1 |
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2004-11-24 12:42 tim |
2 |
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|
3 |
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* src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, |
4 |
+ |
brains/DataStorage.hpp, brains/SimCreator.cpp, |
5 |
+ |
brains/SimCreator.hpp, integrators/Integrator.hpp, |
6 |
+ |
io/ElectrostaticAtomTypesSectionParser.cpp, |
7 |
+ |
primitives/DirectionalAtom.cpp: add SetForceManager method to |
8 |
+ |
integrator |
9 |
+ |
|
10 |
+ |
2004-11-23 18:12 tim |
11 |
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|
12 |
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* src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, |
13 |
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integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
14 |
+ |
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
15 |
+ |
integrators/NPTxyz.cpp, integrators/NPTxyz.hpp, |
16 |
+ |
integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp, |
17 |
+ |
integrators/NVT.hpp, integrators/Velocitizer.cpp, |
18 |
+ |
integrators/VelocityVerletIntegrator.cpp, |
19 |
+ |
integrators/VelocityVerletIntegrator.hpp, |
20 |
+ |
types/UreyBradleyBendType.hpp: refactory NPT integrator |
21 |
+ |
|
22 |
+ |
2004-11-23 17:50 chrisfen |
23 |
+ |
|
24 |
+ |
* samples/water/tip3p_ice/tp3.md: Back to normal... Oh... |
25 |
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Restraints should work in parallel now |
26 |
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|
27 |
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2004-11-23 17:48 chrisfen |
28 |
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|
29 |
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* src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
30 |
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brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
31 |
+ |
integrators/Integrator.cpp, integrators/Integrator.hpp, |
32 |
+ |
io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp, |
33 |
+ |
io/RestraintReader.cpp, io/RestraintWriter.cpp, |
34 |
+ |
restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements |
35 |
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to restraints |
36 |
+ |
|
37 |
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2004-11-23 17:47 chrisfen |
38 |
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|
39 |
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* samples/water/tip3p_ice/tp3.md: just some testing changes, I'll |
40 |
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return to the original on next commit |
41 |
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|
42 |
+ |
2004-11-23 12:53 tim |
43 |
+ |
|
44 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
45 |
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UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
46 |
+ |
applications/simpleBuilder/simpleBuilder.cpp, |
47 |
+ |
io/ChargeAtomTypesSectionParser.cpp, |
48 |
+ |
io/DirectionalAtomTypesSectionParser.hpp, |
49 |
+ |
io/EAMAtomTypesSectionParser.cpp, |
50 |
+ |
io/ElectrostaticAtomTypesSectionParser.cpp, |
51 |
+ |
io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
52 |
+ |
io/SectionParser.hpp, types/DirectionalAtomType.cpp, |
53 |
+ |
utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser |
54 |
+ |
|
55 |
+ |
2004-11-23 12:53 tim |
56 |
+ |
|
57 |
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* src/io/ElectrostaticAtomTypesSectionParser.hpp: file |
58 |
+ |
ElectrostaticAtomTypesSectionParser.hpp was initially added on |
59 |
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branch new_design. |
60 |
+ |
|
61 |
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2004-11-23 12:53 tim |
62 |
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|
63 |
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* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
64 |
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ElectrostaticAtomTypesSectionParser.cpp was initially added on |
65 |
+ |
branch new_design. |
66 |
+ |
|
67 |
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2004-11-23 01:03 tim |
68 |
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|
69 |
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* src/: io/EAMAtomTypesSectionParser.cpp, |
70 |
+ |
io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, |
71 |
+ |
types/AtomType.hpp, types/DirectionalAtomType.cpp, |
72 |
+ |
types/DirectionalAtomType.hpp: add EAM AtomType Section Parser |
73 |
+ |
|
74 |
+ |
2004-11-23 01:03 tim |
75 |
+ |
|
76 |
+ |
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
77 |
+ |
was initially added on branch new_design. |
78 |
+ |
|
79 |
+ |
2004-11-23 01:03 tim |
80 |
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|
81 |
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* src/io/EAMAtomTypesSectionParser.hpp: file |
82 |
+ |
EAMAtomTypesSectionParser.hpp was initially added on branch |
83 |
+ |
new_design. |
84 |
+ |
|
85 |
+ |
2004-11-23 01:03 tim |
86 |
+ |
|
87 |
+ |
* src/io/EAMAtomTypesSectionParser.cpp: file |
88 |
+ |
EAMAtomTypesSectionParser.cpp was initially added on branch |
89 |
+ |
new_design. |
90 |
+ |
|
91 |
+ |
2004-11-22 23:35 tim |
92 |
+ |
|
93 |
+ |
* src/io/TorsionTypesSectionParser.hpp: file |
94 |
+ |
TorsionTypesSectionParser.hpp was initially added on branch |
95 |
+ |
new_design. |
96 |
+ |
|
97 |
+ |
2004-11-22 23:35 tim |
98 |
+ |
|
99 |
+ |
* src/io/BendTypesSectionParser.hpp: file |
100 |
+ |
BendTypesSectionParser.hpp was initially added on branch |
101 |
+ |
new_design. |
102 |
+ |
|
103 |
+ |
2004-11-22 23:35 tim |
104 |
+ |
|
105 |
+ |
* src/io/BondTypesSectionParser.hpp: file |
106 |
+ |
BondTypesSectionParser.hpp was initially added on branch |
107 |
+ |
new_design. |
108 |
+ |
|
109 |
+ |
2004-11-22 23:35 tim |
110 |
+ |
|
111 |
+ |
* src/io/BondTypesSectionParser.cpp: file |
112 |
+ |
BondTypesSectionParser.cpp was initially added on branch |
113 |
+ |
new_design. |
114 |
+ |
|
115 |
+ |
2004-11-22 23:35 tim |
116 |
+ |
|
117 |
+ |
* src/io/TorsionTypesSectionParser.cpp: file |
118 |
+ |
TorsionTypesSectionParser.cpp was initially added on branch |
119 |
+ |
new_design. |
120 |
+ |
|
121 |
+ |
2004-11-22 23:35 tim |
122 |
+ |
|
123 |
+ |
* src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, |
124 |
+ |
BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, |
125 |
+ |
TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add |
126 |
+ |
BondTypesSectionParser, BendTypesSectionParser and |
127 |
+ |
TorsionTypeSectionParser |
128 |
+ |
|
129 |
+ |
2004-11-22 23:35 tim |
130 |
+ |
|
131 |
+ |
* src/io/BendTypesSectionParser.cpp: file |
132 |
+ |
BendTypesSectionParser.cpp was initially added on branch |
133 |
+ |
new_design. |
134 |
+ |
|
135 |
+ |
2004-11-22 18:04 tim |
136 |
+ |
|
137 |
+ |
* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in |
138 |
+ |
DUFF and EAM |
139 |
+ |
|
140 |
+ |
2004-11-22 18:02 tim |
141 |
+ |
|
142 |
+ |
* src/io/: DirectionalAtomTypesParser.hpp, |
143 |
+ |
DirectionalAtomTypesSectionParser.hpp: adding section parsers |
144 |
+ |
|
145 |
+ |
2004-11-22 18:02 tim |
146 |
+ |
|
147 |
+ |
* src/io/DirectionalAtomTypesSectionParser.hpp: file |
148 |
+ |
DirectionalAtomTypesSectionParser.hpp was initially added on branch |
149 |
+ |
new_design. |
150 |
+ |
|
151 |
+ |
2004-11-22 15:55 tim |
152 |
+ |
|
153 |
+ |
* src/io/DipoleAtomTypesSectionParser.hpp: file |
154 |
+ |
DipoleAtomTypesSectionParser.hpp was initially added on branch |
155 |
+ |
new_design. |
156 |
+ |
|
157 |
+ |
2004-11-22 15:55 tim |
158 |
+ |
|
159 |
+ |
* src/io/AtomTypesSectionParser.hpp: file |
160 |
+ |
AtomTypesSectionParser.hpp was initially added on branch |
161 |
+ |
new_design. |
162 |
+ |
|
163 |
+ |
2004-11-22 15:55 tim |
164 |
+ |
|
165 |
+ |
* src/io/HarmonicBondTypesSectionParser.hpp: file |
166 |
+ |
HarmonicBondTypesSectionParser.hpp was initially added on branch |
167 |
+ |
new_design. |
168 |
+ |
|
169 |
+ |
2004-11-22 15:55 tim |
170 |
+ |
|
171 |
+ |
* src/io/StickyAtomTypesSectionParser.cpp: file |
172 |
+ |
StickyAtomTypesSectionParser.cpp was initially added on branch |
173 |
+ |
new_design. |
174 |
+ |
|
175 |
+ |
2004-11-22 15:55 tim |
176 |
+ |
|
177 |
+ |
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
178 |
+ |
LennardJonesAtomTypesSectionParser.hpp was initially added on |
179 |
+ |
branch new_design. |
180 |
+ |
|
181 |
+ |
2004-11-22 15:55 tim |
182 |
+ |
|
183 |
+ |
* src/io/HarmonicBondTypesSectionParser.cpp: file |
184 |
+ |
HarmonicBondTypesSectionParser.cpp was initially added on branch |
185 |
+ |
new_design. |
186 |
+ |
|
187 |
+ |
2004-11-22 15:55 tim |
188 |
+ |
|
189 |
+ |
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
190 |
+ |
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
191 |
+ |
new_design. |
192 |
+ |
|
193 |
+ |
2004-11-22 15:55 tim |
194 |
+ |
|
195 |
+ |
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
196 |
+ |
was initially added on branch new_design. |
197 |
+ |
|
198 |
+ |
2004-11-22 15:55 tim |
199 |
+ |
|
200 |
+ |
* src/io/AtomTypesSectionParser.cpp: file |
201 |
+ |
AtomTypesSectionParser.cpp was initially added on branch |
202 |
+ |
new_design. |
203 |
+ |
|
204 |
+ |
2004-11-22 15:55 tim |
205 |
+ |
|
206 |
+ |
* src/io/ChargeAtomTypesSectionParser.cpp: file |
207 |
+ |
ChargeAtomTypesSectionParser.cpp was initially added on branch |
208 |
+ |
new_design. |
209 |
+ |
|
210 |
+ |
2004-11-22 15:55 tim |
211 |
+ |
|
212 |
+ |
* src/io/DipoleAtomTypesSectionParser.cpp: file |
213 |
+ |
DipoleAtomTypesSectionParser.cpp was initially added on branch |
214 |
+ |
new_design. |
215 |
+ |
|
216 |
+ |
2004-11-22 15:55 tim |
217 |
+ |
|
218 |
+ |
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
219 |
+ |
LennardJonesAtomTypesSectionParser.cpp was initially added on |
220 |
+ |
branch new_design. |
221 |
+ |
|
222 |
+ |
2004-11-22 15:55 tim |
223 |
+ |
|
224 |
+ |
* src/io/ChargeAtomTypesSectionParser.hpp: file |
225 |
+ |
ChargeAtomTypesSectionParser.hpp was initially added on branch |
226 |
+ |
new_design. |
227 |
+ |
|
228 |
+ |
2004-11-22 15:55 tim |
229 |
+ |
|
230 |
+ |
* src/io/StickyAtomTypesSectionParser.hpp: file |
231 |
+ |
StickyAtomTypesSectionParser.hpp was initially added on branch |
232 |
+ |
new_design. |
233 |
+ |
|
234 |
+ |
2004-11-22 15:55 tim |
235 |
+ |
|
236 |
+ |
* src/io/SectionParser.hpp: file SectionParser.hpp was initially |
237 |
+ |
added on branch new_design. |
238 |
+ |
|
239 |
+ |
2004-11-22 15:55 tim |
240 |
+ |
|
241 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
242 |
+ |
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
243 |
+ |
brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
244 |
+ |
integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
245 |
+ |
io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
246 |
+ |
io/ChargeAtomTypesSectionParser.hpp, |
247 |
+ |
io/DipoleAtomTypesSectionParser.cpp, |
248 |
+ |
io/DipoleAtomTypesSectionParser.hpp, |
249 |
+ |
io/DirectionalAtomTypesParser.hpp, |
250 |
+ |
io/DirectionalAtomTypesSectionParser.cpp, |
251 |
+ |
io/HarmonicBondTypesSectionParser.cpp, |
252 |
+ |
io/HarmonicBondTypesSectionParser.hpp, |
253 |
+ |
io/LennardJonesAtomTypesSectionParser.cpp, |
254 |
+ |
io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
255 |
+ |
io/SectionParser.hpp, io/SectionParserManager.cpp, |
256 |
+ |
io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
257 |
+ |
io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
258 |
+ |
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
259 |
+ |
utils/GenericData.hpp: adding section parsers |
260 |
+ |
|
261 |
+ |
2004-11-22 15:55 tim |
262 |
+ |
|
263 |
+ |
* src/io/DirectionalAtomTypesParser.hpp: file |
264 |
+ |
DirectionalAtomTypesParser.hpp was initially added on branch |
265 |
+ |
new_design. |
266 |
+ |
|
267 |
+ |
2004-11-22 15:55 tim |
268 |
+ |
|
269 |
+ |
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
270 |
+ |
was initially added on branch new_design. |
271 |
+ |
|
272 |
+ |
2004-11-22 15:55 tim |
273 |
+ |
|
274 |
+ |
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
275 |
+ |
added on branch new_design. |
276 |
+ |
|
277 |
+ |
2004-11-19 17:12 tim |
278 |
+ |
|
279 |
+ |
* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
280 |
+ |
added on branch new_design. |
281 |
+ |
|
282 |
+ |
2004-11-19 17:12 tim |
283 |
+ |
|
284 |
+ |
* src/: brains/SimState.cpp, brains/SimState.hpp, |
285 |
+ |
io/InitializeFromFile.cpp, types/FixBondType.hpp, |
286 |
+ |
types/FixedBondType.hpp: remove more useless files |
287 |
+ |
|
288 |
+ |
2004-11-19 16:47 tim |
289 |
+ |
|
290 |
+ |
* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, |
291 |
+ |
integrators/Integrator.cpp, applications/Makedepend: remove more |
292 |
+ |
useless files |
293 |
+ |
|
294 |
+ |
2004-11-19 16:38 tim |
295 |
+ |
|
296 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
297 |
+ |
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
298 |
+ |
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
299 |
+ |
integrators/NVT.hpp: refactory integrator |
300 |
+ |
|
301 |
+ |
2004-11-19 16:38 tim |
302 |
+ |
|
303 |
+ |
* src/integrators/NPTi.hpp: file NPTi.hpp was initially added on |
304 |
+ |
branch new_design. |
305 |
+ |
|
306 |
+ |
2004-11-19 16:38 tim |
307 |
+ |
|
308 |
+ |
* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
309 |
+ |
branch new_design. |
310 |
+ |
|
311 |
+ |
2004-11-19 16:38 tim |
312 |
+ |
|
313 |
+ |
* src/integrators/NPT.hpp: file NPT.hpp was initially added on |
314 |
+ |
branch new_design. |
315 |
+ |
|
316 |
+ |
2004-11-19 16:38 tim |
317 |
+ |
|
318 |
+ |
* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
319 |
+ |
on branch new_design. |
320 |
+ |
|
321 |
+ |
2004-11-19 16:38 tim |
322 |
+ |
|
323 |
+ |
* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
324 |
+ |
branch new_design. |
325 |
+ |
|
326 |
+ |
2004-11-19 15:37 tim |
327 |
+ |
|
328 |
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* forceFields/newDUFF.frc: new DUFF forcefield |
329 |
+ |
|
330 |
+ |
2004-11-19 15:23 tim |
331 |
+ |
|
332 |
+ |
* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
333 |
+ |
branch new_design. |
334 |
+ |
|
335 |
+ |
2004-11-19 15:23 tim |
336 |
+ |
|
337 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, |
338 |
+ |
UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, |
339 |
+ |
utils/TypeContainer.hpp: add EAM |
340 |
+ |
|
341 |
+ |
2004-11-19 15:23 tim |
342 |
+ |
|
343 |
+ |
* src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on |
344 |
+ |
branch new_design. |
345 |
+ |
|
346 |
+ |
2004-11-19 13:02 tim |
347 |
+ |
|
348 |
+ |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except |
349 |
+ |
error checking |
350 |
+ |
|
351 |
+ |
2004-11-19 12:56 tim |
352 |
+ |
|
353 |
+ |
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
354 |
+ |
was initially added on branch new_design. |
355 |
+ |
|
356 |
+ |
2004-11-19 12:56 tim |
357 |
+ |
|
358 |
+ |
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
359 |
+ |
was initially added on branch new_design. |
360 |
+ |
|
361 |
+ |
2004-11-19 12:56 tim |
362 |
+ |
|
363 |
+ |
* src/types/FixBondType.hpp: file FixBondType.hpp was initially |
364 |
+ |
added on branch new_design. |
365 |
+ |
|
366 |
+ |
2004-11-19 12:56 tim |
367 |
+ |
|
368 |
+ |
* src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, |
369 |
+ |
UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, |
370 |
+ |
UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, |
371 |
+ |
integrators/IntegratorFactory.cpp, |
372 |
+ |
integrators/IntegratorFactory.hpp, integrators/NVE.hpp, |
373 |
+ |
integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp, |
374 |
+ |
utils/StringTokenizer.cpp: DUFF is almost done except error |
375 |
+ |
checking |
376 |
+ |
|
377 |
+ |
2004-11-18 19:11 tim |
378 |
+ |
|
379 |
+ |
* src/UseTheForce/DUFF.cpp: adding DUFF parser |
380 |
+ |
|
381 |
+ |
2004-11-18 18:26 tim |
382 |
+ |
|
383 |
+ |
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
384 |
+ |
initially added on branch new_design. |
385 |
+ |
|
386 |
+ |
2004-11-18 18:26 tim |
387 |
+ |
|
388 |
+ |
* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, |
389 |
+ |
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
390 |
+ |
integrators/VelocityVerletIntegrator.cpp, |
391 |
+ |
integrators/VelocityVerletIntegrator.hpp, |
392 |
+ |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
393 |
+ |
types/CubicBendType.hpp, types/CubicBondType.hpp, |
394 |
+ |
types/HarmonicBondType.hpp, types/QuadraticBendType.hpp, |
395 |
+ |
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding |
396 |
+ |
DUFF parser |
397 |
+ |
|
398 |
+ |
2004-11-18 16:42 tim |
399 |
+ |
|
400 |
+ |
* forceFields/newDUFF.frc: adding new format DUFF force field |
401 |
+ |
|
402 |
+ |
2004-11-18 10:57 chrisfen |
403 |
+ |
|
404 |
+ |
* src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that |
405 |
+ |
slowed down the force loop |
406 |
+ |
|
407 |
+ |
2004-11-18 00:42 tim |
408 |
+ |
|
409 |
+ |
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
410 |
+ |
initially added on branch new_design. |
411 |
+ |
|
412 |
+ |
2004-11-18 00:42 tim |
413 |
+ |
|
414 |
+ |
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
415 |
+ |
initially added on branch new_design. |
416 |
+ |
|
417 |
+ |
2004-11-18 00:42 tim |
418 |
+ |
|
419 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, |
420 |
+ |
primitives/Bend.cpp, utils/NumericConstant.cpp, |
421 |
+ |
utils/NumericConstant.hpp: Adding NumericConstant class |
422 |
+ |
|
423 |
+ |
2004-11-17 23:16 tim |
424 |
+ |
|
425 |
+ |
* src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, |
426 |
+ |
UseTheForce/ForceFields.hpp: remove more junk files |
427 |
+ |
|
428 |
+ |
2004-11-17 23:12 tim |
429 |
+ |
|
430 |
+ |
* src/: brains/ForceFields.cpp, brains/SimSetup.cpp, |
431 |
+ |
brains/SimSetup.hpp, constraints/AbstractClasses.hpp, |
432 |
+ |
integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp, |
433 |
+ |
primitives/AbstractClasses.hpp, primitives/Bond.cpp, |
434 |
+ |
primitives/BondExtensions.cpp, primitives/SRI.hpp, |
435 |
+ |
primitives/TorsionExtensions.cpp: remove some junk files |
436 |
+ |
|
437 |
+ |
2004-11-17 23:07 tim |
438 |
+ |
|
439 |
+ |
* src/primitives/BendExtensions.cpp: remove some junk files |
440 |
+ |
|
441 |
+ |
2004-11-17 23:04 tim |
442 |
+ |
|
443 |
+ |
* src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, |
444 |
+ |
QuadraticBondType.hpp: refine QudraticBond |
445 |
+ |
|
446 |
+ |
2004-11-17 22:57 tim |
447 |
+ |
|
448 |
+ |
* src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp |
449 |
+ |
|
450 |
+ |
2004-11-17 22:57 tim |
451 |
+ |
|
452 |
+ |
* src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was |
453 |
+ |
initially added on branch new_design. |
454 |
+ |
|
455 |
+ |
2004-11-17 16:47 tim |
456 |
+ |
|
457 |
+ |
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
458 |
+ |
was initially added on branch new_design. |
459 |
+ |
|
460 |
+ |
2004-11-17 16:47 tim |
461 |
+ |
|
462 |
+ |
* src/types/CubicBendType.hpp: file CubicBendType.hpp was initially |
463 |
+ |
added on branch new_design. |
464 |
+ |
|
465 |
+ |
2004-11-17 16:47 tim |
466 |
+ |
|
467 |
+ |
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
468 |
+ |
added on branch new_design. |
469 |
+ |
|
470 |
+ |
2004-11-17 16:47 tim |
471 |
+ |
|
472 |
+ |
* src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was |
473 |
+ |
initially added on branch new_design. |
474 |
+ |
|
475 |
+ |
2004-11-17 16:47 tim |
476 |
+ |
|
477 |
+ |
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
478 |
+ |
initially added on branch new_design. |
479 |
+ |
|
480 |
+ |
2004-11-17 16:47 tim |
481 |
+ |
|
482 |
+ |
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
483 |
+ |
initially added on branch new_design. |
484 |
+ |
|
485 |
+ |
2004-11-17 16:47 tim |
486 |
+ |
|
487 |
+ |
* src/types/CubicBondType.hpp: file CubicBondType.hpp was initially |
488 |
+ |
added on branch new_design. |
489 |
+ |
|
490 |
+ |
2004-11-17 16:47 tim |
491 |
+ |
|
492 |
+ |
* src/: math/ChebyshevPolynomials.cpp, |
493 |
+ |
math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, |
494 |
+ |
primitives/Bend.hpp, primitives/GhostBend.cpp, |
495 |
+ |
primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp, |
496 |
+ |
primitives/UreyBradleyBend.hpp, types/BondType.hpp, |
497 |
+ |
types/CubicBendType.hpp, types/CubicBondType.hpp, |
498 |
+ |
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
499 |
+ |
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: |
500 |
+ |
UreyBradleyBend and GhostBend |
501 |
+ |
|
502 |
+ |
2004-11-17 13:58 tim |
503 |
+ |
|
504 |
+ |
* src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp |
505 |
+ |
was initially added on branch new_design. |
506 |
+ |
|
507 |
+ |
2004-11-17 13:58 tim |
508 |
+ |
|
509 |
+ |
* src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp |
510 |
+ |
was initially added on branch new_design. |
511 |
+ |
|
512 |
+ |
2004-11-17 13:58 tim |
513 |
+ |
|
514 |
+ |
* src/: math/ChebyshevPolynomials.cpp, |
515 |
+ |
math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, |
516 |
+ |
primitives/Bond.hpp, types/CharmmTorsionType.hpp, |
517 |
+ |
types/OplsTorsionType.hpp, types/PolynomialBondType.hpp, |
518 |
+ |
types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types |
519 |
+ |
stuff and Chebyshev Polynomial |
520 |
+ |
|
521 |
+ |
2004-11-17 13:58 tim |
522 |
+ |
|
523 |
+ |
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
524 |
+ |
initially added on branch new_design. |
525 |
+ |
|
526 |
+ |
2004-11-17 01:37 tim |
527 |
+ |
|
528 |
+ |
* src/types/PolynomialTorsionType.hpp: file |
529 |
+ |
PolynomialTorsionType.hpp was initially added on branch new_design. |
530 |
+ |
|
531 |
+ |
2004-11-17 01:37 tim |
532 |
+ |
|
533 |
+ |
* src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was |
534 |
+ |
initially added on branch new_design. |
535 |
+ |
|
536 |
+ |
2004-11-17 01:37 tim |
537 |
+ |
|
538 |
+ |
* src/: math/Polynomial.hpp, primitives/Bend.cpp, |
539 |
+ |
primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, |
540 |
+ |
types/BondType.hpp, types/CharmmTorsionType.cpp, |
541 |
+ |
types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp, |
542 |
+ |
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
543 |
+ |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
544 |
+ |
types/PolynomialTorsionType.hpp, types/TorsionType.hpp, |
545 |
+ |
utils/StringTokenizer.hpp: add PolynomialBondType, |
546 |
+ |
PolynomialBendType, PolynomialTorsionType, HarmonicBendType and |
547 |
+ |
CharmmTorsionType. Need to refine the design and add document for |
548 |
+ |
them |
549 |
+ |
|
550 |
+ |
2004-11-17 01:37 tim |
551 |
+ |
|
552 |
+ |
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
553 |
+ |
initially added on branch new_design. |
554 |
+ |
|
555 |
+ |
2004-11-17 01:37 tim |
556 |
+ |
|
557 |
+ |
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
558 |
+ |
initially added on branch new_design. |
559 |
+ |
|
560 |
+ |
2004-11-17 01:37 tim |
561 |
+ |
|
562 |
+ |
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
563 |
+ |
initially added on branch new_design. |
564 |
+ |
|
565 |
+ |
2004-11-16 20:11 tim |
566 |
+ |
|
567 |
+ |
* src/types/: BendType.hpp, PolynomialBondType.hpp, |
568 |
+ |
TorsionType.hpp: add PolynomialBondType |
569 |
+ |
|
570 |
+ |
2004-11-16 20:11 tim |
571 |
+ |
|
572 |
+ |
* src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was |
573 |
+ |
initially added on branch new_design. |
574 |
+ |
|
575 |
+ |
2004-11-16 18:20 tim |
576 |
+ |
|
577 |
+ |
* src/math/Polynomial.hpp: file Polynomial.hpp was initially added |
578 |
+ |
on branch new_design. |
579 |
+ |
|
580 |
+ |
2004-11-16 18:20 tim |
581 |
+ |
|
582 |
+ |
* src/math/Polynomial.hpp: Adding Polynomial class |
583 |
+ |
|
584 |
+ |
2004-11-16 17:04 gezelter |
585 |
+ |
|
586 |
+ |
* src/types/MorseBondType.hpp: file MorseBondType.hpp was initially |
587 |
+ |
added on branch new_design. |
588 |
+ |
|
589 |
+ |
2004-11-16 17:04 gezelter |
590 |
+ |
|
591 |
+ |
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
592 |
+ |
initially added on branch new_design. |
593 |
+ |
|
594 |
+ |
2004-11-16 17:04 gezelter |
595 |
+ |
|
596 |
+ |
* src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, |
597 |
+ |
MorseBondType.hpp, TorsionType.hpp: added some new stuff |
598 |
+ |
|
599 |
+ |
2004-11-16 15:36 tim |
600 |
+ |
|
601 |
+ |
* src/: primitives/Bend.cpp, primitives/Bend.hpp, |
602 |
+ |
primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, |
603 |
+ |
types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and |
604 |
+ |
TorsionType |
605 |
+ |
|
606 |
+ |
2004-11-15 21:07 tim |
607 |
+ |
|
608 |
+ |
* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on |
609 |
+ |
branch new_design. |
610 |
+ |
|
611 |
+ |
2004-11-15 21:07 tim |
612 |
+ |
|
613 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
614 |
+ |
UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, |
615 |
+ |
utils/StringTokenizer.cpp: adding DUFF class; adding checking |
616 |
+ |
statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer |
617 |
+ |
|
618 |
+ |
2004-11-15 18:00 tim |
619 |
+ |
|
620 |
+ |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
621 |
+ |
UseTheForce/ForceFieldFactory.cpp, |
622 |
+ |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, |
623 |
+ |
UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, |
624 |
+ |
types/AtomType.hpp: adding ForceFieldFactory and LJFF classes |
625 |
+ |
|
626 |
+ |
2004-11-15 18:00 tim |
627 |
+ |
|
628 |
+ |
* src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp |
629 |
+ |
was initially added on branch new_design. |
630 |
+ |
|
631 |
+ |
2004-11-15 18:00 tim |
632 |
+ |
|
633 |
+ |
* src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp |
634 |
+ |
was initially added on branch new_design. |
635 |
+ |
|
636 |
+ |
2004-11-15 18:00 tim |
637 |
+ |
|
638 |
+ |
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
639 |
+ |
branch new_design. |
640 |
+ |
|
641 |
+ |
2004-11-15 13:02 tim |
642 |
+ |
|
643 |
+ |
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
644 |
+ |
initially added on branch new_design. |
645 |
+ |
|
646 |
+ |
2004-11-15 13:02 tim |
647 |
+ |
|
648 |
+ |
* src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on |
649 |
+ |
branch new_design. |
650 |
+ |
|
651 |
+ |
2004-11-15 13:02 tim |
652 |
+ |
|
653 |
+ |
* src/io/DumpReader.hpp: file DumpReader.hpp was initially added on |
654 |
+ |
branch new_design. |
655 |
+ |
|
656 |
+ |
2004-11-15 13:02 tim |
657 |
+ |
|
658 |
+ |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, |
659 |
+ |
brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
660 |
+ |
integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, |
661 |
+ |
io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, |
662 |
+ |
DumpWriter.Next Step is LJFF and integrators |
663 |
+ |
|
664 |
+ |
2004-11-13 00:08 tim |
665 |
+ |
|
666 |
+ |
* src/: brains/ForceManager.cpp, brains/ForceManager.hpp, |
667 |
+ |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
668 |
+ |
brains/SimInfo.hpp, primitives/Molecule.cpp, |
669 |
+ |
primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, |
670 |
+ |
refactory, refactory |
671 |
+ |
|
672 |
+ |
2004-11-12 17:43 tim |
673 |
+ |
|
674 |
+ |
* src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, |
675 |
+ |
StringTokenizer.cpp: bug fix in hasMoreTokens |
676 |
+ |
|
677 |
+ |
2004-11-12 17:28 tim |
678 |
+ |
|
679 |
+ |
* src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was |
680 |
+ |
initially added on branch new_design. |
681 |
+ |
|
682 |
+ |
2004-11-12 17:28 tim |
683 |
+ |
|
684 |
+ |
* src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding |
685 |
+ |
StringUtils, a c-style strtok like class, need unit test |
686 |
+ |
|
687 |
+ |
2004-11-12 12:40 tim |
688 |
+ |
|
689 |
+ |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
690 |
+ |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
691 |
+ |
brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test |
692 |
+ |
|
693 |
+ |
2004-11-12 02:05 tim |
694 |
+ |
|
695 |
+ |
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
696 |
+ |
primitives/CutoffGroup.hpp, primitives/Molecule.cpp: |
697 |
+ |
MoleculeCreator forget to create CutoffGroups for free atoms |
698 |
+ |
|
699 |
+ |
2004-11-12 01:19 tim |
700 |
+ |
|
701 |
+ |
* src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
702 |
+ |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
703 |
+ |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
704 |
+ |
io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: |
705 |
+ |
OOPSE = Object-Obfuscated Parallel Simulation Engine |
706 |
+ |
|
707 |
+ |
2004-11-11 16:48 chrisfen |
708 |
+ |
|
709 |
+ |
* samples/water/tip3p_ice/tp3.md: working sample |
710 |
+ |
|
711 |
+ |
2004-11-11 16:47 chrisfen |
712 |
+ |
|
713 |
+ |
* src/restraints/Restraints.cpp: working towards parallel |
714 |
+ |
restraints |
715 |
+ |
|
716 |
+ |
2004-11-11 16:47 chrisfen |
717 |
+ |
|
718 |
+ |
* src/integrators/Integrator.cpp: Commented out some write |
719 |
+ |
statements |
720 |
+ |
|
721 |
+ |
2004-11-11 16:46 chrisfen |
722 |
+ |
|
723 |
+ |
* src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some |
724 |
+ |
write statements |
725 |
+ |
|
726 |
+ |
2004-11-11 16:46 chrisfen |
727 |
+ |
|
728 |
+ |
* samples/water/tip3p_ice/tp3.md: Fun with ice |
729 |
+ |
|
730 |
+ |
2004-11-11 11:41 tim |
731 |
+ |
|
732 |
+ |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
733 |
+ |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
734 |
+ |
brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h, |
735 |
+ |
brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp, |
736 |
+ |
io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove |
737 |
+ |
useless mpiSimulation |
738 |
+ |
|
739 |
+ |
2004-11-11 11:41 tim |
740 |
+ |
|
741 |
+ |
* src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on |
742 |
+ |
branch new_design. |
743 |
+ |
|
744 |
+ |
2004-11-10 17:50 tim |
745 |
+ |
|
746 |
+ |
* src/: brains/ForceManager.cpp, brains/SimInfo.cpp, |
747 |
+ |
brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, |
748 |
+ |
integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo |
749 |
+ |
|
750 |
+ |
2004-11-10 17:01 tim |
751 |
+ |
|
752 |
+ |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
753 |
+ |
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
754 |
+ |
brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
755 |
+ |
brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp, |
756 |
+ |
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
757 |
+ |
io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp, |
758 |
+ |
visitors/AtomVisitor.cpp: another painful day (1) SimCreator, |
759 |
+ |
SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom |
760 |
+ |
File will be removed) (3) ForceField (at least LJ) and BondType, |
761 |
+ |
BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & |
762 |
+ |
Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint |
763 |
+ |
|
764 |
+ |
2004-11-10 09:52 tim |
765 |
+ |
|
766 |
+ |
* src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a |
767 |
+ |
configurable StatWriter |
768 |
+ |
|
769 |
+ |
2004-11-10 09:52 tim |
770 |
+ |
|
771 |
+ |
* src/io/StatWriter.hpp: file StatWriter.hpp was initially added on |
772 |
+ |
branch new_design. |
773 |
+ |
|
774 |
+ |
2004-11-09 21:58 tim |
775 |
+ |
|
776 |
+ |
* src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation |
777 |
+ |
in progress |
778 |
+ |
|
779 |
+ |
2004-11-09 18:11 tim |
780 |
+ |
|
781 |
+ |
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
782 |
+ |
added on branch new_design. |
783 |
+ |
|
784 |
+ |
2004-11-09 18:11 tim |
785 |
+ |
|
786 |
+ |
* src/integrators/VelocityVerletIntegrator.cpp: file |
787 |
+ |
VelocityVerletIntegrator.cpp was initially added on branch |
788 |
+ |
new_design. |
789 |
+ |
|
790 |
+ |
2004-11-09 18:11 tim |
791 |
+ |
|
792 |
+ |
* src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, |
793 |
+ |
brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
794 |
+ |
brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, |
795 |
+ |
brains/mpiSimulation.hpp, integrators/Integrator.hpp, |
796 |
+ |
integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, |
797 |
+ |
integrators/VelocityVerletIntegrator.hpp: adding ForceManager |
798 |
+ |
|
799 |
+ |
2004-11-09 18:11 tim |
800 |
+ |
|
801 |
+ |
* src/brains/ForceManager.hpp: file ForceManager.hpp was initially |
802 |
+ |
added on branch new_design. |
803 |
+ |
|
804 |
+ |
2004-11-09 18:11 tim |
805 |
+ |
|
806 |
+ |
* src/integrators/NVE.cpp: file NVE.cpp was initially added on |
807 |
+ |
branch new_design. |
808 |
+ |
|
809 |
+ |
2004-11-08 20:08 tim |
810 |
+ |
|
811 |
+ |
* src/integrators/VelocityVerletIntegrator.hpp: file |
812 |
+ |
VelocityVerletIntegrator.hpp was initially added on branch |
813 |
+ |
new_design. |
814 |
+ |
|
815 |
+ |
2004-11-08 20:08 tim |
816 |
+ |
|
817 |
+ |
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
818 |
+ |
branch new_design. |
819 |
+ |
|
820 |
+ |
2004-11-08 20:08 tim |
821 |
+ |
|
822 |
+ |
* src/: brains/Exclude.hpp, brains/Stats.hpp, |
823 |
+ |
integrators/Integrator.hpp, integrators/NVE.hpp, |
824 |
+ |
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
825 |
+ |
utils/TypeContainer.hpp: More to break |
826 |
+ |
|
827 |
+ |
2004-11-06 00:21 tim |
828 |
+ |
|
829 |
+ |
* src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially |
830 |
+ |
added on branch new_design. |
831 |
+ |
|
832 |
+ |
2004-11-06 00:21 tim |
833 |
+ |
|
834 |
+ |
* src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, |
835 |
+ |
UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, |
836 |
+ |
utils/TypeContainer.hpp, utils/next_combination.hpp: adding |
837 |
+ |
ForceField and TypeContainer classes |
838 |
+ |
|
839 |
+ |
2004-11-05 18:38 tim |
840 |
+ |
|
841 |
+ |
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
842 |
+ |
initially added on branch new_design. |
843 |
+ |
|
844 |
+ |
2004-11-05 18:38 tim |
845 |
+ |
|
846 |
+ |
* src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was |
847 |
+ |
initially added on branch new_design. |
848 |
+ |
|
849 |
+ |
2004-11-05 18:38 tim |
850 |
+ |
|
851 |
+ |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
852 |
+ |
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
853 |
+ |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
854 |
+ |
brains/SimInfo.hpp, primitives/Molecule.hpp, |
855 |
+ |
utils/LocalndexManager.hpp: Fix Exclude class etc. |
856 |
+ |
|
857 |
+ |
2004-11-05 16:45 chrisfen |
858 |
+ |
|
859 |
+ |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
860 |
+ |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the |
861 |
+ |
linear visitor |
862 |
+ |
|
863 |
+ |
2004-11-05 16:04 chrisfen |
864 |
+ |
|
865 |
+ |
* src/UseTheForce/DarkSide/shapes.F90: current status of the |
866 |
+ |
debugging process |
867 |
+ |
|
868 |
+ |
2004-11-05 16:04 chrisfen |
869 |
+ |
|
870 |
+ |
* make/Makefile.in: included visitors and minimizer |
871 |
+ |
|
872 |
+ |
2004-11-05 16:03 chrisfen |
873 |
+ |
|
874 |
+ |
* ChangeLog: new changes |
875 |
+ |
|
876 |
+ |
2004-11-04 21:56 tim |
877 |
+ |
|
878 |
+ |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
879 |
+ |
primitives/Molecule.hpp: Pain...... |
880 |
+ |
|
881 |
+ |
2004-11-04 15:55 tim |
882 |
+ |
|
883 |
+ |
* ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, |
884 |
+ |
src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, |
885 |
+ |
src/brains/Stats.hpp: time to break SimSetup |
886 |
+ |
|
887 |
+ |
2004-11-04 15:51 gezelter |
888 |
+ |
|
889 |
+ |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new |
890 |
+ |
classes in progress |
891 |
+ |
|
892 |
+ |
2004-11-04 14:48 tim |
893 |
+ |
|
894 |
+ |
* src/brains/Stats.cpp: file Stats.cpp was initially added on |
895 |
+ |
branch new_design. |
896 |
+ |
|
897 |
+ |
2004-11-04 14:48 tim |
898 |
+ |
|
899 |
+ |
* src/brains/Stats.hpp: file Stats.hpp was initially added on |
900 |
+ |
branch new_design. |
901 |
+ |
|
902 |
+ |
2004-11-04 14:48 tim |
903 |
+ |
|
904 |
+ |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
905 |
+ |
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
906 |
+ |
class |
907 |
+ |
|
908 |
+ |
2004-11-04 11:22 gezelter |
909 |
+ |
|
910 |
+ |
* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
911 |
+ |
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and |
912 |
+ |
linearAxis are virtual in StuntDouble, but are implemented by |
913 |
+ |
DirectionalAtom and RigidBody In StuntDouble, they should return |
914 |
+ |
false and "-1" but there should be logic to figure them out in the |
915 |
+ |
other two classes |
916 |
+ |
|
917 |
+ |
2004-11-04 11:20 gezelter |
918 |
+ |
|
919 |
+ |
* src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't |
920 |
+ |
remember what I did |
921 |
+ |
|
922 |
+ |
2004-11-04 11:20 gezelter |
923 |
+ |
|
924 |
+ |
* src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky |
925 |
+ |
|
926 |
+ |
2004-11-04 11:20 gezelter |
927 |
+ |
|
928 |
+ |
* src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX |
929 |
+ |
in the entry_plug so that it only is set if the atoms really are in |
930 |
+ |
the simulation |
931 |
+ |
|
932 |
+ |
2004-11-04 11:20 gezelter |
933 |
+ |
|
934 |
+ |
* samples/water/ssd/ssd.md: testing force fields |
935 |
+ |
|
936 |
+ |
2004-11-04 11:19 gezelter |
937 |
+ |
|
938 |
+ |
* samples/shape/linear.in: testing shapes |
939 |
+ |
|
940 |
+ |
2004-11-03 14:56 tim |
941 |
+ |
|
942 |
+ |
* src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator |
943 |
+ |
class(similar as SimSetup) |
944 |
+ |
|
945 |
+ |
2004-11-03 14:56 tim |
946 |
+ |
|
947 |
+ |
* src/brains/SimCreator.hpp: file SimCreator.hpp was initially |
948 |
+ |
added on branch new_design. |
949 |
+ |
|
950 |
+ |
2004-11-03 14:56 tim |
951 |
+ |
|
952 |
+ |
* src/brains/SimCreator.cpp: file SimCreator.cpp was initially |
953 |
+ |
added on branch new_design. |
954 |
+ |
|
955 |
+ |
2004-11-03 13:00 tim |
956 |
+ |
|
957 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
958 |
+ |
UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, |
959 |
+ |
UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp, |
960 |
+ |
brains/DataStorage.hpp, primitives/Atom.hpp, |
961 |
+ |
primitives/DirectionalAtom.hpp, restraints/Restraints.hpp, |
962 |
+ |
visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get |
963 |
+ |
compiled. Still a long way to go ...... |
964 |
+ |
|
965 |
+ |
2004-11-03 11:08 tim |
966 |
+ |
|
967 |
+ |
* ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
968 |
+ |
src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, |
969 |
+ |
src/integrators/NPTf.cpp, src/integrators/NPTi.cpp, |
970 |
+ |
src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp, |
971 |
+ |
src/io/ZConsReader.cpp, src/primitives/Bend.cpp, |
972 |
+ |
src/primitives/Bond.cpp, src/primitives/GhostBend.cpp, |
973 |
+ |
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
974 |
+ |
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
975 |
+ |
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
976 |
+ |
src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp, |
977 |
+ |
src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, |
978 |
+ |
src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... |
979 |
+ |
|
980 |
+ |
2004-11-02 17:41 tim |
981 |
+ |
|
982 |
+ |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
983 |
+ |
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
984 |
+ |
Need unit test |
985 |
+ |
|
986 |
+ |
2004-11-02 17:41 tim |
987 |
+ |
|
988 |
+ |
* src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was |
989 |
+ |
initially added on branch new_design. |
990 |
+ |
|
991 |
+ |
2004-11-02 17:41 tim |
992 |
+ |
|
993 |
+ |
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
994 |
+ |
branch new_design. |
995 |
+ |
|
996 |
+ |
2004-11-02 11:59 tim |
997 |
+ |
|
998 |
+ |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
999 |
+ |
branch new_design. |
1000 |
+ |
|
1001 |
+ |
2004-11-02 11:59 tim |
1002 |
+ |
|
1003 |
+ |
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
1004 |
+ |
SimSnapshotManager.hpp: SimModel in progress |
1005 |
+ |
|
1006 |
+ |
2004-11-02 10:28 chrisfen |
1007 |
+ |
|
1008 |
+ |
* src/: UseTheForce/DarkSide/shapes.F90, |
1009 |
+ |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes |
1010 |
+ |
looks like it's working |
1011 |
+ |
|
1012 |
+ |
2004-11-02 10:27 tim |
1013 |
+ |
|
1014 |
+ |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
1015 |
+ |
functions for dealing with memory issue |
1016 |
+ |
|
1017 |
+ |
2004-11-02 10:27 tim |
1018 |
+ |
|
1019 |
+ |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
1020 |
+ |
added on branch new_design. |
1021 |
+ |
|
1022 |
+ |
2004-11-02 10:23 tim |
1023 |
+ |
|
1024 |
+ |
* src/: brains/SimModel.hpp, brains/Snapshot.hpp, |
1025 |
+ |
brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding |
1026 |
+ |
SimModel(something similar as SimInfo) |
1027 |
+ |
|
1028 |
+ |
2004-11-01 17:52 tim |
1029 |
+ |
|
1030 |
+ |
* src/: applications/simpleBuilder/MoLocator.hpp, |
1031 |
+ |
applications/simpleBuilder/simpleBuilder.cpp, |
1032 |
+ |
brains/DataStorage.hpp, brains/ForceFields.cpp, |
1033 |
+ |
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp, |
1034 |
+ |
constraints/ZConstraint.cpp, integrators/Integrator.cpp, |
1035 |
+ |
integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp, |
1036 |
+ |
math/SquareMatrix3.hpp, math/Vector3.hpp, |
1037 |
+ |
minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp, |
1038 |
+ |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
1039 |
+ |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
1040 |
+ |
primitives/RigidBody.hpp, primitives/Torsion.hpp, |
1041 |
+ |
restraints/Restraints.cpp, types/TorsionType.hpp, |
1042 |
+ |
utils/PropertyMap.hpp, utils/StringTokenizer.hpp, |
1043 |
+ |
visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp, |
1044 |
+ |
visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, |
1045 |
+ |
RigidBody and StuntDouble classes get compiled |
1046 |
+ |
|
1047 |
+ |
2004-11-01 16:40 tim |
1048 |
+ |
|
1049 |
+ |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
1050 |
+ |
on branch new_design. |
1051 |
+ |
|
1052 |
+ |
2004-11-01 16:40 tim |
1053 |
+ |
|
1054 |
+ |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
1055 |
+ |
branch new_design. |
1056 |
+ |
|
1057 |
+ |
2004-11-01 16:40 tim |
1058 |
+ |
|
1059 |
+ |
* src/primitives/Bond.hpp: file Bond.hpp was initially added on |
1060 |
+ |
branch new_design. |
1061 |
+ |
|
1062 |
+ |
2004-11-01 16:40 tim |
1063 |
+ |
|
1064 |
+ |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
1065 |
+ |
version of Bond, Bend and Torsion. |
1066 |
+ |
|
1067 |
+ |
2004-11-01 16:37 tim |
1068 |
+ |
|
1069 |
+ |
* src/types/BendType.hpp: file BendType.hpp was initially added on |
1070 |
+ |
branch new_design. |
1071 |
+ |
|
1072 |
+ |
2004-11-01 16:37 tim |
1073 |
+ |
|
1074 |
+ |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
1075 |
+ |
BondType, BendType, TorsionType |
1076 |
+ |
|
1077 |
+ |
2004-11-01 16:37 tim |
1078 |
+ |
|
1079 |
+ |
* src/types/TorsionType.hpp: file TorsionType.hpp was initially |
1080 |
+ |
added on branch new_design. |
1081 |
+ |
|
1082 |
+ |
2004-11-01 16:37 tim |
1083 |
+ |
|
1084 |
+ |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
1085 |
+ |
branch new_design. |
1086 |
+ |
|
1087 |
+ |
2004-11-01 15:15 tim |
1088 |
+ |
|
1089 |
+ |
* src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
1090 |
+ |
CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
1091 |
+ |
GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp, |
1092 |
+ |
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: |
1093 |
+ |
break, break and break..... |
1094 |
+ |
|
1095 |
+ |
2004-11-01 14:57 tim |
1096 |
+ |
|
1097 |
+ |
* test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, |
1098 |
+ |
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, |
1099 |
+ |
StuntDouble.hpp: these core classes get compiled |
1100 |
+ |
|
1101 |
+ |
2004-10-29 17:37 tim |
1102 |
+ |
|
1103 |
+ |
* test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule |
1104 |
+ |
class |
1105 |
+ |
|
1106 |
+ |
2004-10-29 17:28 chrisfen |
1107 |
+ |
|
1108 |
+ |
* src/: UseTheForce/DarkSide/atype.F90, |
1109 |
+ |
UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, |
1110 |
+ |
types/ShapeAtomType.cpp: still debugging |
1111 |
+ |
|
1112 |
+ |
2004-10-29 17:28 chrisfen |
1113 |
+ |
|
1114 |
+ |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: |
1115 |
+ |
shapes rcut calculator added |
1116 |
+ |
|
1117 |
+ |
2004-10-29 17:27 chrisfen |
1118 |
+ |
|
1119 |
+ |
* samples/shape/linear.md: shorter run |
1120 |
+ |
|
1121 |
+ |
2004-10-29 15:54 tim |
1122 |
+ |
|
1123 |
+ |
* test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. |
1124 |
+ |
|
1125 |
+ |
2004-10-29 11:22 tim |
1126 |
+ |
|
1127 |
+ |
* test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, |
1128 |
+ |
ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove |
1129 |
+ |
some deprecated files |
1130 |
+ |
|
1131 |
+ |
2004-10-29 11:20 tim |
1132 |
+ |
|
1133 |
+ |
* test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, |
1134 |
+ |
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: |
1135 |
+ |
More painful reconstruction is coming !!! |
1136 |
+ |
|
1137 |
+ |
2004-10-28 17:34 tim |
1138 |
+ |
|
1139 |
+ |
* src/brains/DataStorage.hpp, src/utils/next_combination.hpp, |
1140 |
+ |
test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, |
1141 |
+ |
test/brains/RigidBody.cpp, test/brains/RigidBody.hpp, |
1142 |
+ |
test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, |
1143 |
+ |
DirectionalAtom and RigidBody |
1144 |
+ |
|
1145 |
+ |
2004-10-28 17:26 tim |
1146 |
+ |
|
1147 |
+ |
* ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, |
1148 |
+ |
src/applications/simpleBuilder/MoLocator.cpp, |
1149 |
+ |
src/applications/simpleBuilder/Vector3d.hpp, |
1150 |
+ |
src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: |
1151 |
+ |
remove old Vector3d.hpp from application/simpleBuilder |
1152 |
+ |
|
1153 |
+ |
2004-10-28 16:42 tim |
1154 |
+ |
|
1155 |
+ |
* src/utils/next_combination.hpp: Minor change in next_combination |
1156 |
+ |
|
1157 |
+ |
2004-10-28 16:28 tim |
1158 |
+ |
|
1159 |
+ |
* src/utils/next_combination.hpp, |
1160 |
+ |
test/utils/NextCombinationTestCase.cpp, |
1161 |
+ |
test/utils/ReplaceWildCardTestCase.cpp: Done with combination |
1162 |
+ |
|
1163 |
+ |
2004-10-28 16:11 tim |
1164 |
+ |
|
1165 |
+ |
* src/utils/next_combination.hpp: change documentation of |
1166 |
+ |
next_combination.hpp |
1167 |
+ |
|
1168 |
+ |
2004-10-28 15:41 tim |
1169 |
+ |
|
1170 |
+ |
* ChangeLog, src/utils/next_combination.hpp, |
1171 |
+ |
test/utils/NextCombinationTestCase.cpp, |
1172 |
+ |
test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working |
1173 |
+ |
|
1174 |
+ |
2004-10-28 15:01 tim |
1175 |
+ |
|
1176 |
+ |
* src/utils/next_combination.hpp: adding replace wildcard function |
1177 |
+ |
|
1178 |
+ |
2004-10-28 14:33 tim |
1179 |
+ |
|
1180 |
+ |
* src/utils/next_combination.hpp: Minor change |
1181 |
+ |
|
1182 |
+ |
2004-10-28 14:06 tim |
1183 |
+ |
|
1184 |
+ |
* ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, |
1185 |
+ |
src/applications/simpleBuilder/simpleBuilder.cpp, |
1186 |
+ |
src/utils/next_combination.hpp, test/utils/Makefile, |
1187 |
+ |
test/utils/NextCombinationTestCase.cpp, |
1188 |
+ |
test/utils/ReplaceWildCardTestCase.cpp, |
1189 |
+ |
test/utils/next_combination.hpp: STL next_permutation like |
1190 |
+ |
next_combination is working |
1191 |
+ |
|
1192 |
+ |
2004-10-28 12:22 chrisfen |
1193 |
+ |
|
1194 |
+ |
* src/UseTheForce/WATER.cpp: fix of setDipoles |
1195 |
+ |
|
1196 |
+ |
2004-10-28 12:20 gezelter |
1197 |
+ |
|
1198 |
+ |
* src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the |
1199 |
+ |
shapeFile |
1200 |
+ |
|
1201 |
+ |
2004-10-28 12:20 gezelter |
1202 |
+ |
|
1203 |
+ |
* samples/shape/linear.md: forgot the orientation line |
1204 |
+ |
|
1205 |
+ |
2004-10-28 11:56 gezelter |
1206 |
+ |
|
1207 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
1208 |
+ |
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
1209 |
+ |
UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate |
1210 |
+ |
declaration foo |
1211 |
+ |
|
1212 |
+ |
2004-10-28 11:55 gezelter |
1213 |
+ |
|
1214 |
+ |
* samples/lipid/5x5.md: uncommented .in line |
1215 |
+ |
|
1216 |
+ |
2004-10-28 10:42 tim |
1217 |
+ |
|
1218 |
+ |
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
1219 |
+ |
NextCombinationTestCase.hpp, next_combination.hpp: next_combination |
1220 |
+ |
in progress |
1221 |
+ |
|
1222 |
+ |
2004-10-28 10:15 tim |
1223 |
+ |
|
1224 |
+ |
* test/utils/: NextCombinationTestCase.cpp, |
1225 |
+ |
NextCombinationTestCase.hpp: adding next_combination test case |
1226 |
+ |
|
1227 |
+ |
2004-10-28 10:02 tim |
1228 |
+ |
|
1229 |
+ |
* test/utils/next_combination.hpp: STL Compatible combination |
1230 |
+ |
sequence generator |
1231 |
+ |
|
1232 |
+ |
2004-10-28 01:23 tim |
1233 |
+ |
|
1234 |
+ |
* test/utils/: GenerateCombination.hpp, |
1235 |
+ |
ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp |
1236 |
+ |
|
1237 |
+ |
2004-10-28 01:16 tim |
1238 |
+ |
|
1239 |
+ |
* test/utils/GenerateCombination.hpp: a STL next_permutaion like |
1240 |
+ |
next_combination function. |
1241 |
+ |
|
1242 |
+ |
2004-10-27 22:27 tim |
1243 |
+ |
|
1244 |
+ |
* test/utils/ReplaceWildCard.hpp: no message |
1245 |
+ |
|
1246 |
+ |
2004-10-27 22:14 tim |
1247 |
+ |
|
1248 |
+ |
* test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: |
1249 |
+ |
ReplaceWildCard(recursive version) is working, need refactoring. An |
1250 |
+ |
iterative version is on the way |
1251 |
+ |
|
1252 |
+ |
2004-10-27 21:28 tim |
1253 |
+ |
|
1254 |
+ |
* test/utils/: Makefile, ReplaceWildCard.hpp, |
1255 |
+ |
ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress |
1256 |
+ |
|
1257 |
+ |
2004-10-27 21:08 tim |
1258 |
+ |
|
1259 |
+ |
* test/utils/: ReplaceWildCardTestCase.cpp, |
1260 |
+ |
ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard |
1261 |
+ |
|
1262 |
+ |
2004-10-27 18:17 tim |
1263 |
+ |
|
1264 |
+ |
* test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need |
1265 |
+ |
test |
1266 |
+ |
|
1267 |
+ |
2004-10-27 01:25 tim |
1268 |
+ |
|
1269 |
+ |
* src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild |
1270 |
+ |
char matching is on the way |
1271 |
+ |
|
1272 |
+ |
2004-10-27 01:07 tim |
1273 |
+ |
|
1274 |
+ |
* src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 |
1275 |
+ |
|
1276 |
+ |
2004-10-26 22:00 gezelter |
1277 |
+ |
|
1278 |
+ |
* src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix |
1279 |
+ |
|
1280 |
+ |
2004-10-26 21:20 gezelter |
1281 |
+ |
|
1282 |
+ |
* src/UseTheForce/ForceFields.hpp: subclass foo |
1283 |
+ |
|
1284 |
+ |
2004-10-26 21:16 gezelter |
1285 |
+ |
|
1286 |
+ |
* src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> |
1287 |
+ |
string conversion |
1288 |
+ |
|
1289 |
+ |
2004-10-26 19:01 gezelter |
1290 |
+ |
|
1291 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
1292 |
+ |
UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, |
1293 |
+ |
brains/SimSetup.hpp: char* -> string |
1294 |
+ |
|
1295 |
+ |
2004-10-26 17:25 gezelter |
1296 |
+ |
|
1297 |
+ |
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, |
1298 |
+ |
Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, |
1299 |
+ |
ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some |
1300 |
+ |
isXXX |
1301 |
+ |
|
1302 |
+ |
2004-10-26 17:25 gezelter |
1303 |
+ |
|
1304 |
+ |
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
1305 |
+ |
define name collision |
1306 |
+ |
|
1307 |
+ |
2004-10-26 17:24 gezelter |
1308 |
+ |
|
1309 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
1310 |
+ |
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
1311 |
+ |
UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp, |
1312 |
+ |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
1313 |
+ |
UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: |
1314 |
+ |
forcefield refactoring for shapes |
1315 |
+ |
|
1316 |
+ |
2004-10-26 17:24 gezelter |
1317 |
+ |
|
1318 |
+ |
* samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, |
1319 |
+ |
Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, |
1320 |
+ |
linear.md, linear.shape, toluene.shape: adding sample shape |
1321 |
+ |
directory |
1322 |
+ |
|
1323 |
+ |
2004-10-26 17:19 tim |
1324 |
+ |
|
1325 |
+ |
* ChangeLog, src/brains/DataStorage.cpp, |
1326 |
+ |
src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, |
1327 |
+ |
test/brains/DataStorageTestCase.cpp, |
1328 |
+ |
test/brains/DataStorageTestCase.hpp, test/brains/Makefile: |
1329 |
+ |
DataStorage passes unit test |
1330 |
+ |
|
1331 |
+ |
2004-10-26 13:03 chrisfen |
1332 |
+ |
|
1333 |
+ |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: |
1334 |
+ |
Changes to help advance shapes |
1335 |
+ |
|
1336 |
+ |
2004-10-26 13:02 chrisfen |
1337 |
+ |
|
1338 |
+ |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to |
1339 |
+ |
Shapes force field reader |
1340 |
+ |
|
1341 |
+ |
2004-10-26 12:28 tim |
1342 |
+ |
|
1343 |
+ |
* src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and |
1344 |
+ |
SnapshotTestCase in progress |
1345 |
+ |
|
1346 |
+ |
2004-10-25 17:46 tim |
1347 |
+ |
|
1348 |
+ |
* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
1349 |
+ |
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
1350 |
+ |
src/math/Vector3.hpp, test/brains/StuntDouble.hpp, |
1351 |
+ |
test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, |
1352 |
+ |
test/math/VectorTestCase.cpp: add getArray function to RectMatrix |
1353 |
+ |
and Vector classes |
1354 |
+ |
|
1355 |
|
2004-10-25 12:03 tim |
1356 |
|
|
1357 |
|
* ChangeLog, src/utils/GenericFactory.hpp, |
2447 |
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
2448 |
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
2449 |
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
2450 |
< |
forceFields/Pt.VC.funcfl: Initial revision |
2450 |
> |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
2451 |
|
|
2452 |
|
2004-09-23 23:16 gezelter |
2453 |
|
|
2622 |
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
2623 |
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
2624 |
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
2625 |
< |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
2625 |
> |
forceFields/Pt.VC.funcfl: Initial revision |
2626 |
|
|