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 |
5744 |
|
|
5745 |
|
2004-09-29 12:56 gezelter |
5746 |
|
|
5747 |
< |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
5747 |
> |
* make/: Make.conf.in, Makefile.in, _files/style.css: Working on |
5748 |
> |
make stuff |
5749 |
|
|
5750 |
|
2004-09-29 12:46 tim |
5751 |
|
|
6011 |
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
6012 |
|
src/visitors/RigidBodyVisitor.cpp, |
6013 |
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
6014 |
< |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
6014 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
6015 |
> |
make/_files/style.css, samples/Makefile.in, |
6016 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
6017 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
6018 |
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
6187 |
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
6188 |
|
src/visitors/RigidBodyVisitor.cpp, |
6189 |
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
6190 |
< |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
6190 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
6191 |
> |
make/_files/style.css, samples/Makefile.in, |
6192 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
6193 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
6194 |
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |