1 |
+ |
2005-09-28 11:55 tim |
2 |
+ |
|
3 |
+ |
* src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid |
4 |
+ |
divergence in rotation matrix to quaternion transformation |
5 |
+ |
|
6 |
+ |
2005-09-28 11:32 gezelter |
7 |
+ |
|
8 |
+ |
* src/primitives/RigidBody.cpp: Rotation matrix multiplication |
9 |
+ |
order error |
10 |
+ |
|
11 |
+ |
2005-09-28 11:32 gezelter |
12 |
+ |
|
13 |
+ |
* src/io/DumpReader.cpp: tracking down quaternion bug |
14 |
+ |
|
15 |
+ |
2005-09-28 11:32 gezelter |
16 |
+ |
|
17 |
+ |
* forceFields/DUFF2.frc: Added DIP atom types for 2-point water |
18 |
+ |
model |
19 |
+ |
|
20 |
+ |
2005-09-27 15:02 tim |
21 |
+ |
|
22 |
+ |
* src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix |
23 |
+ |
to quaternion |
24 |
+ |
|
25 |
+ |
2005-09-26 13:38 chuckv |
26 |
+ |
|
27 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc |
28 |
+ |
7 so derfc is external. Other compilers should treat erfc as |
29 |
+ |
intrinsic. |
30 |
+ |
|
31 |
+ |
2005-09-26 12:07 chuckv |
32 |
+ |
|
33 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc |
34 |
+ |
and declared it to be external to fix issure with ifc7. Hopefully |
35 |
+ |
this will not cause a problem with other compilers where derfc is |
36 |
+ |
an intrinsic function. |
37 |
+ |
|
38 |
+ |
2005-09-26 11:42 chuckv |
39 |
+ |
|
40 |
+ |
* src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype |
41 |
+ |
in simulation module. We needed a seperate receive buffer. |
42 |
+ |
|
43 |
+ |
2005-09-26 10:58 chuckv |
44 |
+ |
|
45 |
+ |
* src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added |
46 |
+ |
support for skinThickness keyword to Globals. |
47 |
+ |
|
48 |
+ |
2005-09-26 10:56 tim |
49 |
+ |
|
50 |
+ |
* src/io/DumpReader.cpp: fix a typo in DumpReader |
51 |
+ |
|
52 |
+ |
2005-09-26 09:27 chrisfen |
53 |
+ |
|
54 |
+ |
* samples/: minimizer/tip4p_two.md, |
55 |
+ |
thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md, |
56 |
+ |
water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md, |
57 |
+ |
water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md, |
58 |
+ |
water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md, |
59 |
+ |
water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md, |
60 |
+ |
water/tip4p/tp4.md: fixing up some samples |
61 |
+ |
|
62 |
+ |
2005-09-24 12:39 chrisfen |
63 |
+ |
|
64 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now |
65 |
+ |
roughly the same speed as the old version when using dipoles |
66 |
+ |
|
67 |
+ |
energies are now exactly the same between the old version of OOPSE |
68 |
+ |
and this version |
69 |
+ |
|
70 |
+ |
2005-09-24 12:38 chrisfen |
71 |
+ |
|
72 |
+ |
* samples/water/ssdrf/ssdrf.md: turned rf on |
73 |
+ |
|
74 |
+ |
2005-09-23 15:31 chuckv |
75 |
+ |
|
76 |
+ |
* src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the |
77 |
+ |
skin thickness and hardcode listSkin to be 1.0. We now get listskin |
78 |
+ |
from skin. This will get fixed to where we can manually set skin |
79 |
+ |
thickness. |
80 |
+ |
|
81 |
+ |
2005-09-22 13:50 gezelter |
82 |
+ |
|
83 |
+ |
* src/math/derfc.F90: added error function |
84 |
+ |
|
85 |
+ |
2005-09-21 19:08 chuckv |
86 |
+ |
|
87 |
+ |
* src/integrators/Velocitizer.cpp: Removed print statement for |
88 |
+ |
angular momentum and inertia tensor from velocitizer. |
89 |
+ |
|
90 |
+ |
2005-09-21 19:04 chuckv |
91 |
+ |
|
92 |
+ |
* src/integrators/Velocitizer.cpp: Removed print statements for |
93 |
+ |
remove angular momentum. |
94 |
+ |
|
95 |
+ |
2005-09-21 18:45 chuckv |
96 |
+ |
|
97 |
+ |
* src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ |
98 |
+ |
(say we are using EAM), we probably shouldn't rebuild the LJ mixing |
99 |
+ |
map. |
100 |
+ |
|
101 |
+ |
2005-09-21 15:59 tim |
102 |
+ |
|
103 |
+ |
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: |
104 |
+ |
DumpReader using pure c++ io |
105 |
+ |
|
106 |
+ |
2005-09-21 12:20 chrisfen |
107 |
+ |
|
108 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a |
109 |
+ |
defaultCutoff bug (HEMES!) |
110 |
+ |
|
111 |
+ |
2005-09-20 17:13 gezelter |
112 |
+ |
|
113 |
+ |
* make/Makefile.in: libz additions |
114 |
+ |
|
115 |
+ |
2005-09-20 17:03 gezelter |
116 |
+ |
|
117 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
118 |
+ |
src/config.h.in: added check for zlib in configure |
119 |
+ |
|
120 |
+ |
2005-09-20 16:22 tim |
121 |
+ |
|
122 |
+ |
* src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, |
123 |
+ |
gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter |
124 |
+ |
|
125 |
+ |
2005-09-20 11:22 tim |
126 |
+ |
|
127 |
+ |
* test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding |
128 |
+ |
testcase for zipstream |
129 |
+ |
|
130 |
+ |
2005-09-20 10:41 tim |
131 |
+ |
|
132 |
+ |
* src/io/zipstream.hpp: adding zipstream.hpp |
133 |
+ |
|
134 |
+ |
2005-09-20 10:34 chrisfen |
135 |
+ |
|
136 |
+ |
* samples/: dipole/splitInWater.md, dipole/split_SSD.md, |
137 |
+ |
dipole/twoSplitDipole.md, minimizer/ssdEM.md, |
138 |
+ |
minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md, |
139 |
+ |
zcons/zconsMoving.md: fixed up some sample md files |
140 |
+ |
|
141 |
+ |
2005-09-19 18:21 chrisfen |
142 |
+ |
|
143 |
+ |
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
144 |
+ |
src/UseTheForce/doForces.F90, |
145 |
+ |
src/UseTheForce/DarkSide/electrostatic.F90, |
146 |
+ |
src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp, |
147 |
+ |
src/brains/fSimulation.h: Fixed bugs in reaction field, now it |
148 |
+ |
appears as though it really is working... |
149 |
+ |
|
150 |
+ |
2005-09-18 15:45 chrisfen |
151 |
+ |
|
152 |
+ |
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
153 |
+ |
src/UseTheForce/doForces.F90, |
154 |
+ |
src/UseTheForce/doForces_interface.F90, |
155 |
+ |
src/UseTheForce/doForces_interface.h, |
156 |
+ |
src/UseTheForce/DarkSide/electrostatic.F90, |
157 |
+ |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
158 |
+ |
src/brains/SimInfo.cpp: reaction field seems to work now, still |
159 |
+ |
need to do some testing... |
160 |
+ |
|
161 |
+ |
2005-09-16 18:04 chuckv |
162 |
+ |
|
163 |
+ |
* src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed |
164 |
+ |
dump files. |
165 |
+ |
|
166 |
+ |
2005-09-16 16:07 chrisfen |
167 |
+ |
|
168 |
+ |
* src/: UseTheForce/doForces_interface.F90, |
169 |
+ |
UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a |
170 |
+ |
bug that ifc missed... |
171 |
+ |
|
172 |
+ |
2005-09-16 15:36 chrisfen |
173 |
+ |
|
174 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
175 |
+ |
fixing some summation method issues |
176 |
+ |
|
177 |
+ |
2005-09-16 14:35 chrisfen |
178 |
+ |
|
179 |
+ |
* src/brains/SimInfo.cpp: fixed a capitalization error |
180 |
+ |
|
181 |
+ |
2005-09-16 14:34 chrisfen |
182 |
+ |
|
183 |
+ |
* src/UseTheForce/: fElectrostaticSummationMethod.h, |
184 |
+ |
DarkSide/fElectrostaticSummationMethod.h: moved a header file |
185 |
+ |
around |
186 |
+ |
|
187 |
+ |
2005-09-16 14:00 chrisfen |
188 |
+ |
|
189 |
+ |
* src/: UseTheForce/DarkSide/electrostatic_interface.F90, |
190 |
+ |
brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there |
191 |
+ |
are known issues - particularly with reaction field... |
192 |
+ |
|
193 |
+ |
2005-09-16 11:07 chrisfen |
194 |
+ |
|
195 |
+ |
* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, |
196 |
+ |
io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking |
197 |
+ |
(cutting out the old way to do reaction field) |
198 |
+ |
|
199 |
+ |
2005-09-15 17:05 gezelter |
200 |
+ |
|
201 |
+ |
* src/UseTheForce/: doForces.F90, fCoulombicCorrection.h, |
202 |
+ |
fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90, |
203 |
+ |
