1 |
+ |
2003-06-25 16:12 mmeineke |
2 |
+ |
|
3 |
+ |
* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
4 |
+ |
to Harmonic bonds in the DUFF frc file |
5 |
+ |
|
6 |
+ |
fixed constraints. |
7 |
+ |
|
8 |
+ |
2003-06-25 16:11 mmeineke |
9 |
+ |
|
10 |
+ |
* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
11 |
+ |
the DUFF frc file |
12 |
+ |
|
13 |
+ |
2003-06-24 17:51 gezelter |
14 |
+ |
|
15 |
+ |
* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
16 |
+ |
|
17 |
+ |
2003-06-24 14:57 mmeineke |
18 |
+ |
|
19 |
+ |
* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
20 |
+ |
libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
21 |
+ |
the DUFF forcefield and BondExtensions.cpp |
22 |
+ |
|
23 |
+ |
2003-06-23 16:24 mmeineke |
24 |
+ |
|
25 |
+ |
* libmdtools/Integrator.cpp: Doing some work to debug the |
26 |
+ |
constraint code. |
27 |
+ |
|
28 |
+ |
2003-06-20 15:50 gezelter |
29 |
+ |
|
30 |
+ |
* libmdtools/Integrator.hpp: NPT fix |
31 |
+ |
|
32 |
+ |
2003-06-20 15:29 mmeineke |
33 |
+ |
|
34 |
+ |
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
35 |
+ |
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
36 |
+ |
libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, |
37 |
+ |
libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, |
38 |
+ |
libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
39 |
+ |
integrator and NVT seem to be working now. |
40 |
+ |
|
41 |
+ |
2003-06-20 11:49 gezelter |
42 |
+ |
|
43 |
+ |
* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
44 |
+ |
|
45 |
+ |
2003-06-19 17:02 mmeineke |
46 |
+ |
|
47 |
+ |
* forceFields/DUFF.frc, forceFields/LJFF.frc, |
48 |
+ |
forceFields/LJ_FF.frc, forceFields/Makefile, |
49 |
+ |
forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, |
50 |
+ |
libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, |
51 |
+ |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
52 |
+ |
libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, |
53 |
+ |
libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
54 |
+ |
forcefield names. |
55 |
+ |
|
56 |
+ |
2003-06-19 14:21 mmeineke |
57 |
+ |
|
58 |
+ |
* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
59 |
+ |
finished the basics of the integrator and SimSetup.cpp |
60 |
+ |
|
61 |
+ |
2003-06-19 14:11 mmeineke |
62 |
+ |
|
63 |
+ |
* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
64 |
+ |
up / get it to work with the new Integrator. |
65 |
+ |
|
66 |
+ |
2003-06-18 17:20 mmeineke |
67 |
+ |
|
68 |
+ |
* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
69 |
+ |
output times. |
70 |
+ |
|
71 |
+ |
2003-06-17 16:56 mmeineke |
72 |
+ |
|
73 |
+ |
* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
74 |
+ |
fro the ghost Bend in TraPPE_Ex |
75 |
+ |
|
76 |
+ |
some work on the integrator. ( incomplete) |
77 |
+ |
|
78 |
+ |
2003-06-17 16:55 mmeineke |
79 |
+ |
|
80 |
+ |
* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
81 |
+ |
Bend in TraPPE_Ex |
82 |
+ |
|
83 |
+ |
2003-06-04 16:06 mmeineke |
84 |
+ |
|
85 |
+ |
* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
86 |
+ |
constrainB to the Symplectic integrator |
87 |
+ |
|
88 |
+ |
2003-05-30 16:32 mmeineke |
89 |
+ |
|
90 |
+ |
* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
91 |
+ |
the basic integrator. |
92 |
+ |
|
93 |
+ |
bilayerSys.cpp altered for building tb3. |
94 |
+ |
|
95 |
+ |
2003-05-30 16:31 mmeineke |
96 |
+ |
|
97 |
+ |
* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
98 |
+ |
TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
99 |
+ |
modifiying Symplectic to become the basic integrator. |
100 |
+ |
|
101 |
+ |
2003-05-30 15:19 mmeineke |
102 |
+ |
|
103 |
+ |
* libmdtools/Integrator.hpp: added some member variables for |
104 |
+ |
position, velocity, etc. |
105 |
+ |
|
106 |
+ |
2003-05-30 14:07 mmeineke |
107 |
+ |
|
108 |
+ |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
109 |
+ |
is now derived from Integrator |
110 |
+ |
|
111 |
+ |
2003-05-20 11:44 mmeineke |
112 |
+ |
|
113 |
+ |
* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
114 |
+ |
|
115 |
+ |
2003-05-17 11:57 mmeineke |
116 |
+ |
|
117 |
+ |
* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
118 |
+ |
working |
119 |
+ |
|
120 |
+ |
2003-05-16 16:37 mmeineke |
121 |
+ |
|
122 |
+ |
* utils/bilayerSys.cpp: still working on the bilayer code |
123 |
+ |
|
124 |
+ |
2003-05-16 09:28 mmeineke |
125 |
+ |
|
126 |
+ |
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
127 |
+ |
work to overhaul sysbuild. |
128 |
+ |
|
129 |
+ |
2003-05-13 16:23 mmeineke |
130 |
+ |
|
131 |
+ |
* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
132 |
+ |
|
133 |
+ |
2003-05-13 15:47 mmeineke |
134 |
+ |
|
135 |
+ |
* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
136 |
+ |
beadLipid/water.mdl: Added bead lipid model to the sample directory |
137 |
+ |
|
138 |
+ |
2003-05-13 15:34 mmeineke |
139 |
+ |
|
140 |
+ |
* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
141 |
+ |
the Trappe extended force field |
142 |
+ |
|
143 |
+ |
2003-05-13 12:01 mmeineke |
144 |
+ |
|
145 |
+ |
* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
146 |
+ |
TraPPe_Ex forceField |
147 |
+ |
|
148 |
+ |
2003-05-09 14:51 mmeineke |
149 |
+ |
|
150 |
+ |
* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
151 |
+ |
there were some duplicate entries |
152 |
+ |
|
153 |
+ |
added a two chain lipid to the lipid.mdl in sample |
154 |
+ |
|
155 |
+ |
2003-05-09 14:51 mmeineke |
156 |
+ |
|
157 |
+ |
* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
158 |
+ |
there were some duplicate entries |
159 |
+ |
|
160 |
+ |
2003-05-09 11:56 mmeineke |
161 |
+ |
|
162 |
+ |
* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
163 |
+ |
configure script |
164 |
+ |
|
165 |
+ |
added the CH branching group to the TraPPE_Ex fource field |
166 |
+ |
|
167 |
+ |
2003-05-09 11:55 mmeineke |
168 |
+ |
|
169 |
+ |
* ac-tools/configure.in: added the utils subdirectory to the |
170 |
+ |
configure script |
171 |
+ |
|
172 |
+ |
2003-04-25 11:02 mmeineke |
173 |
+ |
|
174 |
+ |
* utils/bilayerSys.cpp: i quick fix to th distance in the random |
175 |
+ |
bilayer builder |
176 |
+ |
|
177 |
+ |
2003-04-24 21:00 mmeineke |
178 |
+ |
|
179 |
+ |
* libmdtools/f_verlet_constrained.F90: added a new test for |
180 |
+ |
constraint failure |
181 |
+ |
|
182 |
+ |
2003-04-17 16:54 mmeineke |
183 |
+ |
|
184 |
+ |
* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
185 |
+ |
utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
186 |
+ |
utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
187 |
+ |
build our systems |
188 |
+ |
|
189 |
+ |
2003-04-16 16:11 mmeineke |
190 |
+ |
|
191 |
+ |
* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
192 |
+ |
|
193 |
+ |
2003-04-15 16:47 mmeineke |
194 |
+ |
|
195 |
+ |
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
196 |
+ |
and sysBuild both will build now. woot! |
197 |
+ |
|
198 |
+ |
2003-04-15 16:20 mmeineke |
199 |
+ |
|
200 |
+ |
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
201 |
+ |
bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
202 |
+ |
|
203 |
+ |
sysBuild still need to write the bass file. |
204 |
+ |
|
205 |
+ |
MoLocator.cpp is currently empty |
206 |
+ |
|
207 |
+ |
2003-04-15 15:40 chuckv |
208 |
+ |
|
209 |
+ |
* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
210 |
+ |
forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
211 |
+ |
forceFields/pdu3.eam, forceFields/ptu3.eam, |
212 |
+ |
libmdtools/ForceFields.hpp: Added eam force files... |
213 |
+ |
|
214 |
+ |
2003-04-15 11:37 chuckv |
215 |
+ |
|
216 |
+ |
* libmdtools/EAM_FF.cpp: More eam work. |
217 |
+ |
|
218 |
+ |
2003-04-14 16:22 mmeineke |
219 |
+ |
|
220 |
+ |
* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
221 |
+ |
utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
222 |
+ |
working on the system builder |
223 |
+ |
|
224 |
+ |
2003-04-14 16:16 chuckv |
225 |
+ |
|
226 |
+ |
* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
227 |
+ |
ordering on NVT calculation in integrators. |
228 |
+ |
|
229 |
+ |
2003-04-14 14:51 mmeineke |
230 |
+ |
|
231 |
+ |
* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
232 |
+ |
obj/placeHolder: working on a system builder |
233 |
+ |
|
234 |
+ |
2003-04-14 14:04 mmeineke |
235 |
+ |
|
236 |
+ |
* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
237 |
+ |
|
238 |
+ |
added sysBuild to the utils Makefile |
239 |
+ |
|
240 |
+ |
2003-04-14 14:03 mmeineke |
241 |
+ |
|
242 |
+ |
* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
243 |
+ |
Ghost bends to the TraPPE_Ex forceField |
244 |
+ |
|
245 |
+ |
2003-04-14 13:19 chuckv |
246 |
+ |
|
247 |
+ |
* libmdtools/calc_eam.F90: Added first mangling of EAM. |
248 |
+ |
|
249 |
+ |
2003-04-11 13:46 mmeineke |
250 |
+ |
|
251 |
+ |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
252 |
+ |
simulation_module.F90: fixed a memory bug in Fortran, where |
253 |
+ |
molMembershipArray was declared nLocal instead of nGlobal. |
254 |
+ |
|
255 |
+ |
2003-04-11 10:16 gezelter |
256 |
+ |
|
257 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
258 |
+ |
SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
259 |
+ |
fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
260 |
+ |
for NPT |
261 |
+ |
|
262 |
+ |
2003-04-10 15:08 mmeineke |
263 |
+ |
|
264 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
265 |
+ |
globalIndex counter to Molecule |
266 |
+ |
|
267 |
+ |
2003-04-10 11:35 gezelter |
268 |
+ |
|
269 |
+ |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
270 |
+ |
ConstantStress |
271 |
+ |
|
272 |
+ |
2003-04-10 11:27 mmeineke |
273 |
+ |
|
274 |
+ |
* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
275 |
+ |
caused a miscalculation of nLocal. |
276 |
+ |
|
277 |
+ |
2003-04-10 11:21 mmeineke |
278 |
+ |
|
279 |
+ |
* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
280 |
+ |
do_Forces.F90: fixed a bug in symplectic, where presure was only |
281 |
+ |
being calculated the first time through. |
282 |
+ |
|
283 |
+ |
2003-04-09 11:20 chuckv |
284 |
+ |
|
285 |
+ |
* samples/alkane/alkanes.mdl: added pentane to the alkane model |
286 |
+ |
file |
287 |
+ |
|
288 |
+ |
2003-04-09 08:59 gezelter |
289 |
+ |
|
290 |
+ |
* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
291 |
+ |
Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
292 |
+ |
|
293 |
+ |
2003-04-08 23:06 gezelter |
294 |
+ |
|
295 |
+ |
* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
296 |
+ |
ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
297 |
+ |
SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, |
298 |
+ |
Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
299 |
+ |
calc_reaction_field.F90, calc_sticky_pair.F90, |
300 |
+ |
fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
301 |
+ |
NVT |
302 |
+ |
|
303 |
+ |
2003-04-08 17:38 chuckv |
304 |
+ |
|
305 |
+ |
* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
306 |
+ |
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
307 |
+ |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
308 |
+ |
libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
309 |
+ |
(kinda)... |
310 |
+ |
|
311 |
+ |
2003-04-08 16:35 gezelter |
312 |
+ |
|
313 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
314 |
+ |
libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
315 |
+ |
libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
316 |
+ |
|
317 |
+ |
2003-04-08 12:16 chuckv |
318 |
+ |
|
319 |
+ |
* libmdtools/: do_Forces.F90, neighborLists.F90, |
320 |
+ |
simulation_module.F90: Moved expand neighborlist to init_FF. |
321 |
+ |
|
322 |
+ |
2003-04-08 10:20 chuckv |
323 |
+ |
|
324 |
+ |
* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
325 |
+ |
NVT |
326 |
+ |
|
327 |
+ |
2003-04-08 09:39 gezelter |
328 |
+ |
|
329 |
+ |
* libmdtools/Verlet.cpp: fixes for nvt / npt |
330 |
+ |
|
331 |
+ |
2003-04-08 09:34 gezelter |
332 |
+ |
|
333 |
+ |
* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
334 |
+ |
Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
335 |
+ |
|
336 |
+ |
2003-04-08 07:50 gezelter |
337 |
+ |
|
338 |
+ |
* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
339 |
+ |
|
340 |
+ |
2003-04-08 07:44 gezelter |
341 |
+ |
|
342 |
+ |
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
343 |
+ |
Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
344 |
+ |
NVT and NPT ensembles |
345 |
+ |
|
346 |
+ |
2003-04-07 16:42 gezelter |
347 |
+ |
|
348 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
349 |
+ |
libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
350 |
+ |
libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
351 |
+ |
|
352 |
+ |
2003-04-07 16:20 mmeineke |
353 |
+ |
|
354 |
+ |
* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
355 |
+ |
portion of SSD. |
356 |
+ |
|
357 |
+ |
2003-04-07 16:16 mmeineke |
358 |
+ |
|
359 |
+ |
* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
360 |
+ |
doing some testing in sticky through Symplectic. |
361 |
+ |
|
362 |
+ |
2003-04-07 15:51 gezelter |
363 |
+ |
|
364 |
+ |
* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
365 |
+ |
|
366 |
+ |
2003-04-07 15:50 chuckv |
367 |
+ |
|
368 |
+ |
* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
369 |
+ |
tau and virial. |
370 |
+ |
|
371 |
+ |
2003-04-07 15:06 mmeineke |
372 |
+ |
|
373 |
+ |
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
374 |
+ |
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
375 |
+ |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
376 |
+ |
src/Makefile: bug fixes |
377 |
+ |
|
378 |
+ |
2003-04-07 11:56 gezelter |
379 |
+ |
|
380 |
+ |
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
381 |
+ |
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
382 |
+ |
Many fixes to add extended system |
383 |
+ |
|
384 |
+ |
2003-04-07 09:30 gezelter |
385 |
+ |
|
386 |
+ |
* src/Makefile: Fixed a bug caused by my experimentation |
387 |
+ |
|
388 |
+ |
2003-04-07 09:30 gezelter |
389 |
+ |
|
390 |
+ |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
391 |
+ |
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
392 |
+ |
Added ExtendedSystem infrastructure for NPT and NVT calculations |
393 |
+ |
|
394 |
+ |
2003-04-07 09:30 gezelter |
395 |
+ |
|
396 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
397 |
+ |
|
398 |
+ |
2003-04-04 23:07 gezelter |
399 |
+ |
|
400 |
+ |
* src/Makefile: final mods to try a fortran compiler |
401 |
+ |
|
402 |
+ |
2003-04-04 22:39 gezelter |
403 |
+ |
|
404 |
+ |
* libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, |
405 |
+ |
fortranWrapDefines.hpp: Bug fixes for simulation module rewrites |
406 |
+ |
|
407 |
+ |
2003-04-04 21:56 gezelter |
408 |
+ |
|
409 |
+ |
* libmdtools/: Makefile, atype_module.F90, do_Forces.F90, |
410 |
+ |
fortranWrappers.cpp, wrappers.F90: bug fixes for compilation |
411 |
+ |
|
412 |
+ |
2003-04-04 21:45 gezelter |
413 |
+ |
|
414 |
+ |
* libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug |
415 |
+ |
fixes to fortran wrappers |
416 |
+ |
|
417 |
+ |
2003-04-04 17:22 chuckv |
418 |
+ |
|
419 |
+ |
* libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
420 |
+ |
calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, |
421 |
+ |
do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, |
422 |
+ |
simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets |
423 |
+ |
smarter, fortran gets dumber... |
424 |
+ |
|
425 |
+ |
2003-04-04 14:57 mmeineke |
426 |
+ |
|
427 |
+ |
* libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, |
428 |
+ |
neighborLists.F90: fixed a memory read bug in neighborlist |
429 |
+ |
|
430 |
+ |
2003-04-04 14:47 gezelter |
431 |
+ |
|
432 |
+ |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
433 |
+ |
SimInfo.hpp, Thermo.cpp: Changes for Extended System |
434 |
+ |
|
435 |
+ |
2003-04-04 14:16 gezelter |
436 |
+ |
|
437 |
+ |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
438 |
+ |
SimInfo.hpp: Fixes for ExtendedSystem |
439 |
+ |
|
440 |
+ |
2003-04-03 20:57 gezelter |
441 |
+ |
|
442 |
+ |
* libmdtools/ExtendedSystem.hpp: Added extended system header |
443 |
+ |
|
444 |
+ |
2003-04-03 20:57 gezelter |
445 |
+ |
|
446 |
+ |
* libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes |
447 |
+ |
for extended system code |
448 |
+ |
|
449 |
+ |
2003-04-03 18:49 gezelter |
450 |
+ |
|
451 |
+ |
* libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to |
452 |
+ |
extendedsystem |
453 |
+ |
|
454 |
+ |
2003-04-03 17:19 mmeineke |
455 |
+ |
|
456 |
+ |
* libmdtools/Molecule.hpp: added some little fixes here and there. |
457 |
+ |
|
458 |
+ |
2003-04-03 17:01 mmeineke |
459 |
+ |
|
460 |
+ |
* libmdtools/TraPPE_ExFF.cpp: fixed a possible call before |
461 |
+ |
initialize bug. |
462 |
+ |
|
463 |
+ |
2003-04-03 16:12 mmeineke |
464 |
+ |
|
465 |
+ |
* libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just |
466 |
+ |
little things like deleteing unused variables and such. |
467 |
+ |
|
468 |
+ |
2003-04-03 15:57 mmeineke |
469 |
+ |
|
470 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to |
471 |
+ |
simError.h also some fixes to Molecule.hpp |
472 |
+ |
|
473 |
+ |
2003-04-03 15:57 mmeineke |
474 |
+ |
|
475 |
+ |
* libBASS/simError.h: a few fixes to simError.h |
476 |
+ |
|
477 |
+ |
2003-04-03 15:21 mmeineke |
478 |
+ |
|
479 |
+ |
* libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, |
480 |
+ |
libBASS/simError.h, libmdtools/DumpWriter.cpp, |
481 |
+ |
libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, |
482 |
+ |
libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, |
483 |
+ |
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, |
484 |
+ |
src/Makefile, src/oopse.cpp: fixed some small things with |
485 |
+ |
simError.h |
486 |
+ |
|
487 |
+ |
2003-04-03 15:19 gezelter |
488 |
+ |
|
489 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT |
490 |
+ |
|
491 |
+ |
2003-04-03 14:58 gezelter |
492 |
+ |
|
493 |
+ |
* libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for |
494 |
+ |
now) |
495 |
+ |
|
496 |
+ |
2003-04-03 08:42 gezelter |
497 |
+ |
|
498 |
+ |
* README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: |
499 |
+ |
Changed Readme, added some files |
500 |
+ |
|
501 |
+ |
2003-04-02 17:19 mmeineke |
502 |
+ |
|
503 |
+ |
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, |
504 |
+ |
Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: |
505 |
+ |
dipoles mostly work, but there is a memory leak somewhere. |
506 |
+ |
|
507 |
+ |
2003-04-02 10:01 mmeineke |
508 |
+ |
|
509 |
+ |
* libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting |
510 |
+ |
the proper atomIdents. |
511 |
+ |
|
512 |
+ |
2003-04-01 11:50 chuckv |
513 |
+ |
|
514 |
+ |
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
515 |
+ |
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
516 |
+ |
samples/argon/argon.bass: more bug fixes.... |
517 |
+ |
|
518 |
+ |
2003-04-01 11:49 mmeineke |
519 |
+ |
|
520 |
+ |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed |
521 |
+ |
DumpWriter to be more robust to errors. also added a little |
522 |
+ |
namespace to InitFromFile to wrap it's helper functions in MPI |
523 |
+ |
|
524 |
+ |
2003-03-31 17:09 chuckv |
525 |
+ |
|
526 |
+ |
* libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local |
527 |
+ |
not zeroed. |
528 |
+ |
|
529 |
+ |
2003-03-31 16:50 chuckv |
530 |
+ |
|
531 |
+ |
* libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, |
532 |
+ |
libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
533 |
+ |
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
534 |
+ |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
535 |
+ |
libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, |
536 |
+ |
samples/alkane/butane.bass: Fixes in MPI force calc and in |
537 |
+ |
Trappe_Ex parsing. |
538 |
+ |
|
539 |
+ |
2003-03-28 17:34 chuckv |
540 |
+ |
|
541 |
+ |
* libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp |
542 |
+ |
|
543 |
+ |
2003-03-28 16:45 chuckv |
544 |
+ |
|
545 |
+ |
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
546 |
+ |
libmdtools/InitializeFromFile.cpp: Bug fixes in read-write |
547 |
+ |
routines. |
548 |
+ |
|
549 |
+ |
2003-03-28 14:33 mmeineke |
550 |
+ |
|
551 |
+ |
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, |
552 |
+ |
Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a |
553 |
+ |
bug where the Excludes were not being created properly |
554 |
+ |
|
555 |
+ |
2003-03-28 14:30 chuckv |
556 |
+ |
|
557 |
+ |
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
558 |
+ |
libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, |
559 |
+ |
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes |
560 |
+ |
and debugging mpi read write from file. |
561 |
+ |
|
562 |
+ |
2003-03-28 10:28 mmeineke |
563 |
+ |
|
564 |
+ |
* libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range |
565 |
+ |
interactions in Trappe |
566 |
+ |
|
567 |
+ |
2003-03-27 18:33 chuckv |
568 |
+ |
|
569 |
+ |
* libmdtools/: SimSetup.cpp, mpiSimulation.cpp, |
570 |
+ |
mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. |
571 |
+ |
|
572 |
+ |
2003-03-27 17:16 mmeineke |
573 |
+ |
|
574 |
+ |
* libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where |
575 |
+ |
excludes were not being initialized |
576 |
+ |
|
577 |
+ |
2003-03-27 16:52 mmeineke |
578 |
+ |
|
579 |
+ |
* src/Makefile: [no log message] |
580 |
+ |
|
581 |
+ |
2003-03-27 16:52 mmeineke |
582 |
+ |
|
583 |
+ |
* libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. |
584 |
+ |
|
585 |
+ |
2003-03-27 16:07 mmeineke |
586 |
+ |
|
587 |
+ |
* libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, |
588 |
+ |
Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, |
589 |
+ |
Verlet.cpp: fixed the compile time bugs, Source builds and links |
590 |
+ |
|
591 |
+ |
2003-03-27 15:48 mmeineke |
592 |
+ |
|
593 |
+ |
* libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few |
594 |
+ |
more bugs. |
595 |
+ |
|
596 |
+ |
2003-03-27 15:40 mmeineke |
597 |
+ |
|
598 |
+ |
* libmdtools/Molecule.cpp: added the Molecule.cpp file |
599 |
+ |
|
600 |
+ |
2003-03-27 15:39 mmeineke |
601 |
+ |
|
602 |
+ |
* libmdtools/: Makefile, Molecule.hpp: fixed the makefile |
603 |
+ |
|
604 |
+ |
2003-03-27 15:36 mmeineke |
605 |
+ |
|
606 |
+ |
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
607 |
+ |
ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, |
608 |
+ |
SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs |
609 |
+ |
|
610 |
+ |
2003-03-27 15:12 mmeineke |
611 |
+ |
|
612 |
+ |
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
613 |
+ |
Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, |
614 |
+ |
Verlet.cpp: I have implemeted Molecules everywhere I could remember |
615 |
+ |
to. will now attempt to compile. |
616 |
+ |
|
617 |
+ |
2003-03-27 14:21 mmeineke |
618 |
+ |
|
619 |
+ |
* libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, |
620 |
+ |
SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished |
621 |
+ |
updating SimSetup to initialize and use the new MPI division of |
622 |
+ |
labour, and Molecule class |
623 |
+ |
|
624 |
+ |
2003-03-27 12:55 mmeineke |
625 |
+ |
|
626 |
+ |
* libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to |
627 |
+ |
use Molecule |
628 |
+ |
|
629 |
+ |
2003-03-27 12:32 mmeineke |
630 |
+ |
|
631 |
+ |
* libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, |
632 |
+ |
SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been |
633 |
+ |
converted to the new Molecule model. TraPPE_Ex is currently being |
634 |
+ |
updated. SimSetups routines are writtten, but not yet called. |
635 |
+ |
|
636 |
+ |
2003-03-27 10:07 gezelter |
637 |
+ |
|
638 |
+ |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
639 |
+ |
mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom |
640 |
+ |
numbering in MPI |
641 |
+ |
|
642 |
+ |
2003-03-27 09:30 mmeineke |
643 |
+ |
|
644 |
+ |
* libmdtools/mpiSimulation.cpp: little bug fixes here and there. |
645 |
+ |
|
646 |
+ |
2003-03-26 20:49 gezelter |
647 |
+ |
|
648 |
+ |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to |
649 |
+ |
fileio for MPI |
650 |
+ |
|
651 |
+ |
2003-03-26 18:14 gezelter |
652 |
+ |
|
653 |
+ |
* libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, |
654 |
+ |
mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug |
655 |
+ |
fixes many bug fixes |
656 |
+ |
|
657 |
+ |
2003-03-26 17:24 gezelter |
658 |
+ |
|
659 |
+ |
* libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on |
660 |
+ |
sequence of atoms on the other processors. Node 0 now fires |
661 |
+ |
potatoes at other processors to get them to send french fries back. |
662 |
+ |
|
663 |
+ |
2003-03-26 17:02 mmeineke |
664 |
+ |
|
665 |
+ |
* libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for |
666 |
+ |
making the molecules is in place. ForceField needs to be updated |
667 |
+ |
next. |
668 |
+ |
|
669 |
+ |
2003-03-26 16:54 mmeineke |
670 |
+ |
|
671 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of |
672 |
+ |
the "static" bugs in Atom and Exclude |
673 |
+ |
|
674 |
+ |
2003-03-26 16:50 mmeineke |
675 |
+ |
|
676 |
+ |
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, |
677 |
+ |
SimSetup.cpp: still working on the SimSetup routine. also fixed |
678 |
+ |
some things in Exclude.hpp |
679 |
+ |
|
680 |
+ |
2003-03-26 16:24 gezelter |
681 |
+ |
|
682 |
+ |
* libmdtools/Makefile: Added Atom.cpp and Exclude.cpp |
683 |
+ |
|
684 |
+ |
2003-03-26 16:23 gezelter |
685 |
+ |
|
686 |
+ |
* libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom |
687 |
+ |
and Exclude list |
688 |
+ |
|
689 |
+ |
2003-03-26 16:04 gezelter |
690 |
+ |
|
691 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and |
692 |
+ |
delete ranges of atoms |
693 |
+ |
|
694 |
+ |
2003-03-26 15:45 mmeineke |
695 |
+ |
|
696 |
+ |
* libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class |
697 |
+ |
with static arrays similar to the Atom class |
698 |
+ |
|
699 |
+ |
2003-03-26 15:22 mmeineke |
700 |
+ |
|
701 |
+ |
* libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm |
702 |
+ |
overhauling the molecule class to contain it's own bonds, bends, |
703 |
+ |
and torsions. |
704 |
+ |
|
705 |
+ |
may god have mercy on my soul. |
706 |
+ |
|
707 |
+ |
2003-03-26 14:34 chuckv |
708 |
+ |
|
709 |
+ |
* libmdtools/mpiSimulation.cpp: Finished globalIndex. |
710 |
+ |
|
711 |
+ |
2003-03-26 13:02 gezelter |
712 |
+ |
|
713 |
+ |
* libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, |
714 |
+ |
mpiSimulation.hpp: MPI stuff for passing out molecules |
715 |
+ |
|
716 |
+ |
2003-03-26 11:12 chuckv |
717 |
+ |
|
718 |
+ |
* libmdtools/mpiSimulation.cpp: working on load balancing |
719 |
+ |
|
720 |
+ |
2003-03-26 10:37 chuckv |
721 |
+ |
|
722 |
+ |
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
723 |
+ |
samples/argon/argon.bass: Fixes for Parallel thermalization |
724 |
+ |
|
725 |
+ |
2003-03-26 09:55 mmeineke |
726 |
+ |
|
727 |
+ |
* libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in |
728 |
+ |
THermo.cpp |
729 |
+ |
|
730 |
+ |
2003-03-25 17:54 chuckv |
731 |
+ |
|
732 |
+ |
* libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation |
733 |
+ |
of potential energy and temperature. |
734 |
+ |
|
735 |
+ |
2003-03-25 09:29 mmeineke |
736 |
+ |
|
737 |
+ |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
738 |
+ |
src/MPIobj/dummy, src/obj/dummy: [no log message] |
739 |
+ |
|
740 |
+ |
2003-03-25 09:29 mmeineke |
741 |
+ |
|
742 |
+ |
* libBASS/MPIobj/dummy: added dummy files to keep the build |
743 |
+ |
deirectories from being pruned. |
744 |
+ |
|
745 |
+ |
2003-03-24 20:07 gezelter |
746 |
+ |
|
747 |
+ |
* samples/Makefile: moving tests to samples |
748 |
+ |
|
749 |
+ |
2003-03-24 20:06 gezelter |
750 |
+ |
|
751 |
+ |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
752 |
+ |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
753 |
+ |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
754 |
+ |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
755 |
+ |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
756 |
+ |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
757 |
+ |
samples |
758 |
+ |
|
759 |
+ |
2003-03-24 19:51 gezelter |
760 |
+ |
|
761 |
+ |
* ac-tools/configure.in: Tests are becoming samples |
762 |
+ |
|
763 |
+ |
2003-03-24 19:46 gezelter |
764 |
+ |
|
765 |
+ |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
766 |
+ |
|
767 |
+ |
2003-03-24 16:55 gezelter |
768 |
+ |
|
769 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp, |
770 |
+ |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, |
771 |
+ |
libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90, |
772 |
+ |
libmdtools/calc_reaction_field.F90, |
773 |
+ |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
774 |
+ |
libmdtools/simulation_module.F90: electrostatic changes for dipole |
775 |
+ |
/ RF separation |
776 |
+ |
|
777 |
+ |
2003-03-24 13:33 mmeineke |
778 |
+ |
|
779 |
+ |
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
780 |
+ |
do_Forces.F90: little bug fixes here and there |
781 |
+ |
|
782 |
+ |
2003-03-24 10:26 mmeineke |
783 |
+ |
|
784 |
+ |
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
785 |
+ |
where short range interactions were not being calculated. |
786 |
+ |
|
787 |
+ |
removed some debug print statements |
788 |
+ |
|
789 |
+ |
2003-03-21 17:11 chuckv |
790 |
+ |
|
791 |
+ |
* libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90, |
792 |
+ |
do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90: |
793 |
+ |
various write statements for debugging |
794 |
+ |
|
795 |
+ |
2003-03-21 16:26 chuckv |
796 |
+ |
|
797 |
+ |
* forceFields/Makefile: added links to the makefile in forceFields |
798 |
+ |
|
799 |
+ |
2003-03-21 15:52 gezelter |
800 |
+ |
|
801 |
+ |
* ac-tools/Make.conf.in, ac-tools/configure.in, |
802 |
+ |
libmdtools/Makefile: Fixed F_MACH_DEP bug |
803 |
+ |
|
804 |
+ |
2003-03-21 15:37 gezelter |
805 |
+ |
|
806 |
+ |
* ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in, |
807 |
+ |
ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile, |
808 |
+ |
libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend, |
809 |
+ |
src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org, |
810 |
+ |
autoconf fixes |
811 |
+ |
|
812 |
|
2003-03-21 14:58 gezelter |
813 |
|
|
814 |
|
* LICENSE: Added license file |