1 |
+ |
2004-04-28 21:11 tim |
2 |
+ |
|
3 |
+ |
* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
4 |
+ |
unmatched c/fortran interface |
5 |
+ |
|
6 |
+ |
2004-04-28 18:09 tim |
7 |
+ |
|
8 |
+ |
* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
9 |
+ |
keep the previous position of cantilever in SMD |
10 |
+ |
|
11 |
+ |
2004-04-28 17:34 tim |
12 |
+ |
|
13 |
+ |
* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
14 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
15 |
+ |
in Molecule.cpp which initialize massRatio before creat the array. |
16 |
+ |
fix two bugs in ZconsVisitor |
17 |
+ |
|
18 |
+ |
2004-04-28 17:06 gezelter |
19 |
+ |
|
20 |
+ |
* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
21 |
+ |
Adding molecular cutoffs |
22 |
+ |
|
23 |
+ |
2004-04-28 16:39 gezelter |
24 |
+ |
|
25 |
+ |
* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
26 |
+ |
fSimulation.h, force_globals.F90, simulation_module.F90: work on |
27 |
+ |
molecular cutoffs |
28 |
+ |
|
29 |
+ |
2004-04-28 16:39 gezelter |
30 |
+ |
|
31 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
32 |
+ |
Globals |
33 |
+ |
|
34 |
+ |
2004-04-27 11:26 tim |
35 |
+ |
|
36 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
37 |
+ |
ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
38 |
+ |
fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
39 |
+ |
molecule and massRation into atom class |
40 |
+ |
|
41 |
+ |
2004-04-26 16:16 mmeineke |
42 |
+ |
|
43 |
+ |
* libBASS/Globals.cpp: modified the defaults for the system init |
44 |
+ |
time and system init state. |
45 |
+ |
|
46 |
+ |
2004-04-26 09:29 gezelter |
47 |
+ |
|
48 |
+ |
* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
49 |
+ |
calc_charge_charge.F90 |
50 |
+ |
|
51 |
+ |
2004-04-23 23:31 tim |
52 |
+ |
|
53 |
+ |
* ChangeLog, libmdtools/AtomVisitor.cpp, |
54 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
55 |
+ |
reaction field correction to charge-charge interaction |
56 |
+ |
|
57 |
+ |
2004-04-22 16:33 tim |
58 |
+ |
|
59 |
+ |
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
60 |
+ |
Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
61 |
+ |
calculation of pressure tensor |
62 |
+ |
|
63 |
+ |
2004-04-22 09:55 tim |
64 |
+ |
|
65 |
+ |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
66 |
+ |
another bug in InitFromFile. MPI verion of OOPSE is working again |
67 |
+ |
|
68 |
+ |
2004-04-21 22:29 tim |
69 |
+ |
|
70 |
+ |
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
71 |
+ |
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
72 |
+ |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
73 |
+ |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
74 |
+ |
DumpWriter |
75 |
+ |
|
76 |
+ |
2004-04-21 00:32 tim |
77 |
+ |
|
78 |
+ |
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
79 |
+ |
libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
80 |
+ |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
81 |
+ |
useless files |
82 |
+ |
|
83 |
+ |
2004-04-20 11:56 tim |
84 |
+ |
|
85 |
+ |
* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
86 |
+ |
SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
87 |
+ |
velocitize at thermo |
88 |
+ |
|
89 |
+ |
2004-04-20 00:39 tim |
90 |
+ |
|
91 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
92 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
93 |
+ |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
94 |
+ |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
95 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
96 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
97 |
+ |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
98 |
+ |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
99 |
+ |
|
100 |
+ |
2004-04-19 17:13 gezelter |
101 |
+ |
|
102 |
+ |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
103 |
+ |
Thermo.cpp: Fixed a charge bug |
104 |
+ |
|
105 |
+ |
2004-04-19 15:54 tim |
106 |
+ |
|
107 |
+ |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
108 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
109 |
+ |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
110 |
+ |
a bug in CompositeVisitor which cause the double counting problem |
111 |
+ |
|
112 |
+ |
2004-04-19 12:44 tim |
113 |
+ |
|
114 |
+ |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
115 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
116 |
+ |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
117 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
118 |
+ |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
119 |
+ |
Dump2XYZ is almost working except atoms in rigidbody are double |
120 |
+ |
counted |
121 |
+ |
|
122 |
+ |
2004-04-18 22:52 tim |
123 |
+ |
|
124 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
125 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
126 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
127 |
+ |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
128 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
129 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
130 |
+ |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
131 |
+ |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
132 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
133 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
134 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
135 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
136 |
+ |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
137 |
+ |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
138 |
+ |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
139 |
+ |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
140 |
+ |
implement of quickLate using visitor and composite pattern |
141 |
+ |
|
142 |
+ |
2004-04-15 17:15 tim |
143 |
+ |
|
144 |
+ |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
145 |
+ |
exclude list |
146 |
+ |
|
147 |
+ |
2004-04-15 11:18 tim |
148 |
+ |
|
149 |
+ |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
150 |
+ |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
151 |
+ |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
152 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
153 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
154 |
+ |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
155 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
156 |
+ |
whole bunch of bugs :-) |
157 |
+ |
|
158 |
+ |
2004-04-14 12:20 chrisfen |
159 |
+ |
|
160 |
+ |
* forceFields/WATER.frc: Added the WATER.frc force field |
161 |
+ |
|
162 |
+ |
2004-04-14 11:32 gezelter |
163 |
+ |
|
164 |
+ |
* libmdtools/Molecule.cpp: fixed for get_potential |
165 |
+ |
|
166 |
+ |
2004-04-14 10:37 tim |
167 |
+ |
|
168 |
+ |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
169 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
170 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
171 |
+ |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
172 |
+ |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
173 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
174 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
175 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
176 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
177 |
+ |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
178 |
+ |
Change DumpWriter and InitFromFile |
179 |
+ |
|
180 |
+ |
2004-04-13 11:26 gezelter |
181 |
+ |
|
182 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
183 |
+ |
molecules can keep track of their own IntegrableObjects (and |
184 |
+ |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
185 |
+ |
RigidBodies (which was done incorrectly before). |
186 |
+ |
|
187 |
+ |
2004-04-13 11:25 gezelter |
188 |
+ |
|
189 |
+ |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
190 |
+ |
(will back out momentarily) |
191 |
+ |
|
192 |
+ |
2004-04-13 10:10 gezelter |
193 |
+ |
|
194 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
195 |
+ |
Those were old. |
196 |
+ |
|
197 |
+ |
2004-04-13 10:09 gezelter |
198 |
+ |
|
199 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
200 |
+ |
to add IntegrableObjects |
201 |
+ |
|
202 |
+ |
2004-04-12 16:02 gezelter |
203 |
+ |
|
204 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
205 |
+ |
|
206 |
+ |
2004-04-12 15:32 gezelter |
207 |
+ |
|
208 |
+ |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
209 |
+ |
test run |
210 |
+ |
|
211 |
+ |
2004-04-12 15:32 gezelter |
212 |
+ |
|
213 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
214 |
+ |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
215 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
216 |
+ |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
217 |
+ |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
218 |
+ |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
219 |
+ |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
220 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
221 |
+ |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
222 |
+ |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
223 |
+ |
(Somewhat extensive) |
224 |
+ |
|
225 |
+ |
2004-04-12 15:31 gezelter |
226 |
+ |
|
227 |
+ |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
228 |
+ |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
229 |
+ |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
230 |
+ |
Changes for RigidBody dynamics |
231 |
+ |
|
232 |
+ |
2004-03-17 09:22 tim |
233 |
+ |
|
234 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
235 |
+ |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
236 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
237 |
+ |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
238 |
+ |
does not sound a good choice, next commit will seperate SMD and |
239 |
+ |
ZConstraint |
240 |
+ |
|
241 |
+ |
2004-03-16 14:22 tim |
242 |
+ |
|
243 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
244 |
+ |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
245 |
+ |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
246 |
+ |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
247 |
+ |
now can support sequential moving. Refactorying is needed to |
248 |
+ |
support SMD in ZConstraint |
249 |
+ |
|
250 |
+ |
2004-03-02 15:32 tim |
251 |
+ |
|
252 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
253 |
+ |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
254 |
+ |
support large file |
255 |
+ |
|
256 |
+ |
2004-03-01 16:17 tim |
257 |
+ |
|
258 |
+ |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
259 |
+ |
|
260 |
+ |
2004-03-01 15:01 tim |
261 |
+ |
|
262 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
263 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
264 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
265 |
+ |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
266 |
+ |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
267 |
+ |
program which can be used to replace atom type for zconstraint into |
268 |
+ |
OOPSE |
269 |
+ |
|
270 |
+ |
2004-02-24 11:36 tim |
271 |
+ |
|
272 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
273 |
+ |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
274 |
+ |
message] |
275 |
+ |
|
276 |
+ |
2004-02-24 10:49 tim |
277 |
+ |
|
278 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
279 |
+ |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
280 |
+ |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
281 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
282 |
+ |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
283 |
+ |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
284 |
+ |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
285 |
+ |
|
286 |
+ |
2004-02-24 10:44 tim |
287 |
+ |
|
288 |
+ |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
289 |
+ |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
290 |
+ |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
291 |
+ |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
292 |
+ |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
293 |
+ |
compose to implement Minimizer both versions are working |
294 |
+ |
|
295 |
+ |
2004-02-17 14:23 tim |
296 |
+ |
|
297 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
298 |
+ |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
299 |
+ |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
300 |
+ |
libmdtools/MinimizerParameterSet.hpp, |
301 |
+ |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
302 |
+ |
to remove the constraint force along bond direction |
303 |
+ |
|
304 |
+ |
2004-02-10 16:33 tim |
305 |
+ |
|
306 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
307 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
308 |
+ |
single version of energy minimization is working. |
309 |
+ |
|
310 |
+ |
2004-02-09 15:38 mmeineke |
311 |
+ |
|
312 |
+ |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
313 |
+ |
the massive memory overusage by OOPSE |
314 |
+ |
|
315 |
+ |
2004-02-09 09:48 chrisfen |
316 |
+ |
|
317 |
+ |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
318 |
+ |
hardwired LJ_rcut |
319 |
+ |
|
320 |
+ |
2004-02-06 19:14 tim |
321 |
+ |
|
322 |
+ |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
323 |
+ |
message] |
324 |
+ |
|
325 |
+ |
2004-02-06 16:37 tim |
326 |
+ |
|
327 |
+ |
* ChangeLog, libBASS/Globals.cpp, |
328 |
+ |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
329 |
