1 |
+ |
2003-08-26 15:37 tim |
2 |
+ |
|
3 |
+ |
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
4 |
+ |
mpiSimulation.cpp: set default force substraction policy to |
5 |
+ |
PolicyByMass |
6 |
+ |
|
7 |
+ |
2003-08-26 15:29 tim |
8 |
+ |
|
9 |
+ |
* libmdtools/Integrator.cpp: [no log message] |
10 |
+ |
|
11 |
+ |
2003-08-26 15:13 mmeineke |
12 |
+ |
|
13 |
+ |
* utils/sysbuilder/bilayerSys.cpp: added define statemewnt to |
14 |
+ |
Statwriter and Dumpwriter to handle files larger than 2 gb. |
15 |
+ |
|
16 |
+ |
commented out some print statements in Zconstraint |
17 |
+ |
|
18 |
+ |
hard coding some system init into bilayer.sys |
19 |
+ |
|
20 |
+ |
2003-08-26 15:12 mmeineke |
21 |
+ |
|
22 |
+ |
* libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: |
23 |
+ |
added define statemewnt to Statwriter and Dumpwriter to handle |
24 |
+ |
files larger than 2 gb. |
25 |
+ |
|
26 |
+ |
commented out some print statements in Zconstraint |
27 |
+ |
|
28 |
+ |
2003-08-26 15:02 tim |
29 |
+ |
|
30 |
+ |
* libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed |
31 |
+ |
and check the seed which is specified by user at least contains 9 |
32 |
+ |
digits |
33 |
+ |
|
34 |
+ |
2003-08-26 13:32 mmeineke |
35 |
+ |
|
36 |
+ |
* libmdtools/DUFF.cpp: changed the Makefiel a litle. |
37 |
+ |
|
38 |
+ |
Fixed a bug in MPI_DUFF. The atom block type was not being properly |
39 |
+ |
constucted in MPI. (The MPI struct had 6 doubles declared versus |
40 |
+ |
the actual 11) |
41 |
+ |
|
42 |
+ |
2003-08-26 13:30 mmeineke |
43 |
+ |
|
44 |
+ |
* Makefile: changed the Makefiel a litle. |
45 |
+ |
|
46 |
+ |
2003-08-25 17:17 gezelter |
47 |
+ |
|
48 |
+ |
* utils/sysbuilder/Makefile: More FreeBSD fixes |
49 |
+ |
|
50 |
+ |
2003-08-25 16:51 gezelter |
51 |
+ |
|
52 |
+ |
* libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, |
53 |
+ |
libmdtools/Makefile, src/Makefile: [no log message] |
54 |
+ |
|
55 |
+ |
2003-08-22 15:04 mmeineke |
56 |
+ |
|
57 |
+ |
* libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on |
58 |
+ |
frequency of output dumps. |
59 |
+ |
|
60 |
+ |
2003-08-20 17:23 tim |
61 |
+ |
|
62 |
+ |
* libBASS/Globals.hpp, libmdtools/SimInfo.hpp, |
63 |
+ |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
64 |
+ |
libmdtools/mpiSimulation.cpp: user can setup seed in bass file now, |
65 |
+ |
if he does not specify any value for seed, oopse will take the |
66 |
+ |
value of seconds of system time as seed |
67 |
+ |
|
68 |
+ |
2003-08-20 14:42 mmeineke |
69 |
+ |
|
70 |
+ |
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
71 |
+ |
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, |
72 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimState.cpp, |
73 |
+ |
utils/sysbuilder/bilayerSys.cpp: updated the Changelog. |
74 |
+ |
|
75 |
+ |
added some bug fixes for setting the random number generator seed |
76 |
+ |
value. |
77 |
+ |
|
78 |
+ |
fixed a bug where ghostbend atom b was not being set. ( recent bug |
79 |
+ |
from SimState conversion) |
80 |
+ |
|
81 |
+ |
2003-08-20 14:41 mmeineke |
82 |
+ |
|
83 |
+ |
* libBASS/Globals.hpp: updated the Changelog. |
84 |
+ |
|
85 |
+ |
added some bug fixes for setting the random number generator seed |
86 |
+ |
value. |
87 |
+ |
|
88 |
+ |
2003-08-20 14:41 mmeineke |
89 |
+ |
|
90 |
+ |
* ChangeLog: updated the Changelog. |
91 |
+ |
|
92 |
+ |
2003-08-20 14:11 tim |
93 |
+ |
|
94 |
+ |
* libBASS/Globals.cpp, libmdtools/DUFF.cpp, |
95 |
+ |
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost |
96 |
+ |
bend class |
97 |
+ |
|
98 |
+ |
2003-08-20 10:13 mmeineke |
99 |
+ |
|
100 |
+ |
* utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in |
101 |
+ |
make links. added -f to ln -s. |
102 |
+ |
|
103 |
+ |
2003-08-20 09:50 tim |
104 |
+ |
|
105 |
+ |
* libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] |
106 |
+ |
|
107 |
+ |
2003-08-20 09:34 tim |
108 |
+ |
|
109 |
+ |
* libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp, |
110 |
+ |
ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg |
111 |
+ |
printing |
112 |
+ |
|
113 |
+ |
2003-08-18 15:59 chuckv |
114 |
+ |
|
115 |
+ |
* utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
116 |
+ |
latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, |
117 |
+ |
sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. |
118 |
+ |
Nanobuilder still broke. |
119 |
+ |
|
120 |
+ |
2003-08-15 14:24 tim |
121 |
+ |
|
122 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
123 |
+ |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
124 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
125 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp, |
126 |
+ |
libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint |
127 |
+ |
Method |
128 |
+ |
|
129 |
+ |
2003-08-14 11:16 tim |
130 |
+ |
|
131 |
+ |
* libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint |
132 |
+ |
with average force substraction strategy |
133 |
+ |
|
134 |
+ |
2003-08-13 16:20 chuckv |
135 |
+ |
|
136 |
+ |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some |
137 |
+ |
profiling code -DPROFILE. |
138 |
+ |
|
139 |
+ |
2003-08-13 14:21 tim |
140 |
+ |
|
141 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
142 |
+ |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
143 |
+ |
libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic |
144 |
+ |
potential & z-contraint method |
145 |
+ |
|
146 |
+ |
2003-08-12 16:44 mmeineke |
147 |
+ |
|
148 |
+ |
* libBASS/BASS_interface.cpp, libBASS/Globals.hpp, |
149 |
+ |
libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
150 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
151 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really |
152 |
+ |
annoying bug in Directional Atom, where mu was getting written to |
153 |
+ |
pseudorandom memory location. |
154 |
+ |
|
155 |
+ |
2003-08-12 14:56 tim |
156 |
+ |
|
157 |
+ |
* libBASS/BASS_interface.cpp, libBASS/Globals.cpp, |
158 |
+ |
libBASS/Globals.hpp, libmdtools/Atom.hpp, |
159 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
160 |
+ |
libmdtools/SimSetup.cpp: debugging globals |
161 |
+ |
|
162 |
+ |
2003-08-12 13:40 gezelter |
163 |
+ |
|
164 |
+ |
* forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes |
165 |
+ |
and new atypes in LJFF |
166 |
+ |
|
167 |
+ |
2003-08-12 13:15 gezelter |
168 |
+ |
|
169 |
+ |
* forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older |
170 |
+ |
stuff... |
171 |
+ |
|
172 |
+ |
2003-08-12 13:14 chuckv |
173 |
+ |
|
174 |
+ |
* utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. |
175 |
+ |
|
176 |
+ |
2003-08-12 13:04 chuckv |
177 |
+ |
|
178 |
+ |
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: |
179 |
+ |
Missed del of files before. |
180 |
+ |
|
181 |
+ |
2003-08-12 13:03 chuckv |
182 |
+ |
|
183 |
+ |
* utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log |
184 |
+ |
message] |
185 |
+ |
|
186 |
+ |
2003-08-12 13:01 chuckv |
187 |
+ |
|
188 |
+ |
* utils/sysbuilder/Makefile: commit makefile |
189 |
+ |
|
190 |
+ |
2003-08-12 12:51 tim |
191 |
+ |
|
192 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
193 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
194 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
195 |
+ |
libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added |
196 |
+ |
harmonical potential to z-constraint method |
197 |
+ |
|
198 |
+ |
2003-08-11 17:31 chuckv |
199 |
+ |
|
200 |
+ |
* utils/Makefile: Changed makefile to only build quicklate. |
201 |
+ |
|
202 |
+ |
2003-08-11 17:25 chuckv |
203 |
+ |
|
204 |
+ |
* ac-tools/configure.in: added utils/sysbuilder to be built. |
205 |
+ |
|
206 |
+ |
2003-08-11 17:12 chuckv |
207 |
+ |
|
208 |
+ |
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
209 |
+ |
bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, |
210 |
+ |
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp, |
211 |
+ |
sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp, |
212 |
+ |
sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c, |
213 |
+ |
sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp, |
214 |
+ |
sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp, |
215 |
+ |
sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp, |
216 |
+ |
sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged |
217 |
+ |
sysbuilder into a subdirectory. Fixed some of sysbuilder to work |
218 |
+ |
with new atom allocation in libmdtools. |
219 |
+ |
|
220 |
+ |
2003-08-11 14:41 tim |
221 |
+ |
|
222 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp: added method of |
223 |
+ |
moving zconstraint molecules to specified positions |
224 |
+ |
|
225 |
+ |
2003-08-11 14:39 tim |
226 |
+ |
|
227 |
+ |
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] |
228 |
+ |
|
229 |
+ |
2003-08-11 14:38 mmeineke |
230 |
+ |
|
231 |
+ |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
232 |
+ |
libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, |
233 |
+ |
libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp, |
234 |
+ |
libBASS/ZconStamp.hpp, libBASS/interface.c, libBASS/make_nodes.c, |
235 |
+ |
libBASS/make_nodes.h, libBASS/mpiBASS.c, libBASS/mpiBASS.h, |
236 |
+ |
libBASS/node_list.h, libBASS/parse_interface.h, |
237 |
+ |
libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint |
238 |
+ |
into the BASS language syntax. |
239 |
+ |
|
240 |
+ |
2003-08-11 13:29 mmeineke |
241 |
+ |
|
242 |
+ |
* libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of |
243 |
+ |
degrees of freedom to account for zConstreints |
244 |
+ |
|
245 |
+ |
2003-08-08 16:22 chuckv |
246 |
+ |
|
247 |
+ |
* libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, |
248 |
+ |
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
249 |
+ |
samples/metals/Au.bass: EAM works...... Neighbor list also |
250 |
+ |
works..... |
251 |
+ |
|
252 |
+ |
2003-08-08 13:32 mmeineke |
253 |
+ |
|
254 |
+ |
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
255 |
+ |
moved frameCount's functionality into DumpReader. also split props |
256 |
+ |
into staticProps and dynamicProps. (currently only have |
257 |
+ |
staticProps) |
258 |
+ |
|
259 |
+ |
2003-08-08 12:48 mmeineke |
260 |
+ |
|
261 |
+ |
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
262 |
+ |
instance of Atom::setZ and Atom::getZ in ZConstaint. |
263 |
+ |
|
264 |
+ |
2003-08-07 16:47 mmeineke |
265 |
+ |
|
266 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
267 |
+ |
DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, |
268 |
+ |
GhostBend.cpp, InitializeFromFile.cpp, Makefile, SimInfo.cpp, |
269 |
+ |
SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SimState.cpp, |
270 |
+ |
SimState.hpp, Torsion.cpp: switched SimInfo to use a system |
271 |
+ |
configuration from SimState rather than arrays from Atom |
272 |
+ |
|
273 |
+ |
2003-08-06 19:47 chuckv |
274 |
+ |
|
275 |
+ |
* libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, |
276 |
+ |
libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, |
277 |
+ |
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
278 |
+ |
samples/metals/Au.bass: Bug fixes for eam... |
279 |
+ |
|
280 |
+ |
2003-08-01 11:18 tim |
281 |
+ |
|
282 |
+ |
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of |
283 |
+ |
Z-Constraint |
284 |
+ |
|
285 |
+ |
2003-07-31 14:59 tim |
286 |
+ |
|
287 |
+ |
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
288 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
289 |
+ |
libmdtools/ZConstraint.cpp: add index range checking into |
290 |
+ |
ZConstraint |
291 |
+ |
|
292 |
+ |
2003-07-31 10:38 tim |
293 |
+ |
|
294 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters |
295 |
+ |
to the globals |
296 |
+ |
|
297 |
+ |
2003-07-31 10:35 tim |
298 |
+ |
|
299 |
+ |
* libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, |
300 |
+ |
Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, |
301 |
+ |
NPTfm.cpp, NPTi.cpp, NPTim.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
302 |
+ |
SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: |
303 |
+ |
Added Z constraint. |
304 |
+ |
|
305 |
+ |
2003-07-30 16:17 chuckv |
306 |
+ |
|
307 |
+ |
* libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, |
308 |
+ |
libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, |
309 |
+ |
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, |
310 |
+ |
samples/metals/Au.bass: More bug fixes for eam. |
311 |
+ |
|
312 |
+ |
2003-07-29 11:32 mmeineke |
313 |
+ |
|
314 |
+ |
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
315 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
316 |
+ |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
317 |
+ |
src/Makefile: working on the props code |
318 |
+ |
|
319 |
+ |
2003-07-29 11:32 mmeineke |
320 |
+ |
|
321 |
+ |
* libBASS/Globals.cpp: [no log message] |
322 |
+ |
|
323 |
+ |
2003-07-25 15:05 chuckv |
324 |
+ |
|
325 |
+ |
* samples/metals/: Au.bass, metals.mdl: Added bass models for |
326 |
+ |
metals |
327 |
+ |
|
328 |
+ |
2003-07-25 15:00 chuckv |
329 |
+ |
|
330 |
+ |
* libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, |
331 |
+ |
notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. |
332 |
+ |
|
333 |
+ |
2003-07-24 16:22 chuckv |
334 |
+ |
|
335 |
+ |
* ac-tools/configure.in: Changed configure to look for both upper |
336 |
+ |
and lower cass .mod files |
337 |
+ |
|
338 |
+ |
2003-07-24 14:57 chuckv |
339 |
+ |
|
340 |
+ |
* libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for |
341 |
+ |
eam and do_forces. |
342 |
+ |
|
343 |
+ |
2003-07-23 17:13 chuckv |
344 |
+ |
|
345 |
+ |
* libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, |
346 |
+ |
force_globals.F90, simulation_module.F90, status_module.F90: |
347 |
+ |
Finished most code for eam.... |
348 |
+ |
|
349 |
+ |
2003-07-22 16:49 mmeineke |
350 |
+ |
|
351 |
+ |
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan |
352 |
+ |
function to the DumpReader. It should now save the start of each |
353 |
+ |
frame in a vector. |
354 |
+ |
|
355 |
+ |
2003-07-22 15:05 mmeineke |
356 |
+ |
|
357 |
+ |
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes |
358 |
+ |
to read dump files |
359 |
+ |
|
360 |
+ |
2003-07-22 14:54 tim |
361 |
+ |
|
362 |
+ |
* libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, |
363 |
+ |
Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, |
364 |
+ |
NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log |
365 |
+ |
message] |
366 |
+ |
|
367 |
+ |
2003-07-22 11:41 mmeineke |
368 |
+ |
|
369 |
+ |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, |
370 |
+ |
SimSetup.cpp: Fixed a current time initialization bug in |
371 |
+ |
InitFromFile. |
372 |
+ |
|
373 |
+ |
2003-07-21 16:27 mmeineke |
374 |
+ |
|
375 |
+ |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, |
376 |
+ |
Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and |
377 |
+ |
friends to accomadate random file access |
378 |
+ |
|
379 |
+ |
2003-07-21 11:23 mmeineke |
380 |
+ |
|
381 |
+ |
* libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no |
382 |
+ |
one sets it. |
383 |
+ |
|
384 |
+ |
2003-07-21 11:23 mmeineke |
385 |
+ |
|
386 |
+ |
* libmdtools/: InitializeFromFile.cpp, Integrator.cpp, |
387 |
+ |
ReadWrite.hpp: fixed Initializefrom file to start the simulation |
388 |
+ |
from the time specified in the init file. |
389 |
+ |
|
390 |
+ |
2003-07-17 16:49 gezelter |
391 |
+ |
|
392 |
+ |
* libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, |
393 |
+ |
DumpReader.cpp: Started work on a DumpReader |
394 |
+ |
|
395 |
+ |
2003-07-17 15:38 gezelter |
396 |
+ |
|
397 |
+ |
* libmdtools/calc_sticky_pair.F90: Fixes for SSD/E |
398 |
+ |
|
399 |
+ |
2003-07-17 15:32 gezelter |
400 |
+ |
|
401 |
+ |
* forceFields/DUFF.frc, libmdtools/DUFF.cpp, |
402 |
+ |
libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: |
403 |
+ |
Changes for SSD/E |
404 |
+ |
|
405 |
+ |
2003-07-17 14:38 mmeineke |
406 |
+ |
|
407 |
+ |
* libmdtools/do_Forces.F90: commented out an eam line |
408 |
+ |
|
409 |
+ |
2003-07-17 14:32 chuckv |
410 |
+ |
|
411 |
+ |
* libmdtools/atype_module.F90: fixed spelling issue |
412 |
+ |
|
413 |
+ |
2003-07-17 14:29 chuckv |
414 |
+ |
|
415 |
+ |
* libmdtools/: fInfo.c, status_module.F90: added info module |
416 |
+ |
|
417 |
+ |
2003-07-17 14:25 chuckv |
418 |
+ |
|
419 |
+ |
* libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, |
420 |
+ |
atype_module.F90, calc_eam.F90, do_Forces.F90, |
421 |
+ |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
422 |
+ |
mpiSimulation_module.F90: Added massive changes for eam.... |
423 |
+ |
|
424 |
+ |
2003-07-16 16:49 chuckv |
425 |
+ |
|
426 |
+ |
* libmdtools/EAM_FF.cpp: More up to date version of EAM_FF |
427 |
+ |
|
428 |
+ |
2003-07-16 16:30 mmeineke |
429 |
+ |
|
430 |
+ |
* libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, |
431 |
+ |
SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
432 |
+ |
calc_reaction_field.F90, do_Forces.F90, fSimulation.h, |
433 |
+ |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
434 |
+ |
neighborLists.F90, notifyCutoffs.F90, simulation_module.F90, |
435 |
+ |
wrappers.F90: Changed how cutoffs were handled from C. Now |
436 |
+ |
notifyCutoffs in Fortran notifies those who need the information of |
437 |
+ |
any changes to cutoffs. |
438 |
+ |
|
439 |
+ |
2003-07-16 12:35 gezelter |
440 |
+ |
|
441 |
+ |
* utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. |
442 |
+ |
quickLate is now somewhat more intelligent about periodic |
443 |
+ |
boundaries and wrapping. |
444 |
+ |
|
445 |
+ |
2003-07-16 11:40 chuckv |
446 |
+ |
|
447 |
+ |
* libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists |
448 |
+ |
|
449 |
+ |
2003-07-16 10:34 mmeineke |
450 |
+ |
|
451 |
+ |
* scripts/cleanSrc: added a quick wipe-and-update script for quick |
452 |
+ |
rebuilds on BoB |
453 |
+ |
|
454 |
+ |
2003-07-15 21:11 gezelter |
455 |
+ |
|
456 |
+ |
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, |
457 |
+ |
SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more |
458 |
+ |
fixes for box changes |
459 |
+ |
|
460 |
+ |
2003-07-15 17:29 mmeineke |
461 |
+ |
|
462 |
+ |
* libmdtools/simulation_module.F90: removed some debugging print |
463 |
+ |
statements. |
464 |
+ |
|
465 |
+ |
2003-07-15 17:22 mmeineke |
466 |
+ |
|
467 |
+ |
* libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
468 |
+ |
do_Forces.F90, simulation_module.F90: fixed a long lived bug in |
469 |
+ |
do_forces. Rrf was not being used in the neighborlist correctly. |
470 |
+ |
rcut was conssistently being set lowere than Rrf causing the dipole |
471 |
+ |
cutoff region to be to small. Also led to the removal of the taper |
472 |
+ |
region to buffer the dipole cutoff. |
473 |
+ |
|
474 |
+ |
2003-07-15 16:34 mmeineke |
475 |
+ |
|
476 |
+ |
* libmdtools/: SimInfo.cpp, simulation_module.F90: working on |
477 |
+ |
fixing ssd bug |
478 |
+ |
|
479 |
+ |
2003-07-15 14:56 gezelter |
480 |
+ |
|
481 |
+ |
* libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes |
482 |
+ |
for the NPT ensembles |
483 |
+ |
|
484 |
+ |
2003-07-15 13:52 mmeineke |
485 |
+ |
|
486 |
+ |
* libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up |
487 |
+ |
simSetup |
488 |
+ |
|
489 |
+ |
2003-07-15 12:57 mmeineke |
490 |
+ |
|
491 |
+ |
* libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, |
492 |
+ |
SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: |
493 |
+ |
fixed some bugs, Changed entry_plug to info where appropriate |
494 |
+ |
|
495 |
+ |
2003-07-15 12:25 chuckv |
496 |
+ |
|
497 |
+ |
* utils/sysBuild.ggo: added more command line arguments |
498 |
+ |
|
499 |
+ |
2003-07-15 12:11 gezelter |
500 |
+ |
|
501 |
+ |
* samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: |
502 |
+ |
Fixing force field line |
503 |
+ |
|
504 |
+ |
2003-07-15 12:10 gezelter |
505 |
+ |
|
506 |
+ |
* libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, |
507 |
+ |
calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
508 |
+ |
calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure |
509 |
+ |
tensor |
510 |
+ |
|
511 |
+ |
2003-07-15 10:50 gezelter |
512 |
+ |
|
513 |
+ |
* libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes |
514 |
+ |
|
515 |
+ |
2003-07-15 10:42 gezelter |
516 |
+ |
|
517 |
+ |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: |
518 |
+ |
removed old outdated code |
519 |
+ |
|
520 |
+ |
2003-07-15 09:45 gezelter |
521 |
+ |
|
522 |
+ |
* libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx |
523 |
+ |
|
524 |
+ |
2003-07-15 09:28 gezelter |
525 |
+ |
|
526 |
+ |
* libmdtools/Molecule.cpp: removing get_vx |
527 |
+ |
|
528 |
+ |
2003-07-14 22:28 gezelter |
529 |
+ |
|
530 |
+ |
* libmdtools/NPTfm.cpp: Added NPTfm |
531 |
+ |
|
532 |
+ |
2003-07-14 22:27 gezelter |
533 |
+ |
|
534 |
+ |
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
535 |
+ |
Bugfix in NPTim, fixes for NPTfm |
536 |
+ |
|
537 |
+ |
2003-07-14 22:08 gezelter |
538 |
+ |
|
539 |
+ |
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
540 |
+ |
Checking in changes for NPTim |
541 |
+ |
|
542 |
+ |
2003-07-14 18:06 gezelter |
543 |
+ |
|
544 |
+ |
* utils/Makefile: Broken SysBuilder |
545 |
+ |
|
546 |
+ |
2003-07-14 18:06 gezelter |
547 |
+ |
|
548 |
+ |
* samples/: alkane/init_butane.eor, argon/argon.bass, |
549 |
+ |
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
550 |
+ |
for samples |
551 |
+ |
|
552 |
+ |
2003-07-14 18:06 gezelter |
553 |
+ |
|
554 |
+ |
* libmdtools/: Integrator.cpp, do_Forces.F90: Removed some |
555 |
+ |
debugging write statements |
556 |
+ |
|
557 |
+ |
2003-07-14 17:38 gezelter |
558 |
+ |
|
559 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, |
560 |
+ |
NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom |
561 |
+ |
|
562 |
+ |
2003-07-14 16:48 mmeineke |
563 |
+ |
|
564 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get |
565 |
+ |
and set routines to Atom and DirectionalAtom |
566 |
+ |
|
567 |
+ |
2003-07-14 16:35 chuckv |
568 |
+ |
|
569 |
+ |
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, |
570 |
+ |
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder |
571 |
+ |
that takes different cmd line arguments. |
572 |
+ |
|
573 |
+ |
2003-07-14 16:28 mmeineke |
574 |
+ |
|
575 |
+ |
* libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, |
576 |
+ |
ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, |
577 |
+ |
SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors |
578 |
+ |
were not being updated |
579 |
+ |
|
580 |
+ |
2003-07-14 10:04 gezelter |
581 |
+ |
|
582 |
+ |
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on |
583 |
+ |
NPTim |
584 |
+ |
|
585 |
+ |
2003-07-14 09:55 mmeineke |
586 |
+ |
|
587 |
+ |
* forceFields/DUFF.frc: Switched the bond in the force field back |
588 |
+ |
to constrained, to preserve energy |
589 |
+ |
|
590 |
+ |
2003-07-11 17:34 mmeineke |
591 |
+ |
|
592 |
+ |
* libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, |
593 |
+ |
Integrator.hpp: working on som integrator bugs |
594 |
+ |
|
595 |
+ |
2003-07-11 10:26 gezelter |
596 |
+ |
|
597 |
+ |
* libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting |
598 |
+ |
to worry about all the strtok() calls in our code |
599 |
+ |
|
600 |
+ |
2003-07-11 09:49 gezelter |
601 |
+ |
|
602 |
+ |
* utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness |
603 |
+ |
|
604 |
+ |
2003-07-10 20:15 gezelter |
605 |
+ |
|
606 |
+ |
* libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and |
607 |
+ |
eor. |
608 |
+ |
|
609 |
+ |
2003-07-10 17:15 mmeineke |
610 |
+ |
|
611 |
+ |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, |
612 |
+ |
SimInfo.cpp, Thermo.cpp: fixed some bugs |
613 |
+ |
|
614 |
+ |
2003-07-10 14:53 chuckv |
615 |
+ |
|
616 |
+ |
* utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, |
617 |
+ |
nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added |
618 |
+ |
nanoBuilder and a general Lattice builder. |
619 |
+ |
|
620 |
+ |
2003-07-10 12:10 gezelter |
621 |
+ |
|
622 |
+ |
* libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, |
623 |
+ |
Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff |
624 |
+ |
|
625 |
+ |
2003-07-09 17:14 mmeineke |
626 |
+ |
|
627 |
+ |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
628 |
+ |
Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, |
629 |
+ |
SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the |
630 |
+ |
caclulation of HmatInverse. |
631 |
+ |
|
632 |
+ |
2003-07-09 10:34 mmeineke |
633 |
+ |
|
634 |
+ |
* libBASS/MoleculeStamp.hpp: starting some work for xlate |
635 |
+ |
|
636 |
+ |
2003-07-09 10:33 mmeineke |
637 |
+ |
|
638 |
+ |
* libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff |
639 |
+ |
|
640 |
+ |
2003-07-09 08:56 gezelter |
641 |
+ |
|
642 |
+ |
* libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf |
643 |
+ |
|
644 |
+ |
2003-07-09 08:56 gezelter |
645 |
+ |
|
646 |
+ |
* libBASS/Globals.cpp: Removed Qmass |
647 |
+ |
|
648 |
+ |
2003-07-08 21:15 gezelter |
649 |
+ |
|
650 |
+ |
* libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf |
651 |
+ |
and NPTi |
652 |
+ |
|
653 |
+ |
2003-07-08 20:41 gezelter |
654 |
+ |
|
655 |
+ |
* libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf |
656 |
+ |
|
657 |
+ |
2003-07-08 16:10 gezelter |
658 |
+ |
|
659 |
+ |
* libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] |
660 |
+ |
|
661 |
+ |
2003-07-08 16:06 gezelter |
662 |
+ |
|
663 |
+ |
* libmdtools/NPTi.cpp: fixed box scaling |
664 |
+ |
|
665 |
+ |
2003-07-08 15:56 gezelter |
666 |
+ |
|
667 |
+ |
* libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, |
668 |
+ |
SimInfo.hpp, Thermo.cpp: NPTi |
669 |
+ |
|
670 |
+ |
2003-07-03 14:41 mmeineke |
671 |
+ |
|
672 |
+ |
* libBASS/Makefile, libmdtools/Makefile, src/Makefile, |
673 |
+ |
utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy |
674 |
+ |
scripts in the makefiles |
675 |
+ |
|
676 |
+ |
2003-07-02 16:26 mmeineke |
677 |
+ |
|
678 |
+ |
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
679 |
+ |
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
680 |
+ |
libmdtools/Makefile, libmdtools/ReadWrite.hpp, |
681 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
682 |
+ |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
683 |
+ |
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, src/Makefile, |
684 |
+ |
utils/Makefile: fixed the bugs introduced by switching the periodic |
685 |
+ |
box to a matrix |
686 |
+ |
|
687 |
+ |
2003-07-01 17:39 gezelter |
688 |
+ |
|
689 |
+ |
* libmdtools/do_Forces.F90: Fortran flexi-BOX |
690 |
+ |
|
691 |
+ |
2003-07-01 17:29 gezelter |
692 |
+ |
|
693 |
+ |
* libmdtools/simulation_module.F90: Fixes for flexi-BOX |
694 |
+ |
|
695 |
+ |
2003-07-01 16:33 mmeineke |
696 |
+ |
|
697 |
+ |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, |
698 |
+ |
fortranWrapDefines.hpp, simulation_module.F90: working on adding |
699 |
+ |
the box matrix to everything. |
700 |
+ |
|
701 |
+ |
2003-06-30 17:03 mmeineke |
702 |
+ |
|
703 |
+ |
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
704 |
+ |
src/oopse.cpp: |
705 |
+ |
Updated the ChangeLog, and Converted most of the SImInfo to use |
706 |
+ |
non-Isotropic boxes. wrapVector needs to be finished. |
707 |
+ |
|
708 |
|
2003-06-25 16:12 mmeineke |
709 |
|
|
710 |
|
* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |