineke |
1746 |
|
|
2329 |
|
2003-07-14 18:06 gezelter |
2330 |
|
|
2331 |
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
2332 |
< |
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
2333 |
< |
for samples |
2332 |
> |
argon/init_argon.eor, minimizer/argon/argon.bass, |
2333 |
> |
minimizer/argon/init_argon.eor, lipid/init_5x5.eor, |
2334 |
> |
water/init_ssd.eor: Fixes for samples |
2335 |
|
|
2336 |
|
2003-07-14 18:06 gezelter |
2337 |
|
|
3004 |
|
|
3005 |
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
3006 |
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
3007 |
< |
samples/argon/argon.bass: more bug fixes.... |
3007 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more |
3008 |
> |
bug fixes.... |
3009 |
|
|
3010 |
|
2003-04-01 11:49 mmeineke |
3011 |
|
|
3212 |
|
2003-03-26 10:37 chuckv |
3213 |
|
|
3214 |
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
3215 |
< |
samples/argon/argon.bass: Fixes for Parallel thermalization |
3215 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes |
3216 |
> |
for Parallel thermalization |
3217 |
|
|
3218 |
|
2003-03-26 09:55 mmeineke |
3219 |
|
|
3227 |
|
|
3228 |
|
2003-03-25 09:29 mmeineke |
3229 |
|
|
3230 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
3230 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
3231 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
3232 |
|
|
3233 |
|
2003-03-25 09:29 mmeineke |
3245 |
|
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
3246 |
|
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
3247 |
|
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
3248 |
< |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
3249 |
< |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
3250 |
< |
samples |
3248 |
> |
lipid/lipid.mdl, lipid/water.mdl, minimizer/argon/Makefile, |
3249 |
> |
minimizer/argon/argon.bass, minimizer/argon/init_argon.eor, |
3250 |
> |
minimizer/argon/lj.mdl, water/Makefile, water/init_ssd.eor, |
3251 |
> |
water/ssd.bass, water/water.mdl: moved tests to samples |
3252 |
|
|
3253 |
|
2003-03-24 19:51 gezelter |
3254 |
|
|