+ |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
330 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
331 |
+ |
energy minimization for argon is working, need to add constraint |
332 |
+ |
|
333 |
+ |
2004-02-06 14:05 tim |
334 |
+ |
|
335 |
+ |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
336 |
+ |
one more file into Makefile.in |
337 |
+ |
|
338 |
+ |
2004-02-06 13:58 tim |
339 |
+ |
|
340 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
341 |
+ |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
342 |
+ |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
343 |
+ |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
344 |
+ |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
345 |
+ |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
346 |
+ |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
347 |
+ |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
348 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
349 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
350 |
+ |
some lines into global.cpp to make it work with energy minimization |
351 |
+ |
|
352 |
+ |
2004-02-04 17:26 tim |
353 |
+ |
|
354 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
355 |
+ |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
356 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
357 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
358 |
+ |
Single version of conjugate gradient with golden search linesearch |
359 |
+ |
pass a couple of functions test. Brent's algorithm is still broken |
360 |
+ |
|
361 |
+ |
2004-02-03 17:54 tim |
362 |
+ |
|
363 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
364 |
+ |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
365 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
366 |
+ |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
367 |
+ |
|
368 |
+ |
2004-02-03 15:47 tim |
369 |
+ |
|
370 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
371 |
+ |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
372 |
+ |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
373 |
+ |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
374 |
+ |
SteepestDescent.hpp: [no log message] |
375 |
+ |
|
376 |
+ |
2004-02-03 15:43 tim |
377 |
+ |
|
378 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
379 |
+ |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
380 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
381 |
+ |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
382 |
+ |
constraint class |
383 |
+ |
|
384 |
+ |
2004-02-03 12:10 tim |
385 |
+ |
|
386 |
+ |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
387 |
+ |
|
388 |
+ |
2004-02-03 10:21 tim |
389 |
+ |
|
390 |
+ |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
391 |
+ |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
392 |
+ |
|
393 |
+ |
2004-02-02 15:29 tim |
394 |
+ |
|
395 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
396 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
397 |
+ |
Adding GoldenSection and Brent LineSearch Method |
398 |
+ |
|
399 |
+ |
2004-01-30 16:47 tim |
400 |
+ |
|
401 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
402 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
403 |
+ |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
404 |
+ |
MinimizerBase instead of a functor to do line seach |
405 |
+ |
|
406 |
+ |
2004-01-30 10:00 chrisfen |
407 |
+ |
|
408 |
+ |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
409 |
+ |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
410 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
411 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
412 |
+ |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
413 |
+ |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
414 |
+ |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
415 |
+ |
has a working WATER.cpp forcefield and parser. This involved |
416 |
+ |
changes to WATER.cpp and ForceFields amoung other files. One |
417 |
+ |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
418 |
+ |
This will be removed on the next commit... |
419 |
+ |
|
420 |
+ |
2004-01-29 18:00 gezelter |
421 |
+ |
|
422 |
+ |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
423 |
+ |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
424 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
425 |
+ |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
426 |
+ |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
427 |
+ |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
428 |
+ |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
429 |
+ |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
430 |
+ |
member list fixes for rigid bodies |
431 |
+ |
|
432 |
+ |
2004-01-29 16:44 tim |
433 |
+ |
|
434 |
+ |
* libmdtools/MinimizerParameterSet.hpp: Adding |
435 |
+ |
MinimizerParameterSet class. |
436 |
+ |
|
437 |
+ |
2004-01-28 17:44 tim |
438 |
+ |
|
439 |
+ |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
440 |
+ |
NLModel0 and NLModel1 |
441 |
+ |
|
442 |
+ |
2004-01-28 15:40 tim |
443 |
+ |
|
444 |
+ |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
445 |
+ |
of NLModel |
446 |
+ |
|
447 |
+ |
2004-01-27 15:34 gezelter |
448 |
+ |
|
449 |
+ |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
450 |
+ |
water.mdl file, updated ssd.bass to use new SSD name |
451 |
+ |
|
452 |
+ |
2004-01-27 15:34 gezelter |
453 |
+ |
|
454 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
455 |
+ |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
456 |
+ |
stuff |
457 |
+ |
|
458 |
+ |
2004-01-27 14:39 gezelter |
459 |
+ |
|
460 |
+ |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
461 |
+ |
|
462 |
+ |
2004-01-27 14:39 gezelter |
463 |
+ |
|
464 |
+ |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
465 |
+ |
|
466 |
+ |
2004-01-27 14:38 gezelter |
467 |
+ |
|
468 |
+ |
* samples/argon/argon.bass: Longer run time to test argon |
469 |
+ |
|
470 |
+ |
2004-01-27 14:38 gezelter |
471 |
+ |
|
472 |
+ |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
473 |
+ |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
474 |
+ |
morning |
475 |
+ |
|
476 |
+ |
2004-01-27 14:37 gezelter |
477 |
+ |
|
478 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
479 |
+ |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
480 |
+ |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
481 |
+ |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
482 |
+ |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
483 |
+ |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
484 |
+ |
do new rigidBody scheme |
485 |
+ |
|
486 |
+ |
2004-01-27 14:15 tim |
487 |
+ |
|
488 |
+ |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
489 |
+ |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
490 |
+ |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
491 |
+ |
constraint for Nonlinear Optimization Model |
492 |
+ |
|
493 |
+ |
2004-01-26 17:01 gezelter |
494 |
+ |
|
495 |
+ |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
496 |
+ |
Euler angles for orientation instead of unit vectors required |
497 |
+ |
changes in MoLocator |
498 |
+ |
|
499 |
+ |
2004-01-26 16:53 gezelter |
500 |
+ |
|
501 |
+ |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
502 |
+ |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
503 |
+ |
water/water.mdl: Changed orientation lines from unit vectors to |
504 |
+ |
euler angles |
505 |
+ |
|
506 |
+ |
2004-01-26 16:52 gezelter |
507 |
+ |
|
508 |
+ |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
509 |
+ |
|
510 |
+ |
2004-01-26 16:45 gezelter |
511 |
+ |
|
512 |
+ |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
513 |
+ |
use Euler angles in the following order: phi, theta, psi Removed |
514 |
+ |
the ability to set orientation using a unit vector |
515 |
+ |
|
516 |
+ |
2004-01-26 16:26 gezelter |
517 |
+ |
|
518 |
+ |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
519 |
+ |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
520 |
+ |
Euler angles in the following order: phi, theta, psi Removed the |
521 |
+ |
ability to set orientation using a unit vector |
522 |
+ |
|
523 |
+ |
2004-01-26 13:52 gezelter |
524 |
+ |
|
525 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
526 |
+ |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
527 |
+ |
|
528 |
+ |
2004-01-22 12:34 chrisfen |
529 |
+ |
|
530 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
531 |
+ |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
532 |
+ |
Corrected spelling in several directories, and stated WATER.cpp |
533 |
+ |
|
534 |
+ |
2004-01-21 17:16 tim |
535 |
+ |
|
536 |
+ |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
537 |
+ |
NLOPModel.hpp: constraint class in energy minimization |
538 |
+ |
|
539 |
+ |
2004-01-20 15:34 tim |
540 |
+ |
|
541 |
+ |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
542 |
+ |
|
543 |
+ |
2004-01-20 15:32 tim |
544 |
+ |
|
545 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
546 |
+ |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
547 |
+ |
|
548 |
+ |
2004-01-19 16:17 gezelter |
549 |
+ |
|
550 |
+ |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
551 |
+ |
more user-friendly |
552 |
+ |
|
553 |
+ |
2004-01-19 13:51 chrisfen |
554 |
+ |
|
555 |
+ |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
556 |
+ |
|
557 |
+ |
2004-01-19 13:36 tim |
558 |
+ |
|
559 |
+ |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
560 |
+ |
time, status time, thermal time and reset time are not divisible by |
561 |
+ |
dt |
562 |
+ |
|
563 |
+ |
2004-01-19 11:10 gezelter |
564 |
+ |
|
565 |
+ |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
566 |
+ |
won't complain |
567 |
+ |
|
568 |
+ |
2004-01-19 11:10 gezelter |
569 |
+ |
|
570 |
+ |
* samples/lipid/5x5.bass: Fixed old bass file |
571 |
+ |
|
572 |
+ |
2004-01-19 11:09 gezelter |
573 |
+ |
|
574 |
+ |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
575 |
+ |
required a change in how the MoleculeStamps are used by divideLabor |
576 |
+ |
in mpiSimulation.cpp |
577 |
+ |
|
578 |
+ |
2004-01-19 11:08 gezelter |
579 |
+ |
|
580 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
581 |
+ |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
582 |
+ |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
583 |
+ |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
584 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
585 |
+ |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
586 |
+ |
|
587 |
+ |
2004-01-16 16:55 tim |
588 |
+ |
|
589 |
+ |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
590 |
+ |
eor file |
591 |
+ |
|
592 |
+ |
2004-01-16 16:51 mmeineke |
593 |
+ |
|
594 |
+ |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
595 |
+ |
write eor files |
596 |
+ |
|
597 |
+ |
2004-01-16 10:01 mmeineke |
598 |
+ |
|
599 |
+ |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
600 |
+ |
initialization of the AtomStruct |
601 |
+ |
|
602 |
+ |
2004-01-15 16:57 chuckv |
603 |
+ |
|
604 |
+ |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
605 |
+ |
|
606 |
+ |
2004-01-15 10:51 gezelter |
607 |
+ |
|
608 |
+ |
* ac-tools/aclocal.m4: Changes for altivec |
609 |
+ |
|
610 |
+ |
2004-01-15 09:22 gezelter |
611 |
+ |
|
612 |
+ |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
613 |
+ |
|
614 |
+ |
2004-01-14 23:33 gezelter |
615 |
+ |
|
616 |
+ |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
617 |
+ |
|
618 |
+ |
2004-01-14 20:14 gezelter |
619 |
+ |
|
620 |
+ |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
621 |
+ |
notifyCutoffs.F90: More work for adding charges |
622 |
+ |
|
623 |
+ |
2004-01-14 17:41 gezelter |
624 |
+ |
|
625 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
626 |
+ |
src/Makefile.in: autoconf fixes |
627 |
+ |
|
628 |
+ |
2004-01-14 11:28 mmeineke |
629 |
+ |
|
630 |
+ |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
631 |
+ |
|
632 |
+ |
2004-01-14 10:48 gezelter |
633 |
+ |
|
634 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
635 |
+ |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
636 |
+ |
changes for icc8 |
637 |
+ |
|
638 |
+ |
2004-01-13 18:01 gezelter |
639 |
+ |
|
640 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
641 |
+ |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
642 |
+ |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
643 |
+ |
Changes for adding direct charge-charge interactions (with |
644 |
+ |
switching function) |
645 |
+ |
|
646 |
+ |
2004-01-13 17:34 gezelter |
647 |
+ |
|
648 |
+ |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
649 |
+ |
oopseMPI_module.F90: Some changes for new MPI organization and |
650 |
+ |
direct charge-charge interactions |
651 |
+ |
|
652 |
+ |
2004-01-13 17:11 tim |
653 |
+ |
|
654 |
+ |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
655 |
+ |
|
656 |
+ |
2004-01-13 16:22 tim |
657 |
+ |
|
658 |
+ |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
659 |
+ |
|
660 |
+ |
2004-01-13 15:35 tim |
661 |
+ |
|
662 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
663 |
+ |
eor file whenever it is used instead of rewinding it |
664 |
+ |
|
665 |
+ |
2004-01-13 15:04 tim |
666 |
+ |
|
667 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
668 |
+ |
of writeFrame |
669 |
+ |
|
670 |
+ |
2004-01-13 10:46 tim |
671 |
+ |
|
672 |
+ |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
673 |
+ |
Merge the code of writeFinal and writeDump; |
674 |
+ |
Adding sortingIndex into DumpWriter; |
675 |
+ |
Fix a bug of writing last frame twice in integrator |
676 |
+ |
|
677 |
+ |
2004-01-12 17:54 tim |
678 |
+ |
|
679 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
680 |
+ |
a bug in copying string |
681 |
+ |
|
682 |
|
2004-01-12 15:37 tim |
683 |
|
|
684 |
|
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
1222 |
|
|
1223 |
|
2003-10-10 12:10 mmeineke |
1224 |
|
|
1225 |
< |
* props/AllCorr.cpp, props/AllCorr.hpp, props/CorrWrap.cpp, |
1226 |
< |
props/CorrWrap.hpp, props/GofR.cpp, props/PairCorrList.cpp, |
1227 |
< |
props/PairCorrList.hpp, props/PairCorrType.cpp, |
1228 |
< |
props/PairCorrType.hpp, props/staticProps.cpp, |
1229 |
< |
staticProps/AllCorr.cpp, staticProps/AllCorr.hpp, |
549 |
< |
staticProps/CorrWrap.cpp, staticProps/CorrWrap.hpp, |
550 |
< |
staticProps/GofR.cpp, staticProps/Makefile.in, |
551 |
< |
staticProps/PairCorrList.cpp, staticProps/PairCorrList.hpp, |
552 |
< |
staticProps/PairCorrType.cpp, staticProps/PairCorrType.hpp, |
553 |
< |
staticProps/staticProps.cpp: removed the props directory, and moved |
554 |
< |
everything over to staticProps |
1225 |
> |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
1226 |
> |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
1227 |
> |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1228 |
> |
staticProps.cpp: removed the props directory, and moved everything |
1229 |
> |
over to staticProps |
1230 |
|
|
1231 |
|
2003-10-09 17:09 mmeineke |
1232 |
|
|
1233 |
< |
* libmdtools/Atom.hpp, props/AllCorr.cpp, props/AllCorr.hpp, |
559 |
< |
props/CorrWrap.cpp, props/CorrWrap.hpp, props/GofR.cpp, |
560 |
< |
props/PairCorrType.cpp, props/PairCorrType.hpp, |
561 |
< |
props/staticProps.cpp: Contiuned work on staticProps. should be in |
1233 |
> |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
1234 |
|
a position where it will compile and run first runs. |
1235 |
|
|
1236 |
|
2003-10-04 13:46 chuckv |
1246 |
|
|
1247 |
|
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
1248 |
|
entahlpy from the statwriter and thermo. |
577 |
– |
|
578 |
– |
2003-10-03 17:02 mmeineke |
579 |
– |
|
580 |
– |
* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
581 |
– |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
582 |
– |
staticProps.cpp: changed the formating ogf the error statements in |
583 |
– |
simError |
584 |
– |
|
585 |
– |
added a function to get the maxCutoff |
586 |
– |
|
587 |
– |
near completion of the staticProps code. still needs the pair loop, |
588 |
– |
and the loop to allocate and read each frame. |
1249 |
|
|
1250 |
|
2003-10-03 17:02 mmeineke |
1251 |
|
|
1259 |
|
* libBASS/simError.c: changed the formating ogf the error |
1260 |
|
statements in simError |
1261 |
|
|
602 |
– |
2003-10-02 17:06 mmeineke |
603 |
– |
|
604 |
– |
* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
605 |
– |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
606 |
– |
staticProps.cpp: finishing up the constructs needed to get this |
607 |
– |
program up and running |
608 |
– |
|
1262 |
|
2003-09-30 11:00 mmeineke |
1263 |
|
|
1264 |
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
1415 |
|
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
1416 |
|
statWriter fix bug of vector wrapping at NPTi |
1417 |
|
|
765 |
– |
2003-09-12 15:51 mmeineke |
766 |
– |
|
767 |
– |
* props/: AllCorr.cpp, AllCorr.hpp, GofR.cpp, PairCorrType.cpp, |
768 |
– |
PairCorrType.hpp: added AllCorr. It eill still need some work |
769 |
– |
|
1418 |
|
2003-09-12 11:20 gezelter |
1419 |
|
|
1420 |
|
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
1424 |
|
|
1425 |
|
* ChangeLog: Entered changes for configure into ChangeLog |
1426 |
|
|
779 |
– |
2003-09-10 16:28 mmeineke |
780 |
– |
|
781 |
– |
* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more |
782 |
– |
work on getting gofR working. |
783 |
– |
|
784 |
– |
2003-09-09 16:50 mmeineke |
785 |
– |
|
786 |
– |
* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the |
787 |
– |
beginings of the GofR pair correlation. |
788 |
– |
|
789 |
– |
added identification of identI in matchI. |
790 |
– |
|
1427 |
|
2003-09-09 15:35 mmeineke |
1428 |
|
|
1429 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
1497 |
|
* ChangeLog, libmdtools/GenericData.cpp, |
1498 |
|
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
1499 |
|
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
864 |
– |
|
865 |
– |
2003-08-28 11:59 mmeineke |
866 |
– |
|
867 |
– |
* props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp: |
868 |
– |
added the first functional parts of the PairCorrType Abstract |
869 |
– |
classes. |
1500 |
|
|
1501 |
|
2003-08-27 14:23 tim |
1502 |
|
|
1769 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
1770 |
|
works..... |
1771 |
|
|
1142 |
– |
2003-08-08 13:32 mmeineke |
1143 |
– |
|
1144 |
– |
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
1145 |
– |
moved frameCount's functionality into DumpReader. also split props |
1146 |
– |
into staticProps and dynamicProps. (currently only have |
1147 |
– |
staticProps) |
1148 |
– |
|
1772 |
|
2003-08-08 12:48 mmeineke |
1773 |
|
|
1774 |
|
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
1825 |
|
2003-07-29 11:32 mmeineke |
1826 |
|
|
1827 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
1828 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1829 |
< |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
1207 |
< |
src/Makefile: working on the props code |
1828 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
1829 |
> |
working on the props code |
1830 |
|
|
1831 |
|
2003-07-29 11:32 mmeineke |
1832 |
|
|
2953 |
|
|
2954 |
|
2003-03-25 09:29 mmeineke |
2955 |
|
|
2956 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
2956 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
2957 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
2958 |
|
|
2959 |
|
2003-03-25 09:29 mmeineke |
2963 |
|
|
2964 |
|
2003-03-24 20:07 gezelter |
2965 |
|
|
2966 |
< |
* samples/Makefile, tests/Makefile: moving tests to samples |
2966 |
> |
* samples/Makefile: moving tests to samples |
2967 |
|
|
2968 |
|
2003-03-24 20:06 gezelter |
2969 |
|
|
2970 |
< |
* samples/alkane/Makefile, samples/alkane/alkanes.mdl, |
2971 |
< |
samples/alkane/butane.bass, samples/alkane/init_butane.eor, |
2972 |
< |
samples/argon/Makefile, samples/argon/argon.bass, |
2973 |
< |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
2974 |
< |
samples/lipid/5x5.bass, samples/lipid/Makefile, |
2975 |
< |
samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, |
2976 |
< |
samples/lipid/water.mdl, samples/water/Makefile, |
2355 |
< |
samples/water/init_ssd.eor, samples/water/ssd.bass, |
2356 |
< |
samples/water/water.mdl, tests/alkane/Makefile, |
2357 |
< |
tests/alkane/alkanes.mdl, tests/alkane/butane.bass, |
2358 |
< |
tests/alkane/init_butane.eor, tests/argon/Makefile, |
2359 |
< |
tests/argon/argon.bass, tests/argon/init_argon.eor, |
2360 |
< |
tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile, |
2361 |
< |
tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl, |
2362 |
< |
tests/lipid/water.mdl, tests/water/Makefile, |
2363 |
< |
tests/water/init_ssd.eor, tests/water/ssd.bass, |
2364 |
< |
tests/water/water.mdl: moved tests to samples |
2970 |
> |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
2971 |
> |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
2972 |
> |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
2973 |
> |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
2974 |
> |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
2975 |
> |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
2976 |
> |
samples |
2977 |
|
|
2978 |
|
2003-03-24 19:51 gezelter |
2979 |
|
|
2981 |
|
|
2982 |
|
2003-03-24 19:46 gezelter |
2983 |
|
|
2984 |
< |
* ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile, |
2373 |
< |
tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile: |
2374 |
< |
Added makefiles in tests directories |
2984 |
> |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
2985 |
|
|
2986 |
|
2003-03-24 16:55 gezelter |
2987 |
|
|
2998 |
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
2999 |
|
do_Forces.F90: little bug fixes here and there |
3000 |
|
|
2391 |
– |
2003-03-24 11:04 mmeineke |
2392 |
– |
|
2393 |
– |
* tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon |
2394 |
– |
test simulation |
2395 |
– |
|
2396 |
– |
2003-03-24 11:02 mmeineke |
2397 |
– |
|
2398 |
– |
* tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl, |
2399 |
– |
lipid/water.mdl, water/init_ssd.eor, water/ssd.bass, |
2400 |
– |
water/water.mdl: [no log message] |
2401 |
– |
|
2402 |
– |
2003-03-24 11:02 mmeineke |
2403 |
– |
|
2404 |
– |
* tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added |
2405 |
– |
some test bass files for experimenting with |
2406 |
– |
|
3001 |
|
2003-03-24 10:26 mmeineke |
3002 |
|
|
3003 |
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |