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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|
19 |
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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 |
+ |
DirectionalAtom and RigidBody In StuntDouble, they should return |
23 |
+ |
false and "-1" but there should be logic to figure them out in the |
24 |
+ |
other two classes |
25 |
+ |
|
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 |
+ |
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 |
+ |
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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|
61 |
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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 |
+ |
primitives/DirectionalAtom.hpp, restraints/Restraints.hpp, |
71 |
+ |
visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get |
72 |
+ |
compiled. Still a long way to go ...... |
73 |
+ |
|
74 |
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2004-11-03 11:08 tim |
75 |
+ |
|
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 |
388 |
+ |
|
389 |
+ |
2004-10-26 21:20 gezelter |
390 |
+ |
|
391 |
+ |
* src/UseTheForce/ForceFields.hpp: subclass foo |
392 |
+ |
|
393 |
+ |
2004-10-26 21:16 gezelter |
394 |
+ |
|
395 |
+ |
* src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> |
396 |
+ |
string conversion |
397 |
+ |
|
398 |
+ |
2004-10-26 19:01 gezelter |
399 |
+ |
|
400 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
401 |
+ |
UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, |
402 |
+ |
brains/SimSetup.hpp: char* -> string |
403 |
+ |
|
404 |
+ |
2004-10-26 17:25 gezelter |
405 |
+ |
|
406 |
+ |
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, |
407 |
+ |
Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, |
408 |
+ |
ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some |
409 |
+ |
isXXX |
410 |
+ |
|
411 |
+ |
2004-10-26 17:25 gezelter |
412 |
+ |
|
413 |
+ |
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
414 |
+ |
define name collision |
415 |
+ |
|
416 |
+ |
2004-10-26 17:24 gezelter |
417 |
+ |
|
418 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
419 |
+ |
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
420 |
+ |
UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp, |
421 |
+ |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
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, |
435 |
+ |
src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, |
436 |
+ |
test/brains/DataStorageTestCase.cpp, |
437 |
+ |
test/brains/DataStorageTestCase.hpp, test/brains/Makefile: |
438 |
+ |
DataStorage passes unit test |
439 |
+ |
|
440 |
+ |
2004-10-26 13:03 chrisfen |
441 |
+ |
|
442 |
+ |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: |
443 |
+ |
Changes to help advance shapes |
444 |
+ |
|
445 |
+ |
2004-10-26 13:02 chrisfen |
446 |
+ |
|
447 |
+ |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to |
448 |
+ |
Shapes force field reader |
449 |
+ |
|
450 |
+ |
2004-10-26 12:28 tim |
451 |
+ |
|
452 |
+ |
* src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and |
453 |
+ |
SnapshotTestCase in progress |
454 |
+ |
|
455 |
+ |
2004-10-25 17:46 tim |
456 |
+ |
|
457 |
+ |
* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
458 |
+ |
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
459 |
+ |
src/math/Vector3.hpp, test/brains/StuntDouble.hpp, |
460 |
+ |
test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, |
461 |
+ |
test/math/VectorTestCase.cpp: add getArray function to RectMatrix |
462 |
+ |
and Vector classes |
463 |
+ |
|
464 |
+ |
2004-10-25 12:03 tim |
465 |
+ |
|
466 |
+ |
* ChangeLog, src/utils/GenericFactory.hpp, |
467 |
+ |
test/utils/GenericFactoryTestCase.cpp, |
468 |
+ |
test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding |
469 |
+ |
GenericFactory Test Case. GenericFactory now can bed used to creat |
470 |
+ |
ForcefieldFactory and IntegratorFactory etc. |
471 |
+ |
|
472 |
+ |
2004-10-24 23:08 tim |
473 |
+ |
|
474 |
+ |
* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, |
475 |
+ |
brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, |
476 |
+ |
brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes |
477 |
+ |
get reconstructed |
478 |
+ |
|
479 |
+ |
2004-10-24 02:55 tim |
480 |
+ |
|
481 |
+ |
* src/utils/GenericFactory.hpp: GenericFactory pass unit test |
482 |
+ |
|
483 |
+ |
2004-10-23 18:09 tim |
484 |
+ |
|
485 |
+ |
* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, |
486 |
+ |
StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, |
487 |
+ |
RigidBody.cpp: Refactoring in progress |
488 |
+ |
|
489 |
+ |
2004-10-22 18:09 tim |
490 |
+ |
|
491 |
+ |
* ChangeLog, src/brains/Snapshot.hpp, |
492 |
+ |
src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, |
493 |
+ |
test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, |
494 |
+ |
test/brains/StuntDouble.hpp: more work in Snapshot |
495 |
+ |
|
496 |
+ |
2004-10-22 17:59 chrisfen |
497 |
+ |
|
498 |
+ |
* src/: UseTheForce/LJFF.cpp, |
499 |
+ |
UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear |
500 |
+ |
god! It runs and conserves energy! |
501 |
+ |
|
502 |
+ |
2004-10-22 17:54 chrisfen |
503 |
+ |
|
504 |
+ |
* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY |
505 |
+ |
|
506 |
+ |
2004-10-22 17:53 chrisfen |
507 |
+ |
|
508 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
509 |
+ |
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
510 |
+ |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
511 |
+ |
brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey |
512 |
+ |
breakey |
513 |
+ |
|
514 |
+ |
2004-10-22 17:53 chrisfen |
515 |
+ |
|
516 |
+ |
* make/Makefile.in: compiler flags |
517 |
+ |
|
518 |
+ |
2004-10-22 16:20 gezelter |
519 |
+ |
|
520 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
521 |
+ |
UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, |
522 |
+ |
brains/fSimulation.h, types/AtomType.hpp, |
523 |
+ |
types/DirectionalAtomType.hpp: fixey fixey |
524 |
+ |
|
525 |
+ |
2004-10-22 15:22 gezelter |
526 |
+ |
|
527 |
+ |
* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, |
528 |
+ |
charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, |
529 |
+ |
lj_interface.h, shapes.F90, simulation.F90: Added un-busticated |
530 |
+ |
fortran files and c/Fortran interfaces |
531 |
+ |
|
532 |
+ |
2004-10-22 15:21 gezelter |
533 |
+ |
|
534 |
+ |
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
535 |
+ |
DirectionalAtomType.hpp, Makefile: More on AtomType and |
536 |
+ |
DirectionalAtomType |
537 |
+ |
|
538 |
+ |
2004-10-22 09:47 gezelter |
539 |
+ |
|
540 |
+ |
* src/types/AtomType.hpp: Adding AtomType |
541 |
+ |
|
542 |
+ |
2004-10-21 16:31 tim |
543 |
+ |
|
544 |
+ |
* ChangeLog, src/brains/Snapshot.hpp, |
545 |
+ |
src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, |
546 |
+ |
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
547 |
+ |
src/math/Vector.hpp, src/math/Vector3.hpp, |
548 |
+ |
test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: |
549 |
+ |
Snapshot and SnapshotManager in progress |
550 |
+ |
|
551 |
+ |
2004-10-21 16:30 tim |
552 |
+ |
|
553 |
+ |
* test/brains/: BrainsTest.cpp, Makefile, |
554 |
+ |
SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, |
555 |
+ |
SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for |
556 |
+ |
Snapshot and snapshotManager. |
557 |
+ |
|
558 |
+ |
2004-10-21 15:15 gezelter |
559 |
+ |
|
560 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
561 |
+ |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
562 |
+ |
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
563 |
+ |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
564 |
+ |
UseTheForce/doForces_interface.h, UseTheForce/fForceField.h, |
565 |
+ |
UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h, |
566 |
+ |
brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. |
567 |
+ |
Fixey Fixey. |
568 |
+ |
|
569 |
+ |
2004-10-21 11:32 tim |
570 |
+ |
|
571 |
+ |
* src/utils/GenericData.cpp, src/utils/Makefile, |
572 |
+ |
test/utils/Makefile, test/utils/UtilTest: remove some junk files |
573 |
+ |
|
574 |
+ |
2004-10-21 11:24 tim |
575 |
+ |
|
576 |
+ |
* test/utils/GenericData.hpp: remove backup of GenericData.hpp |
577 |
+ |
|
578 |
+ |
2004-10-21 11:22 tim |
579 |
+ |
|
580 |
+ |
* ChangeLog, src/brains/SimSetup.cpp, |
581 |
+ |
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
582 |
+ |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
583 |
+ |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
584 |
+ |
src/integrators/NVT.cpp, src/io/DumpReader.cpp, |
585 |
+ |
src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp, |
586 |
+ |
src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp, |
587 |
+ |
src/utils/GenericData.cpp, src/utils/GenericData.hpp, |
588 |
+ |
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
589 |
+ |
src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
590 |
+ |
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
591 |
+ |
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
592 |
+ |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
593 |
+ |
src/visitors/ZconsVisitor.hpp: replace old GebericData with new |
594 |
+ |
GenericData |
595 |
+ |
|
596 |
+ |
2004-10-21 10:25 chuckv |
597 |
+ |
|
598 |
+ |
* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj |
599 |
+ |
module. |
600 |
+ |
|
601 |
+ |
2004-10-21 10:24 chuckv |
602 |
+ |
|
603 |
+ |
* src/UseTheForce/DarkSide/lj_interface.h: Added interface for |
604 |
+ |
fortran lj module. |
605 |
+ |
|
606 |
+ |
2004-10-20 17:54 tim |
607 |
+ |
|
608 |
+ |
* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, |
609 |
+ |
test/utils/GenericDataTestCase.cpp, test/utils/Makefile, |
610 |
+ |
test/utils/PropertyMapTestCase.cpp, |
611 |
+ |
test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: |
612 |
+ |
GenericData and PropertyMap pass unit test. |
613 |
+ |
|
614 |
+ |
2004-10-20 16:52 gezelter |
615 |
+ |
|
616 |
+ |
* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, |
617 |
+ |
DarkSide/sticky_interface.h: fixed a fortran name problem |
618 |
+ |
|
619 |
+ |
2004-10-20 16:38 tim |
620 |
+ |
|
621 |
+ |
* test/utils/: GenericData.hpp, GenericDataTestCase.cpp, |
622 |
+ |
GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, |
623 |
+ |
UtilTest, UtilTest.cpp: adding generic data test case |
624 |
+ |
|
625 |
+ |
2004-10-20 16:16 chuckv |
626 |
+ |
|
627 |
+ |
* configure, ac-tools/aclocal.m4, |
628 |
+ |
src/UseTheForce/DarkSide/Makefile, |
629 |
+ |
src/UseTheForce/DarkSide/mpiSimulation.F90, |
630 |
+ |
src/UseTheForce/DarkSide/mpiSimulation_interface.h, |
631 |
+ |
src/UseTheForce/DarkSide/simParallel.F90, |
632 |
+ |
src/UseTheForce/DarkSide/simParallel_interface.h, |
633 |
+ |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: |
634 |
+ |
Fortran/C++ interface de-obfuscation project appears to be |
635 |
+ |
complete! Woo hoo! |
636 |
+ |
|
637 |
+ |
2004-10-20 15:47 chuckv |
638 |
+ |
|
639 |
+ |
* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, |
640 |
+ |
fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project |
641 |
+ |
continues |
642 |
+ |
|
643 |
+ |
2004-10-20 15:46 chuckv |
644 |
+ |
|
645 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
646 |
+ |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
647 |
+ |
UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, |
648 |
+ |
UseTheForce/doForces_interface.h, |
649 |
+ |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, |
650 |
+ |
UseTheForce/DarkSide/atype_interface.h, |
651 |
+ |
UseTheForce/DarkSide/eam_interface.h, |
652 |
+ |
UseTheForce/DarkSide/gb_interface.h, |
653 |
+ |
UseTheForce/DarkSide/mpiSimulation_interface.h, |
654 |
+ |
UseTheForce/DarkSide/shapes_interface.h, |
655 |
+ |
UseTheForce/DarkSide/simulation_interface.h, |
656 |
+ |
UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, |
657 |
+ |
brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface |
658 |
+ |
de-obfuscation project (It is a very long story) |
659 |
+ |
|
660 |
+ |
2004-10-20 13:07 tim |
661 |
+ |
|
662 |
+ |
* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
663 |
+ |
test/math/SquareMatrix3TestCase.cpp, |
664 |
+ |
test/math/SquareMatrixTestCase.cpp, |
665 |
+ |
test/math/SquareMatrixTestCase.hpp: Math library pass the unit test |
666 |
+ |
|
667 |
+ |
2004-10-20 00:52 tim |
668 |
+ |
|
669 |
+ |
* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
670 |
+ |
SnapshotManager in design phase |
671 |
+ |
|
672 |
+ |
2004-10-19 23:54 gezelter |
673 |
+ |
|
674 |
+ |
* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
675 |
+ |
problem prevented linking |
676 |
+ |
|
677 |
+ |
2004-10-19 23:54 gezelter |
678 |
+ |
|
679 |
+ |
* src/UseTheForce/Shapes_FF.cpp: fixed include |
680 |
+ |
|
681 |
+ |
2004-10-19 23:26 gezelter |
682 |
+ |
|
683 |
+ |
* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
684 |
+ |
oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
685 |
+ |
more fortran name mangling |
686 |
+ |
|
687 |
+ |
2004-10-19 23:23 gezelter |
688 |
+ |
|
689 |
+ |
* src/profiling/timing.F90: yet more fortran renaming |
690 |
+ |
|
691 |
+ |
2004-10-19 23:19 gezelter |
692 |
+ |
|
693 |
+ |
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
694 |
+ |
do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
695 |
+ |
notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
696 |
+ |
wrappers.F90: Fortran name cleanup continues |
697 |
+ |
|
698 |
+ |
2004-10-19 23:12 gezelter |
699 |
+ |
|
700 |
+ |
* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
701 |
+ |
broken fortran stuff |
702 |
+ |
|
703 |
+ |
2004-10-19 23:02 gezelter |
704 |
+ |
|
705 |
+ |
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
706 |
+ |
atype_interface.h, atype_module.F90, atype_module_interface.h, |
707 |
+ |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
708 |
+ |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
709 |
+ |
calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, |
710 |
+ |
eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, |
711 |
+ |
gb_interface.h, gb_module_interface.h, mpiSimulation.F90, |
712 |
+ |
mpiSimulation_interface.h, mpiSimulation_module.F90, |
713 |
+ |
mpisimulation_module_interface.h, reactionField.F90, shapes.F90, |
714 |
+ |
shapes_interface.h, shapes_module.h, simulation.F90, |
715 |
+ |
simulation_interface.h, simulation_module.F90, |
716 |
+ |
simulation_module_interface.h, sticky.F90, sticky_interface.h, |
717 |
+ |
sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
718 |
+ |
name sanity on the fortran side |
719 |
+ |
|
720 |
+ |
2004-10-19 19:18 tim |
721 |
+ |
|
722 |
+ |
* test/math/SquareMatrix3TestCase.hpp: [no log message] |
723 |
+ |
|
724 |
+ |
2004-10-19 18:01 tim |
725 |
+ |
|
726 |
+ |
* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
727 |
+ |
src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
728 |
+ |
except diagonalize(), all of functions in math library pass the |
729 |
+ |
test |
730 |
+ |
|
731 |
+ |
2004-10-19 17:43 chuckv |
732 |
+ |
|
733 |
+ |
* src/UseTheForce/do_Forces.h: Added correct prototypes for |
734 |
+ |
C-fortran interface functions. |
735 |
+ |
|
736 |
+ |
2004-10-19 17:37 chuckv |
737 |
+ |
|
738 |
+ |
* src/UseTheForce/DarkSide/: atype_module_interface.h, |
739 |
+ |
eam_module_inteface.h, gb_module_interface.h, |
740 |
+ |
mpisimulation_module_interface.h, simulation_module_interface.h, |
741 |
+ |
sticky_pair_module_interface.h: Added correct prototypes for |
742 |
+ |
C-fortran interface functions. |
743 |
+ |
|
744 |
+ |
2004-10-19 16:28 tim |
745 |
+ |
|
746 |
+ |
* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
747 |
+ |
src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
748 |
+ |
test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, |
749 |
+ |
test/math/RectMatrixTestCase.cpp, |
750 |
+ |
test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, |
751 |
+ |
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
752 |
+ |
bugs get fixed at math library |
753 |
+ |
|
754 |
+ |
2004-10-19 15:43 chuckv |
755 |
+ |
|
756 |
+ |
* src/UseTheForce/: DarkSide/atype_module_interface.h, |
757 |
+ |
DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
758 |
+ |
DarkSide/mpisimulation_module_interface.h, |
759 |
+ |
DarkSide/simulation_module_interface.h, |
760 |
+ |
DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, |
761 |
+ |
DarkSide/atype_module.F90, DarkSide/calc_gb.F90, |
762 |
+ |
DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, |
763 |
+ |
DarkSide/simulation_module.F90, do_Forces.F90, |
764 |
+ |
fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, |
765 |
+ |
notifycutoffs_module_interface.h: Added new files for fortran |
766 |
+ |
interface. |
767 |
+ |
|
768 |
+ |
2004-10-19 15:43 gezelter |
769 |
+ |
|
770 |
+ |
* src/UseTheForce/Makefile: regressing |
771 |
+ |
|
772 |
+ |
2004-10-19 15:40 gezelter |
773 |
+ |
|
774 |
+ |
* src/: UseTheForce/DarkSide/calc_shapes.F90, |
775 |
+ |
UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
776 |
+ |
working on shapes for portability |
777 |
+ |
|
778 |
+ |
2004-10-19 15:40 gezelter |
779 |
+ |
|
780 |
+ |
* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
781 |
+ |
|
782 |
+ |
2004-10-19 13:21 chrisfen |
783 |
+ |
|
784 |
+ |
* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
785 |
+ |
findBegin |
786 |
+ |
|
787 |
|
2004-10-18 23:34 tim |
788 |
|
|
789 |
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |