1 |
+ |
2004-05-11 11:00 gezelter |
2 |
+ |
|
3 |
+ |
* libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
4 |
+ |
fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to |
5 |
+ |
use the simplified cutoff stuff in the BASS library |
6 |
+ |
|
7 |
+ |
2004-05-10 23:21 gezelter |
8 |
+ |
|
9 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, |
10 |
+ |
CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, |
11 |
+ |
Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
12 |
+ |
MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c, |
13 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
14 |
+ |
parse_tree.c: BASS changes for adding CutoffGroups to molecules. |
15 |
+ |
Also restructured the plethora of cutoff radii into one |
16 |
+ |
cutoffRadius and one switchingRadius. Also removed the |
17 |
+ |
useMolecularCutoffs keyword |
18 |
+ |
|
19 |
+ |
2004-05-10 15:28 tim |
20 |
+ |
|
21 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize |
22 |
+ |
DumpWriter |
23 |
+ |
|
24 |
+ |
2004-05-07 16:36 gezelter |
25 |
+ |
|
26 |
+ |
* libmdtools/: fSwitchingFunction.h, switch_module.F90: New module |
27 |
+ |
for fortran group-based switching function |
28 |
+ |
|
29 |
+ |
2004-05-07 16:35 gezelter |
30 |
+ |
|
31 |
+ |
* libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, |
32 |
+ |
Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, |
33 |
+ |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
34 |
+ |
calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, |
35 |
+ |
force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, |
36 |
+ |
mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, |
37 |
+ |
simulation_module.F90: Many changes to get group-based cutoffs to |
38 |
+ |
work |
39 |
+ |
|
40 |
+ |
2004-05-01 13:52 tim |
41 |
+ |
|
42 |
+ |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
43 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, |
44 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, |
45 |
+ |
libmdtools/do_Forces.F90, libmdtools/fSimulation.h, |
46 |
+ |
libmdtools/fortranWrapDefines.hpp, |
47 |
+ |
libmdtools/simulation_module.F90: C++ pass groupList to fortran |
48 |
+ |
|
49 |
+ |
2004-04-29 11:03 tim |
50 |
+ |
|
51 |
+ |
* ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in |
52 |
+ |
calc_charge_charge when using molecular cutoff |
53 |
+ |
|
54 |
+ |
2004-04-28 21:11 tim |
55 |
+ |
|
56 |
+ |
* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
57 |
+ |
unmatched c/fortran interface |
58 |
+ |
|
59 |
+ |
2004-04-28 18:09 tim |
60 |
+ |
|
61 |
+ |
* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
62 |
+ |
keep the previous position of cantilever in SMD |
63 |
+ |
|
64 |
+ |
2004-04-28 17:34 tim |
65 |
+ |
|
66 |
+ |
* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
67 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
68 |
+ |
in Molecule.cpp which initialize massRatio before creat the array. |
69 |
+ |
fix two bugs in ZconsVisitor |
70 |
+ |
|
71 |
+ |
2004-04-28 17:06 gezelter |
72 |
+ |
|
73 |
+ |
* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
74 |
+ |
Adding molecular cutoffs |
75 |
+ |
|
76 |
+ |
2004-04-28 16:39 gezelter |
77 |
+ |
|
78 |
+ |
* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
79 |
+ |
fSimulation.h, force_globals.F90, simulation_module.F90: work on |
80 |
+ |
molecular cutoffs |
81 |
+ |
|
82 |
+ |
2004-04-28 16:39 gezelter |
83 |
+ |
|
84 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
85 |
+ |
Globals |
86 |
+ |
|
87 |
+ |
2004-04-27 11:26 tim |
88 |
+ |
|
89 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
90 |
+ |
ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
91 |
+ |
fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
92 |
+ |
molecule and massRation into atom class |
93 |
+ |
|
94 |
+ |
2004-04-26 16:16 mmeineke |
95 |
+ |
|
96 |
+ |
* libBASS/Globals.cpp: modified the defaults for the system init |
97 |
+ |
time and system init state. |
98 |
+ |
|
99 |
+ |
2004-04-26 09:29 gezelter |
100 |
+ |
|
101 |
+ |
* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
102 |
+ |
calc_charge_charge.F90 |
103 |
+ |
|
104 |
+ |
2004-04-23 23:31 tim |
105 |
+ |
|
106 |
+ |
* ChangeLog, libmdtools/AtomVisitor.cpp, |
107 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
108 |
+ |
reaction field correction to charge-charge interaction |
109 |
+ |
|
110 |
+ |
2004-04-22 16:33 tim |
111 |
+ |
|
112 |
+ |
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
113 |
+ |
Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
114 |
+ |
calculation of pressure tensor |
115 |
+ |
|
116 |
+ |
2004-04-22 09:55 tim |
117 |
+ |
|
118 |
+ |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
119 |
+ |
another bug in InitFromFile. MPI verion of OOPSE is working again |
120 |
+ |
|
121 |
+ |
2004-04-21 22:29 tim |
122 |
+ |
|
123 |
+ |
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
124 |
+ |
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
125 |
+ |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
126 |
+ |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
127 |
+ |
DumpWriter |
128 |
+ |
|
129 |
+ |
2004-04-21 00:32 tim |
130 |
+ |
|
131 |
+ |
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
132 |
+ |
libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
133 |
+ |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
134 |
+ |
useless files |
135 |
+ |
|
136 |
+ |
2004-04-20 11:56 tim |
137 |
+ |
|
138 |
+ |
* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
139 |
+ |
SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
140 |
+ |
velocitize at thermo |
141 |
+ |
|
142 |
+ |
2004-04-20 00:39 tim |
143 |
+ |
|
144 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
145 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
146 |
+ |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
147 |
+ |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
148 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
149 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
150 |
+ |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
151 |
+ |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
152 |
+ |
|
153 |
+ |
2004-04-19 17:13 gezelter |
154 |
+ |
|
155 |
+ |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
156 |
+ |
Thermo.cpp: Fixed a charge bug |
157 |
+ |
|
158 |
+ |
2004-04-19 15:54 tim |
159 |
+ |
|
160 |
+ |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
161 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
162 |
+ |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
163 |
+ |
a bug in CompositeVisitor which cause the double counting problem |
164 |
+ |
|
165 |
+ |
2004-04-19 12:44 tim |
166 |
+ |
|
167 |
+ |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
168 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
169 |
+ |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
170 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
171 |
+ |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
172 |
+ |
Dump2XYZ is almost working except atoms in rigidbody are double |
173 |
+ |
counted |
174 |
+ |
|
175 |
+ |
2004-04-18 22:52 tim |
176 |
+ |
|
177 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
178 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
179 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
180 |
+ |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
181 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
182 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
183 |
+ |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
184 |
+ |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
185 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
186 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
187 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
188 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
189 |
+ |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
190 |
+ |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
191 |
+ |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
192 |
+ |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
193 |
+ |
implement of quickLate using visitor and composite pattern |
194 |
+ |
|
195 |
+ |
2004-04-15 17:15 tim |
196 |
+ |
|
197 |
+ |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
198 |
+ |
exclude list |
199 |
+ |
|
200 |
+ |
2004-04-15 11:18 tim |
201 |
+ |
|
202 |
+ |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
203 |
+ |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
204 |
+ |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
205 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
206 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
207 |
+ |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
208 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
209 |
+ |
whole bunch of bugs :-) |
210 |
+ |
|
211 |
+ |
2004-04-14 12:20 chrisfen |
212 |
+ |
|
213 |
+ |
* forceFields/WATER.frc: Added the WATER.frc force field |
214 |
+ |
|
215 |
+ |
2004-04-14 11:32 gezelter |
216 |
+ |
|
217 |
+ |
* libmdtools/Molecule.cpp: fixed for get_potential |
218 |
+ |
|
219 |
+ |
2004-04-14 10:37 tim |
220 |
+ |
|
221 |
+ |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
222 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
223 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
224 |
+ |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
225 |
+ |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
226 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
227 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
228 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
229 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
230 |
+ |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
231 |
+ |
Change DumpWriter and InitFromFile |
232 |
+ |
|
233 |
+ |
2004-04-13 11:26 gezelter |
234 |
+ |
|
235 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
236 |
+ |
molecules can keep track of their own IntegrableObjects (and |
237 |
+ |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
238 |
+ |
RigidBodies (which was done incorrectly before). |
239 |
+ |
|
240 |
+ |
2004-04-13 11:25 gezelter |
241 |
+ |
|
242 |
+ |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
243 |
+ |
(will back out momentarily) |
244 |
+ |
|
245 |
+ |
2004-04-13 10:10 gezelter |
246 |
+ |
|
247 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
248 |
+ |
Those were old. |
249 |
+ |
|
250 |
+ |
2004-04-13 10:09 gezelter |
251 |
+ |
|
252 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
253 |
+ |
to add IntegrableObjects |
254 |
+ |
|
255 |
+ |
2004-04-12 16:02 gezelter |
256 |
+ |
|
257 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
258 |
+ |
|
259 |
+ |
2004-04-12 15:32 gezelter |
260 |
+ |
|
261 |
+ |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
262 |
+ |
test run |
263 |
+ |
|
264 |
+ |
2004-04-12 15:32 gezelter |
265 |
+ |
|
266 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
267 |
+ |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
268 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
269 |
+ |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
270 |
+ |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
271 |
+ |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
272 |
+ |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
273 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
274 |
+ |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
275 |
+ |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
276 |
+ |
(Somewhat extensive) |
277 |
+ |
|
278 |
+ |
2004-04-12 15:31 gezelter |
279 |
+ |
|
280 |
+ |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
281 |
+ |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
282 |
+ |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
283 |
+ |
Changes for RigidBody dynamics |
284 |
+ |
|
285 |
+ |
2004-03-17 09:22 tim |
286 |
+ |
|
287 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
288 |
+ |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
289 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
290 |
+ |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
291 |
+ |
does not sound a good choice, next commit will seperate SMD and |
292 |
+ |
ZConstraint |
293 |
+ |
|
294 |
+ |
2004-03-16 14:22 tim |
295 |
+ |
|
296 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
297 |
+ |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
298 |
+ |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
299 |
+ |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
300 |
+ |
now can support sequential moving. Refactorying is needed to |
301 |
+ |
support SMD in ZConstraint |
302 |
+ |
|
303 |
+ |
2004-03-02 15:32 tim |
304 |
+ |
|
305 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
306 |
+ |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
307 |
+ |
support large file |
308 |
+ |
|
309 |
+ |
2004-03-01 16:17 tim |
310 |
+ |
|
311 |
+ |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
312 |
+ |
|
313 |
+ |
2004-03-01 15:01 tim |
314 |
+ |
|
315 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
316 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
317 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
318 |
+ |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
319 |
+ |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
320 |
+ |
program which can be used to replace atom type for zconstraint into |
321 |
+ |
OOPSE |
322 |
+ |
|
323 |
+ |
2004-02-24 11:36 tim |
324 |
+ |
|
325 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
326 |
+ |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
327 |
+ |
message] |
328 |
+ |
|
329 |
+ |
2004-02-24 10:49 tim |
330 |
+ |
|
331 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
332 |
+ |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
333 |
+ |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
334 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
335 |
+ |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
336 |
+ |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
337 |
+ |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
338 |
+ |
|
339 |
+ |
2004-02-24 10:44 tim |
340 |
+ |
|
341 |
+ |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
342 |
+ |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
343 |
+ |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
344 |
+ |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
345 |
+ |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
346 |
+ |
compose to implement Minimizer both versions are working |
347 |
+ |
|
348 |
+ |
2004-02-17 14:23 tim |
349 |
+ |
|
350 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
351 |
+ |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
352 |
+ |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
353 |
+ |
libmdtools/MinimizerParameterSet.hpp, |
354 |
+ |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
355 |
+ |
to remove the constraint force along bond direction |
356 |
+ |
|
357 |
+ |
2004-02-10 16:33 tim |
358 |
+ |
|
359 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
360 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
361 |
+ |
single version of energy minimization is working. |
362 |
+ |
|
363 |
+ |
2004-02-09 15:38 mmeineke |
364 |
+ |
|
365 |
+ |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
366 |
+ |
the massive memory overusage by OOPSE |
367 |
+ |
|
368 |
+ |
2004-02-09 09:48 chrisfen |
369 |
+ |
|
370 |
+ |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
371 |
+ |
hardwired LJ_rcut |
372 |
+ |
|
373 |
+ |
2004-02-06 19:14 tim |
374 |
+ |
|
375 |
+ |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
376 |
+ |
message] |
377 |
+ |
|
378 |
+ |
2004-02-06 16:37 tim |
379 |
+ |
|
380 |
+ |
* ChangeLog, libBASS/Globals.cpp, |
381 |
+ |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
382 |
+ |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
383 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
384 |
+ |
energy minimization for argon is working, need to add constraint |
385 |
+ |
|
386 |
+ |
2004-02-06 14:05 tim |
387 |
+ |
|
388 |
+ |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
389 |
+ |
one more file into Makefile.in |
390 |
+ |
|
391 |
+ |
2004-02-06 13:58 tim |
392 |
+ |
|
393 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
394 |
+ |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
395 |
+ |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
396 |
+ |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
397 |
+ |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
398 |
+ |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
399 |
+ |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
400 |
+ |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
401 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
402 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
403 |
+ |
some lines into global.cpp to make it work with energy minimization |
404 |
+ |
|
405 |
+ |
2004-02-04 17:26 tim |
406 |
+ |
|
407 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
408 |
+ |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
409 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
410 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
411 |
+ |
Single version of conjugate gradient with golden search linesearch |
412 |
+ |
pass a couple of functions test. Brent's algorithm is still broken |
413 |
+ |
|
414 |
+ |
2004-02-03 17:54 tim |
415 |
+ |
|
416 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
417 |
+ |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
418 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
419 |
+ |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
420 |
+ |
|
421 |
+ |
2004-02-03 15:47 tim |
422 |
+ |
|
423 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
424 |
+ |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
425 |
+ |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
426 |
+ |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
427 |
+ |
SteepestDescent.hpp: [no log message] |
428 |
+ |
|
429 |
+ |
2004-02-03 15:43 tim |
430 |
+ |
|
431 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
432 |
+ |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
433 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
434 |
+ |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
435 |
+ |
constraint class |
436 |
+ |
|
437 |
+ |
2004-02-03 12:10 tim |
438 |
+ |
|
439 |
+ |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
440 |
+ |
|
441 |
+ |
2004-02-03 10:21 tim |
442 |
+ |
|
443 |
+ |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
444 |
+ |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
445 |
+ |
|
446 |
+ |
2004-02-02 15:29 tim |
447 |
+ |
|
448 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
449 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
450 |
+ |
Adding GoldenSection and Brent LineSearch Method |
451 |
+ |
|
452 |
+ |
2004-01-30 16:47 tim |
453 |
+ |
|
454 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
455 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
456 |
+ |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
457 |
+ |
MinimizerBase instead of a functor to do line seach |
458 |
+ |
|
459 |
+ |
2004-01-30 10:00 chrisfen |
460 |
+ |
|
461 |
+ |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
462 |
+ |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
463 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
464 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
465 |
+ |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
466 |
+ |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
467 |
+ |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
468 |
+ |
has a working WATER.cpp forcefield and parser. This involved |
469 |
+ |
changes to WATER.cpp and ForceFields amoung other files. One |
470 |
+ |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
471 |
+ |
This will be removed on the next commit... |
472 |
+ |
|
473 |
+ |
2004-01-29 18:00 gezelter |
474 |
+ |
|
475 |
+ |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
476 |
+ |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
477 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
478 |
+ |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
479 |
+ |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
480 |
+ |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
481 |
+ |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
482 |
+ |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
483 |
+ |
member list fixes for rigid bodies |
484 |
+ |
|
485 |
+ |
2004-01-29 16:44 tim |
486 |
+ |
|
487 |
+ |
* libmdtools/MinimizerParameterSet.hpp: Adding |
488 |
+ |
MinimizerParameterSet class. |
489 |
+ |
|
490 |
+ |
2004-01-28 17:44 tim |
491 |
+ |
|
492 |
+ |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
493 |
+ |
NLModel0 and NLModel1 |
494 |
+ |
|
495 |
+ |
2004-01-28 15:40 tim |
496 |
+ |
|
497 |
+ |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
498 |
+ |
of NLModel |
499 |
+ |
|
500 |
+ |
2004-01-27 15:34 gezelter |
501 |
+ |
|
502 |
+ |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
503 |
+ |
water.mdl file, updated ssd.bass to use new SSD name |
504 |
+ |
|
505 |
+ |
2004-01-27 15:34 gezelter |
506 |
+ |
|
507 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
508 |
+ |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
509 |
+ |
stuff |
510 |
+ |
|
511 |
+ |
2004-01-27 14:39 gezelter |
512 |
+ |
|
513 |
+ |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
514 |
+ |
|
515 |
+ |
2004-01-27 14:39 gezelter |
516 |
+ |
|
517 |
+ |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
518 |
+ |
|
519 |
+ |
2004-01-27 14:38 gezelter |
520 |
+ |
|
521 |
+ |
* samples/argon/argon.bass: Longer run time to test argon |
522 |
+ |
|
523 |
+ |
2004-01-27 14:38 gezelter |
524 |
+ |
|
525 |
+ |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
526 |
+ |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
527 |
+ |
morning |
528 |
+ |
|
529 |
+ |
2004-01-27 14:37 gezelter |
530 |
+ |
|
531 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
532 |
+ |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
533 |
+ |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
534 |
+ |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
535 |
+ |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
536 |
+ |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
537 |
+ |
do new rigidBody scheme |
538 |
+ |
|
539 |
+ |
2004-01-27 14:15 tim |
540 |
+ |
|
541 |
+ |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
542 |
+ |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
543 |
+ |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
544 |
+ |
constraint for Nonlinear Optimization Model |
545 |
+ |
|
546 |
+ |
2004-01-26 17:01 gezelter |
547 |
+ |
|
548 |
+ |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
549 |
+ |
Euler angles for orientation instead of unit vectors required |
550 |
+ |
changes in MoLocator |
551 |
+ |
|
552 |
+ |
2004-01-26 16:53 gezelter |
553 |
+ |
|
554 |
+ |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
555 |
+ |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
556 |
+ |
water/water.mdl: Changed orientation lines from unit vectors to |
557 |
+ |
euler angles |
558 |
+ |
|
559 |
+ |
2004-01-26 16:52 gezelter |
560 |
+ |
|
561 |
+ |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
562 |
+ |
|
563 |
+ |
2004-01-26 16:45 gezelter |
564 |
+ |
|
565 |
+ |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
566 |
+ |
use Euler angles in the following order: phi, theta, psi Removed |
567 |
+ |
the ability to set orientation using a unit vector |
568 |
+ |
|
569 |
+ |
2004-01-26 16:26 gezelter |
570 |
+ |
|
571 |
+ |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
572 |
+ |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
573 |
+ |
Euler angles in the following order: phi, theta, psi Removed the |
574 |
+ |
ability to set orientation using a unit vector |
575 |
+ |
|
576 |
+ |
2004-01-26 13:52 gezelter |
577 |
+ |
|
578 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
579 |
+ |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
580 |
+ |
|
581 |
+ |
2004-01-22 12:34 chrisfen |
582 |
+ |
|
583 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
584 |
+ |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
585 |
+ |
Corrected spelling in several directories, and stated WATER.cpp |
586 |
+ |
|
587 |
+ |
2004-01-21 17:16 tim |
588 |
+ |
|
589 |
+ |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
590 |
+ |
NLOPModel.hpp: constraint class in energy minimization |
591 |
+ |
|
592 |
+ |
2004-01-20 15:34 tim |
593 |
+ |
|
594 |
+ |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
595 |
+ |
|
596 |
+ |
2004-01-20 15:32 tim |
597 |
+ |
|
598 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
599 |
+ |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
600 |
+ |
|
601 |
+ |
2004-01-19 16:17 gezelter |
602 |
+ |
|
603 |
+ |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
604 |
+ |
more user-friendly |
605 |
+ |
|
606 |
+ |
2004-01-19 13:51 chrisfen |
607 |
+ |
|
608 |
+ |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
609 |
+ |
|
610 |
+ |
2004-01-19 13:36 tim |
611 |
+ |
|
612 |
+ |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
613 |
+ |
time, status time, thermal time and reset time are not divisible by |
614 |
+ |
dt |
615 |
+ |
|
616 |
+ |
2004-01-19 11:10 gezelter |
617 |
+ |
|
618 |
+ |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
619 |
+ |
won't complain |
620 |
+ |
|
621 |
+ |
2004-01-19 11:10 gezelter |
622 |
+ |
|
623 |
+ |
* samples/lipid/5x5.bass: Fixed old bass file |
624 |
+ |
|
625 |
+ |
2004-01-19 11:09 gezelter |
626 |
+ |
|
627 |
+ |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
628 |
+ |
required a change in how the MoleculeStamps are used by divideLabor |
629 |
+ |
in mpiSimulation.cpp |
630 |
+ |
|
631 |
+ |
2004-01-19 11:08 gezelter |
632 |
+ |
|
633 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
634 |
+ |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
635 |
+ |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
636 |
+ |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
637 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
638 |
+ |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
639 |
+ |
|
640 |
+ |
2004-01-16 16:55 tim |
641 |
+ |
|
642 |
+ |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
643 |
+ |
eor file |
644 |
+ |
|
645 |
+ |
2004-01-16 16:51 mmeineke |
646 |
+ |
|
647 |
+ |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
648 |
+ |
write eor files |
649 |
+ |
|
650 |
+ |
2004-01-16 10:01 mmeineke |
651 |
+ |
|
652 |
+ |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
653 |
+ |
initialization of the AtomStruct |
654 |
+ |
|
655 |
+ |
2004-01-15 16:57 chuckv |
656 |
+ |
|
657 |
+ |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
658 |
+ |
|
659 |
+ |
2004-01-15 10:51 gezelter |
660 |
+ |
|
661 |
+ |
* ac-tools/aclocal.m4: Changes for altivec |
662 |
+ |
|
663 |
+ |
2004-01-15 09:22 gezelter |
664 |
+ |
|
665 |
+ |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
666 |
+ |
|
667 |
+ |
2004-01-14 23:33 gezelter |
668 |
+ |
|
669 |
+ |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
670 |
+ |
|
671 |
+ |
2004-01-14 20:14 gezelter |
672 |
+ |
|
673 |
+ |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
674 |
+ |
notifyCutoffs.F90: More work for adding charges |
675 |
+ |
|
676 |
+ |
2004-01-14 17:41 gezelter |
677 |
+ |
|
678 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
679 |
+ |
src/Makefile.in: autoconf fixes |
680 |
+ |
|
681 |
+ |
2004-01-14 11:28 mmeineke |
682 |
+ |
|
683 |
+ |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
684 |
+ |
|
685 |
+ |
2004-01-14 10:48 gezelter |
686 |
+ |
|
687 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
688 |
+ |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
689 |
+ |
changes for icc8 |
690 |
+ |
|
691 |
+ |
2004-01-13 18:01 gezelter |
692 |
+ |
|
693 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
694 |
+ |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
695 |
+ |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
696 |
+ |
Changes for adding direct charge-charge interactions (with |
697 |
+ |
switching function) |
698 |
+ |
|
699 |
+ |
2004-01-13 17:34 gezelter |
700 |
+ |
|
701 |
+ |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
702 |
+ |
oopseMPI_module.F90: Some changes for new MPI organization and |
703 |
+ |
direct charge-charge interactions |
704 |
+ |
|
705 |
+ |
2004-01-13 17:11 tim |
706 |
+ |
|
707 |
+ |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
708 |
+ |
|
709 |
+ |
2004-01-13 16:22 tim |
710 |
+ |
|
711 |
+ |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
712 |
+ |
|
713 |
+ |
2004-01-13 15:35 tim |
714 |
+ |
|
715 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
716 |
+ |
eor file whenever it is used instead of rewinding it |
717 |
+ |
|
718 |
+ |
2004-01-13 15:04 tim |
719 |
+ |
|
720 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
721 |
+ |
of writeFrame |
722 |
+ |
|
723 |
+ |
2004-01-13 10:46 tim |
724 |
+ |
|
725 |
+ |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
726 |
+ |
Merge the code of writeFinal and writeDump; |
727 |
+ |
Adding sortingIndex into DumpWriter; |
728 |
+ |
Fix a bug of writing last frame twice in integrator |
729 |
+ |
|
730 |
+ |
2004-01-12 17:54 tim |
731 |
+ |
|
732 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
733 |
+ |
a bug in copying string |
734 |
+ |
|
735 |
+ |
2004-01-12 15:37 tim |
736 |
+ |
|
737 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
738 |
+ |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
739 |
+ |
master nodes |
740 |
+ |
|
741 |
+ |
2004-01-10 04:46 tim |
742 |
+ |
|
743 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
744 |
+ |
roll it back fix a bug of copying string to a pointer Still have |
745 |
+ |
Seg fault, it looks like a random MPI seg fault in totalview |
746 |
+ |
|
747 |
+ |
2004-01-09 21:15 tim |
748 |
+ |
|
749 |
+ |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
750 |
+ |
|
751 |
+ |
2004-01-09 15:29 gezelter |
752 |
+ |
|
753 |
+ |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
754 |
+ |
|
755 |
+ |
2004-01-08 17:25 chuckv |
756 |
+ |
|
757 |
+ |
* libmdtools/DumpWriter.cpp: A work in progress... |
758 |
+ |
|
759 |
+ |
2004-01-08 13:59 gezelter |
760 |
+ |
|
761 |
+ |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
762 |
+ |
case |
763 |
+ |
|
764 |
+ |
2004-01-08 13:13 mmeineke |
765 |
+ |
|
766 |
+ |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
767 |
+ |
state bug. |
768 |
+ |
|
769 |
+ |
2004-01-08 13:05 gezelter |
770 |
+ |
|
771 |
+ |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
772 |
+ |
|
773 |
+ |
2004-01-08 12:57 mmeineke |
774 |
+ |
|
775 |
+ |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
776 |
+ |
exstended state bug |
777 |
+ |
|
778 |
+ |
2004-01-08 12:40 gezelter |
779 |
+ |
|
780 |
+ |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
781 |
+ |
|
782 |
+ |
2004-01-08 10:44 mmeineke |
783 |
+ |
|
784 |
+ |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
785 |
+ |
XS state info flag |
786 |
+ |
|
787 |
+ |
2004-01-07 14:26 tim |
788 |
+ |
|
789 |
+ |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
790 |
+ |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
791 |
+ |
sending message from master node to itself in DumpWriter.cpp and |
792 |
+ |
InitializeFromFile.cpp |
793 |
+ |
|
794 |
+ |
2004-01-06 14:49 chuckv |
795 |
+ |
|
796 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
797 |
+ |
performance fixes in the dipole dipole and reaction field code |
798 |
+ |
|
799 |
+ |
2004-01-06 13:54 chuckv |
800 |
+ |
|
801 |
+ |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
802 |
+ |
little more sane |
803 |
+ |
|
804 |
+ |
2004-01-05 17:49 chuckv |
805 |
+ |
|
806 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
807 |
+ |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
808 |
+ |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
809 |
+ |
performance by reducing spurious function calls |
810 |
+ |
|
811 |
+ |
2004-01-05 17:18 chuckv |
812 |
+ |
|
813 |
+ |
* libmdtools/do_Forces.F90: mangling forces even further |
814 |
+ |
|
815 |
+ |
2004-01-05 17:18 chuckv |
816 |
+ |
|
817 |
+ |
* configure, ac-tools/configure.in: mpich mucking |
818 |
+ |
|
819 |
+ |
2004-01-05 17:12 chuckv |
820 |
+ |
|
821 |
+ |
* libmdtools/do_Forces.F90: mangled do_forces... |
822 |
+ |
|
823 |
+ |
2004-01-05 16:00 chuckv |
824 |
+ |
|
825 |
+ |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
826 |
+ |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
827 |
+ |
lookup |
828 |
+ |
|
829 |
|
2003-12-29 14:56 chuckv |
830 |
|
|
831 |
|
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
3006 |
|
|
3007 |
|
2003-03-25 09:29 mmeineke |
3008 |
|
|
3009 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
3009 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
3010 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
3011 |
|
|
3012 |
|
2003-03-25 09:29 mmeineke |