1 |
+ |
2004-04-27 11:26 tim |
2 |
+ |
|
3 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
4 |
+ |
ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
5 |
+ |
fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
6 |
+ |
molecule and massRation into atom class |
7 |
+ |
|
8 |
+ |
2004-04-26 16:16 mmeineke |
9 |
+ |
|
10 |
+ |
* libBASS/Globals.cpp: modified the defaults for the system init |
11 |
+ |
time and system init state. |
12 |
+ |
|
13 |
+ |
2004-04-26 09:29 gezelter |
14 |
+ |
|
15 |
+ |
* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
16 |
+ |
calc_charge_charge.F90 |
17 |
+ |
|
18 |
+ |
2004-04-23 23:31 tim |
19 |
+ |
|
20 |
+ |
* ChangeLog, libmdtools/AtomVisitor.cpp, |
21 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
22 |
+ |
reaction field correction to charge-charge interaction |
23 |
+ |
|
24 |
+ |
2004-04-22 16:33 tim |
25 |
+ |
|
26 |
+ |
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
27 |
+ |
Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
28 |
+ |
calculation of pressure tensor |
29 |
+ |
|
30 |
+ |
2004-04-22 09:55 tim |
31 |
+ |
|
32 |
+ |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
33 |
+ |
another bug in InitFromFile. MPI verion of OOPSE is working again |
34 |
+ |
|
35 |
+ |
2004-04-21 22:29 tim |
36 |
+ |
|
37 |
+ |
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
38 |
+ |
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
39 |
+ |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
40 |
+ |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
41 |
+ |
DumpWriter |
42 |
+ |
|
43 |
+ |
2004-04-21 00:32 tim |
44 |
+ |
|
45 |
+ |
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
46 |
+ |
libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
47 |
+ |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
48 |
+ |
useless files |
49 |
+ |
|
50 |
+ |
2004-04-20 11:56 tim |
51 |
+ |
|
52 |
+ |
* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
53 |
+ |
SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
54 |
+ |
velocitize at thermo |
55 |
+ |
|
56 |
+ |
2004-04-20 00:39 tim |
57 |
+ |
|
58 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
59 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
60 |
+ |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
61 |
+ |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
62 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
63 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
64 |
+ |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
65 |
+ |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
66 |
+ |
|
67 |
+ |
2004-04-19 17:13 gezelter |
68 |
+ |
|
69 |
+ |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
70 |
+ |
Thermo.cpp: Fixed a charge bug |
71 |
+ |
|
72 |
+ |
2004-04-19 15:54 tim |
73 |
+ |
|
74 |
+ |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
75 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
76 |
+ |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
77 |
+ |
a bug in CompositeVisitor which cause the double counting problem |
78 |
+ |
|
79 |
+ |
2004-04-19 12:44 tim |
80 |
+ |
|
81 |
+ |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
82 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
83 |
+ |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
84 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
85 |
+ |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
86 |
+ |
Dump2XYZ is almost working except atoms in rigidbody are double |
87 |
+ |
counted |
88 |
+ |
|
89 |
+ |
2004-04-18 22:52 tim |
90 |
+ |
|
91 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
92 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
93 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
94 |
+ |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
95 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
96 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
97 |
+ |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
98 |
+ |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
99 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
100 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
101 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
102 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
103 |
+ |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
104 |
+ |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
105 |
+ |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
106 |
+ |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
107 |
+ |
implement of quickLate using visitor and composite pattern |
108 |
+ |
|
109 |
+ |
2004-04-15 17:15 tim |
110 |
+ |
|
111 |
+ |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
112 |
+ |
exclude list |
113 |
+ |
|
114 |
+ |
2004-04-15 11:18 tim |
115 |
+ |
|
116 |
+ |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
117 |
+ |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
118 |
+ |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
119 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
120 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
121 |
+ |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
122 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
123 |
+ |
whole bunch of bugs :-) |
124 |
+ |
|
125 |
+ |
2004-04-14 12:20 chrisfen |
126 |
+ |
|
127 |
+ |
* forceFields/WATER.frc: Added the WATER.frc force field |
128 |
+ |
|
129 |
+ |
2004-04-14 11:32 gezelter |
130 |
+ |
|
131 |
+ |
* libmdtools/Molecule.cpp: fixed for get_potential |
132 |
+ |
|
133 |
+ |
2004-04-14 10:37 tim |
134 |
+ |
|
135 |
+ |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
136 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
137 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
138 |
+ |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
139 |
+ |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
140 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
141 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
142 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
143 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
144 |
+ |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
145 |
+ |
Change DumpWriter and InitFromFile |
146 |
+ |
|
147 |
+ |
2004-04-13 11:26 gezelter |
148 |
+ |
|
149 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
150 |
+ |
molecules can keep track of their own IntegrableObjects (and |
151 |
+ |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
152 |
+ |
RigidBodies (which was done incorrectly before). |
153 |
+ |
|
154 |
+ |
2004-04-13 11:25 gezelter |
155 |
+ |
|
156 |
+ |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
157 |
+ |
(will back out momentarily) |
158 |
+ |
|
159 |
+ |
2004-04-13 10:10 gezelter |
160 |
+ |
|
161 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
162 |
+ |
Those were old. |
163 |
+ |
|
164 |
+ |
2004-04-13 10:09 gezelter |
165 |
+ |
|
166 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
167 |
+ |
to add IntegrableObjects |
168 |
+ |
|
169 |
+ |
2004-04-12 16:02 gezelter |
170 |
+ |
|
171 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
172 |
+ |
|
173 |
+ |
2004-04-12 15:32 gezelter |
174 |
+ |
|
175 |
+ |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
176 |
+ |
test run |
177 |
+ |
|
178 |
+ |
2004-04-12 15:32 gezelter |
179 |
+ |
|
180 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
181 |
+ |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
182 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
183 |
+ |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
184 |
+ |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
185 |
+ |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
186 |
+ |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
187 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
188 |
+ |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
189 |
+ |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
190 |
+ |
(Somewhat extensive) |
191 |
+ |
|
192 |
+ |
2004-04-12 15:31 gezelter |
193 |
+ |
|
194 |
+ |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
195 |
+ |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
196 |
+ |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
197 |
+ |
Changes for RigidBody dynamics |
198 |
+ |
|
199 |
+ |
2004-03-17 09:22 tim |
200 |
+ |
|
201 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
202 |
+ |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
203 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
204 |
+ |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
205 |
+ |
does not sound a good choice, next commit will seperate SMD and |
206 |
+ |
ZConstraint |
207 |
+ |
|
208 |
+ |
2004-03-16 14:22 tim |
209 |
+ |
|
210 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
211 |
+ |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
212 |
+ |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
213 |
+ |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
214 |
+ |
now can support sequential moving. Refactorying is needed to |
215 |
+ |
support SMD in ZConstraint |
216 |
+ |
|
217 |
+ |
2004-03-02 15:32 tim |
218 |
+ |
|
219 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
220 |
+ |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
221 |
+ |
support large file |
222 |
+ |
|
223 |
+ |
2004-03-01 16:17 tim |
224 |
+ |
|
225 |
+ |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
226 |
+ |
|
227 |
+ |
2004-03-01 15:01 tim |
228 |
+ |
|
229 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
230 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
231 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
232 |
+ |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
233 |
+ |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
234 |
+ |
program which can be used to replace atom type for zconstraint into |
235 |
+ |
OOPSE |
236 |
+ |
|
237 |
+ |
2004-02-24 11:36 tim |
238 |
+ |
|
239 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
240 |
+ |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
241 |
+ |
message] |
242 |
+ |
|
243 |
+ |
2004-02-24 10:49 tim |
244 |
+ |
|
245 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
246 |
+ |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
247 |
+ |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
248 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
249 |
+ |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
250 |
+ |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
251 |
+ |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
252 |
+ |
|
253 |
+ |
2004-02-24 10:44 tim |
254 |
+ |
|
255 |
+ |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
256 |
+ |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
257 |
+ |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
258 |
+ |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
259 |
+ |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
260 |
+ |
compose to implement Minimizer both versions are working |
261 |
+ |
|
262 |
+ |
2004-02-17 14:23 tim |
263 |
+ |
|
264 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
265 |
+ |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
266 |
+ |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
267 |
+ |
libmdtools/MinimizerParameterSet.hpp, |
268 |
+ |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
269 |
+ |
to remove the constraint force along bond direction |
270 |
+ |
|
271 |
+ |
2004-02-10 16:33 tim |
272 |
+ |
|
273 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
274 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
275 |
+ |
single version of energy minimization is working. |
276 |
+ |
|
277 |
+ |
2004-02-09 15:38 mmeineke |
278 |
+ |
|
279 |
+ |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
280 |
+ |
the massive memory overusage by OOPSE |
281 |
+ |
|
282 |
+ |
2004-02-09 09:48 chrisfen |
283 |
+ |
|
284 |
+ |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
285 |
+ |
hardwired LJ_rcut |
286 |
+ |
|
287 |
+ |
2004-02-06 19:14 tim |
288 |
+ |
|
289 |
+ |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
290 |
+ |
message] |
291 |
+ |
|
292 |
+ |
2004-02-06 16:37 tim |
293 |
+ |
|
294 |
+ |
* ChangeLog, libBASS/Globals.cpp, |
295 |
+ |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
296 |
+ |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
297 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
298 |
+ |
energy minimization for argon is working, need to add constraint |
299 |
+ |
|
300 |
+ |
2004-02-06 14:05 tim |
301 |
+ |
|
302 |
+ |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
303 |
+ |
one more file into Makefile.in |
304 |
+ |
|
305 |
+ |
2004-02-06 13:58 tim |
306 |
+ |
|
307 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
308 |
+ |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
309 |
+ |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
310 |
+ |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
311 |
+ |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
312 |
+ |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
313 |
+ |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
314 |
+ |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
315 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
316 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
317 |
+ |
some lines into global.cpp to make it work with energy minimization |
318 |
+ |
|
319 |
+ |
2004-02-04 17:26 tim |
320 |
+ |
|
321 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
322 |
+ |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
323 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
324 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
325 |
+ |
Single version of conjugate gradient with golden search linesearch |
326 |
+ |
pass a couple of functions test. Brent's algorithm is still broken |
327 |
+ |
|
328 |
+ |
2004-02-03 17:54 tim |
329 |
+ |
|
330 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
331 |
+ |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
332 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
333 |
+ |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
334 |
+ |
|
335 |
+ |
2004-02-03 15:47 tim |
336 |
+ |
|
337 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
338 |
+ |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
339 |
+ |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
340 |
+ |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
341 |
+ |
SteepestDescent.hpp: [no log message] |
342 |
+ |
|
343 |
+ |
2004-02-03 15:43 tim |
344 |
+ |
|
345 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
346 |
+ |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
347 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
348 |
+ |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
349 |
+ |
constraint class |
350 |
+ |
|
351 |
+ |
2004-02-03 12:10 tim |
352 |
+ |
|
353 |
+ |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
354 |
+ |
|
355 |
+ |
2004-02-03 10:21 tim |
356 |
+ |
|
357 |
+ |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
358 |
+ |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
359 |
+ |
|
360 |
+ |
2004-02-02 15:29 tim |
361 |
+ |
|
362 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
363 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
364 |
+ |
Adding GoldenSection and Brent LineSearch Method |
365 |
+ |
|
366 |
+ |
2004-01-30 16:47 tim |
367 |
+ |
|
368 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
369 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
370 |
+ |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
371 |
+ |
MinimizerBase instead of a functor to do line seach |
372 |
+ |
|
373 |
+ |
2004-01-30 10:00 chrisfen |
374 |
+ |
|
375 |
+ |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
376 |
+ |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
377 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
378 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
379 |
+ |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
380 |
+ |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
381 |
+ |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
382 |
+ |
has a working WATER.cpp forcefield and parser. This involved |
383 |
+ |
changes to WATER.cpp and ForceFields amoung other files. One |
384 |
+ |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
385 |
+ |
This will be removed on the next commit... |
386 |
+ |
|
387 |
+ |
2004-01-29 18:00 gezelter |
388 |
+ |
|
389 |
+ |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
390 |
+ |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
391 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
392 |
+ |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
393 |
+ |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
394 |
+ |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
395 |
+ |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
396 |
+ |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
397 |
+ |
member list fixes for rigid bodies |
398 |
+ |
|
399 |
+ |
2004-01-29 16:44 tim |
400 |
+ |
|
401 |
+ |
* libmdtools/MinimizerParameterSet.hpp: Adding |
402 |
+ |
MinimizerParameterSet class. |
403 |
+ |
|
404 |
+ |
2004-01-28 17:44 tim |
405 |
+ |
|
406 |
+ |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
407 |
+ |
NLModel0 and NLModel1 |
408 |
+ |
|
409 |
+ |
2004-01-28 15:40 tim |
410 |
+ |
|
411 |
+ |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
412 |
+ |
of NLModel |
413 |
+ |
|
414 |
+ |
2004-01-27 15:34 gezelter |
415 |
+ |
|
416 |
+ |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
417 |
+ |
water.mdl file, updated ssd.bass to use new SSD name |
418 |
+ |
|
419 |
+ |
2004-01-27 15:34 gezelter |
420 |
+ |
|
421 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
422 |
+ |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
423 |
+ |
stuff |
424 |
+ |
|
425 |
+ |
2004-01-27 14:39 gezelter |
426 |
+ |
|
427 |
+ |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
428 |
+ |
|
429 |
+ |
2004-01-27 14:39 gezelter |
430 |
+ |
|
431 |
+ |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
432 |
+ |
|
433 |
+ |
2004-01-27 14:38 gezelter |
434 |
+ |
|
435 |
+ |
* samples/argon/argon.bass: Longer run time to test argon |
436 |
+ |
|
437 |
+ |
2004-01-27 14:38 gezelter |
438 |
+ |
|
439 |
+ |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
440 |
+ |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
441 |
+ |
morning |
442 |
+ |
|
443 |
+ |
2004-01-27 14:37 gezelter |
444 |
+ |
|
445 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
446 |
+ |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
447 |
+ |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
448 |
+ |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
449 |
+ |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
450 |
+ |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
451 |
+ |
do new rigidBody scheme |
452 |
+ |
|
453 |
+ |
2004-01-27 14:15 tim |
454 |
+ |
|
455 |
+ |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
456 |
+ |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
457 |
+ |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
458 |
+ |
constraint for Nonlinear Optimization Model |
459 |
+ |
|
460 |
+ |
2004-01-26 17:01 gezelter |
461 |
+ |
|
462 |
+ |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
463 |
+ |
Euler angles for orientation instead of unit vectors required |
464 |
+ |
changes in MoLocator |
465 |
+ |
|
466 |
+ |
2004-01-26 16:53 gezelter |
467 |
+ |
|
468 |
+ |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
469 |
+ |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
470 |
+ |
water/water.mdl: Changed orientation lines from unit vectors to |
471 |
+ |
euler angles |
472 |
+ |
|
473 |
+ |
2004-01-26 16:52 gezelter |
474 |
+ |
|
475 |
+ |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
476 |
+ |
|
477 |
+ |
2004-01-26 16:45 gezelter |
478 |
+ |
|
479 |
+ |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
480 |
+ |
use Euler angles in the following order: phi, theta, psi Removed |
481 |
+ |
the ability to set orientation using a unit vector |
482 |
+ |
|
483 |
+ |
2004-01-26 16:26 gezelter |
484 |
+ |
|
485 |
+ |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
486 |
+ |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
487 |
+ |
Euler angles in the following order: phi, theta, psi Removed the |
488 |
+ |
ability to set orientation using a unit vector |
489 |
+ |
|
490 |
+ |
2004-01-26 13:52 gezelter |
491 |
+ |
|
492 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
493 |
+ |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
494 |
+ |
|
495 |
+ |
2004-01-22 12:34 chrisfen |
496 |
+ |
|
497 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
498 |
+ |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
499 |
+ |
Corrected spelling in several directories, and stated WATER.cpp |
500 |
+ |
|
501 |
+ |
2004-01-21 17:16 tim |
502 |
+ |
|
503 |
+ |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
504 |
+ |
NLOPModel.hpp: constraint class in energy minimization |
505 |
+ |
|
506 |
+ |
2004-01-20 15:34 tim |
507 |
+ |
|
508 |
+ |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
509 |
+ |
|
510 |
+ |
2004-01-20 15:32 tim |
511 |
+ |
|
512 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
513 |
+ |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
514 |
+ |
|
515 |
+ |
2004-01-19 16:17 gezelter |
516 |
+ |
|
517 |
+ |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
518 |
+ |
more user-friendly |
519 |
+ |
|
520 |
+ |
2004-01-19 13:51 chrisfen |
521 |
+ |
|
522 |
+ |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
523 |
+ |
|
524 |
+ |
2004-01-19 13:36 tim |
525 |
+ |
|
526 |
+ |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
527 |
+ |
time, status time, thermal time and reset time are not divisible by |
528 |
+ |
dt |
529 |
+ |
|
530 |
+ |
2004-01-19 11:10 gezelter |
531 |
+ |
|
532 |
+ |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
533 |
+ |
won't complain |
534 |
+ |
|
535 |
+ |
2004-01-19 11:10 gezelter |
536 |
+ |
|
537 |
+ |
* samples/lipid/5x5.bass: Fixed old bass file |
538 |
+ |
|
539 |
+ |
2004-01-19 11:09 gezelter |
540 |
+ |
|
541 |
+ |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
542 |
+ |
required a change in how the MoleculeStamps are used by divideLabor |
543 |
+ |
in mpiSimulation.cpp |
544 |
+ |
|
545 |
+ |
2004-01-19 11:08 gezelter |
546 |
+ |
|
547 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
548 |
+ |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
549 |
+ |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
550 |
+ |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
551 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
552 |
+ |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
553 |
+ |
|
554 |
+ |
2004-01-16 16:55 tim |
555 |
+ |
|
556 |
+ |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
557 |
+ |
eor file |
558 |
+ |
|
559 |
+ |
2004-01-16 16:51 mmeineke |
560 |
+ |
|
561 |
+ |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
562 |
+ |
write eor files |
563 |
+ |
|
564 |
+ |
2004-01-16 10:01 mmeineke |
565 |
+ |
|
566 |
+ |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
567 |
+ |
initialization of the AtomStruct |
568 |
+ |
|
569 |
+ |
2004-01-15 16:57 chuckv |
570 |
+ |
|
571 |
+ |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
572 |
+ |
|
573 |
+ |
2004-01-15 10:51 gezelter |
574 |
+ |
|
575 |
+ |
* ac-tools/aclocal.m4: Changes for altivec |
576 |
+ |
|
577 |
+ |
2004-01-15 09:22 gezelter |
578 |
+ |
|
579 |
+ |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
580 |
+ |
|
581 |
+ |
2004-01-14 23:33 gezelter |
582 |
+ |
|
583 |
+ |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
584 |
+ |
|
585 |
+ |
2004-01-14 20:14 gezelter |
586 |
+ |
|
587 |
+ |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
588 |
+ |
notifyCutoffs.F90: More work for adding charges |
589 |
+ |
|
590 |
+ |
2004-01-14 17:41 gezelter |
591 |
+ |
|
592 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
593 |
+ |
src/Makefile.in: autoconf fixes |
594 |
+ |
|
595 |
+ |
2004-01-14 11:28 mmeineke |
596 |
+ |
|
597 |
+ |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
598 |
+ |
|
599 |
+ |
2004-01-14 10:48 gezelter |
600 |
+ |
|
601 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
602 |
+ |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
603 |
+ |
changes for icc8 |
604 |
+ |
|
605 |
+ |
2004-01-13 18:01 gezelter |
606 |
+ |
|
607 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
608 |
+ |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
609 |
+ |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
610 |
+ |
Changes for adding direct charge-charge interactions (with |
611 |
+ |
switching function) |
612 |
+ |
|
613 |
+ |
2004-01-13 17:34 gezelter |
614 |
+ |
|
615 |
+ |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
616 |
+ |
oopseMPI_module.F90: Some changes for new MPI organization and |
617 |
+ |
direct charge-charge interactions |
618 |
+ |
|
619 |
+ |
2004-01-13 17:11 tim |
620 |
+ |
|
621 |
+ |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
622 |
+ |
|
623 |
+ |
2004-01-13 16:22 tim |
624 |
+ |
|
625 |
+ |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
626 |
+ |
|
627 |
+ |
2004-01-13 15:35 tim |
628 |
+ |
|
629 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
630 |
+ |
eor file whenever it is used instead of rewinding it |
631 |
+ |
|
632 |
+ |
2004-01-13 15:04 tim |
633 |
+ |
|
634 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
635 |
+ |
of writeFrame |
636 |
+ |
|
637 |
+ |
2004-01-13 10:46 tim |
638 |
+ |
|
639 |
+ |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
640 |
+ |
Merge the code of writeFinal and writeDump; |
641 |
+ |
Adding sortingIndex into DumpWriter; |
642 |
+ |
Fix a bug of writing last frame twice in integrator |
643 |
+ |
|
644 |
+ |
2004-01-12 17:54 tim |
645 |
+ |
|
646 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
647 |
+ |
a bug in copying string |
648 |
+ |
|
649 |
+ |
2004-01-12 15:37 tim |
650 |
+ |
|
651 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
652 |
+ |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
653 |
+ |
master nodes |
654 |
+ |
|
655 |
+ |
2004-01-10 04:46 tim |
656 |
+ |
|
657 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
658 |
+ |
roll it back fix a bug of copying string to a pointer Still have |
659 |
+ |
Seg fault, it looks like a random MPI seg fault in totalview |
660 |
+ |
|
661 |
+ |
2004-01-09 21:15 tim |
662 |
+ |
|
663 |
+ |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
664 |
+ |
|
665 |
+ |
2004-01-09 15:29 gezelter |
666 |
+ |
|
667 |
+ |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
668 |
+ |
|
669 |
+ |
2004-01-08 17:25 chuckv |
670 |
+ |
|
671 |
+ |
* libmdtools/DumpWriter.cpp: A work in progress... |
672 |
+ |
|
673 |
+ |
2004-01-08 13:59 gezelter |
674 |
+ |
|
675 |
+ |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
676 |
+ |
case |
677 |
+ |
|
678 |
+ |
2004-01-08 13:13 mmeineke |
679 |
+ |
|
680 |
+ |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
681 |
+ |
state bug. |
682 |
+ |
|
683 |
+ |
2004-01-08 13:05 gezelter |
684 |
+ |
|
685 |
+ |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
686 |
+ |
|
687 |
+ |
2004-01-08 12:57 mmeineke |
688 |
+ |
|
689 |
+ |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
690 |
+ |
exstended state bug |
691 |
+ |
|
692 |
+ |
2004-01-08 12:40 gezelter |
693 |
+ |
|
694 |
+ |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
695 |
+ |
|
696 |
+ |
2004-01-08 10:44 mmeineke |
697 |
+ |
|
698 |
+ |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
699 |
+ |
XS state info flag |
700 |
+ |
|
701 |
+ |
2004-01-07 14:26 tim |
702 |
+ |
|
703 |
+ |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
704 |
+ |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
705 |
+ |
sending message from master node to itself in DumpWriter.cpp and |
706 |
+ |
InitializeFromFile.cpp |
707 |
+ |
|
708 |
+ |
2004-01-06 14:49 chuckv |
709 |
+ |
|
710 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
711 |
+ |
performance fixes in the dipole dipole and reaction field code |
712 |
+ |
|
713 |
+ |
2004-01-06 13:54 chuckv |
714 |
+ |
|
715 |
+ |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
716 |
+ |
little more sane |
717 |
+ |
|
718 |
+ |
2004-01-05 17:49 chuckv |
719 |
+ |
|
720 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
721 |
+ |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
722 |
+ |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
723 |
+ |
performance by reducing spurious function calls |
724 |
+ |
|
725 |
+ |
2004-01-05 17:18 chuckv |
726 |
+ |
|
727 |
+ |
* libmdtools/do_Forces.F90: mangling forces even further |
728 |
+ |
|
729 |
+ |
2004-01-05 17:18 chuckv |
730 |
+ |
|
731 |
+ |
* configure, ac-tools/configure.in: mpich mucking |
732 |
+ |
|
733 |
+ |
2004-01-05 17:12 chuckv |
734 |
+ |
|
735 |
+ |
* libmdtools/do_Forces.F90: mangled do_forces... |
736 |
+ |
|
737 |
+ |
2004-01-05 16:00 chuckv |
738 |
+ |
|
739 |
+ |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
740 |
+ |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
741 |
+ |
lookup |
742 |
+ |
|
743 |
|
2003-12-29 14:56 chuckv |
744 |
|
|
745 |
|
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
2920 |
|
|
2921 |
|
2003-03-25 09:29 mmeineke |
2922 |
|
|
2923 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
2923 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
2924 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
2925 |
|
|
2926 |
|
2003-03-25 09:29 mmeineke |