1 |
< |
2005-09-18 15:45 chrisfen |
2 |
< |
|
3 |
< |
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
4 |
< |
src/UseTheForce/doForces.F90, |
5 |
< |
src/UseTheForce/doForces_interface.F90, |
6 |
< |
src/UseTheForce/doForces_interface.h, |
7 |
< |
src/UseTheForce/DarkSide/electrostatic.F90, |
8 |
< |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
9 |
< |
src/brains/SimInfo.cpp: reaction field seems to work now, still |
10 |
< |
need to do some testing... |
11 |
< |
|
12 |
< |
2005-09-16 18:04 chuckv |
13 |
< |
|
14 |
< |
* src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed |
15 |
< |
dump files. |
16 |
< |
|
17 |
< |
2005-09-16 16:07 chrisfen |
18 |
< |
|
19 |
< |
* src/: UseTheForce/doForces_interface.F90, |
20 |
< |
UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a |
21 |
< |
bug that ifc missed... |
22 |
< |
|
23 |
< |
2005-09-16 15:36 chrisfen |
24 |
< |
|
25 |
< |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
26 |
< |
fixing some summation method issues |
27 |
< |
|
28 |
< |
2005-09-16 14:35 chrisfen |
29 |
< |
|
30 |
< |
* src/brains/SimInfo.cpp: fixed a capitalization error |
31 |
< |
|
32 |
< |
2005-09-16 14:34 chrisfen |
33 |
< |
|
34 |
< |
* src/UseTheForce/: fElectrostaticSummationMethod.h, |
35 |
< |
DarkSide/fElectrostaticSummationMethod.h: moved a header file |
36 |
< |
around |
37 |
< |
|
38 |
< |
2005-09-16 14:00 chrisfen |
39 |
< |
|
40 |
< |
* src/: UseTheForce/DarkSide/electrostatic_interface.F90, |
41 |
< |
brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there |
42 |
< |
are known issues - particularly with reaction field... |
43 |
< |
|
44 |
< |
2005-09-16 11:07 chrisfen |
45 |
< |
|
46 |
< |
* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, |
47 |
< |
io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking |
48 |
< |
(cutting out the old way to do reaction field) |
49 |
< |
|
50 |
< |
2005-09-15 17:05 gezelter |
51 |
< |
|
52 |
< |
* src/UseTheForce/: doForces.F90, fCoulombicCorrection.h, |
53 |
< |
fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90, |
54 |
< |
DarkSide/electrostatic_interface.F90, |
55 |
< |
DarkSide/electrostatic_interface.h: Working on adding WOLF |
56 |
< |
|
57 |
< |
2005-09-15 14:17 tim |
58 |
< |
|
59 |
< |
* src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame |
60 |
< |
is called without calling getNFrames |
61 |
< |
|
62 |
< |
2005-09-15 08:47 chrisfen |
63 |
< |
|
64 |
< |
* src/UseTheForce/fCoulombicCorrection.h: forgot to add a header |
65 |
< |
|
66 |
< |
2005-09-14 21:48 chuckv |
67 |
< |
|
68 |
< |
* src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was |
69 |
< |
not initialized after creation. When maxval(gtypeMaxCutoff) was |
70 |
< |
called, the largest random garbage value was returned from the |
71 |
< |
array. |
72 |
< |
|
73 |
< |
2005-09-14 19:14 chrisfen |
74 |
< |
|
75 |
< |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, |
76 |
< |
io/Globals.hpp: changes to include the coulombicCorrection selector |
77 |
< |
|
78 |
< |
2005-09-14 19:13 chrisfen |
79 |
< |
|
80 |
< |
* src/UseTheForce/DarkSide/: Makefile, electrostatic.F90, |
81 |
< |
reactionField.F90: added in the undamped wolf, in the process of |
82 |
< |
doing the damped wolf |
83 |
< |
|
84 |
< |
2005-09-14 19:13 chrisfen |
85 |
< |
|
86 |
< |
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
87 |
< |
doForces_interface.h, notifyCutoffs.F90: some changes to activate |
88 |
< |
the coulombicCorrection selector |
89 |
< |
|
90 |
< |
2005-09-14 19:11 chrisfen |
91 |
< |
|
92 |
< |
* samples/water/dimer/: cl.in, cl.md, water.md: just some testing |
93 |
< |
|
94 |
< |
2005-09-14 19:11 chrisfen |
95 |
< |
|
96 |
< |
* samples/argon/: 500.in, 500.md: Equilibrated the sample |
97 |
< |
|
98 |
< |
2005-09-14 19:10 chrisfen |
99 |
< |
|
100 |
< |
* forceFields/DUFF2.frc: re-added Cl- and Na+ |
101 |
< |
|
102 |
< |
2005-09-14 15:31 chuckv |
103 |
< |
|
104 |
< |
* src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup |
105 |
< |
eamAtypes instead of assuming a 1-1 correspondence to atypes. |
106 |
< |
|
107 |
< |
2005-09-14 15:28 gezelter |
108 |
< |
|
109 |
< |
* src/UseTheForce/doForces.F90: fix to put back calculation of r in |
110 |
< |
do_prepair |
111 |
< |
|
112 |
< |
2005-09-14 14:02 gezelter |
113 |
< |
|
114 |
< |
* src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the |
115 |
< |
createMixingMap routine. It should now set doShift correctly |
116 |
< |
|
117 |
< |
2005-09-07 17:44 chuckv |
118 |
< |
|
119 |
< |
* src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. |
120 |
< |
|
121 |
< |
2005-09-07 17:23 chuckv |
122 |
< |
|
123 |
< |
* src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi |
124 |
< |
logical variables |
125 |
< |
|
126 |
< |
2005-09-07 17:08 gezelter |
127 |
< |
|
128 |
< |
* src/UseTheForce/doForces.F90: bugfix on the grouptype finding |
129 |
< |
algorithm |
130 |
< |
|
131 |
< |
2005-09-07 15:46 gezelter |
132 |
< |
|
133 |
< |
* src/: UseTheForce/doForces.F90, |
134 |
< |
UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, |
135 |
< |
UseTheForce/notifyCutoffs_interface.F90, |
136 |
< |
UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp, |
137 |
< |
io/Globals.cpp, io/Globals.hpp: adding c-side interface to change |
138 |
< |
cutoff Policy |
139 |
< |
|
140 |
< |
2005-09-07 14:18 gezelter |
141 |
< |
|
142 |
< |
* src/UseTheForce/doForces.F90: Some bug hunting |
143 |
< |
|
144 |
< |
2005-09-07 14:18 gezelter |
145 |
< |
|
146 |
< |
* samples/argon/argonNVT.md: Just a longer test |
147 |
< |
|
148 |
< |
2005-09-06 12:32 chuckv |
149 |
< |
|
150 |
< |
* src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap |
151 |
< |
etc.. |
152 |
< |
|
153 |
< |
2005-09-01 17:56 gezelter |
154 |
< |
|
155 |
< |
* src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to |
156 |
< |
zero |
157 |
< |
|
158 |
< |
2005-09-01 15:17 gezelter |
159 |
< |
|
160 |
< |
* src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote |
161 |
< |
createGtypeCutoffMap |
162 |
< |
|
163 |
< |
2005-08-30 13:23 chrisfen |
164 |
< |
|
165 |
< |
* src/: UseTheForce/doForces.F90, |
166 |
< |
UseTheForce/doForces_interface.F90, |
167 |
< |
UseTheForce/doForces_interface.h, |
168 |
< |
UseTheForce/DarkSide/electrostatic.F90, |
169 |
< |
UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp, |
170 |
< |
brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some |
171 |
< |
changes for implementing the wolf potential |
172 |
< |
|
173 |
< |
2005-08-26 17:39 chrisfen |
174 |
< |
|
175 |
< |
* src/UseTheForce/DarkSide/eam.F90: updated getEAMCut |
176 |
< |
|
177 |
< |
2005-08-26 16:30 chrisfen |
178 |
< |
|
179 |
< |
* src/UseTheForce/: doForces.F90, DarkSide/eam.F90, |
180 |
< |
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added |
181 |
< |
some probably nonfunctional get*cut routines |
182 |
< |
|
183 |
< |
2005-08-26 15:34 chuckv |
184 |
< |
|
185 |
< |
* src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. |
186 |
< |
|
187 |
< |
2005-08-26 11:36 gezelter |
188 |
< |
|
189 |
< |
* src/UseTheForce/doForces.F90: fixing some of the problems in the |
190 |
< |
interactionHash and gtypeCutoff routines |
191 |
< |
|
192 |
< |
2005-08-17 10:26 gezelter |
193 |
< |
|
194 |
< |
* src/UseTheForce/: doForces.F90, fCutoffPolicy.h, |
195 |
< |
DarkSide/simulation.F90: added fCutoffPolicy.h |
196 |
< |
|
197 |
< |
2005-08-11 16:04 gezelter |
198 |
< |
|
199 |
< |
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in |
200 |
< |
progress |
201 |
< |
|
202 |
< |
2005-08-10 14:17 gezelter |
203 |
< |
|
204 |
< |
* src/primitives/StuntDouble.hpp: putting spaceballs back where |
205 |
< |
they belong |
206 |
< |
|
207 |
< |
2005-08-09 17:33 gezelter |
208 |
< |
|
209 |
< |
* src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard |
210 |
< |
Jones module |
211 |
< |
|
212 |
< |
2005-08-09 17:33 gezelter |
213 |
< |
|
214 |
< |
* src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky |
215 |
< |
|
216 |
< |
2005-08-09 14:40 chuckv |
217 |
< |
|
218 |
< |
* src/UseTheForce/doForces.F90: In process of re-write for group |
219 |
< |
based cutoff.... |
220 |
< |
|
221 |
< |
2005-07-29 14:38 gezelter |
222 |
< |
|
223 |
< |
* src/UseTheForce/doForces.F90: fixes in progress |
224 |
< |
|
225 |
< |
2005-07-29 12:34 tim |
226 |
< |
|
227 |
< |
* src/UseTheForce/doForces.F90: fix a bug which does not update |
228 |
< |
me_i and me_j correctly |
229 |
< |
|
230 |
< |
2005-07-28 17:12 chuckv |
231 |
< |
|
232 |
< |
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed |
233 |
< |
cutoffs... Segfaults nicely now... |
234 |
< |
|
235 |
< |
2005-07-20 12:04 gezelter |
236 |
< |
|
237 |
< |
* configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text |
238 |
< |
error messages from pathscale compiler |
239 |
< |
|
240 |
< |
2005-07-13 11:48 tim |
241 |
< |
|
242 |
< |
* src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in |
243 |
< |
<functional> |
244 |
< |
|
245 |
< |
2005-07-13 10:54 tim |
246 |
< |
|
247 |
< |
* src/: UseTheForce/fSwitchingFunction.h, |
248 |
< |
UseTheForce/mpiComponentPlan.h, |
249 |
< |
UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h, |
250 |
< |
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
251 |
< |
io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c, |
252 |
< |
io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c, |
253 |
< |
io/parse_tree.h, math/MatVec3.c, utils/residentMem.c, |
254 |
< |
utils/simError.c, utils/simError.h: replace c++ style comment in c |
255 |
< |
files |
256 |
< |
|
257 |
< |
2005-07-03 15:53 chuckv |
258 |
< |
|
259 |
< |
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
260 |
< |
UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added |
261 |
< |
subroutine to set cuttoff for Interaction map and function in |
262 |
< |
simulation.F90 to determine if a particular atype is present in a |
263 |
< |
simulation. |
264 |
< |
|
265 |
< |
2005-06-28 08:58 gezelter |
266 |
< |
|
267 |
< |
* src/UseTheForce/doForces.F90: [no log message] |
268 |
< |
|
269 |
< |
2005-06-27 17:21 chuckv |
270 |
< |
|
271 |
< |
* src/UseTheForce/doForces.F90: More breaking and destruction of |
272 |
< |
force code. Does not build at this point... |
273 |
< |
|
274 |
< |
2005-06-27 16:01 gezelter |
275 |
< |
|
276 |
< |
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90, |
277 |
< |
UseTheForce/DarkSide/fInteractionMap.h, |
278 |
< |
UseTheForce/DarkSide/interactions.F90, utils/definitions.F90: |
279 |
< |
Breaky breaky! |
280 |
< |
|
281 |
< |
2005-06-20 11:03 gezelter |
282 |
< |
|
283 |
< |
* samples/water/ssd/ssd.md, |
284 |
< |
src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a |
285 |
< |
simulation |
286 |
< |
|
287 |
< |
2005-06-13 13:25 tim |
288 |
< |
|
289 |
< |
* src/: applications/staticProps/DensityPlot.cpp, |
290 |
< |
applications/staticProps/DensityPlot.hpp, |
291 |
< |
applications/staticProps/SCDOrderParameter.cpp, |
292 |
< |
applications/staticProps/StaticProps.cpp, |
293 |
< |
io/AtomTypesSectionParser.cpp: working version of DensityPlot |
294 |
< |
|
295 |
< |
2005-05-31 17:31 chuckv |
296 |
< |
|
297 |
< |
* src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to |
298 |
< |
remove angular momentum. |
299 |
< |
|
300 |
< |
2005-05-31 12:34 chuckv |
301 |
< |
|
302 |
< |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in |
303 |
< |
typo in nanorodBuilder. |
304 |
< |
|
305 |
< |
2005-05-30 09:01 chuckv |
306 |
< |
|
307 |
< |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
308 |
< |
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, |
309 |
< |
brains/Stats.hpp, integrators/Velocitizer.cpp, |
310 |
< |
integrators/Velocitizer.hpp: Added method to remove system angular |
311 |
< |
momentum to velocitizer and added method to calculate system |
312 |
< |
angular momentum to siminfo. |
313 |
< |
|
314 |
< |
2005-05-29 16:16 chrisfen |
315 |
< |
|
316 |
< |
* src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed |
317 |
< |
balance from the Darkside (files) |
318 |
< |
|
319 |
< |
2005-05-29 16:15 chrisfen |
320 |
< |
|
321 |
< |
* src/UseTheForce/doForces.F90: Removed balance from doForces |
322 |
< |
|
323 |
< |
2005-05-29 16:15 chrisfen |
324 |
< |
|
325 |
< |
* samples/water/tap/: tap.in, tap.md: Updated tap sample |
326 |
< |
|
327 |
< |
2005-05-29 16:15 chrisfen |
328 |
< |
|
329 |
< |
* samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap |
330 |
< |
dimer for testing purposes |
331 |
< |
|
332 |
< |
2005-05-29 16:14 chrisfen |
333 |
< |
|
334 |
< |
* forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It |
335 |
< |
was apparently wiped earlier this month... |
336 |
< |
|
337 |
< |
2005-05-29 16:13 chrisfen |
338 |
< |
|
339 |
< |
* ChangeLog: ran make cvslog |
340 |
< |
|
341 |
< |
2005-05-28 19:16 tim |
342 |
< |
|
343 |
< |
* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding |
344 |
< |
AtomNameVisitor |
345 |
< |
|
346 |
< |
2005-05-28 19:09 tim |
347 |
< |
|
348 |
< |
* src/integrators/Integrator.cpp: dding resetIntegrator |
349 |
< |
|
350 |
< |
2005-05-28 19:06 tim |
351 |
< |
|
352 |
< |
* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, |
353 |
< |
NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, |
354 |
< |
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding |
355 |
< |
resetIntegrator |
356 |
< |
|
357 |
< |
2005-05-27 16:11 tim |
358 |
< |
|
359 |
< |
* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, |
360 |
< |
Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, |
361 |
< |
SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
362 |
< |
StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into |
363 |
< |
StaticProps |
364 |
< |
|
365 |
< |
2005-05-26 23:41 tim |
366 |
< |
|
367 |
< |
* src/: applications/staticProps/Makefile, |
368 |
< |
applications/staticProps/P2OrderParameter.cpp, |
369 |
< |
applications/staticProps/P2OrderParameter.hpp, |
370 |
< |
applications/staticProps/StaticProps.cpp, |
371 |
< |
applications/staticProps/StaticProps.ggo, |
372 |
< |
applications/staticProps/StaticPropsCmd.c, |
373 |
< |
applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, |
374 |
< |
utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps |
375 |
< |
|
376 |
< |
2005-05-26 17:45 tim |
377 |
< |
|
378 |
< |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
379 |
< |
applications/dump2Xyz/Dump2XYZCmd.c, |
380 |
< |
applications/dump2Xyz/Dump2XYZCmd.h, |
381 |
< |
applications/staticProps/Makefile, |
382 |
< |
applications/staticProps/P2OrderParameter.cpp, |
383 |
< |
applications/staticProps/P2OrderParameter.hpp, |
384 |
< |
applications/staticProps/RadialDistrFunc.cpp, |
385 |
< |
applications/staticProps/RadialDistrFunc.hpp, |
386 |
< |
applications/staticProps/StaticAnalyser.hpp, |
387 |
< |
applications/staticProps/StaticProps.cpp, |
388 |
< |
applications/staticProps/StaticProps.ggo, |
389 |
< |
applications/staticProps/StaticPropsCmd.c, |
390 |
< |
applications/staticProps/StaticPropsCmd.h, visitors/Makefile, |
391 |
< |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding |
392 |
< |
AtomNameVisitor to convert atom name to its base name; |
393 |
< |
wrappingvisitor now wrap back to the center of the mass; adding |
394 |
< |
P2OrderParameter into StaticProps |
395 |
< |
|
396 |
< |
2005-05-22 16:36 chuckv |
397 |
< |
|
398 |
< |
* samples/metals/nanorod/Au_nanoparticle_FCC.md, |
399 |
< |
src/applications/nanoRodBuilder/Geometry.cpp, |
400 |
< |
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
401 |
< |
src/applications/nanoRodBuilder/GeometryFactory.cpp, |
402 |
< |
src/applications/nanoRodBuilder/GeometryFactory.hpp, |
403 |
< |
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
404 |
< |
src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
405 |
< |
tensor. |
406 |
< |
|
407 |
< |
2005-05-22 16:05 tim |
408 |
< |
|
409 |
< |
* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
410 |
< |
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
411 |
< |
io/Globals.hpp, io/SectionParserManager.cpp: adding keyword |
412 |
< |
printPressureTensor |
413 |
< |
|
414 |
< |
2005-05-20 14:27 tim |
415 |
< |
|
416 |
< |
* src/integrators/NPrT.cpp: NPrT in progress |
417 |
< |
|
418 |
< |
2005-05-20 11:01 tim |
419 |
< |
|
420 |
< |
* src/: integrators/NPrT.cpp, io/Globals.cpp, |
421 |
< |
utils/OOPSEConstant.hpp: NPrT in progress |
422 |
< |
|
423 |
< |
2005-05-19 16:31 tim |
424 |
< |
|
425 |
< |
* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, |
426 |
< |
integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, |
427 |
< |
io/Globals.hpp: NPAT is working |
428 |
< |
|
429 |
< |
2005-05-19 10:49 tim |
430 |
< |
|
431 |
< |
* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, |
432 |
< |
integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT |
433 |
< |
|
434 |
< |
2005-05-18 23:28 tim |
435 |
< |
|
436 |
< |
* src/: brains/Register.cpp, integrators/NPAT.cpp, |
437 |
< |
integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, |
438 |
< |
io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators |
439 |
< |
|
440 |
< |
2005-05-18 14:06 chrisfen |
441 |
< |
|
442 |
< |
* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just |
443 |
< |
some tap changes |
444 |
< |
|
445 |
< |
2005-05-18 13:31 chrisfen |
446 |
< |
|
447 |
< |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
448 |
< |
DarkSide/sticky.F90: Modifications to temper the dipolar strength |
449 |
< |
in the first solvation shell for tap |
450 |
< |
|
451 |
< |
2005-05-18 07:35 chrisfen |
452 |
< |
|
453 |
< |
* samples/water/tap/: tap.in, tap.md, water.md: added a tap example |
454 |
< |
for testing purposes |
455 |
< |
|
456 |
< |
2005-05-17 17:35 chrisfen |
457 |
< |
|
458 |
< |
* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, |
459 |
< |
samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, |
460 |
< |
src/UseTheForce/doForces.F90, |
461 |
< |
src/UseTheForce/DarkSide/electrostatic.F90, |
462 |
< |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
463 |
< |
src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also |
464 |
< |
correcting changes to the previous merge that were not caught |
465 |
< |
|
466 |
< |
2005-05-16 23:20 chuckv |
467 |
< |
|
468 |
< |
* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: |
469 |
< |
Fixed merge issues between Kyle and Chris so OOPSE will actually |
470 |
< |
build. |
471 |
< |
|
472 |
< |
2005-05-16 22:46 kdaily |
473 |
< |
|
474 |
< |
* src/io/: GayBerneAtomTypesSectionParser.cpp, |
475 |
< |
GayBerneAtomTypesSectionParser.hpp, Makefile: help |
476 |
< |
|
477 |
< |
2005-05-16 21:08 kdaily |
478 |
< |
|
479 |
< |
* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, |
480 |
< |
src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, |
481 |
< |
src/types/DirectionalAtomType.cpp, |
482 |
< |
src/types/DirectionalAtomType.hpp: added gb |
483 |
< |
|
484 |
< |
2005-05-13 15:36 chrisfen |
485 |
< |
|
486 |
< |
* forceFields/DUFF2.frc: Better tap |
487 |
< |
|
488 |
< |
2005-05-12 14:43 chrisfen |
489 |
< |
|
490 |
< |
* forceFields/DUFF2.frc, samples/water/dimer/ssd.in, |
491 |
< |
samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, |
492 |
< |
src/applications/dump2Xyz/Dump2XYZ.cpp, |
493 |
< |
src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. |
494 |
< |
Need to parametrize. |
495 |
< |
|
496 |
< |
2005-05-11 18:15 chuckv |
497 |
< |
|
498 |
< |
* src/: io/ShapeAtomTypesSectionParser.cpp, |
499 |
< |
math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed |
500 |
< |
build issues under ifc7. |
501 |
< |
|
502 |
< |
2005-05-09 17:07 chuckv |
503 |
< |
|
504 |
< |
* src/applications/nanoRodBuilder/Geometry.hpp: More geometry |
505 |
< |
builder changes. |
506 |
< |
|
507 |
< |
2005-05-05 10:06 chrisfen |
508 |
< |
|
509 |
< |
* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED |
510 |
< |
to TAP |
511 |
< |
|
512 |
< |
2005-05-05 09:47 chrisfen |
513 |
< |
|
514 |
< |
* forceFields/DUFF2.frc, samples/water/ssde/ssde.md, |
515 |
< |
samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, |
516 |
< |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, |
517 |
< |
src/UseTheForce/DarkSide/atype.F90, |
518 |
< |
src/UseTheForce/DarkSide/atype_interface.F90, |
519 |
< |
src/UseTheForce/DarkSide/simulation.F90, |
520 |
< |
src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, |
521 |
< |
src/brains/fSimulation.h, src/io/Makefile, |
522 |
< |
src/io/StickyAtomTypesSectionParser.cpp, |
523 |
< |
src/io/StickyPowerAtomTypesSectionParser.cpp, |
524 |
< |
src/io/StickyPowerAtomTypesSectionParser.hpp, |
525 |
< |
src/types/AtomType.cpp, src/types/AtomType.hpp, |
526 |
< |
src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, |
527 |
< |
src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's |
528 |
< |
not parametrized, but OOPSE will now let me run it... |
529 |
< |
|
530 |
< |
2005-05-03 17:55 chuckv |
531 |
< |
|
532 |
< |
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
533 |
< |
GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: |
534 |
< |
Adding support for generic geometry to nanorodbuilder. |
535 |
< |
|
536 |
< |
2005-05-03 12:55 chuckv |
537 |
< |
|
538 |
< |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
539 |
< |
nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, |
540 |
< |
nanorodBuilderCmd.h: More changes to nanoRodBuilder.... |
541 |
< |
|
542 |
< |
2005-04-29 14:16 gezelter |
543 |
< |
|
544 |
< |
* make/Makefile.in: [no log message] |
545 |
< |
|
546 |
< |
2005-04-29 11:26 chrisfen |
547 |
< |
|
548 |
< |
* forceFields/DUFF2.frc, samples/water/spce/water.md, |
549 |
< |
samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, |
550 |
< |
samples/water/ssd-ion/water.md, samples/water/ssde/water.md, |
551 |
< |
samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, |
552 |
< |
samples/water/tip4p/water.md: Added TIP4P-Ew |
553 |
< |
|
554 |
< |
2005-04-27 19:24 chuckv |
555 |
< |
|
556 |
< |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
557 |
< |
GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, |
558 |
< |
nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with |
559 |
< |
nanoRodBuilder.... |
560 |
< |
|
561 |
< |
2005-04-27 15:13 chrisfen |
562 |
< |
|
563 |
< |
* samples/shape/Shapes.frc, samples/shape/linear.shape, |
564 |
< |
src/UseTheForce/DarkSide/atype.F90, |
565 |
< |
src/UseTheForce/DarkSide/shapes.F90, |
566 |
< |
src/UseTheForce/DarkSide/shapes_interface.F90, |
567 |
< |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of |
568 |
< |
write statements and am closer to a working shapes |
569 |
< |
|
570 |
< |
2005-04-22 16:57 chuckv |
571 |
< |
|
572 |
< |
* src/utils/Predicate.hpp: Fixed gcc4 bug... |
573 |
< |
|
574 |
< |
2005-04-22 16:52 tim |
575 |
< |
|
576 |
< |
* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, |
577 |
< |
Trim.hpp: adding CharClassificationFunctor to fix the locale |
578 |
< |
problem of c++ |
579 |
< |
|
580 |
< |
2005-04-21 09:12 chrisfen |
581 |
< |
|
582 |
< |
* samples/shape/Shapes.frc, samples/shape/linear.in, |
583 |
< |
samples/shape/linear.md, src/UseTheForce/ForceField.hpp, |
584 |
< |
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, |
585 |
< |
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
586 |
< |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, |
587 |
< |
src/UseTheForce/DarkSide/shapes.F90, |
588 |
< |
src/UseTheForce/DarkSide/shapes_interface.F90, |
589 |
< |
src/UseTheForce/DarkSide/shapes_interface.h, |
590 |
< |
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
591 |
< |
src/io/Makefile, src/io/SectionParser.cpp, |
592 |
< |
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
593 |
< |
src/io/ShapeAtomTypesSectionParser.cpp, |
594 |
< |
src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, |
595 |
< |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, |
596 |
< |
src/types/ShapeAtomType.hpp: Shapes is limping along with a array |
597 |
< |
bounds overwrite (I think...). At least the parser loads the |
598 |
< |
forcefield fine... |
599 |
< |
|
600 |
< |
2005-04-18 10:44 chrisfen |
601 |
< |
|
602 |
< |
* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on |
603 |
< |
Mac (capitalization confusion of filenames) |
604 |
< |
|
605 |
< |
2005-04-17 22:50 chrisfen |
606 |
< |
|
607 |
< |
* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, |
608 |
< |
UseTheForce/Shapes_FF.cpp, |
609 |
< |
io/DirectionalAtomTypesSectionParser.cpp, |
610 |
< |
io/ShapeAtomTypesSectionParser.cpp, |
611 |
< |
io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... |
612 |
< |
|
613 |
< |
2005-04-15 17:43 gezelter |
614 |
< |
|
615 |
< |
* README: gmake in case people forget |
616 |
< |
|
617 |
< |
2005-04-15 17:40 gezelter |
618 |
< |
|
619 |
< |
* src/applications/oopse/oopse.cpp: fixed the spacing on the |
620 |
< |
banner. Vanity. |
621 |
< |
|
622 |
< |
2005-04-15 17:22 gezelter |
623 |
< |
|
624 |
< |
* src/: config.h.in, applications/oopse/oopse.cpp: Version string |
625 |
< |
in banner (and version numbers in config.h) |
626 |
< |
|
627 |
< |
2005-04-15 17:22 gezelter |
628 |
< |
|
629 |
< |
* ChangeLog, LICENSE, README: Documentation changes |
630 |
< |
|
631 |
< |
2005-04-15 17:03 gezelter |
632 |
< |
|
633 |
< |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
634 |
< |
UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, |
635 |
< |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
636 |
< |
UseTheForce/ForceFieldCreator.hpp, |
637 |
< |
UseTheForce/ForceFieldFactory.cpp, |
638 |
< |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
639 |
< |
UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, |
640 |
< |
UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, |
641 |
< |
UseTheForce/notifyCutoffs.F90, |
642 |
< |
UseTheForce/notifyCutoffs_interface.F90, |
643 |
< |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
644 |
< |
UseTheForce/DarkSide/atype.F90, |
645 |
< |
UseTheForce/DarkSide/atype_interface.F90, |
646 |
< |
UseTheForce/DarkSide/eam.F90, |
647 |
< |
UseTheForce/DarkSide/eam_interface.F90, |
648 |
< |
UseTheForce/DarkSide/eam_interface.h, |
649 |
< |
UseTheForce/DarkSide/electrostatic.F90, |
650 |
< |
UseTheForce/DarkSide/electrostatic_interface.F90, |
651 |
< |
UseTheForce/DarkSide/electrostatic_interface.h, |
652 |
< |
UseTheForce/DarkSide/force_globals.F90, |
653 |
< |
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
654 |
< |
UseTheForce/DarkSide/lj_interface.F90, |
655 |
< |
UseTheForce/DarkSide/lj_interface.h, |
656 |
< |
UseTheForce/DarkSide/neighborLists.F90, |
657 |
< |
UseTheForce/DarkSide/reactionField.F90, |
658 |
< |
UseTheForce/DarkSide/shapes.F90, |
659 |
< |
UseTheForce/DarkSide/shapes_interface.F90, |
660 |
< |
UseTheForce/DarkSide/shapes_interface.h, |
661 |
< |
UseTheForce/DarkSide/simParallel.F90, |
662 |
< |
UseTheForce/DarkSide/simParallel_interface.F90, |
663 |
< |
UseTheForce/DarkSide/simParallel_interface.h, |
664 |
< |
UseTheForce/DarkSide/simulation.F90, |
665 |
< |
UseTheForce/DarkSide/simulation_interface.F90, |
666 |
< |
UseTheForce/DarkSide/simulation_interface.h, |
667 |
< |
UseTheForce/DarkSide/sticky.F90, |
668 |
< |
UseTheForce/DarkSide/sticky_interface.F90, |
669 |
< |
UseTheForce/DarkSide/sticky_interface.h, |
670 |
< |
UseTheForce/DarkSide/switcheroo.F90, |
671 |
< |
applications/dump2Xyz/Dump2XYZ.cpp, |
672 |
< |
applications/dump2Xyz/Dump2XYZCmd.c, |
673 |
< |
applications/dump2Xyz/Dump2XYZCmd.h, |
674 |
< |
applications/dynamicProps/CrossTimeCorrFunc.cpp, |
675 |
< |
applications/dynamicProps/CrossTimeCorrFunc.hpp, |
676 |
< |
applications/dynamicProps/DipoleCorrFunc.cpp, |
677 |
< |
applications/dynamicProps/DipoleCorrFunc.hpp, |
678 |
< |
applications/dynamicProps/DynamicProps.cpp, |
679 |
< |
applications/dynamicProps/DynamicPropsCmd.c, |
680 |
< |
applications/dynamicProps/DynamicPropsCmd.h, |
681 |
< |
applications/dynamicProps/FrameTimeCorrFunc.hpp, |
682 |
< |
applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
683 |
< |
applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
684 |
< |
applications/dynamicProps/RCorrFunc.cpp, |
685 |
< |
applications/dynamicProps/RCorrFunc.hpp, |
686 |
< |
applications/dynamicProps/TimeCorrFunc.cpp, |
687 |
< |
applications/dynamicProps/TimeCorrFunc.hpp, |
688 |
< |
applications/dynamicProps/VCorrFunc.cpp, |
689 |
< |
applications/dynamicProps/VCorrFunc.hpp, |
690 |
< |
applications/nanoRodBuilder/GeometryBuilder.cpp, |
691 |
< |
applications/nanoRodBuilder/GeometryBuilder.hpp, |
692 |
< |
applications/nanoRodBuilder/nanorodBuilder.cpp, |
693 |
< |
applications/nanoRodBuilder/nanorodBuilderCmd.c, |
694 |
< |
applications/nanoRodBuilder/nanorodBuilderCmd.h, |
695 |
< |
applications/oopse/oopse.cpp, |
696 |
< |
applications/simpleBuilder/simpleBuilder.cpp, |
697 |
< |
applications/simpleBuilder/simpleBuilderCmd.c, |
698 |
< |
applications/simpleBuilder/simpleBuilderCmd.h, |
699 |
< |
applications/staticProps/GofAngle2.cpp, |
700 |
< |
applications/staticProps/GofAngle2.hpp, |
701 |
< |
applications/staticProps/GofR.cpp, |
702 |
< |
applications/staticProps/GofR.hpp, |
703 |
< |
applications/staticProps/GofRAngle.cpp, |
704 |
< |
applications/staticProps/GofRAngle.hpp, |
705 |
< |
applications/staticProps/GofXyz.cpp, |
706 |
< |
applications/staticProps/GofXyz.hpp, |
707 |
< |
applications/staticProps/RadialDistrFunc.cpp, |
708 |
< |
applications/staticProps/RadialDistrFunc.hpp, |
709 |
< |
applications/staticProps/StaticProps.cpp, |
710 |
< |
applications/staticProps/StaticPropsCmd.c, |
711 |
< |
applications/staticProps/StaticPropsCmd.h, |
712 |
< |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
713 |
< |
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
714 |
< |
brains/Exclude.hpp, brains/ForceManager.cpp, |
715 |
< |
brains/ForceManager.hpp, brains/MoleculeCreator.cpp, |
716 |
< |
brains/MoleculeCreator.hpp, brains/Register.cpp, |
717 |
< |
brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
718 |
< |
brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
719 |
< |
brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, |
720 |
< |
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, |
721 |
< |
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
722 |
< |
brains/fSimulation.h, constraints/ConstraintElem.hpp, |
723 |
< |
constraints/ConstraintPair.hpp, constraints/Rattle.cpp, |
724 |
< |
constraints/Rattle.hpp, constraints/ZconsStruct.hpp, |
725 |
< |
constraints/ZconstraintForceManager.cpp, |
726 |
< |
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
727 |
< |
integrators/DLM.hpp, integrators/Integrator.cpp, |
728 |
< |
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
729 |
< |
integrators/IntegratorFactory.cpp, |
730 |
< |
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
731 |
< |
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
732 |
< |
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
733 |
< |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
734 |
< |
integrators/NVT.cpp, integrators/NVT.hpp, |
735 |
< |
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
736 |
< |
integrators/Velocitizer.hpp, |
737 |
< |
integrators/VelocityVerletIntegrator.cpp, |
738 |
< |
integrators/VelocityVerletIntegrator.hpp, |
739 |
< |
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
740 |
< |
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
741 |
< |
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
742 |
< |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
743 |
< |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
744 |
< |
io/ChargeAtomTypesSectionParser.hpp, |
745 |
< |
io/DirectionalAtomTypesSectionParser.cpp, |
746 |
< |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
747 |
< |
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
748 |
< |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
749 |
< |
io/Globals.cpp, io/Globals.hpp, |
750 |
< |
io/LennardJonesAtomTypesSectionParser.cpp, |
751 |
< |
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
752 |
< |
io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, |
753 |
< |
io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, |
754 |
< |
io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, |
755 |
< |
io/SectionParser.cpp, io/SectionParser.hpp, |
756 |
< |
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
757 |
< |
io/StatWriter.cpp, io/StatWriter.hpp, |
758 |
< |
io/StickyAtomTypesSectionParser.cpp, |
759 |
< |
io/StickyAtomTypesSectionParser.hpp, |
760 |
< |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
761 |
< |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
762 |
< |
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, |
763 |
< |
io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, |
764 |
< |
io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, |
765 |
< |
io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, |
766 |
< |
lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, |
767 |
< |
lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
768 |
< |
lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, |
769 |
< |
lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, |
770 |
< |
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
771 |
< |
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
772 |
< |
math/ParallelRandNumGen.hpp, math/Polynomial.hpp, |
773 |
< |
math/Quaternion.hpp, math/RandNumGen.hpp, |
774 |
< |
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
775 |
< |
math/RectMatrix.hpp, math/SeqRandNumGen.cpp, |
776 |
< |
math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, |
777 |
< |
math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, |
778 |
< |
minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, |
779 |
< |
minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, |
780 |
< |
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
781 |
< |
minimizers/MinimizerFactory.hpp, |
782 |
< |
minimizers/MinimizerParameterSet.cpp, |
783 |
< |
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
784 |
< |
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
785 |
< |
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
786 |
< |
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
787 |
< |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
788 |
< |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
789 |
< |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
790 |
< |
primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, |
791 |
< |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
792 |
< |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
793 |
< |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
794 |
< |
primitives/Torsion.cpp, primitives/Torsion.hpp, |
795 |
< |
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
796 |
< |
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
797 |
< |
profiling/timing.F90, restraints/Restraints.cpp, |
798 |
< |
restraints/Restraints.hpp, |
799 |
< |
restraints/ThermoIntegrationForceManager.cpp, |
800 |
< |
restraints/ThermoIntegrationForceManager.hpp, |
801 |
< |
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
802 |
< |
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
803 |
< |
selection/NameFinder.cpp, selection/NameFinder.hpp, |
804 |
< |
selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, |
805 |
< |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
806 |
< |
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
807 |
< |
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, |
808 |
< |
selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, |
809 |
< |
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
810 |
< |
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
811 |
< |
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
812 |
< |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
813 |
< |
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
814 |
< |
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
815 |
< |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
816 |
< |
types/DirectionalAtomType.hpp, types/FixedBondType.hpp, |
817 |
< |
types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, |
818 |
< |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
819 |
< |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
820 |
< |
types/MorseBondType.hpp, types/OplsTorsionType.hpp, |
821 |
< |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
822 |
< |
types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, |
823 |
< |
types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, |
824 |
< |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
825 |
< |
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
826 |
< |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
827 |
< |
types/TorsionType.hpp, types/UreyBradleyBendType.hpp, |
828 |
< |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, |
829 |
< |
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
830 |
< |
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
831 |
< |
utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, |
832 |
< |
utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, |
833 |
< |
utils/PropertyMap.cpp, utils/PropertyMap.hpp, |
834 |
< |
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
835 |
< |
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
836 |
< |
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
837 |
< |
utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, |
838 |
< |
utils/any.hpp, utils/definitions.F90, utils/fError.c, |
839 |
< |
utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, |
840 |
< |
utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, |
841 |
< |
utils/residentMem.h, utils/simError.c, utils/simError.h, |
842 |
< |
utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, |
843 |
< |
visitors/AtomData.hpp, visitors/AtomVisitor.cpp, |
844 |
< |
visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, |
845 |
< |
visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, |
846 |
< |
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
847 |
< |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, |
848 |
< |
visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, |
849 |
< |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has |
850 |
< |
been drafted to perform our indentation services |
851 |
< |
|
852 |
< |
2005-04-15 17:03 gezelter |
853 |
< |
|
854 |
< |
* configure, ac-tools/configure.in: Jedi mind-trick warning |
855 |
< |
messages have been added to make users ignore CGAL. |
856 |
< |
|
857 |
< |
2005-04-15 13:41 tim |
858 |
< |
|
859 |
< |
* make/Makefile.in: fix make install |
860 |
< |
|
861 |
< |
2005-04-15 13:41 tim |
862 |
< |
|
863 |
< |
* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: |
864 |
< |
add Makefile of samples |
865 |
< |
|
866 |
< |
2005-04-15 13:33 tim |
867 |
< |
|
868 |
< |
* samples/: lipid/Makefile, water/dimer/Makefile, |
869 |
< |
water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not |
870 |
< |
installed correctly |
871 |
< |
|
872 |
< |
2005-04-14 16:41 gezelter |
873 |
< |
|
874 |
< |
* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
875 |
< |
make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, |
876 |
< |
scripts/filepp, scripts/filepp.in: configure now searches for perl |
877 |
< |
to use with filepp |
878 |
< |
|
879 |
< |
2005-04-14 16:20 gezelter |
880 |
< |
|
881 |
< |
* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |
882 |
< |
MoLocator |
883 |
< |
|
884 |
< |
2005-04-14 14:12 gezelter |
885 |
< |
|
886 |
< |
* LICENSE: [no log message] |
887 |
< |
|
888 |
< |
2005-04-14 11:10 chuckv |
889 |
< |
|
890 |
< |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: |
891 |
< |
nanorodbuilder now exit's when libCGAL is not present. |
892 |
< |
|
893 |
< |
2005-04-14 10:20 tim |
894 |
< |
|
895 |
< |
* src/io/make_nodes.h: fix one more warning message in make_nodes |
896 |
< |
|
897 |
< |
2005-04-13 18:36 chuckv |
898 |
< |
|
899 |
< |
* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed |
900 |
< |
interface name for SGI Compiler |
901 |
< |
|
902 |
< |
2005-04-13 18:29 chrisfen |
903 |
< |
|
904 |
< |
* samples/water/ssde/ssde.md: oops... bad sample |
905 |
< |
|
906 |
< |
2005-04-13 18:00 chuckv |
907 |
< |
|
908 |
< |
* src/config.h.in: Change typo in CGAL. |
909 |
< |
|
910 |
< |
2005-04-13 17:43 tim |
911 |
< |
|
912 |
< |
* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, |
913 |
< |
selection/SelectionCompiler.hpp: fix some warning messages |
914 |
< |
|
915 |
< |
2005-04-13 17:30 gezelter |
916 |
< |
|
917 |
< |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
918 |
< |
make/Makefile.in, src/config.h.in, |
919 |
< |
src/applications/nanoRodBuilder/Makefile, |
920 |
< |
src/applications/nanoRodBuilder/Makefile.in, |
921 |
< |
src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL |
922 |
< |
checks |
923 |
< |
|
924 |
< |
2005-04-13 15:36 chuckv |
925 |
< |
|
926 |
< |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, |
927 |
< |
DarkSide/LJ.F90, DarkSide/electrostatic.F90, |
928 |
< |
DarkSide/electrostatic_interface.F90, |
929 |
< |
DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, |
930 |
< |
DarkSide/lj_interface.h, DarkSide/sticky.F90, |
931 |
< |
DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added |
932 |
< |
destroy methods for Fortran modules. |
933 |
< |
|
934 |
< |
2005-04-13 15:17 chuckv |
935 |
< |
|
936 |
< |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, |
937 |
< |
shapes_interface.h: Added destroy method to clean up memory |
938 |
< |
|
939 |
< |
2005-04-13 13:41 tim |
940 |
< |
|
941 |
< |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
942 |
< |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
943 |
< |
io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, |
944 |
< |
primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, |
945 |
< |
types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are |
946 |
< |
fixed |
947 |
< |
|
948 |
< |
2005-04-12 17:44 chuckv |
949 |
< |
|
950 |
< |
* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed |
951 |
< |
for nanoRodBuilder. |
952 |
< |
|
953 |
< |
2005-04-12 17:42 tim |
954 |
< |
|
955 |
< |
* src/applications/: nanoRodBuilder/nanorodBuilder.cpp, |
956 |
< |
simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder |
957 |
< |
and simpleBuilder(forget to delete lattice) |
958 |
< |
|
959 |
< |
2005-04-12 17:33 tim |
960 |
< |
|
961 |
< |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
962 |
< |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: |
963 |
< |
refactory lattice |
964 |
< |
|
965 |
< |
2005-04-12 17:07 tim |
966 |
< |
|
967 |
< |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, |
968 |
< |
CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, |
969 |
< |
Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory |
970 |
< |
LatticeFactory and LatticeCreator |
971 |
< |
|
972 |
< |
2005-04-12 16:58 tim |
973 |
< |
|
974 |
< |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
975 |
< |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, |
976 |
< |
brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
977 |
< |
lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, |
978 |
< |
lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, |
979 |
< |
lattice/Makefile: refactory LatticeFactory and LatticeCreator |
980 |
< |
|
981 |
< |
2005-04-12 16:28 gezelter |
982 |
< |
|
983 |
< |
* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, |
984 |
< |
vector_class.F90: cleaned up vector_class memory leak fix by |
985 |
< |
deallocating in reverse order of how we allocated. Also migrated |
986 |
< |
MoLocator into utils directory |
987 |
< |
|
988 |
< |
2005-04-12 16:27 gezelter |
989 |
< |
|
990 |
< |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, |
991 |
< |
Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
992 |
< |
LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice |
993 |
< |
directory |
994 |
< |
|
995 |
< |
2005-04-12 16:27 gezelter |
996 |
< |
|
997 |
< |
* src/applications/: nanoRodBuilder/BaseLattice.cpp, |
998 |
< |
nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, |
999 |
< |
nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, |
1000 |
< |
nanoRodBuilder/LatticeCreator.hpp, |
1001 |
< |
nanoRodBuilder/LatticeFactory.cpp, |
1002 |
< |
nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, |
1003 |
< |
nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, |
1004 |
< |
nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, |
1005 |
< |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
1006 |
< |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
1007 |
< |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
1008 |
< |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, |
1009 |
< |
simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, |
1010 |
< |
simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of |
1011 |
< |
these files are now redundant |
1012 |
< |
|
1013 |
< |
2005-04-12 16:27 gezelter |
1014 |
< |
|
1015 |
< |
* src/UseTheForce/DarkSide/: atype_interface.F90, |
1016 |
< |
atype_interface.h: cleaned up memory leak fix |
1017 |
< |
|
1018 |
< |
2005-04-12 16:26 gezelter |
1019 |
< |
|
1020 |
< |
* make/Makefile.in: added lattice subdirectory |
1021 |
< |
|
1022 |
< |
2005-04-12 15:57 chrisfen |
1023 |
< |
|
1024 |
< |
* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added |
1025 |
< |
a space by accident |
1026 |
< |
|
1027 |
< |
2005-04-12 15:56 chrisfen |
1028 |
< |
|
1029 |
< |
* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added |
1030 |
< |
quadrupole sample |
1031 |
< |
|
1032 |
< |
2005-04-12 15:56 chrisfen |
1033 |
< |
|
1034 |
< |
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating |
1035 |
< |
samples |
1036 |
< |
|
1037 |
< |
2005-04-12 13:30 tim |
1038 |
< |
|
1039 |
< |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom |
1040 |
< |
type in fortran side |
1041 |
< |
|
1042 |
< |
2005-04-12 12:45 chuckv |
1043 |
< |
|
1044 |
< |
* src/utils/vector_class.F90: Further changes to vector_class |
1045 |
< |
destroy function. |
1046 |
< |
|
1047 |
< |
2005-04-12 12:39 chuckv |
1048 |
< |
|
1049 |
< |
* src/utils/vector_class.F90: Fixed pointer memory leak in |
1050 |
< |
vector_class. |
1051 |
< |
|
1052 |
< |
2005-04-12 12:12 chuckv |
1053 |
< |
|
1054 |
< |
* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, |
1055 |
< |
DarkSide/atype_interface.F90, DarkSide/atype_interface.h, |
1056 |
< |
DarkSide/eam.F90, DarkSide/eam_interface.F90, |
1057 |
< |
DarkSide/eam_interface.h: Updates to deallocate object in fortran. |
1058 |
< |
|
1059 |
< |
2005-04-12 09:24 chrisfen |
1060 |
< |
|
1061 |
< |
* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI |
1062 |
< |
output |
1063 |
< |
|
1064 |
< |
2005-04-11 19:29 chuckv |
1065 |
< |
|
1066 |
< |
* src/: UseTheForce/DarkSide/atype.F90, |
1067 |
< |
applications/nanoRodBuilder/Makefile: Changes to delete atypes... |
1068 |
< |
|
1069 |
< |
2005-04-11 19:28 chuckv |
1070 |
< |
|
1071 |
< |
* src/utils/vector_class.F90: Added code to delete vector. |
1072 |
< |
|
1073 |
< |
2005-04-11 17:03 chuckv |
1074 |
< |
|
1075 |
< |
* samples/metals/nanorod/: Au_nanoparticle.md, |
1076 |
< |
Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why |
1077 |
< |
aren't these here? |
1 |
> |
2006-04-20 23:19 chrisfen |
2 |
> |
|
3 |
> |
* samples/water/spce/spce.md, |
4 |
> |
src/UseTheForce/DarkSide/electrostatic.F90: Electrosplines added... |
5 |
> |
|
6 |
> |
2006-04-20 17:02 chrisfen |
7 |
> |
|
8 |
> |
* samples/argon/500.md, src/UseTheForce/DarkSide/sticky.F90, |
9 |
> |
src/UseTheForce/DarkSide/switcheroo.F90: splined up sticky |
10 |
> |
|
11 |
> |
2006-04-20 14:24 gezelter |
12 |
> |
|
13 |
> |
* samples/metals/EAM/Au_bulk_voter.md, |
14 |
> |
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
15 |
> |
samples/water/ssde/ssde.md, src/UseTheForce/ForceField.cpp, |
16 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/LJ.F90, |
17 |
> |
src/UseTheForce/DarkSide/eam.F90, |
18 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
19 |
> |
src/UseTheForce/DarkSide/suttonchen.F90, |
20 |
> |
src/UseTheForce/DarkSide/switcheroo.F90, |
21 |
> |
src/UseTheForce/DarkSide/switcheroo_interface.F90, |
22 |
> |
src/UseTheForce/DarkSide/switcheroo_interface.h, |
23 |
> |
src/utils/interpolation.F90: Complete rewrite of spline code and |
24 |
> |
everything that uses it. |
25 |
> |
|
26 |
> |
2006-04-17 17:49 gezelter |
27 |
> |
|
28 |
> |
* configure, ac-tools/aclocal.m4, samples/argon/500.md, |
29 |
> |
samples/metals/EAM/Au_bulk_voter.md, |
30 |
> |
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
31 |
> |
samples/water/ssde/ssde.md, src/UseTheForce/doForces.F90, |
32 |
> |
src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90, |
33 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
34 |
> |
src/UseTheForce/DarkSide/interpolation.F90, |
35 |
> |
src/UseTheForce/DarkSide/sticky.F90, |
36 |
> |
src/UseTheForce/DarkSide/suttonchen.F90, |
37 |
> |
src/UseTheForce/DarkSide/switcheroo.F90, |
38 |
> |
src/applications/hydrodynamics/Hydro.ggo, |
39 |
> |
src/applications/hydrodynamics/HydroCmd.c, |
40 |
> |
src/applications/hydrodynamics/HydroCmd.h, |
41 |
> |
src/mdParser/SimplePreprocessor.hpp, src/types/DataHolder.hpp, |
42 |
> |
src/utils/interpolation.F90: Many performance improvements |
43 |
> |
|
44 |
> |
2006-04-15 22:51 chrisfen |
45 |
> |
|
46 |
> |
* configure, samples/argon/500.md, src/UseTheForce/doForces.F90, |
47 |
> |
src/UseTheForce/fSwitchingFunction.h, |
48 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
49 |
> |
src/UseTheForce/DarkSide/switcheroo.F90: added a cubic spline to |
50 |
> |
switcheroo |
51 |
> |
|
52 |
> |
2006-04-15 17:58 chrisfen |
53 |
> |
|
54 |
> |
* src/utils/Makefile.in: Since status.F90 is used by |
55 |
> |
interpolation.F90, the former needs to be listed above the later in |
56 |
> |
the Makefile. |
57 |
> |
|
58 |
> |
2006-04-14 17:59 gezelter |
59 |
> |
|
60 |
> |
* src/utils/interpolation.F90: changed the interface a bit |
61 |
> |
|
62 |
> |
2006-04-14 17:49 gezelter |
63 |
> |
|
64 |
> |
* src/utils/interpolation.F90: added some logical flags |
65 |
> |
|
66 |
> |
2006-04-14 17:06 chrisfen |
67 |
> |
|
68 |
> |
* src/utils/interpolation.F90: Wiped the spline with derivatives |
69 |
> |
and corrected a boundary comparision error by eliminating the |
70 |
> |
check. This algorithm REQUIRES known first derivatives at the |
71 |
> |
endpoints. |
72 |
> |
|
73 |
> |
2006-04-14 16:04 gezelter |
74 |
> |
|
75 |
> |
* src/utils/: Makefile.in, interpolation.F90: bug fixes for |
76 |
> |
interpolation module |
77 |
> |
|
78 |
> |
2006-04-14 15:57 gezelter |
79 |
> |
|
80 |
> |
* src/utils/interpolation.F90: Heavily modified interpolation |
81 |
> |
module, also moved to "utils" |
82 |
> |
|
83 |
> |
2006-04-12 17:15 chuckv |
84 |
> |
|
85 |
> |
* src/UseTheForce/DarkSide/interpolation.F90: Added interpolation |
86 |
> |
module. |
87 |
> |
|
88 |
> |
2006-04-11 11:33 gezelter |
89 |
> |
|
90 |
> |
* src/applications/staticProps/: StaticProps.ggo, StaticPropsCmd.c, |
91 |
> |
StaticPropsCmd.h: [no log message] |
92 |
> |
|
93 |
> |
2006-04-03 11:37 chuckv |
94 |
> |
|
95 |
> |
* configure, ac-tools/aclocal.m4, make/Makefile.in, |
96 |
> |
src/UseTheForce/DarkSide/simParallel.F90: Added status module to |
97 |
> |
simParallel for error reporting. |
98 |
> |
|
99 |
> |
2006-03-31 13:09 tim |
100 |
> |
|
101 |
> |
* src/: integrators/NPrT.cpp, io/Globals.cpp: NPrT might work now |
102 |
> |
|
103 |
> |
2006-03-30 16:08 chuckv |
104 |
> |
|
105 |
> |
* src/UseTheForce/DarkSide/suttonchen.F90: Fixed memory leak bug |
106 |
> |
where SCList capacity was not reset to zero on destruction. |
107 |
> |
|
108 |
> |
2006-03-30 14:37 chuckv |
109 |
> |
|
110 |
> |
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
111 |
> |
More testing of nanoparticleBuilder. |
112 |
> |
|
113 |
> |
2006-03-29 17:24 chuckv |
114 |
> |
|
115 |
> |
* src/mdParser/SimplePreprocessor.hpp: Added check to make sure md |
116 |
> |
file exists. |
117 |
> |
|
118 |
> |
2006-03-29 14:17 chuckv |
119 |
> |
|
120 |
> |
* src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp, |
121 |
> |
lattice/shapedLattice.cpp, lattice/shapedLattice.hpp: Fixed |
122 |
> |
latticeOrt in shapedlatice and latticebuilder. |
123 |
> |
|
124 |
> |
2006-03-29 13:11 tim |
125 |
> |
|
126 |
> |
* src/applications/dynamicProps/: DipoleCorrFunc.cpp, |
127 |
> |
LegendreCorrFunc.cpp, VCorrFunc.cpp: Fix the normalization problem |
128 |
> |
in calculating correlation functions |
129 |
> |
|
130 |
> |
2006-03-29 13:09 tim |
131 |
> |
|
132 |
> |
* src/applications/hydrodynamics/: ApproximationModel.cpp, |
133 |
> |
ApproximationModel.hpp, CompositeShape.cpp, Hydro.cpp, Hydro.ggo, |
134 |
> |
HydroCmd.c, HydroCmd.h, HydrodynamicsModel.hpp, RoughShell.cpp: (1) |
135 |
> |
RoughShell Model is working; (20)Adding a new option into Hydro |
136 |
> |
which allows user to generate the beads only |
137 |
> |
|
138 |
> |
2006-03-27 11:21 chuckv |
139 |
> |
|
140 |
> |
* src/applications/nanoparticleBuilder/Makefile: Makefile for |
141 |
> |
nanoparticle builder. |
142 |
> |
|
143 |
> |
2006-03-27 11:03 chuckv |
144 |
> |
|
145 |
> |
* make/Makefile.in, src/lattice/shapedLattice.cpp, |
146 |
> |
src/lattice/shapedLattice.hpp: Added nanoparticle builder to |
147 |
> |
makefile |
148 |
> |
|
149 |
> |
2006-03-24 15:46 chuckv |
150 |
> |
|
151 |
> |
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
152 |
> |
Debugging changes to nanoparticle builder. |
153 |
> |
|
154 |
> |
2006-03-24 12:29 tim |
155 |
> |
|
156 |
> |
* src/applications/dynamicProps/: DynamicProps.cpp, |
157 |
> |
DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, |
158 |
> |
RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: back to previous DynamicProps |
159 |
> |
|
160 |
> |
2006-03-24 11:49 tim |
161 |
> |
|
162 |
> |
* src/applications/dynamicProps/: DynamicProps.cpp, |
163 |
> |
DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, |
164 |
> |
RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: Adding position correlation |
165 |
> |
function. The command line option for DynamicProps is now changed. |
166 |
> |
--rcorr is for position correlation and --rmsd is for mean square |
167 |
> |
displacement. |
168 |
> |
|
169 |
> |
2006-03-23 10:03 tim |
170 |
> |
|
171 |
> |
* src/applications/hydrodynamics/: AnalyticalModel.cpp, |
172 |
> |
AnalyticalModel.hpp, ApproximationModel.cpp, |
173 |
> |
ApproximationModel.hpp, HydrodynamicsModel.hpp: update writeBeads |
174 |
> |
method |
175 |
> |
|
176 |
> |
2006-03-23 10:02 tim |
177 |
> |
|
178 |
> |
* src/io/Globals.hpp: remove a unknown method |
179 |
> |
|
180 |
> |
2006-03-23 10:00 tim |
181 |
> |
|
182 |
> |
* src/math/CholeskyDecomposition.hpp: The off diagnal is not set |
183 |
> |
|
184 |
> |
2006-03-23 09:59 tim |
185 |
> |
|
186 |
> |
* src/mdParser/SimplePreprocessor.hpp: Throw exception if the file |
187 |
> |
can not be opened for preprocessing |
188 |
> |
|
189 |
> |
2006-03-22 15:57 chuckv |
190 |
> |
|
191 |
> |
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
192 |
> |
shapedLatticeSpherical.cpp, shapedLatticeSpherical.hpp: Added |
193 |
> |
shaped lattice. |
194 |
> |
|
195 |
> |
2006-03-21 10:33 tim |
196 |
> |
|
197 |
> |
* src/applications/hydrodynamics/ApproximationModel.cpp: fix a bug |
198 |
> |
in calculating hydrodynamics tensor when the radius of beads are |
199 |
> |
not the same |
200 |
> |
|
201 |
> |
2006-03-20 19:26 tim |
202 |
> |
|
203 |
> |
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
204 |
> |
applications/hydrodynamics/BeadModel.cpp, |
205 |
> |
applications/hydrodynamics/ShapeBuilder.cpp, |
206 |
> |
integrators/LDForceManager.cpp: Fix a bug in friction calculation |
207 |
> |
for ellipsoid |
208 |
> |
|
209 |
> |
2006-03-20 14:12 tim |
210 |
> |
|
211 |
> |
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
212 |
> |
applications/hydrodynamics/Ellipsoid.cpp, |
213 |
> |
applications/hydrodynamics/Ellipsoid.hpp, |
214 |
> |
applications/hydrodynamics/ShapeBuilder.cpp, |
215 |
> |
integrators/LDForceManager.cpp: Verify the correctness of |
216 |
> |
Ellipsoid's hydrodynamics properties |
217 |
> |
|
218 |
> |
2006-03-17 18:51 tim |
219 |
> |
|
220 |
> |
* src/applications/hydrodynamics/: Hydro.cpp, ShapeBuilder.cpp: New |
221 |
> |
version of Hydro is working now. |
222 |
> |
|
223 |
> |
2006-03-17 18:20 tim |
224 |
> |
|
225 |
> |
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
226 |
> |
applications/hydrodynamics/AnalyticalModel.hpp, |
227 |
> |
applications/hydrodynamics/ApproximationModel.cpp, |
228 |
> |
applications/hydrodynamics/ApproximationModel.hpp, |
229 |
> |
applications/hydrodynamics/BeadModel.hpp, |
230 |
> |
applications/hydrodynamics/CompositeShape.cpp, |
231 |
> |
applications/hydrodynamics/CompositeShape.hpp, |
232 |
> |
applications/hydrodynamics/Ellipsoid.cpp, |
233 |
> |
applications/hydrodynamics/Ellipsoid.hpp, |
234 |
> |
applications/hydrodynamics/Hydro.cpp, |
235 |
> |
applications/hydrodynamics/Hydro.ggo, |
236 |
> |
applications/hydrodynamics/HydroCmd.c, |
237 |
> |
applications/hydrodynamics/HydroCmd.h, |
238 |
> |
applications/hydrodynamics/HydrodynamicsModel.cpp, |
239 |
> |
applications/hydrodynamics/HydrodynamicsModel.hpp, |
240 |
> |
applications/hydrodynamics/HydrodynamicsModelCreator.hpp, |
241 |
> |
applications/hydrodynamics/HydrodynamicsModelFactory.cpp, |
242 |
> |
applications/hydrodynamics/HydrodynamicsModelFactory.hpp, |
243 |
> |
applications/hydrodynamics/Makefile, |
244 |
> |
applications/hydrodynamics/RoughShell.cpp, |
245 |
> |
applications/hydrodynamics/RoughShell.hpp, |
246 |
> |
applications/hydrodynamics/Shape.hpp, |
247 |
> |
applications/hydrodynamics/ShapeBuilder.cpp, |
248 |
> |
applications/hydrodynamics/ShapeBuilder.hpp, |
249 |
> |
applications/hydrodynamics/Spheric.cpp, |
250 |
> |
applications/hydrodynamics/Spheric.hpp, |
251 |
> |
applications/hydrodynamics/StuntDoubleShape.cpp, |
252 |
> |
applications/hydrodynamics/StuntDoubleShape.hpp, |
253 |
> |
integrators/LDForceManager.cpp, integrators/LDForceManager.hpp, |
254 |
> |
io/Globals.cpp, io/Globals.hpp, math/SquareMatrix.hpp, |
255 |
> |
utils/HydroProps.hpp: refactor Hydrodynamics module. |
256 |
> |
|
257 |
> |
2006-03-17 11:10 chuckv |
258 |
> |
|
259 |
> |
* src/lattice/: shapedLattice.cpp, shapedLattice.hpp, Makefile: |
260 |
> |
Generic Shaped Lattice for oopse. Can overload to get spherical or |
261 |
> |
nanorod. |
262 |
> |
|
263 |
> |
2006-03-16 17:50 tim |
264 |
> |
|
265 |
> |
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
266 |
> |
integrators/LDForceManager.cpp, math/MersenneTwister.hpp: |
267 |
> |
LagevinDynamics is working? |
268 |
> |
|
269 |
> |
2006-03-16 16:52 gezelter |
270 |
> |
|
271 |
> |
* src/applications/hydrodynamics/RoughShell.hpp: fixed a const |
272 |
> |
problem |
273 |
> |
|
274 |
> |
2006-03-15 17:08 tim |
275 |
> |
|
276 |
> |
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: unit |
277 |
> |
conversion for diffusion tensor is wrong |
278 |
> |
|
279 |
> |
2006-03-15 16:28 tim |
280 |
> |
|
281 |
> |
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
282 |
> |
utils/NumericConstant.hpp: change the epsilon of numeric_limit |
283 |
> |
|
284 |
> |
2006-03-15 15:58 tim |
285 |
> |
|
286 |
> |
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: correcting |
287 |
> |
the unit in HydrodynamicsModel |
288 |
> |
|
289 |
> |
2006-03-15 12:35 tim |
290 |
> |
|
291 |
> |
* src/primitives/RigidBody.cpp: using setFrc in |
292 |
> |
RigidBody::calcForcesAndTorques will discard if there are force and |
293 |
> |
torque applied in rigid body itself. use addFrc instead. |
294 |
> |
|
295 |
> |
2006-03-15 10:51 tim |
296 |
> |
|
297 |
> |
* src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp, |
298 |
> |
RoughShell.cpp, RoughShell.hpp: Adding RoughShell and BeadModel |
299 |
> |
|
300 |
> |
2006-03-15 10:50 tim |
301 |
> |
|
302 |
> |
* make/Makefile.in, src/applications/hydrodynamics/Makefile: adding |
303 |
> |
hydrodynamics module into build system |
304 |
> |
|
305 |
> |
2006-03-14 18:46 tim |
306 |
> |
|
307 |
> |
* src/math/CholeskyDecomposition.hpp: adding Cholesky Decomposition |
308 |
> |
|
309 |
> |
2006-03-13 17:42 tim |
310 |
> |
|
311 |
> |
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
312 |
> |
applications/hydrodynamics/HydrodynamicsModel.hpp, |
313 |
> |
applications/hydrodynamics/StuntDoubleShape.cpp, |
314 |
> |
applications/hydrodynamics/StuntDoubleShape.hpp, |
315 |
> |
brains/Register.cpp, integrators/LDForceManager.cpp, |
316 |
> |
integrators/LDForceManager.hpp, integrators/LangevinDynamics.cpp, |
317 |
> |
integrators/LangevinDynamics.hpp, integrators/Makefile, |
318 |
> |
io/Globals.cpp, io/Globals.hpp, math/MersenneTwister.hpp, |
319 |
> |
math/RandNumGen.hpp, math/SquareMatrix3.hpp: LangevinDynamics in |
320 |
> |
progress |
321 |
> |
|
322 |
> |
2006-03-07 11:43 gezelter |
323 |
> |
|
324 |
> |
* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Fixed a |
325 |
> |
double/int bug. Surprised no one ever noticed before... |
326 |
> |
|
327 |
> |
2006-02-24 16:17 tim |
328 |
> |
|
329 |
> |
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: fix bugs |
330 |
> |
in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out |
331 |
> |
product of Rij |
332 |
> |
|
333 |
> |
2006-02-23 18:16 tim |
334 |
> |
|
335 |
> |
* src/applications/hydrodynamics/: Hydro.cpp, Hydro.ggo, |
336 |
> |
HydroCmd.c, HydroCmd.h, HydrodynamicsModel.cpp, |
337 |
> |
HydrodynamicsModel.hpp, HydrodynamicsModelCreator.hpp, |
338 |
> |
HydrodynamicsModelFactory.cpp, HydrodynamicsModelFactory.hpp, |
339 |
> |
MoleculeShape.cpp, MoleculeShape.hpp, StuntDoubleShape.cpp, |
340 |
> |
StuntDoubleShape.hpp: Bead Model is working |
341 |
> |
|
342 |
> |
2006-02-22 15:35 tim |
343 |
> |
|
344 |
> |
* src/: applications/hydrodynamics/Hydro.cpp, |
345 |
> |
applications/hydrodynamics/Hydro.ggo, |
346 |
> |
applications/hydrodynamics/HydroCmd.c, |
347 |
> |
applications/hydrodynamics/HydroCmd.h, |
348 |
> |
applications/hydrodynamics/HydrodynamicsModel.cpp, |
349 |
> |
applications/hydrodynamics/HydrodynamicsModel.hpp, |
350 |
> |
applications/hydrodynamics/HydrodynamicsModelCreator.hpp, |
351 |
> |
applications/hydrodynamics/HydrodynamicsModelFactory.cpp, |
352 |
> |
applications/hydrodynamics/HydrodynamicsModelFactory.hpp, |
353 |
> |
applications/hydrodynamics/MoleculeShape.cpp, |
354 |
> |
applications/hydrodynamics/MoleculeShape.hpp, |
355 |
> |
math/DynamicRectMatrix.hpp, math/DynamicVector.hpp, math/LU.hpp, |
356 |
> |
math/RectMatrix.hpp, math/SquareMatrix3.hpp: Adding Hydrodynamics |
357 |
> |
Module |
358 |
> |
|
359 |
> |
2006-02-16 17:05 gezelter |
360 |
> |
|
361 |
> |
* src/brains/Snapshot.cpp: fixed a spelling error |
362 |
> |
|
363 |
> |
2006-02-16 16:40 gezelter |
364 |
> |
|
365 |
> |
* src/: UseTheForce/doForces.F90, |
366 |
> |
UseTheForce/DarkSide/simulation.F90, math/Makefile, |
367 |
> |
math/linearAlgebra.F90: fixed a problem with cutoff radii being set |
368 |
> |
larger than 1/2 the length of the shortest box dimension. added a |
369 |
> |
few fortran utility routines |
370 |
> |
|
371 |
> |
2006-02-15 15:46 chuckv |
372 |
> |
|
373 |
> |
* src/applications/nanoparticleBuilder/: sphericalNanoparticle.cpp, |
374 |
> |
sphericalNanoparticle.hpp: Changed Names of class files. |
375 |
> |
|
376 |
> |
2006-02-10 10:45 kdaily |
377 |
> |
|
378 |
> |
* src/applications/dynamicProps/LegendreCorrFunc.cpp: [no log |
379 |
> |
message] |
380 |
> |
|
381 |
> |
2006-02-10 10:12 tim |
382 |
> |
|
383 |
> |
* src/math/: LegendrePolynomial.cpp, Vector.hpp: fix a bug in |
384 |
> |
converting integer to double |
385 |
> |
|
386 |
> |
2006-02-08 13:21 chrisfen |
387 |
> |
|
388 |
> |
* forceFields/DUFF2.frc: added DPD molecule type parameters |
389 |
> |
|
390 |
> |
2006-02-07 11:39 tim |
391 |
> |
|
392 |
> |
* src/applications/dynamicProps/: DipoleCorrFunc.cpp, |
393 |
> |
LegendreCorrFunc.cpp: Fixing a bug which reads the wrong frame of |
394 |
> |
trajectory file during analysis |
395 |
> |
|
396 |
> |
2006-02-02 12:14 tim |
397 |
> |
|
398 |
> |
* src/: math/Polynomial.hpp, math/SquareMatrix3.hpp, |
399 |
> |
types/AtomStamp.cpp: adding transpose into SquareMatrix3; fix a bug |
400 |
> |
in AtomStamp where orientation is not set correctly. |
401 |
> |
|
402 |
> |
2006-02-02 11:49 gezelter |
403 |
> |
|
404 |
> |
* src/primitives/RigidBody.cpp: fixed a bug in rigid bodies that |
405 |
> |
contain directional atoms |
406 |
> |
|
407 |
> |
2006-02-02 10:49 xsun |
408 |
> |
|
409 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
410 |
> |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Adding visitor |
411 |
> |
for GBlipid atom type |
412 |
> |
|
413 |
> |
2006-02-01 21:57 gezelter |
414 |
> |
|
415 |
> |
* make/Makefile.in: added CXXFLAGS to the LinkOptions to allow |
416 |
> |
compilation with icc9 (skipping the gcc-4 std c++ libraries). |
417 |
> |
|
418 |
> |
2006-02-01 16:06 chrisfen |
419 |
> |
|
420 |
> |
* src/brains/SimInfo.cpp: Missing brace caused the last commit not |
421 |
> |
to build |
422 |
> |
|
423 |
> |
2006-02-01 15:54 chrisfen |
424 |
> |
|
425 |
> |
* samples/water/spce/spce.md, src/brains/SimInfo.cpp: Changes to |
426 |
> |
cutoff radius setting to a more logical procedure - still may |
427 |
> |
change... |
428 |
> |
|
429 |
> |
2006-02-01 12:26 gezelter |
430 |
> |
|
431 |
> |
* src/: math/Polynomial.hpp, utils/GenericData.hpp, utils/any.hpp: |
432 |
> |
Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X |
433 |
> |
|
434 |
> |
2006-01-30 17:25 tim |
435 |
> |
|
436 |
> |
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
437 |
> |
applications/dynamicProps/DynamicProps.cpp, |
438 |
> |
applications/dynamicProps/DynamicProps.ggo, |
439 |
> |
applications/dynamicProps/DynamicPropsCmd.c, |
440 |
> |
applications/dynamicProps/DynamicPropsCmd.h, |
441 |
> |
applications/dynamicProps/LegendreCorrFunc.cpp, |
442 |
> |
applications/dynamicProps/LegendreCorrFunc.hpp, |
443 |
> |
applications/dynamicProps/Makefile, math/LegendrePolynomial.cpp, |
444 |
> |
math/LegendrePolynomial.hpp, math/Makefile, math/Polynomial.hpp: |
445 |
> |
Adding :LegendrePolynomial |
446 |
> |
|
447 |
> |
2006-01-19 17:54 chuckv |
448 |
> |
|
449 |
> |
* src/applications/nanoparticleBuilder/: Makefile, |
450 |
> |
nanoparticleBuilder.cpp, sphericalNanoparticle.hpp: Changes to |
451 |
> |
nanoparticle builder |
452 |
> |
|
453 |
> |
2006-01-18 16:08 chuckv |
454 |
> |
|
455 |
> |
* src/applications/nanoparticleBuilder/Makefile: Added Makefile for |
456 |
> |
nanoparticle builder. |
457 |
> |
|
458 |
> |
2006-01-17 11:16 gezelter |
459 |
> |
|
460 |
> |
* AUTHORS, README: Cleaning up for 3.0.1 release |
461 |
> |
|
462 |
> |
2006-01-17 10:50 gezelter |
463 |
> |
|
464 |
> |
* ChangeLog: Prepping 3.0.1 release |
465 |
> |
|
466 |
> |
2006-01-17 10:32 gezelter |
467 |
> |
|
468 |
> |
* src/config.h.in: new version number |
469 |
> |
|
470 |
> |
2006-01-17 10:32 gezelter |
471 |
> |
|
472 |
> |
* doc/: OOPSE.pdf, SelectionExpression.html, cppstyle.html, |
473 |
> |
definition.jpg, gofr.jpg, gofrtheta.jpg, heirarchy.png, |
474 |
> |
oopseManual.pdf: Updated Documentation |
475 |
> |
|
476 |
> |
2006-01-16 18:10 gezelter |
477 |
> |
|
478 |
> |
* ChangeLog, README: Getting ready for release! |
479 |
> |
|
480 |
> |
2006-01-16 10:26 gezelter |
481 |
> |
|
482 |
> |
* configure: Testing commit |
483 |
> |
|
484 |
> |
2006-01-13 16:57 chuckv |
485 |
> |
|
486 |
> |
* src/: UseTheForce/SC_FF.cpp, |
487 |
> |
applications/nanoparticleBuilder/sphericalNanoparticle.cpp, |
488 |
> |
io/Globals.cpp, io/Globals.hpp: Removed MixingRule from Globals. |
489 |
> |
Handled by forceField now. |
490 |
> |
|
491 |
> |
2006-01-13 14:17 chuckv |
492 |
> |
|
493 |
> |
* src/io/Globals.cpp: Added NPAT to Globals integrators. |
494 |
> |
|
495 |
> |
2006-01-13 11:33 gezelter |
496 |
> |
|
497 |
> |
* Makefile: [no log message] |
498 |
> |
|
499 |
> |
2006-01-13 11:26 gezelter |
500 |
> |
|
501 |
> |
* Makefile: testing to make sure GNU make is the make that was used |
502 |
> |
to build OOPSE |
503 |
> |
|
504 |
> |
2006-01-13 10:48 gezelter |
505 |
> |
|
506 |
> |
* configure, ac-tools/configure.in: changed compiler search order |
507 |
> |
|
508 |
> |
2006-01-12 19:09 chuckv |
509 |
> |
|
510 |
> |
* forceFields/SuttonChen.QSC.frc, forceFields/SuttonChen.frc, |
511 |
> |
samples/metals/Sutton-Chen/Au_bulk.in, |
512 |
> |
samples/metals/Sutton-Chen/Au_bulk_QSC.md, |
513 |
> |
samples/metals/Sutton-Chen/Au_bulk_SC.md: Changes in Sutton-Chen |
514 |
> |
units |
515 |
> |
|
516 |
> |
2006-01-12 16:16 gezelter |
517 |
> |
|
518 |
> |
* LICENSE, configure, src/applications/oopse/oopse.cpp: fixed some |
519 |
> |
version info and the copyright date |
520 |
> |
|
521 |
> |
2006-01-12 15:52 gezelter |
522 |
> |
|
523 |
> |
* src/config.h.in: added some missing checks for header files |
524 |
> |
(particularly zlib.h), used autoheader to help generate config.h.in |
525 |
> |
|
526 |
> |
2006-01-12 15:51 gezelter |
527 |
> |
|
528 |
> |
* configure, ac-tools/configure.in: added some missing checks for |
529 |
> |
header files (particularly zlib.h) |
530 |
> |
|
531 |
> |
2006-01-12 15:19 gezelter |
532 |
> |
|
533 |
> |
* make/Makefile.in: fixed a dependency problem for the Executable |
534 |
> |
builds |
535 |
> |
|
536 |
> |
2006-01-12 15:02 gezelter |
537 |
> |
|
538 |
> |
* samples/gbljtest/Makefile: Missing Makefile in this sample |
539 |
> |
directory |
540 |
> |
|
541 |
> |
2006-01-12 15:01 gezelter |
542 |
> |
|
543 |
> |
* make/Makefile.in, samples/Makefile.in, samples/cutoff/Makefile: |
544 |
> |
Old makefile.in no longer required |
545 |
> |
|
546 |
> |
2006-01-12 15:01 gezelter |
547 |
> |
|
548 |
> |
* forceFields/: Makefile, Makefile.in: All of the OpenBabel stuff |
549 |
> |
needs to be installed |
550 |
> |
|
551 |
> |
2006-01-12 14:56 chuckv |
552 |
> |
|
553 |
> |
* src/io/DumpWriter.cpp: Changed formating. |
554 |
> |
|
555 |
> |
2006-01-12 11:47 chrisfen |
556 |
> |
|
557 |
> |
* samples/water/tip4p/tp4.md, |
558 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
559 |
> |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
560 |
> |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
561 |
> |
src/brains/SimInfo.cpp: unifying function name in electrostatics |
562 |
> |
|
563 |
> |
2006-01-12 11:04 tim |
564 |
> |
|
565 |
> |
* samples/metals/: EAM/nanoparticle/Makefile, |
566 |
> |
EAM/nanorod/Au_nanoparticle.in, EAM/nanorod/Makefile, |
567 |
> |
Sutton-Chen/Makefile: fix make install problem for metals samples |
568 |
> |
|
569 |
> |
2006-01-12 10:22 tim |
570 |
> |
|
571 |
> |
* make/Makefile.in: remove samples/metals from install list. |
572 |
> |
|
573 |
> |
2006-01-12 09:31 tim |
574 |
> |
|
575 |
> |
* src/io/: ForceFieldOptions.cpp, Globals.cpp: filepp can not |
576 |
> |
handle multiple line macro, just convert multiple line macro into |
577 |
> |
single line macro. |
578 |
> |
|
579 |
> |
2006-01-11 23:13 chrisfen |
580 |
> |
|
581 |
> |
* src/: UseTheForce/DarkSide/electrostatic.F90, |
582 |
> |
UseTheForce/DarkSide/neighborLists.F90, io/Globals.cpp: Made some |
583 |
> |
changes to electrostatics for shifted-potential and shifted-force |
584 |
> |
with mono and multipoles |
585 |
> |
|
586 |
> |
2006-01-11 18:04 gezelter |
587 |
> |
|
588 |
> |
* src/config.h.in, src/UseTheForce/doForces_interface.h, |
589 |
> |
src/UseTheForce/DarkSide/atype_interface.h, |
590 |
> |
src/UseTheForce/DarkSide/eam_interface.h, |
591 |
> |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
592 |
> |
src/UseTheForce/DarkSide/fForceOptions_interface.h, |
593 |
> |
src/UseTheForce/DarkSide/gb_interface.h, |
594 |
> |
src/UseTheForce/DarkSide/lj_interface.h, |
595 |
> |
src/UseTheForce/DarkSide/shapes_interface.h, |
596 |
> |
src/UseTheForce/DarkSide/simParallel_interface.h, |
597 |
> |
src/UseTheForce/DarkSide/simulation_interface.h, |
598 |
> |
src/UseTheForce/DarkSide/sticky_interface.h, |
599 |
> |
src/UseTheForce/DarkSide/suttonchen_interface.h, |
600 |
> |
src/UseTheForce/DarkSide/switcheroo_interface.h, |
601 |
> |
src/mdParser/MDParser.g, src/profiling/mdProfile.cpp, |
602 |
> |
src/utils/fError.c, configure, make/Makefile.in: autoconf |
603 |
> |
modernization and cruft removal |
604 |
> |
|
605 |
> |
2006-01-11 18:04 gezelter |
606 |
> |
|
607 |
> |
* ac-tools/: aclocal.m4, configure.in, fortran90.m4: autoconf |
608 |
> |
modernization and cruft-removal |
609 |
> |
|
610 |
> |
2006-01-11 17:50 tim |
611 |
> |
|
612 |
> |
* src/types/: BendStamp.hpp, BondStamp.hpp, TorsionStamp.hpp: fix |
613 |
> |
some error messages |
614 |
> |
|
615 |
> |
2006-01-11 14:01 tim |
616 |
> |
|
617 |
> |
* src/: applications/staticProps/RhoZ.cpp, brains/SimCreator.cpp, |
618 |
> |
io/Globals.cpp, types/AtomStamp.cpp, types/BendStamp.hpp, |
619 |
> |
types/BondStamp.hpp, types/DataHolder.hpp, types/MoleculeStamp.cpp, |
620 |
> |
types/TorsionStamp.hpp, utils/OOPSEException.hpp, |
621 |
> |
utils/StringUtils.hpp: instead of printing to std::cout, throwing |
622 |
> |
an exception when error is found. |
623 |
> |
|
624 |
> |
2006-01-11 13:41 gezelter |
625 |
> |
|
626 |
> |
* src/types/: AtomStamp.hpp, MoleculeStamp.cpp: Fixed a spelling |
627 |
> |
error |
628 |
> |
|
629 |
> |
2006-01-10 17:55 chuckv |
630 |
> |
|
631 |
> |
* forceFields/SuttonChen.frc: Changed conversion factor. |
632 |
> |
|
633 |
> |
2006-01-10 16:14 chuckv |
634 |
> |
|
635 |
> |
* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
636 |
> |
src/UseTheForce/DarkSide/suttonchen.F90: Sutton and Chen should be |
637 |
> |
working now. |
638 |
> |
|
639 |
> |
2006-01-09 17:22 chuckv |
640 |
> |
|
641 |
> |
* src/UseTheForce/doForces.F90: Fixed SC bug with SIM_uses_SC |
642 |
> |
|
643 |
> |
2006-01-09 17:14 tim |
644 |
> |
|
645 |
> |
* src/applications/staticProps/: Makefile, RhoZ.cpp, RhoZ.hpp, |
646 |
> |
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
647 |
> |
StaticPropsCmd.h: fixing RhoZ |
648 |
> |
|
649 |
> |
2006-01-09 14:26 chuckv |
650 |
> |
|
651 |
> |
* forceFields/SuttonChen.frc, |
652 |
> |
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
653 |
> |
src/io/LennardJonesAtomTypesSectionParser.cpp, |
654 |
> |
src/io/SCAtomTypesSectionParser.cpp: Added energy scaling to |
655 |
> |
section parsers. |
656 |
> |
|
657 |
> |
2006-01-09 14:11 tim |
658 |
> |
|
659 |
> |
* src/: io/ForceFieldOptions.hpp, utils/StringUtils.cpp, |
660 |
> |
utils/StringUtils.hpp: replace isType<int> with isInteger |
661 |
> |
|
662 |
> |
2006-01-06 16:15 tim |
663 |
> |
|
664 |
> |
* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: remove extra |
665 |
> |
forceFieldOptions from SC_FF |
666 |
> |
|
667 |
> |
2006-01-06 15:27 chuckv |
668 |
> |
|
669 |
> |
* forceFields/SuttonChen.frc: Add force file. |
670 |
> |
|
671 |
> |
2005-12-31 17:42 chuckv |
672 |
> |
|
673 |
> |
* src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen no longer |
674 |
> |
segfaults or produces 0 potential, but rather produces Inf for the |
675 |
> |
potential. Progress.... |
676 |
> |
|
677 |
> |
2005-12-30 18:15 chuckv |
678 |
> |
|
679 |
> |
* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
680 |
> |
src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
681 |
> |
src/UseTheForce/DarkSide/suttonchen.F90, src/brains/SimInfo.cpp, |
682 |
> |
src/io/ForceFieldOptions.cpp, src/io/ForceFieldOptions.hpp: More |
683 |
> |
Sutton-Chen bug fixes. |
684 |
> |
|
685 |
> |
2005-12-30 16:25 tim |
686 |
> |
|
687 |
> |
* src/: UseTheForce/doForces.F90, brains/Thermo.cpp: Long range |
688 |
> |
potential return from fortran is already accumulated, it should not |
689 |
> |
be accumulated again; nGroupTypesCol is not initialized; |
690 |
> |
GroupMaxCutoffCol is not allocated; |
691 |
> |
|
692 |
> |
2005-12-30 10:32 tim |
693 |
> |
|
694 |
> |
* make/Makefile.in, src/brains/SimCreator.cpp: In order to compile |
695 |
> |
MPI version, we need to cast const char* to void* for |
696 |
> |
stringstream.str(); Previous Makefile use bjects of single version |
697 |
> |
to make the MPI library; |
698 |
> |
|
699 |
> |
2005-12-29 19:18 chuckv |
700 |
> |
|
701 |
> |
* make/Makefile.in, samples/metals/Makefile, |
702 |
> |
src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
703 |
> |
src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen bug fixes. |
704 |
> |
Almost there... |
705 |
> |
|
706 |
> |
2005-12-29 15:19 chuckv |
707 |
> |
|
708 |
> |
* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Changes in |
709 |
> |
forcefield. |
710 |
> |
|
711 |
> |
2005-12-29 15:07 chuckv |
712 |
> |
|
713 |
> |
* samples/metals/Sutton-Chen/: Au_bulk.in, Au_bulk_SC.md, Makefile, |
714 |
> |
metals.md: added files for sutton-chen |
715 |
> |
|
716 |
> |
2005-12-29 11:37 chuckv |
717 |
> |
|
718 |
> |
* samples/metals/EAM/nanorod/: Au_nanoparticle_FCC.md, Makefile, |
719 |
> |
metals.md: More cvs changing. |
720 |
> |
|
721 |
> |
2005-12-29 11:34 chuckv |
722 |
> |
|
723 |
> |
* samples/metals/Au_nanoparticle.in: More moving... |
724 |
> |
|
725 |
> |
2005-12-29 11:33 chuckv |
726 |
> |
|
727 |
> |
* samples/metals/EAM/nanoparticle/: |
728 |
> |
Au-Core-Ag-Shell_Nanoparticle.in, Au-Core-Ag-Shell_Nanoparticle.md, |
729 |
> |
Au_nanoparticle.in, Au_nanoparticle.md, Makefile, metals.md: More |
730 |
> |
changes to directory structure. |
731 |
> |
|
732 |
> |
2005-12-29 11:21 chuckv |
733 |
> |
|
734 |
> |
* samples/metals/EAM/: Au_bulk.in, Au_bulk_FBD.md, |
735 |
> |
Au_bulk_voter.md, Makefile, metals.md: More Directory changes... |
736 |
> |
|
737 |
> |
2005-12-29 11:17 chuckv |
738 |
> |
|
739 |
> |
* samples/metals/: Au-Core-Ag-Shell_Nanoparticle.in, |
740 |
> |
Au-Core-Ag-Shell_Nanoparticle.md, Au_bulk.in, Au_bulk_FBD.md, |
741 |
> |
Au_bulk_voter.md, Au_nanoparticle.md, metals.md: More changing of |
742 |
> |
directory structure |
743 |
> |
|
744 |
> |
2005-12-29 11:03 chuckv |
745 |
> |
|
746 |
> |
* src/: UseTheForce/DarkSide/fForceOptions_interface.F90, |
747 |
> |
brains/SimCreator.cpp: Fixed issue with symbol naming and added |
748 |
> |
call to set force options in SimCreator. |
749 |
> |
|
750 |
> |
2005-12-28 16:44 chuckv |
751 |
> |
|
752 |
> |
* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp: More |
753 |
> |
changes to forcefield options. |
754 |
> |
|
755 |
> |
2005-12-28 16:42 chuckv |
756 |
> |
|
757 |
> |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: Force options |
758 |
> |
passed to fortran. |
759 |
> |
|
760 |
> |
2005-12-23 18:04 chuckv |
761 |
> |
|
762 |
> |
* src/: UseTheForce/DarkSide/fForceOptions_interface.h, |
763 |
> |
io/ForceFieldOptions.cpp, io/ForceFieldOptions.hpp: Force option |
764 |
> |
changes. |
765 |
> |
|
766 |
> |
2005-12-16 16:52 tim |
767 |
> |
|
768 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
769 |
> |
src/config.h.in, src/UseTheForce/DarkSide/gb.F90, |
770 |
> |
src/openbabel/bitvec.cpp, src/openbabel/bondtyper.cpp, |
771 |
> |
src/openbabel/chains.cpp, src/openbabel/chiral.cpp, |
772 |
> |
src/openbabel/data.cpp, src/openbabel/fingerprint.cpp, |
773 |
> |
src/openbabel/fingerprintformat.cpp, src/openbabel/generic.cpp, |
774 |
> |
src/openbabel/gromos96format.hpp, src/openbabel/kekulize.cpp, |
775 |
> |
src/openbabel/matrix3x3.cpp, src/openbabel/mol.cpp, |
776 |
> |
src/openbabel/molchrg.cpp, src/openbabel/obatom.cpp, |
777 |
> |
src/openbabel/obbond.cpp, src/openbabel/oberror.cpp, |
778 |
> |
src/openbabel/oberror.hpp, src/openbabel/obmolecformat.hpp, |
779 |
> |
src/openbabel/obutil.cpp, src/openbabel/patty.cpp, |
780 |
> |
src/openbabel/pdbformat.cpp, src/openbabel/phmodel.cpp, |
781 |
> |
src/openbabel/povrayformat.hpp, src/openbabel/residue.cpp, |
782 |
> |
src/openbabel/ring.cpp, src/openbabel/rotor.cpp, |
783 |
> |
src/openbabel/smilesformat.cpp, src/openbabel/tinkerformat.hpp, |
784 |
> |
src/openbabel/typer.cpp, src/openbabel/xyzformat.cpp: changed |
785 |
> |
__FUNCTION__ to __func__ to match C99 standard, and then added an |
786 |
> |
autoconf test to check for __func__ usability. Changed some |
787 |
> |
default compile flags for the Sun architecture |
788 |
> |
|
789 |
> |
2005-12-16 14:01 gezelter |
790 |
> |
|
791 |
> |
* ac-tools/AC_CXX_HAVE_STL.m4: added the STL check |
792 |
> |
|
793 |
> |
2005-12-16 13:55 tim |
794 |
> |
|
795 |
> |
* src/utils/: CaseConversion.hpp, ParameterManager.hpp: make minor |
796 |
> |
change to build oopse under solaris |
797 |
> |
|
798 |
> |
2005-12-16 13:26 tim |
799 |
> |
|
800 |
> |
* src/: brains/SimCreator.cpp, io/Globals.cpp, |
801 |
> |
types/MoleculeStamp.cpp, utils/Predicate.hpp: the standard library |
802 |
> |
came with SUN compiler does not have a conforming std::use_facet, |
803 |
> |
define a macro to handle it. Adding exception handling to |
804 |
> |
SimCreator. |
805 |
> |
|
806 |
> |
2005-12-16 10:53 gezelter |
807 |
> |
|
808 |
> |
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
809 |
> |
GB-Ar-traditional.md, gb-ar.in: Removed one parasitic argon atom |
810 |
> |
which was living inside the GB particle. No alien-like ripping out |
811 |
> |
of the stomach was required. |
812 |
> |
|
813 |
> |
2005-12-15 21:57 tim |
814 |
> |
|
815 |
> |
* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
816 |
> |
MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
817 |
> |
MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: |
818 |
> |
replace grammar for numerical parsing |
819 |
> |
|
820 |
> |
2005-12-15 16:43 gezelter |
821 |
> |
|
822 |
> |
* src/UseTheForce/doForces.F90: fixed a cutoff bug |
823 |
> |
|
824 |
> |
2005-12-15 09:48 gezelter |
825 |
> |
|
826 |
> |
* src/antlr/: CharScanner.hpp, config.hpp: Removing compiler |
827 |
> |
dependencies and replacing them with real autoconf checks |
828 |
> |
|
829 |
> |
2005-12-15 09:47 gezelter |
830 |
> |
|
831 |
> |
* configure, ac-tools/AC_CXX_NAMESPACES.m4, ac-tools/AC_CXX_STD.m4, |
832 |
> |
ac-tools/configure.in, src/config.h.in: Adding checks for various |
833 |
> |
features used by ANTLR |
834 |
> |
|
835 |
> |
2005-12-14 13:02 tim |
836 |
> |
|
837 |
> |
* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
838 |
> |
MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
839 |
> |
MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: fix a |
840 |
> |
nasty negative integer parsing problem by refining the grammar |
841 |
> |
|
842 |
> |
2005-12-12 14:32 gezelter |
843 |
> |
|
844 |
> |
* src/: UseTheForce/doForces_interface.F90, |
845 |
> |
UseTheForce/doForces_interface.h, |
846 |
> |
UseTheForce/DarkSide/electrostatic.F90, |
847 |
> |
UseTheForce/DarkSide/electrostatic_interface.F90, |
848 |
> |
UseTheForce/DarkSide/electrostatic_interface.h, |
849 |
> |
brains/MoleculeCreator.cpp, brains/SimInfo.cpp, |
850 |
> |
math/ChebyshevPolynomials.hpp, openbabel/obconversion.hpp: made |
851 |
> |
some minor changes to allow compilation with the portland group |
852 |
> |
compilers |
853 |
> |
|
854 |
> |
2005-12-10 11:54 tim |
855 |
> |
|
856 |
> |
* src/: types/MoleculeStamp.cpp, utils/Tuple.hpp: fixed compilation |
857 |
> |
problem for icc7 |
858 |
> |
|
859 |
> |
2005-12-09 16:18 gezelter |
860 |
> |
|
861 |
> |
* src/utils/CaseConversion.hpp: added missing include |
862 |
> |
|
863 |
> |
2005-12-09 12:11 gezelter |
864 |
> |
|
865 |
> |
* configure, ac-tools/aclocal.m4: added some checks for pathscale |
866 |
> |
compiler |
867 |
> |
|
868 |
> |
2005-12-08 17:05 gezelter |
869 |
> |
|
870 |
> |
* src/io/ForceFieldOptions.cpp: added copyright |
871 |
> |
|
872 |
> |
2005-12-08 17:04 gezelter |
873 |
> |
|
874 |
> |
* src/UseTheForce/doForces.F90: added info printout |
875 |
> |
|
876 |
> |
2005-12-08 17:04 gezelter |
877 |
> |
|
878 |
> |
* configure, ac-tools/configure.in: added pathscale |
879 |
> |
|
880 |
> |
2005-12-08 10:38 chuckv |
881 |
> |
|
882 |
> |
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/DUFF.cpp, |
883 |
> |
UseTheForce/EAM_FF.cpp, UseTheForce/SC_FF.cpp, |
884 |
> |
UseTheForce/SHAPES_FF.cpp, io/BendTypesSectionParser.cpp, |
885 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
886 |
> |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
887 |
> |
io/ChargeAtomTypesSectionParser.hpp, |
888 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
889 |
> |
io/DirectionalAtomTypesSectionParser.hpp, |
890 |
> |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
891 |
> |
io/GayBerneAtomTypesSectionParser.cpp, |
892 |
> |
io/GayBerneAtomTypesSectionParser.hpp, |
893 |
> |
io/MultipoleAtomTypesSectionParser.cpp, |
894 |
> |
io/MultipoleAtomTypesSectionParser.hpp, |
895 |
> |
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
896 |
> |
io/ShapeAtomTypesSectionParser.cpp, |
897 |
> |
io/ShapeAtomTypesSectionParser.hpp, |
898 |
> |
io/StickyAtomTypesSectionParser.cpp, |
899 |
> |
io/StickyAtomTypesSectionParser.hpp, |
900 |
> |
io/StickyPowerAtomTypesSectionParser.cpp, |
901 |
> |
io/StickyPowerAtomTypesSectionParser.hpp, |
902 |
> |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp: |
903 |
> |
Wow thats alot o' files. Now passing forceFieldOptions to all of |
904 |
> |
the parsers. |
905 |
> |
|
906 |
> |
2005-12-07 18:10 chuckv |
907 |
> |
|
908 |
> |
* src/UseTheForce/: CLAYFF.cpp, DUFF.cpp, EAM_FF.cpp, EAM_FF.hpp, |
909 |
> |
SHAPES_FF.cpp, SHAPES_FF.hpp: This should really break things.... |
910 |
> |
Started adding support for ForceOptions to section parsers. |
911 |
> |
|
912 |
> |
2005-12-07 18:01 gezelter |
913 |
> |
|
914 |
> |
* src/UseTheForce/DarkSide/gb_interface.h: [no log message] |
915 |
> |
|
916 |
> |
2005-12-07 18:00 chuckv |
917 |
> |
|
918 |
> |
* src/io/: LennardJonesAtomTypesSectionParser.cpp, |
919 |
> |
LennardJonesAtomTypesSectionParser.hpp: Added forceOptions to |
920 |
> |
section parser |
921 |
> |
|
922 |
> |
2005-12-07 14:58 chuckv |
923 |
> |
|
924 |
> |
* src/UseTheForce/DarkSide/: LJ.F90, lj_interface.F90, |
925 |
> |
lj_interface.h, suttonchen.F90, suttonchen_interface.F90, |
926 |
> |
suttonchen_interface.h: Removed geometric distance mixing from |
927 |
> |
individual modules and now use force options to detemine what the |
928 |
> |
deal is. |
929 |
> |
|
930 |
> |
2005-12-07 14:46 chuckv |
931 |
> |
|
932 |
> |
* src/UseTheForce/: fForceOptions.h, DarkSide/fForceOptions.F90: |
933 |
> |
Further fixes for compiler issues. |
934 |
> |
|
935 |
> |
2005-12-07 14:44 chuckv |
936 |
> |
|
937 |
> |
* src/UseTheForce/fForceOptions.h: Fixed ifc public-private issue. |
938 |
> |
|
939 |
> |
2005-12-07 14:38 chuckv |
940 |
> |
|
941 |
> |
* src/UseTheForce/DarkSide/: Makefile, fForceOptions.F90, |
942 |
> |
fForceOptions_interface.F90, fForceOptions_interface.h: Added |
943 |
> |
support for fortran force options. |
944 |
> |
|
945 |
> |
2005-12-06 16:01 tim |
946 |
> |
|
947 |
> |
* src/types/MoleculeStamp.cpp: Fixed a bug in checkTorsion |
948 |
> |
|
949 |
> |
2005-12-06 14:26 chuckv |
950 |
> |
|
951 |
> |
* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: Changes to SC. |
952 |
> |
|
953 |
> |
2005-12-06 12:53 chuckv |
954 |
> |
|
955 |
> |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
956 |
> |
GeometryBuilder.hpp, nanorodBuilder.cpp: Changes to build twinned |
957 |
> |
crystal |
958 |
> |
|
959 |
> |
2005-12-06 12:52 chuckv |
960 |
> |
|
961 |
> |
* src/io/: DumpWriter.cpp, DumpWriter.hpp: Overloaded interface for |
962 |
> |
dumpwriter. |
963 |
> |
|
964 |
> |
2005-12-06 11:49 tim |
965 |
> |
|
966 |
> |
* samples/: alkane/alkanes.md, alkane/butane.md, argon/500.md, |
967 |
> |
argon/ar864.md, argon/argonNVT.md, argon/lj.md, |
968 |
> |
dipole/splitDipole.md, dipole/splitInWater.md, dipole/split_SSD.md, |
969 |
> |
dipole/twoSplitDipole.md, dipole/water.md, gbljtest/2gb.md, |
970 |
> |
gbljtest/gb.md, gbljtest/gb2lj1.md, gbljtest/gbRotRoundX.md, |
971 |
> |
gbljtest/gbRotRoundY.md, gbljtest/gbRotRoundZ.md, gbljtest/lj.md, |
972 |
> |
lipid/5x5.md, lipid/lipid.md, lipid/water.md, |
973 |
> |
metals/Au-Core-Ag-Shell_Nanoparticle.md, metals/Au_bulk_FBD.md, |
974 |
> |
metals/Au_bulk_voter.md, metals/Au_nanoparticle.md, |
975 |
> |
metals/metals.md, minimizer/ssdEM.md, minimizer/tip4p_two.md, |
976 |
> |
minimizer/water.md, shape/linear.md, |
977 |
> |
thermoIntegration/liquid/ssde.md, |
978 |
> |
thermoIntegration/liquid/water.md, thermoIntegration/solid/ssde.md, |
979 |
> |
thermoIntegration/solid/water.md, water/dimer/cl.md, |
980 |
> |
water/dimer/mix.md, water/dimer/mix2.md, water/dimer/ssd.md, |
981 |
> |
water/dimer/tap.md, water/dimer/two.md, water/dimer/water.md, |
982 |
> |
water/spce/spce.md, water/spce/water.md, water/ssd/ssd.md, |
983 |
> |
water/ssd/water.md, water/ssd-ion/ssdCl.md, water/ssd-ion/water.md, |
984 |
> |
water/ssde/ssde.md, water/ssde/water.md, water/ssdrf/ssdrf.md, |
985 |
> |
water/ssdrf/water.md, water/tap/tap.md, water/tap/water.md, |
986 |
> |
water/tip3p_ice/tp3.md, water/tip3p_ice/water.md, |
987 |
> |
water/tip4p/tp4.md, water/tip4p/water.md, zcons/water.md, |
988 |
> |
zcons/zconsFixed.md, zcons/zconsMoving.md: remove deprecated |
989 |
> |
keywords from samples |
990 |
> |
|
991 |
> |
2005-12-05 18:37 tim |
992 |
> |
|
993 |
> |
* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp, |
994 |
> |
Globals.cpp, Makefile: Fix parsing error in OptionSectionParser |
995 |
> |
|
996 |
> |
2005-12-05 17:23 gezelter |
997 |
> |
|
998 |
> |
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/CLAYFF.hpp, |
999 |
> |
UseTheForce/Makefile, brains/Register.cpp, |
1000 |
> |
io/ForceFieldOptions.hpp, io/OptionSectionParser.cpp: Adding |
1001 |
> |
handler for CLAY force field |
1002 |
> |
|
1003 |
> |
2005-12-05 16:45 chuckv |
1004 |
> |
|
1005 |
> |
* src/openbabel/: zipstream.hpp, zipstreamimpl.hpp: Fixed build bug |
1006 |
> |
in openbabel. |
1007 |
> |
|
1008 |
> |
2005-12-05 14:10 tim |
1009 |
> |
|
1010 |
> |
* src/types/MoleculeStamp.cpp: reformat error message |
1011 |
> |
|
1012 |
> |
2005-12-05 14:07 gezelter |
1013 |
> |
|
1014 |
> |
* forceFields/CLAYFF.frc: Adding .frc file for CLAYFF |
1015 |
> |
|
1016 |
> |
2005-12-05 13:23 tim |
1017 |
> |
|
1018 |
> |
* src/: types/AtomStamp.cpp, types/AtomStamp.hpp, |
1019 |
> |
types/BendStamp.hpp, types/MoleculeStamp.cpp, |
1020 |
> |
types/MoleculeStamp.hpp, types/TorsionStamp.hpp, utils/Tuple.hpp: |
1021 |
> |
adding more checking for topology |
1022 |
> |
|
1023 |
> |
2005-12-02 17:37 gezelter |
1024 |
> |
|
1025 |
> |
* src/antlr/TokenStreamRewriteEngine.cpp: Spurious semicolon |
1026 |
> |
removal |
1027 |
> |
|
1028 |
> |
2005-12-02 17:37 gezelter |
1029 |
> |
|
1030 |
> |
* src/config.h.in: We've made big changes. This isn't 2.0 anymore. |
1031 |
> |
|
1032 |
> |
2005-12-02 17:37 gezelter |
1033 |
> |
|
1034 |
> |
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
1035 |
> |
GB-Ar-traditional.md, cutoff_test.md, gb.md, lj.md, max.md, mix.md, |
1036 |
> |
traditional.md: removing deprecated nAtoms and nComponents lines |
1037 |
> |
|
1038 |
> |
2005-12-02 15:34 tim |
1039 |
> |
|
1040 |
> |
* src/selection/SelectionToken.cpp: adding SelectionToken.cpp |
1041 |
> |
|
1042 |
> |
2005-12-02 15:18 tim |
1043 |
> |
|
1044 |
> |
* src/types/: FragmentStamp.cpp, FragmentStamp.hpp: Adding |
1045 |
> |
FragmentStamp |
1046 |
> |
|
1047 |
> |
2005-12-02 15:11 gezelter |
1048 |
> |
|
1049 |
> |
* src/openbabel/: matrix3x3.cpp, matrix3x3.hpp: Errors are no |
1050 |
> |
longer thrown with consts (fixes compilation bug on the Mac). |
1051 |
> |
|
1052 |
> |
2005-12-02 15:10 gezelter |
1053 |
> |
|
1054 |
> |
* src/integrators/VelocityVerletIntegrator.cpp: Got rid of spurious |
1055 |
> |
printing out of timestep |
1056 |
> |
|
1057 |
> |
2005-12-02 15:10 gezelter |
1058 |
> |
|
1059 |
> |
* src/brains/ForceManager.cpp: Got rid of spurious printing out of |
1060 |
> |
junk |
1061 |
> |
|
1062 |
> |
2005-12-02 15:10 gezelter |
1063 |
> |
|
1064 |
> |
* make/Makefile.in: Change build process for libOOPSE.a so that the |
1065 |
> |
libraries aren't unpacked. libOOPSE.a is now made directly from |
1066 |
> |
the object files |
1067 |
> |
|
1068 |
> |
2005-12-02 15:09 gezelter |
1069 |
> |
|
1070 |
> |
* configure, ac-tools/configure.in: added check for egrep (grep -E) |
1071 |
> |
needed for new build of libOOPSE.a |
1072 |
> |
|
1073 |
> |
2005-12-02 13:43 tim |
1074 |
> |
|
1075 |
> |
* src/types/DataHolder.hpp: adding DataHolder |
1076 |
> |
|
1077 |
> |
2005-12-02 12:01 gezelter |
1078 |
> |
|
1079 |
> |
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
1080 |
> |
GB-Ar-traditional.md, gb-ar.in, gb.md: Added Gay-Berne / Argon test |
1081 |
> |
case for the cutoff policies |
1082 |
> |
|
1083 |
> |
2005-12-02 10:38 tim |
1084 |
> |
|
1085 |
> |
* make/Makefile.in: update Makefile |
1086 |
> |
|
1087 |
> |
2005-12-02 10:38 tim |
1088 |
> |
|
1089 |
> |
* src/: antlr/ANTLRException.hpp, antlr/ANTLRUtil.cpp, |
1090 |
> |
antlr/ANTLRUtil.hpp, antlr/AST.hpp, antlr/ASTArray.hpp, |
1091 |
> |
antlr/ASTFactory.cpp, antlr/ASTFactory.hpp, antlr/ASTNULLType.cpp, |
1092 |
> |
antlr/ASTNULLType.hpp, antlr/ASTPair.hpp, antlr/ASTRefCount.cpp, |
1093 |
> |
antlr/ASTRefCount.hpp, antlr/BaseAST.cpp, antlr/BaseAST.hpp, |
1094 |
> |
antlr/BitSet.cpp, antlr/BitSet.hpp, antlr/CharBuffer.cpp, |
1095 |
> |
antlr/CharBuffer.hpp, antlr/CharInputBuffer.hpp, |
1096 |
> |
antlr/CharScanner.cpp, antlr/CharScanner.hpp, |
1097 |
> |
antlr/CharStreamException.hpp, antlr/CharStreamIOException.hpp, |
1098 |
> |
antlr/CircularQueue.hpp, antlr/CommonAST.cpp, antlr/CommonAST.hpp, |
1099 |
> |
antlr/CommonASTWithHiddenTokens.cpp, |
1100 |
> |
antlr/CommonASTWithHiddenTokens.hpp, |
1101 |
> |
antlr/CommonHiddenStreamToken.cpp, |
1102 |
> |
antlr/CommonHiddenStreamToken.hpp, antlr/CommonToken.cpp, |
1103 |
> |
antlr/CommonToken.hpp, antlr/IOException.hpp, |
1104 |
> |
antlr/InputBuffer.cpp, antlr/InputBuffer.hpp, antlr/LLkParser.cpp, |
1105 |
> |
antlr/LLkParser.hpp, antlr/LexerSharedInputState.hpp, |
1106 |
> |
antlr/Makefile, antlr/MismatchedCharException.cpp, |
1107 |
> |
antlr/MismatchedCharException.hpp, |
1108 |
> |
antlr/MismatchedTokenException.cpp, |
1109 |
> |
antlr/MismatchedTokenException.hpp, antlr/NoViableAltException.cpp, |
1110 |
> |
antlr/NoViableAltException.hpp, |
1111 |
> |
antlr/NoViableAltForCharException.cpp, |
1112 |
> |
antlr/NoViableAltForCharException.hpp, antlr/Parser.cpp, |
1113 |
> |
antlr/Parser.hpp, antlr/ParserSharedInputState.hpp, |
1114 |
> |
antlr/RecognitionException.cpp, antlr/RecognitionException.hpp, |
1115 |
> |
antlr/RefCount.hpp, antlr/SemanticException.hpp, antlr/String.cpp, |
1116 |
> |
antlr/String.hpp, antlr/Token.cpp, antlr/Token.hpp, |
1117 |
> |
antlr/TokenBuffer.cpp, antlr/TokenBuffer.hpp, |
1118 |
> |
antlr/TokenRefCount.cpp, antlr/TokenRefCount.hpp, |
1119 |
> |
antlr/TokenStream.hpp, antlr/TokenStreamBasicFilter.cpp, |
1120 |
> |
antlr/TokenStreamBasicFilter.hpp, antlr/TokenStreamException.hpp, |
1121 |
> |
antlr/TokenStreamHiddenTokenFilter.cpp, |
1122 |
> |
antlr/TokenStreamHiddenTokenFilter.hpp, |
1123 |
> |
antlr/TokenStreamIOException.hpp, |
1124 |
> |
antlr/TokenStreamRecognitionException.hpp, |
1125 |
> |
antlr/TokenStreamRetryException.hpp, |
1126 |
> |
antlr/TokenStreamRewriteEngine.cpp, |
1127 |
> |
antlr/TokenStreamRewriteEngine.hpp, antlr/TokenStreamSelector.cpp, |
1128 |
> |
antlr/TokenStreamSelector.hpp, antlr/TokenWithIndex.hpp, |
1129 |
> |
antlr/TreeParser.cpp, antlr/TreeParser.hpp, |
1130 |
> |
antlr/TreeParserSharedInputState.hpp, antlr/config.hpp, |
1131 |
> |
applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
1132 |
> |
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
1133 |
> |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
1134 |
> |
constraints/ZconstraintForceManager.cpp, |
1135 |
> |
integrators/VelocityVerletIntegrator.cpp, io/BASS_interface.cpp, |
1136 |
> |
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
1137 |
> |
io/BASSlex.l, io/BASSyacc.y, io/Globals.cpp, io/Globals.hpp, |
1138 |
> |
io/LinkedAssign.cpp, io/LinkedAssign.hpp, io/Makefile, |
1139 |
> |
io/ZConsReader.cpp, io/interface.c, io/make_nodes.c, |
1140 |
> |
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, |
1141 |
> |
io/parse_interface.h, io/parse_me.h, io/parse_tree.c, |
1142 |
> |
io/parse_tree.h, mdParser/FilenameObserver.cpp, |
1143 |
> |
mdParser/FilenameObserver.hpp, mdParser/MDLexer.cpp, |
1144 |
> |
mdParser/MDLexer.hpp, mdParser/MDParser.cpp, mdParser/MDParser.g, |
1145 |
> |
mdParser/MDParser.hpp, mdParser/MDTokenTypes.hpp, |
1146 |
> |
mdParser/MDTreeParser.cpp, mdParser/MDTreeParser.g, |
1147 |
> |
mdParser/MDTreeParser.hpp, mdParser/MDTreeParserTokenTypes.hpp, |
1148 |
> |
mdParser/Makefile, mdParser/SimplePreprocessor.hpp, |
1149 |
> |
openbabel/obconversion.cpp, openbabel/oopseformat.cpp, |
1150 |
> |
openbabel/xyzformat.cpp, primitives/RigidBody.cpp, |
1151 |
> |
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
1152 |
> |
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
1153 |
> |
selection/Makefile, selection/NameFinder.cpp, |
1154 |
> |
selection/NameFinder.hpp, selection/SelectionCompiler.hpp, |
1155 |
> |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
1156 |
> |
selection/SelectionManager.hpp, selection/SelectionToken.hpp, |
1157 |
> |
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.hpp, |
1158 |
> |
types/AtomStamp.cpp, types/AtomStamp.hpp, types/BendStamp.cpp, |
1159 |
> |
types/BendStamp.hpp, types/BondStamp.cpp, types/BondStamp.hpp, |
1160 |
> |
types/Component.cpp, types/Component.hpp, |
1161 |
> |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
1162 |
> |
types/MakeStamps.cpp, types/MakeStamps.hpp, types/Makefile, |
1163 |
> |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
1164 |
> |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
1165 |
> |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
1166 |
> |
types/ZconStamp.cpp, types/ZconStamp.hpp, types/ZconsStamp.cpp, |
1167 |
> |
types/ZconsStamp.hpp, utils/BitSet.cpp, utils/BitSet.hpp, |
1168 |
> |
utils/Makefile.in, utils/MoLocator.cpp, utils/OOPSEBitSet.cpp, |
1169 |
> |
utils/OOPSEBitSet.hpp, utils/StringTokenizer.cpp, |
1170 |
> |
utils/StringTokenizer.hpp, visitors/ZconsVisitor.cpp: End of the |
1171 |
> |
Link --> List Return of the Oject-Oriented replace yacc/lex parser |
1172 |
> |
with antlr parser |
1173 |
> |
|
1174 |
> |
2005-11-30 16:00 chuckv |
1175 |
> |
|
1176 |
> |
* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Code to |
1177 |
> |
calculate rho(Z) to calculate density profiles for water slabs. |
1178 |
> |
|
1179 |
> |
2005-11-29 17:54 chuckv |
1180 |
> |
|
1181 |
> |
* configure, ac-tools/configure.in: added checks for some functions |
1182 |
> |
to configure script |
1183 |
> |
|
1184 |
> |
2005-11-22 20:05 chuckv |
1185 |
> |
|
1186 |
> |
* src/openbabel/: Makefile, atom.cpp, bond.cpp, obatom.cpp, |
1187 |
> |
obbond.cpp: Changed file names that conflict w/ oopse file name |
1188 |
> |
object files. |
1189 |
> |
|
1190 |
> |
2005-11-21 17:59 gezelter |
1191 |
> |
|
1192 |
> |
* src/utils/residentMem.c: compilation bug |
1193 |
> |
|
1194 |
> |
2005-11-21 17:59 gezelter |
1195 |
> |
|
1196 |
> |
* src/io/: ForceFieldOptions.hpp, Globals.cpp: parsing by filepp |
1197 |
> |
|
1198 |
> |
2005-11-21 17:59 gezelter |
1199 |
> |
|
1200 |
> |
* src/brains/: SimInfo.cpp, SimInfo.hpp: Cutoff Mixing fixes |
1201 |
> |
|
1202 |
> |
2005-11-21 17:59 gezelter |
1203 |
> |
|
1204 |
> |
* src/applications/atom2mdin/: Makefile, atom2mdin.cpp: compilation |
1205 |
> |
issue |
1206 |
> |
|
1207 |
> |
2005-11-21 17:58 gezelter |
1208 |
> |
|
1209 |
> |
* src/UseTheForce/: ForceField.hpp, Makefile, doForces.F90, |
1210 |
> |
doForces_interface.F90, doForces_interface.h, fForceOptions.h, |
1211 |
> |
notifyCutoffs.F90, notifyCutoffs_interface.F90, |
1212 |
> |
notifyCutoffs_interface.h, DarkSide/LJ.F90, |
1213 |
> |
DarkSide/electrostatic.F90, DarkSide/gb.F90, |
1214 |
> |
DarkSide/suttonchen.F90: Cutoff mixing fixes have been made. |
1215 |
> |
|
1216 |
> |
2005-11-21 11:22 tim |
1217 |
> |
|
1218 |
> |
* src/io/ParamConstraint.cpp: Adding ParamConstraint.cpp |
1219 |
> |
|
1220 |
> |
2005-11-21 09:59 tim |
1221 |
> |
|
1222 |
> |
* forceFields/: SMARTS_InteLigand_051110.txt, aromatic.txt, |
1223 |
> |
atomtyp.txt, bondtyp.txt, element.txt, extable.txt, |
1224 |
> |
isotope-small.txt, isotope.txt, patterns.txt, phmodel.txt, |
1225 |
> |
resdata.txt, torlib.txt, types.txt: adding openbabel data files |
1226 |
> |
|
1227 |
> |
2005-11-18 15:17 tim |
1228 |
> |
|
1229 |
> |
* src/: applications/atom2mdin/Makefile, openbabel/oopseformat.cpp: |
1230 |
> |
adding support for soft linking |
1231 |
> |
|
1232 |
> |
2005-11-18 15:17 tim |
1233 |
> |
|
1234 |
> |
* make/Makefile.in: Adding support for soft linking |
1235 |
> |
|
1236 |
> |
2005-11-18 12:50 gezelter |
1237 |
> |
|
1238 |
> |
* make/Makefile.in: Adding linking stuff |
1239 |
> |
|
1240 |
> |
2005-11-18 11:38 tim |
1241 |
> |
|
1242 |
> |
* make/Makefile.in, src/applications/atom2mdin/Makefile, |
1243 |
> |
src/applications/atom2mdin/atom2mdin.cpp, |
1244 |
> |
src/applications/mdinConverter/Makefile, |
1245 |
> |
src/applications/mdinConverter/mdinConverter.cpp, |
1246 |
> |
src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp: |
1247 |
> |
rename mdinConverter to atom2mdin |
1248 |
> |
|
1249 |
> |
2005-11-17 15:44 gezelter |
1250 |
> |
|
1251 |
> |
* src/openbabel/obconversion.cpp: fixed a bug |
1252 |
> |
|
1253 |
> |
2005-11-17 15:39 gezelter |
1254 |
> |
|
1255 |
> |
* configure: Adding some config checks for OpenBabel codes we are |
1256 |
> |
using |
1257 |
> |
|
1258 |
> |
2005-11-17 15:39 gezelter |
1259 |
> |
|
1260 |
> |
* ac-tools/configure.in: Adding some checks for OpenBabel code |
1261 |
> |
|
1262 |
> |
2005-11-17 15:39 gezelter |
1263 |
> |
|
1264 |
> |
* src/config.h.in: Unifying config.h stuff from OOPSE and OpenBabel |
1265 |
> |
|
1266 |
> |
2005-11-17 15:38 gezelter |
1267 |
> |
|
1268 |
> |
* src/openbabel/: babelconfig.hpp, base.cpp, base.hpp, bitvec.hpp, |
1269 |
> |
bondtyper.cpp, config.h.in, config.hpp, data.cpp, data.hpp, |
1270 |
> |
fingerprint.cpp, generic.hpp, grid.hpp, matrix.hpp, mol.hpp, |
1271 |
> |
obconversion.hpp, oberror.cpp, oberror.hpp, obutil.cpp, obutil.hpp, |
1272 |
> |
patty.cpp, pdbformat.hpp, phmodel.cpp, povrayformat.hpp, |
1273 |
> |
residue.cpp, rotor.cpp, smilesformat.cpp, tokenst.cpp, typer.cpp: |
1274 |
> |
Unifying config.h stuff and making sure the OpenBabel codes can |
1275 |
> |
find our default (and environment variable) Force Field |
1276 |
> |
directories. |
1277 |
> |
|
1278 |
> |
2005-11-17 13:35 tim |
1279 |
> |
|
1280 |
> |
* src/io/ForceFieldOptions.hpp: adding ForceFieldOptions |
1281 |
> |
|
1282 |
> |
2005-11-16 18:10 tim |
1283 |
> |
|
1284 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
1285 |
> |
brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp, |
1286 |
> |
brains/ForceManager.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp, |
1287 |
> |
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
1288 |
> |
io/Globals.hpp, io/Makefile, io/OptionSectionParser.cpp, |
1289 |
> |
io/OptionSectionParser.hpp, io/ParamConstraint.hpp, |
1290 |
> |
io/SectionParser.hpp, io/SectionParserManager.cpp, |
1291 |
> |
io/TorsionTypesSectionParser.cpp, math/ChebyshevPolynomials.hpp, |
1292 |
> |
math/Makefile, math/Polynomial.hpp, primitives/Bend.cpp, |
1293 |
> |
primitives/Bend.hpp, primitives/GhostBend.cpp, |
1294 |
> |
primitives/GhostBend.hpp, primitives/GhostTorsion.cpp, |
1295 |
> |
primitives/GhostTorsion.hpp, primitives/Torsion.cpp, |
1296 |
> |
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
1297 |
> |
primitives/UreyBradleyBend.hpp, types/CharmmTorsionType.cpp, |
1298 |
> |
types/CharmmTorsionType.hpp, types/CubicTorsionType.hpp, |
1299 |
> |
types/PolynomialTorsionType.hpp, types/QuarticTorsionType.hpp, |
1300 |
> |
types/TorsionType.hpp, utils/StringUtils.hpp: OptionSectionParser |
1301 |
> |
get compiled |
1302 |
> |
|
1303 |
> |
2005-11-16 16:37 chuckv |
1304 |
> |
|
1305 |
> |
* src/: io/Globals.cpp, io/Globals.hpp, io/OptionSectionParser.cpp, |
1306 |
> |
io/OptionSectionParser.hpp, io/SCAtomTypesSectionParser.cpp, |
1307 |
> |
UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField |
1308 |
> |
optional parameters.... |
1309 |
> |
|
1310 |
> |
2005-11-16 16:24 tim |
1311 |
> |
|
1312 |
> |
* src/applications/mdinConverter/: Makefile, mdinConverter.cpp: |
1313 |
> |
adding mdinConverter |
1314 |
> |
|
1315 |
> |
2005-11-16 16:22 tim |
1316 |
> |
|
1317 |
> |
* src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp, |
1318 |
> |
fingerprint.hpp, fingerprintformat.cpp, fingerprintformat.hpp, |
1319 |
> |
gromos96format.cpp, gromos96format.hpp, oopseformat.cpp, |
1320 |
> |
oopseformat.hpp, pdbformat.cpp, pdbformat.hpp, povrayformat.cpp, |
1321 |
> |
povrayformat.hpp, smilesformat.cpp, smilesformat.hpp, |
1322 |
> |
tinkerformat.cpp, tinkerformat.hpp, xyzformat.cpp, xyzformat.hpp: |
1323 |
> |
adding more readers/writers |
1324 |
> |
|
1325 |
> |
2005-11-16 16:20 tim |
1326 |
> |
|
1327 |
> |
* make/Makefile.in: adding openbabel |
1328 |
> |
|
1329 |
> |
2005-11-16 16:20 tim |
1330 |
> |
|
1331 |
> |
* src/brains/: Register.cpp, Register.hpp: register openbabel |
1332 |
> |
readers/writers |
1333 |
> |
|
1334 |
> |
2005-11-16 14:57 chrisfen |
1335 |
> |
|
1336 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: included shifted |
1337 |
> |
potential self term |
1338 |
> |
|
1339 |
> |
2005-11-16 14:57 chrisfen |
1340 |
> |
|
1341 |
> |
* samples/water/spce/spce.md: just some parameters |
1342 |
> |
|
1343 |
> |
2005-11-16 14:42 tim |
1344 |
> |
|
1345 |
> |
* src/openbabel/: Makefile, aromatic.hpp, atom.cpp, atomtyp.hpp, |
1346 |
> |
babelconfig.hpp, base.cpp, base.hpp, bitvec.cpp, bitvec.hpp, |
1347 |
> |
bond.cpp, bondtyp.hpp, bondtyper.cpp, bondtyper.hpp, chains.cpp, |
1348 |
> |
chains.hpp, chiral.cpp, chiral.hpp, config.h.in, config.hpp, |
1349 |
> |
data.cpp, data.hpp, element.hpp, extable.hpp, fingerprint.cpp, |
1350 |
> |
fingerprint.hpp, generic.cpp, generic.hpp, grid.cpp, grid.hpp, |
1351 |
> |
isotope.hpp, kekulize.cpp, matrix.cpp, matrix.hpp, matrix3x3.cpp, |
1352 |
> |
matrix3x3.hpp, mol.cpp, mol.hpp, molchrg.cpp, molchrg.hpp, |
1353 |
> |
obconversion.cpp, obconversion.hpp, obconversion.lo, oberror.cpp, |
1354 |
> |
oberror.hpp, obiter.cpp, obiter.hpp, obmolecformat.hpp, obutil.cpp, |
1355 |
> |
obutil.hpp, oopseformat.cpp, parsmart.cpp, parsmart.hpp, patty.cpp, |
1356 |
> |
patty.hpp, pdbformat.cpp, phmodel.cpp, phmodel.hpp, |
1357 |
> |
phmodeldata.hpp, rand.cpp, reaction.hpp, resdata.hpp, residue.cpp, |
1358 |
> |
ring.cpp, ring.hpp, rotamer.cpp, rotamer.hpp, rotor.cpp, rotor.hpp, |
1359 |
> |
snprintf.c, snprintf.h, strncasecmp.c, tinkerformat.cpp, |
1360 |
> |
tokenst.cpp, torlib.hpp, transform.cpp, typer.cpp, typer.hpp, |
1361 |
> |
types.hpp, vector3.cpp, vector3.hpp, xyzformat.cpp, zipstream.hpp, |
1362 |
> |
zipstreamimpl.hpp: adding openbabel |
1363 |
> |
|
1364 |
> |
2005-11-15 14:42 chrisfen |
1365 |
> |
|
1366 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: removed unnecessary |
1367 |
> |
commented code |
1368 |
> |
|
1369 |
> |
2005-11-15 14:04 chrisfen |
1370 |
> |
|
1371 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: cleaned up the |
1372 |
> |
charge-charge interactions a bit... |
1373 |
> |
|
1374 |
> |
2005-11-15 14:03 chrisfen |
1375 |
> |
|
1376 |
> |
* samples/water/spce/: spce.md, water.md: just playing |
1377 |
> |
|
1378 |
> |
2005-11-15 11:38 chrisfen |
1379 |
> |
|
1380 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: fixed a bug in the |
1381 |
> |
shifted_potential case |
1382 |
> |
|
1383 |
> |
2005-11-15 11:37 chrisfen |
1384 |
> |
|
1385 |
> |
* samples/: argon/500.md, water/spce/spce.md, water/spce/water.md: |
1386 |
> |
just playing around - we need to refresh all the samples sometime |
1387 |
> |
soon... |
1388 |
> |
|
1389 |
> |
2005-11-15 11:18 chuckv |
1390 |
> |
|
1391 |
> |
* src/UseTheForce/: SC_FF.cpp, DarkSide/suttonchen.F90: Made |
1392 |
> |
preforce calc public in suttonchen. |
1393 |
> |
|
1394 |
> |
2005-11-15 11:05 chuckv |
1395 |
> |
|
1396 |
> |
* src/brains/: SimInfo.cpp, fSimulation.h: Sutton-Chen added to |
1397 |
> |
SimInfo |
1398 |
> |
|
1399 |
> |
2005-11-15 11:01 chuckv |
1400 |
> |
|
1401 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/fInteractionMap.h, |
1402 |
> |
DarkSide/simulation.F90: Added Sutton-Chen to force loop... |
1403 |
> |
|
1404 |
> |
2005-11-15 10:34 chuckv |
1405 |
> |
|
1406 |
> |
* forceFields/Makefile: Added sutton-chen to makefile. |
1407 |
> |
|
1408 |
> |
2005-11-14 17:20 chuckv |
1409 |
> |
|
1410 |
> |
* src/UseTheForce/DarkSide/: suttonchen.F90, |
1411 |
> |
suttonchen_interface.h: Build Fixes for sutton-chen. |
1412 |
> |
|
1413 |
> |
2005-11-14 17:03 chuckv |
1414 |
> |
|
1415 |
> |
* src/io/Makefile: Missed makefile for sutton-chen. |
1416 |
> |
|
1417 |
> |
2005-11-14 17:03 chuckv |
1418 |
> |
|
1419 |
> |
* src/UseTheForce/: Makefile, DarkSide/Makefile, |
1420 |
> |
DarkSide/atype.F90, DarkSide/atype_interface.F90: Sutton-chen stuff |
1421 |
> |
|
1422 |
> |
2005-11-14 16:29 chuckv |
1423 |
> |
|
1424 |
> |
* src/: UseTheForce/SC_FF.cpp, UseTheForce/SC_FF.hpp, |
1425 |
> |
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
1426 |
> |
UseTheForce/DarkSide/suttonchen.F90, |
1427 |
> |
UseTheForce/DarkSide/suttonchen_interface.F90, |
1428 |
> |
UseTheForce/DarkSide/suttonchen_interface.h, brains/Register.cpp, |
1429 |
> |
brains/fSimulation.h, types/AtomType.cpp, types/AtomType.hpp, |
1430 |
> |
types/AtomTypeProperties.h: Sutton-Chen almost done. Just need to |
1431 |
> |
fix do_forces to use Sutton-Chen. |
1432 |
> |
|
1433 |
> |
2005-11-11 12:21 chrisfen |
1434 |
> |
|
1435 |
> |
* src/UseTheForce/DarkSide/: fSwitchingFunctionType.h, |
1436 |
> |
switcheroo_interface.F90, switcheroo_interface.h: Forgot to add |
1437 |
> |
some files |
1438 |
> |
|
1439 |
> |
2005-11-11 10:22 chrisfen |
1440 |
> |
|
1441 |
> |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/DumpWriter.cpp, |
1442 |
> |
io/Globals.cpp, io/Globals.hpp: added in a 5th order polynomial |
1443 |
> |
switching function option |
1444 |
> |
|
1445 |
> |
2005-11-11 10:21 chrisfen |
1446 |
> |
|
1447 |
> |
* src/UseTheForce/DarkSide/: Makefile, switcheroo.F90: added in a |
1448 |
> |
5th order polynomial switching function |
1449 |
> |
|
1450 |
> |
2005-11-11 10:21 chrisfen |
1451 |
> |
|
1452 |
> |
* samples/water/ssd/ssd.md: playing with switching functions again |
1453 |
> |
|
1454 |
> |
2005-11-11 10:21 chrisfen |
1455 |
> |
|
1456 |
> |
* samples/argon/500.md: playing with switching functions |
1457 |
> |
|
1458 |
> |
2005-11-08 19:11 chuckv |
1459 |
> |
|
1460 |
> |
* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Added force |
1461 |
> |
files for Sutton-Chen and Quantum Sutton-Chen |
1462 |
> |
|
1463 |
> |
2005-11-08 08:32 chrisfen |
1464 |
> |
|
1465 |
> |
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp, |
1466 |
> |
DumpWriter.hpp, Globals.cpp, Globals.hpp: Added a keyword and |
1467 |
> |
ability to output forces and torques |
1468 |
> |
|
1469 |
> |
2005-11-08 08:32 chrisfen |
1470 |
> |
|
1471 |
> |
* src/brains/: SimInfo.cpp, fSimulation.h: Added a keyword for |
1472 |
> |
output of forces and torques |
1473 |
> |
|
1474 |
> |
2005-11-08 08:31 chrisfen |
1475 |
> |
|
1476 |
> |
* src/UseTheForce/DarkSide/: electrostatic.F90, simulation.F90: |
1477 |
> |
Working on shifted_force... |
1478 |
> |
|
1479 |
> |
2005-11-08 08:31 chrisfen |
1480 |
> |
|
1481 |
> |
* samples/water/: spce/spce.md, ssde/ssde.md: Just testing... |
1482 |
> |
|
1483 |
> |
2005-11-03 18:22 chrisfen |
1484 |
> |
|
1485 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: removed a poorly |
1486 |
> |
commented section |
1487 |
> |
|
1488 |
> |
2005-11-03 18:12 chrisfen |
1489 |
> |
|
1490 |
> |
* src/: UseTheForce/DarkSide/electrostatic.F90, |
1491 |
> |
UseTheForce/DarkSide/fElectrostaticScreeningMethod.h, |
1492 |
> |
UseTheForce/DarkSide/fScreeningMethod.h, brains/SimInfo.cpp, |
1493 |
> |
io/Globals.cpp, io/Globals.hpp: improvements in shifted-force |
1494 |
> |
|
1495 |
> |
2005-11-03 18:11 chrisfen |
1496 |
> |
|
1497 |
> |
* samples/water/spce/spce.md: mmm... damped shifted force... |
1498 |
> |
|
1499 |
> |
2005-11-03 18:06 chuckv |
1500 |
> |
|
1501 |
> |
* src/UseTheForce/DarkSide/suttonchen.F90: More work on SC. |
1502 |
> |
|
1503 |
> |
2005-11-02 18:50 chuckv |
1504 |
> |
|
1505 |
> |
* src/UseTheForce/DarkSide/suttonchen.F90: More work on suttonchen. |
1506 |
> |
|
1507 |
> |
2005-11-02 16:01 chrisfen |
1508 |
> |
|
1509 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
1510 |
> |
removed some test code |
1511 |
> |
|
1512 |
> |
2005-11-02 15:45 chrisfen |
1513 |
> |
|
1514 |
> |
* src/UseTheForce/DarkSide/fScreeningMethod.h: forgot to add the |
1515 |
> |
screening method header |
1516 |
> |
|
1517 |
> |
2005-11-02 15:36 chrisfen |
1518 |
> |
|
1519 |
> |
* src/brains/SimInfo.cpp: again, changing how we deal with |
1520 |
> |
summation and screening methods |
1521 |
> |
|
1522 |
> |
2005-11-02 15:36 chrisfen |
1523 |
> |
|
1524 |
> |
* src/: UseTheForce/DarkSide/electrostatic.F90, |
1525 |
> |
UseTheForce/DarkSide/electrostatic_interface.F90, |
1526 |
> |
UseTheForce/DarkSide/electrostatic_interface.h, |
1527 |
> |
UseTheForce/DarkSide/fElectrostaticSummationMethod.h, |
1528 |
> |
io/Globals.cpp, io/Globals.hpp: changing how we deal with summation |
1529 |
> |
and screening methods |
1530 |
> |
|
1531 |
> |
2005-11-02 15:35 chrisfen |
1532 |
> |
|
1533 |
> |
* src/UseTheForce/doForces.F90: debug stuff for rf removed |
1534 |
> |
|
1535 |
> |
2005-11-01 18:32 chuckv |
1536 |
> |
|
1537 |
> |
* src/: UseTheForce/DarkSide/atype.F90, |
1538 |
> |
UseTheForce/DarkSide/atype_interface.F90, |
1539 |
> |
UseTheForce/DarkSide/suttonchen.F90, types/AtomType.cpp, |
1540 |
> |
types/AtomTypeProperties.h: Added suppport to atypes for MEAM and |
1541 |
> |
sutton-chen |
1542 |
> |
|
1543 |
> |
2005-11-01 14:24 chrisfen |
1544 |
> |
|
1545 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
1546 |
> |
removed some testing code... |
1547 |
> |
|
1548 |
> |
2005-11-01 14:14 chrisfen |
1549 |
> |
|
1550 |
> |
* src/: brains/Register.cpp, brains/SimInfo.cpp, |
1551 |
> |
brains/fSimulation.h, integrators/IntegratorFactory.hpp, |
1552 |
> |
io/Globals.cpp: fixed a capitalization problem with NPT integrator |
1553 |
> |
initialization |
1554 |
> |
|
1555 |
> |
2005-11-01 14:13 chrisfen |
1556 |
> |
|
1557 |
> |
* src/applications/oopse/oopse.cpp: nothing |
1558 |
> |
|
1559 |
> |
2005-11-01 14:09 chrisfen |
1560 |
> |
|
1561 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
1562 |
> |
DarkSide/simulation.F90: still fixing up wolf... |
1563 |
> |
|
1564 |
> |
2005-11-01 13:29 chuckv |
1565 |
> |
|
1566 |
> |
* src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In |
1567 |
> |
process of adding sutton-chen forcefield. |
1568 |
> |
|
1569 |
> |
2005-10-26 18:32 chrisfen |
1570 |
> |
|
1571 |
> |
* src/brains/SimInfo.cpp: changed the default switching radius to |
1572 |
> |
85% of rcut |
1573 |
> |
|
1574 |
> |
2005-10-26 18:31 chrisfen |
1575 |
> |
|
1576 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks |
1577 |
> |
to be working now - for charges and dipoles alike |
1578 |
> |
|
1579 |
> |
2005-10-26 18:31 chrisfen |
1580 |
> |
|
1581 |
> |
* src/UseTheForce/doForces.F90: reaction field looks to be working |
1582 |
> |
now |
1583 |
> |
|
1584 |
> |
2005-10-26 18:30 chrisfen |
1585 |
> |
|
1586 |
> |
* samples/water/ssdrf/water.md: added a test molecule |
1587 |
> |
|
1588 |
> |
2005-10-26 18:30 chrisfen |
1589 |
> |
|
1590 |
> |
* forceFields/DUFF2.frc: added a test atom type |
1591 |
> |
|
1592 |
> |
2005-10-24 09:06 chrisfen |
1593 |
> |
|
1594 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole |
1595 |
> |
reaction field - don't know if it works... |
1596 |
> |
|
1597 |
> |
2005-10-23 16:08 chrisfen |
1598 |
> |
|
1599 |
> |
* src/: UseTheForce/doForces.F90, |
1600 |
> |
UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp: |
1601 |
> |
streamlined reaction field for dipoles (now a good bit faster) and |
1602 |
> |
added reaction field for charges - still need to do charge-dipole |
1603 |
> |
RF |
1604 |
> |
|
1605 |
> |
2005-10-23 16:07 chrisfen |
1606 |
> |
|
1607 |
> |
* samples/water/ssdrf/ssdrf.md: minor changes when testing reaction |
1608 |
> |
field |
1609 |
> |
|
1610 |
> |
2005-10-23 16:06 chrisfen |
1611 |
> |
|
1612 |
> |
* samples/water/spce/spce.md: reaction field now works for charges |
1613 |
> |
|
1614 |
> |
2005-10-20 15:27 tim |
1615 |
> |
|
1616 |
> |
* src/primitives/Torsion.cpp: Fix the other branch of force |
1617 |
> |
calculation in Torision.cpp |
1618 |
> |
|
1619 |
> |
2005-10-19 14:24 chrisfen |
1620 |
> |
|
1621 |
> |
* src/: UseTheForce/doForces.F90, |
1622 |
> |
UseTheForce/DarkSide/electrostatic.F90, |
1623 |
> |
UseTheForce/DarkSide/simulation.F90, applications/oopse/oopse.cpp, |
1624 |
> |
brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals |
1625 |
> |
toUpper problems - these changes should fix those... |
1626 |
> |
|
1627 |
> |
2005-10-19 14:23 chrisfen |
1628 |
> |
|
1629 |
> |
* samples/water/ssdrf/ssdrf.md: nothing |
1630 |
> |
|
1631 |
> |
2005-10-19 12:03 gezelter |
1632 |
> |
|
1633 |
> |
* src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in |
1634 |
> |
GayBerne |
1635 |
> |
|
1636 |
> |
2005-10-19 11:49 tim |
1637 |
> |
|
1638 |
> |
* src/: UseTheForce/DarkSide/fInteractionMap.h, |
1639 |
> |
brains/ForceManager.cpp: fix an index mismathcing between c and |
1640 |
> |
fortran |
1641 |
> |
|
1642 |
> |
2005-10-18 18:03 gezelter |
1643 |
> |
|
1644 |
> |
* samples/cutoff/: lj.md, max.md, mix.md, traditional.md: added |
1645 |
> |
samples for the cutoff methods that Yang Zheng has been working on |
1646 |
> |
|
1647 |
> |
2005-10-18 16:13 gezelter |
1648 |
> |
|
1649 |
> |
* src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques |
1650 |
> |
and a rotation matrix bug |
1651 |
> |
|
1652 |
> |
2005-10-18 16:13 gezelter |
1653 |
> |
|
1654 |
> |
* samples/gbljtest/: 2gb.in, 2gb.md, gb.md, gb2lj1.in, gb2lj1.md, |
1655 |
> |
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
1656 |
> |
added a few GB test cases |
1657 |
> |
|
1658 |
> |
2005-10-18 16:13 gezelter |
1659 |
> |
|
1660 |
> |
* forceFields/DUFF2.frc: Fixing GB parameters |
1661 |
> |
|
1662 |
> |
2005-10-18 13:36 kdaily |
1663 |
> |
|
1664 |
> |
* forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne |
1665 |
> |
type |
1666 |
> |
|
1667 |
> |
2005-10-18 10:01 chrisfen |
1668 |
> |
|
1669 |
> |
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
1670 |
> |
UseTheForce/DarkSide/Makefile, |
1671 |
> |
UseTheForce/DarkSide/electrostatic.F90, |
1672 |
> |
UseTheForce/DarkSide/electrostatic_interface.F90, |
1673 |
> |
UseTheForce/DarkSide/electrostatic_interface.h, |
1674 |
> |
UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged |
1675 |
> |
reaction field with electrostatics.F90 |
1676 |
> |
|
1677 |
> |
2005-10-17 18:13 tim |
1678 |
> |
|
1679 |
> |
* src/: brains/ForceManager.cpp, brains/Stats.cpp, |
1680 |
> |
brains/Stats.hpp, integrators/VelocityVerletIntegrator.cpp, |
1681 |
> |
io/BASS_interface.h, io/Globals.cpp, io/StatWriter.cpp, |
1682 |
> |
io/StatWriter.hpp: Customized StatWriter is working |
1683 |
> |
|
1684 |
> |
2005-10-17 17:42 kdaily |
1685 |
> |
|
1686 |
> |
* src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver |
1687 |
> |
paper |
1688 |
> |
|
1689 |
> |
2005-10-17 16:47 gezelter |
1690 |
> |
|
1691 |
> |
* src/UseTheForce/DarkSide/gb.F90: bugtracking gb |
1692 |
> |
|
1693 |
> |
2005-10-17 14:24 tim |
1694 |
> |
|
1695 |
> |
* src/io/ParamConstraint.hpp: Another bug fix |
1696 |
> |
|
1697 |
> |
2005-10-17 14:22 tim |
1698 |
> |
|
1699 |
> |
* src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace |
1700 |
> |
issues in Globals |
1701 |
> |
|
1702 |
> |
2005-10-17 14:12 gezelter |
1703 |
> |
|
1704 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90, |
1705 |
> |
UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90, |
1706 |
> |
UseTheForce/DarkSide/gb_interface.F90, |
1707 |
> |
UseTheForce/DarkSide/gb_interface.h, |
1708 |
> |
io/GayBerneAtomTypesSectionParser.cpp, |
1709 |
> |
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
1710 |
> |
changing GB architecture |
1711 |
> |
|
1712 |
> |
2005-10-17 14:12 gezelter |
1713 |
> |
|
1714 |
> |
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in, |
1715 |
> |
gbRotRoundZ.in: Adding samples for gb tests |
1716 |
> |
|
1717 |
> |
2005-10-16 22:06 tim |
1718 |
> |
|
1719 |
> |
* src/io/: Globals.cpp, Globals.hpp: fix a seg fault when try copy |
1720 |
> |
a string to event's err_msg, there are still tons of memory |
1721 |
> |
leaking problem in Globals |
1722 |
> |
|
1723 |
> |
2005-10-16 19:51 tim |
1724 |
> |
|
1725 |
> |
* src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change |
1726 |
> |
error message in Globals |
1727 |
> |
|
1728 |
> |
2005-10-14 16:43 tim |
1729 |
> |
|
1730 |
> |
* src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for |
1731 |
> |
parameters are working now |
1732 |
> |
|
1733 |
> |
2005-10-14 11:43 gezelter |
1734 |
> |
|
1735 |
> |
* samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests |
1736 |
> |
|
1737 |
> |
2005-10-14 11:05 gezelter |
1738 |
> |
|
1739 |
> |
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md, |
1740 |
> |
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
1741 |
> |
Adding some Gay Berne tests |
1742 |
> |
|
1743 |
> |
2005-10-14 11:05 gezelter |
1744 |
> |
|
1745 |
> |
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some |
1746 |
> |
cutoff tests |
1747 |
> |
|
1748 |
> |
2005-10-14 10:44 kdaily |
1749 |
> |
|
1750 |
> |
* forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, |
1751 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90, |
1752 |
> |
src/UseTheForce/DarkSide/gb_interface.F90, |
1753 |
> |
src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne |
1754 |
> |
LJ |
1755 |
> |
|
1756 |
> |
2005-10-14 09:48 tim |
1757 |
> |
|
1758 |
> |
* src/io/ParamConstraint.hpp: Adding Parameter Constraint class |
1759 |
> |
|
1760 |
> |
2005-10-14 09:18 chrisfen |
1761 |
> |
|
1762 |
> |
* samples/thermoIntegration/liquid/ssde.md, |
1763 |
> |
samples/thermoIntegration/solid/ssde.md, src/io/Globals.cpp, |
1764 |
> |
src/restraints/Restraints.cpp: added default restraint spring |
1765 |
> |
constants into Globals |
1766 |
> |
|
1767 |
> |
2005-10-13 17:26 tim |
1768 |
> |
|
1769 |
> |
* src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
1770 |
> |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp, |
1771 |
> |
constraints/ZconstraintForceManager.cpp, |
1772 |
> |
integrators/Integrator.cpp, integrators/NPT.cpp, |
1773 |
> |
integrators/NVT.cpp, integrators/Velocitizer.cpp, io/Globals.cpp, |
1774 |
> |
io/Globals.hpp, io/ZConsReader.cpp, minimizers/Minimizer.cpp, |
1775 |
> |
minimizers/MinimizerParameterSet.cpp, restraints/Restraints.cpp, |
1776 |
> |
restraints/ThermoIntegrationForceManager.cpp, |
1777 |
> |
visitors/ZconsVisitor.cpp: rewrite Globals |
1778 |
> |
|
1779 |
> |
2005-10-12 16:57 chuckv |
1780 |
> |
|
1781 |
> |
* src/brains/ForceManager.cpp: Fix to forceManager to pass |
1782 |
> |
potential array to fortran. |
1783 |
> |
|
1784 |
> |
2005-10-12 16:00 gezelter |
1785 |
> |
|
1786 |
> |
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't |
1787 |
> |
remember what we did |
1788 |
> |
|
1789 |
> |
2005-10-12 16:00 gezelter |
1790 |
> |
|
1791 |
> |
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
1792 |
> |
DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/fInteractionMap.h, |
1793 |
> |
DarkSide/force_globals.F90, DarkSide/gb.F90, DarkSide/shapes.F90, |
1794 |
> |
DarkSide/sticky.F90: simplifying long range potential array |
1795 |
> |
|
1796 |
> |
2005-10-12 16:00 gezelter |
1797 |
> |
|
1798 |
> |
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new |
1799 |
> |
cutoff methods |
1800 |
> |
|
1801 |
> |
2005-10-12 16:00 gezelter |
1802 |
> |
|
1803 |
> |
* forceFields/DUFF2.frc: Messing with 2-point water models |
1804 |
> |
|
1805 |
> |
2005-10-12 15:22 chuckv |
1806 |
> |
|
1807 |
> |
* src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran |
1808 |
> |
interface now expects an array for pot. |
1809 |
> |
|
1810 |
> |
2005-10-12 15:18 chuckv |
1811 |
> |
|
1812 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/gb.F90, |
1813 |
> |
DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for |
1814 |
> |
calculation of potential. |
1815 |
> |
|
1816 |
> |
2005-10-12 14:55 chuckv |
1817 |
> |
|
1818 |
> |
* src/UseTheForce/doForces.F90: More changes to MPI potential |
1819 |
> |
calculations. |
1820 |
> |
|
1821 |
> |
2005-10-12 13:59 chuckv |
1822 |
> |
|
1823 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90, |
1824 |
> |
DarkSide/eam.F90, DarkSide/electrostatic.F90, |
1825 |
> |
DarkSide/fInteractionMap.h, DarkSide/force_globals.F90, |
1826 |
> |
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky |
1827 |
> |
Breaky: Add Support for seperating potential contributions. |
1828 |
> |
|
1829 |
> |
2005-10-11 17:00 chuckv |
1830 |
> |
|
1831 |
> |
* src/UseTheForce/doForces.F90: Free some variables that weren't |
1832 |
> |
freed before. |
1833 |
> |
|
1834 |
> |
2005-10-11 16:59 chuckv |
1835 |
> |
|
1836 |
> |
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
1837 |
> |
GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod |
1838 |
> |
builder --twinned. |
1839 |
> |
|
1840 |
> |
2005-10-11 16:57 chuckv |
1841 |
> |
|
1842 |
> |
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
1843 |
> |
nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c, |
1844 |
> |
nanoparticleBuilderCmd.h, sphericalNanoparticle.cpp, |
1845 |
> |
sphericalNanoparticle.hpp: Added code for nanoparticle builder to |
1846 |
> |
cvs. |
1847 |
> |
|
1848 |
> |
2005-10-10 16:34 chuckv |
1849 |
> |
|
1850 |
> |
* src/UseTheForce/doForces.F90: Bug fix, undeclared local variable |
1851 |
> |
in MPI. |
1852 |
> |
|
1853 |
> |
2005-10-10 16:20 chuckv |
1854 |
> |
|
1855 |
> |
* src/UseTheForce/doForces.F90: Fixed MPI bug with Row and Column |
1856 |
> |
indexing of groupToGtype. We now have two seperate maps |
1857 |
> |
groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer |
1858 |
> |
that is set to groupToGtypeRow in the single processor version. |
1859 |
> |
|
1860 |
> |
2005-10-06 13:44 chrisfen |
1861 |
> |
|
1862 |
> |
* samples/water/: dimer/water.md, spce/water.md, ssd/water.md, |
1863 |
> |
ssd-ion/water.md, ssde/water.md, ssdrf/water.md, tap/water.md, |
1864 |
> |
tip3p_ice/water.md, tip4p/water.md: fixing up the samples |
1865 |
> |
|
1866 |
> |
2005-10-05 16:12 tim |
1867 |
> |
|
1868 |
> |
* src/primitives/RigidBody.cpp: There is still something wrong with |
1869 |
> |
inertia tensor projection |
1870 |
> |
|
1871 |
> |
2005-10-05 14:35 tim |
1872 |
> |
|
1873 |
> |
* src/primitives/RigidBody.cpp: erase output of inertia tensor. |
1874 |
> |
There is still something wrong with current implementation. |
1875 |
> |
|
1876 |
> |
2005-10-05 14:34 tim |
1877 |
> |
|
1878 |
> |
* src/brains/MoleculeCreator.cpp: fix a bug in creating |
1879 |
> |
cutoffGroup. When cutoffGroup is turned off, there is a mismatch |
1880 |
> |
between group and center of mass array |
1881 |
> |
|
1882 |
> |
2005-10-05 14:12 tim |
1883 |
> |
|
1884 |
> |
* src/primitives/RigidBody.cpp: fix a bug in creating cutoffGroup. |
1885 |
> |
When cutoffGroup is turned off, there is a mismatch between group |
1886 |
> |
and center of mass array |
1887 |
> |
|
1888 |
> |
2005-10-04 14:34 chrisfen |
1889 |
> |
|
1890 |
> |
* src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying |
1891 |
> |
mass ratio bug that results in simulation failure with massless |
1892 |
> |
particles |
1893 |
> |
|
1894 |
> |
2005-10-04 14:33 chrisfen |
1895 |
> |
|
1896 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on |
1897 |
> |
wolf |
1898 |
> |
|
1899 |
> |
2005-10-04 14:32 chrisfen |
1900 |
> |
|
1901 |
> |
* samples/water/dimer/two.md, samples/water/dimer/water.md, |
1902 |
> |
samples/water/tip3p_ice/tp3.md, samples/water/tip3p_ice/water.md, |
1903 |
> |
samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90: just some |
1904 |
> |
random changes when testing |
1905 |
> |
|
1906 |
> |
2005-10-03 10:54 tim |
1907 |
> |
|
1908 |
> |
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: fix a bug in |
1909 |
> |
projecting the inertia tensor of directional atom in rigibody into |
1910 |
> |
rigidbody's body frame (previous commit is wrong) |
1911 |
> |
|
1912 |
> |
2005-10-03 09:31 tim |
1913 |
> |
|
1914 |
> |
* src/primitives/RigidBody.cpp: fix a bug in projecting the inertia |
1915 |
> |
tensor of directional atom in rigibody into rigidbody's body frame |
1916 |
> |
|
1917 |
> |
2005-09-28 13:47 chrisfen |
1918 |
> |
|
1919 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: working on wolf |
1920 |
> |
|
1921 |
> |
2005-09-28 13:46 chrisfen |
1922 |
> |
|
1923 |
> |
* samples/water/: dimer/cl.md, dimer/mix.md, dimer/mix2.md, |
1924 |
> |
dimer/ssd.md, dimer/tap.md, dimer/two.md, spce/spce.md, ssd/ssd.md, |
1925 |
> |
ssd-ion/ssdCl.md, ssde/ssde.md, tap/tap.md, tip3p_ice/tp3.md, |
1926 |
> |
tip4p/tp4.md: fixed some samples |
1927 |
> |
|
1928 |
> |
2005-09-28 13:46 chrisfen |
1929 |
> |
|
1930 |
> |
* ChangeLog: updated |
1931 |
> |
|
1932 |
> |
2005-09-28 11:55 tim |
1933 |
> |
|
1934 |
> |
* src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid |
1935 |
> |
divergence in rotation matrix to quaternion transformation |
1936 |
> |
|
1937 |
> |
2005-09-28 11:32 gezelter |
1938 |
> |
|
1939 |
> |
* src/primitives/RigidBody.cpp: Rotation matrix multiplication |
1940 |
> |
order error |
1941 |
> |
|
1942 |
> |
2005-09-28 11:32 gezelter |
1943 |
> |
|
1944 |
> |
* src/io/DumpReader.cpp: tracking down quaternion bug |
1945 |
> |
|
1946 |
> |
2005-09-28 11:32 gezelter |
1947 |
> |
|
1948 |
> |
* forceFields/DUFF2.frc: Added DIP atom types for 2-point water |
1949 |
> |
model |
1950 |
> |
|
1951 |
> |
2005-09-27 15:02 tim |
1952 |
> |
|
1953 |
> |
* src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix |
1954 |
> |
to quaternion |
1955 |
> |
|
1956 |
> |
2005-09-26 13:38 chuckv |
1957 |
> |
|
1958 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc |
1959 |
> |
7 so derfc is external. Other compilers should treat erfc as |
1960 |
> |
intrinsic. |
1961 |
> |
|
1962 |
> |
2005-09-26 12:07 chuckv |
1963 |
> |
|
1964 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc |
1965 |
> |
and declared it to be external to fix issure with ifc7. Hopefully |
1966 |
> |
this will not cause a problem with other compilers where derfc is |
1967 |
> |
an intrinsic function. |
1968 |
> |
|
1969 |
> |
2005-09-26 11:42 chuckv |
1970 |
> |
|
1971 |
> |
* src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype |
1972 |
> |
in simulation module. We needed a seperate receive buffer. |
1973 |
> |
|
1974 |
> |
2005-09-26 10:58 chuckv |
1975 |
> |
|
1976 |
> |
* src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added |
1977 |
> |
support for skinThickness keyword to Globals. |
1978 |
> |
|
1979 |
> |
2005-09-26 10:56 tim |
1980 |
> |
|
1981 |
> |
* src/io/DumpReader.cpp: fix a typo in DumpReader |
1982 |
> |
|
1983 |
> |
2005-09-26 09:27 chrisfen |
1984 |
> |
|
1985 |
> |
* samples/: minimizer/tip4p_two.md, |
1986 |
> |
thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md, |
1987 |
> |
water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md, |
1988 |
> |
water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md, |
1989 |
> |
water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md, |
1990 |
> |
water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md, |
1991 |
> |
water/tip4p/tp4.md: fixing up some samples |
1992 |
> |
|
1993 |
> |
2005-09-24 12:39 chrisfen |
1994 |
> |
|
1995 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now |
1996 |
> |
roughly the same speed as the old version when using dipoles |
1997 |
> |
|
1998 |
> |
energies are now exactly the same between the old version of OOPSE |
1999 |
> |
and this version |
2000 |
> |
|
2001 |
> |
2005-09-24 12:38 chrisfen |
2002 |
> |
|
2003 |
> |
* samples/water/ssdrf/ssdrf.md: turned rf on |
2004 |
> |
|
2005 |
> |
2005-09-23 15:31 chuckv |
2006 |
> |
|
2007 |
> |
* src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the |
2008 |
> |
skin thickness and hardcode listSkin to be 1.0. We now get listskin |
2009 |
> |
from skin. This will get fixed to where we can manually set skin |
2010 |
> |
thickness. |
2011 |
> |
|
2012 |
> |
2005-09-22 13:50 gezelter |
2013 |
> |
|
2014 |
> |
* src/math/derfc.F90: added error function |
2015 |
> |
|
2016 |
> |
2005-09-21 19:08 chuckv |
2017 |
> |
|
2018 |
> |
* src/integrators/Velocitizer.cpp: Removed print statement for |
2019 |
> |
angular momentum and inertia tensor from velocitizer. |
2020 |
> |
|
2021 |
> |
2005-09-21 19:04 chuckv |
2022 |
> |
|
2023 |
> |
* src/integrators/Velocitizer.cpp: Removed print statements for |
2024 |
> |
remove angular momentum. |
2025 |
> |
|
2026 |
> |
2005-09-21 18:45 chuckv |
2027 |
> |
|
2028 |
> |
* src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ |
2029 |
> |
(say we are using EAM), we probably shouldn't rebuild the LJ mixing |
2030 |
> |
map. |
2031 |
> |
|
2032 |
> |
2005-09-21 15:59 tim |
2033 |
> |
|
2034 |
> |
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: |
2035 |
> |
DumpReader using pure c++ io |
2036 |
> |
|
2037 |
> |
2005-09-21 12:20 chrisfen |
2038 |
> |
|
2039 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a |
2040 |
> |
defaultCutoff bug (HEMES!) |
2041 |
> |
|
2042 |
> |
2005-09-20 17:13 gezelter |
2043 |
> |
|
2044 |
> |
* make/Makefile.in: libz additions |
2045 |
> |
|
2046 |
> |
2005-09-20 17:03 gezelter |
2047 |
> |
|
2048 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
2049 |
> |
src/config.h.in: added check for zlib in configure |
2050 |
> |
|
2051 |
> |
2005-09-20 16:22 tim |
2052 |
> |
|
2053 |
> |
* src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, |
2054 |
> |
gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter |
2055 |
> |
|
2056 |
> |
2005-09-20 11:22 tim |
2057 |
> |
|
2058 |
> |
* test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding |
2059 |
> |
testcase for zipstream |
2060 |
> |
|
2061 |
> |
2005-09-20 10:41 tim |
2062 |
> |
|
2063 |
> |
* src/io/zipstream.hpp: adding zipstream.hpp |
2064 |
> |
|
2065 |
> |
2005-09-20 10:34 chrisfen |
2066 |
> |
|
2067 |
> |
* samples/: dipole/splitInWater.md, dipole/split_SSD.md, |
2068 |
> |
dipole/twoSplitDipole.md, minimizer/ssdEM.md, |
2069 |
> |
minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md, |
2070 |
> |
zcons/zconsMoving.md: fixed up some sample md files |
2071 |
> |
|
2072 |
> |
2005-09-19 18:21 chrisfen |
2073 |
> |
|
2074 |
> |
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
2075 |
> |
src/UseTheForce/doForces.F90, |
2076 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
2077 |
> |
src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp, |
2078 |
> |
src/brains/fSimulation.h: Fixed bugs in reaction field, now it |
2079 |
> |
appears as though it really is working... |
2080 |
> |
|
2081 |
> |
2005-09-18 15:45 chrisfen |
2082 |
> |
|
2083 |
> |
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
2084 |
> |
src/UseTheForce/doForces.F90, |
2085 |
> |
src/UseTheForce/doForces_interface.F90, |
2086 |
> |
src/UseTheForce/doForces_interface.h, |
2087 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
2088 |
> |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
2089 |
> |
src/brains/SimInfo.cpp: reaction field seems to work now, still |
2090 |
> |
need to do some testing... |
2091 |
> |
|
2092 |
> |
2005-09-16 18:04 chuckv |
2093 |
> |
|
2094 |
> |
* src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed |
2095 |
> |
dump files. |
2096 |
> |
|
2097 |
> |
2005-09-16 16:07 chrisfen |
2098 |
> |
|
2099 |
> |
* src/: UseTheForce/doForces_interface.F90, |
2100 |
> |
UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a |
2101 |
> |
bug that ifc missed... |
2102 |
> |
|
2103 |
> |
2005-09-16 15:36 chrisfen |
2104 |
> |
|
2105 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
2106 |
> |
fixing some summation method issues |
2107 |
> |
|
2108 |
> |
2005-09-16 14:35 chrisfen |
2109 |
> |
|
2110 |
> |
* src/brains/SimInfo.cpp: fixed a capitalization error |
2111 |
> |
|
2112 |
> |
2005-09-16 14:34 chrisfen |
2113 |
> |
|
2114 |
> |
* src/UseTheForce/: fElectrostaticSummationMethod.h, |
2115 |
> |
DarkSide/fElectrostaticSummationMethod.h: moved a header file |
2116 |
> |
around |
2117 |
> |
|
2118 |
> |
2005-09-16 14:00 chrisfen |
2119 |
> |
|
2120 |
> |
* src/: UseTheForce/DarkSide/electrostatic_interface.F90, |
2121 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there |
2122 |
> |
are known issues - particularly with reaction field... |
2123 |
> |
|
2124 |
> |
2005-09-16 11:07 chrisfen |
2125 |
> |
|
2126 |
> |
* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, |
2127 |
> |
io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking |
2128 |
> |
(cutting out the old way to do reaction field) |
2129 |
> |
|
2130 |
> |
2005-09-15 17:05 gezelter |
2131 |
> |
|
2132 |
> |
* src/UseTheForce/: doForces.F90, fCoulombicCorrection.h, |
2133 |
> |
fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90, |
2134 |
> |
DarkSide/electrostatic_interface.F90, |
2135 |
> |
DarkSide/electrostatic_interface.h: Working on adding WOLF |
2136 |
> |
|
2137 |
> |
2005-09-15 14:17 tim |
2138 |
> |
|
2139 |
> |
* src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame |
2140 |
> |
is called without calling getNFrames |
2141 |
> |
|
2142 |
> |
2005-09-15 08:47 chrisfen |
2143 |
> |
|
2144 |
> |
* src/UseTheForce/fCoulombicCorrection.h: forgot to add a header |
2145 |
> |
|
2146 |
> |
2005-09-14 21:48 chuckv |
2147 |
> |
|
2148 |
> |
* src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was |
2149 |
> |
not initialized after creation. When maxval(gtypeMaxCutoff) was |
2150 |
> |
called, the largest random garbage value was returned from the |
2151 |
> |
array. |
2152 |
> |
|
2153 |
> |
2005-09-14 19:14 chrisfen |
2154 |
> |
|
2155 |
> |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, |
2156 |
> |
io/Globals.hpp: changes to include the coulombicCorrection selector |
2157 |
> |
|
2158 |
> |
2005-09-14 19:13 chrisfen |
2159 |
> |
|
2160 |
> |
* src/UseTheForce/DarkSide/: Makefile, electrostatic.F90, |
2161 |
> |
reactionField.F90: added in the undamped wolf, in the process of |
2162 |
> |
doing the damped wolf |
2163 |
> |
|
2164 |
> |
2005-09-14 19:13 chrisfen |
2165 |
> |
|
2166 |
> |
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
2167 |
> |
doForces_interface.h, notifyCutoffs.F90: some changes to activate |
2168 |
> |
the coulombicCorrection selector |
2169 |
> |
|
2170 |
> |
2005-09-14 19:11 chrisfen |
2171 |
> |
|
2172 |
> |
* samples/water/dimer/: cl.in, cl.md, water.md: just some testing |
2173 |
> |
|
2174 |
> |
2005-09-14 19:11 chrisfen |
2175 |
> |
|
2176 |
> |
* samples/argon/: 500.in, 500.md: Equilibrated the sample |
2177 |
> |
|
2178 |
> |
2005-09-14 19:10 chrisfen |
2179 |
> |
|
2180 |
> |
* forceFields/DUFF2.frc: re-added Cl- and Na+ |
2181 |
> |
|
2182 |
> |
2005-09-14 15:31 chuckv |
2183 |
> |
|
2184 |
> |
* src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup |
2185 |
> |
eamAtypes instead of assuming a 1-1 correspondence to atypes. |
2186 |
> |
|
2187 |
> |
2005-09-14 15:28 gezelter |
2188 |
> |
|
2189 |
> |
* src/UseTheForce/doForces.F90: fix to put back calculation of r in |
2190 |
> |
do_prepair |
2191 |
> |
|
2192 |
> |
2005-09-14 14:02 gezelter |
2193 |
> |
|
2194 |
> |
* src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the |
2195 |
> |
createMixingMap routine. It should now set doShift correctly |
2196 |
> |
|
2197 |
> |
2005-09-07 17:44 chuckv |
2198 |
> |
|
2199 |
> |
* src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. |
2200 |
> |
|
2201 |
> |
2005-09-07 17:23 chuckv |
2202 |
> |
|
2203 |
> |
* src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi |
2204 |
> |
logical variables |
2205 |
> |
|
2206 |
> |
2005-09-07 17:08 gezelter |
2207 |
> |
|
2208 |
> |
* src/UseTheForce/doForces.F90: bugfix on the grouptype finding |
2209 |
> |
algorithm |
2210 |
> |
|
2211 |
> |
2005-09-07 15:46 gezelter |
2212 |
> |
|
2213 |
> |
* src/: UseTheForce/doForces.F90, |
2214 |
> |
UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, |
2215 |
> |
UseTheForce/notifyCutoffs_interface.F90, |
2216 |
> |
UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp, |
2217 |
> |
io/Globals.cpp, io/Globals.hpp: adding c-side interface to change |
2218 |
> |
cutoff Policy |
2219 |
> |
|
2220 |
> |
2005-09-07 14:18 gezelter |
2221 |
> |
|
2222 |
> |
* src/UseTheForce/doForces.F90: Some bug hunting |
2223 |
> |
|
2224 |
> |
2005-09-07 14:18 gezelter |
2225 |
> |
|
2226 |
> |
* samples/argon/argonNVT.md: Just a longer test |
2227 |
> |
|
2228 |
> |
2005-09-06 12:32 chuckv |
2229 |
> |
|
2230 |
> |
* src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap |
2231 |
> |
etc.. |
2232 |
> |
|
2233 |
> |
2005-09-01 17:56 gezelter |
2234 |
> |
|
2235 |
> |
* src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to |
2236 |
> |
zero |
2237 |
> |
|
2238 |
> |
2005-09-01 15:17 gezelter |
2239 |
> |
|
2240 |
> |
* src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote |
2241 |
> |
createGtypeCutoffMap |
2242 |
> |
|
2243 |
> |
2005-08-30 13:23 chrisfen |
2244 |
> |
|
2245 |
> |
* src/: UseTheForce/doForces.F90, |
2246 |
> |
UseTheForce/doForces_interface.F90, |
2247 |
> |
UseTheForce/doForces_interface.h, |
2248 |
> |
UseTheForce/DarkSide/electrostatic.F90, |
2249 |
> |
UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp, |
2250 |
> |
brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some |
2251 |
> |
changes for implementing the wolf potential |
2252 |
> |
|
2253 |
> |
2005-08-26 17:39 chrisfen |
2254 |
> |
|
2255 |
> |
* src/UseTheForce/DarkSide/eam.F90: updated getEAMCut |
2256 |
> |
|
2257 |
> |
2005-08-26 16:30 chrisfen |
2258 |
> |
|
2259 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/eam.F90, |
2260 |
> |
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added |
2261 |
> |
some probably nonfunctional get*cut routines |
2262 |
> |
|
2263 |
> |
2005-08-26 15:34 chuckv |
2264 |
> |
|
2265 |
> |
* src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. |
2266 |
> |
|
2267 |
> |
2005-08-26 11:36 gezelter |
2268 |
> |
|
2269 |
> |
* src/UseTheForce/doForces.F90: fixing some of the problems in the |
2270 |
> |
interactionHash and gtypeCutoff routines |
2271 |
> |
|
2272 |
> |
2005-08-17 10:26 gezelter |
2273 |
> |
|
2274 |
> |
* src/UseTheForce/: doForces.F90, fCutoffPolicy.h, |
2275 |
> |
DarkSide/simulation.F90: added fCutoffPolicy.h |
2276 |
> |
|
2277 |
> |
2005-08-11 16:04 gezelter |
2278 |
> |
|
2279 |
> |
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in |
2280 |
> |
progress |
2281 |
> |
|
2282 |
> |
2005-08-10 14:17 gezelter |
2283 |
> |
|
2284 |
> |
* src/primitives/StuntDouble.hpp: putting spaceballs back where |
2285 |
> |
they belong |
2286 |
> |
|
2287 |
> |
2005-08-09 17:33 gezelter |
2288 |
> |
|
2289 |
> |
* src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard |
2290 |
> |
Jones module |
2291 |
> |
|
2292 |
> |
2005-08-09 17:33 gezelter |
2293 |
> |
|
2294 |
> |
* src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky |
2295 |
> |
|
2296 |
> |
2005-08-09 14:40 chuckv |
2297 |
> |
|
2298 |
> |
* src/UseTheForce/doForces.F90: In process of re-write for group |
2299 |
> |
based cutoff.... |
2300 |
> |
|
2301 |
> |
2005-07-29 14:38 gezelter |
2302 |
> |
|
2303 |
> |
* src/UseTheForce/doForces.F90: fixes in progress |
2304 |
> |
|
2305 |
> |
2005-07-29 12:34 tim |
2306 |
> |
|
2307 |
> |
* src/UseTheForce/doForces.F90: fix a bug which does not update |
2308 |
> |
me_i and me_j correctly |
2309 |
> |
|
2310 |
> |
2005-07-28 17:12 chuckv |
2311 |
> |
|
2312 |
> |
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed |
2313 |
> |
cutoffs... Segfaults nicely now... |
2314 |
> |
|
2315 |
> |
2005-07-20 12:04 gezelter |
2316 |
> |
|
2317 |
> |
* configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text |
2318 |
> |
error messages from pathscale compiler |
2319 |
> |
|
2320 |
> |
2005-07-13 11:48 tim |
2321 |
> |
|
2322 |
> |
* src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in |
2323 |
> |
<functional> |
2324 |
> |
|
2325 |
> |
2005-07-13 10:54 tim |
2326 |
> |
|
2327 |
> |
* src/: UseTheForce/fSwitchingFunction.h, |
2328 |
> |
UseTheForce/mpiComponentPlan.h, |
2329 |
> |
UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h, |
2330 |
> |
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
2331 |
> |
io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c, |
2332 |
> |
io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c, |
2333 |
> |
io/parse_tree.h, math/MatVec3.c, utils/residentMem.c, |
2334 |
> |
utils/simError.c, utils/simError.h: replace c++ style comment in c |
2335 |
> |
files |
2336 |
> |
|
2337 |
> |
2005-07-03 15:53 chuckv |
2338 |
> |
|
2339 |
> |
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
2340 |
> |
UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added |
2341 |
> |
subroutine to set cuttoff for Interaction map and function in |
2342 |
> |
simulation.F90 to determine if a particular atype is present in a |
2343 |
> |
simulation. |
2344 |
> |
|
2345 |
> |
2005-06-28 08:58 gezelter |
2346 |
> |
|
2347 |
> |
* src/UseTheForce/doForces.F90: [no log message] |
2348 |
> |
|
2349 |
> |
2005-06-27 17:21 chuckv |
2350 |
> |
|
2351 |
> |
* src/UseTheForce/doForces.F90: More breaking and destruction of |
2352 |
> |
force code. Does not build at this point... |
2353 |
> |
|
2354 |
> |
2005-06-27 16:01 gezelter |
2355 |
> |
|
2356 |
> |
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90, |
2357 |
> |
UseTheForce/DarkSide/fInteractionMap.h, |
2358 |
> |
UseTheForce/DarkSide/interactions.F90, utils/definitions.F90: |
2359 |
> |
Breaky breaky! |
2360 |
> |
|
2361 |
> |
2005-06-20 11:03 gezelter |
2362 |
> |
|
2363 |
> |
* samples/water/ssd/ssd.md, |
2364 |
> |
src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a |
2365 |
> |
simulation |
2366 |
> |
|
2367 |
> |
2005-06-13 13:25 tim |
2368 |
> |
|
2369 |
> |
* src/: applications/staticProps/DensityPlot.cpp, |
2370 |
> |
applications/staticProps/DensityPlot.hpp, |
2371 |
> |
applications/staticProps/SCDOrderParameter.cpp, |
2372 |
> |
applications/staticProps/StaticProps.cpp, |
2373 |
> |
io/AtomTypesSectionParser.cpp: working version of DensityPlot |
2374 |
> |
|
2375 |
> |
2005-05-31 17:31 chuckv |
2376 |
> |
|
2377 |
> |
* src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to |
2378 |
> |
remove angular momentum. |
2379 |
> |
|
2380 |
> |
2005-05-31 12:34 chuckv |
2381 |
> |
|
2382 |
> |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in |
2383 |
> |
typo in nanorodBuilder. |
2384 |
> |
|
2385 |
> |
2005-05-30 09:01 chuckv |
2386 |
> |
|
2387 |
> |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
2388 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, |
2389 |
> |
brains/Stats.hpp, integrators/Velocitizer.cpp, |
2390 |
> |
integrators/Velocitizer.hpp: Added method to remove system angular |
2391 |
> |
momentum to velocitizer and added method to calculate system |
2392 |
> |
angular momentum to siminfo. |
2393 |
> |
|
2394 |
> |
2005-05-29 16:16 chrisfen |
2395 |
> |
|
2396 |
> |
* src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed |
2397 |
> |
balance from the Darkside (files) |
2398 |
> |
|
2399 |
> |
2005-05-29 16:15 chrisfen |
2400 |
> |
|
2401 |
> |
* src/UseTheForce/doForces.F90: Removed balance from doForces |
2402 |
> |
|
2403 |
> |
2005-05-29 16:15 chrisfen |
2404 |
> |
|
2405 |
> |
* samples/water/tap/: tap.in, tap.md: Updated tap sample |
2406 |
> |
|
2407 |
> |
2005-05-29 16:15 chrisfen |
2408 |
> |
|
2409 |
> |
* samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap |
2410 |
> |
dimer for testing purposes |
2411 |
> |
|
2412 |
> |
2005-05-29 16:14 chrisfen |
2413 |
> |
|
2414 |
> |
* forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It |
2415 |
> |
was apparently wiped earlier this month... |
2416 |
> |
|
2417 |
> |
2005-05-29 16:13 chrisfen |
2418 |
> |
|
2419 |
> |
* ChangeLog: ran make cvslog |
2420 |
> |
|
2421 |
> |
2005-05-28 19:16 tim |
2422 |
> |
|
2423 |
> |
* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding |
2424 |
> |
AtomNameVisitor |
2425 |
> |
|
2426 |
> |
2005-05-28 19:09 tim |
2427 |
> |
|
2428 |
> |
* src/integrators/Integrator.cpp: dding resetIntegrator |
2429 |
> |
|
2430 |
> |
2005-05-28 19:06 tim |
2431 |
> |
|
2432 |
> |
* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, |
2433 |
> |
NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, |
2434 |
> |
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding |
2435 |
> |
resetIntegrator |
2436 |
> |
|
2437 |
> |
2005-05-27 16:11 tim |
2438 |
> |
|
2439 |
> |
* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, |
2440 |
> |
Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, |
2441 |
> |
SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
2442 |
> |
StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into |
2443 |
> |
StaticProps |
2444 |
> |
|
2445 |
> |
2005-05-26 23:41 tim |
2446 |
> |
|
2447 |
> |
* src/: applications/staticProps/Makefile, |
2448 |
> |
applications/staticProps/P2OrderParameter.cpp, |
2449 |
> |
applications/staticProps/P2OrderParameter.hpp, |
2450 |
> |
applications/staticProps/StaticProps.cpp, |
2451 |
> |
applications/staticProps/StaticProps.ggo, |
2452 |
> |
applications/staticProps/StaticPropsCmd.c, |
2453 |
> |
applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, |
2454 |
> |
utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps |
2455 |
> |
|
2456 |
> |
2005-05-26 17:45 tim |
2457 |
> |
|
2458 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
2459 |
> |
applications/dump2Xyz/Dump2XYZCmd.c, |
2460 |
> |
applications/dump2Xyz/Dump2XYZCmd.h, |
2461 |
> |
applications/staticProps/Makefile, |
2462 |
> |
applications/staticProps/P2OrderParameter.cpp, |
2463 |
> |
applications/staticProps/P2OrderParameter.hpp, |
2464 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
2465 |
> |
applications/staticProps/RadialDistrFunc.hpp, |
2466 |
> |
applications/staticProps/StaticAnalyser.hpp, |
2467 |
> |
applications/staticProps/StaticProps.cpp, |
2468 |
> |
applications/staticProps/StaticProps.ggo, |
2469 |
> |
applications/staticProps/StaticPropsCmd.c, |
2470 |
> |
applications/staticProps/StaticPropsCmd.h, visitors/Makefile, |
2471 |
> |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding |
2472 |
> |
AtomNameVisitor to convert atom name to its base name; |
2473 |
> |
wrappingvisitor now wrap back to the center of the mass; adding |
2474 |
> |
P2OrderParameter into StaticProps |
2475 |
> |
|
2476 |
> |
2005-05-22 16:36 chuckv |
2477 |
> |
|
2478 |
> |
* src/: applications/nanoRodBuilder/Geometry.cpp, |
2479 |
> |
applications/nanoRodBuilder/GeometryBuilder.cpp, |
2480 |
> |
applications/nanoRodBuilder/GeometryFactory.cpp, |
2481 |
> |
applications/nanoRodBuilder/GeometryFactory.hpp, |
2482 |
> |
applications/nanoRodBuilder/nanorodBuilder.cpp, |
2483 |
> |
integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
2484 |
> |
tensor. |
2485 |
> |
|
2486 |
> |
2005-05-22 16:05 tim |
2487 |
> |
|
2488 |
> |
* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
2489 |
> |
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
2490 |
> |
io/Globals.hpp, io/SectionParserManager.cpp: adding keyword |
2491 |
> |
printPressureTensor |
2492 |
> |
|
2493 |
> |
2005-05-20 14:27 tim |
2494 |
> |
|
2495 |
> |
* src/integrators/NPrT.cpp: NPrT in progress |
2496 |
> |
|
2497 |
> |
2005-05-20 11:01 tim |
2498 |
> |
|
2499 |
> |
* src/: integrators/NPrT.cpp, io/Globals.cpp, |
2500 |
> |
utils/OOPSEConstant.hpp: NPrT in progress |
2501 |
> |
|
2502 |
> |
2005-05-19 16:31 tim |
2503 |
> |
|
2504 |
> |
* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, |
2505 |
> |
integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, |
2506 |
> |
io/Globals.hpp: NPAT is working |
2507 |
> |
|
2508 |
> |
2005-05-19 10:49 tim |
2509 |
> |
|
2510 |
> |
* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, |
2511 |
> |
integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT |
2512 |
> |
|
2513 |
> |
2005-05-18 23:28 tim |
2514 |
> |
|
2515 |
> |
* src/: brains/Register.cpp, integrators/NPAT.cpp, |
2516 |
> |
integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, |
2517 |
> |
io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators |
2518 |
> |
|
2519 |
> |
2005-05-18 14:06 chrisfen |
2520 |
> |
|
2521 |
> |
* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just |
2522 |
> |
some tap changes |
2523 |
> |
|
2524 |
> |
2005-05-18 13:31 chrisfen |
2525 |
> |
|
2526 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
2527 |
> |
DarkSide/sticky.F90: Modifications to temper the dipolar strength |
2528 |
> |
in the first solvation shell for tap |
2529 |
> |
|
2530 |
> |
2005-05-18 07:35 chrisfen |
2531 |
> |
|
2532 |
> |
* samples/water/tap/: tap.in, tap.md, water.md: added a tap example |
2533 |
> |
for testing purposes |
2534 |
> |
|
2535 |
> |
2005-05-17 17:35 chrisfen |
2536 |
> |
|
2537 |
> |
* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, |
2538 |
> |
samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, |
2539 |
> |
src/UseTheForce/doForces.F90, |
2540 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
2541 |
> |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
2542 |
> |
src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also |
2543 |
> |
correcting changes to the previous merge that were not caught |
2544 |
> |
|
2545 |
> |
2005-05-16 23:20 chuckv |
2546 |
> |
|
2547 |
> |
* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: |
2548 |
> |
Fixed merge issues between Kyle and Chris so OOPSE will actually |
2549 |
> |
build. |
2550 |
> |
|
2551 |
> |
2005-05-16 22:46 kdaily |
2552 |
> |
|
2553 |
> |
* src/io/: GayBerneAtomTypesSectionParser.cpp, |
2554 |
> |
GayBerneAtomTypesSectionParser.hpp, Makefile: help |
2555 |
> |
|
2556 |
> |
2005-05-16 21:08 kdaily |
2557 |
> |
|
2558 |
> |
* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, |
2559 |
> |
src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, |
2560 |
> |
src/types/DirectionalAtomType.cpp, |
2561 |
> |
src/types/DirectionalAtomType.hpp: added gb |
2562 |
> |
|
2563 |
> |
2005-05-13 15:36 chrisfen |
2564 |
> |
|
2565 |
> |
* forceFields/DUFF2.frc: Better tap |
2566 |
> |
|
2567 |
> |
2005-05-12 14:43 chrisfen |
2568 |
> |
|
2569 |
> |
* forceFields/DUFF2.frc, samples/water/dimer/ssd.in, |
2570 |
> |
samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, |
2571 |
> |
src/applications/dump2Xyz/Dump2XYZ.cpp, |
2572 |
> |
src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. |
2573 |
> |
Need to parametrize. |
2574 |
> |
|
2575 |
> |
2005-05-11 18:15 chuckv |
2576 |
> |
|
2577 |
> |
* src/: io/ShapeAtomTypesSectionParser.cpp, |
2578 |
> |
math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed |
2579 |
> |
build issues under ifc7. |
2580 |
> |
|
2581 |
> |
2005-05-09 17:07 chuckv |
2582 |
> |
|
2583 |
> |
* src/applications/nanoRodBuilder/Geometry.hpp: More geometry |
2584 |
> |
builder changes. |
2585 |
> |
|
2586 |
> |
2005-05-05 10:06 chrisfen |
2587 |
> |
|
2588 |
> |
* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED |
2589 |
> |
to TAP |
2590 |
> |
|
2591 |
> |
2005-05-05 09:47 chrisfen |
2592 |
> |
|
2593 |
> |
* forceFields/DUFF2.frc, samples/water/ssde/ssde.md, |
2594 |
> |
samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, |
2595 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, |
2596 |
> |
src/UseTheForce/DarkSide/atype.F90, |
2597 |
> |
src/UseTheForce/DarkSide/atype_interface.F90, |
2598 |
> |
src/UseTheForce/DarkSide/simulation.F90, |
2599 |
> |
src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, |
2600 |
> |
src/brains/fSimulation.h, src/io/Makefile, |
2601 |
> |
src/io/StickyAtomTypesSectionParser.cpp, |
2602 |
> |
src/io/StickyPowerAtomTypesSectionParser.cpp, |
2603 |
> |
src/io/StickyPowerAtomTypesSectionParser.hpp, |
2604 |
> |
src/types/AtomType.cpp, src/types/AtomType.hpp, |
2605 |
> |
src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, |
2606 |
> |
src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's |
2607 |
> |
not parametrized, but OOPSE will now let me run it... |
2608 |
> |
|
2609 |
> |
2005-05-03 17:55 chuckv |
2610 |
> |
|
2611 |
> |
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
2612 |
> |
GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: |
2613 |
> |
Adding support for generic geometry to nanorodbuilder. |
2614 |
> |
|
2615 |
> |
2005-05-03 12:55 chuckv |
2616 |
> |
|
2617 |
> |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
2618 |
> |
nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, |
2619 |
> |
nanorodBuilderCmd.h: More changes to nanoRodBuilder.... |
2620 |
> |
|
2621 |
> |
2005-04-29 14:16 gezelter |
2622 |
> |
|
2623 |
> |
* make/Makefile.in: [no log message] |
2624 |
> |
|
2625 |
> |
2005-04-29 11:26 chrisfen |
2626 |
> |
|
2627 |
> |
* forceFields/DUFF2.frc, samples/water/spce/water.md, |
2628 |
> |
samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, |
2629 |
> |
samples/water/ssd-ion/water.md, samples/water/ssde/water.md, |
2630 |
> |
samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, |
2631 |
> |
samples/water/tip4p/water.md: Added TIP4P-Ew |
2632 |
> |
|
2633 |
> |
2005-04-27 19:24 chuckv |
2634 |
> |
|
2635 |
> |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
2636 |
> |
GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, |
2637 |
> |
nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with |
2638 |
> |
nanoRodBuilder.... |
2639 |
> |
|
2640 |
> |
2005-04-27 15:13 chrisfen |
2641 |
> |
|
2642 |
> |
* samples/shape/Shapes.frc, samples/shape/linear.shape, |
2643 |
> |
src/UseTheForce/DarkSide/atype.F90, |
2644 |
> |
src/UseTheForce/DarkSide/shapes.F90, |
2645 |
> |
src/UseTheForce/DarkSide/shapes_interface.F90, |
2646 |
> |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of |
2647 |
> |
write statements and am closer to a working shapes |
2648 |
> |
|
2649 |
> |
2005-04-22 16:57 chuckv |
2650 |
> |
|
2651 |
> |
* src/utils/Predicate.hpp: Fixed gcc4 bug... |
2652 |
> |
|
2653 |
> |
2005-04-22 16:52 tim |
2654 |
> |
|
2655 |
> |
* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, |
2656 |
> |
Trim.hpp: adding CharClassificationFunctor to fix the locale |
2657 |
> |
problem of c++ |
2658 |
> |
|
2659 |
> |
2005-04-21 09:12 chrisfen |
2660 |
> |
|
2661 |
> |
* samples/shape/Shapes.frc, samples/shape/linear.in, |
2662 |
> |
samples/shape/linear.md, src/UseTheForce/ForceField.hpp, |
2663 |
> |
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, |
2664 |
> |
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
2665 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, |
2666 |
> |
src/UseTheForce/DarkSide/shapes.F90, |
2667 |
> |
src/UseTheForce/DarkSide/shapes_interface.F90, |
2668 |
> |
src/UseTheForce/DarkSide/shapes_interface.h, |
2669 |
> |
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
2670 |
> |
src/io/Makefile, src/io/SectionParser.cpp, |
2671 |
> |
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
2672 |
> |
src/io/ShapeAtomTypesSectionParser.cpp, |
2673 |
> |
src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, |
2674 |
> |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, |
2675 |
> |
src/types/ShapeAtomType.hpp: Shapes is limping along with a array |
2676 |
> |
bounds overwrite (I think...). At least the parser loads the |
2677 |
> |
forcefield fine... |
2678 |
> |
|
2679 |
> |
2005-04-18 10:44 chrisfen |
2680 |
> |
|
2681 |
> |
* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on |
2682 |
> |
Mac (capitalization confusion of filenames) |
2683 |
> |
|
2684 |
> |
2005-04-17 22:50 chrisfen |
2685 |
> |
|
2686 |
> |
* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, |
2687 |
> |
UseTheForce/Shapes_FF.cpp, |
2688 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
2689 |
> |
io/ShapeAtomTypesSectionParser.cpp, |
2690 |
> |
io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... |
2691 |
> |
|
2692 |
> |
2005-04-15 17:43 gezelter |
2693 |
> |
|
2694 |
> |
* README: gmake in case people forget |
2695 |
> |
|
2696 |
> |
2005-04-15 17:40 gezelter |
2697 |
> |
|
2698 |
> |
* src/applications/oopse/oopse.cpp: fixed the spacing on the |
2699 |
> |
banner. Vanity. |
2700 |
> |
|
2701 |
> |
2005-04-15 17:22 gezelter |
2702 |
> |
|
2703 |
> |
* src/: config.h.in, applications/oopse/oopse.cpp: Version string |
2704 |
> |
in banner (and version numbers in config.h) |
2705 |
> |
|
2706 |
> |
2005-04-15 17:22 gezelter |
2707 |
> |
|
2708 |
> |
* ChangeLog, LICENSE, README: Documentation changes |
2709 |
> |
|
2710 |
> |
2005-04-15 17:03 gezelter |
2711 |
> |
|
2712 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
2713 |
> |
UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, |
2714 |
> |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
2715 |
> |
UseTheForce/ForceFieldCreator.hpp, |
2716 |
> |
UseTheForce/ForceFieldFactory.cpp, |
2717 |
> |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
2718 |
> |
UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, |
2719 |
> |
UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, |
2720 |
> |
UseTheForce/notifyCutoffs.F90, |
2721 |
> |
UseTheForce/notifyCutoffs_interface.F90, |
2722 |
> |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
2723 |
> |
UseTheForce/DarkSide/atype.F90, |
2724 |
> |
UseTheForce/DarkSide/atype_interface.F90, |
2725 |
> |
UseTheForce/DarkSide/eam.F90, |
2726 |
> |
UseTheForce/DarkSide/eam_interface.F90, |
2727 |
> |
UseTheForce/DarkSide/eam_interface.h, |
2728 |
> |
UseTheForce/DarkSide/electrostatic.F90, |
2729 |
> |
UseTheForce/DarkSide/electrostatic_interface.F90, |
2730 |
> |
UseTheForce/DarkSide/electrostatic_interface.h, |
2731 |
> |
UseTheForce/DarkSide/force_globals.F90, |
2732 |
> |
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
2733 |
> |
UseTheForce/DarkSide/lj_interface.F90, |
2734 |
> |
UseTheForce/DarkSide/lj_interface.h, |
2735 |
> |
UseTheForce/DarkSide/neighborLists.F90, |
2736 |
> |
UseTheForce/DarkSide/reactionField.F90, |
2737 |
> |
UseTheForce/DarkSide/shapes.F90, |
2738 |
> |
UseTheForce/DarkSide/shapes_interface.F90, |
2739 |
> |
UseTheForce/DarkSide/shapes_interface.h, |
2740 |
> |
UseTheForce/DarkSide/simParallel.F90, |
2741 |
> |
UseTheForce/DarkSide/simParallel_interface.F90, |
2742 |
> |
UseTheForce/DarkSide/simParallel_interface.h, |
2743 |
> |
UseTheForce/DarkSide/simulation.F90, |
2744 |
> |
UseTheForce/DarkSide/simulation_interface.F90, |
2745 |
> |
UseTheForce/DarkSide/simulation_interface.h, |
2746 |
> |
UseTheForce/DarkSide/sticky.F90, |
2747 |
> |
UseTheForce/DarkSide/sticky_interface.F90, |
2748 |
> |
UseTheForce/DarkSide/sticky_interface.h, |
2749 |
> |
UseTheForce/DarkSide/switcheroo.F90, |
2750 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, |
2751 |
> |
applications/dump2Xyz/Dump2XYZCmd.c, |
2752 |
> |
applications/dump2Xyz/Dump2XYZCmd.h, |
2753 |
> |
applications/dynamicProps/CrossTimeCorrFunc.cpp, |
2754 |
> |
applications/dynamicProps/CrossTimeCorrFunc.hpp, |
2755 |
> |
applications/dynamicProps/DipoleCorrFunc.cpp, |
2756 |
> |
applications/dynamicProps/DipoleCorrFunc.hpp, |
2757 |
> |
applications/dynamicProps/DynamicProps.cpp, |
2758 |
> |
applications/dynamicProps/DynamicPropsCmd.c, |
2759 |
> |
applications/dynamicProps/DynamicPropsCmd.h, |
2760 |
> |
applications/dynamicProps/FrameTimeCorrFunc.hpp, |
2761 |
> |
applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
2762 |
> |
applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
2763 |
> |
applications/dynamicProps/RCorrFunc.cpp, |
2764 |
> |
applications/dynamicProps/RCorrFunc.hpp, |
2765 |
> |
applications/dynamicProps/TimeCorrFunc.cpp, |
2766 |
> |
applications/dynamicProps/TimeCorrFunc.hpp, |
2767 |
> |
applications/dynamicProps/VCorrFunc.cpp, |
2768 |
> |
applications/dynamicProps/VCorrFunc.hpp, |
2769 |
> |
applications/nanoRodBuilder/GeometryBuilder.cpp, |
2770 |
> |
applications/nanoRodBuilder/GeometryBuilder.hpp, |
2771 |
> |
applications/nanoRodBuilder/nanorodBuilder.cpp, |
2772 |
> |
applications/nanoRodBuilder/nanorodBuilderCmd.c, |
2773 |
> |
applications/nanoRodBuilder/nanorodBuilderCmd.h, |
2774 |
> |
applications/oopse/oopse.cpp, |
2775 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
2776 |
> |
applications/simpleBuilder/simpleBuilderCmd.c, |
2777 |
> |
applications/simpleBuilder/simpleBuilderCmd.h, |
2778 |
> |
applications/staticProps/GofAngle2.cpp, |
2779 |
> |
applications/staticProps/GofAngle2.hpp, |
2780 |
> |
applications/staticProps/GofR.cpp, |
2781 |
> |
applications/staticProps/GofR.hpp, |
2782 |
> |
applications/staticProps/GofRAngle.cpp, |
2783 |
> |
applications/staticProps/GofRAngle.hpp, |
2784 |
> |
applications/staticProps/GofXyz.cpp, |
2785 |
> |
applications/staticProps/GofXyz.hpp, |
2786 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
2787 |
> |
applications/staticProps/RadialDistrFunc.hpp, |
2788 |
> |
applications/staticProps/StaticProps.cpp, |
2789 |
> |
applications/staticProps/StaticPropsCmd.c, |
2790 |
> |
applications/staticProps/StaticPropsCmd.h, |
2791 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
2792 |
> |
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
2793 |
> |
brains/Exclude.hpp, brains/ForceManager.cpp, |
2794 |
> |
brains/ForceManager.hpp, brains/MoleculeCreator.cpp, |
2795 |
> |
brains/MoleculeCreator.hpp, brains/Register.cpp, |
2796 |
> |
brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
2797 |
> |
brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
2798 |
> |
brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, |
2799 |
> |
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, |
2800 |
> |
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
2801 |
> |
brains/fSimulation.h, constraints/ConstraintElem.hpp, |
2802 |
> |
constraints/ConstraintPair.hpp, constraints/Rattle.cpp, |
2803 |
> |
constraints/Rattle.hpp, constraints/ZconsStruct.hpp, |
2804 |
> |
constraints/ZconstraintForceManager.cpp, |
2805 |
> |
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
2806 |
> |
integrators/DLM.hpp, integrators/Integrator.cpp, |
2807 |
> |
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
2808 |
> |
integrators/IntegratorFactory.cpp, |
2809 |
> |
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
2810 |
> |
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
2811 |
> |
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
2812 |
> |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
2813 |
> |
integrators/NVT.cpp, integrators/NVT.hpp, |
2814 |
> |
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
2815 |
> |
integrators/Velocitizer.hpp, |
2816 |
> |
integrators/VelocityVerletIntegrator.cpp, |
2817 |
> |
integrators/VelocityVerletIntegrator.hpp, |
2818 |
> |
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
2819 |
> |
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
2820 |
> |
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
2821 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
2822 |
> |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
2823 |
> |
io/ChargeAtomTypesSectionParser.hpp, |
2824 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
2825 |
> |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
2826 |
> |
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
2827 |
> |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
2828 |
> |
io/Globals.cpp, io/Globals.hpp, |
2829 |
> |
io/LennardJonesAtomTypesSectionParser.cpp, |
2830 |
> |
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
2831 |
> |
io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, |
2832 |
> |
io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, |
2833 |
> |
io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, |
2834 |
> |
io/SectionParser.cpp, io/SectionParser.hpp, |
2835 |
> |
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
2836 |
> |
io/StatWriter.cpp, io/StatWriter.hpp, |
2837 |
> |
io/StickyAtomTypesSectionParser.cpp, |
2838 |
> |
io/StickyAtomTypesSectionParser.hpp, |
2839 |
> |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
2840 |
> |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
2841 |
> |
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, |
2842 |
> |
io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, |
2843 |
> |
io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, |
2844 |
> |
io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, |
2845 |
> |
lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, |
2846 |
> |
lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
2847 |
> |
lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, |
2848 |
> |
lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, |
2849 |
> |
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
2850 |
> |
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
2851 |
> |
math/ParallelRandNumGen.hpp, math/Polynomial.hpp, |
2852 |
> |
math/Quaternion.hpp, math/RandNumGen.hpp, |
2853 |
> |
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
2854 |
> |
math/RectMatrix.hpp, math/SeqRandNumGen.cpp, |
2855 |
> |
math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, |
2856 |
> |
math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, |
2857 |
> |
minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, |
2858 |
> |
minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, |
2859 |
> |
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
2860 |
> |
minimizers/MinimizerFactory.hpp, |
2861 |
> |
minimizers/MinimizerParameterSet.cpp, |
2862 |
> |
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
2863 |
> |
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
2864 |
> |
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
2865 |
> |
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
2866 |
> |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
2867 |
> |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
2868 |
> |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
2869 |
> |
primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, |
2870 |
> |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
2871 |
> |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
2872 |
> |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
2873 |
> |
primitives/Torsion.cpp, primitives/Torsion.hpp, |
2874 |
> |
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
2875 |
> |
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
2876 |
> |
profiling/timing.F90, restraints/Restraints.cpp, |
2877 |
> |
restraints/Restraints.hpp, |
2878 |
> |
restraints/ThermoIntegrationForceManager.cpp, |
2879 |
> |
restraints/ThermoIntegrationForceManager.hpp, |
2880 |
> |
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
2881 |
> |
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
2882 |
> |
selection/NameFinder.cpp, selection/NameFinder.hpp, |
2883 |
> |
selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, |
2884 |
> |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
2885 |
> |
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
2886 |
> |
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, |
2887 |
> |
selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, |
2888 |
> |
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
2889 |
> |
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
2890 |
> |
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
2891 |
> |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
2892 |
> |
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
2893 |
> |
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
2894 |
> |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
2895 |
> |
types/DirectionalAtomType.hpp, types/FixedBondType.hpp, |
2896 |
> |
types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, |
2897 |
> |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
2898 |
> |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
2899 |
> |
types/MorseBondType.hpp, types/OplsTorsionType.hpp, |
2900 |
> |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
2901 |
> |
types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, |
2902 |
> |
types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, |
2903 |
> |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
2904 |
> |
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
2905 |
> |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
2906 |
> |
types/TorsionType.hpp, types/UreyBradleyBendType.hpp, |
2907 |
> |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, |
2908 |
> |
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
2909 |
> |
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
2910 |
> |
utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, |
2911 |
> |
utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, |
2912 |
> |
utils/PropertyMap.cpp, utils/PropertyMap.hpp, |
2913 |
> |
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
2914 |
> |
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
2915 |
> |
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
2916 |
> |
utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, |
2917 |
> |
utils/any.hpp, utils/definitions.F90, utils/fError.c, |
2918 |
> |
utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, |
2919 |
> |
utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, |
2920 |
> |
utils/residentMem.h, utils/simError.c, utils/simError.h, |
2921 |
> |
utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, |
2922 |
> |
visitors/AtomData.hpp, visitors/AtomVisitor.cpp, |
2923 |
> |
visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, |
2924 |
> |
visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, |
2925 |
> |
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
2926 |
> |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, |
2927 |
> |
visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, |
2928 |
> |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has |
2929 |
> |
been drafted to perform our indentation services |
2930 |
> |
|
2931 |
> |
2005-04-15 17:03 gezelter |
2932 |
> |
|
2933 |
> |
* configure, ac-tools/configure.in: Jedi mind-trick warning |
2934 |
> |
messages have been added to make users ignore CGAL. |
2935 |
> |
|
2936 |
> |
2005-04-15 13:41 tim |
2937 |
> |
|
2938 |
> |
* make/Makefile.in: fix make install |
2939 |
> |
|
2940 |
> |
2005-04-15 13:41 tim |
2941 |
> |
|
2942 |
> |
* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: |
2943 |
> |
add Makefile of samples |
2944 |
> |
|
2945 |
> |
2005-04-15 13:33 tim |
2946 |
> |
|
2947 |
> |
* samples/: lipid/Makefile, water/dimer/Makefile, |
2948 |
> |
water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not |
2949 |
> |
installed correctly |
2950 |
> |
|
2951 |
> |
2005-04-14 16:41 gezelter |
2952 |
> |
|
2953 |
> |
* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
2954 |
> |
make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, |
2955 |
> |
scripts/filepp, scripts/filepp.in: configure now searches for perl |
2956 |
> |
to use with filepp |
2957 |
> |
|
2958 |
> |
2005-04-14 16:20 gezelter |
2959 |
> |
|
2960 |
> |
* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |
2961 |
> |
MoLocator |
2962 |
> |
|
2963 |
> |
2005-04-14 14:12 gezelter |
2964 |
> |
|
2965 |
> |
* LICENSE: [no log message] |
2966 |
> |
|
2967 |
> |
2005-04-14 11:10 chuckv |
2968 |
> |
|
2969 |
> |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: |
2970 |
> |
nanorodbuilder now exit's when libCGAL is not present. |
2971 |
> |
|
2972 |
> |
2005-04-14 10:20 tim |
2973 |
> |
|
2974 |
> |
* src/io/make_nodes.h: fix one more warning message in make_nodes |
2975 |
> |
|
2976 |
> |
2005-04-13 18:36 chuckv |
2977 |
> |
|
2978 |
> |
* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed |
2979 |
> |
interface name for SGI Compiler |
2980 |
> |
|
2981 |
> |
2005-04-13 18:29 chrisfen |
2982 |
> |
|
2983 |
> |
* samples/water/ssde/ssde.md: oops... bad sample |
2984 |
> |
|
2985 |
> |
2005-04-13 18:00 chuckv |
2986 |
> |
|
2987 |
> |
* src/config.h.in: Change typo in CGAL. |
2988 |
> |
|
2989 |
> |
2005-04-13 17:43 tim |
2990 |
> |
|
2991 |
> |
* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, |
2992 |
> |
selection/SelectionCompiler.hpp: fix some warning messages |
2993 |
> |
|
2994 |
> |
2005-04-13 17:30 gezelter |
2995 |
> |
|
2996 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
2997 |
> |
make/Makefile.in, src/config.h.in, |
2998 |
> |
src/applications/nanoRodBuilder/Makefile, |
2999 |
> |
src/applications/nanoRodBuilder/Makefile.in, |
3000 |
> |
src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL |
3001 |
> |
checks |
3002 |
> |
|
3003 |
> |
2005-04-13 15:36 chuckv |
3004 |
> |
|
3005 |
> |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, |
3006 |
> |
DarkSide/LJ.F90, DarkSide/electrostatic.F90, |
3007 |
> |
DarkSide/electrostatic_interface.F90, |
3008 |
> |
DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, |
3009 |
> |
DarkSide/lj_interface.h, DarkSide/sticky.F90, |
3010 |
> |
DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added |
3011 |
> |
destroy methods for Fortran modules. |
3012 |
> |
|
3013 |
> |
2005-04-13 15:17 chuckv |
3014 |
> |
|
3015 |
> |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, |
3016 |
> |
shapes_interface.h: Added destroy method to clean up memory |
3017 |
> |
|
3018 |
> |
2005-04-13 13:41 tim |
3019 |
> |
|
3020 |
> |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
3021 |
> |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
3022 |
> |
io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, |
3023 |
> |
primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, |
3024 |
> |
types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are |
3025 |
> |
fixed |
3026 |
> |
|
3027 |
> |
2005-04-12 17:44 chuckv |
3028 |
> |
|
3029 |
> |
* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed |
3030 |
> |
for nanoRodBuilder. |
3031 |
> |
|
3032 |
> |
2005-04-12 17:42 tim |
3033 |
> |
|
3034 |
> |
* src/applications/: nanoRodBuilder/nanorodBuilder.cpp, |
3035 |
> |
simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder |
3036 |
> |
and simpleBuilder(forget to delete lattice) |
3037 |
> |
|
3038 |
> |
2005-04-12 17:33 tim |
3039 |
> |
|
3040 |
> |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
3041 |
> |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: |
3042 |
> |
refactory lattice |
3043 |
> |
|
3044 |
> |
2005-04-12 17:07 tim |
3045 |
> |
|
3046 |
> |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, |
3047 |
> |
CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, |
3048 |
> |
Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory |
3049 |
> |
LatticeFactory and LatticeCreator |
3050 |
> |
|
3051 |
> |
2005-04-12 16:58 tim |
3052 |
> |
|
3053 |
> |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
3054 |
> |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, |
3055 |
> |
brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
3056 |
> |
lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, |
3057 |
> |
lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, |
3058 |
> |
lattice/Makefile: refactory LatticeFactory and LatticeCreator |
3059 |
> |
|
3060 |
> |
2005-04-12 16:28 gezelter |
3061 |
> |
|
3062 |
> |
* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, |
3063 |
> |
vector_class.F90: cleaned up vector_class memory leak fix by |
3064 |
> |
deallocating in reverse order of how we allocated. Also migrated |
3065 |
> |
MoLocator into utils directory |
3066 |
> |
|
3067 |
> |
2005-04-12 16:27 gezelter |
3068 |
> |
|
3069 |
> |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, |
3070 |
> |
Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
3071 |
> |
LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice |
3072 |
> |
directory |
3073 |
> |
|
3074 |
> |
2005-04-12 16:27 gezelter |
3075 |
> |
|
3076 |
> |
* src/applications/: nanoRodBuilder/BaseLattice.cpp, |
3077 |
> |
nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, |
3078 |
> |
nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, |
3079 |
> |
nanoRodBuilder/LatticeCreator.hpp, |
3080 |
> |
nanoRodBuilder/LatticeFactory.cpp, |
3081 |
> |
nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, |
3082 |
> |
nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, |
3083 |
> |
nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, |
3084 |
> |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
3085 |
> |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
3086 |
> |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
3087 |
> |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, |
3088 |
> |
simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, |
3089 |
> |
simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of |
3090 |
> |
these files are now redundant |
3091 |
> |
|
3092 |
> |
2005-04-12 16:27 gezelter |
3093 |
> |
|
3094 |
> |
* src/UseTheForce/DarkSide/: atype_interface.F90, |
3095 |
> |
atype_interface.h: cleaned up memory leak fix |
3096 |
> |
|
3097 |
> |
2005-04-12 16:26 gezelter |
3098 |
> |
|
3099 |
> |
* make/Makefile.in: added lattice subdirectory |
3100 |
> |
|
3101 |
> |
2005-04-12 15:57 chrisfen |
3102 |
> |
|
3103 |
> |
* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added |
3104 |
> |
a space by accident |
3105 |
> |
|
3106 |
> |
2005-04-12 15:56 chrisfen |
3107 |
> |
|
3108 |
> |
* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added |
3109 |
> |
quadrupole sample |
3110 |
> |
|
3111 |
> |
2005-04-12 15:56 chrisfen |
3112 |
> |
|
3113 |
> |
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating |
3114 |
> |
samples |
3115 |
> |
|
3116 |
> |
2005-04-12 13:30 tim |
3117 |
> |
|
3118 |
> |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom |
3119 |
> |
type in fortran side |
3120 |
> |
|
3121 |
> |
2005-04-12 12:45 chuckv |
3122 |
> |
|
3123 |
> |
* src/utils/vector_class.F90: Further changes to vector_class |
3124 |
> |
destroy function. |
3125 |
> |
|
3126 |
> |
2005-04-12 12:39 chuckv |
3127 |
> |
|
3128 |
> |
* src/utils/vector_class.F90: Fixed pointer memory leak in |
3129 |
> |
vector_class. |
3130 |
> |
|
3131 |
> |
2005-04-12 12:12 chuckv |
3132 |
> |
|
3133 |
> |
* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, |
3134 |
> |
DarkSide/atype_interface.F90, DarkSide/atype_interface.h, |
3135 |
> |
DarkSide/eam.F90, DarkSide/eam_interface.F90, |
3136 |
> |
DarkSide/eam_interface.h: Updates to deallocate object in fortran. |
3137 |
> |
|
3138 |
> |
2005-04-12 09:24 chrisfen |
3139 |
> |
|
3140 |
> |
* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI |
3141 |
> |
output |
3142 |
> |
|
3143 |
> |
2005-04-11 19:29 chuckv |
3144 |
> |
|
3145 |
> |
* src/: UseTheForce/DarkSide/atype.F90, |
3146 |
> |
applications/nanoRodBuilder/Makefile: Changes to delete atypes... |
3147 |
> |
|
3148 |
> |
2005-04-11 19:28 chuckv |
3149 |
> |
|
3150 |
> |
* src/utils/vector_class.F90: Added code to delete vector. |
3151 |
|
|
3152 |
|
2005-04-11 16:58 tim |
3153 |
|
|