DarkSide/electrostatic_interface.F90, |
204 |
+ |
DarkSide/electrostatic_interface.h: Working on adding WOLF |
205 |
+ |
|
206 |
+ |
2005-09-15 14:17 tim |
207 |
+ |
|
208 |
+ |
* src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame |
209 |
+ |
is called without calling getNFrames |
210 |
+ |
|
211 |
+ |
2005-09-15 08:47 chrisfen |
212 |
+ |
|
213 |
+ |
* src/UseTheForce/fCoulombicCorrection.h: forgot to add a header |
214 |
+ |
|
215 |
+ |
2005-09-14 21:48 chuckv |
216 |
+ |
|
217 |
+ |
* src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was |
218 |
+ |
not initialized after creation. When maxval(gtypeMaxCutoff) was |
219 |
+ |
called, the largest random garbage value was returned from the |
220 |
+ |
array. |
221 |
+ |
|
222 |
+ |
2005-09-14 19:14 chrisfen |
223 |
+ |
|
224 |
+ |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, |
225 |
+ |
io/Globals.hpp: changes to include the coulombicCorrection selector |
226 |
+ |
|
227 |
+ |
2005-09-14 19:13 chrisfen |
228 |
+ |
|
229 |
+ |
* src/UseTheForce/DarkSide/: Makefile, electrostatic.F90, |
230 |
+ |
reactionField.F90: added in the undamped wolf, in the process of |
231 |
+ |
doing the damped wolf |
232 |
+ |
|
233 |
+ |
2005-09-14 19:13 chrisfen |
234 |
+ |
|
235 |
+ |
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
236 |
+ |
doForces_interface.h, notifyCutoffs.F90: some changes to activate |
237 |
+ |
the coulombicCorrection selector |
238 |
+ |
|
239 |
+ |
2005-09-14 19:11 chrisfen |
240 |
+ |
|
241 |
+ |
* samples/water/dimer/: cl.in, cl.md, water.md: just some testing |
242 |
+ |
|
243 |
+ |
2005-09-14 19:11 chrisfen |
244 |
+ |
|
245 |
+ |
* samples/argon/: 500.in, 500.md: Equilibrated the sample |
246 |
+ |
|
247 |
+ |
2005-09-14 19:10 chrisfen |
248 |
+ |
|
249 |
+ |
* forceFields/DUFF2.frc: re-added Cl- and Na+ |
250 |
+ |
|
251 |
+ |
2005-09-14 15:31 chuckv |
252 |
+ |
|
253 |
+ |
* src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup |
254 |
+ |
eamAtypes instead of assuming a 1-1 correspondence to atypes. |
255 |
+ |
|
256 |
+ |
2005-09-14 15:28 gezelter |
257 |
+ |
|
258 |
+ |
* src/UseTheForce/doForces.F90: fix to put back calculation of r in |
259 |
+ |
do_prepair |
260 |
+ |
|
261 |
+ |
2005-09-14 14:02 gezelter |
262 |
+ |
|
263 |
+ |
* src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the |
264 |
+ |
createMixingMap routine. It should now set doShift correctly |
265 |
+ |
|
266 |
+ |
2005-09-07 17:44 chuckv |
267 |
+ |
|
268 |
+ |
* src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. |
269 |
+ |
|
270 |
+ |
2005-09-07 17:23 chuckv |
271 |
+ |
|
272 |
+ |
* src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi |
273 |
+ |
logical variables |
274 |
+ |
|
275 |
+ |
2005-09-07 17:08 gezelter |
276 |
+ |
|
277 |
+ |
* src/UseTheForce/doForces.F90: bugfix on the grouptype finding |
278 |
+ |
algorithm |
279 |
+ |
|
280 |
+ |
2005-09-07 15:46 gezelter |
281 |
+ |
|
282 |
+ |
* src/: UseTheForce/doForces.F90, |
283 |
+ |
UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, |
284 |
+ |
UseTheForce/notifyCutoffs_interface.F90, |
285 |
+ |
UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp, |
286 |
+ |
io/Globals.cpp, io/Globals.hpp: adding c-side interface to change |
287 |
+ |
cutoff Policy |
288 |
+ |
|
289 |
+ |
2005-09-07 14:18 gezelter |
290 |
+ |
|
291 |
+ |
* src/UseTheForce/doForces.F90: Some bug hunting |
292 |
+ |
|
293 |
+ |
2005-09-07 14:18 gezelter |
294 |
+ |
|
295 |
+ |
* samples/argon/argonNVT.md: Just a longer test |
296 |
+ |
|
297 |
+ |
2005-09-06 12:32 chuckv |
298 |
+ |
|
299 |
+ |
* src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap |
300 |
+ |
etc.. |
301 |
+ |
|
302 |
+ |
2005-09-01 17:56 gezelter |
303 |
+ |
|
304 |
+ |
* src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to |
305 |
+ |
zero |
306 |
+ |
|
307 |
+ |
2005-09-01 15:17 gezelter |
308 |
+ |
|
309 |
+ |
* src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote |
310 |
+ |
createGtypeCutoffMap |
311 |
+ |
|
312 |
+ |
2005-08-30 13:23 chrisfen |
313 |
+ |
|
314 |
+ |
* src/: UseTheForce/doForces.F90, |
315 |
+ |
UseTheForce/doForces_interface.F90, |
316 |
+ |
UseTheForce/doForces_interface.h, |
317 |
+ |
UseTheForce/DarkSide/electrostatic.F90, |
318 |
+ |
UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp, |
319 |
+ |
brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some |
320 |
+ |
changes for implementing the wolf potential |
321 |
+ |
|
322 |
+ |
2005-08-26 17:39 chrisfen |
323 |
+ |
|
324 |
+ |
* src/UseTheForce/DarkSide/eam.F90: updated getEAMCut |
325 |
+ |
|
326 |
+ |
2005-08-26 16:30 chrisfen |
327 |
+ |
|
328 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/eam.F90, |
329 |
+ |
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added |
330 |
+ |
some probably nonfunctional get*cut routines |
331 |
+ |
|
332 |
+ |
2005-08-26 15:34 chuckv |
333 |
+ |
|
334 |
+ |
* src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. |
335 |
+ |
|
336 |
+ |
2005-08-26 11:36 gezelter |
337 |
+ |
|
338 |
+ |
* src/UseTheForce/doForces.F90: fixing some of the problems in the |
339 |
+ |
interactionHash and gtypeCutoff routines |
340 |
+ |
|
341 |
+ |
2005-08-17 10:26 gezelter |
342 |
+ |
|
343 |
+ |
* src/UseTheForce/: doForces.F90, fCutoffPolicy.h, |
344 |
+ |
DarkSide/simulation.F90: added fCutoffPolicy.h |
345 |
+ |
|
346 |
+ |
2005-08-11 16:04 gezelter |
347 |
+ |
|
348 |
+ |
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in |
349 |
+ |
progress |
350 |
+ |
|
351 |
+ |
2005-08-10 14:17 gezelter |
352 |
+ |
|
353 |
+ |
* src/primitives/StuntDouble.hpp: putting spaceballs back where |
354 |
+ |
they belong |
355 |
+ |
|
356 |
+ |
2005-08-09 17:33 gezelter |
357 |
+ |
|
358 |
+ |
* src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard |
359 |
+ |
Jones module |
360 |
+ |
|
361 |
+ |
2005-08-09 17:33 gezelter |
362 |
+ |
|
363 |
+ |
* src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky |
364 |
+ |
|
365 |
+ |
2005-08-09 14:40 chuckv |
366 |
+ |
|
367 |
+ |
* src/UseTheForce/doForces.F90: In process of re-write for group |
368 |
+ |
based cutoff.... |
369 |
+ |
|
370 |
+ |
2005-07-29 14:38 gezelter |
371 |
+ |
|
372 |
+ |
* src/UseTheForce/doForces.F90: fixes in progress |
373 |
+ |
|
374 |
+ |
2005-07-29 12:34 tim |
375 |
+ |
|
376 |
+ |
* src/UseTheForce/doForces.F90: fix a bug which does not update |
377 |
+ |
me_i and me_j correctly |
378 |
+ |
|
379 |
+ |
2005-07-28 17:12 chuckv |
380 |
+ |
|
381 |
+ |
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed |
382 |
+ |
cutoffs... Segfaults nicely now... |
383 |
+ |
|
384 |
+ |
2005-07-20 12:04 gezelter |
385 |
+ |
|
386 |
+ |
* configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text |
387 |
+ |
error messages from pathscale compiler |
388 |
+ |
|
389 |
+ |
2005-07-13 11:48 tim |
390 |
+ |
|
391 |
+ |
* src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in |
392 |
+ |
<functional> |
393 |
+ |
|
394 |
+ |
2005-07-13 10:54 tim |
395 |
+ |
|
396 |
+ |
* src/: UseTheForce/fSwitchingFunction.h, |
397 |
+ |
UseTheForce/mpiComponentPlan.h, |
398 |
+ |
UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h, |
399 |
+ |
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
400 |
+ |
io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c, |
401 |
+ |
io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c, |
402 |
+ |
io/parse_tree.h, math/MatVec3.c, utils/residentMem.c, |
403 |
+ |
utils/simError.c, utils/simError.h: replace c++ style comment in c |
404 |
+ |
files |
405 |
+ |
|
406 |
+ |
2005-07-03 15:53 chuckv |
407 |
+ |
|
408 |
+ |
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
409 |
+ |
UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added |
410 |
+ |
subroutine to set cuttoff for Interaction map and function in |
411 |
+ |
simulation.F90 to determine if a particular atype is present in a |
412 |
+ |
simulation. |
413 |
+ |
|
414 |
+ |
2005-06-28 08:58 gezelter |
415 |
+ |
|
416 |
+ |
* src/UseTheForce/doForces.F90: [no log message] |
417 |
+ |
|
418 |
+ |
2005-06-27 17:21 chuckv |
419 |
+ |
|
420 |
+ |
* src/UseTheForce/doForces.F90: More breaking and destruction of |
421 |
+ |
force code. Does not build at this point... |
422 |
+ |
|
423 |
+ |
2005-06-27 16:01 gezelter |
424 |
+ |
|
425 |
+ |
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90, |
426 |
+ |
UseTheForce/DarkSide/fInteractionMap.h, |
427 |
+ |
UseTheForce/DarkSide/interactions.F90, utils/definitions.F90: |
428 |
+ |
Breaky breaky! |
429 |
+ |
|
430 |
+ |
2005-06-20 11:03 gezelter |
431 |
+ |
|
432 |
+ |
* samples/water/ssd/ssd.md, |
433 |
+ |
src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a |
434 |
+ |
simulation |
435 |
+ |
|
436 |
+ |
2005-06-13 13:25 tim |
437 |
+ |
|
438 |
+ |
* src/: applications/staticProps/DensityPlot.cpp, |
439 |
+ |
applications/staticProps/DensityPlot.hpp, |
440 |
+ |
applications/staticProps/SCDOrderParameter.cpp, |
441 |
+ |
applications/staticProps/StaticProps.cpp, |
442 |
+ |
io/AtomTypesSectionParser.cpp: working version of DensityPlot |
443 |
+ |
|
444 |
+ |
2005-05-31 17:31 chuckv |
445 |
+ |
|
446 |
+ |
* src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to |
447 |
+ |
remove angular momentum. |
448 |
+ |
|
449 |
+ |
2005-05-31 12:34 chuckv |
450 |
+ |
|
451 |
+ |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in |
452 |
+ |
typo in nanorodBuilder. |
453 |
+ |
|
454 |
+ |
2005-05-30 09:01 chuckv |
455 |
+ |
|
456 |
+ |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
457 |
+ |
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, |
458 |
+ |
brains/Stats.hpp, integrators/Velocitizer.cpp, |
459 |
+ |
integrators/Velocitizer.hpp: Added method to remove system angular |
460 |
+ |
momentum to velocitizer and added method to calculate system |
461 |
+ |
angular momentum to siminfo. |
462 |
+ |
|
463 |
+ |
2005-05-29 16:16 chrisfen |
464 |
+ |
|
465 |
+ |
* src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed |
466 |
+ |
balance from the Darkside (files) |
467 |
+ |
|
468 |
+ |
2005-05-29 16:15 chrisfen |
469 |
+ |
|
470 |
+ |
* src/UseTheForce/doForces.F90: Removed balance from doForces |
471 |
+ |
|
472 |
+ |
2005-05-29 16:15 chrisfen |
473 |
+ |
|
474 |
+ |
* samples/water/tap/: tap.in, tap.md: Updated tap sample |
475 |
+ |
|
476 |
+ |
2005-05-29 16:15 chrisfen |
477 |
+ |
|
478 |
+ |
* samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap |
479 |
+ |
dimer for testing purposes |
480 |
+ |
|
481 |
+ |
2005-05-29 16:14 chrisfen |
482 |
+ |
|
483 |
+ |
* forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It |
484 |
+ |
was apparently wiped earlier this month... |
485 |
+ |
|
486 |
+ |
2005-05-29 16:13 chrisfen |
487 |
+ |
|
488 |
+ |
* ChangeLog: ran make cvslog |
489 |
+ |
|
490 |
+ |
2005-05-28 19:16 tim |
491 |
+ |
|
492 |
+ |
* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding |
493 |
+ |
AtomNameVisitor |
494 |
+ |
|
495 |
+ |
2005-05-28 19:09 tim |
496 |
+ |
|
497 |
+ |
* src/integrators/Integrator.cpp: dding resetIntegrator |
498 |
+ |
|
499 |
+ |
2005-05-28 19:06 tim |
500 |
+ |
|
501 |
+ |
* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, |
502 |
+ |
NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, |
503 |
+ |
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding |
504 |
+ |
resetIntegrator |
505 |
+ |
|
506 |
+ |
2005-05-27 16:11 tim |
507 |
+ |
|
508 |
+ |
* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, |
509 |
+ |
Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, |
510 |
+ |
SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
511 |
+ |
StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into |
512 |
+ |
StaticProps |
513 |
+ |
|
514 |
+ |
2005-05-26 23:41 tim |
515 |
+ |
|
516 |
+ |
* src/: applications/staticProps/Makefile, |
517 |
+ |
applications/staticProps/P2OrderParameter.cpp, |
518 |
+ |
applications/staticProps/P2OrderParameter.hpp, |
519 |
+ |
applications/staticProps/StaticProps.cpp, |
520 |
+ |
applications/staticProps/StaticProps.ggo, |
521 |
+ |
applications/staticProps/StaticPropsCmd.c, |
522 |
+ |
applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, |
523 |
+ |
utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps |
524 |
+ |
|
525 |
+ |
2005-05-26 17:45 tim |
526 |
+ |
|
527 |
+ |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
528 |
+ |
applications/dump2Xyz/Dump2XYZCmd.c, |
529 |
+ |
applications/dump2Xyz/Dump2XYZCmd.h, |
530 |
+ |
applications/staticProps/Makefile, |
531 |
+ |
applications/staticProps/P2OrderParameter.cpp, |
532 |
+ |
applications/staticProps/P2OrderParameter.hpp, |
533 |
+ |
applications/staticProps/RadialDistrFunc.cpp, |
534 |
+ |
applications/staticProps/RadialDistrFunc.hpp, |
535 |
+ |
applications/staticProps/StaticAnalyser.hpp, |
536 |
+ |
applications/staticProps/StaticProps.cpp, |
537 |
+ |
applications/staticProps/StaticProps.ggo, |
538 |
+ |
applications/staticProps/StaticPropsCmd.c, |
539 |
+ |
applications/staticProps/StaticPropsCmd.h, visitors/Makefile, |
540 |
+ |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding |
541 |
+ |
AtomNameVisitor to convert atom name to its base name; |
542 |
+ |
wrappingvisitor now wrap back to the center of the mass; adding |
543 |
+ |
P2OrderParameter into StaticProps |
544 |
+ |
|
545 |
+ |
2005-05-22 16:36 chuckv |
546 |
+ |
|
547 |
+ |
* samples/metals/nanorod/Au_nanoparticle_FCC.md, |
548 |
+ |
src/applications/nanoRodBuilder/Geometry.cpp, |
549 |
+ |
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
550 |
+ |
src/applications/nanoRodBuilder/GeometryFactory.cpp, |
551 |
+ |
src/applications/nanoRodBuilder/GeometryFactory.hpp, |
552 |
+ |
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
553 |
+ |
src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
554 |
+ |
tensor. |
555 |
+ |
|
556 |
+ |
2005-05-22 16:05 tim |
557 |
+ |
|
558 |
+ |
* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
559 |
+ |
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
560 |
+ |
io/Globals.hpp, io/SectionParserManager.cpp: adding keyword |
561 |
+ |
printPressureTensor |
562 |
+ |
|
563 |
+ |
2005-05-20 14:27 tim |
564 |
+ |
|
565 |
+ |
* src/integrators/NPrT.cpp: NPrT in progress |
566 |
+ |
|
567 |
+ |
2005-05-20 11:01 tim |
568 |
+ |
|
569 |
+ |
* src/: integrators/NPrT.cpp, io/Globals.cpp, |
570 |
+ |
utils/OOPSEConstant.hpp: NPrT in progress |
571 |
+ |
|
572 |
+ |
2005-05-19 16:31 tim |
573 |
+ |
|
574 |
+ |
* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, |
575 |
+ |
integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, |
576 |
+ |
io/Globals.hpp: NPAT is working |
577 |
+ |
|
578 |
+ |
2005-05-19 10:49 tim |
579 |
+ |
|
580 |
+ |
* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, |
581 |
+ |
integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT |
582 |
+ |
|
583 |
+ |
2005-05-18 23:28 tim |
584 |
+ |
|
585 |
+ |
* src/: brains/Register.cpp, integrators/NPAT.cpp, |
586 |
+ |
integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, |
587 |
+ |
io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators |
588 |
+ |
|
589 |
+ |
2005-05-18 14:06 chrisfen |
590 |
+ |
|
591 |
+ |
* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just |
592 |
+ |
some tap changes |
593 |
+ |
|
594 |
+ |
2005-05-18 13:31 chrisfen |
595 |
+ |
|
596 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
597 |
+ |
DarkSide/sticky.F90: Modifications to temper the dipolar strength |
598 |
+ |
in the first solvation shell for tap |
599 |
+ |
|
600 |
+ |
2005-05-18 07:35 chrisfen |
601 |
+ |
|
602 |
+ |
* samples/water/tap/: tap.in, tap.md, water.md: added a tap example |
603 |
+ |
for testing purposes |
604 |
+ |
|
605 |
+ |
2005-05-17 17:35 chrisfen |
606 |
+ |
|
607 |
+ |
* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, |
608 |
+ |
samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, |
609 |
+ |
src/UseTheForce/doForces.F90, |
610 |
+ |
src/UseTheForce/DarkSide/electrostatic.F90, |
611 |
+ |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
612 |
+ |
src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also |
613 |
+ |
correcting changes to the previous merge that were not caught |
614 |
+ |
|
615 |
+ |
2005-05-16 23:20 chuckv |
616 |
+ |
|
617 |
+ |
* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: |
618 |
+ |
Fixed merge issues between Kyle and Chris so OOPSE will actually |
619 |
+ |
build. |
620 |
+ |
|
621 |
+ |
2005-05-16 22:46 kdaily |
622 |
+ |
|
623 |
+ |
* src/io/: GayBerneAtomTypesSectionParser.cpp, |
624 |
+ |
GayBerneAtomTypesSectionParser.hpp, Makefile: help |
625 |
+ |
|
626 |
+ |
2005-05-16 21:08 kdaily |
627 |
+ |
|
628 |
+ |
* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, |
629 |
+ |
src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, |
630 |
+ |
src/types/DirectionalAtomType.cpp, |
631 |
+ |
src/types/DirectionalAtomType.hpp: added gb |
632 |
+ |
|
633 |
+ |
2005-05-13 15:36 chrisfen |
634 |
+ |
|
635 |
+ |
* forceFields/DUFF2.frc: Better tap |
636 |
+ |
|
637 |
+ |
2005-05-12 14:43 chrisfen |
638 |
+ |
|
639 |
+ |
* forceFields/DUFF2.frc, samples/water/dimer/ssd.in, |
640 |
+ |
samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, |
641 |
+ |
src/applications/dump2Xyz/Dump2XYZ.cpp, |
642 |
+ |
src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. |
643 |
+ |
Need to parametrize. |
644 |
+ |
|
645 |
+ |
2005-05-11 18:15 chuckv |
646 |
+ |
|
647 |
+ |
* src/: io/ShapeAtomTypesSectionParser.cpp, |
648 |
+ |
math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed |
649 |
+ |
build issues under ifc7. |
650 |
+ |
|
651 |
+ |
2005-05-09 17:07 chuckv |
652 |
+ |
|
653 |
+ |
* src/applications/nanoRodBuilder/Geometry.hpp: More geometry |
654 |
+ |
builder changes. |
655 |
+ |
|
656 |
+ |
2005-05-05 10:06 chrisfen |
657 |
+ |
|
658 |
+ |
* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED |
659 |
+ |
to TAP |
660 |
+ |
|
661 |
+ |
2005-05-05 09:47 chrisfen |
662 |
+ |
|
663 |
+ |
* forceFields/DUFF2.frc, samples/water/ssde/ssde.md, |
664 |
+ |
samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, |
665 |
+ |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, |
666 |
+ |
src/UseTheForce/DarkSide/atype.F90, |
667 |
+ |
src/UseTheForce/DarkSide/atype_interface.F90, |
668 |
+ |
src/UseTheForce/DarkSide/simulation.F90, |
669 |
+ |
src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, |
670 |
+ |
src/brains/fSimulation.h, src/io/Makefile, |
671 |
+ |
src/io/StickyAtomTypesSectionParser.cpp, |
672 |
+ |
src/io/StickyPowerAtomTypesSectionParser.cpp, |
673 |
+ |
src/io/StickyPowerAtomTypesSectionParser.hpp, |
674 |
+ |
src/types/AtomType.cpp, src/types/AtomType.hpp, |
675 |
+ |
src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, |
676 |
+ |
src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's |
677 |
+ |
not parametrized, but OOPSE will now let me run it... |
678 |
+ |
|
679 |
+ |
2005-05-03 17:55 chuckv |
680 |
+ |
|
681 |
+ |
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
682 |
+ |
GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: |
683 |
+ |
Adding support for generic geometry to nanorodbuilder. |
684 |
+ |
|
685 |
+ |
2005-05-03 12:55 chuckv |
686 |
+ |
|
687 |
+ |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
688 |
+ |
nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, |
689 |
+ |
nanorodBuilderCmd.h: More changes to nanoRodBuilder.... |
690 |
+ |
|
691 |
+ |
2005-04-29 14:16 gezelter |
692 |
+ |
|
693 |
+ |
* make/Makefile.in: [no log message] |
694 |
+ |
|
695 |
+ |
2005-04-29 11:26 chrisfen |
696 |
+ |
|
697 |
+ |
* forceFields/DUFF2.frc, samples/water/spce/water.md, |
698 |
+ |
samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, |
699 |
+ |
samples/water/ssd-ion/water.md, samples/water/ssde/water.md, |
700 |
+ |
samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, |
701 |
+ |
samples/water/tip4p/water.md: Added TIP4P-Ew |
702 |
+ |
|
703 |
+ |
2005-04-27 19:24 chuckv |
704 |
+ |
|
705 |
+ |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
706 |
+ |
GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, |
707 |
+ |
nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with |
708 |
+ |
nanoRodBuilder.... |
709 |
+ |
|
710 |
+ |
2005-04-27 15:13 chrisfen |
711 |
+ |
|
712 |
+ |
* samples/shape/Shapes.frc, samples/shape/linear.shape, |
713 |
+ |
src/UseTheForce/DarkSide/atype.F90, |
714 |
+ |
src/UseTheForce/DarkSide/shapes.F90, |
715 |
+ |
src/UseTheForce/DarkSide/shapes_interface.F90, |
716 |
+ |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of |
717 |
+ |
write statements and am closer to a working shapes |
718 |
+ |
|
719 |
+ |
2005-04-22 16:57 chuckv |
720 |
+ |
|
721 |
+ |
* src/utils/Predicate.hpp: Fixed gcc4 bug... |
722 |
+ |
|
723 |
+ |
2005-04-22 16:52 tim |
724 |
+ |
|
725 |
+ |
* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, |
726 |
+ |
Trim.hpp: adding CharClassificationFunctor to fix the locale |
727 |
+ |
problem of c++ |
728 |
+ |
|
729 |
+ |
2005-04-21 09:12 chrisfen |
730 |
+ |
|
731 |
+ |
* samples/shape/Shapes.frc, samples/shape/linear.in, |
732 |
+ |
samples/shape/linear.md, src/UseTheForce/ForceField.hpp, |
733 |
+ |
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, |
734 |
+ |
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
735 |
+ |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, |
736 |
+ |
src/UseTheForce/DarkSide/shapes.F90, |
737 |
+ |
src/UseTheForce/DarkSide/shapes_interface.F90, |
738 |
+ |
src/UseTheForce/DarkSide/shapes_interface.h, |
739 |
+ |
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
740 |
+ |
src/io/Makefile, src/io/SectionParser.cpp, |
741 |
+ |
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
742 |
+ |
src/io/ShapeAtomTypesSectionParser.cpp, |
743 |
+ |
src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, |
744 |
+ |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, |
745 |
+ |
src/types/ShapeAtomType.hpp: Shapes is limping along with a array |
746 |
+ |
bounds overwrite (I think...). At least the parser loads the |
747 |
+ |
forcefield fine... |
748 |
+ |
|
749 |
+ |
2005-04-18 10:44 chrisfen |
750 |
+ |
|
751 |
+ |
* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on |
752 |
+ |
Mac (capitalization confusion of filenames) |
753 |
+ |
|
754 |
+ |
2005-04-17 22:50 chrisfen |
755 |
+ |
|
756 |
+ |
* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, |
757 |
+ |
UseTheForce/Shapes_FF.cpp, |
758 |
+ |
io/DirectionalAtomTypesSectionParser.cpp, |
759 |
+ |
io/ShapeAtomTypesSectionParser.cpp, |
760 |
+ |
io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... |
761 |
+ |
|
762 |
+ |
2005-04-15 17:43 gezelter |
763 |
+ |
|
764 |
+ |
* README: gmake in case people forget |
765 |
+ |
|
766 |
+ |
2005-04-15 17:40 gezelter |
767 |
+ |
|
768 |
+ |
* src/applications/oopse/oopse.cpp: fixed the spacing on the |
769 |
+ |
banner. Vanity. |
770 |
+ |
|
771 |
+ |
2005-04-15 17:22 gezelter |
772 |
+ |
|
773 |
+ |
* src/: config.h.in, applications/oopse/oopse.cpp: Version string |
774 |
+ |
in banner (and version numbers in config.h) |
775 |
+ |
|
776 |
+ |
2005-04-15 17:22 gezelter |
777 |
+ |
|
778 |
+ |
* ChangeLog, LICENSE, README: Documentation changes |
779 |
+ |
|
780 |
|
2005-04-15 17:03 gezelter |
781 |
|
|
782 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |