1 |
+ |
2006-01-16 10:26 gezelter |
2 |
+ |
|
3 |
+ |
* configure: Testing commit |
4 |
+ |
|
5 |
+ |
2006-01-13 16:57 chuckv |
6 |
+ |
|
7 |
+ |
* src/: UseTheForce/SC_FF.cpp, |
8 |
+ |
applications/nanoparticleBuilder/sphericalNanoparticle.cpp, |
9 |
+ |
io/Globals.cpp, io/Globals.hpp: Removed MixingRule from Globals. |
10 |
+ |
Handled by forceField now. |
11 |
+ |
|
12 |
+ |
2006-01-13 14:17 chuckv |
13 |
+ |
|
14 |
+ |
* src/io/Globals.cpp: Added NPAT to Globals integrators. |
15 |
+ |
|
16 |
+ |
2006-01-13 11:33 gezelter |
17 |
+ |
|
18 |
+ |
* Makefile: [no log message] |
19 |
+ |
|
20 |
+ |
2006-01-13 11:26 gezelter |
21 |
+ |
|
22 |
+ |
* Makefile: testing to make sure GNU make is the make that was used |
23 |
+ |
to build OOPSE |
24 |
+ |
|
25 |
+ |
2006-01-13 10:48 gezelter |
26 |
+ |
|
27 |
+ |
* configure, ac-tools/configure.in: changed compiler search order |
28 |
+ |
|
29 |
+ |
2006-01-12 19:09 chuckv |
30 |
+ |
|
31 |
+ |
* forceFields/SuttonChen.QSC.frc, forceFields/SuttonChen.frc, |
32 |
+ |
samples/metals/Sutton-Chen/Au_bulk.in, |
33 |
+ |
samples/metals/Sutton-Chen/Au_bulk_QSC.md, |
34 |
+ |
samples/metals/Sutton-Chen/Au_bulk_SC.md: Changes in Sutton-Chen |
35 |
+ |
units |
36 |
+ |
|
37 |
+ |
2006-01-12 16:16 gezelter |
38 |
+ |
|
39 |
+ |
* LICENSE, configure, src/applications/oopse/oopse.cpp: fixed some |
40 |
+ |
version info and the copyright date |
41 |
+ |
|
42 |
+ |
2006-01-12 15:52 gezelter |
43 |
+ |
|
44 |
+ |
* src/config.h.in: added some missing checks for header files |
45 |
+ |
(particularly zlib.h), used autoheader to help generate config.h.in |
46 |
+ |
|
47 |
+ |
2006-01-12 15:51 gezelter |
48 |
+ |
|
49 |
+ |
* configure, ac-tools/configure.in: added some missing checks for |
50 |
+ |
header files (particularly zlib.h) |
51 |
+ |
|
52 |
+ |
2006-01-12 15:19 gezelter |
53 |
+ |
|
54 |
+ |
* make/Makefile.in: fixed a dependency problem for the Executable |
55 |
+ |
builds |
56 |
+ |
|
57 |
+ |
2006-01-12 15:02 gezelter |
58 |
+ |
|
59 |
+ |
* samples/gbljtest/Makefile: Missing Makefile in this sample |
60 |
+ |
directory |
61 |
+ |
|
62 |
+ |
2006-01-12 15:01 gezelter |
63 |
+ |
|
64 |
+ |
* make/Makefile.in, samples/Makefile.in, samples/cutoff/Makefile: |
65 |
+ |
Old makefile.in no longer required |
66 |
+ |
|
67 |
+ |
2006-01-12 15:01 gezelter |
68 |
+ |
|
69 |
+ |
* forceFields/: Makefile, Makefile.in: All of the OpenBabel stuff |
70 |
+ |
needs to be installed |
71 |
+ |
|
72 |
+ |
2006-01-12 14:56 chuckv |
73 |
+ |
|
74 |
+ |
* src/io/DumpWriter.cpp: Changed formating. |
75 |
+ |
|
76 |
+ |
2006-01-12 11:47 chrisfen |
77 |
+ |
|
78 |
+ |
* samples/water/tip4p/tp4.md, |
79 |
+ |
src/UseTheForce/DarkSide/electrostatic.F90, |
80 |
+ |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
81 |
+ |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
82 |
+ |
src/brains/SimInfo.cpp: unifying function name in electrostatics |
83 |
+ |
|
84 |
+ |
2006-01-12 11:04 tim |
85 |
+ |
|
86 |
+ |
* samples/metals/: EAM/nanoparticle/Makefile, |
87 |
+ |
EAM/nanorod/Au_nanoparticle.in, EAM/nanorod/Makefile, |
88 |
+ |
Sutton-Chen/Makefile: fix make install problem for metals samples |
89 |
+ |
|
90 |
+ |
2006-01-12 10:22 tim |
91 |
+ |
|
92 |
+ |
* make/Makefile.in: remove samples/metals from install list. |
93 |
+ |
|
94 |
+ |
2006-01-12 09:31 tim |
95 |
+ |
|
96 |
+ |
* src/io/: ForceFieldOptions.cpp, Globals.cpp: filepp can not |
97 |
+ |
handle multiple line macro, just convert multiple line macro into |
98 |
+ |
single line macro. |
99 |
+ |
|
100 |
+ |
2006-01-11 23:13 chrisfen |
101 |
+ |
|
102 |
+ |
* src/: UseTheForce/DarkSide/electrostatic.F90, |
103 |
+ |
UseTheForce/DarkSide/neighborLists.F90, io/Globals.cpp: Made some |
104 |
+ |
changes to electrostatics for shifted-potential and shifted-force |
105 |
+ |
with mono and multipoles |
106 |
+ |
|
107 |
+ |
2006-01-11 18:04 gezelter |
108 |
+ |
|
109 |
+ |
* src/config.h.in, src/UseTheForce/doForces_interface.h, |
110 |
+ |
src/UseTheForce/DarkSide/atype_interface.h, |
111 |
+ |
src/UseTheForce/DarkSide/eam_interface.h, |
112 |
+ |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
113 |
+ |
src/UseTheForce/DarkSide/fForceOptions_interface.h, |
114 |
+ |
src/UseTheForce/DarkSide/gb_interface.h, |
115 |
+ |
src/UseTheForce/DarkSide/lj_interface.h, |
116 |
+ |
src/UseTheForce/DarkSide/shapes_interface.h, |
117 |
+ |
src/UseTheForce/DarkSide/simParallel_interface.h, |
118 |
+ |
src/UseTheForce/DarkSide/simulation_interface.h, |
119 |
+ |
src/UseTheForce/DarkSide/sticky_interface.h, |
120 |
+ |
src/UseTheForce/DarkSide/suttonchen_interface.h, |
121 |
+ |
src/UseTheForce/DarkSide/switcheroo_interface.h, |
122 |
+ |
src/mdParser/MDParser.g, src/profiling/mdProfile.cpp, |
123 |
+ |
src/utils/fError.c, configure, make/Makefile.in: autoconf |
124 |
+ |
modernization and cruft removal |
125 |
+ |
|
126 |
+ |
2006-01-11 18:04 gezelter |
127 |
+ |
|
128 |
+ |
* ac-tools/: aclocal.m4, configure.in, fortran90.m4: autoconf |
129 |
+ |
modernization and cruft-removal |
130 |
+ |
|
131 |
+ |
2006-01-11 17:50 tim |
132 |
+ |
|
133 |
+ |
* src/types/: BendStamp.hpp, BondStamp.hpp, TorsionStamp.hpp: fix |
134 |
+ |
some error messages |
135 |
+ |
|
136 |
+ |
2006-01-11 14:01 tim |
137 |
+ |
|
138 |
+ |
* src/: applications/staticProps/RhoZ.cpp, brains/SimCreator.cpp, |
139 |
+ |
io/Globals.cpp, types/AtomStamp.cpp, types/BendStamp.hpp, |
140 |
+ |
types/BondStamp.hpp, types/DataHolder.hpp, types/MoleculeStamp.cpp, |
141 |
+ |
types/TorsionStamp.hpp, utils/OOPSEException.hpp, |
142 |
+ |
utils/StringUtils.hpp: instead of printing to std::cout, throwing |
143 |
+ |
an exception when error is found. |
144 |
+ |
|
145 |
+ |
2006-01-11 13:41 gezelter |
146 |
+ |
|
147 |
+ |
* src/types/: AtomStamp.hpp, MoleculeStamp.cpp: Fixed a spelling |
148 |
+ |
error |
149 |
+ |
|
150 |
+ |
2006-01-10 17:55 chuckv |
151 |
+ |
|
152 |
+ |
* forceFields/SuttonChen.frc: Changed conversion factor. |
153 |
+ |
|
154 |
+ |
2006-01-10 16:14 chuckv |
155 |
+ |
|
156 |
+ |
* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
157 |
+ |
src/UseTheForce/DarkSide/suttonchen.F90: Sutton and Chen should be |
158 |
+ |
working now. |
159 |
+ |
|
160 |
+ |
2006-01-09 17:22 chuckv |
161 |
+ |
|
162 |
+ |
* src/UseTheForce/doForces.F90: Fixed SC bug with SIM_uses_SC |
163 |
+ |
|
164 |
+ |
2006-01-09 17:14 tim |
165 |
+ |
|
166 |
+ |
* src/applications/staticProps/: Makefile, RhoZ.cpp, RhoZ.hpp, |
167 |
+ |
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
168 |
+ |
StaticPropsCmd.h: fixing RhoZ |
169 |
+ |
|
170 |
+ |
2006-01-09 14:26 chuckv |
171 |
+ |
|
172 |
+ |
* forceFields/SuttonChen.frc, |
173 |
+ |
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
174 |
+ |
src/io/LennardJonesAtomTypesSectionParser.cpp, |
175 |
+ |
src/io/SCAtomTypesSectionParser.cpp: Added energy scaling to |
176 |
+ |
section parsers. |
177 |
+ |
|
178 |
+ |
2006-01-09 14:11 tim |
179 |
+ |
|
180 |
+ |
* src/: io/ForceFieldOptions.hpp, utils/StringUtils.cpp, |
181 |
+ |
utils/StringUtils.hpp: replace isType<int> with isInteger |
182 |
+ |
|
183 |
+ |
2006-01-06 16:15 tim |
184 |
+ |
|
185 |
+ |
* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: remove extra |
186 |
+ |
forceFieldOptions from SC_FF |
187 |
+ |
|
188 |
+ |
2006-01-06 15:27 chuckv |
189 |
+ |
|
190 |
+ |
* forceFields/SuttonChen.frc: Add force file. |
191 |
+ |
|
192 |
+ |
2005-12-31 17:42 chuckv |
193 |
+ |
|
194 |
+ |
* src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen no longer |
195 |
+ |
segfaults or produces 0 potential, but rather produces Inf for the |
196 |
+ |
potential. Progress.... |
197 |
+ |
|
198 |
+ |
2005-12-30 18:15 chuckv |
199 |
+ |
|
200 |
+ |
* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
201 |
+ |
src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
202 |
+ |
src/UseTheForce/DarkSide/suttonchen.F90, src/brains/SimInfo.cpp, |
203 |
+ |
src/io/ForceFieldOptions.cpp, src/io/ForceFieldOptions.hpp: More |
204 |
+ |
Sutton-Chen bug fixes. |
205 |
+ |
|
206 |
+ |
2005-12-30 16:25 tim |
207 |
+ |
|
208 |
+ |
* src/: UseTheForce/doForces.F90, brains/Thermo.cpp: Long range |
209 |
+ |
potential return from fortran is already accumulated, it should not |
210 |
+ |
be accumulated again; nGroupTypesCol is not initialized; |
211 |
+ |
GroupMaxCutoffCol is not allocated; |
212 |
+ |
|
213 |
+ |
2005-12-30 10:32 tim |
214 |
+ |
|
215 |
+ |
* make/Makefile.in, src/brains/SimCreator.cpp: In order to compile |
216 |
+ |
MPI version, we need to cast const char* to void* for |
217 |
+ |
stringstream.str(); Previous Makefile use bjects of single version |
218 |
+ |
to make the MPI library; |
219 |
+ |
|
220 |
+ |
2005-12-29 19:18 chuckv |
221 |
+ |
|
222 |
+ |
* make/Makefile.in, samples/metals/Makefile, |
223 |
+ |
src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
224 |
+ |
src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen bug fixes. |
225 |
+ |
Almost there... |
226 |
+ |
|
227 |
+ |
2005-12-29 15:19 chuckv |
228 |
+ |
|
229 |
+ |
* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Changes in |
230 |
+ |
forcefield. |
231 |
+ |
|
232 |
+ |
2005-12-29 15:07 chuckv |
233 |
+ |
|
234 |
+ |
* samples/metals/Sutton-Chen/: Au_bulk.in, Au_bulk_SC.md, Makefile, |
235 |
+ |
metals.md: added files for sutton-chen |
236 |
+ |
|
237 |
+ |
2005-12-29 11:37 chuckv |
238 |
+ |
|
239 |
+ |
* samples/metals/EAM/nanorod/: Au_nanoparticle_FCC.md, Makefile, |
240 |
+ |
metals.md: More cvs changing. |
241 |
+ |
|
242 |
+ |
2005-12-29 11:34 chuckv |
243 |
+ |
|
244 |
+ |
* samples/metals/Au_nanoparticle.in: More moving... |
245 |
+ |
|
246 |
+ |
2005-12-29 11:33 chuckv |
247 |
+ |
|
248 |
+ |
* samples/metals/EAM/nanoparticle/: |
249 |
+ |
Au-Core-Ag-Shell_Nanoparticle.in, Au-Core-Ag-Shell_Nanoparticle.md, |
250 |
+ |
Au_nanoparticle.in, Au_nanoparticle.md, Makefile, metals.md: More |
251 |
+ |
changes to directory structure. |
252 |
+ |
|
253 |
+ |
2005-12-29 11:21 chuckv |
254 |
+ |
|
255 |
+ |
* samples/metals/EAM/: Au_bulk.in, Au_bulk_FBD.md, |
256 |
+ |
Au_bulk_voter.md, Makefile, metals.md: More Directory changes... |
257 |
+ |
|
258 |
+ |
2005-12-29 11:17 chuckv |
259 |
+ |
|
260 |
+ |
* samples/metals/: Au-Core-Ag-Shell_Nanoparticle.in, |
261 |
+ |
Au-Core-Ag-Shell_Nanoparticle.md, Au_bulk.in, Au_bulk_FBD.md, |
262 |
+ |
Au_bulk_voter.md, Au_nanoparticle.md, metals.md: More changing of |
263 |
+ |
directory structure |
264 |
+ |
|
265 |
+ |
2005-12-29 11:03 chuckv |
266 |
+ |
|
267 |
+ |
* src/: UseTheForce/DarkSide/fForceOptions_interface.F90, |
268 |
+ |
brains/SimCreator.cpp: Fixed issue with symbol naming and added |
269 |
+ |
call to set force options in SimCreator. |
270 |
+ |
|
271 |
+ |
2005-12-28 16:44 chuckv |
272 |
+ |
|
273 |
+ |
* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp: More |
274 |
+ |
changes to forcefield options. |
275 |
+ |
|
276 |
+ |
2005-12-28 16:42 chuckv |
277 |
+ |
|
278 |
+ |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: Force options |
279 |
+ |
passed to fortran. |
280 |
+ |
|
281 |
+ |
2005-12-23 18:04 chuckv |
282 |
+ |
|
283 |
+ |
* src/: UseTheForce/DarkSide/fForceOptions_interface.h, |
284 |
+ |
io/ForceFieldOptions.cpp, io/ForceFieldOptions.hpp: Force option |
285 |
+ |
changes. |
286 |
+ |
|
287 |
+ |
2005-12-16 16:52 tim |
288 |
+ |
|
289 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
290 |
+ |
src/config.h.in, src/UseTheForce/DarkSide/gb.F90, |
291 |
+ |
src/openbabel/bitvec.cpp, src/openbabel/bondtyper.cpp, |
292 |
+ |
src/openbabel/chains.cpp, src/openbabel/chiral.cpp, |
293 |
+ |
src/openbabel/data.cpp, src/openbabel/fingerprint.cpp, |
294 |
+ |
src/openbabel/fingerprintformat.cpp, src/openbabel/generic.cpp, |
295 |
+ |
src/openbabel/gromos96format.hpp, src/openbabel/kekulize.cpp, |
296 |
+ |
src/openbabel/matrix3x3.cpp, src/openbabel/mol.cpp, |
297 |
+ |
src/openbabel/molchrg.cpp, src/openbabel/obatom.cpp, |
298 |
+ |
src/openbabel/obbond.cpp, src/openbabel/oberror.cpp, |
299 |
+ |
src/openbabel/oberror.hpp, src/openbabel/obmolecformat.hpp, |
300 |
+ |
src/openbabel/obutil.cpp, src/openbabel/patty.cpp, |
301 |
+ |
src/openbabel/pdbformat.cpp, src/openbabel/phmodel.cpp, |
302 |
+ |
src/openbabel/povrayformat.hpp, src/openbabel/residue.cpp, |
303 |
+ |
src/openbabel/ring.cpp, src/openbabel/rotor.cpp, |
304 |
+ |
src/openbabel/smilesformat.cpp, src/openbabel/tinkerformat.hpp, |
305 |
+ |
src/openbabel/typer.cpp, src/openbabel/xyzformat.cpp: changed |
306 |
+ |
__FUNCTION__ to __func__ to match C99 standard, and then added an |
307 |
+ |
autoconf test to check for __func__ usability. Changed some |
308 |
+ |
default compile flags for the Sun architecture |
309 |
+ |
|
310 |
+ |
2005-12-16 14:01 gezelter |
311 |
+ |
|
312 |
+ |
* ac-tools/AC_CXX_HAVE_STL.m4: added the STL check |
313 |
+ |
|
314 |
+ |
2005-12-16 13:55 tim |
315 |
+ |
|
316 |
+ |
* src/utils/: CaseConversion.hpp, ParameterManager.hpp: make minor |
317 |
+ |
change to build oopse under solaris |
318 |
+ |
|
319 |
+ |
2005-12-16 13:26 tim |
320 |
+ |
|
321 |
+ |
* src/: brains/SimCreator.cpp, io/Globals.cpp, |
322 |
+ |
types/MoleculeStamp.cpp, utils/Predicate.hpp: the standard library |
323 |
+ |
came with SUN compiler does not have a conforming std::use_facet, |
324 |
+ |
define a macro to handle it. Adding exception handling to |
325 |
+ |
SimCreator. |
326 |
+ |
|
327 |
+ |
2005-12-16 10:53 gezelter |
328 |
+ |
|
329 |
+ |
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
330 |
+ |
GB-Ar-traditional.md, gb-ar.in: Removed one parasitic argon atom |
331 |
+ |
which was living inside the GB particle. No alien-like ripping out |
332 |
+ |
of the stomach was required. |
333 |
+ |
|
334 |
+ |
2005-12-15 21:57 tim |
335 |
+ |
|
336 |
+ |
* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
337 |
+ |
MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
338 |
+ |
MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: |
339 |
+ |
replace grammar for numerical parsing |
340 |
+ |
|
341 |
+ |
2005-12-15 16:43 gezelter |
342 |
+ |
|
343 |
+ |
* src/UseTheForce/doForces.F90: fixed a cutoff bug |
344 |
+ |
|
345 |
+ |
2005-12-15 09:48 gezelter |
346 |
+ |
|
347 |
+ |
* src/antlr/: CharScanner.hpp, config.hpp: Removing compiler |
348 |
+ |
dependencies and replacing them with real autoconf checks |
349 |
+ |
|
350 |
+ |
2005-12-15 09:47 gezelter |
351 |
+ |
|
352 |
+ |
* configure, ac-tools/AC_CXX_NAMESPACES.m4, ac-tools/AC_CXX_STD.m4, |
353 |
+ |
ac-tools/configure.in, src/config.h.in: Adding checks for various |
354 |
+ |
features used by ANTLR |
355 |
+ |
|
356 |
+ |
2005-12-14 13:02 tim |
357 |
+ |
|
358 |
+ |
* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
359 |
+ |
MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
360 |
+ |
MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: fix a |
361 |
+ |
nasty negative integer parsing problem by refining the grammar |
362 |
+ |
|
363 |
+ |
2005-12-12 14:32 gezelter |
364 |
+ |
|
365 |
+ |
* src/: UseTheForce/doForces_interface.F90, |
366 |
+ |
UseTheForce/doForces_interface.h, |
367 |
+ |
UseTheForce/DarkSide/electrostatic.F90, |
368 |
+ |
UseTheForce/DarkSide/electrostatic_interface.F90, |
369 |
+ |
UseTheForce/DarkSide/electrostatic_interface.h, |
370 |
+ |
brains/MoleculeCreator.cpp, brains/SimInfo.cpp, |
371 |
+ |
math/ChebyshevPolynomials.hpp, openbabel/obconversion.hpp: made |
372 |
+ |
some minor changes to allow compilation with the portland group |
373 |
+ |
compilers |
374 |
+ |
|
375 |
+ |
2005-12-10 11:54 tim |
376 |
+ |
|
377 |
+ |
* src/: types/MoleculeStamp.cpp, utils/Tuple.hpp: fixed compilation |
378 |
+ |
problem for icc7 |
379 |
+ |
|
380 |
+ |
2005-12-09 16:18 gezelter |
381 |
+ |
|
382 |
+ |
* src/utils/CaseConversion.hpp: added missing include |
383 |
+ |
|
384 |
+ |
2005-12-09 12:11 gezelter |
385 |
+ |
|
386 |
+ |
* configure, ac-tools/aclocal.m4: added some checks for pathscale |
387 |
+ |
compiler |
388 |
+ |
|
389 |
+ |
2005-12-08 17:05 gezelter |
390 |
+ |
|
391 |
+ |
* src/io/ForceFieldOptions.cpp: added copyright |
392 |
+ |
|
393 |
+ |
2005-12-08 17:04 gezelter |
394 |
+ |
|
395 |
+ |
* src/UseTheForce/doForces.F90: added info printout |
396 |
+ |
|
397 |
+ |
2005-12-08 17:04 gezelter |
398 |
+ |
|
399 |
+ |
* configure, ac-tools/configure.in: added pathscale |
400 |
+ |
|
401 |
+ |
2005-12-08 10:38 chuckv |
402 |
+ |
|
403 |
+ |
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/DUFF.cpp, |
404 |
+ |
UseTheForce/EAM_FF.cpp, UseTheForce/SC_FF.cpp, |
405 |
+ |
UseTheForce/SHAPES_FF.cpp, io/BendTypesSectionParser.cpp, |
406 |
+ |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
407 |
+ |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
408 |
+ |
io/ChargeAtomTypesSectionParser.hpp, |
409 |
+ |
io/DirectionalAtomTypesSectionParser.cpp, |
410 |
+ |
io/DirectionalAtomTypesSectionParser.hpp, |
411 |
+ |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
412 |
+ |
io/GayBerneAtomTypesSectionParser.cpp, |
413 |
+ |
io/GayBerneAtomTypesSectionParser.hpp, |
414 |
+ |
io/MultipoleAtomTypesSectionParser.cpp, |
415 |
+ |
io/MultipoleAtomTypesSectionParser.hpp, |
416 |
+ |
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
417 |
+ |
io/ShapeAtomTypesSectionParser.cpp, |
418 |
+ |
io/ShapeAtomTypesSectionParser.hpp, |
419 |
+ |
io/StickyAtomTypesSectionParser.cpp, |
420 |
+ |
io/StickyAtomTypesSectionParser.hpp, |
421 |
+ |
io/StickyPowerAtomTypesSectionParser.cpp, |
422 |
+ |
io/StickyPowerAtomTypesSectionParser.hpp, |
423 |
+ |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp: |
424 |
+ |
Wow thats alot o' files. Now passing forceFieldOptions to all of |
425 |
+ |
the parsers. |
426 |
+ |
|
427 |
+ |
2005-12-07 18:10 chuckv |
428 |
+ |
|
429 |
+ |
* src/UseTheForce/: CLAYFF.cpp, DUFF.cpp, EAM_FF.cpp, EAM_FF.hpp, |
430 |
+ |
SHAPES_FF.cpp, SHAPES_FF.hpp: This should really break things.... |
431 |
+ |
Started adding support for ForceOptions to section parsers. |
432 |
+ |
|
433 |
+ |
2005-12-07 18:01 gezelter |
434 |
+ |
|
435 |
+ |
* src/UseTheForce/DarkSide/gb_interface.h: [no log message] |
436 |
+ |
|
437 |
+ |
2005-12-07 18:00 chuckv |
438 |
+ |
|
439 |
+ |
* src/io/: LennardJonesAtomTypesSectionParser.cpp, |
440 |
+ |
LennardJonesAtomTypesSectionParser.hpp: Added forceOptions to |
441 |
+ |
section parser |
442 |
+ |
|
443 |
+ |
2005-12-07 14:58 chuckv |
444 |
+ |
|
445 |
+ |
* src/UseTheForce/DarkSide/: LJ.F90, lj_interface.F90, |
446 |
+ |
lj_interface.h, suttonchen.F90, suttonchen_interface.F90, |
447 |
+ |
suttonchen_interface.h: Removed geometric distance mixing from |
448 |
+ |
individual modules and now use force options to detemine what the |
449 |
+ |
deal is. |
450 |
+ |
|
451 |
+ |
2005-12-07 14:46 chuckv |
452 |
+ |
|
453 |
+ |
* src/UseTheForce/: fForceOptions.h, DarkSide/fForceOptions.F90: |
454 |
+ |
Further fixes for compiler issues. |
455 |
+ |
|
456 |
+ |
2005-12-07 14:44 chuckv |
457 |
+ |
|
458 |
+ |
* src/UseTheForce/fForceOptions.h: Fixed ifc public-private issue. |
459 |
+ |
|
460 |
+ |
2005-12-07 14:38 chuckv |
461 |
+ |
|
462 |
+ |
* src/UseTheForce/DarkSide/: Makefile, fForceOptions.F90, |
463 |
+ |
fForceOptions_interface.F90, fForceOptions_interface.h: Added |
464 |
+ |
support for fortran force options. |
465 |
+ |
|
466 |
+ |
2005-12-06 16:01 tim |
467 |
+ |
|
468 |
+ |
* src/types/MoleculeStamp.cpp: Fixed a bug in checkTorsion |
469 |
+ |
|
470 |
+ |
2005-12-06 14:26 chuckv |
471 |
+ |
|
472 |
+ |
* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: Changes to SC. |
473 |
+ |
|
474 |
+ |
2005-12-06 12:53 chuckv |
475 |
+ |
|
476 |
+ |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
477 |
+ |
GeometryBuilder.hpp, nanorodBuilder.cpp: Changes to build twinned |
478 |
+ |
crystal |
479 |
+ |
|
480 |
+ |
2005-12-06 12:52 chuckv |
481 |
+ |
|
482 |
+ |
* src/io/: DumpWriter.cpp, DumpWriter.hpp: Overloaded interface for |
483 |
+ |
dumpwriter. |
484 |
+ |
|
485 |
+ |
2005-12-06 11:49 tim |
486 |
+ |
|
487 |
+ |
* samples/: alkane/alkanes.md, alkane/butane.md, argon/500.md, |
488 |
+ |
argon/ar864.md, argon/argonNVT.md, argon/lj.md, |
489 |
+ |
dipole/splitDipole.md, dipole/splitInWater.md, dipole/split_SSD.md, |
490 |
+ |
dipole/twoSplitDipole.md, dipole/water.md, gbljtest/2gb.md, |
491 |
+ |
gbljtest/gb.md, gbljtest/gb2lj1.md, gbljtest/gbRotRoundX.md, |
492 |
+ |
gbljtest/gbRotRoundY.md, gbljtest/gbRotRoundZ.md, gbljtest/lj.md, |
493 |
+ |
lipid/5x5.md, lipid/lipid.md, lipid/water.md, |
494 |
+ |
metals/Au-Core-Ag-Shell_Nanoparticle.md, metals/Au_bulk_FBD.md, |
495 |
+ |
metals/Au_bulk_voter.md, metals/Au_nanoparticle.md, |
496 |
+ |
metals/metals.md, minimizer/ssdEM.md, minimizer/tip4p_two.md, |
497 |
+ |
minimizer/water.md, shape/linear.md, |
498 |
+ |
thermoIntegration/liquid/ssde.md, |
499 |
+ |
thermoIntegration/liquid/water.md, thermoIntegration/solid/ssde.md, |
500 |
+ |
thermoIntegration/solid/water.md, water/dimer/cl.md, |
501 |
+ |
water/dimer/mix.md, water/dimer/mix2.md, water/dimer/ssd.md, |
502 |
+ |
water/dimer/tap.md, water/dimer/two.md, water/dimer/water.md, |
503 |
+ |
water/spce/spce.md, water/spce/water.md, water/ssd/ssd.md, |
504 |
+ |
water/ssd/water.md, water/ssd-ion/ssdCl.md, water/ssd-ion/water.md, |
505 |
+ |
water/ssde/ssde.md, water/ssde/water.md, water/ssdrf/ssdrf.md, |
506 |
+ |
water/ssdrf/water.md, water/tap/tap.md, water/tap/water.md, |
507 |
+ |
water/tip3p_ice/tp3.md, water/tip3p_ice/water.md, |
508 |
+ |
water/tip4p/tp4.md, water/tip4p/water.md, zcons/water.md, |
509 |
+ |
zcons/zconsFixed.md, zcons/zconsMoving.md: remove deprecated |
510 |
+ |
keywords from samples |
511 |
+ |
|
512 |
+ |
2005-12-05 18:37 tim |
513 |
+ |
|
514 |
+ |
* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp, |
515 |
+ |
Globals.cpp, Makefile: Fix parsing error in OptionSectionParser |
516 |
+ |
|
517 |
+ |
2005-12-05 17:23 gezelter |
518 |
+ |
|
519 |
+ |
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/CLAYFF.hpp, |
520 |
+ |
UseTheForce/Makefile, brains/Register.cpp, |
521 |
+ |
io/ForceFieldOptions.hpp, io/OptionSectionParser.cpp: Adding |
522 |
+ |
handler for CLAY force field |
523 |
+ |
|
524 |
+ |
2005-12-05 16:45 chuckv |
525 |
+ |
|
526 |
+ |
* src/openbabel/: zipstream.hpp, zipstreamimpl.hpp: Fixed build bug |
527 |
+ |
in openbabel. |
528 |
+ |
|
529 |
+ |
2005-12-05 14:10 tim |
530 |
+ |
|
531 |
+ |
* src/types/MoleculeStamp.cpp: reformat error message |
532 |
+ |
|
533 |
+ |
2005-12-05 14:07 gezelter |
534 |
+ |
|
535 |
+ |
* forceFields/CLAYFF.frc: Adding .frc file for CLAYFF |
536 |
+ |
|
537 |
+ |
2005-12-05 13:23 tim |
538 |
+ |
|
539 |
+ |
* src/: types/AtomStamp.cpp, types/AtomStamp.hpp, |
540 |
+ |
types/BendStamp.hpp, types/MoleculeStamp.cpp, |
541 |
+ |
types/MoleculeStamp.hpp, types/TorsionStamp.hpp, utils/Tuple.hpp: |
542 |
+ |
adding more checking for topology |
543 |
+ |
|
544 |
+ |
2005-12-02 17:37 gezelter |
545 |
+ |
|
546 |
+ |
* src/antlr/TokenStreamRewriteEngine.cpp: Spurious semicolon |
547 |
+ |
removal |
548 |
+ |
|
549 |
+ |
2005-12-02 17:37 gezelter |
550 |
+ |
|
551 |
+ |
* src/config.h.in: We've made big changes. This isn't 2.0 anymore. |
552 |
+ |
|
553 |
+ |
2005-12-02 17:37 gezelter |
554 |
+ |
|
555 |
+ |
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
556 |
+ |
GB-Ar-traditional.md, cutoff_test.md, gb.md, lj.md, max.md, mix.md, |
557 |
+ |
traditional.md: removing deprecated nAtoms and nComponents lines |
558 |
+ |
|
559 |
+ |
2005-12-02 15:34 tim |
560 |
+ |
|
561 |
+ |
* src/selection/SelectionToken.cpp: adding SelectionToken.cpp |
562 |
+ |
|
563 |
+ |
2005-12-02 15:18 tim |
564 |
+ |
|
565 |
+ |
* src/types/: FragmentStamp.cpp, FragmentStamp.hpp: Adding |
566 |
+ |
FragmentStamp |
567 |
+ |
|
568 |
+ |
2005-12-02 15:11 gezelter |
569 |
+ |
|
570 |
+ |
* src/openbabel/: matrix3x3.cpp, matrix3x3.hpp: Errors are no |
571 |
+ |
longer thrown with consts (fixes compilation bug on the Mac). |
572 |
+ |
|
573 |
+ |
2005-12-02 15:10 gezelter |
574 |
+ |
|
575 |
+ |
* src/integrators/VelocityVerletIntegrator.cpp: Got rid of spurious |
576 |
+ |
printing out of timestep |
577 |
+ |
|
578 |
+ |
2005-12-02 15:10 gezelter |
579 |
+ |
|
580 |
+ |
* src/brains/ForceManager.cpp: Got rid of spurious printing out of |
581 |
+ |
junk |
582 |
+ |
|
583 |
+ |
2005-12-02 15:10 gezelter |
584 |
+ |
|
585 |
+ |
* make/Makefile.in: Change build process for libOOPSE.a so that the |
586 |
+ |
libraries aren't unpacked. libOOPSE.a is now made directly from |
587 |
+ |
the object files |
588 |
+ |
|
589 |
+ |
2005-12-02 15:09 gezelter |
590 |
+ |
|
591 |
+ |
* configure, ac-tools/configure.in: added check for egrep (grep -E) |
592 |
+ |
needed for new build of libOOPSE.a |
593 |
+ |
|
594 |
+ |
2005-12-02 13:43 tim |
595 |
+ |
|
596 |
+ |
* src/types/DataHolder.hpp: adding DataHolder |
597 |
+ |
|
598 |
+ |
2005-12-02 12:01 gezelter |
599 |
+ |
|
600 |
+ |
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
601 |
+ |
GB-Ar-traditional.md, gb-ar.in, gb.md: Added Gay-Berne / Argon test |
602 |
+ |
case for the cutoff policies |
603 |
+ |
|
604 |
+ |
2005-12-02 10:38 tim |
605 |
+ |
|
606 |
+ |
* make/Makefile.in: update Makefile |
607 |
+ |
|
608 |
+ |
2005-12-02 10:38 tim |
609 |
+ |
|
610 |
+ |
* src/: antlr/ANTLRException.hpp, antlr/ANTLRUtil.cpp, |
611 |
+ |
antlr/ANTLRUtil.hpp, antlr/AST.hpp, antlr/ASTArray.hpp, |
612 |
+ |
antlr/ASTFactory.cpp, antlr/ASTFactory.hpp, antlr/ASTNULLType.cpp, |
613 |
+ |
antlr/ASTNULLType.hpp, antlr/ASTPair.hpp, antlr/ASTRefCount.cpp, |
614 |
+ |
antlr/ASTRefCount.hpp, antlr/BaseAST.cpp, antlr/BaseAST.hpp, |
615 |
+ |
antlr/BitSet.cpp, antlr/BitSet.hpp, antlr/CharBuffer.cpp, |
616 |
+ |
antlr/CharBuffer.hpp, antlr/CharInputBuffer.hpp, |
617 |
+ |
antlr/CharScanner.cpp, antlr/CharScanner.hpp, |
618 |
+ |
antlr/CharStreamException.hpp, antlr/CharStreamIOException.hpp, |
619 |
+ |
antlr/CircularQueue.hpp, antlr/CommonAST.cpp, antlr/CommonAST.hpp, |
620 |
+ |
antlr/CommonASTWithHiddenTokens.cpp, |
621 |
+ |
antlr/CommonASTWithHiddenTokens.hpp, |
622 |
+ |
antlr/CommonHiddenStreamToken.cpp, |
623 |
+ |
antlr/CommonHiddenStreamToken.hpp, antlr/CommonToken.cpp, |
624 |
+ |
antlr/CommonToken.hpp, antlr/IOException.hpp, |
625 |
+ |
antlr/InputBuffer.cpp, antlr/InputBuffer.hpp, antlr/LLkParser.cpp, |
626 |
+ |
antlr/LLkParser.hpp, antlr/LexerSharedInputState.hpp, |
627 |
+ |
antlr/Makefile, antlr/MismatchedCharException.cpp, |
628 |
+ |
antlr/MismatchedCharException.hpp, |
629 |
+ |
antlr/MismatchedTokenException.cpp, |
630 |
+ |
antlr/MismatchedTokenException.hpp, antlr/NoViableAltException.cpp, |
631 |
+ |
antlr/NoViableAltException.hpp, |
632 |
+ |
antlr/NoViableAltForCharException.cpp, |
633 |
+ |
antlr/NoViableAltForCharException.hpp, antlr/Parser.cpp, |
634 |
+ |
antlr/Parser.hpp, antlr/ParserSharedInputState.hpp, |
635 |
+ |
antlr/RecognitionException.cpp, antlr/RecognitionException.hpp, |
636 |
+ |
antlr/RefCount.hpp, antlr/SemanticException.hpp, antlr/String.cpp, |
637 |
+ |
antlr/String.hpp, antlr/Token.cpp, antlr/Token.hpp, |
638 |
+ |
antlr/TokenBuffer.cpp, antlr/TokenBuffer.hpp, |
639 |
+ |
antlr/TokenRefCount.cpp, antlr/TokenRefCount.hpp, |
640 |
+ |
antlr/TokenStream.hpp, antlr/TokenStreamBasicFilter.cpp, |
641 |
+ |
antlr/TokenStreamBasicFilter.hpp, antlr/TokenStreamException.hpp, |
642 |
+ |
antlr/TokenStreamHiddenTokenFilter.cpp, |
643 |
+ |
antlr/TokenStreamHiddenTokenFilter.hpp, |
644 |
+ |
antlr/TokenStreamIOException.hpp, |
645 |
+ |
antlr/TokenStreamRecognitionException.hpp, |
646 |
+ |
antlr/TokenStreamRetryException.hpp, |
647 |
+ |
antlr/TokenStreamRewriteEngine.cpp, |
648 |
+ |
antlr/TokenStreamRewriteEngine.hpp, antlr/TokenStreamSelector.cpp, |
649 |
+ |
antlr/TokenStreamSelector.hpp, antlr/TokenWithIndex.hpp, |
650 |
+ |
antlr/TreeParser.cpp, antlr/TreeParser.hpp, |
651 |
+ |
antlr/TreeParserSharedInputState.hpp, antlr/config.hpp, |
652 |
+ |
applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
653 |
+ |
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
654 |
+ |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
655 |
+ |
constraints/ZconstraintForceManager.cpp, |
656 |
+ |
integrators/VelocityVerletIntegrator.cpp, io/BASS_interface.cpp, |
657 |
+ |
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
658 |
+ |
io/BASSlex.l, io/BASSyacc.y, io/Globals.cpp, io/Globals.hpp, |
659 |
+ |
io/LinkedAssign.cpp, io/LinkedAssign.hpp, io/Makefile, |
660 |
+ |
io/ZConsReader.cpp, io/interface.c, io/make_nodes.c, |
661 |
+ |
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, |
662 |
+ |
io/parse_interface.h, io/parse_me.h, io/parse_tree.c, |
663 |
+ |
io/parse_tree.h, mdParser/FilenameObserver.cpp, |
664 |
+ |
mdParser/FilenameObserver.hpp, mdParser/MDLexer.cpp, |
665 |
+ |
mdParser/MDLexer.hpp, mdParser/MDParser.cpp, mdParser/MDParser.g, |
666 |
+ |
mdParser/MDParser.hpp, mdParser/MDTokenTypes.hpp, |
667 |
+ |
mdParser/MDTreeParser.cpp, mdParser/MDTreeParser.g, |
668 |
+ |
mdParser/MDTreeParser.hpp, mdParser/MDTreeParserTokenTypes.hpp, |
669 |
+ |
mdParser/Makefile, mdParser/SimplePreprocessor.hpp, |
670 |
+ |
openbabel/obconversion.cpp, openbabel/oopseformat.cpp, |
671 |
+ |
openbabel/xyzformat.cpp, primitives/RigidBody.cpp, |
672 |
+ |
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
673 |
+ |
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
674 |
+ |
selection/Makefile, selection/NameFinder.cpp, |
675 |
+ |
selection/NameFinder.hpp, selection/SelectionCompiler.hpp, |
676 |
+ |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
677 |
+ |
selection/SelectionManager.hpp, selection/SelectionToken.hpp, |
678 |
+ |
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.hpp, |
679 |
+ |
types/AtomStamp.cpp, types/AtomStamp.hpp, types/BendStamp.cpp, |
680 |
+ |
types/BendStamp.hpp, types/BondStamp.cpp, types/BondStamp.hpp, |
681 |
+ |
types/Component.cpp, types/Component.hpp, |
682 |
+ |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
683 |
+ |
types/MakeStamps.cpp, types/MakeStamps.hpp, types/Makefile, |
684 |
+ |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
685 |
+ |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
686 |
+ |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
687 |
+ |
types/ZconStamp.cpp, types/ZconStamp.hpp, types/ZconsStamp.cpp, |
688 |
+ |
types/ZconsStamp.hpp, utils/BitSet.cpp, utils/BitSet.hpp, |
689 |
+ |
utils/Makefile.in, utils/MoLocator.cpp, utils/OOPSEBitSet.cpp, |
690 |
+ |
utils/OOPSEBitSet.hpp, utils/StringTokenizer.cpp, |
691 |
+ |
utils/StringTokenizer.hpp, visitors/ZconsVisitor.cpp: End of the |
692 |
+ |
Link --> List Return of the Oject-Oriented replace yacc/lex parser |
693 |
+ |
with antlr parser |
694 |
+ |
|
695 |
+ |
2005-11-30 16:00 chuckv |
696 |
+ |
|
697 |
+ |
* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Code to |
698 |
+ |
calculate rho(Z) to calculate density profiles for water slabs. |
699 |
+ |
|
700 |
+ |
2005-11-29 17:54 chuckv |
701 |
+ |
|
702 |
+ |
* configure, ac-tools/configure.in: added checks for some functions |
703 |
+ |
to configure script |
704 |
+ |
|
705 |
+ |
2005-11-22 20:05 chuckv |
706 |
+ |
|
707 |
+ |
* src/openbabel/: Makefile, atom.cpp, bond.cpp, obatom.cpp, |
708 |
+ |
obbond.cpp: Changed file names that conflict w/ oopse file name |
709 |
+ |
object files. |
710 |
+ |
|
711 |
+ |
2005-11-21 17:59 gezelter |
712 |
+ |
|
713 |
+ |
* src/utils/residentMem.c: compilation bug |
714 |
+ |
|
715 |
+ |
2005-11-21 17:59 gezelter |
716 |
+ |
|
717 |
+ |
* src/io/: ForceFieldOptions.hpp, Globals.cpp: parsing by filepp |
718 |
+ |
|
719 |
+ |
2005-11-21 17:59 gezelter |
720 |
+ |
|
721 |
+ |
* src/brains/: SimInfo.cpp, SimInfo.hpp: Cutoff Mixing fixes |
722 |
+ |
|
723 |
+ |
2005-11-21 17:59 gezelter |
724 |
+ |
|
725 |
+ |
* src/applications/atom2mdin/: Makefile, atom2mdin.cpp: compilation |
726 |
+ |
issue |
727 |
+ |
|
728 |
+ |
2005-11-21 17:58 gezelter |
729 |
+ |
|
730 |
+ |
* src/UseTheForce/: ForceField.hpp, Makefile, doForces.F90, |
731 |
+ |
doForces_interface.F90, doForces_interface.h, fForceOptions.h, |
732 |
+ |
notifyCutoffs.F90, notifyCutoffs_interface.F90, |
733 |
+ |
notifyCutoffs_interface.h, DarkSide/LJ.F90, |
734 |
+ |
DarkSide/electrostatic.F90, DarkSide/gb.F90, |
735 |
+ |
DarkSide/suttonchen.F90: Cutoff mixing fixes have been made. |
736 |
+ |
|
737 |
+ |
2005-11-21 11:22 tim |
738 |
+ |
|
739 |
+ |
* src/io/ParamConstraint.cpp: Adding ParamConstraint.cpp |
740 |
+ |
|
741 |
+ |
2005-11-21 09:59 tim |
742 |
+ |
|
743 |
+ |
* forceFields/: SMARTS_InteLigand_051110.txt, aromatic.txt, |
744 |
+ |
atomtyp.txt, bondtyp.txt, element.txt, extable.txt, |
745 |
+ |
isotope-small.txt, isotope.txt, patterns.txt, phmodel.txt, |
746 |
+ |
resdata.txt, torlib.txt, types.txt: adding openbabel data files |
747 |
+ |
|
748 |
+ |
2005-11-18 15:17 tim |
749 |
+ |
|
750 |
+ |
* src/: applications/atom2mdin/Makefile, openbabel/oopseformat.cpp: |
751 |
+ |
adding support for soft linking |
752 |
+ |
|
753 |
+ |
2005-11-18 15:17 tim |
754 |
+ |
|
755 |
+ |
* make/Makefile.in: Adding support for soft linking |
756 |
+ |
|
757 |
+ |
2005-11-18 12:50 gezelter |
758 |
+ |
|
759 |
+ |
* make/Makefile.in: Adding linking stuff |
760 |
+ |
|
761 |
+ |
2005-11-18 11:38 tim |
762 |
+ |
|
763 |
+ |
* make/Makefile.in, src/applications/atom2mdin/Makefile, |
764 |
+ |
src/applications/atom2mdin/atom2mdin.cpp, |
765 |
+ |
src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp: |
766 |
+ |
rename mdinConverter to atom2mdin |
767 |
+ |
|
768 |
+ |
2005-11-17 15:44 gezelter |
769 |
+ |
|
770 |
+ |
* src/openbabel/obconversion.cpp: fixed a bug |
771 |
+ |
|
772 |
+ |
2005-11-17 15:39 gezelter |
773 |
+ |
|
774 |
+ |
* configure: Adding some config checks for OpenBabel codes we are |
775 |
+ |
using |
776 |
+ |
|
777 |
+ |
2005-11-17 15:39 gezelter |
778 |
+ |
|
779 |
+ |
* ac-tools/configure.in: Adding some checks for OpenBabel code |
780 |
+ |
|
781 |
+ |
2005-11-17 15:39 gezelter |
782 |
+ |
|
783 |
+ |
* src/config.h.in: Unifying config.h stuff from OOPSE and OpenBabel |
784 |
+ |
|
785 |
+ |
2005-11-17 15:38 gezelter |
786 |
+ |
|
787 |
+ |
* src/openbabel/: babelconfig.hpp, base.cpp, base.hpp, bitvec.hpp, |
788 |
+ |
bondtyper.cpp, config.h.in, config.hpp, data.cpp, data.hpp, |
789 |
+ |
fingerprint.cpp, generic.hpp, grid.hpp, matrix.hpp, mol.hpp, |
790 |
+ |
obconversion.hpp, oberror.cpp, oberror.hpp, obutil.cpp, obutil.hpp, |
791 |
+ |
patty.cpp, pdbformat.hpp, phmodel.cpp, povrayformat.hpp, |
792 |
+ |
residue.cpp, rotor.cpp, smilesformat.cpp, tokenst.cpp, typer.cpp: |
793 |
+ |
Unifying config.h stuff and making sure the OpenBabel codes can |
794 |
+ |
find our default (and environment variable) Force Field |
795 |
+ |
directories. |
796 |
+ |
|
797 |
+ |
2005-11-17 13:35 tim |
798 |
+ |
|
799 |
+ |
* src/io/ForceFieldOptions.hpp: adding ForceFieldOptions |
800 |
+ |
|
801 |
+ |
2005-11-16 18:10 tim |
802 |
+ |
|
803 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
804 |
+ |
brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp, |
805 |
+ |
brains/ForceManager.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp, |
806 |
+ |
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
807 |
+ |
io/Globals.hpp, io/Makefile, io/OptionSectionParser.cpp, |
808 |
+ |
io/OptionSectionParser.hpp, io/ParamConstraint.hpp, |
809 |
+ |
io/SectionParser.hpp, io/SectionParserManager.cpp, |
810 |
+ |
io/TorsionTypesSectionParser.cpp, math/ChebyshevPolynomials.hpp, |
811 |
+ |
math/Makefile, math/Polynomial.hpp, primitives/Bend.cpp, |
812 |
+ |
primitives/Bend.hpp, primitives/GhostBend.cpp, |
813 |
+ |
primitives/GhostBend.hpp, primitives/GhostTorsion.cpp, |
814 |
+ |
primitives/GhostTorsion.hpp, primitives/Torsion.cpp, |
815 |
+ |
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
816 |
+ |
primitives/UreyBradleyBend.hpp, types/CharmmTorsionType.cpp, |
817 |
+ |
types/CharmmTorsionType.hpp, types/CubicTorsionType.hpp, |
818 |
+ |
types/PolynomialTorsionType.hpp, types/QuarticTorsionType.hpp, |
819 |
+ |
types/TorsionType.hpp, utils/StringUtils.hpp: OptionSectionParser |
820 |
+ |
get compiled |
821 |
+ |
|
822 |
+ |
2005-11-16 16:37 chuckv |
823 |
+ |
|
824 |
+ |
* src/: io/Globals.cpp, io/Globals.hpp, io/OptionSectionParser.cpp, |
825 |
+ |
io/OptionSectionParser.hpp, io/SCAtomTypesSectionParser.cpp, |
826 |
+ |
UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField |
827 |
+ |
optional parameters.... |
828 |
+ |
|
829 |
+ |
2005-11-16 16:22 tim |
830 |
+ |
|
831 |
+ |
* src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp, |
832 |
+ |
fingerprint.hpp, fingerprintformat.cpp, fingerprintformat.hpp, |
833 |
+ |
gromos96format.cpp, gromos96format.hpp, oopseformat.cpp, |
834 |
+ |
oopseformat.hpp, pdbformat.cpp, pdbformat.hpp, povrayformat.cpp, |
835 |
+ |
povrayformat.hpp, smilesformat.cpp, smilesformat.hpp, |
836 |
+ |
tinkerformat.cpp, tinkerformat.hpp, xyzformat.cpp, xyzformat.hpp: |
837 |
+ |
adding more readers/writers |
838 |
+ |
|
839 |
+ |
2005-11-16 16:20 tim |
840 |
+ |
|
841 |
+ |
* make/Makefile.in: adding openbabel |
842 |
+ |
|
843 |
+ |
2005-11-16 16:20 tim |
844 |
+ |
|
845 |
+ |
* src/brains/: Register.cpp, Register.hpp: register openbabel |
846 |
+ |
readers/writers |
847 |
+ |
|
848 |
+ |
2005-11-16 14:57 chrisfen |
849 |
+ |
|
850 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: included shifted |
851 |
+ |
potential self term |
852 |
+ |
|
853 |
+ |
2005-11-16 14:57 chrisfen |
854 |
+ |
|
855 |
+ |
* samples/water/spce/spce.md: just some parameters |
856 |
+ |
|
857 |
+ |
2005-11-16 14:42 tim |
858 |
+ |
|
859 |
+ |
* src/openbabel/: Makefile, aromatic.hpp, atom.cpp, atomtyp.hpp, |
860 |
+ |
babelconfig.hpp, base.cpp, base.hpp, bitvec.cpp, bitvec.hpp, |
861 |
+ |
bond.cpp, bondtyp.hpp, bondtyper.cpp, bondtyper.hpp, chains.cpp, |
862 |
+ |
chains.hpp, chiral.cpp, chiral.hpp, config.h.in, config.hpp, |
863 |
+ |
data.cpp, data.hpp, element.hpp, extable.hpp, fingerprint.cpp, |
864 |
+ |
fingerprint.hpp, generic.cpp, generic.hpp, grid.cpp, grid.hpp, |
865 |
+ |
isotope.hpp, kekulize.cpp, matrix.cpp, matrix.hpp, matrix3x3.cpp, |
866 |
+ |
matrix3x3.hpp, mol.cpp, mol.hpp, molchrg.cpp, molchrg.hpp, |
867 |
+ |
obconversion.cpp, obconversion.hpp, obconversion.lo, oberror.cpp, |
868 |
+ |
oberror.hpp, obiter.cpp, obiter.hpp, obmolecformat.hpp, obutil.cpp, |
869 |
+ |
obutil.hpp, oopseformat.cpp, parsmart.cpp, parsmart.hpp, patty.cpp, |
870 |
+ |
patty.hpp, pdbformat.cpp, phmodel.cpp, phmodel.hpp, |
871 |
+ |
phmodeldata.hpp, rand.cpp, reaction.hpp, resdata.hpp, residue.cpp, |
872 |
+ |
ring.cpp, ring.hpp, rotamer.cpp, rotamer.hpp, rotor.cpp, rotor.hpp, |
873 |
+ |
snprintf.c, snprintf.h, strncasecmp.c, tinkerformat.cpp, |
874 |
+ |
tokenst.cpp, torlib.hpp, transform.cpp, typer.cpp, typer.hpp, |
875 |
+ |
types.hpp, vector3.cpp, vector3.hpp, xyzformat.cpp, zipstream.hpp, |
876 |
+ |
zipstreamimpl.hpp: adding openbabel |
877 |
+ |
|
878 |
+ |
2005-11-15 14:42 chrisfen |
879 |
+ |
|
880 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: removed unnecessary |
881 |
+ |
commented code |
882 |
+ |
|
883 |
+ |
2005-11-15 14:04 chrisfen |
884 |
+ |
|
885 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: cleaned up the |
886 |
+ |
charge-charge interactions a bit... |
887 |
+ |
|
888 |
+ |
2005-11-15 14:03 chrisfen |
889 |
+ |
|
890 |
+ |
* samples/water/spce/: spce.md, water.md: just playing |
891 |
+ |
|
892 |
+ |
2005-11-15 11:38 chrisfen |
893 |
+ |
|
894 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: fixed a bug in the |
895 |
+ |
shifted_potential case |
896 |
+ |
|
897 |
+ |
2005-11-15 11:37 chrisfen |
898 |
+ |
|
899 |
+ |
* samples/: argon/500.md, water/spce/spce.md, water/spce/water.md: |
900 |
+ |
just playing around - we need to refresh all the samples sometime |
901 |
+ |
soon... |
902 |
+ |
|
903 |
+ |
2005-11-15 11:18 chuckv |
904 |
+ |
|
905 |
+ |
* src/UseTheForce/: SC_FF.cpp, DarkSide/suttonchen.F90: Made |
906 |
+ |
preforce calc public in suttonchen. |
907 |
+ |
|
908 |
+ |
2005-11-15 11:05 chuckv |
909 |
+ |
|
910 |
+ |
* src/brains/: SimInfo.cpp, fSimulation.h: Sutton-Chen added to |
911 |
+ |
SimInfo |
912 |
+ |
|
913 |
+ |
2005-11-15 11:01 chuckv |
914 |
+ |
|
915 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/fInteractionMap.h, |
916 |
+ |
DarkSide/simulation.F90: Added Sutton-Chen to force loop... |
917 |
+ |
|
918 |
+ |
2005-11-15 10:34 chuckv |
919 |
+ |
|
920 |
+ |
* forceFields/Makefile: Added sutton-chen to makefile. |
921 |
+ |
|
922 |
+ |
2005-11-14 17:20 chuckv |
923 |
+ |
|
924 |
+ |
* src/UseTheForce/DarkSide/: suttonchen.F90, |
925 |
+ |
suttonchen_interface.h: Build Fixes for sutton-chen. |
926 |
+ |
|
927 |
+ |
2005-11-14 17:03 chuckv |
928 |
+ |
|
929 |
+ |
* src/io/Makefile: Missed makefile for sutton-chen. |
930 |
+ |
|
931 |
+ |
2005-11-14 17:03 chuckv |
932 |
+ |
|
933 |
+ |
* src/UseTheForce/: Makefile, DarkSide/Makefile, |
934 |
+ |
DarkSide/atype.F90, DarkSide/atype_interface.F90: Sutton-chen stuff |
935 |
+ |
|
936 |
+ |
2005-11-14 16:29 chuckv |
937 |
+ |
|
938 |
+ |
* src/: UseTheForce/SC_FF.cpp, UseTheForce/SC_FF.hpp, |
939 |
+ |
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
940 |
+ |
UseTheForce/DarkSide/suttonchen.F90, |
941 |
+ |
UseTheForce/DarkSide/suttonchen_interface.F90, |
942 |
+ |
UseTheForce/DarkSide/suttonchen_interface.h, brains/Register.cpp, |
943 |
+ |
brains/fSimulation.h, types/AtomType.cpp, types/AtomType.hpp, |
944 |
+ |
types/AtomTypeProperties.h: Sutton-Chen almost done. Just need to |
945 |
+ |
fix do_forces to use Sutton-Chen. |
946 |
+ |
|
947 |
+ |
2005-11-11 12:21 chrisfen |
948 |
+ |
|
949 |
+ |
* src/UseTheForce/DarkSide/: fSwitchingFunctionType.h, |
950 |
+ |
switcheroo_interface.F90, switcheroo_interface.h: Forgot to add |
951 |
+ |
some files |
952 |
+ |
|
953 |
+ |
2005-11-11 10:22 chrisfen |
954 |
+ |
|
955 |
+ |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/DumpWriter.cpp, |
956 |
+ |
io/Globals.cpp, io/Globals.hpp: added in a 5th order polynomial |
957 |
+ |
switching function option |
958 |
+ |
|
959 |
+ |
2005-11-11 10:21 chrisfen |
960 |
+ |
|
961 |
+ |
* src/UseTheForce/DarkSide/: Makefile, switcheroo.F90: added in a |
962 |
+ |
5th order polynomial switching function |
963 |
+ |
|
964 |
+ |
2005-11-11 10:21 chrisfen |
965 |
+ |
|
966 |
+ |
* samples/water/ssd/ssd.md: playing with switching functions again |
967 |
+ |
|
968 |
+ |
2005-11-11 10:21 chrisfen |
969 |
+ |
|
970 |
+ |
* samples/argon/500.md: playing with switching functions |
971 |
+ |
|
972 |
+ |
2005-11-08 19:11 chuckv |
973 |
+ |
|
974 |
+ |
* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Added force |
975 |
+ |
files for Sutton-Chen and Quantum Sutton-Chen |
976 |
+ |
|
977 |
+ |
2005-11-08 08:32 chrisfen |
978 |
+ |
|
979 |
+ |
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp, |
980 |
+ |
DumpWriter.hpp, Globals.cpp, Globals.hpp: Added a keyword and |
981 |
+ |
ability to output forces and torques |
982 |
+ |
|
983 |
+ |
2005-11-08 08:32 chrisfen |
984 |
+ |
|
985 |
+ |
* src/brains/: SimInfo.cpp, fSimulation.h: Added a keyword for |
986 |
+ |
output of forces and torques |
987 |
+ |
|
988 |
+ |
2005-11-08 08:31 chrisfen |
989 |
+ |
|
990 |
+ |
* src/UseTheForce/DarkSide/: electrostatic.F90, simulation.F90: |
991 |
+ |
Working on shifted_force... |
992 |
+ |
|
993 |
+ |
2005-11-08 08:31 chrisfen |
994 |
+ |
|
995 |
+ |
* samples/water/: spce/spce.md, ssde/ssde.md: Just testing... |
996 |
+ |
|
997 |
+ |
2005-11-03 18:22 chrisfen |
998 |
+ |
|
999 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: removed a poorly |
1000 |
+ |
commented section |
1001 |
+ |
|
1002 |
+ |
2005-11-03 18:12 chrisfen |
1003 |
+ |
|
1004 |
+ |
* src/: UseTheForce/DarkSide/electrostatic.F90, |
1005 |
+ |
UseTheForce/DarkSide/fElectrostaticScreeningMethod.h, |
1006 |
+ |
UseTheForce/DarkSide/fScreeningMethod.h, brains/SimInfo.cpp, |
1007 |
+ |
io/Globals.cpp, io/Globals.hpp: improvements in shifted-force |
1008 |
+ |
|
1009 |
+ |
2005-11-03 18:11 chrisfen |
1010 |
+ |
|
1011 |
+ |
* samples/water/spce/spce.md: mmm... damped shifted force... |
1012 |
+ |
|
1013 |
+ |
2005-11-03 18:06 chuckv |
1014 |
+ |
|
1015 |
+ |
* src/UseTheForce/DarkSide/suttonchen.F90: More work on SC. |
1016 |
+ |
|
1017 |
+ |
2005-11-02 18:50 chuckv |
1018 |
+ |
|
1019 |
+ |
* src/UseTheForce/DarkSide/suttonchen.F90: More work on suttonchen. |
1020 |
+ |
|
1021 |
+ |
2005-11-02 16:01 chrisfen |
1022 |
+ |
|
1023 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
1024 |
+ |
removed some test code |
1025 |
+ |
|
1026 |
+ |
2005-11-02 15:45 chrisfen |
1027 |
+ |
|
1028 |
+ |
* src/UseTheForce/DarkSide/fScreeningMethod.h: forgot to add the |
1029 |
+ |
screening method header |
1030 |
+ |
|
1031 |
+ |
2005-11-02 15:36 chrisfen |
1032 |
+ |
|
1033 |
+ |
* src/brains/SimInfo.cpp: again, changing how we deal with |
1034 |
+ |
summation and screening methods |
1035 |
+ |
|
1036 |
+ |
2005-11-02 15:36 chrisfen |
1037 |
+ |
|
1038 |
+ |
* src/: UseTheForce/DarkSide/electrostatic.F90, |
1039 |
+ |
UseTheForce/DarkSide/electrostatic_interface.F90, |
1040 |
+ |
UseTheForce/DarkSide/electrostatic_interface.h, |
1041 |
+ |
UseTheForce/DarkSide/fElectrostaticSummationMethod.h, |
1042 |
+ |
io/Globals.cpp, io/Globals.hpp: changing how we deal with summation |
1043 |
+ |
and screening methods |
1044 |
+ |
|
1045 |
+ |
2005-11-02 15:35 chrisfen |
1046 |
+ |
|
1047 |
+ |
* src/UseTheForce/doForces.F90: debug stuff for rf removed |
1048 |
+ |
|
1049 |
+ |
2005-11-01 18:32 chuckv |
1050 |
+ |
|
1051 |
+ |
* src/: UseTheForce/DarkSide/atype.F90, |
1052 |
+ |
UseTheForce/DarkSide/atype_interface.F90, |
1053 |
+ |
UseTheForce/DarkSide/suttonchen.F90, types/AtomType.cpp, |
1054 |
+ |
types/AtomTypeProperties.h: Added suppport to atypes for MEAM and |
1055 |
+ |
sutton-chen |
1056 |
+ |
|
1057 |
+ |
2005-11-01 14:24 chrisfen |
1058 |
+ |
|
1059 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
1060 |
+ |
removed some testing code... |
1061 |
+ |
|
1062 |
+ |
2005-11-01 14:14 chrisfen |
1063 |
+ |
|
1064 |
+ |
* src/: brains/Register.cpp, brains/SimInfo.cpp, |
1065 |
+ |
brains/fSimulation.h, integrators/IntegratorFactory.hpp, |
1066 |
+ |
io/Globals.cpp: fixed a capitalization problem with NPT integrator |
1067 |
+ |
initialization |
1068 |
+ |
|
1069 |
+ |
2005-11-01 14:13 chrisfen |
1070 |
+ |
|
1071 |
+ |
* src/applications/oopse/oopse.cpp: nothing |
1072 |
+ |
|
1073 |
+ |
2005-11-01 14:09 chrisfen |
1074 |
+ |
|
1075 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
1076 |
+ |
DarkSide/simulation.F90: still fixing up wolf... |
1077 |
+ |
|
1078 |
+ |
2005-11-01 13:29 chuckv |
1079 |
+ |
|
1080 |
+ |
* src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In |
1081 |
+ |
process of adding sutton-chen forcefield. |
1082 |
+ |
|
1083 |
+ |
2005-10-26 18:32 chrisfen |
1084 |
+ |
|
1085 |
+ |
* src/brains/SimInfo.cpp: changed the default switching radius to |
1086 |
+ |
85% of rcut |
1087 |
+ |
|
1088 |
+ |
2005-10-26 18:31 chrisfen |
1089 |
+ |
|
1090 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks |
1091 |
+ |
to be working now - for charges and dipoles alike |
1092 |
+ |
|
1093 |
+ |
2005-10-26 18:31 chrisfen |
1094 |
+ |
|
1095 |
+ |
* src/UseTheForce/doForces.F90: reaction field looks to be working |
1096 |
+ |
now |
1097 |
+ |
|
1098 |
+ |
2005-10-26 18:30 chrisfen |
1099 |
+ |
|
1100 |
+ |
* samples/water/ssdrf/water.md: added a test molecule |
1101 |
+ |
|
1102 |
+ |
2005-10-26 18:30 chrisfen |
1103 |
+ |
|
1104 |
+ |
* forceFields/DUFF2.frc: added a test atom type |
1105 |
+ |
|
1106 |
+ |
2005-10-24 09:06 chrisfen |
1107 |
+ |
|
1108 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole |
1109 |
+ |
reaction field - don't know if it works... |
1110 |
+ |
|
1111 |
+ |
2005-10-23 16:08 chrisfen |
1112 |
+ |
|
1113 |
+ |
* src/: UseTheForce/doForces.F90, |
1114 |
+ |
UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp: |
1115 |
+ |
streamlined reaction field for dipoles (now a good bit faster) and |
1116 |
+ |
added reaction field for charges - still need to do charge-dipole |
1117 |
+ |
RF |
1118 |
+ |
|
1119 |
+ |
2005-10-23 16:07 chrisfen |
1120 |
+ |
|
1121 |
+ |
* samples/water/ssdrf/ssdrf.md: minor changes when testing reaction |
1122 |
+ |
field |
1123 |
+ |
|
1124 |
+ |
2005-10-23 16:06 chrisfen |
1125 |
+ |
|
1126 |
+ |
* samples/water/spce/spce.md: reaction field now works for charges |
1127 |
+ |
|
1128 |
+ |
2005-10-20 15:27 tim |
1129 |
+ |
|
1130 |
+ |
* src/primitives/Torsion.cpp: Fix the other branch of force |
1131 |
+ |
calculation in Torision.cpp |
1132 |
+ |
|
1133 |
+ |
2005-10-19 14:24 chrisfen |
1134 |
+ |
|
1135 |
+ |
* src/: UseTheForce/doForces.F90, |
1136 |
+ |
UseTheForce/DarkSide/electrostatic.F90, |
1137 |
+ |
UseTheForce/DarkSide/simulation.F90, applications/oopse/oopse.cpp, |
1138 |
+ |
brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals |
1139 |
+ |
toUpper problems - these changes should fix those... |
1140 |
+ |
|
1141 |
+ |
2005-10-19 14:23 chrisfen |
1142 |
+ |
|
1143 |
+ |
* samples/water/ssdrf/ssdrf.md: nothing |
1144 |
+ |
|
1145 |
+ |
2005-10-19 12:03 gezelter |
1146 |
+ |
|
1147 |
+ |
* src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in |
1148 |
+ |
GayBerne |
1149 |
+ |
|
1150 |
+ |
2005-10-19 11:49 tim |
1151 |
+ |
|
1152 |
+ |
* src/: UseTheForce/DarkSide/fInteractionMap.h, |
1153 |
+ |
brains/ForceManager.cpp: fix an index mismathcing between c and |
1154 |
+ |
fortran |
1155 |
+ |
|
1156 |
+ |
2005-10-18 18:03 gezelter |
1157 |
+ |
|
1158 |
+ |
* samples/cutoff/: lj.md, max.md, mix.md, traditional.md: added |
1159 |
+ |
samples for the cutoff methods that Yang Zheng has been working on |
1160 |
+ |
|
1161 |
+ |
2005-10-18 16:13 gezelter |
1162 |
+ |
|
1163 |
+ |
* src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques |
1164 |
+ |
and a rotation matrix bug |
1165 |
+ |
|
1166 |
+ |
2005-10-18 16:13 gezelter |
1167 |
+ |
|
1168 |
+ |
* samples/gbljtest/: 2gb.in, 2gb.md, gb.md, gb2lj1.in, gb2lj1.md, |
1169 |
+ |
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
1170 |
+ |
added a few GB test cases |
1171 |
+ |
|
1172 |
+ |
2005-10-18 16:13 gezelter |
1173 |
+ |
|
1174 |
+ |
* forceFields/DUFF2.frc: Fixing GB parameters |
1175 |
+ |
|
1176 |
+ |
2005-10-18 13:36 kdaily |
1177 |
+ |
|
1178 |
+ |
* forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne |
1179 |
+ |
type |
1180 |
+ |
|
1181 |
+ |
2005-10-18 10:01 chrisfen |
1182 |
+ |
|
1183 |
+ |
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
1184 |
+ |
UseTheForce/DarkSide/Makefile, |
1185 |
+ |
UseTheForce/DarkSide/electrostatic.F90, |
1186 |
+ |
UseTheForce/DarkSide/electrostatic_interface.F90, |
1187 |
+ |
UseTheForce/DarkSide/electrostatic_interface.h, |
1188 |
+ |
UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged |
1189 |
+ |
reaction field with electrostatics.F90 |
1190 |
+ |
|
1191 |
+ |
2005-10-17 18:13 tim |
1192 |
+ |
|
1193 |
+ |
* src/: brains/ForceManager.cpp, brains/Stats.cpp, |
1194 |
+ |
brains/Stats.hpp, integrators/VelocityVerletIntegrator.cpp, |
1195 |
+ |
io/BASS_interface.h, io/Globals.cpp, io/StatWriter.cpp, |
1196 |
+ |
io/StatWriter.hpp: Customized StatWriter is working |
1197 |
+ |
|
1198 |
+ |
2005-10-17 17:42 kdaily |
1199 |
+ |
|
1200 |
+ |
* src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver |
1201 |
+ |
paper |
1202 |
+ |
|
1203 |
+ |
2005-10-17 16:47 gezelter |
1204 |
+ |
|
1205 |
+ |
* src/UseTheForce/DarkSide/gb.F90: bugtracking gb |
1206 |
+ |
|
1207 |
+ |
2005-10-17 14:24 tim |
1208 |
+ |
|
1209 |
+ |
* src/io/ParamConstraint.hpp: Another bug fix |
1210 |
+ |
|
1211 |
+ |
2005-10-17 14:22 tim |
1212 |
+ |
|
1213 |
+ |
* src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace |
1214 |
+ |
issues in Globals |
1215 |
+ |
|
1216 |
+ |
2005-10-17 14:12 gezelter |
1217 |
+ |
|
1218 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90, |
1219 |
+ |
UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90, |
1220 |
+ |
UseTheForce/DarkSide/gb_interface.F90, |
1221 |
+ |
UseTheForce/DarkSide/gb_interface.h, |
1222 |
+ |
io/GayBerneAtomTypesSectionParser.cpp, |
1223 |
+ |
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
1224 |
+ |
changing GB architecture |
1225 |
+ |
|
1226 |
+ |
2005-10-17 14:12 gezelter |
1227 |
+ |
|
1228 |
+ |
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in, |
1229 |
+ |
gbRotRoundZ.in: Adding samples for gb tests |
1230 |
+ |
|
1231 |
+ |
2005-10-16 22:06 tim |
1232 |
+ |
|
1233 |
+ |
* src/io/: Globals.cpp, Globals.hpp: fix a seg fault when try copy |
1234 |
+ |
a string to event's err_msg, there are still tons of memory |
1235 |
+ |
leaking problem in Globals |
1236 |
+ |
|
1237 |
+ |
2005-10-16 19:51 tim |
1238 |
+ |
|
1239 |
+ |
* src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change |
1240 |
+ |
error message in Globals |
1241 |
+ |
|
1242 |
+ |
2005-10-14 16:43 tim |
1243 |
+ |
|
1244 |
+ |
* src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for |
1245 |
+ |
parameters are working now |
1246 |
+ |
|
1247 |
+ |
2005-10-14 11:43 gezelter |
1248 |
+ |
|
1249 |
+ |
* samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests |
1250 |
+ |
|
1251 |
+ |
2005-10-14 11:05 gezelter |
1252 |
+ |
|
1253 |
+ |
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md, |
1254 |
+ |
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
1255 |
+ |
Adding some Gay Berne tests |
1256 |
+ |
|
1257 |
+ |
2005-10-14 11:05 gezelter |
1258 |
+ |
|
1259 |
+ |
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some |
1260 |
+ |
cutoff tests |
1261 |
+ |
|
1262 |
+ |
2005-10-14 10:44 kdaily |
1263 |
+ |
|
1264 |
+ |
* forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, |
1265 |
+ |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90, |
1266 |
+ |
src/UseTheForce/DarkSide/gb_interface.F90, |
1267 |
+ |
src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne |
1268 |
+ |
LJ |
1269 |
+ |
|
1270 |
+ |
2005-10-14 09:48 tim |
1271 |
+ |
|
1272 |
+ |
* src/io/ParamConstraint.hpp: Adding Parameter Constraint class |
1273 |
+ |
|
1274 |
+ |
2005-10-14 09:18 chrisfen |
1275 |
+ |
|
1276 |
+ |
* samples/thermoIntegration/liquid/ssde.md, |
1277 |
+ |
samples/thermoIntegration/solid/ssde.md, src/io/Globals.cpp, |
1278 |
+ |
src/restraints/Restraints.cpp: added default restraint spring |
1279 |
+ |
constants into Globals |
1280 |
+ |
|
1281 |
+ |
2005-10-13 17:26 tim |
1282 |
+ |
|
1283 |
+ |
* src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
1284 |
+ |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp, |
1285 |
+ |
constraints/ZconstraintForceManager.cpp, |
1286 |
+ |
integrators/Integrator.cpp, integrators/NPT.cpp, |
1287 |
+ |
integrators/NVT.cpp, integrators/Velocitizer.cpp, io/Globals.cpp, |
1288 |
+ |
io/Globals.hpp, io/ZConsReader.cpp, minimizers/Minimizer.cpp, |
1289 |
+ |
minimizers/MinimizerParameterSet.cpp, restraints/Restraints.cpp, |
1290 |
+ |
restraints/ThermoIntegrationForceManager.cpp, |
1291 |
+ |
visitors/ZconsVisitor.cpp: rewrite Globals |
1292 |
+ |
|
1293 |
+ |
2005-10-12 16:57 chuckv |
1294 |
+ |
|
1295 |
+ |
* src/brains/ForceManager.cpp: Fix to forceManager to pass |
1296 |
+ |
potential array to fortran. |
1297 |
+ |
|
1298 |
+ |
2005-10-12 16:00 gezelter |
1299 |
+ |
|
1300 |
+ |
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't |
1301 |
+ |
remember what we did |
1302 |
+ |
|
1303 |
+ |
2005-10-12 16:00 gezelter |
1304 |
+ |
|
1305 |
+ |
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
1306 |
+ |
DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/fInteractionMap.h, |
1307 |
+ |
DarkSide/force_globals.F90, DarkSide/gb.F90, DarkSide/shapes.F90, |
1308 |
+ |
DarkSide/sticky.F90: simplifying long range potential array |
1309 |
+ |
|
1310 |
+ |
2005-10-12 16:00 gezelter |
1311 |
+ |
|
1312 |
+ |
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new |
1313 |
+ |
cutoff methods |
1314 |
+ |
|
1315 |
+ |
2005-10-12 16:00 gezelter |
1316 |
+ |
|
1317 |
+ |
* forceFields/DUFF2.frc: Messing with 2-point water models |
1318 |
+ |
|
1319 |
+ |
2005-10-12 15:22 chuckv |
1320 |
+ |
|
1321 |
+ |
* src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran |
1322 |
+ |
interface now expects an array for pot. |
1323 |
+ |
|
1324 |
+ |
2005-10-12 15:18 chuckv |
1325 |
+ |
|
1326 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/gb.F90, |
1327 |
+ |
DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for |
1328 |
+ |
calculation of potential. |
1329 |
+ |
|
1330 |
+ |
2005-10-12 14:55 chuckv |
1331 |
+ |
|
1332 |
+ |
* src/UseTheForce/doForces.F90: More changes to MPI potential |
1333 |
+ |
calculations. |
1334 |
+ |
|
1335 |
+ |
2005-10-12 13:59 chuckv |
1336 |
+ |
|
1337 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90, |
1338 |
+ |
DarkSide/eam.F90, DarkSide/electrostatic.F90, |
1339 |
+ |
DarkSide/fInteractionMap.h, DarkSide/force_globals.F90, |
1340 |
+ |
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky |
1341 |
+ |
Breaky: Add Support for seperating potential contributions. |
1342 |
+ |
|
1343 |
+ |
2005-10-11 17:00 chuckv |
1344 |
+ |
|
1345 |
+ |
* src/UseTheForce/doForces.F90: Free some variables that weren't |
1346 |
+ |
freed before. |
1347 |
+ |
|
1348 |
+ |
2005-10-11 16:59 chuckv |
1349 |
+ |
|
1350 |
+ |
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
1351 |
+ |
GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod |
1352 |
+ |
builder --twinned. |
1353 |
+ |
|
1354 |
+ |
2005-10-11 16:57 chuckv |
1355 |
+ |
|
1356 |
+ |
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
1357 |
+ |
nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c, |
1358 |
+ |
nanoparticleBuilderCmd.h, sphericalNanoparticle.cpp, |
1359 |
+ |
sphericalNanoparticle.hpp: Added code for nanoparticle builder to |
1360 |
+ |
cvs. |
1361 |
+ |
|
1362 |
+ |
2005-10-10 16:34 chuckv |
1363 |
+ |
|
1364 |
+ |
* src/UseTheForce/doForces.F90: Bug fix, undeclared local variable |
1365 |
+ |
in MPI. |
1366 |
+ |
|
1367 |
+ |
2005-10-10 16:20 chuckv |
1368 |
+ |
|
1369 |
+ |
* src/UseTheForce/doForces.F90: Fixed MPI bug with Row and Column |
1370 |
+ |
indexing of groupToGtype. We now have two seperate maps |
1371 |
+ |
groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer |
1372 |
+ |
that is set to groupToGtypeRow in the single processor version. |
1373 |
+ |
|
1374 |
+ |
2005-10-06 13:44 chrisfen |
1375 |
+ |
|
1376 |
+ |
* samples/water/: dimer/water.md, spce/water.md, ssd/water.md, |
1377 |
+ |
ssd-ion/water.md, ssde/water.md, ssdrf/water.md, tap/water.md, |
1378 |
+ |
tip3p_ice/water.md, tip4p/water.md: fixing up the samples |
1379 |
+ |
|
1380 |
+ |
2005-10-05 16:12 tim |
1381 |
+ |
|
1382 |
+ |
* src/primitives/RigidBody.cpp: There is still something wrong with |
1383 |
+ |
inertia tensor projection |
1384 |
+ |
|
1385 |
+ |
2005-10-05 14:35 tim |
1386 |
+ |
|
1387 |
+ |
* src/primitives/RigidBody.cpp: erase output of inertia tensor. |
1388 |
+ |
There is still something wrong with current implementation. |
1389 |
+ |
|
1390 |
+ |
2005-10-05 14:34 tim |
1391 |
+ |
|
1392 |
+ |
* src/brains/MoleculeCreator.cpp: fix a bug in creating |
1393 |
+ |
cutoffGroup. When cutoffGroup is turned off, there is a mismatch |
1394 |
+ |
between group and center of mass array |
1395 |
+ |
|
1396 |
+ |
2005-10-05 14:12 tim |
1397 |
+ |
|
1398 |
+ |
* src/primitives/RigidBody.cpp: fix a bug in creating cutoffGroup. |
1399 |
+ |
When cutoffGroup is turned off, there is a mismatch between group |
1400 |
+ |
and center of mass array |
1401 |
+ |
|
1402 |
+ |
2005-10-04 14:34 chrisfen |
1403 |
+ |
|
1404 |
+ |
* src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying |
1405 |
+ |
mass ratio bug that results in simulation failure with massless |
1406 |
+ |
particles |
1407 |
+ |
|
1408 |
+ |
2005-10-04 14:33 chrisfen |
1409 |
+ |
|
1410 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on |
1411 |
+ |
wolf |
1412 |
+ |
|
1413 |
+ |
2005-10-04 14:32 chrisfen |
1414 |
+ |
|
1415 |
+ |
* samples/water/dimer/two.md, samples/water/dimer/water.md, |
1416 |
+ |
samples/water/tip3p_ice/tp3.md, samples/water/tip3p_ice/water.md, |
1417 |
+ |
samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90: just some |
1418 |
+ |
random changes when testing |
1419 |
+ |
|
1420 |
+ |
2005-10-03 10:54 tim |
1421 |
+ |
|
1422 |
+ |
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: fix a bug in |
1423 |
+ |
projecting the inertia tensor of directional atom in rigibody into |
1424 |
+ |
rigidbody's body frame (previous commit is wrong) |
1425 |
+ |
|
1426 |
+ |
2005-10-03 09:31 tim |
1427 |
+ |
|
1428 |
+ |
* src/primitives/RigidBody.cpp: fix a bug in projecting the inertia |
1429 |
+ |
tensor of directional atom in rigibody into rigidbody's body frame |
1430 |
+ |
|
1431 |
+ |
2005-09-28 13:47 chrisfen |
1432 |
+ |
|
1433 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: working on wolf |
1434 |
+ |
|
1435 |
+ |
2005-09-28 13:46 chrisfen |
1436 |
+ |
|
1437 |
+ |
* samples/water/: dimer/cl.md, dimer/mix.md, dimer/mix2.md, |
1438 |
+ |
dimer/ssd.md, dimer/tap.md, dimer/two.md, spce/spce.md, ssd/ssd.md, |
1439 |
+ |
ssd-ion/ssdCl.md, ssde/ssde.md, tap/tap.md, tip3p_ice/tp3.md, |
1440 |
+ |
tip4p/tp4.md: fixed some samples |
1441 |
+ |
|
1442 |
+ |
2005-09-28 13:46 chrisfen |
1443 |
+ |
|
1444 |
+ |
* ChangeLog: updated |
1445 |
+ |
|
1446 |
+ |
2005-09-28 11:55 tim |
1447 |
+ |
|
1448 |
+ |
* src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid |
1449 |
+ |
divergence in rotation matrix to quaternion transformation |
1450 |
+ |
|
1451 |
+ |
2005-09-28 11:32 gezelter |
1452 |
+ |
|
1453 |
+ |
* src/primitives/RigidBody.cpp: Rotation matrix multiplication |
1454 |
+ |
order error |
1455 |
+ |
|
1456 |
+ |
2005-09-28 11:32 gezelter |
1457 |
+ |
|
1458 |
+ |
* src/io/DumpReader.cpp: tracking down quaternion bug |
1459 |
+ |
|
1460 |
+ |
2005-09-28 11:32 gezelter |
1461 |
+ |
|
1462 |
+ |
* forceFields/DUFF2.frc: Added DIP atom types for 2-point water |
1463 |
+ |
model |
1464 |
+ |
|
1465 |
+ |
2005-09-27 15:02 tim |
1466 |
+ |
|
1467 |
+ |
* src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix |
1468 |
+ |
to quaternion |
1469 |
+ |
|
1470 |
+ |
2005-09-26 13:38 chuckv |
1471 |
+ |
|
1472 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc |
1473 |
+ |
7 so derfc is external. Other compilers should treat erfc as |
1474 |
+ |
intrinsic. |
1475 |
+ |
|
1476 |
+ |
2005-09-26 12:07 chuckv |
1477 |
+ |
|
1478 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc |
1479 |
+ |
and declared it to be external to fix issure with ifc7. Hopefully |
1480 |
+ |
this will not cause a problem with other compilers where derfc is |
1481 |
+ |
an intrinsic function. |
1482 |
+ |
|
1483 |
+ |
2005-09-26 11:42 chuckv |
1484 |
+ |
|
1485 |
+ |
* src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype |
1486 |
+ |
in simulation module. We needed a seperate receive buffer. |
1487 |
+ |
|
1488 |
+ |
2005-09-26 10:58 chuckv |
1489 |
+ |
|
1490 |
+ |
* src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added |
1491 |
+ |
support for skinThickness keyword to Globals. |
1492 |
+ |
|
1493 |
+ |
2005-09-26 10:56 tim |
1494 |
+ |
|
1495 |
+ |
* src/io/DumpReader.cpp: fix a typo in DumpReader |
1496 |
+ |
|
1497 |
+ |
2005-09-26 09:27 chrisfen |
1498 |
+ |
|
1499 |
+ |
* samples/: minimizer/tip4p_two.md, |
1500 |
+ |
thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md, |
1501 |
+ |
water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md, |
1502 |
+ |
water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md, |
1503 |
+ |
water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md, |
1504 |
+ |
water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md, |
1505 |
+ |
water/tip4p/tp4.md: fixing up some samples |
1506 |
+ |
|
1507 |
+ |
2005-09-24 12:39 chrisfen |
1508 |
+ |
|
1509 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now |
1510 |
+ |
roughly the same speed as the old version when using dipoles |
1511 |
+ |
|
1512 |
+ |
energies are now exactly the same between the old version of OOPSE |
1513 |
+ |
and this version |
1514 |
+ |
|
1515 |
+ |
2005-09-24 12:38 chrisfen |
1516 |
+ |
|
1517 |
+ |
* samples/water/ssdrf/ssdrf.md: turned rf on |
1518 |
+ |
|
1519 |
+ |
2005-09-23 15:31 chuckv |
1520 |
+ |
|
1521 |
+ |
* src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the |
1522 |
+ |
skin thickness and hardcode listSkin to be 1.0. We now get listskin |
1523 |
+ |
from skin. This will get fixed to where we can manually set skin |
1524 |
+ |
thickness. |
1525 |
+ |
|
1526 |
+ |
2005-09-22 13:50 gezelter |
1527 |
+ |
|
1528 |
+ |
* src/math/derfc.F90: added error function |
1529 |
+ |
|
1530 |
+ |
2005-09-21 19:08 chuckv |
1531 |
+ |
|
1532 |
+ |
* src/integrators/Velocitizer.cpp: Removed print statement for |
1533 |
+ |
angular momentum and inertia tensor from velocitizer. |
1534 |
+ |
|
1535 |
+ |
2005-09-21 19:04 chuckv |
1536 |
+ |
|
1537 |
+ |
* src/integrators/Velocitizer.cpp: Removed print statements for |
1538 |
+ |
remove angular momentum. |
1539 |
+ |
|
1540 |
+ |
2005-09-21 18:45 chuckv |
1541 |
+ |
|
1542 |
+ |
* src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ |
1543 |
+ |
(say we are using EAM), we probably shouldn't rebuild the LJ mixing |
1544 |
+ |
map. |
1545 |
+ |
|
1546 |
+ |
2005-09-21 15:59 tim |
1547 |
+ |
|
1548 |
+ |
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: |
1549 |
+ |
DumpReader using pure c++ io |
1550 |
+ |
|
1551 |
+ |
2005-09-21 12:20 chrisfen |
1552 |
+ |
|
1553 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a |
1554 |
+ |
defaultCutoff bug (HEMES!) |
1555 |
+ |
|
1556 |
+ |
2005-09-20 17:13 gezelter |
1557 |
+ |
|
1558 |
+ |
* make/Makefile.in: libz additions |
1559 |
+ |
|
1560 |
+ |
2005-09-20 17:03 gezelter |
1561 |
+ |
|
1562 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1563 |
+ |
src/config.h.in: added check for zlib in configure |
1564 |
+ |
|
1565 |
+ |
2005-09-20 16:22 tim |
1566 |
+ |
|
1567 |
+ |
* src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, |
1568 |
+ |
gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter |
1569 |
+ |
|
1570 |
+ |
2005-09-20 11:22 tim |
1571 |
+ |
|
1572 |
+ |
* test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding |
1573 |
+ |
testcase for zipstream |
1574 |
+ |
|
1575 |
+ |
2005-09-20 10:41 tim |
1576 |
+ |
|
1577 |
+ |
* src/io/zipstream.hpp: adding zipstream.hpp |
1578 |
+ |
|
1579 |
+ |
2005-09-20 10:34 chrisfen |
1580 |
+ |
|
1581 |
+ |
* samples/: dipole/splitInWater.md, dipole/split_SSD.md, |
1582 |
+ |
dipole/twoSplitDipole.md, minimizer/ssdEM.md, |
1583 |
+ |
minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md, |
1584 |
+ |
zcons/zconsMoving.md: fixed up some sample md files |
1585 |
+ |
|
1586 |
+ |
2005-09-19 18:21 chrisfen |
1587 |
+ |
|
1588 |
+ |
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
1589 |
+ |
src/UseTheForce/doForces.F90, |
1590 |
+ |
src/UseTheForce/DarkSide/electrostatic.F90, |
1591 |
+ |
src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp, |
1592 |
+ |
src/brains/fSimulation.h: Fixed bugs in reaction field, now it |
1593 |
+ |
appears as though it really is working... |
1594 |
+ |
|
1595 |
|
2005-09-18 15:45 chrisfen |
1596 |
|
|
1597 |
|
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
1989 |
|
|
1990 |
|
2005-05-22 16:36 chuckv |
1991 |
|
|
1992 |
< |
* samples/metals/nanorod/Au_nanoparticle_FCC.md, |
1993 |
< |
src/applications/nanoRodBuilder/Geometry.cpp, |
1994 |
< |
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
1995 |
< |
src/applications/nanoRodBuilder/GeometryFactory.cpp, |
1996 |
< |
src/applications/nanoRodBuilder/GeometryFactory.hpp, |
1997 |
< |
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
404 |
< |
src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
1992 |
> |
* src/: applications/nanoRodBuilder/Geometry.cpp, |
1993 |
> |
applications/nanoRodBuilder/GeometryBuilder.cpp, |
1994 |
> |
applications/nanoRodBuilder/GeometryFactory.cpp, |
1995 |
> |
applications/nanoRodBuilder/GeometryFactory.hpp, |
1996 |
> |
applications/nanoRodBuilder/nanorodBuilder.cpp, |
1997 |
> |
integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
1998 |
|
tensor. |
1999 |
|
|
2000 |
|
2005-05-22 16:05 tim |
2662 |
|
2005-04-11 19:28 chuckv |
2663 |
|
|
2664 |
|
* 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? |
2665 |
|
|
2666 |
|
2005-04-11 16:58 tim |
2667 |
|
|
7671 |
|
|
7672 |
|
2004-09-29 12:56 gezelter |
7673 |
|
|
7674 |
< |
* make/: Make.conf.in, Makefile.in, _files/style.css: Working on |
6088 |
< |
make stuff |
7674 |
> |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
7675 |
|
|
7676 |
|
2004-09-29 12:46 tim |
7677 |
|
|
7937 |
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
7938 |
|
src/visitors/RigidBodyVisitor.cpp, |
7939 |
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
7940 |
< |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
6355 |
< |
make/_files/style.css, samples/Makefile.in, |
7940 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
7941 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
7942 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
7943 |
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
8112 |
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
8113 |
|
src/visitors/RigidBodyVisitor.cpp, |
8114 |
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
8115 |
< |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
6531 |
< |
make/_files/style.css, samples/Makefile.in, |
8115 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
8116 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
8117 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
8118 |
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |