1 |
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2004-11-04 14:48 tim |
2 |
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|
3 |
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* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
4 |
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SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
5 |
+ |
class |
6 |
+ |
|
7 |
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2004-11-04 14:48 tim |
8 |
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|
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* src/brains/Stats.cpp: file Stats.cpp was initially added on |
10 |
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branch new_design. |
11 |
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|
12 |
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2004-11-04 14:48 tim |
13 |
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|
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* src/brains/Stats.hpp: file Stats.hpp was initially added on |
15 |
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branch new_design. |
16 |
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|
17 |
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2004-11-04 11:22 gezelter |
18 |
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|
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* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
20 |
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RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and |
21 |
+ |
linearAxis are virtual in StuntDouble, but are implemented by |
22 |
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DirectionalAtom and RigidBody In StuntDouble, they should return |
23 |
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false and "-1" but there should be logic to figure them out in the |
24 |
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other two classes |
25 |
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|
26 |
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2004-11-04 11:20 gezelter |
27 |
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|
28 |
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* src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't |
29 |
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remember what I did |
30 |
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|
31 |
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2004-11-04 11:20 gezelter |
32 |
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|
33 |
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* src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky |
34 |
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|
35 |
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2004-11-04 11:20 gezelter |
36 |
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|
37 |
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* src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX |
38 |
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in the entry_plug so that it only is set if the atoms really are in |
39 |
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the simulation |
40 |
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|
41 |
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2004-11-04 11:20 gezelter |
42 |
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|
43 |
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* samples/water/ssd/ssd.md: testing force fields |
44 |
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|
45 |
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2004-11-04 11:19 gezelter |
46 |
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|
47 |
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* samples/shape/linear.in: testing shapes |
48 |
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|
49 |
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2004-11-03 14:56 tim |
50 |
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|
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* src/brains/SimCreator.cpp: file SimCreator.cpp was initially |
52 |
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added on branch new_design. |
53 |
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|
54 |
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2004-11-03 14:56 tim |
55 |
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|
56 |
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* src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator |
57 |
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class(similar as SimSetup) |
58 |
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|
59 |
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2004-11-03 14:56 tim |
60 |
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|
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* src/brains/SimCreator.hpp: file SimCreator.hpp was initially |
62 |
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added on branch new_design. |
63 |
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|
64 |
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2004-11-03 13:00 tim |
65 |
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|
66 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
67 |
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UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, |
68 |
+ |
UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp, |
69 |
+ |
brains/DataStorage.hpp, primitives/Atom.hpp, |
70 |
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primitives/DirectionalAtom.hpp, restraints/Restraints.hpp, |
71 |
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visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get |
72 |
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compiled. Still a long way to go ...... |
73 |
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|
74 |
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2004-11-03 11:08 tim |
75 |
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|
76 |
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* ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
77 |
+ |
src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, |
78 |
+ |
src/integrators/NPTf.cpp, src/integrators/NPTi.cpp, |
79 |
+ |
src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp, |
80 |
+ |
src/io/ZConsReader.cpp, src/primitives/Bend.cpp, |
81 |
+ |
src/primitives/Bond.cpp, src/primitives/GhostBend.cpp, |
82 |
+ |
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
83 |
+ |
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
84 |
+ |
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
85 |
+ |
src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp, |
86 |
+ |
src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, |
87 |
+ |
src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... |
88 |
+ |
|
89 |
+ |
2004-11-02 17:41 tim |
90 |
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|
91 |
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* src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was |
92 |
+ |
initially added on branch new_design. |
93 |
+ |
|
94 |
+ |
2004-11-02 17:41 tim |
95 |
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|
96 |
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* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
97 |
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branch new_design. |
98 |
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|
99 |
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2004-11-02 17:41 tim |
100 |
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|
101 |
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* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
102 |
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utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
103 |
+ |
Need unit test |
104 |
+ |
|
105 |
+ |
2004-11-02 11:59 tim |
106 |
+ |
|
107 |
+ |
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
108 |
+ |
SimSnapshotManager.hpp: SimModel in progress |
109 |
+ |
|
110 |
+ |
2004-11-02 11:59 tim |
111 |
+ |
|
112 |
+ |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
113 |
+ |
branch new_design. |
114 |
+ |
|
115 |
+ |
2004-11-02 10:28 chrisfen |
116 |
+ |
|
117 |
+ |
* src/: UseTheForce/DarkSide/shapes.F90, |
118 |
+ |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes |
119 |
+ |
looks like it's working |
120 |
+ |
|
121 |
+ |
2004-11-02 10:27 tim |
122 |
+ |
|
123 |
+ |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
124 |
+ |
added on branch new_design. |
125 |
+ |
|
126 |
+ |
2004-11-02 10:27 tim |
127 |
+ |
|
128 |
+ |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
129 |
+ |
functions for dealing with memory issue |
130 |
+ |
|
131 |
+ |
2004-11-02 10:23 tim |
132 |
+ |
|
133 |
+ |
* src/: brains/SimModel.hpp, brains/Snapshot.hpp, |
134 |
+ |
brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding |
135 |
+ |
SimModel(something similar as SimInfo) |
136 |
+ |
|
137 |
+ |
2004-11-01 17:52 tim |
138 |
+ |
|
139 |
+ |
* src/: applications/simpleBuilder/MoLocator.hpp, |
140 |
+ |
applications/simpleBuilder/simpleBuilder.cpp, |
141 |
+ |
brains/DataStorage.hpp, brains/ForceFields.cpp, |
142 |
+ |
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp, |
143 |
+ |
constraints/ZConstraint.cpp, integrators/Integrator.cpp, |
144 |
+ |
integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp, |
145 |
+ |
math/SquareMatrix3.hpp, math/Vector3.hpp, |
146 |
+ |
minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp, |
147 |
+ |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
148 |
+ |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
149 |
+ |
primitives/RigidBody.hpp, primitives/Torsion.hpp, |
150 |
+ |
restraints/Restraints.cpp, types/TorsionType.hpp, |
151 |
+ |
utils/PropertyMap.hpp, utils/StringTokenizer.hpp, |
152 |
+ |
visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp, |
153 |
+ |
visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, |
154 |
+ |
RigidBody and StuntDouble classes get compiled |
155 |
+ |
|
156 |
+ |
2004-11-01 16:40 tim |
157 |
+ |
|
158 |
+ |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
159 |
+ |
on branch new_design. |
160 |
+ |
|
161 |
+ |
2004-11-01 16:40 tim |
162 |
+ |
|
163 |
+ |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
164 |
+ |
branch new_design. |
165 |
+ |
|
166 |
+ |
2004-11-01 16:40 tim |
167 |
+ |
|
168 |
+ |
* src/primitives/Bond.hpp: file Bond.hpp was initially added on |
169 |
+ |
branch new_design. |
170 |
+ |
|
171 |
+ |
2004-11-01 16:40 tim |
172 |
+ |
|
173 |
+ |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
174 |
+ |
version of Bond, Bend and Torsion. |
175 |
+ |
|
176 |
+ |
2004-11-01 16:37 tim |
177 |
+ |
|
178 |
+ |
* src/types/BendType.hpp: file BendType.hpp was initially added on |
179 |
+ |
branch new_design. |
180 |
+ |
|
181 |
+ |
2004-11-01 16:37 tim |
182 |
+ |
|
183 |
+ |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
184 |
+ |
BondType, BendType, TorsionType |
185 |
+ |
|
186 |
+ |
2004-11-01 16:37 tim |
187 |
+ |
|
188 |
+ |
* src/types/TorsionType.hpp: file TorsionType.hpp was initially |
189 |
+ |
added on branch new_design. |
190 |
+ |
|
191 |
+ |
2004-11-01 16:37 tim |
192 |
+ |
|
193 |
+ |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
194 |
+ |
branch new_design. |
195 |
+ |
|
196 |
+ |
2004-11-01 15:15 tim |
197 |
+ |
|
198 |
+ |
* src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
199 |
+ |
CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
200 |
+ |
GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp, |
201 |
+ |
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: |
202 |
+ |
break, break and break..... |
203 |
+ |
|
204 |
+ |
2004-11-01 14:57 tim |
205 |
+ |
|
206 |
+ |
* test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, |
207 |
+ |
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, |
208 |
+ |
StuntDouble.hpp: these core classes get compiled |
209 |
+ |
|
210 |
+ |
2004-10-29 17:37 tim |
211 |
+ |
|
212 |
+ |
* test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule |
213 |
+ |
class |
214 |
+ |
|
215 |
+ |
2004-10-29 17:28 chrisfen |
216 |
+ |
|
217 |
+ |
* src/: UseTheForce/DarkSide/atype.F90, |
218 |
+ |
UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, |
219 |
+ |
types/ShapeAtomType.cpp: still debugging |
220 |
+ |
|
221 |
+ |
2004-10-29 17:28 chrisfen |
222 |
+ |
|
223 |
+ |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: |
224 |
+ |
shapes rcut calculator added |
225 |
+ |
|
226 |
+ |
2004-10-29 17:27 chrisfen |
227 |
+ |
|
228 |
+ |
* samples/shape/linear.md: shorter run |
229 |
+ |
|
230 |
+ |
2004-10-29 15:54 tim |
231 |
+ |
|
232 |
+ |
* test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. |
233 |
+ |
|
234 |
+ |
2004-10-29 11:22 tim |
235 |
+ |
|
236 |
+ |
* test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, |
237 |
+ |
ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove |
238 |
+ |
some deprecated files |
239 |
+ |
|
240 |
+ |
2004-10-29 11:20 tim |
241 |
+ |
|
242 |
+ |
* test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, |
243 |
+ |
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: |
244 |
+ |
More painful reconstruction is coming !!! |
245 |
+ |
|
246 |
+ |
2004-10-28 17:34 tim |
247 |
+ |
|
248 |
+ |
* src/brains/DataStorage.hpp, src/utils/next_combination.hpp, |
249 |
+ |
test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, |
250 |
+ |
test/brains/RigidBody.cpp, test/brains/RigidBody.hpp, |
251 |
+ |
test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, |
252 |
+ |
DirectionalAtom and RigidBody |
253 |
+ |
|
254 |
+ |
2004-10-28 17:26 tim |
255 |
+ |
|
256 |
+ |
* ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, |
257 |
+ |
src/applications/simpleBuilder/MoLocator.cpp, |
258 |
+ |
src/applications/simpleBuilder/Vector3d.hpp, |
259 |
+ |
src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: |
260 |
+ |
remove old Vector3d.hpp from application/simpleBuilder |
261 |
+ |
|
262 |
+ |
2004-10-28 16:42 tim |
263 |
+ |
|
264 |
+ |
* src/utils/next_combination.hpp: Minor change in next_combination |
265 |
+ |
|
266 |
+ |
2004-10-28 16:28 tim |
267 |
+ |
|
268 |
+ |
* src/utils/next_combination.hpp, |
269 |
+ |
test/utils/NextCombinationTestCase.cpp, |
270 |
+ |
test/utils/ReplaceWildCardTestCase.cpp: Done with combination |
271 |
+ |
|
272 |
+ |
2004-10-28 16:11 tim |
273 |
+ |
|
274 |
+ |
* src/utils/next_combination.hpp: change documentation of |
275 |
+ |
next_combination.hpp |
276 |
+ |
|
277 |
+ |
2004-10-28 15:41 tim |
278 |
+ |
|
279 |
+ |
* ChangeLog, src/utils/next_combination.hpp, |
280 |
+ |
test/utils/NextCombinationTestCase.cpp, |
281 |
+ |
test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working |
282 |
+ |
|
283 |
+ |
2004-10-28 15:01 tim |
284 |
+ |
|
285 |
+ |
* src/utils/next_combination.hpp: adding replace wildcard function |
286 |
+ |
|
287 |
+ |
2004-10-28 14:33 tim |
288 |
+ |
|
289 |
+ |
* src/utils/next_combination.hpp: Minor change |
290 |
+ |
|
291 |
+ |
2004-10-28 14:06 tim |
292 |
+ |
|
293 |
+ |
* ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, |
294 |
+ |
src/applications/simpleBuilder/simpleBuilder.cpp, |
295 |
+ |
src/utils/next_combination.hpp, test/utils/Makefile, |
296 |
+ |
test/utils/NextCombinationTestCase.cpp, |
297 |
+ |
test/utils/ReplaceWildCardTestCase.cpp, |
298 |
+ |
test/utils/next_combination.hpp: STL next_permutation like |
299 |
+ |
next_combination is working |
300 |
+ |
|
301 |
+ |
2004-10-28 12:22 chrisfen |
302 |
+ |
|
303 |
+ |
* src/UseTheForce/WATER.cpp: fix of setDipoles |
304 |
+ |
|
305 |
+ |
2004-10-28 12:20 gezelter |
306 |
+ |
|
307 |
+ |
* src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the |
308 |
+ |
shapeFile |
309 |
+ |
|
310 |
+ |
2004-10-28 12:20 gezelter |
311 |
+ |
|
312 |
+ |
* samples/shape/linear.md: forgot the orientation line |
313 |
+ |
|
314 |
+ |
2004-10-28 11:56 gezelter |
315 |
+ |
|
316 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
317 |
+ |
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
318 |
+ |
UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate |
319 |
+ |
declaration foo |
320 |
+ |
|
321 |
+ |
2004-10-28 11:55 gezelter |
322 |
+ |
|
323 |
+ |
* samples/lipid/5x5.md: uncommented .in line |
324 |
+ |
|
325 |
+ |
2004-10-28 10:42 tim |
326 |
+ |
|
327 |
+ |
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
328 |
+ |
NextCombinationTestCase.hpp, next_combination.hpp: next_combination |
329 |
+ |
in progress |
330 |
+ |
|
331 |
+ |
2004-10-28 10:15 tim |
332 |
+ |
|
333 |
+ |
* test/utils/: NextCombinationTestCase.cpp, |
334 |
+ |
NextCombinationTestCase.hpp: adding next_combination test case |
335 |
+ |
|
336 |
+ |
2004-10-28 10:02 tim |
337 |
+ |
|
338 |
+ |
* test/utils/next_combination.hpp: STL Compatible combination |
339 |
+ |
sequence generator |
340 |
+ |
|
341 |
+ |
2004-10-28 01:23 tim |
342 |
+ |
|
343 |
+ |
* test/utils/: GenerateCombination.hpp, |
344 |
+ |
ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp |
345 |
+ |
|
346 |
+ |
2004-10-28 01:16 tim |
347 |
+ |
|
348 |
+ |
* test/utils/GenerateCombination.hpp: a STL next_permutaion like |
349 |
+ |
next_combination function. |
350 |
+ |
|
351 |
+ |
2004-10-27 22:27 tim |
352 |
+ |
|
353 |
+ |
* test/utils/ReplaceWildCard.hpp: no message |
354 |
+ |
|
355 |
+ |
2004-10-27 22:14 tim |
356 |
+ |
|
357 |
+ |
* test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: |
358 |
+ |
ReplaceWildCard(recursive version) is working, need refactoring. An |
359 |
+ |
iterative version is on the way |
360 |
+ |
|
361 |
+ |
2004-10-27 21:28 tim |
362 |
+ |
|
363 |
+ |
* test/utils/: Makefile, ReplaceWildCard.hpp, |
364 |
+ |
ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress |
365 |
+ |
|
366 |
+ |
2004-10-27 21:08 tim |
367 |
+ |
|
368 |
+ |
* test/utils/: ReplaceWildCardTestCase.cpp, |
369 |
+ |
ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard |
370 |
+ |
|
371 |
+ |
2004-10-27 18:17 tim |
372 |
+ |
|
373 |
+ |
* test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need |
374 |
+ |
test |
375 |
+ |
|
376 |
+ |
2004-10-27 01:25 tim |
377 |
+ |
|
378 |
+ |
* src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild |
379 |
+ |
char matching is on the way |
380 |
+ |
|
381 |
+ |
2004-10-27 01:07 tim |
382 |
+ |
|
383 |
+ |
* src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 |
384 |
+ |
|
385 |
|
2004-10-26 22:00 gezelter |
386 |
|
|
387 |
|
* src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix |
422 |
|
UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: |
423 |
|
forcefield refactoring for shapes |
424 |
|
|
425 |
+ |
2004-10-26 17:24 gezelter |
426 |
+ |
|
427 |
+ |
* samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, |
428 |
+ |
Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, |
429 |
+ |
linear.md, linear.shape, toluene.shape: adding sample shape |
430 |
+ |
directory |
431 |
+ |
|
432 |
|
2004-10-26 17:19 tim |
433 |
|
|
434 |
|
* ChangeLog, src/brains/DataStorage.cpp, |