1 |
+ |
2004-04-19 15:54 tim |
2 |
+ |
|
3 |
+ |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
4 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
5 |
+ |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
6 |
+ |
a bug in CompositeVisitor which cause the double counting problem |
7 |
+ |
|
8 |
+ |
2004-04-19 12:44 tim |
9 |
+ |
|
10 |
+ |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
11 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
12 |
+ |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
13 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
14 |
+ |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
15 |
+ |
Dump2XYZ is almost working except atoms in rigidbody are double |
16 |
+ |
counted |
17 |
+ |
|
18 |
+ |
2004-04-18 22:52 tim |
19 |
+ |
|
20 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
21 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
22 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
23 |
+ |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
24 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
25 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
26 |
+ |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
27 |
+ |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
28 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
29 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
30 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
31 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
32 |
+ |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
33 |
+ |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
34 |
+ |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
35 |
+ |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
36 |
+ |
implement of quickLate using visitor and composite pattern |
37 |
+ |
|
38 |
+ |
2004-04-15 17:15 tim |
39 |
+ |
|
40 |
+ |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
41 |
+ |
exclude list |
42 |
+ |
|
43 |
+ |
2004-04-15 11:18 tim |
44 |
+ |
|
45 |
+ |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
46 |
+ |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
47 |
+ |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
48 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
49 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
50 |
+ |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
51 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
52 |
+ |
whole bunch of bugs :-) |
53 |
+ |
|
54 |
+ |
2004-04-14 12:20 chrisfen |
55 |
+ |
|
56 |
+ |
* forceFields/WATER.frc: Added the WATER.frc force field |
57 |
+ |
|
58 |
+ |
2004-04-14 11:32 gezelter |
59 |
+ |
|
60 |
+ |
* libmdtools/Molecule.cpp: fixed for get_potential |
61 |
+ |
|
62 |
+ |
2004-04-14 10:37 tim |
63 |
+ |
|
64 |
+ |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
65 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
66 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
67 |
+ |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
68 |
+ |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
69 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
70 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
71 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
72 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
73 |
+ |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
74 |
+ |
Change DumpWriter and InitFromFile |
75 |
+ |
|
76 |
+ |
2004-04-13 11:26 gezelter |
77 |
+ |
|
78 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
79 |
+ |
molecules can keep track of their own IntegrableObjects (and |
80 |
+ |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
81 |
+ |
RigidBodies (which was done incorrectly before). |
82 |
+ |
|
83 |
+ |
2004-04-13 11:25 gezelter |
84 |
+ |
|
85 |
+ |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
86 |
+ |
(will back out momentarily) |
87 |
+ |
|
88 |
+ |
2004-04-13 10:10 gezelter |
89 |
+ |
|
90 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
91 |
+ |
Those were old. |
92 |
+ |
|
93 |
+ |
2004-04-13 10:09 gezelter |
94 |
+ |
|
95 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
96 |
+ |
to add IntegrableObjects |
97 |
+ |
|
98 |
+ |
2004-04-12 16:02 gezelter |
99 |
+ |
|
100 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
101 |
+ |
|
102 |
+ |
2004-04-12 15:32 gezelter |
103 |
+ |
|
104 |
+ |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
105 |
+ |
test run |
106 |
+ |
|
107 |
+ |
2004-04-12 15:32 gezelter |
108 |
+ |
|
109 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
110 |
+ |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
111 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
112 |
+ |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
113 |
+ |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
114 |
+ |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
115 |
+ |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
116 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
117 |
+ |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
118 |
+ |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
119 |
+ |
(Somewhat extensive) |
120 |
+ |
|
121 |
+ |
2004-04-12 15:31 gezelter |
122 |
+ |
|
123 |
+ |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
124 |
+ |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
125 |
+ |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
126 |
+ |
Changes for RigidBody dynamics |
127 |
+ |
|
128 |
+ |
2004-03-17 09:22 tim |
129 |
+ |
|
130 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
131 |
+ |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
132 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
133 |
+ |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
134 |
+ |
does not sound a good choice, next commit will seperate SMD and |
135 |
+ |
ZConstraint |
136 |
+ |
|
137 |
+ |
2004-03-16 14:22 tim |
138 |
+ |
|
139 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
140 |
+ |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
141 |
+ |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
142 |
+ |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
143 |
+ |
now can support sequential moving. Refactorying is needed to |
144 |
+ |
support SMD in ZConstraint |
145 |
+ |
|
146 |
+ |
2004-03-02 15:32 tim |
147 |
+ |
|
148 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
149 |
+ |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
150 |
+ |
support large file |
151 |
+ |
|
152 |
+ |
2004-03-01 16:17 tim |
153 |
+ |
|
154 |
+ |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
155 |
+ |
|
156 |
+ |
2004-03-01 15:01 tim |
157 |
+ |
|
158 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
159 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
160 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
161 |
+ |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
162 |
+ |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
163 |
+ |
program which can be used to replace atom type for zconstraint into |
164 |
+ |
OOPSE |
165 |
+ |
|
166 |
+ |
2004-02-24 11:36 tim |
167 |
+ |
|
168 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
169 |
+ |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
170 |
+ |
message] |
171 |
+ |
|
172 |
+ |
2004-02-24 10:49 tim |
173 |
+ |
|
174 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
175 |
+ |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
176 |
+ |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
177 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
178 |
+ |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
179 |
+ |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
180 |
+ |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
181 |
+ |
|
182 |
+ |
2004-02-24 10:44 tim |
183 |
+ |
|
184 |
+ |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
185 |
+ |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
186 |
+ |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
187 |
+ |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
188 |
+ |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
189 |
+ |
compose to implement Minimizer both versions are working |
190 |
+ |
|
191 |
+ |
2004-02-17 14:23 tim |
192 |
+ |
|
193 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
194 |
+ |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
195 |
+ |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
196 |
+ |
libmdtools/MinimizerParameterSet.hpp, |
197 |
+ |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
198 |
+ |
to remove the constraint force along bond direction |
199 |
+ |
|
200 |
+ |
2004-02-10 16:33 tim |
201 |
+ |
|
202 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
203 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
204 |
+ |
single version of energy minimization is working. |
205 |
+ |
|
206 |
+ |
2004-02-09 15:38 mmeineke |
207 |
+ |
|
208 |
+ |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
209 |
+ |
the massive memory overusage by OOPSE |
210 |
+ |
|
211 |
+ |
2004-02-09 09:48 chrisfen |
212 |
+ |
|
213 |
+ |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
214 |
+ |
hardwired LJ_rcut |
215 |
+ |
|
216 |
+ |
2004-02-06 19:14 tim |
217 |
+ |
|
218 |
+ |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
219 |
+ |
message] |
220 |
+ |
|
221 |
+ |
2004-02-06 16:37 tim |
222 |
+ |
|
223 |
+ |
* ChangeLog, libBASS/Globals.cpp, |
224 |
+ |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
225 |
+ |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
226 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
227 |
+ |
energy minimization for argon is working, need to add constraint |
228 |
+ |
|
229 |
+ |
2004-02-06 14:05 tim |
230 |
+ |
|
231 |
+ |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
232 |
+ |
one more file into Makefile.in |
233 |
+ |
|
234 |
+ |
2004-02-06 13:58 tim |
235 |
+ |
|
236 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
237 |
+ |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
238 |
+ |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
239 |
+ |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
240 |
+ |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
241 |
+ |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
242 |
+ |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
243 |
+ |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
244 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
245 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
246 |
+ |
some lines into global.cpp to make it work with energy minimization |
247 |
+ |
|
248 |
+ |
2004-02-04 17:26 tim |
249 |
+ |
|
250 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
251 |
+ |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
252 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
253 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
254 |
+ |
Single version of conjugate gradient with golden search linesearch |
255 |
+ |
pass a couple of functions test. Brent's algorithm is still broken |
256 |
+ |
|
257 |
+ |
2004-02-03 17:54 tim |
258 |
+ |
|
259 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
260 |
+ |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
261 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
262 |
+ |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
263 |
+ |
|
264 |
+ |
2004-02-03 15:47 tim |
265 |
+ |
|
266 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
267 |
+ |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
268 |
+ |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
269 |
+ |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
270 |
+ |
SteepestDescent.hpp: [no log message] |
271 |
+ |
|
272 |
+ |
2004-02-03 15:43 tim |
273 |
+ |
|
274 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
275 |
+ |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
276 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
277 |
+ |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
278 |
+ |
constraint class |
279 |
+ |
|
280 |
+ |
2004-02-03 12:10 tim |
281 |
+ |
|
282 |
+ |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
283 |
+ |
|
284 |
+ |
2004-02-03 10:21 tim |
285 |
+ |
|
286 |
+ |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
287 |
+ |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
288 |
+ |
|
289 |
|
2004-02-02 15:29 tim |
290 |
|
|
291 |
|
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
2849 |
|
|
2850 |
|
2003-03-25 09:29 mmeineke |
2851 |
|
|
2852 |
< |
* libBASS/obj/dummy, libmdtools/obj/dummy, src/MPIobj/dummy, |
2853 |
< |
src/obj/dummy: [no log message] |
2852 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
2853 |
> |
src/MPIobj/dummy, src/obj/dummy: [no log message] |
2854 |
|
|
2855 |
|
2003-03-25 09:29 mmeineke |
2856 |
|
|