1 |
+ |
2005-05-28 19:16 tim |
2 |
+ |
|
3 |
+ |
* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding |
4 |
+ |
AtomNameVisitor |
5 |
+ |
|
6 |
+ |
2005-05-28 19:09 tim |
7 |
+ |
|
8 |
+ |
* src/integrators/Integrator.cpp: dding resetIntegrator |
9 |
+ |
|
10 |
+ |
2005-05-28 19:06 tim |
11 |
+ |
|
12 |
+ |
* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, |
13 |
+ |
NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, |
14 |
+ |
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding |
15 |
+ |
resetIntegrator |
16 |
+ |
|
17 |
+ |
2005-05-27 16:11 tim |
18 |
+ |
|
19 |
+ |
* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, |
20 |
+ |
Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, |
21 |
+ |
SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
22 |
+ |
StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into |
23 |
+ |
StaticProps |
24 |
+ |
|
25 |
+ |
2005-05-26 23:41 tim |
26 |
+ |
|
27 |
+ |
* src/: applications/staticProps/Makefile, |
28 |
+ |
applications/staticProps/P2OrderParameter.cpp, |
29 |
+ |
applications/staticProps/P2OrderParameter.hpp, |
30 |
+ |
applications/staticProps/StaticProps.cpp, |
31 |
+ |
applications/staticProps/StaticProps.ggo, |
32 |
+ |
applications/staticProps/StaticPropsCmd.c, |
33 |
+ |
applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, |
34 |
+ |
utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps |
35 |
+ |
|
36 |
+ |
2005-05-26 17:45 tim |
37 |
+ |
|
38 |
+ |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
39 |
+ |
applications/dump2Xyz/Dump2XYZCmd.c, |
40 |
+ |
applications/dump2Xyz/Dump2XYZCmd.h, |
41 |
+ |
applications/staticProps/Makefile, |
42 |
+ |
applications/staticProps/P2OrderParameter.cpp, |
43 |
+ |
applications/staticProps/P2OrderParameter.hpp, |
44 |
+ |
applications/staticProps/RadialDistrFunc.cpp, |
45 |
+ |
applications/staticProps/RadialDistrFunc.hpp, |
46 |
+ |
applications/staticProps/StaticAnalyser.hpp, |
47 |
+ |
applications/staticProps/StaticProps.cpp, |
48 |
+ |
applications/staticProps/StaticProps.ggo, |
49 |
+ |
applications/staticProps/StaticPropsCmd.c, |
50 |
+ |
applications/staticProps/StaticPropsCmd.h, visitors/Makefile, |
51 |
+ |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding |
52 |
+ |
AtomNameVisitor to convert atom name to its base name; |
53 |
+ |
wrappingvisitor now wrap back to the center of the mass; adding |
54 |
+ |
P2OrderParameter into StaticProps |
55 |
+ |
|
56 |
+ |
2005-05-22 16:36 chuckv |
57 |
+ |
|
58 |
+ |
* samples/metals/nanorod/Au_nanoparticle_FCC.md, |
59 |
+ |
src/applications/nanoRodBuilder/Geometry.cpp, |
60 |
+ |
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
61 |
+ |
src/applications/nanoRodBuilder/GeometryFactory.cpp, |
62 |
+ |
src/applications/nanoRodBuilder/GeometryFactory.hpp, |
63 |
+ |
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
64 |
+ |
src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
65 |
+ |
tensor. |
66 |
+ |
|
67 |
+ |
2005-05-22 16:05 tim |
68 |
+ |
|
69 |
+ |
* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
70 |
+ |
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
71 |
+ |
io/Globals.hpp, io/SectionParserManager.cpp: adding keyword |
72 |
+ |
printPressureTensor |
73 |
+ |
|
74 |
+ |
2005-05-20 14:27 tim |
75 |
+ |
|
76 |
+ |
* src/integrators/NPrT.cpp: NPrT in progress |
77 |
+ |
|
78 |
+ |
2005-05-20 11:01 tim |
79 |
+ |
|
80 |
+ |
* src/: integrators/NPrT.cpp, io/Globals.cpp, |
81 |
+ |
utils/OOPSEConstant.hpp: NPrT in progress |
82 |
+ |
|
83 |
+ |
2005-05-19 16:31 tim |
84 |
+ |
|
85 |
+ |
* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, |
86 |
+ |
integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, |
87 |
+ |
io/Globals.hpp: NPAT is working |
88 |
+ |
|
89 |
+ |
2005-05-19 10:49 tim |
90 |
+ |
|
91 |
+ |
* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, |
92 |
+ |
integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT |
93 |
+ |
|
94 |
+ |
2005-05-18 23:28 tim |
95 |
+ |
|
96 |
+ |
* src/: brains/Register.cpp, integrators/NPAT.cpp, |
97 |
+ |
integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, |
98 |
+ |
io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators |
99 |
+ |
|
100 |
+ |
2005-05-18 14:06 chrisfen |
101 |
+ |
|
102 |
+ |
* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just |
103 |
+ |
some tap changes |
104 |
+ |
|
105 |
+ |
2005-05-18 13:31 chrisfen |
106 |
+ |
|
107 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
108 |
+ |
DarkSide/sticky.F90: Modifications to temper the dipolar strength |
109 |
+ |
in the first solvation shell for tap |
110 |
+ |
|
111 |
+ |
2005-05-18 07:35 chrisfen |
112 |
+ |
|
113 |
+ |
* samples/water/tap/: tap.in, tap.md, water.md: added a tap example |
114 |
+ |
for testing purposes |
115 |
+ |
|
116 |
+ |
2005-05-17 17:35 chrisfen |
117 |
+ |
|
118 |
+ |
* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, |
119 |
+ |
samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, |
120 |
+ |
src/UseTheForce/doForces.F90, |
121 |
+ |
src/UseTheForce/DarkSide/electrostatic.F90, |
122 |
+ |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
123 |
+ |
src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also |
124 |
+ |
correcting changes to the previous merge that were not caught |
125 |
+ |
|
126 |
+ |
2005-05-16 23:20 chuckv |
127 |
+ |
|
128 |
+ |
* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: |
129 |
+ |
Fixed merge issues between Kyle and Chris so OOPSE will actually |
130 |
+ |
build. |
131 |
+ |
|
132 |
+ |
2005-05-16 22:46 kdaily |
133 |
+ |
|
134 |
+ |
* src/io/: GayBerneAtomTypesSectionParser.cpp, |
135 |
+ |
GayBerneAtomTypesSectionParser.hpp, Makefile: help |
136 |
+ |
|
137 |
+ |
2005-05-16 21:08 kdaily |
138 |
+ |
|
139 |
+ |
* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, |
140 |
+ |
src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, |
141 |
+ |
src/types/DirectionalAtomType.cpp, |
142 |
+ |
src/types/DirectionalAtomType.hpp: added gb |
143 |
+ |
|
144 |
+ |
2005-05-13 15:36 chrisfen |
145 |
+ |
|
146 |
+ |
* forceFields/DUFF2.frc: Better tap |
147 |
+ |
|
148 |
+ |
2005-05-12 14:43 chrisfen |
149 |
+ |
|
150 |
+ |
* forceFields/DUFF2.frc, samples/water/dimer/ssd.in, |
151 |
+ |
samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, |
152 |
+ |
src/applications/dump2Xyz/Dump2XYZ.cpp, |
153 |
+ |
src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. |
154 |
+ |
Need to parametrize. |
155 |
+ |
|
156 |
+ |
2005-05-11 18:15 chuckv |
157 |
+ |
|
158 |
+ |
* src/: io/ShapeAtomTypesSectionParser.cpp, |
159 |
+ |
math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed |
160 |
+ |
build issues under ifc7. |
161 |
+ |
|
162 |
+ |
2005-05-09 17:07 chuckv |
163 |
+ |
|
164 |
+ |
* src/applications/nanoRodBuilder/Geometry.hpp: More geometry |
165 |
+ |
builder changes. |
166 |
+ |
|
167 |
+ |
2005-05-05 10:06 chrisfen |
168 |
+ |
|
169 |
+ |
* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED |
170 |
+ |
to TAP |
171 |
+ |
|
172 |
+ |
2005-05-05 09:47 chrisfen |
173 |
+ |
|
174 |
+ |
* forceFields/DUFF2.frc, samples/water/ssde/ssde.md, |
175 |
+ |
samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, |
176 |
+ |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, |
177 |
+ |
src/UseTheForce/DarkSide/atype.F90, |
178 |
+ |
src/UseTheForce/DarkSide/atype_interface.F90, |
179 |
+ |
src/UseTheForce/DarkSide/simulation.F90, |
180 |
+ |
src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, |
181 |
+ |
src/brains/fSimulation.h, src/io/Makefile, |
182 |
+ |
src/io/StickyAtomTypesSectionParser.cpp, |
183 |
+ |
src/io/StickyPowerAtomTypesSectionParser.cpp, |
184 |
+ |
src/io/StickyPowerAtomTypesSectionParser.hpp, |
185 |
+ |
src/types/AtomType.cpp, src/types/AtomType.hpp, |
186 |
+ |
src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, |
187 |
+ |
src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's |
188 |
+ |
not parametrized, but OOPSE will now let me run it... |
189 |
+ |
|
190 |
+ |
2005-05-03 17:55 chuckv |
191 |
+ |
|
192 |
+ |
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
193 |
+ |
GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: |
194 |
+ |
Adding support for generic geometry to nanorodbuilder. |
195 |
+ |
|
196 |
+ |
2005-05-03 12:55 chuckv |
197 |
+ |
|
198 |
+ |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
199 |
+ |
nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, |
200 |
+ |
nanorodBuilderCmd.h: More changes to nanoRodBuilder.... |
201 |
+ |
|
202 |
+ |
2005-04-29 14:16 gezelter |
203 |
+ |
|
204 |
+ |
* make/Makefile.in: [no log message] |
205 |
+ |
|
206 |
+ |
2005-04-29 11:26 chrisfen |
207 |
+ |
|
208 |
+ |
* forceFields/DUFF2.frc, samples/water/spce/water.md, |
209 |
+ |
samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, |
210 |
+ |
samples/water/ssd-ion/water.md, samples/water/ssde/water.md, |
211 |
+ |
samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, |
212 |
+ |
samples/water/tip4p/water.md: Added TIP4P-Ew |
213 |
+ |
|
214 |
+ |
2005-04-27 19:24 chuckv |
215 |
+ |
|
216 |
+ |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
217 |
+ |
GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, |
218 |
+ |
nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with |
219 |
+ |
nanoRodBuilder.... |
220 |
+ |
|
221 |
+ |
2005-04-27 15:13 chrisfen |
222 |
+ |
|
223 |
+ |
* samples/shape/Shapes.frc, samples/shape/linear.shape, |
224 |
+ |
src/UseTheForce/DarkSide/atype.F90, |
225 |
+ |
src/UseTheForce/DarkSide/shapes.F90, |
226 |
+ |
src/UseTheForce/DarkSide/shapes_interface.F90, |
227 |
+ |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of |
228 |
+ |
write statements and am closer to a working shapes |
229 |
+ |
|
230 |
+ |
2005-04-22 16:57 chuckv |
231 |
+ |
|
232 |
+ |
* src/utils/Predicate.hpp: Fixed gcc4 bug... |
233 |
+ |
|
234 |
+ |
2005-04-22 16:52 tim |
235 |
+ |
|
236 |
+ |
* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, |
237 |
+ |
Trim.hpp: adding CharClassificationFunctor to fix the locale |
238 |
+ |
problem of c++ |
239 |
+ |
|
240 |
+ |
2005-04-21 09:12 chrisfen |
241 |
+ |
|
242 |
+ |
* samples/shape/Shapes.frc, samples/shape/linear.in, |
243 |
+ |
samples/shape/linear.md, src/UseTheForce/ForceField.hpp, |
244 |
+ |
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, |
245 |
+ |
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
246 |
+ |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, |
247 |
+ |
src/UseTheForce/DarkSide/shapes.F90, |
248 |
+ |
src/UseTheForce/DarkSide/shapes_interface.F90, |
249 |
+ |
src/UseTheForce/DarkSide/shapes_interface.h, |
250 |
+ |
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
251 |
+ |
src/io/Makefile, src/io/SectionParser.cpp, |
252 |
+ |
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
253 |
+ |
src/io/ShapeAtomTypesSectionParser.cpp, |
254 |
+ |
src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, |
255 |
+ |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, |
256 |
+ |
src/types/ShapeAtomType.hpp: Shapes is limping along with a array |
257 |
+ |
bounds overwrite (I think...). At least the parser loads the |
258 |
+ |
forcefield fine... |
259 |
+ |
|
260 |
+ |
2005-04-18 10:44 chrisfen |
261 |
+ |
|
262 |
+ |
* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on |
263 |
+ |
Mac (capitalization confusion of filenames) |
264 |
+ |
|
265 |
+ |
2005-04-17 22:50 chrisfen |
266 |
+ |
|
267 |
+ |
* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, |
268 |
+ |
UseTheForce/Shapes_FF.cpp, |
269 |
+ |
io/DirectionalAtomTypesSectionParser.cpp, |
270 |
+ |
io/ShapeAtomTypesSectionParser.cpp, |
271 |
+ |
io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... |
272 |
+ |
|
273 |
+ |
2005-04-15 17:43 gezelter |
274 |
+ |
|
275 |
+ |
* README: gmake in case people forget |
276 |
+ |
|
277 |
+ |
2005-04-15 17:40 gezelter |
278 |
+ |
|
279 |
+ |
* src/applications/oopse/oopse.cpp: fixed the spacing on the |
280 |
+ |
banner. Vanity. |
281 |
+ |
|
282 |
+ |
2005-04-15 17:22 gezelter |
283 |
+ |
|
284 |
+ |
* src/: config.h.in, applications/oopse/oopse.cpp: Version string |
285 |
+ |
in banner (and version numbers in config.h) |
286 |
+ |
|
287 |
+ |
2005-04-15 17:22 gezelter |
288 |
+ |
|
289 |
+ |
* ChangeLog, LICENSE, README: Documentation changes |
290 |
+ |
|
291 |
+ |
2005-04-15 17:03 gezelter |
292 |
+ |
|
293 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
294 |
+ |
UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, |
295 |
+ |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
296 |
+ |
UseTheForce/ForceFieldCreator.hpp, |
297 |
+ |
UseTheForce/ForceFieldFactory.cpp, |
298 |
+ |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
299 |
+ |
UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, |
300 |
+ |
UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, |
301 |
+ |
UseTheForce/notifyCutoffs.F90, |
302 |
+ |
UseTheForce/notifyCutoffs_interface.F90, |
303 |
+ |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
304 |
+ |
UseTheForce/DarkSide/atype.F90, |
305 |
+ |
UseTheForce/DarkSide/atype_interface.F90, |
306 |
+ |
UseTheForce/DarkSide/eam.F90, |
307 |
+ |
UseTheForce/DarkSide/eam_interface.F90, |
308 |
+ |
UseTheForce/DarkSide/eam_interface.h, |
309 |
+ |
UseTheForce/DarkSide/electrostatic.F90, |
310 |
+ |
UseTheForce/DarkSide/electrostatic_interface.F90, |
311 |
+ |
UseTheForce/DarkSide/electrostatic_interface.h, |
312 |
+ |
UseTheForce/DarkSide/force_globals.F90, |
313 |
+ |
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
314 |
+ |
UseTheForce/DarkSide/lj_interface.F90, |
315 |
+ |
UseTheForce/DarkSide/lj_interface.h, |
316 |
+ |
UseTheForce/DarkSide/neighborLists.F90, |
317 |
+ |
UseTheForce/DarkSide/reactionField.F90, |
318 |
+ |
UseTheForce/DarkSide/shapes.F90, |
319 |
+ |
UseTheForce/DarkSide/shapes_interface.F90, |
320 |
+ |
UseTheForce/DarkSide/shapes_interface.h, |
321 |
+ |
UseTheForce/DarkSide/simParallel.F90, |
322 |
+ |
UseTheForce/DarkSide/simParallel_interface.F90, |
323 |
+ |
UseTheForce/DarkSide/simParallel_interface.h, |
324 |
+ |
UseTheForce/DarkSide/simulation.F90, |
325 |
+ |
UseTheForce/DarkSide/simulation_interface.F90, |
326 |
+ |
UseTheForce/DarkSide/simulation_interface.h, |
327 |
+ |
UseTheForce/DarkSide/sticky.F90, |
328 |
+ |
UseTheForce/DarkSide/sticky_interface.F90, |
329 |
+ |
UseTheForce/DarkSide/sticky_interface.h, |
330 |
+ |
UseTheForce/DarkSide/switcheroo.F90, |
331 |
+ |
applications/dump2Xyz/Dump2XYZ.cpp, |
332 |
+ |
applications/dump2Xyz/Dump2XYZCmd.c, |
333 |
+ |
applications/dump2Xyz/Dump2XYZCmd.h, |
334 |
+ |
applications/dynamicProps/CrossTimeCorrFunc.cpp, |
335 |
+ |
applications/dynamicProps/CrossTimeCorrFunc.hpp, |
336 |
+ |
applications/dynamicProps/DipoleCorrFunc.cpp, |
337 |
+ |
applications/dynamicProps/DipoleCorrFunc.hpp, |
338 |
+ |
applications/dynamicProps/DynamicProps.cpp, |
339 |
+ |
applications/dynamicProps/DynamicPropsCmd.c, |
340 |
+ |
applications/dynamicProps/DynamicPropsCmd.h, |
341 |
+ |
applications/dynamicProps/FrameTimeCorrFunc.hpp, |
342 |
+ |
applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
343 |
+ |
applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
344 |
+ |
applications/dynamicProps/RCorrFunc.cpp, |
345 |
+ |
applications/dynamicProps/RCorrFunc.hpp, |
346 |
+ |
applications/dynamicProps/TimeCorrFunc.cpp, |
347 |
+ |
applications/dynamicProps/TimeCorrFunc.hpp, |
348 |
+ |
applications/dynamicProps/VCorrFunc.cpp, |
349 |
+ |
applications/dynamicProps/VCorrFunc.hpp, |
350 |
+ |
applications/nanoRodBuilder/GeometryBuilder.cpp, |
351 |
+ |
applications/nanoRodBuilder/GeometryBuilder.hpp, |
352 |
+ |
applications/nanoRodBuilder/nanorodBuilder.cpp, |
353 |
+ |
applications/nanoRodBuilder/nanorodBuilderCmd.c, |
354 |
+ |
applications/nanoRodBuilder/nanorodBuilderCmd.h, |
355 |
+ |
applications/oopse/oopse.cpp, |
356 |
+ |
applications/simpleBuilder/simpleBuilder.cpp, |
357 |
+ |
applications/simpleBuilder/simpleBuilderCmd.c, |
358 |
+ |
applications/simpleBuilder/simpleBuilderCmd.h, |
359 |
+ |
applications/staticProps/GofAngle2.cpp, |
360 |
+ |
applications/staticProps/GofAngle2.hpp, |
361 |
+ |
applications/staticProps/GofR.cpp, |
362 |
+ |
applications/staticProps/GofR.hpp, |
363 |
+ |
applications/staticProps/GofRAngle.cpp, |
364 |
+ |
applications/staticProps/GofRAngle.hpp, |
365 |
+ |
applications/staticProps/GofXyz.cpp, |
366 |
+ |
applications/staticProps/GofXyz.hpp, |
367 |
+ |
applications/staticProps/RadialDistrFunc.cpp, |
368 |
+ |
applications/staticProps/RadialDistrFunc.hpp, |
369 |
+ |
applications/staticProps/StaticProps.cpp, |
370 |
+ |
applications/staticProps/StaticPropsCmd.c, |
371 |
+ |
applications/staticProps/StaticPropsCmd.h, |
372 |
+ |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
373 |
+ |
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
374 |
+ |
brains/Exclude.hpp, brains/ForceManager.cpp, |
375 |
+ |
brains/ForceManager.hpp, brains/MoleculeCreator.cpp, |
376 |
+ |
brains/MoleculeCreator.hpp, brains/Register.cpp, |
377 |
+ |
brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
378 |
+ |
brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
379 |
+ |
brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, |
380 |
+ |
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, |
381 |
+ |
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
382 |
+ |
brains/fSimulation.h, constraints/ConstraintElem.hpp, |
383 |
+ |
constraints/ConstraintPair.hpp, constraints/Rattle.cpp, |
384 |
+ |
constraints/Rattle.hpp, constraints/ZconsStruct.hpp, |
385 |
+ |
constraints/ZconstraintForceManager.cpp, |
386 |
+ |
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
387 |
+ |
integrators/DLM.hpp, integrators/Integrator.cpp, |
388 |
+ |
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
389 |
+ |
integrators/IntegratorFactory.cpp, |
390 |
+ |
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
391 |
+ |
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
392 |
+ |
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
393 |
+ |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
394 |
+ |
integrators/NVT.cpp, integrators/NVT.hpp, |
395 |
+ |
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
396 |
+ |
integrators/Velocitizer.hpp, |
397 |
+ |
integrators/VelocityVerletIntegrator.cpp, |
398 |
+ |
integrators/VelocityVerletIntegrator.hpp, |
399 |
+ |
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
400 |
+ |
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
401 |
+ |
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
402 |
+ |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
403 |
+ |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
404 |
+ |
io/ChargeAtomTypesSectionParser.hpp, |
405 |
+ |
io/DirectionalAtomTypesSectionParser.cpp, |
406 |
+ |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
407 |
+ |
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
408 |
+ |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
409 |
+ |
io/Globals.cpp, io/Globals.hpp, |
410 |
+ |
io/LennardJonesAtomTypesSectionParser.cpp, |
411 |
+ |
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
412 |
+ |
io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, |
413 |
+ |
io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, |
414 |
+ |
io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, |
415 |
+ |
io/SectionParser.cpp, io/SectionParser.hpp, |
416 |
+ |
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
417 |
+ |
io/StatWriter.cpp, io/StatWriter.hpp, |
418 |
+ |
io/StickyAtomTypesSectionParser.cpp, |
419 |
+ |
io/StickyAtomTypesSectionParser.hpp, |
420 |
+ |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
421 |
+ |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
422 |
+ |
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, |
423 |
+ |
io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, |
424 |
+ |
io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, |
425 |
+ |
io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, |
426 |
+ |
lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, |
427 |
+ |
lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
428 |
+ |
lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, |
429 |
+ |
lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, |
430 |
+ |
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
431 |
+ |
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
432 |
+ |
math/ParallelRandNumGen.hpp, math/Polynomial.hpp, |
433 |
+ |
math/Quaternion.hpp, math/RandNumGen.hpp, |
434 |
+ |
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
435 |
+ |
math/RectMatrix.hpp, math/SeqRandNumGen.cpp, |
436 |
+ |
math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, |
437 |
+ |
math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, |
438 |
+ |
minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, |
439 |
+ |
minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, |
440 |
+ |
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
441 |
+ |
minimizers/MinimizerFactory.hpp, |
442 |
+ |
minimizers/MinimizerParameterSet.cpp, |
443 |
+ |
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
444 |
+ |
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
445 |
+ |
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
446 |
+ |
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
447 |
+ |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
448 |
+ |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
449 |
+ |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
450 |
+ |
primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, |
451 |
+ |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
452 |
+ |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
453 |
+ |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
454 |
+ |
primitives/Torsion.cpp, primitives/Torsion.hpp, |
455 |
+ |
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
456 |
+ |
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
457 |
+ |
profiling/timing.F90, restraints/Restraints.cpp, |
458 |
+ |
restraints/Restraints.hpp, |
459 |
+ |
restraints/ThermoIntegrationForceManager.cpp, |
460 |
+ |
restraints/ThermoIntegrationForceManager.hpp, |
461 |
+ |
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
462 |
+ |
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
463 |
+ |
selection/NameFinder.cpp, selection/NameFinder.hpp, |
464 |
+ |
selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, |
465 |
+ |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
466 |
+ |
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
467 |
+ |
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, |
468 |
+ |
selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, |
469 |
+ |
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
470 |
+ |
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
471 |
+ |
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
472 |
+ |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
473 |
+ |
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
474 |
+ |
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
475 |
+ |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
476 |
+ |
types/DirectionalAtomType.hpp, types/FixedBondType.hpp, |
477 |
+ |
types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, |
478 |
+ |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
479 |
+ |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
480 |
+ |
types/MorseBondType.hpp, types/OplsTorsionType.hpp, |
481 |
+ |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
482 |
+ |
types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, |
483 |
+ |
types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, |
484 |
+ |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
485 |
+ |
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
486 |
+ |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
487 |
+ |
types/TorsionType.hpp, types/UreyBradleyBendType.hpp, |
488 |
+ |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, |
489 |
+ |
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
490 |
+ |
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
491 |
+ |
utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, |
492 |
+ |
utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, |
493 |
+ |
utils/PropertyMap.cpp, utils/PropertyMap.hpp, |
494 |
+ |
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
495 |
+ |
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
496 |
+ |
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
497 |
+ |
utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, |
498 |
+ |
utils/any.hpp, utils/definitions.F90, utils/fError.c, |
499 |
+ |
utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, |
500 |
+ |
utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, |
501 |
+ |
utils/residentMem.h, utils/simError.c, utils/simError.h, |
502 |
+ |
utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, |
503 |
+ |
visitors/AtomData.hpp, visitors/AtomVisitor.cpp, |
504 |
+ |
visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, |
505 |
+ |
visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, |
506 |
+ |
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
507 |
+ |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, |
508 |
+ |
visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, |
509 |
+ |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has |
510 |
+ |
been drafted to perform our indentation services |
511 |
+ |
|
512 |
+ |
2005-04-15 17:03 gezelter |
513 |
+ |
|
514 |
+ |
* configure, ac-tools/configure.in: Jedi mind-trick warning |
515 |
+ |
messages have been added to make users ignore CGAL. |
516 |
+ |
|
517 |
+ |
2005-04-15 13:41 tim |
518 |
+ |
|
519 |
+ |
* make/Makefile.in: fix make install |
520 |
+ |
|
521 |
+ |
2005-04-15 13:41 tim |
522 |
+ |
|
523 |
+ |
* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: |
524 |
+ |
add Makefile of samples |
525 |
+ |
|
526 |
+ |
2005-04-15 13:33 tim |
527 |
+ |
|
528 |
+ |
* samples/: lipid/Makefile, water/dimer/Makefile, |
529 |
+ |
water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not |
530 |
+ |
installed correctly |
531 |
+ |
|
532 |
+ |
2005-04-14 16:41 gezelter |
533 |
+ |
|
534 |
+ |
* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
535 |
+ |
make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, |
536 |
+ |
scripts/filepp, scripts/filepp.in: configure now searches for perl |
537 |
+ |
to use with filepp |
538 |
+ |
|
539 |
+ |
2005-04-14 16:20 gezelter |
540 |
+ |
|
541 |
+ |
* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |
542 |
+ |
MoLocator |
543 |
+ |
|
544 |
+ |
2005-04-14 14:12 gezelter |
545 |
+ |
|
546 |
+ |
* LICENSE: [no log message] |
547 |
+ |
|
548 |
+ |
2005-04-14 11:10 chuckv |
549 |
+ |
|
550 |
+ |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: |
551 |
+ |
nanorodbuilder now exit's when libCGAL is not present. |
552 |
+ |
|
553 |
+ |
2005-04-14 10:20 tim |
554 |
+ |
|
555 |
+ |
* src/io/make_nodes.h: fix one more warning message in make_nodes |
556 |
+ |
|
557 |
+ |
2005-04-13 18:36 chuckv |
558 |
+ |
|
559 |
+ |
* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed |
560 |
+ |
interface name for SGI Compiler |
561 |
+ |
|
562 |
+ |
2005-04-13 18:29 chrisfen |
563 |
+ |
|
564 |
+ |
* samples/water/ssde/ssde.md: oops... bad sample |
565 |
+ |
|
566 |
+ |
2005-04-13 18:00 chuckv |
567 |
+ |
|
568 |
+ |
* src/config.h.in: Change typo in CGAL. |
569 |
+ |
|
570 |
+ |
2005-04-13 17:43 tim |
571 |
+ |
|
572 |
+ |
* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, |
573 |
+ |
selection/SelectionCompiler.hpp: fix some warning messages |
574 |
+ |
|
575 |
+ |
2005-04-13 17:30 gezelter |
576 |
+ |
|
577 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
578 |
+ |
make/Makefile.in, src/config.h.in, |
579 |
+ |
src/applications/nanoRodBuilder/Makefile, |
580 |
+ |
src/applications/nanoRodBuilder/Makefile.in, |
581 |
+ |
src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL |
582 |
+ |
checks |
583 |
+ |
|
584 |
+ |
2005-04-13 15:36 chuckv |
585 |
+ |
|
586 |
+ |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, |
587 |
+ |
DarkSide/LJ.F90, DarkSide/electrostatic.F90, |
588 |
+ |
DarkSide/electrostatic_interface.F90, |
589 |
+ |
DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, |
590 |
+ |
DarkSide/lj_interface.h, DarkSide/sticky.F90, |
591 |
+ |
DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added |
592 |
+ |
destroy methods for Fortran modules. |
593 |
+ |
|
594 |
+ |
2005-04-13 15:17 chuckv |
595 |
+ |
|
596 |
+ |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, |
597 |
+ |
shapes_interface.h: Added destroy method to clean up memory |
598 |
+ |
|
599 |
+ |
2005-04-13 13:41 tim |
600 |
+ |
|
601 |
+ |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
602 |
+ |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
603 |
+ |
io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, |
604 |
+ |
primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, |
605 |
+ |
types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are |
606 |
+ |
fixed |
607 |
+ |
|
608 |
+ |
2005-04-12 17:44 chuckv |
609 |
+ |
|
610 |
+ |
* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed |
611 |
+ |
for nanoRodBuilder. |
612 |
+ |
|
613 |
+ |
2005-04-12 17:42 tim |
614 |
+ |
|
615 |
+ |
* src/applications/: nanoRodBuilder/nanorodBuilder.cpp, |
616 |
+ |
simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder |
617 |
+ |
and simpleBuilder(forget to delete lattice) |
618 |
+ |
|
619 |
+ |
2005-04-12 17:33 tim |
620 |
+ |
|
621 |
+ |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
622 |
+ |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: |
623 |
+ |
refactory lattice |
624 |
+ |
|
625 |
+ |
2005-04-12 17:07 tim |
626 |
+ |
|
627 |
+ |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, |
628 |
+ |
CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, |
629 |
+ |
Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory |
630 |
+ |
LatticeFactory and LatticeCreator |
631 |
+ |
|
632 |
+ |
2005-04-12 16:58 tim |
633 |
+ |
|
634 |
+ |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
635 |
+ |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, |
636 |
+ |
brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
637 |
+ |
lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, |
638 |
+ |
lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, |
639 |
+ |
lattice/Makefile: refactory LatticeFactory and LatticeCreator |
640 |
+ |
|
641 |
+ |
2005-04-12 16:28 gezelter |
642 |
+ |
|
643 |
+ |
* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, |
644 |
+ |
vector_class.F90: cleaned up vector_class memory leak fix by |
645 |
+ |
deallocating in reverse order of how we allocated. Also migrated |
646 |
+ |
MoLocator into utils directory |
647 |
+ |
|
648 |
+ |
2005-04-12 16:27 gezelter |
649 |
+ |
|
650 |
+ |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, |
651 |
+ |
Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
652 |
+ |
LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice |
653 |
+ |
directory |
654 |
+ |
|
655 |
+ |
2005-04-12 16:27 gezelter |
656 |
+ |
|
657 |
+ |
* src/applications/: nanoRodBuilder/BaseLattice.cpp, |
658 |
+ |
nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, |
659 |
+ |
nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, |
660 |
+ |
nanoRodBuilder/LatticeCreator.hpp, |
661 |
+ |
nanoRodBuilder/LatticeFactory.cpp, |
662 |
+ |
nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, |
663 |
+ |
nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, |
664 |
+ |
nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, |
665 |
+ |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
666 |
+ |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
667 |
+ |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
668 |
+ |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, |
669 |
+ |
simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, |
670 |
+ |
simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of |
671 |
+ |
these files are now redundant |
672 |
+ |
|
673 |
+ |
2005-04-12 16:27 gezelter |
674 |
+ |
|
675 |
+ |
* src/UseTheForce/DarkSide/: atype_interface.F90, |
676 |
+ |
atype_interface.h: cleaned up memory leak fix |
677 |
+ |
|
678 |
+ |
2005-04-12 16:26 gezelter |
679 |
+ |
|
680 |
+ |
* make/Makefile.in: added lattice subdirectory |
681 |
+ |
|
682 |
+ |
2005-04-12 15:57 chrisfen |
683 |
+ |
|
684 |
+ |
* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added |
685 |
+ |
a space by accident |
686 |
+ |
|
687 |
+ |
2005-04-12 15:56 chrisfen |
688 |
+ |
|
689 |
+ |
* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added |
690 |
+ |
quadrupole sample |
691 |
+ |
|
692 |
+ |
2005-04-12 15:56 chrisfen |
693 |
+ |
|
694 |
+ |
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating |
695 |
+ |
samples |
696 |
+ |
|
697 |
+ |
2005-04-12 13:30 tim |
698 |
+ |
|
699 |
+ |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom |
700 |
+ |
type in fortran side |
701 |
+ |
|
702 |
+ |
2005-04-12 12:45 chuckv |
703 |
+ |
|
704 |
+ |
* src/utils/vector_class.F90: Further changes to vector_class |
705 |
+ |
destroy function. |
706 |
+ |
|
707 |
+ |
2005-04-12 12:39 chuckv |
708 |
+ |
|
709 |
+ |
* src/utils/vector_class.F90: Fixed pointer memory leak in |
710 |
+ |
vector_class. |
711 |
+ |
|
712 |
+ |
2005-04-12 12:12 chuckv |
713 |
+ |
|
714 |
+ |
* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, |
715 |
+ |
DarkSide/atype_interface.F90, DarkSide/atype_interface.h, |
716 |
+ |
DarkSide/eam.F90, DarkSide/eam_interface.F90, |
717 |
+ |
DarkSide/eam_interface.h: Updates to deallocate object in fortran. |
718 |
+ |
|
719 |
+ |
2005-04-12 09:24 chrisfen |
720 |
+ |
|
721 |
+ |
* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI |
722 |
+ |
output |
723 |
+ |
|
724 |
+ |
2005-04-11 19:29 chuckv |
725 |
+ |
|
726 |
+ |
* src/: UseTheForce/DarkSide/atype.F90, |
727 |
+ |
applications/nanoRodBuilder/Makefile: Changes to delete atypes... |
728 |
+ |
|
729 |
+ |
2005-04-11 19:28 chuckv |
730 |
+ |
|
731 |
+ |
* src/utils/vector_class.F90: Added code to delete vector. |
732 |
+ |
|
733 |
+ |
2005-04-11 17:03 chuckv |
734 |
+ |
|
735 |
+ |
* samples/metals/nanorod/: Au_nanoparticle.md, |
736 |
+ |
Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why |
737 |
+ |
aren't these here? |
738 |
+ |
|
739 |
+ |
2005-04-11 16:58 tim |
740 |
+ |
|
741 |
+ |
* src/io/basic_ifstrstream.hpp: avoid multiple inherit in |
742 |
+ |
basic_ifstrstream |
743 |
+ |
|
744 |
+ |
2005-04-11 16:37 chuckv |
745 |
+ |
|
746 |
+ |
* make/Makefile.in, |
747 |
+ |
src/applications/nanoRodBuilder/BaseLattice.cpp, |
748 |
+ |
src/applications/nanoRodBuilder/BaseLattice.hpp, |
749 |
+ |
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
750 |
+ |
src/applications/nanoRodBuilder/GeometryBuilder.hpp, |
751 |
+ |
src/applications/nanoRodBuilder/Lattice.cpp, |
752 |
+ |
src/applications/nanoRodBuilder/Lattice.hpp, |
753 |
+ |
src/applications/nanoRodBuilder/LatticeCreator.cpp, |
754 |
+ |
src/applications/nanoRodBuilder/LatticeCreator.hpp, |
755 |
+ |
src/applications/nanoRodBuilder/LatticeFactory.cpp, |
756 |
+ |
src/applications/nanoRodBuilder/LatticeFactory.hpp, |
757 |
+ |
src/applications/nanoRodBuilder/Makefile, |
758 |
+ |
src/applications/nanoRodBuilder/MoLocator.cpp, |
759 |
+ |
src/applications/nanoRodBuilder/MoLocator.hpp, |
760 |
+ |
src/applications/nanoRodBuilder/nanoBuilder.ggo, |
761 |
+ |
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
762 |
+ |
src/applications/nanoRodBuilder/nanorodBuilder.ggo, |
763 |
+ |
src/applications/nanoRodBuilder/nanorodBuilderCmd.c, |
764 |
+ |
src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing |
765 |
+ |
nanoRodBuilder application (may not work yet). ((Doesn't work |
766 |
+ |
yet.)) (((May never work....))) |
767 |
+ |
|
768 |
+ |
2005-04-11 15:54 tim |
769 |
+ |
|
770 |
+ |
* src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete |
771 |
+ |
prepareVisitor in Dump2XYZ |
772 |
+ |
|
773 |
+ |
2005-04-11 15:19 chrisfen |
774 |
+ |
|
775 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: fixing of the |
776 |
+ |
quadrupoles. look! it's divide by 3 like stone says! |
777 |
+ |
|
778 |
+ |
2005-04-11 15:18 chrisfen |
779 |
+ |
|
780 |
+ |
* forceFields/DUFF2.frc: fixing of the quadrupoles |
781 |
+ |
|
782 |
+ |
2005-04-11 15:16 tim |
783 |
+ |
|
784 |
+ |
* src/selection/Token.hpp: change the parameter name in |
785 |
+ |
constructors |
786 |
+ |
|
787 |
+ |
2005-04-11 14:49 gezelter |
788 |
+ |
|
789 |
+ |
* make/Makefile.in: One more bug fix for GNU make versions < 3.80 |
790 |
+ |
|
791 |
+ |
2005-04-11 14:06 gezelter |
792 |
+ |
|
793 |
+ |
* make/Makefile.in: Fixed the uc and lc functions for GNU make |
794 |
+ |
versions < 3.80 |
795 |
+ |
|
796 |
+ |
2005-04-11 11:13 gezelter |
797 |
+ |
|
798 |
+ |
* make/Makefile.in, src/UseTheForce/Makefile, |
799 |
+ |
src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added |
800 |
+ |
some stuff to clean out module files during "make clean" |
801 |
+ |
|
802 |
+ |
2005-04-08 17:13 chrisfen |
803 |
+ |
|
804 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: quadrupole |
805 |
+ |
interactions should be working with a remaining question of |
806 |
+ |
interaction magnitude |
807 |
+ |
|
808 |
+ |
2005-04-08 17:12 chrisfen |
809 |
+ |
|
810 |
+ |
* samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with |
811 |
+ |
samples |
812 |
+ |
|
813 |
+ |
2005-04-08 13:48 chrisfen |
814 |
+ |
|
815 |
+ |
* samples/water/ssd/ssd.md: oops... messed up a sample |
816 |
+ |
|
817 |
+ |
2005-04-08 09:43 chrisfen |
818 |
+ |
|
819 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix |
820 |
+ |
charge-dipole interactions |
821 |
+ |
|
822 |
+ |
2005-04-08 09:42 chrisfen |
823 |
+ |
|
824 |
+ |
* samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md, |
825 |
+ |
ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole |
826 |
+ |
|
827 |
+ |
2005-04-08 09:41 chrisfen |
828 |
+ |
|
829 |
+ |
* forceFields/DUFF2.frc: added Cl- and Na+ |
830 |
+ |
|
831 |
+ |
2005-04-06 18:59 tim |
832 |
+ |
|
833 |
+ |
* src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser |
834 |
+ |
|
835 |
+ |
2005-04-05 18:09 tim |
836 |
+ |
|
837 |
+ |
* src/selection/: NameFinder.cpp, SelectionCompiler.cpp, |
838 |
+ |
SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-' |
839 |
+ |
in atom type name;clean the code a little bit |
840 |
+ |
|
841 |
+ |
2005-03-29 16:00 tim |
842 |
+ |
|
843 |
+ |
* src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug |
844 |
+ |
in converting rotation matrix to quaternion |
845 |
+ |
|
846 |
+ |
2005-03-28 17:41 tim |
847 |
+ |
|
848 |
+ |
* src/visitors/LipidTransVisitor.cpp: fixed the wrapping |
849 |
+ |
|
850 |
+ |
2005-03-28 17:30 tim |
851 |
+ |
|
852 |
+ |
* src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do |
853 |
+ |
the wrapping |
854 |
+ |
|
855 |
+ |
2005-03-28 10:54 tim |
856 |
+ |
|
857 |
+ |
* src/applications/staticProps/GofXyz.cpp: fix a bug in getting the |
858 |
+ |
dimension of histogram |
859 |
+ |
|
860 |
+ |
2005-03-22 11:38 tim |
861 |
+ |
|
862 |
+ |
* make/Makefile.in, src/applications/dump2Xyz/Makefile, |
863 |
+ |
src/applications/dynamicProps/Makefile, |
864 |
+ |
src/applications/oopse/Makefile, |
865 |
+ |
src/applications/simpleBuilder/Makefile, |
866 |
+ |
src/applications/staticProps/Makefile: avoid building parallel |
867 |
+ |
executable for dump2XYZ, simpleBuilder, staticProps and |
868 |
+ |
dynamicProps |
869 |
+ |
|
870 |
+ |
2005-03-21 17:34 chrisfen |
871 |
+ |
|
872 |
+ |
* forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the |
873 |
+ |
forcefield files |
874 |
+ |
|
875 |
+ |
2005-03-21 15:51 chrisfen |
876 |
+ |
|
877 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
878 |
+ |
DarkSide/reactionField.F90: Make sure electrostatic_module provides |
879 |
+ |
data for reaction_field |
880 |
+ |
|
881 |
+ |
2005-03-21 15:50 chrisfen |
882 |
+ |
|
883 |
+ |
* forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff. HE |
884 |
+ |
WILL CHANGE THIS BACK, RIGHT? |
885 |
+ |
|
886 |
+ |
2005-03-21 14:23 gezelter |
887 |
+ |
|
888 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: constant back to |
889 |
+ |
correct value |
890 |
+ |
|
891 |
+ |
2005-03-21 14:22 gezelter |
892 |
+ |
|
893 |
+ |
* make/Makefile.in: fixed an install-related bug. |
894 |
+ |
$(InstallCommand) had been set to $(InstallData) |
895 |
+ |
|
896 |
+ |
2005-03-15 09:21 gezelter |
897 |
+ |
|
898 |
+ |
* src/integrators/Integrator.cpp: VelocityVerletIntegrator already |
899 |
+ |
deletes and Nullifies restWriter, so Integrator shouldn't do it. |
900 |
+ |
|
901 |
+ |
2005-03-15 09:20 gezelter |
902 |
+ |
|
903 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos |
904 |
+ |
|
905 |
+ |
2005-03-13 02:39 gezelter |
906 |
+ |
|
907 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: first run at |
908 |
+ |
charge-quadrupole interactions |
909 |
+ |
|
910 |
+ |
2005-03-12 14:12 chrisfen |
911 |
+ |
|
912 |
+ |
* samples/: Makefile.in, thermoIntegration/liquid/Makefile, |
913 |
+ |
thermoIntegration/solid/Makefile: forgot a couple of makefiles |
914 |
+ |
|
915 |
+ |
2005-03-12 14:05 chrisfen |
916 |
+ |
|
917 |
+ |
* samples/thermoIntegration/liquid/ssde.in, |
918 |
+ |
samples/thermoIntegration/liquid/ssde.md, |
919 |
+ |
samples/thermoIntegration/liquid/water.md, |
920 |
+ |
samples/thermoIntegration/solid/idealCrystal.in, |
921 |
+ |
samples/thermoIntegration/solid/ssde.in, |
922 |
+ |
samples/thermoIntegration/solid/ssde.md, |
923 |
+ |
samples/thermoIntegration/solid/ssde.zang0, |
924 |
+ |
samples/thermoIntegration/solid/water.md, |
925 |
+ |
samples/water/tip3p_ice/tp3.md, |
926 |
+ |
src/UseTheForce/DarkSide/sticky.F90, |
927 |
+ |
src/restraints/ThermoIntegrationForceManager.cpp: added some |
928 |
+ |
samples |
929 |
+ |
|
930 |
+ |
2005-03-11 12:50 tim |
931 |
+ |
|
932 |
+ |
* src/: brains/SimCreator.cpp, |
933 |
+ |
io/MultipoleAtomTypesSectionParser.cpp: fix a typo in |
934 |
+ |
MultipoleAtomTypesSectionParser |
935 |
+ |
|
936 |
+ |
2005-03-11 10:55 tim |
937 |
+ |
|
938 |
+ |
* src/brains/SimInfo.cpp: pairs inside cutoff group should not be |
939 |
+ |
excluded |
940 |
+ |
|
941 |
+ |
2005-03-11 10:53 gezelter |
942 |
+ |
|
943 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for |
944 |
+ |
quadrupoles |
945 |
+ |
|
946 |
+ |
2005-03-11 10:52 gezelter |
947 |
+ |
|
948 |
+ |
* forceFields/DUFF2.frc: quadrupoles for SSD models |
949 |
+ |
|
950 |
+ |
2005-03-11 10:00 tim |
951 |
+ |
|
952 |
+ |
* ChangeLog, doc/SelectionExpression.html, |
953 |
+ |
doc/classoopse_1_1StuntDouble.png, doc/definition.jpg, |
954 |
+ |
doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png, |
955 |
+ |
src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp, |
956 |
+ |
src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp, |
957 |
+ |
src/selection/TokenMap.cpp: clean up SimInfo; modify the images of |
958 |
+ |
SelectionExpression.html |
959 |
+ |
|
960 |
+ |
2005-03-10 19:43 chrisfen |
961 |
+ |
|
962 |
+ |
* samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md, |
963 |
+ |
src/io/RestReader.cpp, src/restraints/Restraints.cpp, |
964 |
+ |
src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in |
965 |
+ |
MPI restraints |
966 |
+ |
|
967 |
+ |
2005-03-10 18:56 tim |
968 |
+ |
|
969 |
+ |
* doc/SelectionExpression.html, src/brains/SimInfo.cpp, |
970 |
+ |
src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody |
971 |
+ |
and cutoff group |
972 |
+ |
|
973 |
+ |
2005-03-10 17:06 gezelter |
974 |
+ |
|
975 |
+ |
* src/types/MorseBondType.hpp: fixed a doxygen problem |
976 |
+ |
|
977 |
+ |
2005-03-10 16:51 gezelter |
978 |
+ |
|
979 |
+ |
* samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with |
980 |
+ |
the split dipole test cases |
981 |
+ |
|
982 |
+ |
2005-03-10 16:51 gezelter |
983 |
+ |
|
984 |
+ |
* doc/SelectionExpression.html: updated some documentation |
985 |
+ |
|
986 |
+ |
2005-03-10 15:40 gezelter |
987 |
+ |
|
988 |
+ |
* src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp, |
989 |
+ |
Makefile: LinkedList removal project starts now |
990 |
+ |
|
991 |
+ |
2005-03-10 15:28 tim |
992 |
+ |
|
993 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
994 |
+ |
io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp: |
995 |
+ |
using map to replace link list |
996 |
+ |
|
997 |
+ |
2005-03-10 14:11 tim |
998 |
+ |
|
999 |
+ |
* samples/dipole/: splitInWater.in, splitInWater.md: adding test |
1000 |
+ |
case of split dipole |
1001 |
+ |
|
1002 |
+ |
2005-03-10 14:10 chrisfen |
1003 |
+ |
|
1004 |
+ |
* samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, |
1005 |
+ |
src/io/RestWriter.cpp, |
1006 |
+ |
src/restraints/ThermoIntegrationForceManager.cpp: Oops... MPI now |
1007 |
+ |
builds... |
1008 |
+ |
|
1009 |
+ |
2005-03-10 13:44 tim |
1010 |
+ |
|
1011 |
+ |
* samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in, |
1012 |
+ |
split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md: |
1013 |
+ |
adding test case for split dipole |
1014 |
+ |
|
1015 |
+ |
2005-03-10 12:54 gezelter |
1016 |
+ |
|
1017 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side |
1018 |
+ |
support for split dipoles |
1019 |
+ |
|
1020 |
+ |
2005-03-10 11:27 chrisfen |
1021 |
+ |
|
1022 |
+ |
* samples/water/tip3p_ice/tp3.md, |
1023 |
+ |
src/restraints/ThermoIntegrationForceManager.cpp: fixes to |
1024 |
+ |
restraints |
1025 |
+ |
|
1026 |
+ |
2005-03-10 11:15 chrisfen |
1027 |
+ |
|
1028 |
+ |
* samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp, |
1029 |
+ |
src/UseTheForce/ForceFields.hpp, |
1030 |
+ |
src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints |
1031 |
+ |
|
1032 |
+ |
2005-03-10 11:14 tim |
1033 |
+ |
|
1034 |
+ |
* ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc, |
1035 |
+ |
src/io/MultipoleAtomTypesSectionParser.cpp, |
1036 |
+ |
src/selection/SelectionEvaluator.cpp: minor change |
1037 |
+ |
|
1038 |
|
2005-03-10 10:10 chrisfen |
1039 |
|
|
1040 |
|
* make/Makefile.in, samples/water/tip3p_ice/tp3.md, |
1311 |
|
adding basic_teebuf which can operate on multiple stream |
1312 |
|
simutaneously. |
1313 |
|
|
1314 |
+ |
2005-02-22 14:26 chrisfen |
1315 |
+ |
|
1316 |
+ |
* samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf |
1317 |
+ |
sample |
1318 |
+ |
|
1319 |
|
2005-02-22 13:56 tim |
1320 |
|
|
1321 |
|
* src/: UseTheForce/DarkSide/reactionField.F90, |
2521 |
|
|
2522 |
|
2005-01-11 10:52 tim |
2523 |
|
|
2524 |
< |
* src/constraints/Rattle.cpp: file Rattle.cpp was initially added |
2524 |
> |
* src/constraints/Rattle.hpp: file Rattle.hpp was initially added |
2525 |
|
on branch new_design. |
2526 |
|
|
2527 |
|
2005-01-11 10:52 tim |
2528 |
|
|
2529 |
< |
* src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm |
2529 |
> |
* src/constraints/Rattle.cpp: file Rattle.cpp was initially added |
2530 |
> |
on branch new_design. |
2531 |
|
|
2532 |
|
2005-01-11 10:52 tim |
2533 |
|
|
2534 |
< |
* src/constraints/Rattle.hpp: file Rattle.hpp was initially added |
1492 |
< |
on branch new_design. |
2534 |
> |
* src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm |
2535 |
|
|
2536 |
|
2005-01-11 10:47 tim |
2537 |
|
|
2596 |
|
|
2597 |
|
* src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was |
2598 |
|
initially added on branch new_design. |
2599 |
+ |
|
2600 |
+ |
2005-01-07 16:50 tim |
2601 |
+ |
|
2602 |
+ |
* src/constraints/ZconstraintForceManager.cpp: file |
2603 |
+ |
ZconstraintForceManager.cpp was initially added on branch |
2604 |
+ |
new_design. |
2605 |
+ |
|
2606 |
+ |
2005-01-07 16:50 tim |
2607 |
|
|
2608 |
+ |
* src/constraints/ZconstraintForceManager.hpp: file |
2609 |
+ |
ZconstraintForceManager.hpp was initially added on branch |
2610 |
+ |
new_design. |
2611 |
+ |
|
2612 |
|
2005-01-07 16:50 tim |
2613 |
|
|
2614 |
|
* src/: applications/simpleBuilder/BaseLattice.hpp, |
2628 |
|
* src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was |
2629 |
|
initially added on branch new_design. |
2630 |
|
|
1577 |
– |
2005-01-07 16:50 tim |
1578 |
– |
|
1579 |
– |
* src/constraints/ZconstraintForceManager.cpp: file |
1580 |
– |
ZconstraintForceManager.cpp was initially added on branch |
1581 |
– |
new_design. |
1582 |
– |
|
1583 |
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2005-01-07 16:50 tim |
1584 |
– |
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1585 |
– |
* src/constraints/ZconstraintForceManager.hpp: file |
1586 |
– |
ZconstraintForceManager.hpp was initially added on branch |
1587 |
– |
new_design. |
1588 |
– |
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2631 |
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2005-01-06 17:31 tim |
2632 |
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2633 |
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* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
2664 |
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|
2665 |
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2005-01-05 12:35 tim |
2666 |
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|
2667 |
+ |
* src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially |
2668 |
+ |
added on branch new_design. |
2669 |
+ |
|
2670 |
+ |
2005-01-05 12:35 tim |
2671 |
+ |
|
2672 |
|
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
2673 |
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Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, |
2674 |
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MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp, |
2677 |
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|
2678 |
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2005-01-05 12:35 tim |
2679 |
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|
2680 |
< |
* src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially |
2681 |
< |
added on branch new_design. |
2680 |
> |
* src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp |
2681 |
> |
was initially added on branch new_design. |
2682 |
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2683 |
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2005-01-05 12:35 tim |
2684 |
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2685 |
< |
* src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp |
2685 |
> |
* src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp |
2686 |
|
was initially added on branch new_design. |
2687 |
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|
2688 |
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2005-01-05 12:35 tim |
2689 |
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2690 |
< |
* src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp |
2690 |
> |
* src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp |
2691 |
|
was initially added on branch new_design. |
2692 |
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|
2693 |
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2005-01-05 12:35 tim |
2695 |
|
* src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially |
2696 |
|
added on branch new_design. |
2697 |
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1651 |
– |
2005-01-05 12:35 tim |
1652 |
– |
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1653 |
– |
* src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp |
1654 |
– |
was initially added on branch new_design. |
1655 |
– |
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2698 |
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2005-01-04 17:18 tim |
2699 |
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1658 |
– |
* src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was |
1659 |
– |
initially added on branch new_design. |
1660 |
– |
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1661 |
– |
2005-01-04 17:18 tim |
1662 |
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2700 |
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* src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
2701 |
|
brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, |
2702 |
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brains/Thermo.cpp, constraints/ConstraintPair.hpp, |
2708 |
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2709 |
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2005-01-04 17:18 tim |
2710 |
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|
2711 |
< |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
2712 |
< |
Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, |
1676 |
< |
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, |
1677 |
< |
SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress |
2711 |
> |
* src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was |
2712 |
> |
initially added on branch new_design. |
2713 |
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|
2714 |
|
2005-01-04 17:18 tim |
2715 |
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1681 |
– |
* src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp |
1682 |
– |
was initially added on branch new_design. |
1683 |
– |
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1684 |
– |
2005-01-04 17:18 tim |
1685 |
– |
|
2716 |
|
* src/minimizers/MinimizerParameterSet.cpp: file |
2717 |
|
MinimizerParameterSet.cpp was initially added on branch new_design. |
2718 |
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2723 |
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2724 |
|
2005-01-04 17:18 tim |
2725 |
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|
2726 |
+ |
* src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp |
2727 |
+ |
was initially added on branch new_design. |
2728 |
+ |
|
2729 |
+ |
2005-01-04 17:18 tim |
2730 |
+ |
|
2731 |
+ |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
2732 |
+ |
Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, |
2733 |
+ |
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, |
2734 |
+ |
SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress |
2735 |
+ |
|
2736 |
+ |
2005-01-04 17:18 tim |
2737 |
+ |
|
2738 |
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* src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on |
2739 |
|
branch new_design. |
2740 |
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|
3050 |
|
io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp, |
3051 |
|
io/SectionParserManager.cpp, utils/LocalIndexManager.hpp, |
3052 |
|
utils/TypeContainer.hpp: begin to fix bugs |
3053 |
+ |
|
3054 |
+ |
2004-12-02 19:26 tim |
3055 |
+ |
|
3056 |
+ |
* src/utils/Trim.cpp: file Trim.cpp was initially added on branch |
3057 |
+ |
new_design. |
3058 |
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|
3059 |
|
2004-12-02 19:26 tim |
3060 |
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|
3067 |
|
utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a |
3068 |
|
bug in countTokens in StringTokenizer |
3069 |
|
|
2023 |
– |
2004-12-02 19:26 tim |
2024 |
– |
|
2025 |
– |
* src/utils/Trim.cpp: file Trim.cpp was initially added on branch |
2026 |
– |
new_design. |
2027 |
– |
|
3070 |
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2004-12-02 19:06 tim |
3071 |
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|
3072 |
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* forceFields/newDUFF.frc: minor fix |
3074 |
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2004-12-02 18:15 tim |
3075 |
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3076 |
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* forceFields/newDUFF.frc: new ForceField format |
2035 |
– |
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2036 |
– |
2004-12-02 17:15 tim |
2037 |
– |
|
2038 |
– |
* src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp |
2039 |
– |
was initially added on branch new_design. |
2040 |
– |
|
2041 |
– |
2004-12-02 17:15 tim |
3077 |
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2043 |
– |
* src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp |
2044 |
– |
was initially added on branch new_design. |
2045 |
– |
|
3078 |
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2004-12-02 17:15 tim |
3079 |
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2048 |
– |
* src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp |
2049 |
– |
was initially added on branch new_design. |
2050 |
– |
|
2051 |
– |
2004-12-02 17:15 tim |
2052 |
– |
|
3080 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
3081 |
|
UseTheForce/ForceFieldCreator.cpp, |
3082 |
|
UseTheForce/ForceFieldCreator.hpp, |
3099 |
|
* src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp |
3100 |
|
was initially added on branch new_design. |
3101 |
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|
3102 |
+ |
2004-12-02 17:15 tim |
3103 |
+ |
|
3104 |
+ |
* src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp |
3105 |
+ |
was initially added on branch new_design. |
3106 |
+ |
|
3107 |
+ |
2004-12-02 17:15 tim |
3108 |
+ |
|
3109 |
+ |
* src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp |
3110 |
+ |
was initially added on branch new_design. |
3111 |
+ |
|
3112 |
+ |
2004-12-02 17:15 tim |
3113 |
+ |
|
3114 |
+ |
* src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp |
3115 |
+ |
was initially added on branch new_design. |
3116 |
+ |
|
3117 |
|
2004-12-02 11:53 tim |
3118 |
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|
3119 |
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* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, |
3272 |
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|
3273 |
|
2004-12-01 19:09 tim |
3274 |
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|
3275 |
< |
* src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp |
3276 |
< |
was initially added on branch new_design. |
3275 |
> |
* src/integrators/DLM.cpp: file DLM.cpp was initially added on |
3276 |
> |
branch new_design. |
3277 |
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|
3278 |
|
2004-12-01 19:09 tim |
3279 |
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|
3280 |
+ |
* src/integrators/DLM.hpp: file DLM.hpp was initially added on |
3281 |
+ |
branch new_design. |
3282 |
+ |
|
3283 |
+ |
2004-12-01 19:09 tim |
3284 |
+ |
|
3285 |
|
* src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, |
3286 |
|
brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
3287 |
|
brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp, |
3294 |
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|
3295 |
|
2004-12-01 19:09 tim |
3296 |
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|
3297 |
< |
* src/integrators/DLM.hpp: file DLM.hpp was initially added on |
3298 |
< |
branch new_design. |
3297 |
> |
* src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp |
3298 |
> |
was initially added on branch new_design. |
3299 |
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|
2253 |
– |
2004-12-01 19:09 tim |
2254 |
– |
|
2255 |
– |
* src/integrators/DLM.cpp: file DLM.cpp was initially added on |
2256 |
– |
branch new_design. |
2257 |
– |
|
3300 |
|
2004-12-01 17:45 tim |
3301 |
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|
3302 |
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* src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp, |
3395 |
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|
3396 |
|
2004-11-30 14:58 tim |
3397 |
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|
2356 |
– |
* src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially |
2357 |
– |
added on branch new_design. |
2358 |
– |
|
2359 |
– |
2004-11-30 14:58 tim |
2360 |
– |
|
3398 |
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
3399 |
|
brains/ForceManager.cpp, brains/ForceManager.hpp, |
3400 |
|
brains/MoleculeCreator.cpp, brains/SimCreator.hpp, |
3404 |
|
brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, |
3405 |
|
math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo |
3406 |
|
|
3407 |
+ |
2004-11-30 14:58 tim |
3408 |
+ |
|
3409 |
+ |
* src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially |
3410 |
+ |
added on branch new_design. |
3411 |
+ |
|
3412 |
|
2004-11-30 12:54 tim |
3413 |
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|
3414 |
|
* src/: primitives/Bend.hpp, primitives/Bond.hpp, |
3417 |
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|
3418 |
|
2004-11-30 00:03 tim |
3419 |
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|
3420 |
< |
* src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename |
3421 |
< |
LocalndexManager.hpp to LocalIndexManager.hpp |
3420 |
> |
* src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was |
3421 |
> |
initially added on branch new_design. |
3422 |
|
|
3423 |
|
2004-11-30 00:03 tim |
3424 |
|
|
3425 |
< |
* src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was |
3426 |
< |
initially added on branch new_design. |
3425 |
> |
* src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename |
3426 |
> |
LocalndexManager.hpp to LocalIndexManager.hpp |
3427 |
|
|
3428 |
|
2004-11-29 23:43 tim |
3429 |
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|
3551 |
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|
3552 |
|
2004-11-25 15:18 tim |
3553 |
|
|
3554 |
+ |
* src/types/QuarticBondType.hpp: file QuarticBondType.hpp was |
3555 |
+ |
initially added on branch new_design. |
3556 |
+ |
|
3557 |
+ |
2004-11-25 15:18 tim |
3558 |
+ |
|
3559 |
|
* src/: io/AtomTypesSectionParser.cpp, |
3560 |
|
io/BondTypesSectionParser.cpp, |
3561 |
|
io/DirectionalAtomTypesSectionParser.cpp, |
3568 |
|
* src/types/QuarticBendType.hpp: file QuarticBendType.hpp was |
3569 |
|
initially added on branch new_design. |
3570 |
|
|
2524 |
– |
2004-11-25 15:18 tim |
2525 |
– |
|
2526 |
– |
* src/types/QuarticBondType.hpp: file QuarticBondType.hpp was |
2527 |
– |
initially added on branch new_design. |
2528 |
– |
|
3571 |
|
2004-11-24 17:12 tim |
3572 |
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|
3573 |
|
* src/: io/AtomTypesSectionParser.cpp, |
3680 |
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|
3681 |
|
2004-11-23 12:53 tim |
3682 |
|
|
2641 |
– |
* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
2642 |
– |
ElectrostaticAtomTypesSectionParser.cpp was initially added on |
2643 |
– |
branch new_design. |
2644 |
– |
|
2645 |
– |
2004-11-23 12:53 tim |
2646 |
– |
|
3683 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
3684 |
|
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
3685 |
|
applications/simpleBuilder/simpleBuilder.cpp, |
3697 |
|
ElectrostaticAtomTypesSectionParser.hpp was initially added on |
3698 |
|
branch new_design. |
3699 |
|
|
3700 |
< |
2004-11-23 01:03 tim |
3700 |
> |
2004-11-23 12:53 tim |
3701 |
|
|
3702 |
< |
* src/io/EAMAtomTypesSectionParser.cpp: file |
3703 |
< |
EAMAtomTypesSectionParser.cpp was initially added on branch |
3704 |
< |
new_design. |
3702 |
> |
* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
3703 |
> |
ElectrostaticAtomTypesSectionParser.cpp was initially added on |
3704 |
> |
branch new_design. |
3705 |
|
|
3706 |
|
2004-11-23 01:03 tim |
3707 |
|
|
3712 |
|
|
3713 |
|
2004-11-23 01:03 tim |
3714 |
|
|
3715 |
+ |
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
3716 |
+ |
was initially added on branch new_design. |
3717 |
+ |
|
3718 |
+ |
2004-11-23 01:03 tim |
3719 |
+ |
|
3720 |
|
* src/io/EAMAtomTypesSectionParser.hpp: file |
3721 |
|
EAMAtomTypesSectionParser.hpp was initially added on branch |
3722 |
|
new_design. |
3723 |
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|
3724 |
|
2004-11-23 01:03 tim |
3725 |
|
|
3726 |
< |
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
3727 |
< |
was initially added on branch new_design. |
3726 |
> |
* src/io/EAMAtomTypesSectionParser.cpp: file |
3727 |
> |
EAMAtomTypesSectionParser.cpp was initially added on branch |
3728 |
> |
new_design. |
3729 |
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|
3730 |
|
2004-11-22 23:35 tim |
3731 |
|
|
3732 |
< |
* src/io/TorsionTypesSectionParser.cpp: file |
3733 |
< |
TorsionTypesSectionParser.cpp was initially added on branch |
3732 |
> |
* src/io/TorsionTypesSectionParser.hpp: file |
3733 |
> |
TorsionTypesSectionParser.hpp was initially added on branch |
3734 |
|
new_design. |
3735 |
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|
3736 |
|
2004-11-22 23:35 tim |
3741 |
|
|
3742 |
|
2004-11-22 23:35 tim |
3743 |
|
|
2702 |
– |
* src/io/BondTypesSectionParser.cpp: file |
2703 |
– |
BondTypesSectionParser.cpp was initially added on branch |
2704 |
– |
new_design. |
2705 |
– |
|
2706 |
– |
2004-11-22 23:35 tim |
2707 |
– |
|
3744 |
|
* src/io/BondTypesSectionParser.hpp: file |
3745 |
|
BondTypesSectionParser.hpp was initially added on branch |
3746 |
|
new_design. |
3747 |
|
|
3748 |
|
2004-11-22 23:35 tim |
3749 |
|
|
3750 |
< |
* src/io/TorsionTypesSectionParser.hpp: file |
3751 |
< |
TorsionTypesSectionParser.hpp was initially added on branch |
3750 |
> |
* src/io/BondTypesSectionParser.cpp: file |
3751 |
> |
BondTypesSectionParser.cpp was initially added on branch |
3752 |
|
new_design. |
3753 |
|
|
3754 |
|
2004-11-22 23:35 tim |
3755 |
|
|
3756 |
< |
* src/io/BendTypesSectionParser.cpp: file |
3757 |
< |
BendTypesSectionParser.cpp was initially added on branch |
3756 |
> |
* src/io/TorsionTypesSectionParser.cpp: file |
3757 |
> |
TorsionTypesSectionParser.cpp was initially added on branch |
3758 |
|
new_design. |
3759 |
|
|
3760 |
|
2004-11-22 23:35 tim |
3765 |
|
BondTypesSectionParser, BendTypesSectionParser and |
3766 |
|
TorsionTypeSectionParser |
3767 |
|
|
3768 |
+ |
2004-11-22 23:35 tim |
3769 |
+ |
|
3770 |
+ |
* src/io/BendTypesSectionParser.cpp: file |
3771 |
+ |
BendTypesSectionParser.cpp was initially added on branch |
3772 |
+ |
new_design. |
3773 |
+ |
|
3774 |
|
2004-11-22 18:04 tim |
3775 |
|
|
3776 |
|
* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in |
3778 |
|
|
3779 |
|
2004-11-22 18:02 tim |
3780 |
|
|
3781 |
+ |
* src/io/: DirectionalAtomTypesParser.hpp, |
3782 |
+ |
DirectionalAtomTypesSectionParser.hpp: adding section parsers |
3783 |
+ |
|
3784 |
+ |
2004-11-22 18:02 tim |
3785 |
+ |
|
3786 |
|
* src/io/DirectionalAtomTypesSectionParser.hpp: file |
3787 |
|
DirectionalAtomTypesSectionParser.hpp was initially added on branch |
3788 |
|
new_design. |
3789 |
|
|
2743 |
– |
2004-11-22 18:02 tim |
2744 |
– |
|
2745 |
– |
* src/io/: DirectionalAtomTypesParser.hpp, |
2746 |
– |
DirectionalAtomTypesSectionParser.hpp: adding section parsers |
2747 |
– |
|
3790 |
|
2004-11-22 15:55 tim |
3791 |
|
|
3792 |
< |
* src/io/DirectionalAtomTypesParser.hpp: file |
3793 |
< |
DirectionalAtomTypesParser.hpp was initially added on branch |
3792 |
> |
* src/io/DipoleAtomTypesSectionParser.hpp: file |
3793 |
> |
DipoleAtomTypesSectionParser.hpp was initially added on branch |
3794 |
|
new_design. |
3795 |
|
|
3796 |
|
2004-11-22 15:55 tim |
3797 |
|
|
3798 |
< |
* src/io/HarmonicBondTypesSectionParser.hpp: file |
3799 |
< |
HarmonicBondTypesSectionParser.hpp was initially added on branch |
3798 |
> |
* src/io/AtomTypesSectionParser.hpp: file |
3799 |
> |
AtomTypesSectionParser.hpp was initially added on branch |
3800 |
|
new_design. |
3801 |
|
|
3802 |
|
2004-11-22 15:55 tim |
3803 |
|
|
3804 |
< |
* src/io/ChargeAtomTypesSectionParser.hpp: file |
3805 |
< |
ChargeAtomTypesSectionParser.hpp was initially added on branch |
3804 |
> |
* src/io/HarmonicBondTypesSectionParser.hpp: file |
3805 |
> |
HarmonicBondTypesSectionParser.hpp was initially added on branch |
3806 |
|
new_design. |
3807 |
|
|
3808 |
|
2004-11-22 15:55 tim |
3809 |
|
|
3810 |
< |
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
3811 |
< |
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
3810 |
> |
* src/io/StickyAtomTypesSectionParser.cpp: file |
3811 |
> |
StickyAtomTypesSectionParser.cpp was initially added on branch |
3812 |
|
new_design. |
3813 |
|
|
3814 |
|
2004-11-22 15:55 tim |
3815 |
|
|
3816 |
< |
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
3817 |
< |
LennardJonesAtomTypesSectionParser.cpp was initially added on |
3816 |
> |
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
3817 |
> |
LennardJonesAtomTypesSectionParser.hpp was initially added on |
3818 |
|
branch new_design. |
3819 |
|
|
3820 |
|
2004-11-22 15:55 tim |
3821 |
|
|
3822 |
< |
* src/io/DipoleAtomTypesSectionParser.cpp: file |
3823 |
< |
DipoleAtomTypesSectionParser.cpp was initially added on branch |
3822 |
> |
* src/io/HarmonicBondTypesSectionParser.cpp: file |
3823 |
> |
HarmonicBondTypesSectionParser.cpp was initially added on branch |
3824 |
|
new_design. |
3825 |
|
|
3826 |
|
2004-11-22 15:55 tim |
3827 |
|
|
3828 |
< |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
3829 |
< |
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
2788 |
< |
brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
2789 |
< |
integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
2790 |
< |
io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
2791 |
< |
io/ChargeAtomTypesSectionParser.hpp, |
2792 |
< |
io/DipoleAtomTypesSectionParser.cpp, |
2793 |
< |
io/DipoleAtomTypesSectionParser.hpp, |
2794 |
< |
io/DirectionalAtomTypesParser.hpp, |
2795 |
< |
io/DirectionalAtomTypesSectionParser.cpp, |
2796 |
< |
io/HarmonicBondTypesSectionParser.cpp, |
2797 |
< |
io/HarmonicBondTypesSectionParser.hpp, |
2798 |
< |
io/LennardJonesAtomTypesSectionParser.cpp, |
2799 |
< |
io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
2800 |
< |
io/SectionParser.hpp, io/SectionParserManager.cpp, |
2801 |
< |
io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
2802 |
< |
io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
2803 |
< |
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
2804 |
< |
utils/GenericData.hpp: adding section parsers |
2805 |
< |
|
2806 |
< |
2004-11-22 15:55 tim |
2807 |
< |
|
2808 |
< |
* src/io/DipoleAtomTypesSectionParser.hpp: file |
2809 |
< |
DipoleAtomTypesSectionParser.hpp was initially added on branch |
3828 |
> |
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
3829 |
> |
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
3830 |
|
new_design. |
3831 |
|
|
3832 |
|
2004-11-22 15:55 tim |
3833 |
|
|
3834 |
< |
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
2815 |
< |
added on branch new_design. |
2816 |
< |
|
2817 |
< |
2004-11-22 15:55 tim |
2818 |
< |
|
2819 |
< |
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
3834 |
> |
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
3835 |
|
was initially added on branch new_design. |
3836 |
|
|
3837 |
|
2004-11-22 15:55 tim |
3842 |
|
|
3843 |
|
2004-11-22 15:55 tim |
3844 |
|
|
3845 |
< |
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
3846 |
< |
LennardJonesAtomTypesSectionParser.hpp was initially added on |
3847 |
< |
branch new_design. |
3845 |
> |
* src/io/ChargeAtomTypesSectionParser.cpp: file |
3846 |
> |
ChargeAtomTypesSectionParser.cpp was initially added on branch |
3847 |
> |
new_design. |
3848 |
|
|
3849 |
|
2004-11-22 15:55 tim |
3850 |
|
|
3851 |
< |
* src/io/HarmonicBondTypesSectionParser.cpp: file |
3852 |
< |
HarmonicBondTypesSectionParser.cpp was initially added on branch |
3851 |
> |
* src/io/DipoleAtomTypesSectionParser.cpp: file |
3852 |
> |
DipoleAtomTypesSectionParser.cpp was initially added on branch |
3853 |
|
new_design. |
3854 |
|
|
3855 |
|
2004-11-22 15:55 tim |
3856 |
|
|
3857 |
< |
* src/io/AtomTypesSectionParser.hpp: file |
3858 |
< |
AtomTypesSectionParser.hpp was initially added on branch |
3857 |
> |
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
3858 |
> |
LennardJonesAtomTypesSectionParser.cpp was initially added on |
3859 |
> |
branch new_design. |
3860 |
> |
|
3861 |
> |
2004-11-22 15:55 tim |
3862 |
> |
|
3863 |
> |
* src/io/ChargeAtomTypesSectionParser.hpp: file |
3864 |
> |
ChargeAtomTypesSectionParser.hpp was initially added on branch |
3865 |
|
new_design. |
3866 |
|
|
3867 |
|
2004-11-22 15:55 tim |
3868 |
|
|
3869 |
< |
* src/io/StickyAtomTypesSectionParser.cpp: file |
3870 |
< |
StickyAtomTypesSectionParser.cpp was initially added on branch |
3869 |
> |
* src/io/StickyAtomTypesSectionParser.hpp: file |
3870 |
> |
StickyAtomTypesSectionParser.hpp was initially added on branch |
3871 |
|
new_design. |
3872 |
|
|
3873 |
|
2004-11-22 15:55 tim |
3877 |
|
|
3878 |
|
2004-11-22 15:55 tim |
3879 |
|
|
3880 |
< |
* src/io/ChargeAtomTypesSectionParser.cpp: file |
3881 |
< |
ChargeAtomTypesSectionParser.cpp was initially added on branch |
3880 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
3881 |
> |
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
3882 |
> |
brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
3883 |
> |
integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
3884 |
> |
io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
3885 |
> |
io/ChargeAtomTypesSectionParser.hpp, |
3886 |
> |
io/DipoleAtomTypesSectionParser.cpp, |
3887 |
> |
io/DipoleAtomTypesSectionParser.hpp, |
3888 |
> |
io/DirectionalAtomTypesParser.hpp, |
3889 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
3890 |
> |
io/HarmonicBondTypesSectionParser.cpp, |
3891 |
> |
io/HarmonicBondTypesSectionParser.hpp, |
3892 |
> |
io/LennardJonesAtomTypesSectionParser.cpp, |
3893 |
> |
io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
3894 |
> |
io/SectionParser.hpp, io/SectionParserManager.cpp, |
3895 |
> |
io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
3896 |
> |
io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
3897 |
> |
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
3898 |
> |
utils/GenericData.hpp: adding section parsers |
3899 |
> |
|
3900 |
> |
2004-11-22 15:55 tim |
3901 |
> |
|
3902 |
> |
* src/io/DirectionalAtomTypesParser.hpp: file |
3903 |
> |
DirectionalAtomTypesParser.hpp was initially added on branch |
3904 |
|
new_design. |
3905 |
|
|
3906 |
|
2004-11-22 15:55 tim |
3907 |
|
|
3908 |
< |
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
3908 |
> |
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
3909 |
|
was initially added on branch new_design. |
3910 |
|
|
3911 |
|
2004-11-22 15:55 tim |
3912 |
|
|
3913 |
< |
* src/io/StickyAtomTypesSectionParser.hpp: file |
3914 |
< |
StickyAtomTypesSectionParser.hpp was initially added on branch |
2872 |
< |
new_design. |
3913 |
> |
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
3914 |
> |
added on branch new_design. |
3915 |
|
|
3916 |
|
2004-11-19 17:12 tim |
3917 |
|
|
3918 |
+ |
* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
3919 |
+ |
added on branch new_design. |
3920 |
+ |
|
3921 |
+ |
2004-11-19 17:12 tim |
3922 |
+ |
|
3923 |
|
* src/: brains/SimState.cpp, brains/SimState.hpp, |
3924 |
|
io/InitializeFromFile.cpp, types/FixBondType.hpp, |
3925 |
|
types/FixedBondType.hpp: remove more useless files |
3926 |
|
|
2880 |
– |
2004-11-19 17:12 tim |
2881 |
– |
|
2882 |
– |
* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
2883 |
– |
added on branch new_design. |
2884 |
– |
|
3927 |
|
2004-11-19 16:47 tim |
3928 |
|
|
3929 |
|
* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, |
3932 |
|
|
3933 |
|
2004-11-19 16:38 tim |
3934 |
|
|
3935 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
3936 |
+ |
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
3937 |
+ |
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
3938 |
+ |
integrators/NVT.hpp: refactory integrator |
3939 |
+ |
|
3940 |
+ |
2004-11-19 16:38 tim |
3941 |
+ |
|
3942 |
|
* src/integrators/NPTi.hpp: file NPTi.hpp was initially added on |
3943 |
|
branch new_design. |
3944 |
|
|
3945 |
|
2004-11-19 16:38 tim |
3946 |
|
|
3947 |
< |
* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
3948 |
< |
on branch new_design. |
3947 |
> |
* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
3948 |
> |
branch new_design. |
3949 |
|
|
3950 |
|
2004-11-19 16:38 tim |
3951 |
|
|
3954 |
|
|
3955 |
|
2004-11-19 16:38 tim |
3956 |
|
|
3957 |
< |
* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
3958 |
< |
branch new_design. |
3957 |
> |
* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
3958 |
> |
on branch new_design. |
3959 |
|
|
3960 |
|
2004-11-19 16:38 tim |
3961 |
|
|
3962 |
< |
* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
3962 |
> |
* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
3963 |
|
branch new_design. |
3964 |
|
|
2916 |
– |
2004-11-19 16:38 tim |
2917 |
– |
|
2918 |
– |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
2919 |
– |
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
2920 |
– |
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
2921 |
– |
integrators/NVT.hpp: refactory integrator |
2922 |
– |
|
3965 |
|
2004-11-19 15:37 tim |
3966 |
|
|
3967 |
|
* forceFields/newDUFF.frc: new DUFF forcefield |
3968 |
|
|
3969 |
|
2004-11-19 15:23 tim |
3970 |
|
|
3971 |
+ |
* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
3972 |
+ |
branch new_design. |
3973 |
+ |
|
3974 |
+ |
2004-11-19 15:23 tim |
3975 |
+ |
|
3976 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, |
3977 |
|
UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, |
3978 |
|
utils/TypeContainer.hpp: add EAM |
3982 |
|
* src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on |
3983 |
|
branch new_design. |
3984 |
|
|
2938 |
– |
2004-11-19 15:23 tim |
2939 |
– |
|
2940 |
– |
* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
2941 |
– |
branch new_design. |
2942 |
– |
|
3985 |
|
2004-11-19 13:02 tim |
3986 |
|
|
3987 |
|
* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except |
3989 |
|
|
3990 |
|
2004-11-19 12:56 tim |
3991 |
|
|
3992 |
< |
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
3992 |
> |
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
3993 |
|
was initially added on branch new_design. |
3994 |
|
|
3995 |
|
2004-11-19 12:56 tim |
3996 |
|
|
3997 |
< |
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
3997 |
> |
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
3998 |
|
was initially added on branch new_design. |
3999 |
|
|
4000 |
|
2004-11-19 12:56 tim |
4019 |
|
|
4020 |
|
2004-11-18 18:26 tim |
4021 |
|
|
4022 |
+ |
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
4023 |
+ |
initially added on branch new_design. |
4024 |
+ |
|
4025 |
+ |
2004-11-18 18:26 tim |
4026 |
+ |
|
4027 |
|
* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, |
4028 |
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
4029 |
|
integrators/VelocityVerletIntegrator.cpp, |
4034 |
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding |
4035 |
|
DUFF parser |
4036 |
|
|
2990 |
– |
2004-11-18 18:26 tim |
2991 |
– |
|
2992 |
– |
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
2993 |
– |
initially added on branch new_design. |
2994 |
– |
|
4037 |
|
2004-11-18 16:42 tim |
4038 |
|
|
4039 |
|
* forceFields/newDUFF.frc: adding new format DUFF force field |
4045 |
|
|
4046 |
|
2004-11-18 00:42 tim |
4047 |
|
|
4048 |
< |
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
4048 |
> |
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
4049 |
|
initially added on branch new_design. |
4050 |
|
|
4051 |
|
2004-11-18 00:42 tim |
4052 |
|
|
4053 |
< |
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
4053 |
> |
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
4054 |
|
initially added on branch new_design. |
4055 |
|
|
4056 |
|
2004-11-18 00:42 tim |
4093 |
|
|
4094 |
|
2004-11-17 16:47 tim |
4095 |
|
|
4096 |
+ |
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
4097 |
+ |
was initially added on branch new_design. |
4098 |
+ |
|
4099 |
+ |
2004-11-17 16:47 tim |
4100 |
+ |
|
4101 |
|
* src/types/CubicBendType.hpp: file CubicBendType.hpp was initially |
4102 |
|
added on branch new_design. |
4103 |
|
|
4104 |
|
2004-11-17 16:47 tim |
4105 |
|
|
4106 |
+ |
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
4107 |
+ |
added on branch new_design. |
4108 |
+ |
|
4109 |
+ |
2004-11-17 16:47 tim |
4110 |
+ |
|
4111 |
|
* src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was |
4112 |
|
initially added on branch new_design. |
4113 |
|
|
4114 |
|
2004-11-17 16:47 tim |
4115 |
|
|
4116 |
< |
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
4116 |
> |
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
4117 |
|
initially added on branch new_design. |
4118 |
|
|
4119 |
|
2004-11-17 16:47 tim |
4120 |
|
|
4121 |
< |
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
4121 |
> |
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
4122 |
|
initially added on branch new_design. |
4123 |
|
|
4124 |
|
2004-11-17 16:47 tim |
4138 |
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: |
4139 |
|
UreyBradleyBend and GhostBend |
4140 |
|
|
3089 |
– |
2004-11-17 16:47 tim |
3090 |
– |
|
3091 |
– |
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
3092 |
– |
added on branch new_design. |
3093 |
– |
|
3094 |
– |
2004-11-17 16:47 tim |
3095 |
– |
|
3096 |
– |
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
3097 |
– |
was initially added on branch new_design. |
3098 |
– |
|
4141 |
|
2004-11-17 13:58 tim |
4142 |
|
|
4143 |
|
* src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp |
4145 |
|
|
4146 |
|
2004-11-17 13:58 tim |
4147 |
|
|
3106 |
– |
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
3107 |
– |
initially added on branch new_design. |
3108 |
– |
|
3109 |
– |
2004-11-17 13:58 tim |
3110 |
– |
|
4148 |
|
* src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp |
4149 |
|
was initially added on branch new_design. |
4150 |
|
|
4157 |
|
types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types |
4158 |
|
stuff and Chebyshev Polynomial |
4159 |
|
|
4160 |
< |
2004-11-17 01:37 tim |
3124 |
< |
|
3125 |
< |
* src/types/PolynomialTorsionType.hpp: file |
3126 |
< |
PolynomialTorsionType.hpp was initially added on branch new_design. |
3127 |
< |
|
3128 |
< |
2004-11-17 01:37 tim |
4160 |
> |
2004-11-17 13:58 tim |
4161 |
|
|
4162 |
< |
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
4162 |
> |
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
4163 |
|
initially added on branch new_design. |
4164 |
|
|
4165 |
|
2004-11-17 01:37 tim |
4166 |
|
|
4167 |
< |
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
4168 |
< |
initially added on branch new_design. |
4167 |
> |
* src/types/PolynomialTorsionType.hpp: file |
4168 |
> |
PolynomialTorsionType.hpp was initially added on branch new_design. |
4169 |
|
|
4170 |
|
2004-11-17 01:37 tim |
4171 |
|
|
4174 |
|
|
4175 |
|
2004-11-17 01:37 tim |
4176 |
|
|
3145 |
– |
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
3146 |
– |
initially added on branch new_design. |
3147 |
– |
|
3148 |
– |
2004-11-17 01:37 tim |
3149 |
– |
|
4177 |
|
* src/: math/Polynomial.hpp, primitives/Bend.cpp, |
4178 |
|
primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, |
4179 |
|
types/BondType.hpp, types/CharmmTorsionType.cpp, |
4186 |
|
CharmmTorsionType. Need to refine the design and add document for |
4187 |
|
them |
4188 |
|
|
4189 |
+ |
2004-11-17 01:37 tim |
4190 |
+ |
|
4191 |
+ |
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
4192 |
+ |
initially added on branch new_design. |
4193 |
+ |
|
4194 |
+ |
2004-11-17 01:37 tim |
4195 |
+ |
|
4196 |
+ |
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
4197 |
+ |
initially added on branch new_design. |
4198 |
+ |
|
4199 |
+ |
2004-11-17 01:37 tim |
4200 |
+ |
|
4201 |
+ |
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
4202 |
+ |
initially added on branch new_design. |
4203 |
+ |
|
4204 |
|
2004-11-16 20:11 tim |
4205 |
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|
4206 |
|
* src/types/: BendType.hpp, PolynomialBondType.hpp, |
4213 |
|
|
4214 |
|
2004-11-16 18:20 tim |
4215 |
|
|
3174 |
– |
* src/math/Polynomial.hpp: Adding Polynomial class |
3175 |
– |
|
3176 |
– |
2004-11-16 18:20 tim |
3177 |
– |
|
4216 |
|
* src/math/Polynomial.hpp: file Polynomial.hpp was initially added |
4217 |
|
on branch new_design. |
4218 |
|
|
4219 |
< |
2004-11-16 17:04 gezelter |
4219 |
> |
2004-11-16 18:20 tim |
4220 |
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|
4221 |
< |
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
3184 |
< |
initially added on branch new_design. |
4221 |
> |
* src/math/Polynomial.hpp: Adding Polynomial class |
4222 |
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|
4223 |
|
2004-11-16 17:04 gezelter |
4224 |
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|
4227 |
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|
4228 |
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2004-11-16 17:04 gezelter |
4229 |
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|
4230 |
+ |
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
4231 |
+ |
initially added on branch new_design. |
4232 |
+ |
|
4233 |
+ |
2004-11-16 17:04 gezelter |
4234 |
+ |
|
4235 |
|
* src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, |
4236 |
|
MorseBondType.hpp, TorsionType.hpp: added some new stuff |
4237 |
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|
4244 |
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|
4245 |
|
2004-11-15 21:07 tim |
4246 |
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|
3205 |
– |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
3206 |
– |
UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, |
3207 |
– |
utils/StringTokenizer.cpp: adding DUFF class; adding checking |
3208 |
– |
statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer |
3209 |
– |
|
3210 |
– |
2004-11-15 21:07 tim |
3211 |
– |
|
4247 |
|
* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on |
4248 |
|
branch new_design. |
4249 |
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|
4250 |
< |
2004-11-15 18:00 tim |
3216 |
< |
|
3217 |
< |
* src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp |
3218 |
< |
was initially added on branch new_design. |
3219 |
< |
|
3220 |
< |
2004-11-15 18:00 tim |
4250 |
> |
2004-11-15 21:07 tim |
4251 |
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|
4252 |
< |
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
4253 |
< |
branch new_design. |
4252 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
4253 |
> |
UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, |
4254 |
> |
utils/StringTokenizer.cpp: adding DUFF class; adding checking |
4255 |
> |
statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer |
4256 |
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|
4257 |
|
2004-11-15 18:00 tim |
4258 |
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4264 |
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4265 |
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2004-11-15 18:00 tim |
4266 |
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4267 |
+ |
* src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp |
4268 |
+ |
was initially added on branch new_design. |
4269 |
+ |
|
4270 |
+ |
2004-11-15 18:00 tim |
4271 |
+ |
|
4272 |
|
* src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp |
4273 |
|
was initially added on branch new_design. |
4274 |
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|
4275 |
+ |
2004-11-15 18:00 tim |
4276 |
+ |
|
4277 |
+ |
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
4278 |
+ |
branch new_design. |
4279 |
+ |
|
4280 |
|
2004-11-15 13:02 tim |
4281 |
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|
4282 |
+ |
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
4283 |
+ |
initially added on branch new_design. |
4284 |
+ |
|
4285 |
+ |
2004-11-15 13:02 tim |
4286 |
+ |
|
4287 |
|
* src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on |
4288 |
|
branch new_design. |
4289 |
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4294 |
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4295 |
|
2004-11-15 13:02 tim |
4296 |
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3250 |
– |
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
3251 |
– |
initially added on branch new_design. |
3252 |
– |
|
3253 |
– |
2004-11-15 13:02 tim |
3254 |
– |
|
4297 |
|
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, |
4298 |
|
brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
4299 |
|
integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, |
4417 |
|
|
4418 |
|
2004-11-09 18:11 tim |
4419 |
|
|
4420 |
+ |
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
4421 |
+ |
added on branch new_design. |
4422 |
+ |
|
4423 |
+ |
2004-11-09 18:11 tim |
4424 |
+ |
|
4425 |
+ |
* src/integrators/VelocityVerletIntegrator.cpp: file |
4426 |
+ |
VelocityVerletIntegrator.cpp was initially added on branch |
4427 |
+ |
new_design. |
4428 |
+ |
|
4429 |
+ |
2004-11-09 18:11 tim |
4430 |
+ |
|
4431 |
|
* src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, |
4432 |
|
brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
4433 |
|
brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, |
4442 |
|
|
4443 |
|
2004-11-09 18:11 tim |
4444 |
|
|
3392 |
– |
* src/integrators/VelocityVerletIntegrator.cpp: file |
3393 |
– |
VelocityVerletIntegrator.cpp was initially added on branch |
3394 |
– |
new_design. |
3395 |
– |
|
3396 |
– |
2004-11-09 18:11 tim |
3397 |
– |
|
4445 |
|
* src/integrators/NVE.cpp: file NVE.cpp was initially added on |
4446 |
|
branch new_design. |
4447 |
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|
3401 |
– |
2004-11-09 18:11 tim |
3402 |
– |
|
3403 |
– |
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
3404 |
– |
added on branch new_design. |
3405 |
– |
|
4448 |
|
2004-11-08 20:08 tim |
4449 |
|
|
4450 |
|
* src/integrators/VelocityVerletIntegrator.hpp: file |
4451 |
|
VelocityVerletIntegrator.hpp was initially added on branch |
4452 |
|
new_design. |
4453 |
+ |
|
4454 |
+ |
2004-11-08 20:08 tim |
4455 |
+ |
|
4456 |
+ |
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
4457 |
+ |
branch new_design. |
4458 |
|
|
4459 |
|
2004-11-08 20:08 tim |
4460 |
|
|
4463 |
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
4464 |
|
utils/TypeContainer.hpp: More to break |
4465 |
|
|
3419 |
– |
2004-11-08 20:08 tim |
3420 |
– |
|
3421 |
– |
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
3422 |
– |
branch new_design. |
3423 |
– |
|
4466 |
|
2004-11-06 00:21 tim |
4467 |
|
|
4468 |
|
* src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially |
4477 |
|
|
4478 |
|
2004-11-05 18:38 tim |
4479 |
|
|
4480 |
+ |
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
4481 |
+ |
initially added on branch new_design. |
4482 |
+ |
|
4483 |
+ |
2004-11-05 18:38 tim |
4484 |
+ |
|
4485 |
|
* src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was |
4486 |
|
initially added on branch new_design. |
4487 |
|
|
4493 |
|
brains/SimInfo.hpp, primitives/Molecule.hpp, |
4494 |
|
utils/LocalndexManager.hpp: Fix Exclude class etc. |
4495 |
|
|
3449 |
– |
2004-11-05 18:38 tim |
3450 |
– |
|
3451 |
– |
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
3452 |
– |
initially added on branch new_design. |
3453 |
– |
|
4496 |
|
2004-11-05 16:45 chrisfen |
4497 |
|
|
4498 |
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
4530 |
|
|
4531 |
|
2004-11-04 14:48 tim |
4532 |
|
|
3491 |
– |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
3492 |
– |
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
3493 |
– |
class |
3494 |
– |
|
3495 |
– |
2004-11-04 14:48 tim |
3496 |
– |
|
4533 |
|
* src/brains/Stats.cpp: file Stats.cpp was initially added on |
4534 |
|
branch new_design. |
4535 |
|
|
4538 |
|
* src/brains/Stats.hpp: file Stats.hpp was initially added on |
4539 |
|
branch new_design. |
4540 |
|
|
4541 |
+ |
2004-11-04 14:48 tim |
4542 |
+ |
|
4543 |
+ |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
4544 |
+ |
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
4545 |
+ |
class |
4546 |
+ |
|
4547 |
|
2004-11-04 11:22 gezelter |
4548 |
|
|
4549 |
|
* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
4618 |
|
|
4619 |
|
2004-11-02 17:41 tim |
4620 |
|
|
4621 |
< |
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
4622 |
< |
branch new_design. |
4621 |
> |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
4622 |
> |
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
4623 |
> |
Need unit test |
4624 |
|
|
4625 |
|
2004-11-02 17:41 tim |
4626 |
|
|
4629 |
|
|
4630 |
|
2004-11-02 17:41 tim |
4631 |
|
|
4632 |
< |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
4633 |
< |
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
3591 |
< |
Need unit test |
4632 |
> |
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
4633 |
> |
branch new_design. |
4634 |
|
|
4635 |
|
2004-11-02 11:59 tim |
4636 |
|
|
4637 |
< |
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
4638 |
< |
SimSnapshotManager.hpp: SimModel in progress |
4637 |
> |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
4638 |
> |
branch new_design. |
4639 |
|
|
4640 |
|
2004-11-02 11:59 tim |
4641 |
|
|
4642 |
< |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
4643 |
< |
branch new_design. |
4642 |
> |
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
4643 |
> |
SimSnapshotManager.hpp: SimModel in progress |
4644 |
|
|
4645 |
|
2004-11-02 10:28 chrisfen |
4646 |
|
|
4650 |
|
|
4651 |
|
2004-11-02 10:27 tim |
4652 |
|
|
4653 |
< |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
4654 |
< |
added on branch new_design. |
4653 |
> |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
4654 |
> |
functions for dealing with memory issue |
4655 |
|
|
4656 |
|
2004-11-02 10:27 tim |
4657 |
|
|
4658 |
< |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
4659 |
< |
functions for dealing with memory issue |
4658 |
> |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
4659 |
> |
added on branch new_design. |
4660 |
|
|
4661 |
|
2004-11-02 10:23 tim |
4662 |
|
|
4685 |
|
|
4686 |
|
2004-11-01 16:40 tim |
4687 |
|
|
4688 |
< |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
4689 |
< |
branch new_design. |
4688 |
> |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
4689 |
> |
on branch new_design. |
4690 |
|
|
4691 |
|
2004-11-01 16:40 tim |
4692 |
|
|
4693 |
< |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
4694 |
< |
version of Bond, Bend and Torsion. |
4693 |
> |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
4694 |
> |
branch new_design. |
4695 |
|
|
4696 |
|
2004-11-01 16:40 tim |
4697 |
|
|
4700 |
|
|
4701 |
|
2004-11-01 16:40 tim |
4702 |
|
|
4703 |
< |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
4704 |
< |
on branch new_design. |
4703 |
> |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
4704 |
> |
version of Bond, Bend and Torsion. |
4705 |
|
|
4706 |
|
2004-11-01 16:37 tim |
4707 |
|
|
4710 |
|
|
4711 |
|
2004-11-01 16:37 tim |
4712 |
|
|
4713 |
< |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
4714 |
< |
branch new_design. |
4713 |
> |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
4714 |
> |
BondType, BendType, TorsionType |
4715 |
|
|
4716 |
|
2004-11-01 16:37 tim |
4717 |
|
|
4720 |
|
|
4721 |
|
2004-11-01 16:37 tim |
4722 |
|
|
4723 |
< |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
4724 |
< |
BondType, BendType, TorsionType |
4723 |
> |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
4724 |
> |
branch new_design. |
4725 |
|
|
4726 |
|
2004-11-01 15:15 tim |
4727 |
|
|
5554 |
|
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
5555 |
|
directory |
5556 |
|
|
5557 |
+ |
2004-10-11 09:23 tim |
5558 |
+ |
|
5559 |
+ |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
5560 |
+ |
Makefile |
5561 |
+ |
|
5562 |
|
2004-10-09 01:01 tim |
5563 |
|
|
5564 |
< |
* samples/: alkane/Makefile.in, lipid/Makefile.in, |
5565 |
< |
metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in |
5564 |
> |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
5565 |
> |
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
5566 |
> |
Remove some Makefile.in |
5567 |
|
|
5568 |
|
2004-10-08 18:15 tim |
5569 |
|
|
5579 |
|
|
5580 |
|
2004-10-08 17:04 tim |
5581 |
|
|
5582 |
< |
* samples/: alkane/Makefile, lipid/Makefile, metals/Makefile, |
5583 |
< |
minimizer/Makefile, water/Makefile.in, water/dimer/Makefile, |
5584 |
< |
water/dimer/Makefile.in, water/spce/Makefile, |
5582 |
> |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
5583 |
> |
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
5584 |
> |
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
5585 |
|
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
5586 |
|
water/ssde/Makefile, water/ssde/Makefile.in, |
5587 |
|
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
6060 |
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
6061 |
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
6062 |
|
samples/alkane/butane.in, samples/alkane/butane.md, |
6063 |
+ |
samples/argon/500.in, samples/argon/500.md, |
6064 |
+ |
samples/argon/Makefile.in, samples/argon/ar864.in, |
6065 |
+ |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
6066 |
+ |
samples/argon/argonNVT.md, samples/argon/lj.md, |
6067 |
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
6068 |
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
6069 |
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
6236 |
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
6237 |
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
6238 |
|
samples/alkane/butane.in, samples/alkane/butane.md, |
6239 |
+ |
samples/argon/500.in, samples/argon/500.md, |
6240 |
+ |
samples/argon/Makefile.in, samples/argon/ar864.in, |
6241 |
+ |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
6242 |
+ |
samples/argon/argonNVT.md, samples/argon/lj.md, |
6243 |
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
6244 |
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
6245 |
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |